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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LL3G9

Calculation Name: 6W4B-AB-Xray101

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6W4B

Chain ID: AB

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2020-04-16

Reference: K. Kato, Y. Handa, Y. Kawashima, K. Fukuzawa et. Al., FMO Calculation for SARS Cov-2 related proteins. To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2483151.747973
FMO2-HF: Nuclear repulsion 2395813.856844
FMO2-HF: Total energy -87337.891129
FMO2-MP2: Total energy -87588.447218


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER )


Summations of interaction energy for fragment #1(A:6:SER )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
0.2152.7830.762-1.261-2.0690.007
Interaction energy analysis for fragmet #1(A:6:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : ******
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A8VAL 0-0.0112.7050.3832.7970.764-1.239-1.9390.007
4A9ALA 00.0505.273-0.180-0.116-0.001-0.009-0.0540.000
5A10LEU 0-0.0159.0280.2550.2550.0000.0000.0000.000
6A11ARG 10.94011.4180.2180.2180.0000.0000.0000.000
7A12GLN 00.03914.6220.0010.0010.0000.0000.0000.000
8A13MET 0-0.07317.7480.0230.0230.0000.0000.0000.000
9A14SER 00.03620.655-0.012-0.0120.0000.0000.0000.000
10A15CYS 0-0.05622.7630.0080.0080.0000.0000.0000.000
11A16ALA 00.04624.843-0.005-0.0050.0000.0000.0000.000
12A17ALA 00.02326.1240.0030.0030.0000.0000.0000.000
13A18GLY 00.08128.0870.0010.0010.0000.0000.0000.000
14A19THR 00.03830.232-0.001-0.0010.0000.0000.0000.000
15A20THR 00.01032.8510.0030.0030.0000.0000.0000.000
16A21GLN 00.05228.8290.0020.0020.0000.0000.0000.000
17A22THR 00.01532.4050.0010.0010.0000.0000.0000.000
18A23ALA 0-0.02833.832-0.001-0.0010.0000.0000.0000.000
19A24CYS 0-0.10329.513-0.005-0.0050.0000.0000.0000.000
20A25THR 0-0.03531.4060.0070.0070.0000.0000.0000.000
21A26ASP -1-0.91731.951-0.038-0.0380.0000.0000.0000.000
22A27ASP -1-0.91727.731-0.066-0.0660.0000.0000.0000.000
23A28ASN 0-0.00429.408-0.008-0.0080.0000.0000.0000.000
24A29ALA 0-0.01225.148-0.006-0.0060.0000.0000.0000.000
25A30LEU 0-0.00520.7740.0030.0030.0000.0000.0000.000
26A31ALA 00.03218.982-0.010-0.0100.0000.0000.0000.000
27A32TYR 00.03514.7120.0020.0020.0000.0000.0000.000
28A33TYR 0-0.02413.6160.0330.0330.0000.0000.0000.000
29A34ASN 00.0336.7050.0480.0480.0000.0000.0000.000
30A35THR 0-0.0038.7360.0090.0090.0000.0000.0000.000
31A36THR 0-0.0037.1900.2270.2270.0000.0000.0000.000
32A37LYS 10.9499.312-0.826-0.8260.0000.0000.0000.000
33A38GLY 00.06711.476-0.060-0.0600.0000.0000.0000.000
34A39GLY 0-0.02014.108-0.060-0.0600.0000.0000.0000.000
35A40ARG 10.95013.1670.0020.0020.0000.0000.0000.000
36A41PHE 0-0.0339.6620.0180.0180.0000.0000.0000.000
37A42VAL 00.05312.578-0.063-0.0630.0000.0000.0000.000
38A43LEU 0-0.06310.0020.0110.0110.0000.0000.0000.000
39A44ALA 00.03714.3140.0050.0050.0000.0000.0000.000
40A45LEU 0-0.02317.5790.0110.0110.0000.0000.0000.000
41A46LEU 00.00121.012-0.008-0.0080.0000.0000.0000.000
42A47SER 00.00622.9860.0100.0100.0000.0000.0000.000
43A48ASP -1-0.80526.726-0.119-0.1190.0000.0000.0000.000
44A49LEU 00.03329.5600.0060.0060.0000.0000.0000.000
45A50GLN 00.02029.582-0.006-0.0060.0000.0000.0000.000
46A51ASP -1-0.90231.152-0.052-0.0520.0000.0000.0000.000
47A52LEU 0-0.07027.0030.0070.0070.0000.0000.0000.000
48A53LYS 10.95527.8990.0440.0440.0000.0000.0000.000
49A54TRP 0-0.00126.1150.0040.0040.0000.0000.0000.000
50A55ALA 00.04923.281-0.008-0.0080.0000.0000.0000.000
51A56ARG 10.95124.8890.0210.0210.0000.0000.0000.000
52A57PHE 00.00620.700-0.007-0.0070.0000.0000.0000.000
53A58PRO 00.01324.3260.0100.0100.0000.0000.0000.000
54A59LYS 10.84123.581-0.085-0.0850.0000.0000.0000.000
55A60SER 00.00221.549-0.002-0.0020.0000.0000.0000.000
56A61ASP -1-0.84923.6010.0800.0800.0000.0000.0000.000
57A62GLY 00.07225.931-0.006-0.0060.0000.0000.0000.000
58A63THR 0-0.07727.419-0.003-0.0030.0000.0000.0000.000
59A64GLY 00.05128.359-0.004-0.0040.0000.0000.0000.000
60A65THR 0-0.04626.913-0.003-0.0030.0000.0000.0000.000
61A66ILE 0-0.03821.3930.0070.0070.0000.0000.0000.000
62A67TYR 00.01224.907-0.009-0.0090.0000.0000.0000.000
63A68THR 0-0.04119.8580.0110.0110.0000.0000.0000.000
64A69GLU -1-0.85423.004-0.013-0.0130.0000.0000.0000.000
65A70LEU 0-0.04522.370-0.004-0.0040.0000.0000.0000.000
66A71GLU -1-0.82820.437-0.097-0.0970.0000.0000.0000.000
67A72PRO 0-0.02023.955-0.002-0.0020.0000.0000.0000.000
68A73PRO 0-0.02425.034-0.010-0.0100.0000.0000.0000.000
69A74CYS -1-0.80223.443-0.151-0.1510.0000.0000.0000.000
70A75ARG 10.75325.6070.0960.0960.0000.0000.0000.000
71A76PHE 00.03623.807-0.012-0.0120.0000.0000.0000.000
72A77VAL 00.04227.5320.0080.0080.0000.0000.0000.000
73A78THR 0-0.06325.701-0.012-0.0120.0000.0000.0000.000
74A79ASP -1-0.79628.263-0.123-0.1230.0000.0000.0000.000
75A80THR 0-0.11929.628-0.006-0.0060.0000.0000.0000.000
76A81PRO 00.04331.4480.0060.0060.0000.0000.0000.000
77A82LYS 10.90934.2800.0940.0940.0000.0000.0000.000
78A83GLY 00.05135.9480.0050.0050.0000.0000.0000.000
79A84PRO 00.01832.960-0.005-0.0050.0000.0000.0000.000
80A85LYS 10.90030.4450.1190.1190.0000.0000.0000.000
81A86VAL 00.00630.593-0.010-0.0100.0000.0000.0000.000
82A87LYS 10.77426.2400.1370.1370.0000.0000.0000.000
83A88TYR 00.03826.837-0.001-0.0010.0000.0000.0000.000
84A89LEU 0-0.03219.196-0.003-0.0030.0000.0000.0000.000
85A90TYR 00.00822.2700.0080.0080.0000.0000.0000.000
86A91PHE 00.06115.664-0.022-0.0220.0000.0000.0000.000
87A92ILE 00.00516.6350.0250.0250.0000.0000.0000.000
88A93LYS 10.87518.447-0.020-0.0200.0000.0000.0000.000
89A94GLY 0-0.01518.5930.0200.0200.0000.0000.0000.000
90A95LEU 0-0.04812.3940.0090.0090.0000.0000.0000.000
91A96ASN 00.0749.536-0.080-0.0800.0000.0000.0000.000
92A97ASN 00.05513.250-0.038-0.0380.0000.0000.0000.000
93A98LEU 00.0055.9190.0460.0460.0000.0000.0000.000
94A99ASN 00.0178.412-0.271-0.2710.0000.0000.0000.000
95A100ARG 10.81210.3820.1680.1680.0000.0000.0000.000
96A101GLY 00.05312.3160.0200.0200.0000.0000.0000.000
97A102MET 0-0.0316.432-0.110-0.1100.0000.0000.0000.000
98A103VAL 00.03110.8550.0350.0350.0000.0000.0000.000
99A104LEU 00.01114.2380.0310.0310.0000.0000.0000.000
100A105GLY 0-0.02813.2470.0370.0370.0000.0000.0000.000
101A106SER 0-0.00613.2840.0130.0130.0000.0000.0000.000
102A107LEU 0-0.02414.7760.0490.0490.0000.0000.0000.000
103A108ALA 00.02017.7370.0280.0280.0000.0000.0000.000
104A109ALA 0-0.04816.2850.0230.0230.0000.0000.0000.000
105A110THR 0-0.06717.2960.0270.0270.0000.0000.0000.000
106A111VAL 0-0.02419.9720.0360.0360.0000.0000.0000.000
107A112ARG 10.92323.0160.1700.1700.0000.0000.0000.000
108A113LEU 00.00922.4240.0100.0100.0000.0000.0000.000
109A114GLN -1-0.96226.547-0.127-0.1270.0000.0000.0000.000
110B-1ASN 0-0.01435.5370.0030.0030.0000.0000.0000.000
111B0ALA 0-0.00933.719-0.004-0.0040.0000.0000.0000.000
112B1MET 00.00928.0930.0040.0040.0000.0000.0000.000
113B2ASN 0-0.03632.042-0.002-0.0020.0000.0000.0000.000
114B3ASN 0-0.05525.0250.0100.0100.0000.0000.0000.000
115B4GLU -1-0.78827.511-0.108-0.1080.0000.0000.0000.000
116B5LEU 0-0.03221.188-0.007-0.0070.0000.0000.0000.000
117B6SER 0-0.01925.1320.0050.0050.0000.0000.0000.000
118B7PRO 00.03324.506-0.020-0.0200.0000.0000.0000.000
119B8VAL 0-0.04420.3690.0040.0040.0000.0000.0000.000
120B9ALA 00.01121.375-0.017-0.0170.0000.0000.0000.000
121B10LEU 0-0.02415.0630.0020.0020.0000.0000.0000.000
122B11ARG 10.93619.1690.2090.2090.0000.0000.0000.000
123B12GLN 00.01816.6710.0180.0180.0000.0000.0000.000
124B13MET 0-0.08320.0540.0270.0270.0000.0000.0000.000
125B14SER 00.02721.393-0.020-0.0200.0000.0000.0000.000
126B15CYS 0-0.02721.6420.0020.0020.0000.0000.0000.000
127B16ALA 00.02923.4890.0000.0000.0000.0000.0000.000
128B17ALA 00.02920.835-0.003-0.0030.0000.0000.0000.000
129B18GLY 00.07622.5860.0020.0020.0000.0000.0000.000
130B19THR 00.05722.4650.0010.0010.0000.0000.0000.000
131B20THR 0-0.01223.8930.0040.0040.0000.0000.0000.000
132B21GLN 00.06326.896-0.010-0.0100.0000.0000.0000.000
133B22THR 00.01228.637-0.005-0.0050.0000.0000.0000.000
134B23ALA 0-0.04926.805-0.003-0.0030.0000.0000.0000.000
135B24CYS 0-0.08825.582-0.005-0.0050.0000.0000.0000.000
136B25THR 00.01026.776-0.001-0.0010.0000.0000.0000.000
137B26ASP -1-0.84826.802-0.073-0.0730.0000.0000.0000.000
138B27ASP -1-0.93625.025-0.115-0.1150.0000.0000.0000.000
139B28ASN 00.03623.168-0.009-0.0090.0000.0000.0000.000
140B29ALA 0-0.04918.597-0.001-0.0010.0000.0000.0000.000
141B30LEU 00.02417.0230.0010.0010.0000.0000.0000.000
142B31ALA 00.01417.005-0.019-0.0190.0000.0000.0000.000
143B32TYR 0-0.01214.383-0.001-0.0010.0000.0000.0000.000
144B33TYR 0-0.02416.8470.0230.0230.0000.0000.0000.000
145B34ASN 00.07218.852-0.033-0.0330.0000.0000.0000.000
146B35THR 0-0.04821.0460.0200.0200.0000.0000.0000.000
147B36THR 00.03924.6610.0000.0000.0000.0000.0000.000
148B37LYS 11.00326.4210.0890.0890.0000.0000.0000.000
149B38GLY 0-0.04028.9440.0070.0070.0000.0000.0000.000
150B39GLY 00.04328.4560.0020.0020.0000.0000.0000.000
151B40ARG 10.93324.0460.1360.1360.0000.0000.0000.000
152B41PHE 00.01919.0890.0070.0070.0000.0000.0000.000
153B42VAL 00.00118.205-0.029-0.0290.0000.0000.0000.000
154B43LEU 0-0.03014.4210.0090.0090.0000.0000.0000.000
155B44ALA 00.00012.0840.0090.0090.0000.0000.0000.000
156B45LEU 0-0.01013.7550.0010.0010.0000.0000.0000.000
157B46LEU 0-0.00911.814-0.002-0.0020.0000.0000.0000.000
158B47SER 00.00614.4770.0200.0200.0000.0000.0000.000
159B48ASP -1-0.82014.858-0.217-0.2170.0000.0000.0000.000
160B49LEU 00.03616.7240.0200.0200.0000.0000.0000.000
161B50GLN 0-0.01314.243-0.016-0.0160.0000.0000.0000.000
162B51ASP -1-0.90215.8290.0760.0760.0000.0000.0000.000
163B52LEU 0-0.02717.460-0.019-0.0190.0000.0000.0000.000
164B53LYS 10.93218.024-0.061-0.0610.0000.0000.0000.000
165B54TRP 0-0.00720.226-0.005-0.0050.0000.0000.0000.000
166B55ALA 00.05120.497-0.005-0.0050.0000.0000.0000.000
167B56ARG 10.86222.5760.0750.0750.0000.0000.0000.000
168B57PHE 00.02520.292-0.015-0.0150.0000.0000.0000.000
169B58PRO 00.02326.3670.0080.0080.0000.0000.0000.000
170B59LYS 10.86228.8750.0560.0560.0000.0000.0000.000
171B60SER 0-0.01829.295-0.001-0.0010.0000.0000.0000.000
172B61ASP -1-0.84930.967-0.071-0.0710.0000.0000.0000.000
173B62GLY 00.06034.0630.0010.0010.0000.0000.0000.000
174B63THR 0-0.07535.3740.0040.0040.0000.0000.0000.000
175B64GLY 00.04734.4890.0050.0050.0000.0000.0000.000
176B65THR 0-0.03330.239-0.005-0.0050.0000.0000.0000.000
177B66ILE 0-0.04225.5560.0050.0050.0000.0000.0000.000
178B67TYR 00.03525.618-0.005-0.0050.0000.0000.0000.000
179B68THR 0-0.07719.995-0.004-0.0040.0000.0000.0000.000
180B69GLU -1-0.79120.1440.0310.0310.0000.0000.0000.000
181B70LEU 0-0.04316.337-0.019-0.0190.0000.0000.0000.000
182B71GLU -1-0.85111.8830.1370.1370.0000.0000.0000.000
183B72PRO 0-0.03412.179-0.025-0.0250.0000.0000.0000.000
184B73PRO 00.00411.2840.0610.0610.0000.0000.0000.000
185B74CYS 0-0.0535.8930.2890.2890.0000.0000.0000.000
186B75ARG 10.9597.397-0.597-0.5970.0000.0000.0000.000
187B76PHE 0-0.0285.4790.0920.0920.0000.0000.0000.000
188B77VAL 00.0186.8170.1810.1810.0000.0000.0000.000
189B78THR 0-0.0349.380-0.188-0.1880.0000.0000.0000.000
190B79ASP -1-0.73712.032-0.208-0.2080.0000.0000.0000.000
191B80THR 0-0.04914.8430.0110.0110.0000.0000.0000.000
192B81PRO 00.00617.9330.0230.0230.0000.0000.0000.000
193B82LYS 10.88221.3470.1620.1620.0000.0000.0000.000
194B83GLY 00.06020.0170.0160.0160.0000.0000.0000.000
195B84PRO 00.02114.502-0.017-0.0170.0000.0000.0000.000
196B85LYS 10.93815.1250.1880.1880.0000.0000.0000.000
197B86VAL 0-0.01610.879-0.071-0.0710.0000.0000.0000.000
198B87LYS 10.83311.1940.3110.3110.0000.0000.0000.000
199B88TYR 00.01110.3970.0350.0350.0000.0000.0000.000
200B89LEU 0-0.0117.875-0.071-0.0710.0000.0000.0000.000
201B90TYR 0-0.00110.2900.1830.1830.0000.0000.0000.000
202B91PHE 00.0706.748-0.123-0.1230.0000.0000.0000.000
203B92ILE 00.04612.3950.0510.0510.0000.0000.0000.000
204B93LYS 10.81814.997-0.036-0.0360.0000.0000.0000.000
205B94GLY 00.03516.8840.0180.0180.0000.0000.0000.000
206B95LEU 0-0.05212.169-0.019-0.0190.0000.0000.0000.000
207B96ASN 00.09613.972-0.021-0.0210.0000.0000.0000.000
208B97ASN 00.0569.5320.0040.0040.0000.0000.0000.000
209B98LEU 00.01611.016-0.131-0.1310.0000.0000.0000.000
210B99ASN 00.02312.762-0.090-0.0900.0000.0000.0000.000
211B100ARG 10.7468.4490.0210.0210.0000.0000.0000.000
212B101GLY 00.0298.319-0.245-0.2450.0000.0000.0000.000
213B102MET 0-0.0129.385-0.106-0.1060.0000.0000.0000.000
214B103VAL 00.0209.407-0.001-0.0010.0000.0000.0000.000
215B104LEU 0-0.0144.273-0.113-0.023-0.001-0.013-0.0760.000
216B105GLY 00.0017.861-0.036-0.0360.0000.0000.0000.000
217B106SER 00.00810.6960.1160.1160.0000.0000.0000.000
218B107LEU 0-0.0237.8510.0810.0810.0000.0000.0000.000
219B108ALA 00.0028.9870.0920.0920.0000.0000.0000.000
220B109ALA 0-0.02910.8120.1400.1400.0000.0000.0000.000
221B110THR 0-0.05113.8840.0980.0980.0000.0000.0000.000
222B111VAL 0-0.04411.8610.0930.0930.0000.0000.0000.000
223B112ARG 10.82913.1500.2650.2650.0000.0000.0000.000
224B113LEU 0-0.0457.263-0.021-0.0210.0000.0000.0000.000
225B114GLN -1-0.9376.023-0.224-0.2240.0000.0000.0000.000