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Simulation report and files

General information

Name: Fully-glycosylated S protein (head) in open-open-closed state in complex with antibody c105

Included proteins: Spike

Uniprot ID: P0DTC2

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

PDB ID: 6XCM

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: 71414

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-closed state in complex with antibody c105 ( 6XCM)

Selection

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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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Protein CA, CB, C, N, O
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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
S
13
2
N(A)
17
3
L
18
4
T
22
5
Q
23
6
P
25
7
P
26
8
A
27
11
Y
28
28
T
29
29
N
30
30
S
31
12
F
32
32
T
33
33
R
34
34
G
35
13
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
14
T
51
51
Q
52
52
D
53
53
L
54
54
F
55
55
L
56
56
P
57
15
F(G)
58
16
F(Q)
59
17
S
60
18
N
61
61
V
62
19
T
63
20
W
64
64
F
65
65
I
68
21
H
69
69
S
71
22
G(C)
72
23
T
73
24
G
75
25
T
76
26
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
28
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
29
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
30
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
G
142
31
Y(G)
144
32
Y
145
33
K
150
34
F
157
157
Y
160
35
S(V)
161
36
S
162
37
N
164
164
N
165
165
C
166
166
T
167
167
F
168
168
E(W)
169
38
Y
170
39
V
171
171
S(Q)
172
40
Q
173
41
P
174
43
G
181
44
K
182
45
N(A)
185
46
F(P)
186
47
K
187
48
N
188
188
L
189
49
R
190
190
E
191
191
F
192
192
V
193
193
F
194
194
K
195
195
N(M)
196
50
I
197
51
Y
200
52
F
201
201
K
202
202
I(E)
203
53
Y(V)
204
54
S
205
55
K
206
56
H
207
207
T
208
208
P
209
209
I
210
210
N
211
211
R
214
57
D
215
215
L
216
216
P
217
58
Q
218
218
G
219
219
F
220
220
S
221
59
A
222
222
L
223
223
E
224
224
P
225
225
L(G)
226
60
V
227
61
D
228
228
L
229
229
P
230
62
I
231
231
G
232
232
I
233
233
N
234
234
I
235
235
T(D)
236
63
R
237
64
F
238
65
Q
239
3
T
240
240
L
244
244
S
247
66
L
249
4
G
252
67
S
254
68
S(K)
255
69
S
256
70
G
257
71
W(N)
258
72
T
259
73
G
261
9
A
263
74
A(S)
264
75
Y(L)
265
76
Y(T)
266
77
V
267
78
G
268
80
Y
269
269
L
270
81
Q
271
82
P
272
14
R
273
273
T
274
274
F
275
275
L
276
276
L
277
277
K
278
278
Y
279
279
N(A)
280
83
E
281
84
N
282
282
G
283
15
T
284
284
I
285
285
T
286
286
D
287
85
A
288
87
V
289
289
D
290
88
C
291
91
A(S)
292
17
L
293
18
D
294
294
P(R)
295
19
L
296
20
S
297
92
E
298
298
T
299
299
K
300
300
C
301
22
T
302
302
L(A)
303
23
K(A)
304
24
S
305
93
F
306
27
T
307
28
V(Y)
308
94
E
309
95
K
310
310
G
311
96
I
312
312
Y
313
313
Q
314
314
T(S)
315
30
S
316
97
N
317
32
F
318
100
R
319
319
V
320
101
Q
321
321
P
322
322
T(Y)
323
33
E(M)
324
34
S
325
35
I(W)
326
36
V
327
102
R
328
38
F
329
103
P(G)
330
104
N(G)
331
105
I(G)
332
106
T
333
107
N(K)
334
108
L
335
109
T
336
110
P(V)
337
111
F(L)
338
117
G
339
118
E
340
46
V
341
341
F
342
342
N
343
343
A
344
344
T
345
345
R
346
346
F
347
347
A
348
348
S
349
349
V
350
350
Y
351
351
A
352
352
W
353
47
N
354
354
R
355
355
K
356
356
R
357
357
I
358
358
S
359
359
N
360
360
C
361
361
V
362
48
A
363
363
D
364
364
Y
365
365
S
366
49
V
367
50
L(I)
368
51
Y
369
52
N
370
370
S
371
371
A
372
372
S
373
373
F
374
374
S
375
53
T
376
376
F
377
377
K
378
378
C
379
379
Y
380
380
G
381
54
V(G)
382
55
S
383
56
P
384
384
T
385
385
K
386
386
L
387
387
N
388
388
D
389
389
L
390
390
C
391
391
F
392
392
T
393
57
N
394
394
V(Y)
395
58
Y
396
59
A
397
60
D
398
61
S
399
62
F
400
400
V
401
63
I
402
402
R(K)
403
64
G
404
65
D
405
405
E
406
406
V
407
407
R
408
66
Q
409
409
I
410
410
A
411
411
P
412
412
G
413
413
Q
414
414
T
415
415
G
416
416
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
425
425
P
426
426
D
427
427
D
428
428
F
429
67
T
430
68
G
431
431
C
432
432
V
433
433
I
434
69
A
435
435
W
436
436
N
437
437
S
438
70
N
439
439
N
440
440
L(R)
441
71
D
442
72
S
443
74
K
444
75
V
445
445
G
446
446
G
447
447
N
448
448
Y
449
449
N
450
76
Y(T)
451
77
L
452
78
Y
453
79
R
454
454
L
455
80
F(Q)
456
81
R(M)
457
82
K(N)
458
83
S
459
84
N
460
460
L
461
85
K
462
462
P(R)
463
86
F(A)
464
87
E
465
88
R
466
466
D
467
89
I
468
468
S
469
469
T
470
90
E
471
471
I
472
472
Y
473
473
Q
474
474
A
475
91
G
476
476
S(V)
477
92
T(Y)
478
93
P(Y)
479
94
C
480
95
N(A)
481
96
G
482
98
V
483
483
E
484
99
G
485
100
F
486
486
N
487
487
C(W)
488
101
Y(E)
489
102
F(L)
490
103
P
491
104
L
492
492
Q(Y)
493
105
S(D)
494
106
Y
495
107
G
496
109
F
497
497
Q
498
110
P
499
499
T
500
500
N
501
501
G
502
502
V
503
503
G
504
111
Y
505
505
Q
506
506
P
507
507
Y(T)
508
112
R(L)
509
113
V
510
114
V(T)
511
115
V
512
116
L
513
513
S
514
117
F
515
515
E
516
516
L
517
517
L
518
518
A
520
520
P
521
521
A
522
522
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
533
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
542
542
F
543
543
N
544
544
G
545
545
L
546
546
T
547
547
G
548
548
T
549
549
G
550
550
V
551
551
L
552
552
T
553
553
E
554
554
S
555
555
N
556
556
K
557
557
K
558
558
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
567
D
568
568
I
569
569
A
570
570
D
571
571
T
572
572
T
573
573
D
574
574
A
575
575
V
576
576
R
577
577
D
578
578
P
579
579
Q
580
580
T
581
581
L
582
582
E
583
583
I
584
584
L
585
585
D
586
586
I
587
587
T
588
588
P
589
589
C
590
590
S
591
591
F
592
592
G
593
593
G
594
594
V
595
595
S
596
596
V
597
597
I
598
598
T
599
599
P
600
600
G
601
601
T
602
602
N
603
603
T
604
604
S
605
605
N
606
606
Q
607
607
V
608
608
A
609
609
V
610
610
L
611
611
Y
612
612
Q
613
613
D
614
614
V
615
615
N
616
616
C
617
617
T
618
618
E
619
619
V
635
635
N
641
641
V
642
642
F
643
643
Q
644
644
T
645
645
R
646
646
A
647
647
G
648
648
C
649
649
L
650
650
I
651
651
G
652
652
A
653
653
E
654
654
H
655
655
V
656
656
N
657
657
N
658
658
S
659
659
Y
660
660
E
661
661
C
662
662
D
663
663
I
664
664
P
665
665
I
666
666
G
667
667
A
668
668
G
669
669
I
670
670
C
671
671
A
672
672
S
673
673
Y
674
674
Q
677
677
T
678
678
S
689
689
Q
690
690
S
691
691
I
692
692
I
693
693
A
694
694
Y
695
695
T
696
696
M
697
697
S
698
698
L
699
699
G
700
700
A
701
701
E
702
702
N
703
703
S
704
704
V
705
705
A
706
706
Y
707
707
S
708
708
N
709
709
N
710
710
S
711
711
I
712
712
A
713
713
I
714
714
P
715
715
T
716
716
N
717
717
F
718
718
T
719
719
I
720
720
S
721
721
V
722
722
T
723
723
T
724
724
E
725
725
I
726
726
L
727
727
P
728
728
V
729
729
S
730
730
M
731
731
T
732
732
K
733
733
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
745
S
746
746
T
747
747
E
748
748
C
749
749
S
750
750
N
751
751
L
752
752
L
753
753
L
754
754
Q
755
755
Y
756
756
G
757
757
S
758
758
F
759
759
C
760
760
T
761
761
Q
762
762
L
763
763
N
764
764
R
765
765
A
766
766
L
767
767
T
768
768
G
769
769
I
770
770
A
771
771
V
772
772
E
773
773
Q
774
774
D
775
775
K
776
776
N
777
777
T
778
778
Q
779
779
E
780
780
V
781
781
F
782
782
A
783
783
Q
784
784
V
785
785
K
786
786
Q
787
787
I
788
788
Y
789
789
K
790
790
T
791
791
P
792
792
P
793
793
I
794
794
K
795
795
D
796
796
F
797
797
G
798
798
G
799
799
F
800
800
N
801
801
F
802
802
S
803
803
Q
804
804
I
805
805
L
806
806
P
807
807
D
808
808
P
809
809
S
810
810
K
811
811
S
813
813
K
814
814
R
815
815
S
816
816
F
817
817
I
818
818
E
819
819
D
820
820
L
821
821
L
822
822
F
823
823
N
824
824
K
825
825
V
826
826
T
827
827
K
854
854
F
855
855
N
856
856
G
857
857
L
858
858
T
859
859
V
860
860
L
861
861
P
862
862
P
863
863
L
864
864
L
865
865
T
866
866
D
867
867
E
868
868
M
869
869
I
870
870
A
871
871
Q
872
872
Y
873
873
T
874
874
S
875
875
A
876
876
L
877
877
L
878
878
A
879
879
G
880
880
T
881
881
I
882
882
T
883
883
S
884
884
G
885
885
W
886
886
T
887
887
F
888
888
G
889
889
A
890
890
G
891
891
A
892
892
A
893
893
L
894
894
Q
895
895
I
896
896
P
897
897
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
914
914
V
915
915
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
927
N
928
928
S
929
929
A
930
930
I
931
931
G
932
932
K
933
933
I
934
934
Q
935
935
D
936
936
S
937
937
L
938
938
S
939
939
S
940
940
T
941
941
A
942
942
S
943
943
A
944
944
L
945
945
G
946
946
K
947
947
L
948
948
Q
949
949
D
950
950
V
951
951
V
952
952
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
961
L
962
962
V
963
963
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
975
V
976
976
L
977
977
N
978
978
D
979
979
I
980
980
L
981
981
S
982
982
R
983
983
L
984
984
D
985
985
K
986
986
V
987
987
E
988
988
A
989
989
E
990
990
V
991
991
Q
992
992
I
993
993
D
994
994
R
995
995
L
996
996
I
997
997
T
998
998
G
999
999
R
1000
1000
L
1001
1001
Q
1002
1002
S
1003
1003
L
1004
1004
Q
1005
1005
T
1006
1006
Y
1007
1007
V
1008
1008
T
1009
1009
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
1024
1024
A
1025
1025
A
1026
1026
T
1027
1027
K
1028
1028
M
1029
1029
S
1030
1030
E
1031
1031
C
1032
1032
V
1033
1033
L
1034
1034
G
1035
1035
Q
1036
1036
S
1037
1037
K
1038
1038
R
1039
1039
V
1040
1040
D
1041
1041
F
1042
1042
C
1043
1043
G
1044
1044
K
1045
1045
G
1046
1046
Y
1047
1047
H
1048
1048
L
1049
1049
M
1050
1050
S
1051
1051
F
1052
1052
P
1053
1053
Q
1054
1054
S
1055
1055
A
1056
1056
P
1057
1057
H
1058
1058
G
1059
1059
V
1060
1060
V
1061
1061
F
1062
1062
L
1063
1063
H
1064
1064
V
1065
1065
T
1066
1066
Y
1067
1067
V
1068
1068
P
1069
1069
A
1070
1070
Q
1071
1071
E
1072
1072
K
1073
1073
N
1074
1074
F
1075
1075
T
1076
1076
T
1077
1077
A
1078
1078
P
1079
1079
A
1080
1080
I
1081
1081
C
1082
1082
H
1083
1083
D
1084
1084
G
1085
1085
K
1086
1086
A
1087
1087
H
1088
1088
F
1089
1089
P
1090
1090
R
1091
1091
E
1092
1092
G
1093
1093
V
1094
1094
F
1095
1095
V
1096
1096
S
1097
1097
N
1098
1098
G
1099
1099
T
1100
1100
H
1101
1101
W
1102
1102
F
1103
1103
V
1104
1104
T
1105
1105
Q
1106
1106
R
1107
1107
N
1108
1108
F
1109
1109
Y
1110
1110
E
1111
1111
P
1112
1112
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
1122
1122
S
1123
1123
G
1124
1124
N
1125
1125
C
1126
1126
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.