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: QYVLY

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 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 206
LigandCharge DGL=-1,DAR=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2360495.71875
FMO2-HF: Nuclear repulsion 2280865.616476
FMO2-HF: Total energy -79630.102273
FMO2-MP2: Total energy -79862.926569


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.
-8.535-3.6111.432-2.799-3.557-0.014
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 : 0.024 / 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].
3A11VAL00.003-0.0032.923-3.847-1.3410.162-1.165-1.5040.007
4A12ALA00.0180.0122.455-4.808-2.4871.271-1.614-1.977-0.021
5A13PRO00.0370.0014.310-0.0410.056-0.001-0.020-0.0760.000
6A14VAL0-0.0300.0027.710-0.406-0.4060.0000.0000.0000.000
7A15TYR00.0100.01410.3400.2260.2260.0000.0000.0000.000
8A16VAL00.008-0.00513.425-0.111-0.1110.0000.0000.0000.000
9A17GLY00.0300.01916.5590.0620.0620.0000.0000.0000.000
10A18GLY00.0580.02119.956-0.025-0.0250.0000.0000.0000.000
11A19PHE0-0.0310.00723.3740.0200.0200.0000.0000.0000.000
12A20LEU00.0200.00324.7570.0040.0040.0000.0000.0000.000
13A21ALA0-0.043-0.03428.2780.0170.0170.0000.0000.0000.000
14A22ARG10.8190.89928.7590.1990.1990.0000.0000.0000.000
15A23TYR0-0.073-0.02633.5540.0130.0130.0000.0000.0000.000
16A24ASP-1-0.818-0.89334.955-0.125-0.1250.0000.0000.0000.000
17A56ALA00.0410.01322.2940.0010.0010.0000.0000.0000.000
18A57LEU0-0.063-0.02523.5580.0130.0130.0000.0000.0000.000
19A58PRO00.0470.02821.266-0.008-0.0080.0000.0000.0000.000
20A59LEU0-0.012-0.00517.174-0.021-0.0210.0000.0000.0000.000
21A60ASN0-0.020-0.01418.9160.0050.0050.0000.0000.0000.000
22A61ILE00.0180.02116.912-0.034-0.0340.0000.0000.0000.000
23A62ASN0-0.013-0.03520.9340.0050.0050.0000.0000.0000.000
24A63HIS00.0150.00724.491-0.004-0.0040.0000.0000.0000.000
25A64ASP-1-0.718-0.80823.5770.0670.0670.0000.0000.0000.000
26A65ASP-1-0.817-0.90623.2550.0120.0120.0000.0000.0000.000
27A66THR0-0.053-0.05423.3560.0200.0200.0000.0000.0000.000
28A67ALA0-0.016-0.00919.7740.0260.0260.0000.0000.0000.000
29A68VAL0-0.026-0.01818.784-0.028-0.0280.0000.0000.0000.000
30A69VAL0-0.003-0.01214.4290.0360.0360.0000.0000.0000.000
31A70GLY00.0340.01314.042-0.002-0.0020.0000.0000.0000.000
32A71HIS0-0.040-0.00115.394-0.020-0.0200.0000.0000.0000.000
33A72VAL00.000-0.01418.097-0.043-0.0430.0000.0000.0000.000
34A73ALA00.0140.01017.6480.0240.0240.0000.0000.0000.000
35A74ALA00.0250.00519.8010.0120.0120.0000.0000.0000.000
36A75MET0-0.045-0.02922.916-0.013-0.0130.0000.0000.0000.000
37A76GLN00.0480.02726.0470.0160.0160.0000.0000.0000.000
38A77SER0-0.022-0.00428.373-0.010-0.0100.0000.0000.0000.000
39A78VAL00.0180.02527.5610.0050.0050.0000.0000.0000.000
40A79ARG10.8220.88330.8400.1960.1960.0000.0000.0000.000
41A80ASP-1-0.748-0.84331.926-0.167-0.1670.0000.0000.0000.000
42A81GLY00.005-0.01331.8390.0000.0000.0000.0000.0000.000
43A82LEU0-0.0310.00229.037-0.002-0.0020.0000.0000.0000.000
44A83PHE00.0330.01421.543-0.005-0.0050.0000.0000.0000.000
45A84CYS0-0.078-0.03823.3660.0260.0260.0000.0000.0000.000
46A85LEU00.0140.01616.701-0.040-0.0400.0000.0000.0000.000
47A86GLY00.0210.00618.2010.0520.0520.0000.0000.0000.000
48A87CYS0-0.045-0.01512.768-0.054-0.0540.0000.0000.0000.000
49A88VAL0-0.0070.00711.3340.0830.0830.0000.0000.0000.000
50A89THR0-0.007-0.03110.134-0.075-0.0750.0000.0000.0000.000
51A90SER0-0.036-0.02910.3600.0940.0940.0000.0000.0000.000
52A91PRO00.0380.0178.440-0.027-0.0270.0000.0000.0000.000
53A92ARG10.8030.8869.385-0.181-0.1810.0000.0000.0000.000
54A93PHE00.0350.01412.1100.0190.0190.0000.0000.0000.000
55A94LEU00.0160.0056.703-0.027-0.0270.0000.0000.0000.000
56A95GLU-1-0.729-0.8338.5271.5591.5590.0000.0000.0000.000
57A96ILE0-0.060-0.0279.414-0.023-0.0230.0000.0000.0000.000
58A97VAL00.0010.00210.865-0.044-0.0440.0000.0000.0000.000
59A98ARG10.7580.8386.785-1.471-1.4710.0000.0000.0000.000
60A99ARG10.8580.9229.804-0.877-0.8770.0000.0000.0000.000
61A100ALA00.0270.01612.842-0.077-0.0770.0000.0000.0000.000
62A101SER0-0.036-0.03111.207-0.118-0.1180.0000.0000.0000.000
63A102GLU-1-0.824-0.8699.6500.6270.6270.0000.0000.0000.000
64A103LYS10.8350.91213.808-0.066-0.0660.0000.0000.0000.000
65A104SER00.0440.03416.558-0.023-0.0230.0000.0000.0000.000
66A105GLU-1-0.773-0.85317.187-0.285-0.2850.0000.0000.0000.000
67A106LEU00.0580.02718.759-0.050-0.0500.0000.0000.0000.000
68A107VAL0-0.034-0.00212.981-0.069-0.0690.0000.0000.0000.000
69A108SER0-0.044-0.04513.785-0.080-0.0800.0000.0000.0000.000
70A109ARG10.8120.88315.8610.2670.2670.0000.0000.0000.000
71A110GLY00.0180.04414.325-0.015-0.0150.0000.0000.0000.000
72A111PRO0-0.012-0.01412.6000.1110.1110.0000.0000.0000.000
73A112VAL00.0220.01715.8450.0320.0320.0000.0000.0000.000
74A113SER0-0.039-0.03817.3840.0860.0860.0000.0000.0000.000
75A114PRO0-0.0250.00516.091-0.036-0.0360.0000.0000.0000.000
76A115LEU0-0.0220.00712.840-0.125-0.1250.0000.0000.0000.000
77A116GLN00.0540.0207.532-0.284-0.2840.0000.0000.0000.000
78A117PRO00.0190.0029.770-0.094-0.0940.0000.0000.0000.000
79A118ASP-1-0.796-0.8626.441-3.694-3.6940.0000.0000.0000.000
80A119LYS10.8670.9188.1240.7950.7950.0000.0000.0000.000
81A120VAL00.0310.0187.0800.2770.2770.0000.0000.0000.000
82A121VAL00.0340.0148.6300.2280.2280.0000.0000.0000.000
83A122GLU-1-0.781-0.88910.928-0.884-0.8840.0000.0000.0000.000
84A123PHE00.0210.00912.7480.1210.1210.0000.0000.0000.000
85A124LEU0-0.0040.01111.9030.0930.0930.0000.0000.0000.000
86A125SER0-0.007-0.02314.5260.0620.0620.0000.0000.0000.000
87A126GLY0-0.017-0.00116.9880.0170.0170.0000.0000.0000.000
88A127SER0-0.061-0.02017.8840.0610.0610.0000.0000.0000.000
89A128TYR0-0.042-0.03517.3080.0420.0420.0000.0000.0000.000
90A129ALA00.0750.05220.257-0.026-0.0260.0000.0000.0000.000
91A130GLY00.0310.01821.686-0.009-0.0090.0000.0000.0000.000
92A131LEU0-0.0120.01820.9780.0120.0120.0000.0000.0000.000
93A132SER0-0.044-0.05824.6190.0160.0160.0000.0000.0000.000
94A133LEU00.0150.02626.4990.0070.0070.0000.0000.0000.000
95A134SER0-0.038-0.03928.1180.0030.0030.0000.0000.0000.000
96A135SER00.0550.00530.076-0.001-0.0010.0000.0000.0000.000
97A136ARG10.8460.93132.714-0.014-0.0140.0000.0000.0000.000
98A137ARG10.7730.85434.8280.0100.0100.0000.0000.0000.000
99A138CYS00.014-0.00937.9940.0030.0030.0000.0000.0000.000
100A139ASP-1-0.818-0.88739.534-0.003-0.0030.0000.0000.0000.000
101A140ASP-1-0.823-0.87234.857-0.006-0.0060.0000.0000.0000.000
102A141VAL00.0480.01935.4570.0020.0020.0000.0000.0000.000
103A142GLU-1-0.905-0.93933.8800.0340.0340.0000.0000.0000.000
104A154PRO0-0.029-0.03129.9880.0010.0010.0000.0000.0000.000
105A155PHE00.012-0.00231.0590.0040.0040.0000.0000.0000.000
106A156LYS10.8260.92828.6990.0190.0190.0000.0000.0000.000
107A157HIS00.0320.02824.494-0.004-0.0040.0000.0000.0000.000
108A158VAL0-0.008-0.00422.400-0.010-0.0100.0000.0000.0000.000
109A159ALA00.0130.02422.5530.0090.0090.0000.0000.0000.000
110A160LEU00.0270.01716.642-0.020-0.0200.0000.0000.0000.000
111A161CYS0-0.029-0.01021.1490.0370.0370.0000.0000.0000.000
112A162SER00.0150.00823.205-0.028-0.0280.0000.0000.0000.000
113A163VAL0-0.038-0.01924.365-0.020-0.0200.0000.0000.0000.000
114A164GLY00.0430.05126.8420.0160.0160.0000.0000.0000.000
115A165ARG10.8620.90228.3190.0860.0860.0000.0000.0000.000
116A166ARG10.8690.93530.7380.1120.1120.0000.0000.0000.000
117A167ARG10.8230.90431.3400.1170.1170.0000.0000.0000.000
118A168GLY00.0520.01229.4200.0050.0050.0000.0000.0000.000
119A169THR0-0.114-0.05327.331-0.017-0.0170.0000.0000.0000.000
120A170LEU00.0210.00322.4820.0030.0030.0000.0000.0000.000
121A171ALA0-0.051-0.00919.852-0.004-0.0040.0000.0000.0000.000
122A172VAL0-0.002-0.00617.241-0.036-0.0360.0000.0000.0000.000
123A173TYR0-0.008-0.03013.3730.0160.0160.0000.0000.0000.000
124A174GLY00.031-0.00611.136-0.076-0.0760.0000.0000.0000.000
125A175ARG10.7640.8475.8112.6242.6240.0000.0000.0000.000
126A176ASP-1-0.811-0.9008.813-0.618-0.6180.0000.0000.0000.000
127A177PRO00.0200.02310.987-0.013-0.0130.0000.0000.0000.000
128A178GLU-1-0.727-0.82714.434-0.330-0.3300.0000.0000.0000.000
129A179TRP0-0.028-0.01412.705-0.008-0.0080.0000.0000.0000.000
130A180VAL0-0.018-0.00713.6270.0190.0190.0000.0000.0000.000
131A181THR0-0.017-0.03016.0750.0610.0610.0000.0000.0000.000
132A182GLN0-0.085-0.07417.7760.0840.0840.0000.0000.0000.000
133A183ARG10.7900.90816.0960.7330.7330.0000.0000.0000.000
134A184PHE00.0100.00519.9490.0330.0330.0000.0000.0000.000
135A185PRO00.0220.01823.4280.0170.0170.0000.0000.0000.000
136A186ASP-1-0.840-0.89426.364-0.218-0.2180.0000.0000.0000.000
137A187LEU0-0.050-0.01223.1890.0240.0240.0000.0000.0000.000
138A188THR0-0.002-0.02026.483-0.015-0.0150.0000.0000.0000.000
139A189ALA0-0.007-0.01525.497-0.011-0.0110.0000.0000.0000.000
140A190ALA00.0730.03125.857-0.002-0.0020.0000.0000.0000.000
141A191ASP-1-0.800-0.89526.936-0.180-0.1800.0000.0000.0000.000
142A192ARG10.8660.92820.7780.3540.3540.0000.0000.0000.000
143A193ASP-1-0.845-0.90522.877-0.196-0.1960.0000.0000.0000.000
144A194GLY00.0000.01024.9170.0160.0160.0000.0000.0000.000
145A195LEU0-0.038-0.02021.7490.0140.0140.0000.0000.0000.000
146A196ARG10.8400.89219.8170.2770.2770.0000.0000.0000.000
147A197ALA00.0200.00521.0580.0220.0220.0000.0000.0000.000
148A198GLN0-0.093-0.05523.1990.0360.0360.0000.0000.0000.000
149A199TRP00.1010.04416.4450.0160.0160.0000.0000.0000.000
150A200GLN0-0.081-0.03918.2390.0160.0160.0000.0000.0000.000
151A201ARG10.8750.93919.5040.0680.0680.0000.0000.0000.000
152A202CYS0-0.045-0.00319.2430.0320.0320.0000.0000.0000.000
153A203GLY00.0740.01815.056-0.063-0.0630.0000.0000.0000.000
154A204SER0-0.051-0.03010.4770.0460.0460.0000.0000.0000.000
155A205THR0-0.010-0.00811.604-0.069-0.0690.0000.0000.0000.000
156A206ALA00.0410.03614.1160.0410.0410.0000.0000.0000.000
157A207VAL0-0.038-0.02915.9110.0410.0410.0000.0000.0000.000
158A208ASP-1-0.881-0.92918.1920.2470.2470.0000.0000.0000.000
159A209ALA0-0.010-0.01018.252-0.029-0.0290.0000.0000.0000.000
160A210SER0-0.012-0.02020.3850.0100.0100.0000.0000.0000.000
161A211GLY00.0140.02617.1690.0000.0000.0000.0000.0000.000
162A212ASP-1-0.771-0.87613.3610.3170.3170.0000.0000.0000.000
163A213PRO00.0250.01914.950-0.014-0.0140.0000.0000.0000.000
164A214PHE00.0130.02015.653-0.032-0.0320.0000.0000.0000.000
165A215ARG10.8130.88117.578-0.087-0.0870.0000.0000.0000.000
166A216SER00.0190.03420.2410.0050.0050.0000.0000.0000.000
167A217ASP-1-0.827-0.92918.8450.1890.1890.0000.0000.0000.000
168A218SER00.013-0.00818.075-0.015-0.0150.0000.0000.0000.000
169A219TYR0-0.027-0.00719.305-0.023-0.0230.0000.0000.0000.000
170A220GLY00.0360.03222.804-0.021-0.0210.0000.0000.0000.000
171A221LEU0-0.028-0.02416.705-0.019-0.0190.0000.0000.0000.000
172A222LEU0-0.0070.00821.181-0.024-0.0240.0000.0000.0000.000
173A223GLY00.0410.03223.215-0.018-0.0180.0000.0000.0000.000
174A224ASN00.0370.01822.804-0.019-0.0190.0000.0000.0000.000
175A225SER0-0.084-0.06322.658-0.020-0.0200.0000.0000.0000.000
176A226VAL00.005-0.00224.624-0.015-0.0150.0000.0000.0000.000
177A227ASP-1-0.870-0.93528.258-0.034-0.0340.0000.0000.0000.000
178A228ALA0-0.050-0.03725.822-0.010-0.0100.0000.0000.0000.000
179A229LEU0-0.0210.00227.494-0.015-0.0150.0000.0000.0000.000
180A230TYR0-0.003-0.00329.654-0.005-0.0050.0000.0000.0000.000
181A231ILE0-0.0040.01128.6360.0020.0020.0000.0000.0000.000
182A232DAR10.8080.88931.9030.0900.0900.0000.0000.0000.000
183A233DGL-1-0.793-0.90032.138-0.137-0.1370.0000.0000.0000.000
184A234ARG10.8680.93623.0830.1850.1850.0000.0000.0000.000
185A235LEU00.0240.00827.161-0.017-0.0170.0000.0000.0000.000
186A236PRO0-0.035-0.03029.342-0.017-0.0170.0000.0000.0000.000
187A237LYS10.8210.91230.4050.1640.1640.0000.0000.0000.000
188A238LEU00.0250.00824.824-0.004-0.0040.0000.0000.0000.000
189A239ARG10.9240.95927.5680.1880.1880.0000.0000.0000.000
190A240TYR00.0360.02229.010-0.009-0.0090.0000.0000.0000.000
191A241ASP-1-0.756-0.86427.581-0.198-0.1980.0000.0000.0000.000
192A242LYS10.8260.89624.6020.3420.3420.0000.0000.0000.000
193A243GLN0-0.016-0.00326.580-0.001-0.0010.0000.0000.0000.000
194A244LEU0-0.057-0.02029.7120.0020.0020.0000.0000.0000.000
195A245VAL0-0.031-0.02224.9470.0060.0060.0000.0000.0000.000
196A246GLY00.0270.01626.354-0.016-0.0160.0000.0000.0000.000
197A247VAL0-0.0200.00620.792-0.017-0.0170.0000.0000.0000.000
198A248THR0-0.035-0.03222.0300.0210.0210.0000.0000.0000.000
199A249GLU-1-0.836-0.90219.926-0.452-0.4520.0000.0000.0000.000
200A250ARG10.9080.93619.3810.5120.5120.0000.0000.0000.000
201A251GLU-1-0.803-0.88018.089-0.606-0.6060.0000.0000.0000.000
202A252SER0-0.006-0.01016.069-0.071-0.0710.0000.0000.0000.000
203A253TYR0-0.005-0.0309.7910.0580.0580.0000.0000.0000.000
204A254VAL0-0.032-0.00315.6990.0500.0500.0000.0000.0000.000
205A255LYS10.8510.91415.5690.6850.6850.0000.0000.0000.000
206A256ALA0-0.039-0.00720.2370.0560.0560.0000.0000.0000.000