Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z6VZN

Calculation Name: 1LAY-A-Xray372

Preferred Name: Human herpes virus 5 capsid protein P40

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1LAY

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:


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 206
LigandCharge DGL=-1,DAR=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2359279.452865
FMO2-HF: Nuclear repulsion 2279651.867357
FMO2-HF: Total energy -79627.585508
FMO2-MP2: Total energy -79860.563912


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:9:GLN)


Summations of interaction energy for fragment #1(A:9:GLN)
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.
-6.981-2.1260.699-2.304-3.251-0.005
Interaction energy analysis for fragmet #1(A:9:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.011
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].
3A11VAL00.0150.0202.974-3.949-1.3730.165-1.125-1.6170.008
4A12ALA0-0.0100.0052.754-3.258-1.0880.534-1.151-1.552-0.013
5A13PRO00.0300.0004.0420.0030.1120.000-0.028-0.0820.000
6A14VAL00.0030.0137.812-0.299-0.2990.0000.0000.0000.000
7A15TYR00.0030.00110.2140.1810.1810.0000.0000.0000.000
8A16VAL00.0230.00613.526-0.104-0.1040.0000.0000.0000.000
9A17GLY00.0160.00816.6450.0520.0520.0000.0000.0000.000
10A18GLY00.0510.01719.883-0.031-0.0310.0000.0000.0000.000
11A19PHE0-0.0040.01623.3600.0260.0260.0000.0000.0000.000
12A20LEU00.0150.00724.923-0.001-0.0010.0000.0000.0000.000
13A21ALA0-0.082-0.06527.9660.0100.0100.0000.0000.0000.000
14A22ARG10.8910.96529.6120.1590.1590.0000.0000.0000.000
15A23TYR0-0.044-0.01533.7800.0100.0100.0000.0000.0000.000
16A24ASP-1-0.824-0.89535.497-0.110-0.1100.0000.0000.0000.000
17A56ALA00.0300.01221.9750.0000.0000.0000.0000.0000.000
18A57LEU0-0.060-0.03122.7780.0100.0100.0000.0000.0000.000
19A58PRO00.0380.04220.808-0.002-0.0020.0000.0000.0000.000
20A59LEU00.015-0.01716.358-0.024-0.0240.0000.0000.0000.000
21A60ASN00.009-0.00419.1330.0130.0130.0000.0000.0000.000
22A61ILE00.0270.01917.038-0.034-0.0340.0000.0000.0000.000
23A62ASN0-0.004-0.01920.8440.0010.0010.0000.0000.0000.000
24A63HIS0-0.006-0.00924.197-0.009-0.0090.0000.0000.0000.000
25A64ASP-1-0.804-0.87023.6610.0790.0790.0000.0000.0000.000
26A65ASP-1-0.873-0.96323.6650.0620.0620.0000.0000.0000.000
27A66THR0-0.111-0.03923.5480.0210.0210.0000.0000.0000.000
28A67ALA0-0.019-0.00919.9460.0310.0310.0000.0000.0000.000
29A68VAL00.016-0.00618.335-0.026-0.0260.0000.0000.0000.000
30A69VAL0-0.013-0.02014.4270.0350.0350.0000.0000.0000.000
31A70GLY00.0200.01113.9330.0160.0160.0000.0000.0000.000
32A71HIS0-0.0070.03614.598-0.028-0.0280.0000.0000.0000.000
33A72VAL0-0.011-0.01317.597-0.031-0.0310.0000.0000.0000.000
34A73ALA00.004-0.01017.4630.0200.0200.0000.0000.0000.000
35A74ALA00.0260.00319.5790.0120.0120.0000.0000.0000.000
36A75MET0-0.033-0.01822.785-0.017-0.0170.0000.0000.0000.000
37A76GLN00.0310.02325.7690.0210.0210.0000.0000.0000.000
38A77SER0-0.0140.01828.517-0.009-0.0090.0000.0000.0000.000
39A78VAL00.0080.01628.3300.0040.0040.0000.0000.0000.000
40A79ARG10.8590.90031.3340.1530.1530.0000.0000.0000.000
41A80ASP-1-0.791-0.89732.082-0.134-0.1340.0000.0000.0000.000
42A81GLY0-0.021-0.01731.937-0.003-0.0030.0000.0000.0000.000
43A82LEU0-0.048-0.00228.7200.0030.0030.0000.0000.0000.000
44A83PHE00.001-0.00221.874-0.004-0.0040.0000.0000.0000.000
45A84CYS0-0.034-0.02422.6360.0230.0230.0000.0000.0000.000
46A85LEU00.0380.02616.802-0.033-0.0330.0000.0000.0000.000
47A86GLY0-0.028-0.02217.9360.0400.0400.0000.0000.0000.000
48A87CYS0-0.045-0.01812.473-0.029-0.0290.0000.0000.0000.000
49A88VAL00.0020.00111.2500.0620.0620.0000.0000.0000.000
50A89THR00.006-0.0169.962-0.051-0.0510.0000.0000.0000.000
51A90SER0-0.042-0.01910.1440.0950.0950.0000.0000.0000.000
52A91PRO00.0470.0218.376-0.011-0.0110.0000.0000.0000.000
53A92ARG10.8290.9249.457-0.225-0.2250.0000.0000.0000.000
54A93PHE00.0310.02212.360-0.023-0.0230.0000.0000.0000.000
55A94LEU00.013-0.0086.821-0.033-0.0330.0000.0000.0000.000
56A95GLU-1-0.793-0.8928.8701.5211.5210.0000.0000.0000.000
57A96ILE0-0.081-0.02510.059-0.080-0.0800.0000.0000.0000.000
58A97VAL00.005-0.01611.162-0.053-0.0530.0000.0000.0000.000
59A98ARG10.8030.9036.324-1.348-1.3480.0000.0000.0000.000
60A99ARG10.9370.98710.014-0.795-0.7950.0000.0000.0000.000
61A100ALA00.0130.01212.586-0.083-0.0830.0000.0000.0000.000
62A101SER0-0.052-0.03411.360-0.102-0.1020.0000.0000.0000.000
63A102GLU-1-0.896-0.9559.9630.1930.1930.0000.0000.0000.000
64A103LYS10.8870.95213.5250.0270.0270.0000.0000.0000.000
65A104SER00.0130.01516.042-0.002-0.0020.0000.0000.0000.000
66A105GLU-1-0.869-0.93917.019-0.331-0.3310.0000.0000.0000.000
67A106LEU0-0.020-0.01318.490-0.051-0.0510.0000.0000.0000.000
68A107VAL00.009-0.00612.522-0.050-0.0500.0000.0000.0000.000
69A108SER0-0.057-0.03714.106-0.143-0.1430.0000.0000.0000.000
70A109ARG10.8720.95115.6790.3400.3400.0000.0000.0000.000
71A110GLY00.0070.03514.088-0.027-0.0270.0000.0000.0000.000
72A111PRO0-0.039-0.03712.3960.1310.1310.0000.0000.0000.000
73A112VAL0-0.0010.02115.5500.0270.0270.0000.0000.0000.000
74A113SER00.029-0.04417.2470.0610.0610.0000.0000.0000.000
75A114PRO0-0.0570.00115.991-0.017-0.0170.0000.0000.0000.000
76A115LEU0-0.0120.01712.854-0.106-0.1060.0000.0000.0000.000
77A116GLN00.0470.0287.197-0.394-0.3940.0000.0000.0000.000
78A117PRO00.0210.0369.1630.0020.0020.0000.0000.0000.000
79A118ASP-1-0.760-0.8476.756-3.664-3.6640.0000.0000.0000.000
80A119LYS11.0150.9847.9151.3711.3710.0000.0000.0000.000
81A120VAL00.0520.0247.4190.2420.2420.0000.0000.0000.000
82A121VAL00.0180.0228.4990.2330.2330.0000.0000.0000.000
83A122GLU-1-0.812-0.88910.671-0.954-0.9540.0000.0000.0000.000
84A123PHE00.0130.00812.4020.1210.1210.0000.0000.0000.000
85A124LEU0-0.026-0.00711.7680.0900.0900.0000.0000.0000.000
86A125SER0-0.020-0.04014.4710.0650.0650.0000.0000.0000.000
87A126GLY0-0.021-0.00616.8720.0350.0350.0000.0000.0000.000
88A127SER0-0.071-0.01917.8420.0600.0600.0000.0000.0000.000
89A128TYR0-0.057-0.04516.8300.0390.0390.0000.0000.0000.000
90A129ALA00.0520.02520.179-0.018-0.0180.0000.0000.0000.000
91A130GLY00.0340.01621.820-0.007-0.0070.0000.0000.0000.000
92A131LEU0-0.0200.01020.5090.0160.0160.0000.0000.0000.000
93A132SER0-0.065-0.04624.3990.0100.0100.0000.0000.0000.000
94A133LEU00.0390.02926.1140.0060.0060.0000.0000.0000.000
95A134SER0-0.040-0.05927.9260.0010.0010.0000.0000.0000.000
96A135SER00.0100.00429.8140.0040.0040.0000.0000.0000.000
97A136ARG10.8730.91332.012-0.039-0.0390.0000.0000.0000.000
98A137ARG10.8730.92634.532-0.005-0.0050.0000.0000.0000.000
99A138CYS0-0.010-0.01837.7670.0030.0030.0000.0000.0000.000
100A139ASP-1-0.946-0.96939.3110.0120.0120.0000.0000.0000.000
101A140ASP-1-0.863-0.92734.4530.0150.0150.0000.0000.0000.000
102A141VAL00.0390.02535.0430.0010.0010.0000.0000.0000.000
103A142GLU-1-0.866-0.90033.4120.0540.0540.0000.0000.0000.000
104A154PRO0-0.014-0.01729.8510.0000.0000.0000.0000.0000.000
105A155PHE0-0.028-0.03630.4390.0060.0060.0000.0000.0000.000
106A156LYS10.9440.98629.024-0.005-0.0050.0000.0000.0000.000
107A157HIS00.0790.07224.392-0.002-0.0020.0000.0000.0000.000
108A158VAL0-0.028-0.01022.421-0.014-0.0140.0000.0000.0000.000
109A159ALA00.0000.01922.3490.0110.0110.0000.0000.0000.000
110A160LEU0-0.018-0.00616.669-0.021-0.0210.0000.0000.0000.000
111A161CYS0-0.005-0.01421.2750.0280.0280.0000.0000.0000.000
112A162SER0-0.0110.00623.249-0.027-0.0270.0000.0000.0000.000
113A163VAL00.018-0.01024.825-0.024-0.0240.0000.0000.0000.000
114A164GLY00.0420.05026.9250.0170.0170.0000.0000.0000.000
115A165ARG10.8790.91528.2780.0560.0560.0000.0000.0000.000
116A166ARG10.9430.98030.8620.0740.0740.0000.0000.0000.000
117A167ARG10.8160.88531.0990.0990.0990.0000.0000.0000.000
118A168GLY00.0470.00829.3360.0070.0070.0000.0000.0000.000
119A169THR0-0.086-0.03626.933-0.012-0.0120.0000.0000.0000.000
120A170LEU0-0.0010.01422.4930.0050.0050.0000.0000.0000.000
121A171ALA0-0.040-0.00919.5380.0020.0020.0000.0000.0000.000
122A172VAL0-0.0040.00817.169-0.039-0.0390.0000.0000.0000.000
123A173TYR0-0.012-0.03013.1990.0550.0550.0000.0000.0000.000
124A174GLY00.018-0.00611.882-0.081-0.0810.0000.0000.0000.000
125A175ARG10.7200.8385.5712.0922.0920.0000.0000.0000.000
126A176ASP-1-0.833-0.9149.430-0.304-0.3040.0000.0000.0000.000
127A177PRO00.0470.02211.610-0.031-0.0310.0000.0000.0000.000
128A178GLU-1-0.798-0.89914.880-0.221-0.2210.0000.0000.0000.000
129A179TRP0-0.054-0.01913.248-0.037-0.0370.0000.0000.0000.000
130A180VAL00.0180.01114.4030.0010.0010.0000.0000.0000.000
131A181THR0-0.042-0.01616.7740.0310.0310.0000.0000.0000.000
132A182GLN0-0.073-0.06318.2540.0370.0370.0000.0000.0000.000
133A183ARG10.8190.91716.7020.5870.5870.0000.0000.0000.000
134A184PHE00.0130.01020.4420.0170.0170.0000.0000.0000.000
135A185PRO00.0630.03523.9120.0190.0190.0000.0000.0000.000
136A186ASP-1-0.872-0.92826.870-0.186-0.1860.0000.0000.0000.000
137A187LEU0-0.068-0.02823.4090.0220.0220.0000.0000.0000.000
138A188THR0-0.0130.02526.518-0.018-0.0180.0000.0000.0000.000
139A189ALA00.005-0.02226.081-0.004-0.0040.0000.0000.0000.000
140A190ALA00.0880.02926.7210.0050.0050.0000.0000.0000.000
141A191ASP-1-0.833-0.92327.226-0.128-0.1280.0000.0000.0000.000
142A192ARG10.8830.92521.7750.2500.2500.0000.0000.0000.000
143A193ASP-1-0.886-0.92623.516-0.108-0.1080.0000.0000.0000.000
144A194GLY0-0.028-0.01325.6110.0170.0170.0000.0000.0000.000
145A195LEU0-0.017-0.02022.6420.0140.0140.0000.0000.0000.000
146A196ARG10.9300.95019.5270.1740.1740.0000.0000.0000.000
147A197ALA00.0080.00021.5670.0250.0250.0000.0000.0000.000
148A198GLN0-0.065-0.04723.2820.0310.0310.0000.0000.0000.000
149A199TRP00.0590.05016.9030.0140.0140.0000.0000.0000.000
150A200GLN0-0.050-0.01918.1970.0310.0310.0000.0000.0000.000
151A201ARG10.8660.94319.997-0.012-0.0120.0000.0000.0000.000
152A202CYS0-0.0520.00618.5690.0150.0150.0000.0000.0000.000
153A203GLY00.0420.01014.605-0.042-0.0420.0000.0000.0000.000
154A204SER0-0.044-0.0519.0590.0090.0090.0000.0000.0000.000
155A205THR0-0.039-0.02611.073-0.049-0.0490.0000.0000.0000.000
156A206ALA00.0520.04913.4410.0420.0420.0000.0000.0000.000
157A207VAL0-0.038-0.02615.4360.0480.0480.0000.0000.0000.000
158A208ASP-1-0.886-0.94117.8390.2850.2850.0000.0000.0000.000
159A209ALA0-0.0080.00518.146-0.024-0.0240.0000.0000.0000.000
160A210SER0-0.009-0.02119.9940.0020.0020.0000.0000.0000.000
161A211GLY0-0.0050.01416.688-0.001-0.0010.0000.0000.0000.000
162A212ASP-1-0.762-0.90013.2960.4480.4480.0000.0000.0000.000
163A213PRO0-0.025-0.00414.887-0.021-0.0210.0000.0000.0000.000
164A214PHE0-0.023-0.00815.710-0.035-0.0350.0000.0000.0000.000
165A215ARG10.9270.94217.548-0.143-0.1430.0000.0000.0000.000
166A216SER00.0800.08819.754-0.010-0.0100.0000.0000.0000.000
167A217ASP-1-0.861-0.97819.0490.1960.1960.0000.0000.0000.000
168A218SER0-0.011-0.02118.846-0.029-0.0290.0000.0000.0000.000
169A219TYR00.0140.00319.664-0.030-0.0300.0000.0000.0000.000
170A220GLY00.0410.04522.674-0.020-0.0200.0000.0000.0000.000
171A221LEU0-0.022-0.01017.252-0.018-0.0180.0000.0000.0000.000
172A222LEU0-0.029-0.01421.443-0.026-0.0260.0000.0000.0000.000
173A223GLY00.0280.02423.473-0.016-0.0160.0000.0000.0000.000
174A224ASN00.0280.01322.9730.0020.0020.0000.0000.0000.000
175A225SER0-0.103-0.05123.204-0.021-0.0210.0000.0000.0000.000
176A226VAL00.0480.00224.995-0.018-0.0180.0000.0000.0000.000
177A227ASP-1-0.835-0.91028.566-0.031-0.0310.0000.0000.0000.000
178A228ALA0-0.051-0.02626.414-0.009-0.0090.0000.0000.0000.000
179A229LEU0-0.046-0.01727.249-0.013-0.0130.0000.0000.0000.000
180A230TYR0-0.055-0.03130.004-0.004-0.0040.0000.0000.0000.000
181A231ILE0-0.0050.02829.1220.0050.0050.0000.0000.0000.000
182A232DAR10.7900.86832.1030.0940.0940.0000.0000.0000.000
183A233DGL-1-0.790-0.90232.213-0.134-0.1340.0000.0000.0000.000
184A234ARG10.9541.00622.9920.1940.1940.0000.0000.0000.000
185A235LEU00.0310.00127.157-0.012-0.0120.0000.0000.0000.000
186A236PRO0-0.014-0.01229.177-0.013-0.0130.0000.0000.0000.000
187A237LYS10.8770.97230.2010.1360.1360.0000.0000.0000.000
188A238LEU00.020-0.00224.549-0.006-0.0060.0000.0000.0000.000
189A239ARG10.8800.93827.4190.1930.1930.0000.0000.0000.000
190A240TYR00.0190.00929.064-0.004-0.0040.0000.0000.0000.000
191A241ASP-1-0.721-0.86427.584-0.172-0.1720.0000.0000.0000.000
192A242LYS10.8390.92824.4000.3500.3500.0000.0000.0000.000
193A243GLN0-0.043-0.02526.6640.0010.0010.0000.0000.0000.000
194A244LEU0-0.040-0.00629.7070.0030.0030.0000.0000.0000.000
195A245VAL0-0.046-0.03825.3380.0060.0060.0000.0000.0000.000
196A246GLY00.0250.02427.073-0.007-0.0070.0000.0000.0000.000
197A247VAL0-0.0060.02520.957-0.017-0.0170.0000.0000.0000.000
198A248THR00.007-0.00222.819-0.002-0.0020.0000.0000.0000.000
199A249GLU-1-0.913-0.95920.153-0.438-0.4380.0000.0000.0000.000
200A250ARG10.9450.95218.8790.5200.5200.0000.0000.0000.000
201A251GLU-1-0.880-0.94718.576-0.512-0.5120.0000.0000.0000.000
202A252SER00.006-0.01416.000-0.027-0.0270.0000.0000.0000.000
203A253TYR0-0.020-0.0659.8740.0560.0560.0000.0000.0000.000
204A254VAL0-0.0010.01215.9130.0360.0360.0000.0000.0000.000
205A255LYS10.8710.92215.6430.7240.7240.0000.0000.0000.000
206A256ALA0-0.0080.00520.3310.0300.0300.0000.0000.0000.000