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: LZNG9

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 OptAll
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 -1864337.152054
FMO2-HF: Nuclear repulsion 1788880.912296
FMO2-HF: Total energy -75456.239758
FMO2-MP2: Total energy -75658.378255


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.
-6.006-1.0693.53-2.408-6.058-0.007
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 : 0.026 / q_NPA : 0.010
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].
3A13PRO00.0410.0192.700-3.0110.1490.601-1.702-2.060-0.008
4A14VAL0-0.046-0.0144.7470.5360.634-0.001-0.005-0.0920.000
5A15TYR00.0110.0037.3790.0150.0150.0000.0000.0000.000
6A16VAL00.015-0.00210.8530.0860.0860.0000.0000.0000.000
7A17GLY00.0310.01213.783-0.016-0.0160.0000.0000.0000.000
8A18GLY00.0340.01417.5390.0210.0210.0000.0000.0000.000
9A19PHE0-0.036-0.01720.974-0.006-0.0060.0000.0000.0000.000
10A20LEU0-0.015-0.00621.1390.0070.0070.0000.0000.0000.000
11A21ALA00.0050.00324.7320.0160.0160.0000.0000.0000.000
12A22ARG10.8170.88728.4310.1540.1540.0000.0000.0000.000
13A23TYR0-0.040-0.03330.8800.0030.0030.0000.0000.0000.000
14A24ASP-1-0.960-0.96334.221-0.114-0.1140.0000.0000.0000.000
15A34LEU0-0.015-0.02630.2560.0030.0030.0000.0000.0000.000
16A35PRO00.0230.01634.021-0.006-0.0060.0000.0000.0000.000
17A36ARG10.8490.91133.6540.1360.1360.0000.0000.0000.000
18A37ASP-1-0.895-0.95535.146-0.114-0.1140.0000.0000.0000.000
19A38VAL0-0.014-0.00834.724-0.002-0.0020.0000.0000.0000.000
20A39VAL0-0.080-0.03829.914-0.005-0.0050.0000.0000.0000.000
21A40GLU-1-0.858-0.89431.745-0.154-0.1540.0000.0000.0000.000
22A41HIS0-0.009-0.00632.739-0.009-0.0090.0000.0000.0000.000
23A42TRP0-0.070-0.03531.1350.0040.0040.0000.0000.0000.000
24A55VAL00.012-0.01320.715-0.006-0.0060.0000.0000.0000.000
25A56ALA0-0.0100.00817.1290.0060.0060.0000.0000.0000.000
26A57LEU00.0220.01618.7430.0110.0110.0000.0000.0000.000
27A58PRO00.0240.01815.564-0.056-0.0560.0000.0000.0000.000
28A59LEU00.002-0.00712.6560.0440.0440.0000.0000.0000.000
29A60ASN0-0.011-0.01013.993-0.031-0.0310.0000.0000.0000.000
30A61ILE0-0.0060.01212.569-0.018-0.0180.0000.0000.0000.000
31A62ASN00.021-0.01916.5450.0180.0180.0000.0000.0000.000
32A63HIS00.0070.00419.8750.0230.0230.0000.0000.0000.000
33A64ASP-1-0.766-0.83518.747-0.072-0.0720.0000.0000.0000.000
34A65ASP-1-0.940-0.97618.248-0.119-0.1190.0000.0000.0000.000
35A66THR0-0.007-0.02717.619-0.002-0.0020.0000.0000.0000.000
36A67ALA0-0.011-0.01614.5410.0170.0170.0000.0000.0000.000
37A68VAL00.017-0.00212.925-0.052-0.0520.0000.0000.0000.000
38A69VAL0-0.046-0.0309.7040.0250.0250.0000.0000.0000.000
39A70GLY00.0450.0258.816-0.271-0.2710.0000.0000.0000.000
40A71HIS0-0.054-0.02310.6090.2150.2150.0000.0000.0000.000
41A72VAL0-0.014-0.01113.613-0.089-0.0890.0000.0000.0000.000
42A73ALA0-0.035-0.02714.721-0.004-0.0040.0000.0000.0000.000
43A74ALA0-0.031-0.01216.8080.0330.0330.0000.0000.0000.000
44A75MET0-0.014-0.01120.140-0.007-0.0070.0000.0000.0000.000
45A76GLN00.0310.02523.1460.0000.0000.0000.0000.0000.000
46A77SER00.0140.02026.1420.0030.0030.0000.0000.0000.000
47A78VAL0-0.0180.00126.7170.0050.0050.0000.0000.0000.000
48A79ARG10.8280.87229.9030.1620.1620.0000.0000.0000.000
49A80ASP-1-0.714-0.82530.469-0.141-0.1410.0000.0000.0000.000
50A81GLY00.026-0.00429.5530.0050.0050.0000.0000.0000.000
51A82LEU0-0.0090.03025.611-0.006-0.0060.0000.0000.0000.000
52A83PHE00.016-0.00220.429-0.007-0.0070.0000.0000.0000.000
53A84CYS0-0.072-0.02919.860-0.010-0.0100.0000.0000.0000.000
54A85LEU00.0080.00814.831-0.006-0.0060.0000.0000.0000.000
55A86GLY00.0360.01114.5250.0270.0270.0000.0000.0000.000
56A87CAS0-0.060-0.0239.9000.0090.0090.0000.0000.0000.000
57A88VAL00.0320.0217.8020.0500.0500.0000.0000.0000.000
58A89THR0-0.031-0.0615.356-0.333-0.3330.0000.0000.0000.000
59A90SER0-0.024-0.0293.941-0.900-0.7250.001-0.063-0.1120.000
60A91PRO00.014-0.0022.379-1.331-0.2551.557-0.586-2.0460.002
61A92ARG10.8550.9353.361-0.073-0.158-0.0020.344-0.2570.000
62A93PHE00.0490.0266.5850.0330.0330.0000.0000.0000.000
63A94LEU00.0140.0032.338-0.524-0.1911.376-0.384-1.325-0.001
64A95GLU-1-0.776-0.8584.7051.0361.164-0.001-0.007-0.1200.000
65A96ILE0-0.048-0.0255.807-0.029-0.0290.0000.0000.0000.000
66A97VAL00.0130.0087.8320.0040.0040.0000.0000.0000.000
67A98ARG10.7760.8646.427-0.651-0.6510.0000.0000.0000.000
68A99ARG10.8610.9308.518-0.621-0.6210.0000.0000.0000.000
69A100ALA00.0480.02911.235-0.014-0.0140.0000.0000.0000.000
70A101SER0-0.037-0.02211.207-0.015-0.0150.0000.0000.0000.000
71A102GLU-1-0.808-0.90111.6480.3320.3320.0000.0000.0000.000
72A103LYS10.7680.89414.193-0.234-0.2340.0000.0000.0000.000
73A104SER00.0000.00116.572-0.019-0.0190.0000.0000.0000.000
74A105GLU-1-0.769-0.86018.7970.0260.0260.0000.0000.0000.000
75A106LEU0-0.062-0.01818.233-0.008-0.0080.0000.0000.0000.000
76A107VAL0-0.0210.00214.986-0.025-0.0250.0000.0000.0000.000
77A108SER0-0.021-0.04618.1400.0220.0220.0000.0000.0000.000
78A109ARG10.7800.85318.278-0.044-0.0440.0000.0000.0000.000
79A110GLY00.0250.01618.653-0.006-0.0060.0000.0000.0000.000
80A111PRO0-0.041-0.01717.4910.0020.0020.0000.0000.0000.000
81A112VAL00.0280.01514.374-0.012-0.0120.0000.0000.0000.000
82A113SER00.0150.00616.8680.0020.0020.0000.0000.0000.000
83A114PRO00.023-0.01916.168-0.015-0.0150.0000.0000.0000.000
84A115LEU0-0.030-0.00217.252-0.032-0.0320.0000.0000.0000.000
85A116GLN0-0.038-0.01417.183-0.004-0.0040.0000.0000.0000.000
86A117PRO0-0.014-0.00814.116-0.013-0.0130.0000.0000.0000.000
87A118ASP-1-0.743-0.8539.011-0.448-0.4480.0000.0000.0000.000
88A119LYS10.8610.89611.6800.0410.0410.0000.0000.0000.000
89A120VAL00.0040.0156.5460.0190.0190.0000.0000.0000.000
90A121VAL00.0140.0169.430-0.034-0.0340.0000.0000.0000.000
91A122GLU-1-0.752-0.81111.410-0.088-0.0880.0000.0000.0000.000
92A123PHE00.0630.02412.2570.0120.0120.0000.0000.0000.000
93A124LEU0-0.0210.0138.9210.0160.0160.0000.0000.0000.000
94A125SER0-0.014-0.02413.3990.0060.0060.0000.0000.0000.000
95A126GLY00.0030.01316.3020.0210.0210.0000.0000.0000.000
96A127SER0-0.094-0.05714.9470.0170.0170.0000.0000.0000.000
97A128TYR00.0740.01713.4760.0230.0230.0000.0000.0000.000
98A129ALA00.0490.04317.287-0.034-0.0340.0000.0000.0000.000
99A130GLY00.0130.00519.5170.0100.0100.0000.0000.0000.000
100A131LEU0-0.002-0.00117.231-0.023-0.0230.0000.0000.0000.000
101A132SER0-0.014-0.01020.6050.0240.0240.0000.0000.0000.000
102A133LEU00.0670.04122.212-0.015-0.0150.0000.0000.0000.000
103A134SER0-0.0040.00324.3000.0160.0160.0000.0000.0000.000
104A155PHE00.006-0.01524.7080.0030.0030.0000.0000.0000.000
105A156LYS10.9360.98123.7380.1430.1430.0000.0000.0000.000
106A157HIS0-0.001-0.01319.6300.0030.0030.0000.0000.0000.000
107A158VAL0-0.004-0.00118.5440.0190.0190.0000.0000.0000.000
108A159ALA0-0.0020.02318.103-0.027-0.0270.0000.0000.0000.000
109A160LEU00.012-0.00112.4040.0000.0000.0000.0000.0000.000
110A161CAS0-0.047-0.01617.0760.0390.0390.0000.0000.0000.000
111A162SER00.0540.02818.915-0.007-0.0070.0000.0000.0000.000
112A163VAL0-0.034-0.02320.4780.0140.0140.0000.0000.0000.000
113A164GLY00.0400.05224.353-0.011-0.0110.0000.0000.0000.000
114A165ARG10.8880.94424.5690.1610.1610.0000.0000.0000.000
115A166ARG10.9210.93727.4140.0880.0880.0000.0000.0000.000
116A167ARG10.9030.94120.9100.1010.1010.0000.0000.0000.000
117A168GLY00.0440.02622.805-0.012-0.0120.0000.0000.0000.000
118A169THR0-0.015-0.02023.2790.0130.0130.0000.0000.0000.000
119A170LEU0-0.0580.00621.8500.0000.0000.0000.0000.0000.000
120A171ALA00.0000.01917.401-0.014-0.0140.0000.0000.0000.000
121A172VAL0-0.008-0.00516.8130.0220.0220.0000.0000.0000.000
122A173TYR00.011-0.01511.413-0.064-0.0640.0000.0000.0000.000
123A174GLY00.019-0.01011.6360.0870.0870.0000.0000.0000.000
124A175ARG10.7840.8554.2191.0681.120-0.001-0.005-0.0460.000
125A176ASP-1-0.768-0.88310.144-0.692-0.6920.0000.0000.0000.000
126A177PRO00.0290.02412.5940.0700.0700.0000.0000.0000.000
127A178GLU-1-0.820-0.86515.250-0.307-0.3070.0000.0000.0000.000
128A179TRP0-0.035-0.02115.6710.0390.0390.0000.0000.0000.000
129A180VAL00.008-0.00113.8090.0470.0470.0000.0000.0000.000
130A181THR00.002-0.02116.9960.0480.0480.0000.0000.0000.000
131A182GLN0-0.032-0.02920.1840.0490.0490.0000.0000.0000.000
132A183ARG10.8140.92519.1370.3290.3290.0000.0000.0000.000
133A184PHE00.0010.00919.3440.0220.0220.0000.0000.0000.000
134A185PRO0-0.007-0.01524.3180.0000.0000.0000.0000.0000.000
135A186ASP-1-0.838-0.88727.702-0.164-0.1640.0000.0000.0000.000
136A187LEU0-0.0370.00423.5110.0070.0070.0000.0000.0000.000
137A188THR00.009-0.01827.615-0.001-0.0010.0000.0000.0000.000
138A189ALA0-0.003-0.01727.984-0.015-0.0150.0000.0000.0000.000
139A190ALA00.0720.03527.891-0.015-0.0150.0000.0000.0000.000
140A191ASP-1-0.785-0.87226.941-0.211-0.2110.0000.0000.0000.000
141A192ARG10.8410.91323.8200.2100.2100.0000.0000.0000.000
142A193ASP-1-0.827-0.91823.483-0.286-0.2860.0000.0000.0000.000
143A194GLY00.0200.02225.215-0.012-0.0120.0000.0000.0000.000
144A195LEU0-0.030-0.01820.638-0.014-0.0140.0000.0000.0000.000
145A196ARG10.7990.86920.4920.2890.2890.0000.0000.0000.000
146A197ALA00.0070.00320.803-0.030-0.0300.0000.0000.0000.000
147A198GLN0-0.088-0.04921.0680.0050.0050.0000.0000.0000.000
148A199TRP00.0970.03616.033-0.046-0.0460.0000.0000.0000.000
149A200GLN0-0.003-0.00815.894-0.056-0.0560.0000.0000.0000.000
150A201ARG10.9110.95817.0370.3150.3150.0000.0000.0000.000
151A202CAS0-0.036-0.00412.8380.0090.0090.0000.0000.0000.000
152A203GLY0-0.0060.01612.936-0.098-0.0980.0000.0000.0000.000
153A204SER0-0.052-0.03014.2100.0310.0310.0000.0000.0000.000
154A205THR0-0.040-0.03214.8970.0920.0920.0000.0000.0000.000
155A206ALA0-0.026-0.00913.654-0.088-0.0880.0000.0000.0000.000
156A207VAL00.0460.01610.0250.0480.0480.0000.0000.0000.000
157A208ASP-1-0.801-0.8798.371-1.128-1.1280.0000.0000.0000.000
158A209ALA00.0160.0149.9230.1110.1110.0000.0000.0000.000
159A210SER0-0.035-0.00911.9770.0690.0690.0000.0000.0000.000
160A211GLY0-0.016-0.0039.7020.1060.1060.0000.0000.0000.000
161A212ASP-1-0.768-0.8767.025-0.106-0.1060.0000.0000.0000.000
162A213PRO00.0240.0288.5850.1220.1220.0000.0000.0000.000
163A214PHE0-0.0060.0079.9000.0510.0510.0000.0000.0000.000
164A215ARG10.7790.86411.8460.0960.0960.0000.0000.0000.000
165A216SER00.0570.03914.6220.0520.0520.0000.0000.0000.000
166A217ASP-1-0.830-0.91112.9540.1950.1950.0000.0000.0000.000
167A218SER00.015-0.00313.791-0.026-0.0260.0000.0000.0000.000
168A219TYR0-0.040-0.01914.887-0.028-0.0280.0000.0000.0000.000
169A220GLY00.0220.01817.622-0.019-0.0190.0000.0000.0000.000
170A221LEU0-0.029-0.02011.970-0.027-0.0270.0000.0000.0000.000
171A222LEU0-0.019-0.00416.652-0.019-0.0190.0000.0000.0000.000
172A223GLY00.0230.01619.387-0.009-0.0090.0000.0000.0000.000
173A224ASN00.002-0.01318.558-0.018-0.0180.0000.0000.0000.000
174A225TYR0-0.093-0.07217.550-0.007-0.0070.0000.0000.0000.000
175A226VAL0-0.026-0.01320.722-0.005-0.0050.0000.0000.0000.000
176A227ASP-1-0.888-0.94424.009-0.028-0.0280.0000.0000.0000.000
177A228ALA0-0.044-0.01522.594-0.003-0.0030.0000.0000.0000.000
178A229LEU0-0.104-0.04724.567-0.006-0.0060.0000.0000.0000.000
179A230TYR0-0.079-0.04326.3250.0030.0030.0000.0000.0000.000