FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 82YVY

Calculation Name: 3VX8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX8

Chain ID: D

ChEMBL ID:

UniProt ID: Q0WWQ1

Base Structure: X-ray

Registration Date: 2023-06-20

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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4458713.538202
FMO2-HF: Nuclear repulsion 4339928.660262
FMO2-HF: Total energy -118784.877939
FMO2-MP2: Total energy -119135.005039


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(D:9:ILE)


Summations of interaction energy for fragment #1(D:9:ILE)
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.
-7.856-2.6061.247-2.338-4.16-0.009
Interaction energy analysis for fragmet #1(D:9:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.008
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].
3D11LEU00.011-0.0033.029-2.753-0.1080.135-1.317-1.463-0.004
4D12GLN0-0.035-0.0155.1300.6840.6840.0000.0000.0000.000
5D13PHE00.0160.0036.957-0.089-0.0890.0000.0000.0000.000
6D14ALA00.0050.00510.5790.1130.1130.0000.0000.0000.000
7D15PRO0-0.056-0.03813.1440.0040.0040.0000.0000.0000.000
8D16LEU00.0320.02316.273-0.013-0.0130.0000.0000.0000.000
9D17ASN0-0.037-0.01319.3180.0430.0430.0000.0000.0000.000
10D18SER0-0.027-0.04222.384-0.011-0.0110.0000.0000.0000.000
11D19SER0-0.041-0.01826.0340.0070.0070.0000.0000.0000.000
12D20VAL0-0.015-0.00629.233-0.003-0.0030.0000.0000.0000.000
13D21ASP-1-0.847-0.90732.726-0.063-0.0630.0000.0000.0000.000
14D22GLU-1-0.853-0.95235.619-0.038-0.0380.0000.0000.0000.000
15D23GLY00.0370.00638.7870.0040.0040.0000.0000.0000.000
16D24PHE0-0.020-0.00136.1740.0030.0030.0000.0000.0000.000
17D25TRP00.0420.00134.3190.0040.0040.0000.0000.0000.000
18D26HIS0-0.0320.01440.0030.0040.0040.0000.0000.0000.000
19D27SER00.0300.00341.8140.0020.0020.0000.0000.0000.000
20D28PHE00.018-0.00140.2080.0020.0020.0000.0000.0000.000
21D29SER0-0.034-0.03142.3450.0040.0040.0000.0000.0000.000
22D30SER00.0120.00844.9570.0020.0020.0000.0000.0000.000
23D31LEU0-0.0070.00342.7310.0010.0010.0000.0000.0000.000
24D32LYS10.8660.92643.9950.0170.0170.0000.0000.0000.000
25D33LEU0-0.060-0.03246.2960.0030.0030.0000.0000.0000.000
26D34ASP-1-0.916-0.93849.735-0.024-0.0240.0000.0000.0000.000
27D35LYS10.8920.95145.9670.0350.0350.0000.0000.0000.000
28D36LEU0-0.052-0.02443.3890.0010.0010.0000.0000.0000.000
29D37GLY00.0610.03648.0230.0020.0020.0000.0000.0000.000
30D38ILE0-0.061-0.05348.0920.0000.0000.0000.0000.0000.000
31D39ASP-1-0.863-0.92045.775-0.017-0.0170.0000.0000.0000.000
32D40ASP-1-0.991-1.00142.409-0.008-0.0080.0000.0000.0000.000
33D41SER0-0.030-0.01541.3020.0010.0010.0000.0000.0000.000
34D42PRO0-0.064-0.03036.972-0.002-0.0020.0000.0000.0000.000
35D43ILE00.0250.02137.850-0.001-0.0010.0000.0000.0000.000
36D44SER0-0.038-0.01735.926-0.001-0.0010.0000.0000.0000.000
37D45ILE0-0.040-0.01732.8180.0020.0020.0000.0000.0000.000
38D46THR00.0070.00833.045-0.004-0.0040.0000.0000.0000.000
39D47GLY0-0.046-0.01629.7430.0040.0040.0000.0000.0000.000
40D48PHE00.0160.00430.042-0.004-0.0040.0000.0000.0000.000
41D49TYR00.0170.00422.3260.0070.0070.0000.0000.0000.000
42D50GLY00.0540.01825.3580.0060.0060.0000.0000.0000.000
43D51PRO00.0290.02622.581-0.004-0.0040.0000.0000.0000.000
44D52CYS0-0.045-0.01720.8290.0250.0250.0000.0000.0000.000
45D53GLY00.0460.04022.772-0.008-0.0080.0000.0000.0000.000
46D54HIS0-0.002-0.02024.3960.0040.0040.0000.0000.0000.000
47D55PRO00.0520.01421.454-0.007-0.0070.0000.0000.0000.000
48D56GLN0-0.016-0.02420.469-0.012-0.0120.0000.0000.0000.000
49D57VAL0-0.048-0.01521.9860.0130.0130.0000.0000.0000.000
50D58SER0-0.043-0.00319.367-0.002-0.0020.0000.0000.0000.000
51D59ASN0-0.024-0.01221.5010.0370.0370.0000.0000.0000.000
52D60HIS0-0.028-0.02322.496-0.005-0.0050.0000.0000.0000.000
53D61LEU0-0.022-0.00924.605-0.003-0.0030.0000.0000.0000.000
54D62THR0-0.043-0.02126.1010.0140.0140.0000.0000.0000.000
55D63LEU00.0080.00629.618-0.003-0.0030.0000.0000.0000.000
56D64LEU00.0260.00032.6280.0040.0040.0000.0000.0000.000
57D65SER00.021-0.00236.1460.0030.0030.0000.0000.0000.000
58D66GLU-1-0.907-0.96937.668-0.075-0.0750.0000.0000.0000.000
59D67SER0-0.044-0.00834.473-0.001-0.0010.0000.0000.0000.000
60D68LEU0-0.023-0.01036.9070.0020.0020.0000.0000.0000.000
61D69PRO00.0010.01240.0310.0000.0000.0000.0000.0000.000
62D82GLY00.0670.03936.1620.0030.0030.0000.0000.0000.000
63D83ASN0-0.083-0.05435.170-0.003-0.0030.0000.0000.0000.000
64D84ARG10.9530.96231.9620.1540.1540.0000.0000.0000.000
65D85ASN0-0.050-0.03230.669-0.018-0.0180.0000.0000.0000.000
66D86LYS10.8820.94631.1700.0980.0980.0000.0000.0000.000
67D87CYS00.0030.02128.0960.0010.0010.0000.0000.0000.000
68D88PRO00.0350.00629.7130.0010.0010.0000.0000.0000.000
69D89VAL00.0100.02326.468-0.007-0.0070.0000.0000.0000.000
70D90PRO00.0150.01629.2240.0120.0120.0000.0000.0000.000
71D91GLY00.0640.01329.547-0.006-0.0060.0000.0000.0000.000
72D92ILE0-0.096-0.04231.0260.0050.0050.0000.0000.0000.000
73D93LEU00.003-0.00232.3140.0000.0000.0000.0000.0000.000
74D94TYR00.0390.00333.3850.0040.0040.0000.0000.0000.000
75D95ASN00.0510.03236.0520.0020.0020.0000.0000.0000.000
76D96THR00.0200.00837.9670.0010.0010.0000.0000.0000.000
77D97ASN00.0370.01640.587-0.003-0.0030.0000.0000.0000.000
78D98THR00.0230.01143.4690.0000.0000.0000.0000.0000.000
79D99VAL00.0590.01839.5180.0000.0000.0000.0000.0000.000
80D100GLU-1-0.926-0.98239.6490.0170.0170.0000.0000.0000.000
81D101SER0-0.012-0.00739.9030.0030.0030.0000.0000.0000.000
82D102PHE0-0.0070.00832.7080.0020.0020.0000.0000.0000.000
83D103ASN0-0.068-0.04235.4740.0010.0010.0000.0000.0000.000
84D104LYS10.8900.94335.539-0.025-0.0250.0000.0000.0000.000
85D105LEU00.0330.03634.2590.0020.0020.0000.0000.0000.000
86D106ASP-1-0.863-0.92031.7720.0410.0410.0000.0000.0000.000
87D107LYS10.9630.97827.903-0.032-0.0320.0000.0000.0000.000
88D108GLN00.000-0.00925.710-0.009-0.0090.0000.0000.0000.000
89D109SER0-0.040-0.03827.662-0.007-0.0070.0000.0000.0000.000
90D110LEU00.0470.03029.835-0.005-0.0050.0000.0000.0000.000
91D111LEU0-0.013-0.00722.236-0.008-0.0080.0000.0000.0000.000
92D112LYS10.9580.97124.176-0.070-0.0700.0000.0000.0000.000
93D113ALA00.0090.01726.812-0.005-0.0050.0000.0000.0000.000
94D114GLU-1-0.839-0.92827.750-0.051-0.0510.0000.0000.0000.000
95D115ALA00.0060.00623.770-0.012-0.0120.0000.0000.0000.000
96D116ASN0-0.028-0.02125.625-0.014-0.0140.0000.0000.0000.000
97D117LYS10.8970.94728.2070.0440.0440.0000.0000.0000.000
98D118ILE00.0090.01723.275-0.004-0.0040.0000.0000.0000.000
99D119TRP0-0.014-0.01621.067-0.021-0.0210.0000.0000.0000.000
100D120GLU-1-0.904-0.95626.285-0.054-0.0540.0000.0000.0000.000
101D121ASP-1-0.882-0.94028.478-0.096-0.0960.0000.0000.0000.000
102D122ILE0-0.065-0.03622.504-0.011-0.0110.0000.0000.0000.000
103D123GLN0-0.028-0.01824.422-0.002-0.0020.0000.0000.0000.000
104D124SER0-0.063-0.01928.3600.0000.0000.0000.0000.0000.000
105D125GLY00.0120.01229.0850.0000.0000.0000.0000.0000.000
106D126LYS10.9710.96830.1510.0710.0710.0000.0000.0000.000
107D127ALA0-0.0020.00126.165-0.003-0.0030.0000.0000.0000.000
108D128LEU0-0.048-0.02026.872-0.018-0.0180.0000.0000.0000.000
109D129GLU-1-1.005-1.01428.145-0.116-0.1160.0000.0000.0000.000
110D130ASP-1-0.809-0.88830.624-0.143-0.1430.0000.0000.0000.000
111D131PRO00.0160.02225.1750.0010.0010.0000.0000.0000.000
112D132SER0-0.078-0.06225.611-0.011-0.0110.0000.0000.0000.000
113D133VAL00.007-0.00727.6470.0060.0060.0000.0000.0000.000
114D134LEU0-0.020-0.00921.7160.0060.0060.0000.0000.0000.000
115D135PRO0-0.096-0.03622.2250.0000.0000.0000.0000.0000.000
116D136ARG10.9691.00523.3170.0960.0960.0000.0000.0000.000
117D137PHE0-0.038-0.02324.5990.0000.0000.0000.0000.0000.000
118D138LEU0-0.034-0.01926.5530.0080.0080.0000.0000.0000.000
119D139VAL0-0.0050.00728.0190.0000.0000.0000.0000.0000.000
120D140ILE0-0.0130.01330.3820.0040.0040.0000.0000.0000.000
121D141SER0-0.021-0.06332.730-0.002-0.0020.0000.0000.0000.000
122D142PHE0-0.0250.00035.4930.0030.0030.0000.0000.0000.000
123D143ALA00.0290.01538.794-0.001-0.0010.0000.0000.0000.000
124D144ASP-1-0.844-0.91541.107-0.004-0.0040.0000.0000.0000.000
125D145LEU00.0250.00243.863-0.001-0.0010.0000.0000.0000.000
126D146LYS10.8940.95446.5210.0050.0050.0000.0000.0000.000
127D147LYS10.9040.94245.447-0.001-0.0010.0000.0000.0000.000
128D148TRP00.0520.02844.1130.0010.0010.0000.0000.0000.000
129D149SER0-0.039-0.00740.510-0.002-0.0020.0000.0000.0000.000
130D150PHE00.0670.02937.7100.0010.0010.0000.0000.0000.000
131D151ARG10.9140.96133.647-0.012-0.0120.0000.0000.0000.000
132D152TYR00.0350.01229.906-0.001-0.0010.0000.0000.0000.000
133D153TRP0-0.063-0.06125.0780.0110.0110.0000.0000.0000.000
134D154PHE00.0690.04325.6340.0010.0010.0000.0000.0000.000
135D155ALA00.024-0.00924.0130.0090.0090.0000.0000.0000.000
136D156PHE0-0.007-0.00220.586-0.007-0.0070.0000.0000.0000.000
137D157PRO0-0.028-0.01320.352-0.008-0.0080.0000.0000.0000.000
138D158ALA00.0470.05116.790-0.016-0.0160.0000.0000.0000.000
139D159PHE00.014-0.01018.2010.0350.0350.0000.0000.0000.000
140D160VAL0-0.089-0.05813.537-0.057-0.0570.0000.0000.0000.000
141D161LEU0-0.018-0.00612.7840.0280.0280.0000.0000.0000.000
142D162ASP-1-0.833-0.90513.3850.1290.1290.0000.0000.0000.000
143D163PRO0-0.025-0.00110.3840.1280.1280.0000.0000.0000.000
144D164PRO0-0.042-0.0257.813-0.167-0.1670.0000.0000.0000.000
145D165VAL00.0550.0257.4460.0510.0510.0000.0000.0000.000
146D166SER00.0400.0333.174-0.2010.2050.012-0.125-0.2930.000
147D167LEU0-0.040-0.0212.370-0.1420.8791.022-0.419-1.625-0.002
148D168ILE0-0.026-0.0033.423-3.103-2.1070.079-0.458-0.617-0.003
149D169GLU-1-0.928-0.9794.322-1.581-1.399-0.001-0.019-0.1620.000
150D170LEU0-0.052-0.0376.4480.0960.0960.0000.0000.0000.000
151D171LYS10.9300.9708.6020.8280.8280.0000.0000.0000.000
152D172PRO00.0540.02911.9310.0120.0120.0000.0000.0000.000
153D173ALA0-0.008-0.00815.422-0.003-0.0030.0000.0000.0000.000
154D174SER00.001-0.00417.6410.0110.0110.0000.0000.0000.000
155D175GLU-1-0.934-0.96715.259-0.432-0.4320.0000.0000.0000.000
156D176TYR0-0.114-0.04414.4010.0110.0110.0000.0000.0000.000
157D177PHE0-0.028-0.01116.5760.0170.0170.0000.0000.0000.000
158D178SER00.0420.03520.2340.0120.0120.0000.0000.0000.000
159D179SER00.012-0.02023.2100.0020.0020.0000.0000.0000.000
160D180GLU-1-0.936-0.96525.888-0.188-0.1880.0000.0000.0000.000
161D181GLU-1-0.863-0.93622.863-0.330-0.3300.0000.0000.0000.000
162D182ALA0-0.032-0.02224.1280.0000.0000.0000.0000.0000.000
163D183GLU-1-0.898-0.95225.269-0.181-0.1810.0000.0000.0000.000
164D184SER00.0020.00728.2950.0120.0120.0000.0000.0000.000
165D185VAL0-0.002-0.00423.3760.0060.0060.0000.0000.0000.000
166D186SER0-0.003-0.00326.6270.0000.0000.0000.0000.0000.000
167D187ALA00.0000.00727.8540.0080.0080.0000.0000.0000.000
168D188ALA00.0560.03928.4520.0070.0070.0000.0000.0000.000
169D189CYS0-0.077-0.04325.481-0.006-0.0060.0000.0000.0000.000
170D190ASN0-0.006-0.02928.282-0.003-0.0030.0000.0000.0000.000
171D191ASP-1-0.881-0.92631.449-0.153-0.1530.0000.0000.0000.000
172D192TRP0-0.076-0.03328.3880.0110.0110.0000.0000.0000.000
173D193ARG10.7910.89428.0050.1990.1990.0000.0000.0000.000
174D194ASP-1-0.883-0.95232.160-0.137-0.1370.0000.0000.0000.000
175D195SER0-0.044-0.00335.3100.0140.0140.0000.0000.0000.000
176D196ASP-1-0.885-0.95735.450-0.113-0.1130.0000.0000.0000.000
177D197LEU0-0.048-0.01536.736-0.001-0.0010.0000.0000.0000.000
178D198THR0-0.046-0.03032.0430.0010.0010.0000.0000.0000.000
179D199THR00.0040.02631.259-0.010-0.0100.0000.0000.0000.000
180D200ASP-1-0.931-0.97330.245-0.148-0.1480.0000.0000.0000.000
181D201VAL00.0400.03427.9470.0020.0020.0000.0000.0000.000
182D202PRO0-0.020-0.02324.277-0.013-0.0130.0000.0000.0000.000
183D203PHE0-0.032-0.02920.110-0.033-0.0330.0000.0000.0000.000
184D204PHE00.0140.01022.6510.0140.0140.0000.0000.0000.000
185D205LEU00.0360.01822.513-0.035-0.0350.0000.0000.0000.000
186D206VAL0-0.011-0.01521.4930.0230.0230.0000.0000.0000.000
187D207SER0-0.031-0.00922.816-0.018-0.0180.0000.0000.0000.000
188D208VAL00.028-0.00922.8730.0160.0160.0000.0000.0000.000
189D209SER00.1250.07625.820-0.003-0.0030.0000.0000.0000.000
190D210SER0-0.055-0.00426.589-0.015-0.0150.0000.0000.0000.000
191D211ASP-1-1.015-1.06127.996-0.163-0.1630.0000.0000.0000.000
192D212SER0-0.002-0.00627.125-0.004-0.0040.0000.0000.0000.000
193D213LYS10.9600.99928.2040.1710.1710.0000.0000.0000.000
194D214ALA0-0.026-0.00326.144-0.007-0.0070.0000.0000.0000.000
195D215SER0-0.036-0.01427.9830.0180.0180.0000.0000.0000.000
196D216ILE00.0050.00325.468-0.010-0.0100.0000.0000.0000.000
197D217ARG10.8960.95827.5830.2070.2070.0000.0000.0000.000
198D218HIS00.0690.02727.550-0.021-0.0210.0000.0000.0000.000
199D219LEU00.008-0.01123.015-0.007-0.0070.0000.0000.0000.000
200D220LYS10.9360.97226.9070.1330.1330.0000.0000.0000.000
201D221ASP-1-0.892-0.93329.673-0.158-0.1580.0000.0000.0000.000
202D222LEU00.0090.01022.893-0.009-0.0090.0000.0000.0000.000
203D223GLU-1-0.955-0.99127.000-0.168-0.1680.0000.0000.0000.000
204D224ALA0-0.043-0.00728.6570.0120.0120.0000.0000.0000.000
205D225CYS0-0.094-0.05027.955-0.002-0.0020.0000.0000.0000.000
206D226GLN00.0220.02422.7030.0040.0040.0000.0000.0000.000
207D227GLY00.010-0.00526.1710.0190.0190.0000.0000.0000.000
208D228ASP-1-0.951-0.96526.131-0.203-0.2030.0000.0000.0000.000
209D229HIS0-0.079-0.04926.671-0.005-0.0050.0000.0000.0000.000
210D230GLN00.0400.01825.6880.0090.0090.0000.0000.0000.000
211D231LYS10.9270.98819.2020.4040.4040.0000.0000.0000.000
212D232LEU00.0470.01320.6800.0180.0180.0000.0000.0000.000
213D233LEU0-0.037-0.01516.051-0.058-0.0580.0000.0000.0000.000
214D234PHE00.0300.01217.4510.0500.0500.0000.0000.0000.000
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