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Simulation report and files

General information

Name: Fully-glycosylated S protein (head) in open-open-open state in complex with antibody ey6a

Included proteins: Spike

Uniprot ID: P0DTC2

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6ZDH

Submitted by: Lehigh University, Bethlehem (CHARMM-GUI)

Submission date: May 20, 2021

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P (water was filtered out of the simulation output)

Total number of atoms: 84309

Simulation details

Software and version: GROMACS 2018.6

Forcefield and version: CHARMM36(m) -

Time step : 4.0 fs

Delta : 1.0 ns

Replicates: 1

Accumulated simulation time: 0.5210 µs

References

Cao, Y.; Choi, Y.K.; Frank, M.; Woo, H.; Park, S.-J.; Yeom, M.S.; Seok, C.; Im, W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. bioRxiv 2021, 2021.05.10.443519. DOI: 10.1101/2021.05.10.443519

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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

Viewer

Fully-glycosylated S protein (head) in open-open-open state in complex with antibody ey6a ( 6ZDH)

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Coiled-coil region

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Toolkit

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RMSD
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Selection:
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RMSF
Trajectory:
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Stride:
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact

Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:

Display isolate: All isolates
Spike
AA
Seq. pos.
PDB resID
A
27
27
Y
28
28
T
29
29
N
30
30
S
31
31
F
32
32
T
33
33
R
34
34
G
35
35
V
36
36
Y
37
37
Y
38
38
P
39
39
D
40
40
K
41
41
V
42
42
F
43
43
R
44
44
S
45
45
S
46
46
V
47
47
L
48
48
H
49
49
S
50
50
T
51
51
Q
52
52
D
53
53
L
54
54
F
55
55
L
56
56
P
57
57
F
58
58
F
59
59
S
60
60
N
61
61
V
62
62
T
63
63
W
64
64
F
65
65
H
66
66
A
67
67
I
68
68
H
69
69
D
80
80
N
81
81
P
82
82
V
83
83
L
84
84
P
85
85
F
86
86
N
87
87
D
88
88
G
89
89
V
90
90
Y
91
91
F
92
92
A
93
93
S
94
94
T
95
95
E
96
96
K
97
97
S
98
98
N
99
99
I
100
100
I
101
101
R
102
102
G
103
103
W
104
104
I
105
105
F
106
106
G
107
107
T
108
108
T
109
109
L
110
110
D
111
111
S
112
112
K
113
113
T
114
114
Q
115
115
S
116
116
L
117
117
L
118
118
I
119
119
V
120
120
N
121
121
N
122
122
A
123
123
T
124
124
N
125
125
V
126
126
V
127
127
I
128
128
K
129
129
V
130
130
C
131
131
E
132
132
F
133
133
Q
134
134
F
135
135
C
136
136
N
137
137
D
138
138
P
139
139
F
140
140
L
141
141
G
142
142
V
159
159
N
165
165
C
166
166
T
167
167
F
168
168
E
169
169
Y
170
170
V
171
171
S
172
172
F
186
186
K
187
187
N
188
188
L
189
189
R
190
190
E
191
191
F
192
192
V
193
193
F
194
194
K
195
195
N
196
196
I
197
197
D
198
198
G
199
199
Y
200
200
F
201
201
K
202
202
I
203
203
Y
204
204
S
205
205
K
206
206
H
207
207
T
208
208
P
209
209
I
210
210
N
211
211
L
212
212
V
213
213
R
214
214
D
215
215
L
216
216
P
217
217
Q
218
218
G
219
219
F
220
220
S
221
221
A
222
222
L
223
223
E
224
224
P
225
225
L
226
226
V
227
227
D
228
228
L
229
229
P
230
230
I
231
231
G
232
232
I
233
233
N
234
234
I
235
235
T
236
236
R
237
237
F
238
238
Q
239
239
T
240
240
L
241
241
L
242
242
A
243
243
L
244
244
H
245
245
A
263
263
A
264
264
Y
265
265
Y
266
266
V
267
267
G
268
268
Y
269
269
L
270
270
Q
271
271
P
272
272
R
273
273
T
274
274
F
275
275
L
276
276
L
277
277
K
278
278
Y
279
279
N
280
280
E
281
281
N
282
282
G
283
283
T(D)
284
1
I
285
2
T
286
5
D
287
287
A
288
288
V
289
289
D
290
290
C
291
291
A
292
292
L(Q)
293
6
D(S)
294
7
P
295
8
L
296
296
S
297
9
E
298
298
T
299
299
K
300
300
C
301
301
T(S)
302
10
L
303
11
K
304
304
S
305
12
F(A)
306
13
T(S)
307
14
V
308
15
E
309
309
K
310
310
G
311
16
I
312
312
Y
313
313
Q
314
314
T
315
315
S
316
316
N
317
317
F(D)
318
17
R
319
18
V
320
19
Q
321
321
P
322
322
T
323
20
E
324
324
S
325
325
I
326
326
V
327
327
R
328
328
F
329
329
P
330
330
N
331
331
I
332
21
T
333
22
N
334
334
L
335
335
C
336
23
P
337
337
F
338
338
G
339
339
E
340
340
V
341
341
F
342
342
N
343
343
A
344
344
T
345
345
R
346
24
F
347
347
A
348
25
S
349
26
V
350
350
Y
351
351
A
352
352
W
353
353
N
354
354
R
355
355
K(Q)
356
27
R(S)
357
28
I
358
29
S
359
30
N
360
360
C
361
361
V
362
362
A
363
363
D
364
364
Y
365
365
S
366
31
V(Y)
367
32
L
368
33
Y
369
369
N
370
34
S
371
371
A
372
372
S
373
373
F(W)
374
35
S(Y)
375
36
T(Q)
376
37
F(Q)
377
38
K
378
39
C
379
379
Y(P)
380
40
G
381
41
V(K)
382
42
S(A)
383
43
P
384
44
T
385
385
K
386
45
L
387
46
N
388
388
D
389
389
L
390
47
C
391
391
F
392
392
T
393
393
N
394
394
V(I)
395
48
Y
396
49
A
397
50
D(A)
398
51
S
399
52
S
400
53
V(L)
401
54
I(Q)
402
55
R(S)
403
56
G
404
57
D
405
405
E
406
406
V
407
58
R
408
61
Q
409
409
I
410
410
A(F)
411
62
P(S)
412
63
G
413
64
Q
414
414
T(S)
415
65
G
416
66
K
417
417
I
418
418
A
419
419
D
420
420
Y
421
421
N
422
422
Y
423
423
K
424
424
L(S)
425
67
P(G)
426
68
D(T)
427
69
D
428
70
F
429
71
T
430
72
G
431
431
C(L)
432
73
V(T)
433
74
I
434
75
A
435
435
W
436
436
N
437
437
S
438
438
N
439
439
N
440
440
L
441
441
D
442
442
S
443
76
K
444
444
V
445
445
G
446
446
G
447
447
N
448
448
Y
449
449
N
450
450
Y
451
451
L
452
452
Y
453
453
R
454
454
L
455
455
F
456
456
R
457
457
K
458
458
S
459
77
N
460
460
L
461
78
K(Q)
462
79
P
463
80
F
464
464
E
465
81
R
466
466
D
467
82
I
468
468
S
469
469
T
470
470
E
471
471
I
472
472
Y
473
473
Q(F)
474
83
A
475
84
G
476
476
S
477
477
T
478
85
P
479
479
C
480
480
N
481
481
G
482
482
V
483
483
E
484
484
G
485
485
F
486
486
N
487
487
C
488
488
Y
489
86
F
490
490
P
491
491
L
492
492
Q
493
493
S
494
494
Y
495
87
G
496
496
C
497
88
Q
498
89
P
499
499
T
500
500
N
501
501
G
502
502
V
503
503
G
504
504
Y
505
505
Q
506
90
P(S)
507
91
Y
508
92
R
509
509
V
510
510
V
511
511
V
512
512
L
513
513
S
514
93
F
515
515
E
516
516
L(T)
517
94
L
518
95
H
519
519
A
520
520
P
521
521
A
522
96
T
523
523
V
524
524
C
525
525
G
526
526
P
527
527
K
528
528
K
529
529
S
530
530
T
531
531
N
532
532
L
533
97
V
534
534
K
535
535
N
536
536
K
537
537
C
538
538
V
539
539
N
540
540
F
541
541
N(T)
542
98
F
543
99
N
544
544
G
545
100
L
546
546
T(G)
547
101
G
548
102
T
549
103
G(K)
550
104
V
551
105
L
552
552
T
553
553
E
554
106
S
555
555
N
556
556
K(I)
557
107
K
558
108
F
559
559
L
560
560
P
561
561
F
562
562
Q
563
563
Q
564
564
F
565
565
G
566
566
R
567
109
D
568
568
I
569
569
A
570
570
D
571
571
T
572
572
T
573
110
D
574
574
A(E)
575
1
V
576
111
R
577
577
D
578
578
P
579
579
Q
580
3
T
581
581
L
582
4
E
583
6
I
584
584
L
585
585
D
586
586
I(A)
587
112
T(A)
588
113
P
589
114
C
590
590
S
591
115
F(G)
592
8
G
593
9
G
594
10
V
595
116
S
596
596
V(F)
597
117
I
598
118
T(F)
599
119
P
600
120
G
601
15
T
602
602
N
603
603
T(P)
604
121
S
605
122
N
606
606
Q
607
607
V
608
608
A
609
609
V
610
610
L
611
18
Y
612
612
Q
613
613
D
614
123
V(L)
615
20
N(S)
616
21
C
617
22
T
618
618
E
619
124
A
623
23
A
626
24
Q
628
125
L
629
126
T(A)
630
26
P(F)
631
27
T
632
28
V
635
635
Y(K)
636
127
S
637
128
T
638
130
G(A)
639
131
S
640
132
N(Y)
641
32
V
642
133
F(R)
643
38
Q
644
39
T
645
645
R
646
646
A
647
40
V
648
134
C
649
135
L
650
136
I(K)
651
43
G
652
44
A(L)
653
45
E
654
46
H(W)
655
47
V(L)
656
137
N
657
138
N
658
139
S
659
52
Y
660
53
E
661
661
C
662
662
D
663
54
I
664
664
P
665
665
I
666
666
G
667
667
A
668
668
G
669
55
I
670
670
C
671
671
A
672
672
S(F)
673
140
Y
674
141
Q
677
677
T
678
678
N
679
57
P
681
142
R
682
143
R(E)
683
144
A
684
145
S(K)
686
146
V
687
147
S
689
689
Q
690
148
S
691
691
I
692
692
I
693
693
A(K)
694
58
Y
695
59
T
696
696
M
697
697
S
698
698
L(W)
699
149
G(K)
700
150
A(V)
701
151
E(D)
702
152
N
703
153
S
704
63
V
705
64
A
706
154
Y(L)
707
155
S
708
157
N(G)
709
158
N
710
159
S
711
160
I
712
712
A
713
713
I
714
714
P(K)
715
65
T(G)
716
66
N(R)
717
67
F
718
68
T(Q)
719
161
I(E)
720
162
S
721
163
V
722
164
T
723
723
T
724
165
E
725
166
I
726
726
L(R)
727
72
P(Q)
728
167
V(D)
729
168
S
730
169
M
731
731
T
732
732
K
733
170
T
734
734
S
735
735
V
736
736
D
737
737
C
738
738
T
739
739
M
740
740
Y
741
741
I
742
742
C
743
743
G
744
744
D
745
171
S
746
172
T
747
173
E
748
748
Y
749
174
S
750
175
N
751
751
L
752
79
L(Y)
753
80
L
754
176
Q
755
82
Y(M)
756
83
G(N)
757
84
S
758
177
F
759
759
S
760
178
T
761
179
Q
762
762
L
763
180
N
764
764
R
765
87
A(T)
766
181
L
767
182
T
768
768
G(S)
769
183
I(K)
770
184
A
771
185
V(D)
772
186
E
773
188
Q
774
774
D
775
90
K
776
189
N
777
777
T
778
91
Q(H)
779
190
E(K)
780
191
V
781
192
F(Y)
782
193
A
783
194
Q(C)
784
195
V
785
197
K
786
786
Q
787
787
I
788
788
Y
789
94
K
790
790
T
791
198
P(Y)
792
95
P(C)
793
96
I(A)
794
97
K
795
98
D
796
99
F
797
797
G
798
100
G
799
101
F
800
800
N
801
801
F
802
802
S(H)
803
199
Q
804
200
I(G)
805
201
L
806
202
P
807
807
D
808
808
P
809
809
S
810
203
K(S)
811
204
P
812
205
S(V)
813
206
K
814
208
R
815
815
S
816
209
F
817
817
I
818
818
E
819
819
D
820
820
L
821
821
L
822
103
F
823
210
N
824
211
K(W)
825
104
V
826
105
T
827
827
Q(Y)
836
106
Y(R)
837
212
G
838
213
D(E)
839
214
C
840
215
L(W)
841
111
G
842
112
Q
853
113
K
854
854
F
855
855
N
856
856
G
857
114
L
858
858
T
859
115
V
860
860
L
861
861
P
862
862
P
863
863
L
864
116
L(V)
865
117
T
866
118
D
867
867
E
868
868
M
869
869
I
870
870
A
871
871
Q
872
872
Y
873
873
T(V)
874
119
S
875
120
A
876
876
L
877
877
L(S)
878
121
A
879
122
G
880
880
T
881
881
I
882
882
T
883
883
S
884
123
G
885
885
W
886
886
T
887
124
F
888
888
G
889
889
A(K)
890
125
G
891
126
A
892
892
A
893
893
L
894
894
Q
895
895
I
896
896
P
897
127
F
898
898
A
899
899
M
900
900
Q
901
901
M
902
902
A
903
903
Y
904
904
R
905
905
F
906
906
N
907
907
G
908
908
I
909
909
G
910
910
V
911
911
T
912
912
Q
913
913
N(S)
914
128
V
915
129
L
916
916
Y
917
917
E
918
918
N
919
919
Q
920
920
K
921
921
L
922
922
I
923
923
A
924
924
N
925
925
Q
926
926
F
927
130
N(P)
928
131
S(L)
929
132
A
930
133
I
931
931
G
932
932
K
933
933
I
934
934
Q
935
935
D(P)
936
134
S
937
135
L
938
938
S
939
136
S(G)
940
142
T
941
143
A
942
144
S
943
943
A
944
145
L
945
146
G
946
147
K(C)
947
148
L
948
149
Q(V)
949
150
D
950
152
V(Y)
951
153
V
952
158
N
953
953
Q
954
954
N
955
955
A
956
956
Q
957
957
A
958
958
L
959
959
N
960
960
T
961
159
L
962
962
V
963
160
K
964
964
Q
965
965
L
966
966
S
967
967
S
968
968
N
969
969
F
970
970
G
971
971
A
972
972
I
973
973
S
974
974
S
975
161
V
976
976
L(W)
977
162
N
978
163
D
979
979
I
980
980
L
981
981
S
982
164
R
983
983
L
984
984
D
985
985
K
986
986
V
987
987
E(G)
988
165
A
989
166
E
990
990
V
991
991
Q
992
992
I
993
993
D
994
994
R
995
995
L
996
167
I
997
997
T
998
168
G
999
999
R
1000
1000
L
1001
1001
Q
1002
1002
S
1003
169
L
1004
1004
Q
1005
1005
T
1006
1006
Y(G)
1007
170
V
1008
171
T
1009
173
Q
1010
1010
Q
1011
1011
L
1012
1012
I
1013
1013
R
1014
1014
A
1015
1015
A
1016
1016
E
1017
1017
I
1018
1018
R
1019
1019
A
1020
1020
S
1021
1021
A
1022
1022
N
1023
1023
L(F)
1024
174
A(P)
1025
175
A
1026
176
T
1027
1027
K
1028
1028
M
1029
1029
S
1030
1030
E
1031
1031
C
1032
1032
V
1033
177
L
1034
178
G
1035
1035
Q
1036
179
S
1037
180
K
1038
1038
R
1039
1039
V
1040
1040
D
1041
1041
F
1042
1042
C(S)
1043
181
G
1044
182
K
1045
1045
G(L)
1046
183
Y
1047
184
H(S)
1048
185
L
1049
186
M
1050
1050
S
1051
187
F
1052
1052
P
1053
1053
Q
1054
1054
S
1055
188
A
1056
1056
P
1057
1057
H
1058
1058
G
1059
1059
V
1060
1060
V
1061
189
F
1062
1062
L
1063
1063
H
1064
1064
V
1065
190
T
1066
191
Y
1067
1067
V
1068
192
P
1069
193
A
1070
1070
Q(S)
1071
194
E(S)
1072
195
K(S)
1073
196
N(L)
1074
197
F(G)
1075
198
T
1076
199
T
1077
201
A
1078
1078
P
1079
1079
A(Y)
1080
202
I
1081
203
C
1082
204
H
1083
208
D
1084
1084
G
1085
1085
K
1086
209
A
1087
1087
H
1088
1088
F
1089
1089
P
1090
210
R
1091
1091
E
1092
1092
G
1093
1093
V
1094
1094
F
1095
1095
V
1096
1096
S
1097
211
N
1098
212
G
1099
1099
T
1100
213
H
1101
1101
W
1102
1102
F(K)
1103
214
V
1104
215
T(D)
1105
216
Q(K)
1106
217
R
1107
218
N
1108
1108
F
1109
1109
Y(V)
1110
219
E
1111
220
P
1112
221
Q
1113
1113
I
1114
1114
I
1115
1115
T
1116
1116
T
1117
1117
D
1118
1118
N
1119
1119
T
1120
1120
F
1121
1121
V(K)
1122
222
S
1123
223
G
1124
1124
N
1125
1125
C
1126
224
D
1127
1127
V
1128
1128
V
1129
1129
I
1130
1130
G
1131
1131
I
1132
1132
V
1133
1133
N
1134
1134
N
1135
1135
T
1136
1136
V
1137
1137
Y
1138
1138
D
1139
1139
P
1140
1140
L
1141
1141
Q
1142
1142
P
1143
1143
E
1144
1144
L
1145
1145
D
1146
1146
Impact score

Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.

Mutation effect 0/16
Substitution scores
0
 BLOSUM90 score
0
 Δ charge
0
 Epstein's coefficient of difference
0
 Experimental exchangeability
0
 Grantham's distance
0
 Miyata's distance
0
 Sneath's index
0
 Δ hydrophobicity
Conservation
0
 Frequency (‰)
0
 SIFT4G Score
0
 SIFT4G Median IC
Structure
0
 Post-translational modification
0
 Surface accessibility
0
 FoldX ΔΔG
Experimental
0
 Mean Experimental Antibody Escape
0
 Max. Experimental Antibody Escape
Others
Annotation
Time-dependent 0/28
Parameter Average Weight average SD Weight SD
RMSD
0
0

Please select a variant from the sequence above.
RMSF
0
0

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SASA
0
0

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CHI1
0
0

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All contacts
0
0

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Hydrogen bond contacts
0
0

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Salt bridge contacts
0
0

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Hydrophobic contacts
0
0

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Pi-cation contacts
0
0

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Pi-stacking contacts
0
0

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T-stacking contacts
0
0

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Van der Waals contacts
0
0

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Water bridge contacts
0
0

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Extended water bridge contacts
0
0

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User-provided descriptors 0/0

Upload your own descriptors according to this template.