FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 39JZL

Calculation Name: 1JQ6-A-Xray372

Preferred Name: Human herpes virus 5 capsid protein P40

Target Type: SINGLE PROTEIN

Ligand Name: s-(dimethylarsenic)cysteine

ligand 3-letter code: CAS

PDB ID: 1JQ6

Chain ID: A

ChEMBL ID: CHEMBL3771

UniProt ID: P16753

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1862399.255144
FMO2-HF: Nuclear repulsion 1786943.495787
FMO2-HF: Total energy -75455.759357
FMO2-MP2: Total energy -75657.95852


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:11:VAL)


Summations of interaction energy for fragment #1(A:11:VAL)
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.
-6.996-1.3252.111-2.559-5.226-0.004
Interaction energy analysis for fragmet #1(A:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.003
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].
3A13PRO00.0390.0172.680-3.787-0.1510.597-1.925-2.308-0.006
4A14VAL0-0.047-0.0185.0520.5260.618-0.001-0.005-0.0860.000
5A15TYR00.004-0.0097.494-0.056-0.0560.0000.0000.0000.000
6A16VAL00.0270.00511.0360.0970.0970.0000.0000.0000.000
7A17GLY00.0350.02613.999-0.014-0.0140.0000.0000.0000.000
8A18GLY00.0530.03217.6820.0250.0250.0000.0000.0000.000
9A19PHE0-0.044-0.01621.092-0.010-0.0100.0000.0000.0000.000
10A20LEU0-0.028-0.01621.3240.0030.0030.0000.0000.0000.000
11A21ALA00.007-0.00724.9260.0160.0160.0000.0000.0000.000
12A22ARG10.8320.92428.1800.1630.1630.0000.0000.0000.000
13A23TYR0-0.013-0.02130.9460.0010.0010.0000.0000.0000.000
14A24ASP-1-0.966-0.96234.282-0.114-0.1140.0000.0000.0000.000
15A34LEU0-0.017-0.02730.6050.0030.0030.0000.0000.0000.000
16A35PRO00.0310.02134.175-0.005-0.0050.0000.0000.0000.000
17A36ARG10.8450.91933.5580.1400.1400.0000.0000.0000.000
18A37ASP-1-0.895-0.95635.108-0.121-0.1210.0000.0000.0000.000
19A38VAL0-0.0030.00434.732-0.002-0.0020.0000.0000.0000.000
20A39VAL0-0.080-0.04429.861-0.005-0.0050.0000.0000.0000.000
21A40GLU-1-0.848-0.90031.893-0.161-0.1610.0000.0000.0000.000
22A41HIS0-0.057-0.03632.606-0.013-0.0130.0000.0000.0000.000
23A42TRP0-0.088-0.04931.1880.0060.0060.0000.0000.0000.000
24A55VAL00.010-0.01320.682-0.007-0.0070.0000.0000.0000.000
25A56ALA0-0.026-0.00117.2560.0110.0110.0000.0000.0000.000
26A57LEU00.0200.01718.4600.0000.0000.0000.0000.0000.000
27A58PRO00.0510.03515.804-0.058-0.0580.0000.0000.0000.000
28A59LEU00.002-0.00912.9320.0420.0420.0000.0000.0000.000
29A60ASN0-0.003-0.01114.157-0.035-0.0350.0000.0000.0000.000
30A61ILE0-0.0100.00512.970-0.012-0.0120.0000.0000.0000.000
31A62ASN00.022-0.01216.8980.0190.0190.0000.0000.0000.000
32A63HIS0-0.031-0.01420.3650.0230.0230.0000.0000.0000.000
33A64ASP-1-0.737-0.81519.029-0.091-0.0910.0000.0000.0000.000
34A65ASP-1-0.960-0.97818.327-0.142-0.1420.0000.0000.0000.000
35A66THR0-0.032-0.03318.005-0.004-0.0040.0000.0000.0000.000
36A67ALA0-0.045-0.04414.8410.0150.0150.0000.0000.0000.000
37A68VAL00.0130.00412.917-0.051-0.0510.0000.0000.0000.000
38A69VAL0-0.033-0.0369.8660.0000.0000.0000.0000.0000.000
39A70GLY00.0360.0178.955-0.296-0.2960.0000.0000.0000.000
40A71HIS0-0.060-0.02110.9190.2330.2330.0000.0000.0000.000
41A72VAL0-0.026-0.01213.964-0.077-0.0770.0000.0000.0000.000
42A73ALA0-0.037-0.02914.551-0.003-0.0030.0000.0000.0000.000
43A74ALA0-0.024-0.01616.5020.0410.0410.0000.0000.0000.000
44A75MET0-0.019-0.01520.096-0.008-0.0080.0000.0000.0000.000
45A76GLN00.0490.03723.1190.0030.0030.0000.0000.0000.000
46A77SER00.0060.03525.9090.0040.0040.0000.0000.0000.000
47A78VAL00.027-0.00527.2560.0040.0040.0000.0000.0000.000
48A79ARG10.8730.92830.1680.1590.1590.0000.0000.0000.000
49A80ASP-1-0.728-0.84729.987-0.150-0.1500.0000.0000.0000.000
50A81GLY00.0350.00529.8190.0050.0050.0000.0000.0000.000
51A82LEU0-0.0050.02825.680-0.008-0.0080.0000.0000.0000.000
52A83PHE0-0.005-0.00620.288-0.007-0.0070.0000.0000.0000.000
53A84CYS0-0.049-0.01219.809-0.016-0.0160.0000.0000.0000.000
54A85LEU00.0250.00714.823-0.004-0.0040.0000.0000.0000.000
55A86GLY00.0170.00414.5060.0070.0070.0000.0000.0000.000
56A87CAS0-0.051-0.0249.7680.0210.0210.0000.0000.0000.000
57A88VAL00.0130.0037.8160.0810.0810.0000.0000.0000.000
58A89THR0-0.004-0.0535.434-0.338-0.3380.0000.0000.0000.000
59A90SER0-0.025-0.0254.218-0.751-0.648-0.001-0.029-0.0740.000
60A91PRO00.0240.0042.411-1.181-0.0940.942-0.412-1.6180.002
61A92ARG10.8860.9493.809-0.1690.0030.0010.040-0.2140.000
62A93PHE00.0330.0186.8370.0370.0370.0000.0000.0000.000
63A94LEU00.024-0.0032.466-0.5170.0130.574-0.224-0.8790.000
64A95GLU-1-0.797-0.8705.0571.0051.0050.0000.0000.0000.000
65A96ILE0-0.048-0.0266.0260.0230.0230.0000.0000.0000.000
66A97VAL00.0080.0057.9930.0200.0200.0000.0000.0000.000
67A98ARG10.8050.8836.525-0.611-0.6110.0000.0000.0000.000
68A99ARG10.8710.9428.652-0.498-0.4980.0000.0000.0000.000
69A100ALA00.0300.02011.453-0.007-0.0070.0000.0000.0000.000
70A101SER0-0.036-0.02011.299-0.018-0.0180.0000.0000.0000.000
71A102GLU-1-0.899-0.94411.7160.3250.3250.0000.0000.0000.000
72A103LYS10.7870.88714.584-0.193-0.1930.0000.0000.0000.000
73A104SER00.0180.01516.788-0.022-0.0220.0000.0000.0000.000
74A105GLU-1-0.782-0.87019.1070.0270.0270.0000.0000.0000.000
75A106LEU0-0.037-0.01418.238-0.008-0.0080.0000.0000.0000.000
76A107VAL0-0.043-0.00314.792-0.018-0.0180.0000.0000.0000.000
77A108SER0-0.014-0.01118.0790.0230.0230.0000.0000.0000.000
78A109ARG10.8170.87318.644-0.042-0.0420.0000.0000.0000.000
79A110GLY00.0220.02519.712-0.009-0.0090.0000.0000.0000.000
80A111PRO0-0.002-0.00717.5060.0000.0000.0000.0000.0000.000
81A112VAL00.0520.02514.038-0.015-0.0150.0000.0000.0000.000
82A113SER0-0.009-0.00116.5380.0070.0070.0000.0000.0000.000
83A114PRO00.036-0.01415.835-0.016-0.0160.0000.0000.0000.000
84A115LEU0-0.030-0.00616.910-0.032-0.0320.0000.0000.0000.000
85A116GLN0-0.052-0.01517.201-0.013-0.0130.0000.0000.0000.000
86A117PRO0-0.018-0.00514.239-0.010-0.0100.0000.0000.0000.000
87A118ASP-1-0.744-0.8599.284-0.369-0.3690.0000.0000.0000.000
88A119LYS10.8930.92911.7090.0100.0100.0000.0000.0000.000
89A120VAL00.0210.0216.6090.0020.0020.0000.0000.0000.000
90A121VAL0-0.0010.0049.311-0.050-0.0500.0000.0000.0000.000
91A122GLU-1-0.772-0.87211.237-0.093-0.0930.0000.0000.0000.000
92A123PHE00.0340.01212.4390.0160.0160.0000.0000.0000.000
93A124LEU0-0.0120.0098.8810.0110.0110.0000.0000.0000.000
94A125SER0-0.035-0.02913.3720.0000.0000.0000.0000.0000.000
95A126GLY0-0.0060.00816.2210.0210.0210.0000.0000.0000.000
96A127SER0-0.084-0.03715.1110.0080.0080.0000.0000.0000.000
97A128TYR00.0590.01613.9840.0210.0210.0000.0000.0000.000
98A129ALA00.0480.03917.314-0.033-0.0330.0000.0000.0000.000
99A130GLY00.0140.00719.7280.0020.0020.0000.0000.0000.000
100A131LEU00.0230.02617.036-0.019-0.0190.0000.0000.0000.000
101A132SER0-0.023-0.01220.6950.0270.0270.0000.0000.0000.000
102A133LEU00.0470.02722.392-0.018-0.0180.0000.0000.0000.000
103A134SER0-0.0070.00024.0860.0200.0200.0000.0000.0000.000
104A155PHE00.012-0.01124.7240.0030.0030.0000.0000.0000.000
105A156LYS10.9671.00423.7290.1620.1620.0000.0000.0000.000
106A157HIS00.033-0.01019.601-0.002-0.0020.0000.0000.0000.000
107A158VAL0-0.0090.00218.5690.0250.0250.0000.0000.0000.000
108A159ALA0-0.0060.01618.187-0.029-0.0290.0000.0000.0000.000
109A160LEU0-0.012-0.00612.6800.0040.0040.0000.0000.0000.000
110A161CAS0-0.042-0.02817.3460.0350.0350.0000.0000.0000.000
111A162SER00.0440.02119.434-0.008-0.0080.0000.0000.0000.000
112A163VAL0-0.037-0.02020.9560.0160.0160.0000.0000.0000.000
113A164GLY00.0540.04924.751-0.010-0.0100.0000.0000.0000.000
114A165ARG10.8870.94524.8790.1660.1660.0000.0000.0000.000
115A166ARG10.9170.93727.8700.0930.0930.0000.0000.0000.000
116A167ARG10.9070.94321.1090.1100.1100.0000.0000.0000.000
117A168GLY00.0410.02322.913-0.012-0.0120.0000.0000.0000.000
118A169THR0-0.013-0.02523.2010.0130.0130.0000.0000.0000.000
119A170LEU0-0.0360.01421.8070.0000.0000.0000.0000.0000.000
120A171ALA0-0.0030.01517.488-0.012-0.0120.0000.0000.0000.000
121A172VAL0-0.009-0.00516.7760.0160.0160.0000.0000.0000.000
122A173TYR00.015-0.01911.513-0.073-0.0730.0000.0000.0000.000
123A174GLY00.018-0.00611.9750.0890.0890.0000.0000.0000.000
124A175ARG10.8100.8894.2350.8500.901-0.001-0.004-0.0470.000
125A176ASP-1-0.784-0.8999.955-0.724-0.7240.0000.0000.0000.000
126A177PRO00.0370.02812.4950.0790.0790.0000.0000.0000.000
127A178GLU-1-0.822-0.87215.105-0.313-0.3130.0000.0000.0000.000
128A179TRP0-0.004-0.00315.6260.0440.0440.0000.0000.0000.000
129A180VAL00.004-0.00313.9670.0510.0510.0000.0000.0000.000
130A181THR00.008-0.01717.0770.0480.0480.0000.0000.0000.000
131A182GLN0-0.069-0.03020.1860.0490.0490.0000.0000.0000.000
132A183ARG10.8360.93219.1610.3150.3150.0000.0000.0000.000
133A184PHE0-0.031-0.01519.5290.0230.0230.0000.0000.0000.000
134A185PRO0-0.027-0.02124.3180.0000.0000.0000.0000.0000.000
135A186ASP-1-0.903-0.94627.778-0.171-0.1710.0000.0000.0000.000
136A187LEU00.0000.00923.4170.0060.0060.0000.0000.0000.000
137A188THR00.002-0.01427.4480.0020.0020.0000.0000.0000.000
138A189ALA0-0.004-0.01627.630-0.016-0.0160.0000.0000.0000.000
139A190ALA00.0800.04127.626-0.015-0.0150.0000.0000.0000.000
140A191ASP-1-0.798-0.87426.913-0.215-0.2150.0000.0000.0000.000
141A192ARG10.8640.91223.5510.2130.2130.0000.0000.0000.000
142A193ASP-1-0.850-0.92923.448-0.287-0.2870.0000.0000.0000.000
143A194GLY0-0.0100.00525.179-0.011-0.0110.0000.0000.0000.000
144A195LEU0-0.041-0.03420.827-0.016-0.0160.0000.0000.0000.000
145A196ARG10.7900.87320.3030.2940.2940.0000.0000.0000.000
146A197ALA00.0150.00820.345-0.032-0.0320.0000.0000.0000.000
147A198GLN0-0.073-0.03620.761-0.018-0.0180.0000.0000.0000.000
148A199TRP00.1060.03915.691-0.047-0.0470.0000.0000.0000.000
149A200GLN0-0.012-0.01015.818-0.053-0.0530.0000.0000.0000.000
150A201ARG10.9270.96917.0680.3380.3380.0000.0000.0000.000
151A202CAS0-0.041-0.00712.7110.0010.0010.0000.0000.0000.000
152A203GLY0-0.0030.02012.588-0.088-0.0880.0000.0000.0000.000
153A204SER0-0.036-0.01813.6750.0210.0210.0000.0000.0000.000
154A205THR0-0.054-0.03414.4460.1010.1010.0000.0000.0000.000
155A206ALA0-0.023-0.01113.277-0.090-0.0900.0000.0000.0000.000
156A207VAL00.0310.0079.4510.0580.0580.0000.0000.0000.000
157A208ASP-1-0.797-0.8757.908-1.305-1.3050.0000.0000.0000.000
158A209ALA00.0240.0269.7650.1190.1190.0000.0000.0000.000
159A210SER0-0.040-0.01711.9780.0790.0790.0000.0000.0000.000
160A211GLY0-0.017-0.0149.7550.1010.1010.0000.0000.0000.000
161A212ASP-1-0.763-0.8757.587-0.251-0.2510.0000.0000.0000.000
162A213PRO00.0260.0288.9450.1420.1420.0000.0000.0000.000
163A214PHE00.0100.01310.2660.0490.0490.0000.0000.0000.000
164A215ARG10.7470.85311.9650.1410.1410.0000.0000.0000.000
165A216SER00.1010.06313.8610.0250.0250.0000.0000.0000.000
166A217ASP-1-0.847-0.92813.2920.1630.1630.0000.0000.0000.000
167A218SER00.014-0.00814.019-0.024-0.0240.0000.0000.0000.000
168A219TYR0-0.040-0.01915.101-0.026-0.0260.0000.0000.0000.000
169A220GLY00.0410.02617.795-0.017-0.0170.0000.0000.0000.000
170A221LEU0-0.020-0.00912.221-0.025-0.0250.0000.0000.0000.000
171A222LEU0-0.0100.00916.921-0.018-0.0180.0000.0000.0000.000
172A223GLY00.0200.01519.702-0.008-0.0080.0000.0000.0000.000
173A224ASN00.009-0.00718.796-0.016-0.0160.0000.0000.0000.000
174A225TYR0-0.109-0.08518.054-0.006-0.0060.0000.0000.0000.000
175A226VAL0-0.033-0.02121.107-0.004-0.0040.0000.0000.0000.000
176A227ASP-1-0.889-0.94424.184-0.045-0.0450.0000.0000.0000.000
177A228ALA0-0.049-0.02423.018-0.003-0.0030.0000.0000.0000.000
178A229LEU0-0.110-0.05624.966-0.002-0.0020.0000.0000.0000.000
179A230TYR0-0.076-0.02526.5840.0060.0060.0000.0000.0000.000