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

tag_button

FMODB ID: R98L8

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 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 206
LigandCharge DGL=-1,DAR=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357942.274569
FMO2-HF: Nuclear repulsion 2278313.23632
FMO2-HF: Total energy -79629.03825
FMO2-MP2: Total energy -79861.877113


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.
-7.054-2.0730.759-2.401-3.339-0.005
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 : 0.026 / q_NPA : 0.006
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].
3A11VAL00.0100.0032.976-3.989-1.3420.157-1.178-1.6260.008
4A12ALA0-0.0100.0062.744-3.280-1.0690.602-1.194-1.619-0.013
5A13PRO00.029-0.0044.0380.0020.1250.000-0.029-0.0940.000
6A14VAL00.0030.0147.807-0.351-0.3510.0000.0000.0000.000
7A15TYR00.0020.00610.2060.2140.2140.0000.0000.0000.000
8A16VAL00.0270.00713.493-0.107-0.1070.0000.0000.0000.000
9A17GLY00.0180.00916.6150.0530.0530.0000.0000.0000.000
10A18GLY00.0500.01619.857-0.029-0.0290.0000.0000.0000.000
11A19PHE0-0.0110.01823.3350.0240.0240.0000.0000.0000.000
12A20LEU00.0270.02024.5890.0010.0010.0000.0000.0000.000
13A21ALA0-0.053-0.04627.9570.0130.0130.0000.0000.0000.000
14A22ARG10.8580.94029.1040.1810.1810.0000.0000.0000.000
15A23TYR0-0.0520.00233.7540.0110.0110.0000.0000.0000.000
16A24ASP-1-0.835-0.89335.516-0.116-0.1160.0000.0000.0000.000
17A56ALA00.0270.01121.9230.0000.0000.0000.0000.0000.000
18A57LEU0-0.049-0.02722.7760.0110.0110.0000.0000.0000.000
19A58PRO00.0330.03420.801-0.005-0.0050.0000.0000.0000.000
20A59LEU0-0.012-0.01916.773-0.025-0.0250.0000.0000.0000.000
21A60ASN0-0.003-0.01919.1230.0120.0120.0000.0000.0000.000
22A61ILE00.0370.02316.852-0.036-0.0360.0000.0000.0000.000
23A62ASN0-0.022-0.03220.8290.0020.0020.0000.0000.0000.000
24A63HIS00.006-0.00224.216-0.007-0.0070.0000.0000.0000.000
25A64ASP-1-0.764-0.83623.8800.0800.0800.0000.0000.0000.000
26A65ASP-1-0.842-0.94623.6510.0440.0440.0000.0000.0000.000
27A66THR0-0.072-0.04523.5350.0190.0190.0000.0000.0000.000
28A67ALA0-0.035-0.01519.9250.0310.0310.0000.0000.0000.000
29A68VAL0-0.015-0.01518.458-0.028-0.0280.0000.0000.0000.000
30A69VAL0-0.013-0.02014.3990.0360.0360.0000.0000.0000.000
31A70GLY00.0220.01413.9230.0100.0100.0000.0000.0000.000
32A71HIS0-0.0220.03115.048-0.032-0.0320.0000.0000.0000.000
33A72VAL0-0.002-0.01117.594-0.036-0.0360.0000.0000.0000.000
34A73ALA00.014-0.00817.4470.0230.0230.0000.0000.0000.000
35A74ALA00.0210.00819.5800.0130.0130.0000.0000.0000.000
36A75MET0-0.029-0.02322.786-0.014-0.0140.0000.0000.0000.000
37A76GLN00.0340.01525.7680.0180.0180.0000.0000.0000.000
38A77SER0-0.0110.00928.483-0.011-0.0110.0000.0000.0000.000
39A78VAL0-0.0030.01127.9050.0040.0040.0000.0000.0000.000
40A79ARG10.8640.90631.1630.1730.1730.0000.0000.0000.000
41A80ASP-1-0.780-0.89531.997-0.148-0.1480.0000.0000.0000.000
42A81GLY00.015-0.00731.906-0.002-0.0020.0000.0000.0000.000
43A82LEU0-0.059-0.00728.7460.0020.0020.0000.0000.0000.000
44A83PHE00.008-0.00221.635-0.005-0.0050.0000.0000.0000.000
45A84CYS0-0.017-0.01721.7280.0300.0300.0000.0000.0000.000
46A85LEU00.0080.01416.931-0.035-0.0350.0000.0000.0000.000
47A86GLY0-0.029-0.02317.9320.0440.0440.0000.0000.0000.000
48A87CYS0-0.044-0.02312.760-0.042-0.0420.0000.0000.0000.000
49A88VAL0-0.0010.00411.3210.0730.0730.0000.0000.0000.000
50A89THR0-0.012-0.0309.969-0.059-0.0590.0000.0000.0000.000
51A90SER0-0.034-0.03510.1390.1020.1020.0000.0000.0000.000
52A91PRO00.0430.0168.268-0.015-0.0150.0000.0000.0000.000
53A92ARG10.7960.8879.446-0.210-0.2100.0000.0000.0000.000
54A93PHE00.0320.02112.371-0.020-0.0200.0000.0000.0000.000
55A94LEU00.014-0.0056.500-0.024-0.0240.0000.0000.0000.000
56A95GLU-1-0.725-0.8379.0901.4871.4870.0000.0000.0000.000
57A96ILE0-0.062-0.01610.039-0.070-0.0700.0000.0000.0000.000
58A97VAL0-0.003-0.02011.192-0.052-0.0520.0000.0000.0000.000
59A98ARG10.7760.8556.467-1.293-1.2930.0000.0000.0000.000
60A99ARG10.8560.91910.157-0.880-0.8800.0000.0000.0000.000
61A100ALA00.0040.01212.731-0.084-0.0840.0000.0000.0000.000
62A101SER0-0.043-0.02811.347-0.127-0.1270.0000.0000.0000.000
63A102GLU-1-0.852-0.9019.6060.3340.3340.0000.0000.0000.000
64A103LYS10.8930.95413.6390.0060.0060.0000.0000.0000.000
65A104SER00.0150.01316.268-0.014-0.0140.0000.0000.0000.000
66A105GLU-1-0.799-0.88017.230-0.325-0.3250.0000.0000.0000.000
67A106LEU00.007-0.00318.500-0.049-0.0490.0000.0000.0000.000
68A107VAL00.001-0.01012.658-0.054-0.0540.0000.0000.0000.000
69A108SER0-0.053-0.04014.288-0.140-0.1400.0000.0000.0000.000
70A109ARG10.8070.90515.8700.3120.3120.0000.0000.0000.000
71A110GLY00.0050.03514.239-0.026-0.0260.0000.0000.0000.000
72A111PRO0-0.031-0.03312.5140.1310.1310.0000.0000.0000.000
73A112VAL00.0150.01715.7280.0320.0320.0000.0000.0000.000
74A113SER0-0.033-0.04017.4500.0710.0710.0000.0000.0000.000
75A114PRO0-0.0070.00916.100-0.014-0.0140.0000.0000.0000.000
76A115LEU0-0.0280.00112.917-0.121-0.1210.0000.0000.0000.000
77A116GLN00.0310.0187.216-0.379-0.3790.0000.0000.0000.000
78A117PRO00.0440.0189.591-0.010-0.0100.0000.0000.0000.000
79A118ASP-1-0.774-0.8356.732-3.709-3.7090.0000.0000.0000.000
80A119LYS10.9660.9668.0871.1001.1000.0000.0000.0000.000
81A120VAL00.0570.0307.5390.2470.2470.0000.0000.0000.000
82A121VAL00.0200.0118.6200.2390.2390.0000.0000.0000.000
83A122GLU-1-0.804-0.89810.795-0.968-0.9680.0000.0000.0000.000
84A123PHE00.0160.00512.5770.1270.1270.0000.0000.0000.000
85A124LEU0-0.0260.00211.6310.0950.0950.0000.0000.0000.000
86A125SER0-0.005-0.02114.6620.0730.0730.0000.0000.0000.000
87A126GLY0-0.0160.00117.0010.0370.0370.0000.0000.0000.000
88A127SER0-0.083-0.03717.8090.0650.0650.0000.0000.0000.000
89A128TYR0-0.059-0.05017.1760.0400.0400.0000.0000.0000.000
90A129ALA00.0550.04020.164-0.022-0.0220.0000.0000.0000.000
91A130GLY00.0350.02121.941-0.007-0.0070.0000.0000.0000.000
92A131LEU0-0.0260.00820.5480.0160.0160.0000.0000.0000.000
93A132SER0-0.052-0.04124.3870.0120.0120.0000.0000.0000.000
94A133LEU00.0150.01726.1030.0050.0050.0000.0000.0000.000
95A134SER0-0.029-0.03528.0900.0010.0010.0000.0000.0000.000
96A135SER00.0140.00829.8060.0030.0030.0000.0000.0000.000
97A136ARG10.8540.90332.000-0.031-0.0310.0000.0000.0000.000
98A137ARG10.8180.89734.5240.0000.0000.0000.0000.0000.000
99A138CYS0-0.035-0.02737.7580.0030.0030.0000.0000.0000.000
100A139ASP-1-0.848-0.91839.4150.0060.0060.0000.0000.0000.000
101A140ASP-1-0.810-0.89334.9390.0090.0090.0000.0000.0000.000
102A141VAL00.0340.01635.1360.0020.0020.0000.0000.0000.000
103A142GLU-1-0.857-0.89033.4660.0460.0460.0000.0000.0000.000
104A154PRO0-0.016-0.02029.7500.0000.0000.0000.0000.0000.000
105A155PHE0-0.027-0.03930.4150.0060.0060.0000.0000.0000.000
106A156LYS10.8950.95728.795-0.002-0.0020.0000.0000.0000.000
107A157HIS00.0350.04724.399-0.003-0.0030.0000.0000.0000.000
108A158VAL0-0.029-0.01522.383-0.013-0.0130.0000.0000.0000.000
109A159ALA00.0190.03122.3390.0100.0100.0000.0000.0000.000
110A160LEU0-0.032-0.01616.773-0.022-0.0220.0000.0000.0000.000
111A161CYS0-0.007-0.01121.2610.0310.0310.0000.0000.0000.000
112A162SER00.0310.02523.233-0.031-0.0310.0000.0000.0000.000
113A163VAL00.009-0.00524.839-0.024-0.0240.0000.0000.0000.000
114A164GLY00.0320.04627.0020.0180.0180.0000.0000.0000.000
115A165ARG10.8720.91028.2640.0690.0690.0000.0000.0000.000
116A166ARG10.8860.94430.5970.0910.0910.0000.0000.0000.000
117A167ARG10.8180.88531.0870.1070.1070.0000.0000.0000.000
118A168GLY00.0450.01029.4010.0070.0070.0000.0000.0000.000
119A169THR0-0.091-0.03926.996-0.014-0.0140.0000.0000.0000.000
120A170LEU00.0060.00822.6900.0050.0050.0000.0000.0000.000
121A171ALA0-0.039-0.00419.6070.0000.0000.0000.0000.0000.000
122A172VAL00.0010.00217.116-0.038-0.0380.0000.0000.0000.000
123A173TYR0-0.023-0.04313.3580.0440.0440.0000.0000.0000.000
124A174GLY00.034-0.00211.731-0.075-0.0750.0000.0000.0000.000
125A175ARG10.7440.8416.0432.3952.3950.0000.0000.0000.000
126A176ASP-1-0.825-0.9179.238-0.446-0.4460.0000.0000.0000.000
127A177PRO00.0290.02711.345-0.014-0.0140.0000.0000.0000.000
128A178GLU-1-0.730-0.84014.602-0.264-0.2640.0000.0000.0000.000
129A179TRP0-0.035-0.02213.091-0.016-0.0160.0000.0000.0000.000
130A180VAL00.0050.00214.2160.0100.0100.0000.0000.0000.000
131A181THR0-0.033-0.01716.6070.0440.0440.0000.0000.0000.000
132A182GLN0-0.084-0.07218.0140.0650.0650.0000.0000.0000.000
133A183ARG10.7720.89616.3550.6580.6580.0000.0000.0000.000
134A184PHE00.008-0.00220.3210.0240.0240.0000.0000.0000.000
135A185PRO00.0560.03723.7870.0170.0170.0000.0000.0000.000
136A186ASP-1-0.863-0.91626.767-0.198-0.1980.0000.0000.0000.000
137A187LEU0-0.061-0.02723.4100.0230.0230.0000.0000.0000.000
138A188THR00.0010.00026.334-0.017-0.0170.0000.0000.0000.000
139A189ALA0-0.009-0.01925.840-0.005-0.0050.0000.0000.0000.000
140A190ALA00.0830.03726.4460.0040.0040.0000.0000.0000.000
141A191ASP-1-0.820-0.89727.125-0.152-0.1520.0000.0000.0000.000
142A192ARG10.8550.90321.4310.3020.3020.0000.0000.0000.000
143A193ASP-1-0.846-0.89723.207-0.144-0.1440.0000.0000.0000.000
144A194GLY0-0.015-0.00625.2620.0160.0160.0000.0000.0000.000
145A195LEU0-0.035-0.02122.3690.0130.0130.0000.0000.0000.000
146A196ARG10.8630.89119.7520.2160.2160.0000.0000.0000.000
147A197ALA00.0260.01121.3570.0240.0240.0000.0000.0000.000
148A198GLN0-0.078-0.04923.3520.0330.0330.0000.0000.0000.000
149A199TRP00.0690.04416.7890.0120.0120.0000.0000.0000.000
150A200GLN0-0.052-0.02218.1570.0220.0220.0000.0000.0000.000
151A201ARG10.8750.94519.9610.0190.0190.0000.0000.0000.000
152A202CYS0-0.0520.00418.5720.0210.0210.0000.0000.0000.000
153A203GLY00.0540.01414.611-0.050-0.0500.0000.0000.0000.000
154A204SER0-0.032-0.0349.2010.0210.0210.0000.0000.0000.000
155A205THR0-0.031-0.01811.010-0.051-0.0510.0000.0000.0000.000
156A206ALA00.0490.04113.4300.0390.0390.0000.0000.0000.000
157A207VAL0-0.041-0.03215.5210.0460.0460.0000.0000.0000.000
158A208ASP-1-0.888-0.93817.9910.2790.2790.0000.0000.0000.000
159A209ALA0-0.0130.00218.100-0.026-0.0260.0000.0000.0000.000
160A210SER00.005-0.01119.9540.0010.0010.0000.0000.0000.000
161A211GLY0-0.0070.01116.6880.0000.0000.0000.0000.0000.000
162A212ASP-1-0.752-0.86813.2740.4160.4160.0000.0000.0000.000
163A213PRO00.0050.00914.938-0.020-0.0200.0000.0000.0000.000
164A214PHE00.0110.00615.655-0.041-0.0410.0000.0000.0000.000
165A215ARG10.8630.91417.536-0.133-0.1330.0000.0000.0000.000
166A216SER00.0630.07719.748-0.008-0.0080.0000.0000.0000.000
167A217ASP-1-0.835-0.94919.0170.2040.2040.0000.0000.0000.000
168A218SER00.007-0.01118.763-0.017-0.0170.0000.0000.0000.000
169A219TYR0-0.024-0.01619.644-0.030-0.0300.0000.0000.0000.000
170A220GLY00.0450.04922.611-0.021-0.0210.0000.0000.0000.000
171A221LEU0-0.026-0.01717.035-0.018-0.0180.0000.0000.0000.000
172A222LEU0-0.023-0.01321.423-0.026-0.0260.0000.0000.0000.000
173A223GLY00.0270.02423.452-0.016-0.0160.0000.0000.0000.000
174A224ASN00.0160.00423.200-0.002-0.0020.0000.0000.0000.000
175A225SER0-0.105-0.04823.083-0.021-0.0210.0000.0000.0000.000
176A226VAL00.0430.00224.974-0.017-0.0170.0000.0000.0000.000
177A227ASP-1-0.830-0.90728.501-0.033-0.0330.0000.0000.0000.000
178A228ALA0-0.059-0.03126.371-0.009-0.0090.0000.0000.0000.000
179A229LEU0-0.024-0.00727.454-0.014-0.0140.0000.0000.0000.000
180A230TYR0-0.050-0.03030.191-0.005-0.0050.0000.0000.0000.000
181A231ILE0-0.0080.02728.9010.0040.0040.0000.0000.0000.000
182A232DAR10.7920.87232.2420.0970.0970.0000.0000.0000.000
183A233DGL-1-0.801-0.91232.300-0.139-0.1390.0000.0000.0000.000
184A234ARG10.9240.98323.1060.1950.1950.0000.0000.0000.000
185A235LEU00.0420.00926.958-0.013-0.0130.0000.0000.0000.000
186A236PRO0-0.020-0.01829.321-0.013-0.0130.0000.0000.0000.000
187A237LYS10.8470.92230.4930.1540.1540.0000.0000.0000.000
188A238LEU00.0280.00324.906-0.006-0.0060.0000.0000.0000.000
189A239ARG10.8970.94627.5200.1920.1920.0000.0000.0000.000
190A240TYR00.0140.00829.171-0.006-0.0060.0000.0000.0000.000
191A241ASP-1-0.721-0.84527.815-0.182-0.1820.0000.0000.0000.000
192A242LYS10.8350.91124.7410.3500.3500.0000.0000.0000.000
193A243GLN0-0.045-0.01826.621-0.002-0.0020.0000.0000.0000.000
194A244LEU0-0.051-0.01229.6660.0030.0030.0000.0000.0000.000
195A245VAL0-0.035-0.03225.2780.0060.0060.0000.0000.0000.000
196A246GLY00.0250.02126.939-0.008-0.0080.0000.0000.0000.000
197A247VAL0-0.0210.01820.775-0.016-0.0160.0000.0000.0000.000
198A248THR00.0190.00422.6800.0050.0050.0000.0000.0000.000
199A249GLU-1-0.883-0.92520.189-0.445-0.4450.0000.0000.0000.000
200A250ARG10.9280.94019.5240.5250.5250.0000.0000.0000.000
201A251GLU-1-0.843-0.92618.460-0.581-0.5810.0000.0000.0000.000
202A252SER00.0150.00615.958-0.037-0.0370.0000.0000.0000.000
203A253TYR0-0.015-0.0339.8680.0650.0650.0000.0000.0000.000
204A254VAL00.0030.01515.9470.0420.0420.0000.0000.0000.000
205A255LYS10.8830.93415.7480.7220.7220.0000.0000.0000.000
206A256ALA0-0.0160.00720.4640.0340.0340.0000.0000.0000.000