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: JLQY9

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 OptH
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 -1861244.74738
FMO2-HF: Nuclear repulsion 1785789.767967
FMO2-HF: Total energy -75454.979413
FMO2-MP2: Total energy -75657.202039


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.
-6.038-1.4132.072-1.92-4.778-0.012
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 : 0.005 / q_NPA : -0.015
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].
3A13PRO00.0310.0172.533-3.772-1.2341.078-1.402-2.214-0.013
4A14VAL0-0.032-0.0084.9160.6630.760-0.001-0.005-0.0910.000
5A15TYR0-0.005-0.0097.380-0.049-0.0490.0000.0000.0000.000
6A16VAL00.0270.00710.9140.0850.0850.0000.0000.0000.000
7A17GLY00.0310.02113.8980.0010.0010.0000.0000.0000.000
8A18GLY00.0570.03217.5740.0150.0150.0000.0000.0000.000
9A19PHE0-0.038-0.01320.994-0.008-0.0080.0000.0000.0000.000
10A20LEU0-0.033-0.01721.242-0.006-0.0060.0000.0000.0000.000
11A21ALA00.010-0.00524.8470.0140.0140.0000.0000.0000.000
12A22ARG10.8630.92428.0050.1970.1970.0000.0000.0000.000
13A23TYR0-0.038-0.02530.8550.0000.0000.0000.0000.0000.000
14A24ASP-1-0.971-0.96534.186-0.128-0.1280.0000.0000.0000.000
15A34LEU0-0.008-0.02530.4380.0020.0020.0000.0000.0000.000
16A35PRO00.0160.01934.097-0.004-0.0040.0000.0000.0000.000
17A36ARG10.8670.91933.4610.1470.1470.0000.0000.0000.000
18A37ASP-1-0.896-0.95735.006-0.132-0.1320.0000.0000.0000.000
19A38VAL0-0.0070.00434.650-0.002-0.0020.0000.0000.0000.000
20A39VAL0-0.073-0.03929.784-0.006-0.0060.0000.0000.0000.000
21A40GLU-1-0.878-0.92531.797-0.171-0.1710.0000.0000.0000.000
22A41HIS0-0.068-0.04432.499-0.016-0.0160.0000.0000.0000.000
23A42TRP0-0.073-0.02931.0180.0100.0100.0000.0000.0000.000
24A55VAL00.017-0.00820.832-0.004-0.0040.0000.0000.0000.000
25A56ALA0-0.024-0.00317.2860.0080.0080.0000.0000.0000.000
26A57LEU00.0230.01518.622-0.015-0.0150.0000.0000.0000.000
27A58PRO00.0410.03415.714-0.062-0.0620.0000.0000.0000.000
28A59LEU00.011-0.01212.9330.0580.0580.0000.0000.0000.000
29A60ASN0-0.008-0.00314.070-0.068-0.0680.0000.0000.0000.000
30A61ILE00.0070.01013.212-0.002-0.0020.0000.0000.0000.000
31A62ASN00.015-0.02117.0080.0370.0370.0000.0000.0000.000
32A63HIS0-0.041-0.02620.2370.0360.0360.0000.0000.0000.000
33A64ASP-1-0.748-0.82518.981-0.295-0.2950.0000.0000.0000.000
34A65ASP-1-0.944-0.97418.280-0.335-0.3350.0000.0000.0000.000
35A66THR0-0.034-0.03818.016-0.031-0.0310.0000.0000.0000.000
36A67ALA0-0.061-0.04914.827-0.033-0.0330.0000.0000.0000.000
37A68VAL00.0150.00212.912-0.046-0.0460.0000.0000.0000.000
38A69VAL0-0.023-0.0339.741-0.071-0.0710.0000.0000.0000.000
39A70GLY00.0320.0138.862-0.400-0.4000.0000.0000.0000.000
40A71HIS0-0.057-0.01010.8200.2970.2970.0000.0000.0000.000
41A72VAL0-0.027-0.00713.832-0.076-0.0760.0000.0000.0000.000
42A73ALA0-0.030-0.02414.5210.0070.0070.0000.0000.0000.000
43A74ALA0-0.043-0.02916.3850.0600.0600.0000.0000.0000.000
44A75MET0-0.009-0.00719.952-0.022-0.0220.0000.0000.0000.000
45A76GLN00.0570.04723.0090.0110.0110.0000.0000.0000.000
46A77SER00.0070.04525.789-0.003-0.0030.0000.0000.0000.000
47A78VAL00.0250.00627.2250.0090.0090.0000.0000.0000.000
48A79ARG10.9530.97930.0450.1500.1500.0000.0000.0000.000
49A80ASP-1-0.753-0.86629.781-0.164-0.1640.0000.0000.0000.000
50A81GLY00.001-0.02329.6920.0000.0000.0000.0000.0000.000
51A82LEU00.0090.03125.553-0.003-0.0030.0000.0000.0000.000
52A83PHE0-0.002-0.00319.957-0.014-0.0140.0000.0000.0000.000
53A84CYS0-0.043-0.01319.377-0.018-0.0180.0000.0000.0000.000
54A85LEU00.0240.00914.654-0.004-0.0040.0000.0000.0000.000
55A86GLY00.0090.00014.4060.0170.0170.0000.0000.0000.000
56A87CAS0-0.035-0.0219.6430.0290.0290.0000.0000.0000.000
57A88VAL00.0010.0047.1500.0700.0700.0000.0000.0000.000
58A89THR00.007-0.0315.286-0.386-0.3860.0000.0000.0000.000
59A90SER0-0.028-0.0314.150-1.094-0.979-0.001-0.037-0.0780.000
60A91PRO00.0220.0022.494-1.206-0.1560.940-0.419-1.5710.001
61A92ARG10.8990.9593.6930.7740.9120.0010.073-0.2120.000
62A93PHE00.0380.0246.7660.1690.1690.0000.0000.0000.000
63A94LEU00.030-0.0023.210-0.3600.2590.056-0.122-0.5530.000
64A95GLU-1-0.816-0.8785.0430.4720.4720.0000.0000.0000.000
65A96ILE0-0.047-0.0256.1850.2090.2090.0000.0000.0000.000
66A97VAL00.0030.0048.0840.1170.1170.0000.0000.0000.000
67A98ARG10.8750.9216.549-0.066-0.0660.0000.0000.0000.000
68A99ARG10.8970.9698.6590.0640.0640.0000.0000.0000.000
69A100ALA00.0150.00711.5090.0470.0470.0000.0000.0000.000
70A101SER0-0.045-0.02711.2800.0270.0270.0000.0000.0000.000
71A102GLU-1-0.998-1.01011.7780.0760.0760.0000.0000.0000.000
72A103LYS10.7970.90114.6910.0760.0760.0000.0000.0000.000
73A104SER00.0100.01317.002-0.016-0.0160.0000.0000.0000.000
74A105GLU-1-0.888-0.95119.093-0.078-0.0780.0000.0000.0000.000
75A106LEU0-0.047-0.02218.238-0.001-0.0010.0000.0000.0000.000
76A107VAL0-0.0100.00514.822-0.013-0.0130.0000.0000.0000.000
77A108SER0-0.0190.00617.9840.0300.0300.0000.0000.0000.000
78A109ARG10.9080.94818.6340.0430.0430.0000.0000.0000.000
79A110GLY00.0270.02219.7030.0000.0000.0000.0000.0000.000
80A111PRO0-0.021-0.01517.533-0.006-0.0060.0000.0000.0000.000
81A112VAL00.0560.02613.916-0.012-0.0120.0000.0000.0000.000
82A113SER00.0050.00016.4780.0200.0200.0000.0000.0000.000
83A114PRO00.022-0.01615.685-0.025-0.0250.0000.0000.0000.000
84A115LEU0-0.033-0.01116.763-0.020-0.0200.0000.0000.0000.000
85A116GLN0-0.0090.00917.324-0.013-0.0130.0000.0000.0000.000
86A117PRO0-0.043-0.01114.147-0.008-0.0080.0000.0000.0000.000
87A118ASP-1-0.742-0.8689.350-0.564-0.5640.0000.0000.0000.000
88A119LYS10.9980.98811.5090.0460.0460.0000.0000.0000.000
89A120VAL00.0070.0106.815-0.004-0.0040.0000.0000.0000.000
90A121VAL00.0100.0069.344-0.061-0.0610.0000.0000.0000.000
91A122GLU-1-0.843-0.92611.181-0.200-0.2000.0000.0000.0000.000
92A123PHE00.0180.00512.3950.0230.0230.0000.0000.0000.000
93A124LEU0-0.0170.0028.8520.0170.0170.0000.0000.0000.000
94A125SER0-0.031-0.03013.3540.0210.0210.0000.0000.0000.000
95A126GLY0-0.0110.00816.1770.0390.0390.0000.0000.0000.000
96A127SER0-0.084-0.04215.2020.0120.0120.0000.0000.0000.000
97A128TYR00.0520.01013.7610.0360.0360.0000.0000.0000.000
98A129ALA00.0500.04317.277-0.032-0.0320.0000.0000.0000.000
99A130GLY00.0140.00719.6890.0170.0170.0000.0000.0000.000
100A131LEU00.0210.02617.022-0.036-0.0360.0000.0000.0000.000
101A132SER0-0.033-0.01720.6400.0430.0430.0000.0000.0000.000
102A133LEU00.0380.02222.352-0.027-0.0270.0000.0000.0000.000
103A134SER0-0.006-0.00123.7830.0230.0230.0000.0000.0000.000
104A155PHE00.027-0.00324.5380.0010.0010.0000.0000.0000.000
105A156LYS10.9490.99623.8790.2550.2550.0000.0000.0000.000
106A157HIS00.042-0.00119.490-0.010-0.0100.0000.0000.0000.000
107A158VAL00.0100.01118.4080.0370.0370.0000.0000.0000.000
108A159ALA0-0.0150.00718.074-0.049-0.0490.0000.0000.0000.000
109A160LEU0-0.014-0.00412.6430.0190.0190.0000.0000.0000.000
110A161CAS0-0.033-0.02517.3200.0240.0240.0000.0000.0000.000
111A162SER00.0260.01219.564-0.002-0.0020.0000.0000.0000.000
112A163VAL00.0030.00321.0220.0240.0240.0000.0000.0000.000
113A164GLY00.0270.04024.769-0.005-0.0050.0000.0000.0000.000
114A165ARG10.8790.93225.0400.2430.2430.0000.0000.0000.000
115A166ARG10.9030.93227.9430.1650.1650.0000.0000.0000.000
116A167ARG10.9250.95221.2090.2390.2390.0000.0000.0000.000
117A168GLY00.0370.02322.787-0.011-0.0110.0000.0000.0000.000
118A169THR0-0.004-0.02523.0560.0200.0200.0000.0000.0000.000
119A170LEU0-0.0350.01821.6540.0050.0050.0000.0000.0000.000
120A171ALA0-0.0030.01217.489-0.006-0.0060.0000.0000.0000.000
121A172VAL0-0.009-0.00116.5420.0110.0110.0000.0000.0000.000
122A173TYR00.013-0.02611.497-0.086-0.0860.0000.0000.0000.000
123A174GLY00.026-0.00111.8610.1090.1090.0000.0000.0000.000
124A175ARG10.8100.9054.0181.2601.328-0.001-0.008-0.0590.000
125A176ASP-1-0.823-0.9189.814-0.531-0.5310.0000.0000.0000.000
126A177PRO00.0300.01912.3870.0430.0430.0000.0000.0000.000
127A178GLU-1-0.796-0.87914.956-0.248-0.2480.0000.0000.0000.000
128A179TRP0-0.004-0.00115.4090.0230.0230.0000.0000.0000.000
129A180VAL00.004-0.00513.9190.0350.0350.0000.0000.0000.000
130A181THR00.0190.00616.9440.0430.0430.0000.0000.0000.000
131A182GLN0-0.078-0.03820.0480.0390.0390.0000.0000.0000.000
132A183ARG10.8590.94519.0060.2980.2980.0000.0000.0000.000
133A184PHE0-0.033-0.01519.6200.0140.0140.0000.0000.0000.000
134A185PRO0-0.033-0.02424.1940.0050.0050.0000.0000.0000.000
135A186ASP-1-0.927-0.95127.649-0.175-0.1750.0000.0000.0000.000
136A187LEU0-0.021-0.00523.1750.0090.0090.0000.0000.0000.000
137A188THR00.0000.00327.3120.0080.0080.0000.0000.0000.000
138A189ALA0-0.023-0.02527.479-0.014-0.0140.0000.0000.0000.000
139A190ALA00.0860.04327.475-0.010-0.0100.0000.0000.0000.000
140A191ASP-1-0.800-0.90126.638-0.203-0.2030.0000.0000.0000.000
141A192ARG10.9120.94223.3760.1780.1780.0000.0000.0000.000
142A193ASP-1-0.876-0.95023.300-0.207-0.2070.0000.0000.0000.000
143A194GLY0-0.023-0.01224.768-0.005-0.0050.0000.0000.0000.000
144A195LEU0-0.045-0.02420.749-0.015-0.0150.0000.0000.0000.000
145A196ARG10.8170.90319.8460.2140.2140.0000.0000.0000.000
146A197ALA00.0040.00219.918-0.019-0.0190.0000.0000.0000.000
147A198GLN0-0.089-0.05120.549-0.015-0.0150.0000.0000.0000.000
148A199TRP00.1100.04115.364-0.029-0.0290.0000.0000.0000.000
149A200GLN0-0.026-0.01815.432-0.034-0.0340.0000.0000.0000.000
150A201ARG10.9580.98516.6710.3020.3020.0000.0000.0000.000
151A202CAS0-0.0340.00412.3610.0010.0010.0000.0000.0000.000
152A203GLY0-0.0070.01412.257-0.055-0.0550.0000.0000.0000.000
153A204SER0-0.065-0.02913.3370.0750.0750.0000.0000.0000.000
154A205THR0-0.023-0.02314.1000.0530.0530.0000.0000.0000.000
155A206ALA0-0.027-0.01413.053-0.062-0.0620.0000.0000.0000.000
156A207VAL00.0310.0099.3730.0270.0270.0000.0000.0000.000
157A208ASP-1-0.819-0.9238.193-1.688-1.6880.0000.0000.0000.000
158A209ALA00.0200.02410.0470.0820.0820.0000.0000.0000.000
159A210SER0-0.051-0.02512.1440.0790.0790.0000.0000.0000.000
160A211GLY0-0.019-0.0139.7530.0800.0800.0000.0000.0000.000
161A212ASP-1-0.752-0.8597.451-1.305-1.3050.0000.0000.0000.000
162A213PRO00.0210.0398.9020.2270.2270.0000.0000.0000.000
163A214PHE00.0070.01310.1930.1150.1150.0000.0000.0000.000
164A215ARG10.7440.83411.9780.5050.5050.0000.0000.0000.000
165A216SER00.0980.06613.7840.0640.0640.0000.0000.0000.000
166A217ASP-1-0.848-0.94013.230-0.200-0.2000.0000.0000.0000.000
167A218SER00.003-0.01614.043-0.013-0.0130.0000.0000.0000.000
168A219TYR0-0.042-0.01515.1290.0020.0020.0000.0000.0000.000
169A220GLY00.0520.02717.7370.0050.0050.0000.0000.0000.000
170A221LEU0-0.021-0.01012.396-0.013-0.0130.0000.0000.0000.000
171A222LEU0-0.0130.01017.1130.0020.0020.0000.0000.0000.000
172A223GLY00.0210.01319.8750.0090.0090.0000.0000.0000.000
173A224ASN00.0250.02118.9870.0000.0000.0000.0000.0000.000
174A225TYR0-0.087-0.06718.3970.0150.0150.0000.0000.0000.000
175A226VAL0-0.042-0.02621.2540.0110.0110.0000.0000.0000.000
176A227ASP-1-0.899-0.95224.275-0.173-0.1730.0000.0000.0000.000
177A228ALA0-0.058-0.02523.1650.0060.0060.0000.0000.0000.000
178A229LEU0-0.109-0.05125.1100.0080.0080.0000.0000.0000.000
179A230TYR0-0.049-0.01426.7050.0200.0200.0000.0000.0000.000