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: N1YGQ

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 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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4462954.450873
FMO2-HF: Nuclear repulsion 4344167.679977
FMO2-HF: Total energy -118786.770896
FMO2-MP2: Total energy -119136.984261


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.
-7.605-2.581.598-2.332-4.292-0.011
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 : -0.006 / 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].
3D11LEU00.010-0.0022.860-3.054-0.2530.307-1.430-1.678-0.006
4D12GLN0-0.041-0.0184.9140.6440.6440.0000.0000.0000.000
5D13PHE00.0360.0066.804-0.094-0.0940.0000.0000.0000.000
6D14ALA00.0130.01010.3710.1030.1030.0000.0000.0000.000
7D15PRO0-0.056-0.04012.9980.0060.0060.0000.0000.0000.000
8D16LEU00.0310.02616.157-0.014-0.0140.0000.0000.0000.000
9D17ASN0-0.058-0.02519.1450.0400.0400.0000.0000.0000.000
10D18SER0-0.038-0.04922.253-0.009-0.0090.0000.0000.0000.000
11D19SER0-0.027-0.01525.8880.0050.0050.0000.0000.0000.000
12D20VAL0-0.017-0.00829.085-0.002-0.0020.0000.0000.0000.000
13D21ASP-1-0.839-0.90532.577-0.054-0.0540.0000.0000.0000.000
14D22GLU-1-0.884-0.96435.459-0.032-0.0320.0000.0000.0000.000
15D23GLY00.0610.02538.6490.0040.0040.0000.0000.0000.000
16D24PHE0-0.0150.01235.8200.0030.0030.0000.0000.0000.000
17D25TRP00.0460.00234.3240.0040.0040.0000.0000.0000.000
18D26HIS0-0.0190.02239.8610.0040.0040.0000.0000.0000.000
19D27SER00.018-0.00941.6120.0020.0020.0000.0000.0000.000
20D28PHE00.008-0.00340.0180.0020.0020.0000.0000.0000.000
21D29SER0-0.027-0.02842.1720.0030.0030.0000.0000.0000.000
22D30SER00.003-0.00144.8120.0020.0020.0000.0000.0000.000
23D31LEU0-0.0070.00542.5520.0010.0010.0000.0000.0000.000
24D32LYS10.7980.88043.9920.0100.0100.0000.0000.0000.000
25D33LEU0-0.055-0.02846.1360.0020.0020.0000.0000.0000.000
26D34ASP-1-0.925-0.94349.586-0.018-0.0180.0000.0000.0000.000
27D35LYS10.9030.95445.9890.0260.0260.0000.0000.0000.000
28D36LEU0-0.049-0.02043.2750.0010.0010.0000.0000.0000.000
29D37GLY00.0670.03947.8430.0020.0020.0000.0000.0000.000
30D38ILE0-0.025-0.02747.9550.0000.0000.0000.0000.0000.000
31D39ASP-1-0.825-0.88645.553-0.009-0.0090.0000.0000.0000.000
32D40ASP-1-0.924-0.96442.1850.0000.0000.0000.0000.0000.000
33D41SER0-0.047-0.03241.1590.0020.0020.0000.0000.0000.000
34D42PRO0-0.069-0.03536.780-0.002-0.0020.0000.0000.0000.000
35D43ILE00.0180.01637.647-0.001-0.0010.0000.0000.0000.000
36D44SER0-0.027-0.00935.677-0.001-0.0010.0000.0000.0000.000
37D45ILE0-0.045-0.02032.4370.0010.0010.0000.0000.0000.000
38D46THR00.0150.01332.783-0.003-0.0030.0000.0000.0000.000
39D47GLY0-0.051-0.01029.4850.0040.0040.0000.0000.0000.000
40D48PHE00.0120.00129.771-0.004-0.0040.0000.0000.0000.000
41D49TYR0-0.002-0.00221.9560.0070.0070.0000.0000.0000.000
42D50GLY00.0740.03125.1010.0050.0050.0000.0000.0000.000
43D51PRO0-0.0040.01622.266-0.005-0.0050.0000.0000.0000.000
44D52CYS0-0.046-0.01520.4280.0240.0240.0000.0000.0000.000
45D53GLY00.0600.04422.506-0.008-0.0080.0000.0000.0000.000
46D54HIS0-0.006-0.01324.2400.0020.0020.0000.0000.0000.000
47D55PRO00.0480.01721.312-0.007-0.0070.0000.0000.0000.000
48D56GLN0-0.017-0.02620.340-0.010-0.0100.0000.0000.0000.000
49D57VAL0-0.052-0.02121.8880.0110.0110.0000.0000.0000.000
50D58SER0-0.015-0.01419.255-0.001-0.0010.0000.0000.0000.000
51D59ASN0-0.045-0.01921.3250.0340.0340.0000.0000.0000.000
52D60HIS0-0.016-0.02022.295-0.001-0.0010.0000.0000.0000.000
53D61LEU0-0.034-0.01124.322-0.002-0.0020.0000.0000.0000.000
54D62THR0-0.050-0.02525.8730.0130.0130.0000.0000.0000.000
55D63LEU0-0.0010.00129.405-0.002-0.0020.0000.0000.0000.000
56D64LEU00.0400.01032.4110.0030.0030.0000.0000.0000.000
57D65SER00.032-0.00335.9280.0030.0030.0000.0000.0000.000
58D66GLU-1-0.882-0.94637.438-0.064-0.0640.0000.0000.0000.000
59D67SER0-0.052-0.02534.151-0.001-0.0010.0000.0000.0000.000
60D68LEU0-0.024-0.00936.6550.0020.0020.0000.0000.0000.000
61D69PRO00.0030.01239.7870.0000.0000.0000.0000.0000.000
62D82GLY00.0710.04535.8150.0030.0030.0000.0000.0000.000
63D83ASN0-0.097-0.06934.741-0.004-0.0040.0000.0000.0000.000
64D84ARG10.9310.94931.5950.1390.1390.0000.0000.0000.000
65D85ASN0-0.060-0.03630.357-0.014-0.0140.0000.0000.0000.000
66D86LYS10.8510.91530.8790.0840.0840.0000.0000.0000.000
67D87CYS0-0.0040.01727.7490.0010.0010.0000.0000.0000.000
68D88PRO00.0320.00529.3930.0010.0010.0000.0000.0000.000
69D89VAL00.0060.02026.193-0.006-0.0060.0000.0000.0000.000
70D90PRO00.0230.02028.8340.0100.0100.0000.0000.0000.000
71D91GLY00.0560.01229.264-0.004-0.0040.0000.0000.0000.000
72D92ILE0-0.087-0.03830.8710.0040.0040.0000.0000.0000.000
73D93LEU0-0.004-0.00132.1210.0000.0000.0000.0000.0000.000
74D94TYR00.028-0.00232.8890.0040.0040.0000.0000.0000.000
75D95ASN00.0500.02735.9340.0010.0010.0000.0000.0000.000
76D96THR0-0.010-0.01337.8130.0010.0010.0000.0000.0000.000
77D97ASN00.001-0.00940.497-0.003-0.0030.0000.0000.0000.000
78D98THR00.0110.01543.4420.0000.0000.0000.0000.0000.000
79D99VAL00.0500.02439.4810.0000.0000.0000.0000.0000.000
80D100GLU-1-0.894-0.96739.6460.0190.0190.0000.0000.0000.000
81D101SER0-0.025-0.02039.9000.0030.0030.0000.0000.0000.000
82D102PHE00.0050.01732.5620.0030.0030.0000.0000.0000.000
83D103ASN0-0.026-0.02835.4510.0020.0020.0000.0000.0000.000
84D104LYS10.9030.94835.555-0.029-0.0290.0000.0000.0000.000
85D105LEU00.0420.04533.8100.0020.0020.0000.0000.0000.000
86D106ASP-1-0.825-0.88431.3650.0500.0500.0000.0000.0000.000
87D107LYS10.8860.93828.014-0.035-0.0350.0000.0000.0000.000
88D108GLN00.0450.02125.598-0.003-0.0030.0000.0000.0000.000
89D109SER0-0.049-0.05827.566-0.005-0.0050.0000.0000.0000.000
90D110LEU00.0400.02629.725-0.005-0.0050.0000.0000.0000.000
91D111LEU0-0.015-0.00922.156-0.007-0.0070.0000.0000.0000.000
92D112LYS10.8940.93523.997-0.092-0.0920.0000.0000.0000.000
93D113ALA00.0180.02426.655-0.004-0.0040.0000.0000.0000.000
94D114GLU-1-0.783-0.88927.607-0.033-0.0330.0000.0000.0000.000
95D115ALA00.0000.00223.596-0.010-0.0100.0000.0000.0000.000
96D116ASN0-0.032-0.01925.393-0.011-0.0110.0000.0000.0000.000
97D117LYS10.8830.93127.9640.0230.0230.0000.0000.0000.000
98D118ILE00.0050.01023.015-0.004-0.0040.0000.0000.0000.000
99D119TRP0-0.004-0.00821.139-0.016-0.0160.0000.0000.0000.000
100D120GLU-1-0.908-0.95526.013-0.033-0.0330.0000.0000.0000.000
101D121ASP-1-0.844-0.90128.415-0.069-0.0690.0000.0000.0000.000
102D122ILE0-0.060-0.02822.393-0.010-0.0100.0000.0000.0000.000
103D123GLN0-0.011-0.00824.499-0.005-0.0050.0000.0000.0000.000
104D124SER0-0.072-0.04428.4810.0000.0000.0000.0000.0000.000
105D125GLY00.0240.02229.179-0.001-0.0010.0000.0000.0000.000
106D126LYS10.8870.91730.2460.0540.0540.0000.0000.0000.000
107D127ALA0-0.023-0.01025.924-0.003-0.0030.0000.0000.0000.000
108D128LEU0-0.051-0.01526.843-0.015-0.0150.0000.0000.0000.000
109D129GLU-1-0.902-0.93728.250-0.098-0.0980.0000.0000.0000.000
110D130ASP-1-0.797-0.87030.223-0.120-0.1200.0000.0000.0000.000
111D131PRO00.0190.01724.9020.0020.0020.0000.0000.0000.000
112D132SER0-0.071-0.06125.225-0.009-0.0090.0000.0000.0000.000
113D133VAL00.012-0.01227.3120.0060.0060.0000.0000.0000.000
114D134LEU0-0.014-0.00121.3990.0080.0080.0000.0000.0000.000
115D135PRO0-0.081-0.02721.9400.0020.0020.0000.0000.0000.000
116D136ARG10.9600.98723.0020.0700.0700.0000.0000.0000.000
117D137PHE0-0.058-0.03124.3420.0010.0010.0000.0000.0000.000
118D138LEU0-0.049-0.02226.3230.0070.0070.0000.0000.0000.000
119D139VAL0-0.0010.00827.8630.0000.0000.0000.0000.0000.000
120D140ILE0-0.0090.01330.3660.0040.0040.0000.0000.0000.000
121D141SER0-0.012-0.04932.637-0.002-0.0020.0000.0000.0000.000
122D142PHE0-0.026-0.00835.4030.0030.0030.0000.0000.0000.000
123D143ALA00.0450.02438.726-0.001-0.0010.0000.0000.0000.000
124D144ASP-1-0.857-0.91541.0250.0000.0000.0000.0000.0000.000
125D145LEU00.0350.00843.808-0.001-0.0010.0000.0000.0000.000
126D146LYS10.8890.94746.4420.0010.0010.0000.0000.0000.000
127D147LYS10.9040.94545.438-0.004-0.0040.0000.0000.0000.000
128D148TRP00.0430.02144.1760.0000.0000.0000.0000.0000.000
129D149SER0-0.0300.00140.501-0.001-0.0010.0000.0000.0000.000
130D150PHE00.0380.01137.6470.0020.0020.0000.0000.0000.000
131D151ARG10.8850.94533.994-0.017-0.0170.0000.0000.0000.000
132D152TYR00.0330.01129.5900.0020.0020.0000.0000.0000.000
133D153TRP0-0.055-0.05125.1890.0090.0090.0000.0000.0000.000
134D154PHE00.0830.04325.4660.0010.0010.0000.0000.0000.000
135D155ALA00.008-0.01323.8770.0080.0080.0000.0000.0000.000
136D156PHE00.0230.00620.450-0.007-0.0070.0000.0000.0000.000
137D157PRO0-0.019-0.00920.156-0.005-0.0050.0000.0000.0000.000
138D158ALA00.0530.05316.495-0.014-0.0140.0000.0000.0000.000
139D159PHE00.028-0.00117.8920.0350.0350.0000.0000.0000.000
140D160VAL0-0.080-0.04813.539-0.047-0.0470.0000.0000.0000.000
141D161LEU0-0.023-0.00812.8890.0210.0210.0000.0000.0000.000
142D162ASP-1-0.778-0.87313.4480.1820.1820.0000.0000.0000.000
143D163PRO0-0.0020.00910.6940.1150.1150.0000.0000.0000.000
144D164PRO0-0.047-0.0277.862-0.145-0.1450.0000.0000.0000.000
145D165VAL00.0500.0247.6100.1220.1220.0000.0000.0000.000
146D166SER00.0430.0343.311-0.1950.1630.007-0.106-0.2590.000
147D167LEU0-0.038-0.0182.389-0.2520.6471.258-0.399-1.759-0.002
148D168ILE0-0.027-0.0033.492-2.955-2.1320.027-0.390-0.460-0.003
149D169GLU-1-0.853-0.9334.582-1.400-1.256-0.001-0.007-0.1360.000
150D170LEU0-0.049-0.0326.8170.0970.0970.0000.0000.0000.000
151D171LYS10.8440.9219.0370.8830.8830.0000.0000.0000.000
152D172PRO00.0520.02712.3130.0130.0130.0000.0000.0000.000
153D173ALA0-0.012-0.01615.651-0.003-0.0030.0000.0000.0000.000
154D174SER0-0.014-0.03218.0570.0120.0120.0000.0000.0000.000
155D175GLU-1-0.925-0.94215.546-0.404-0.4040.0000.0000.0000.000
156D176TYR0-0.094-0.03114.6660.0150.0150.0000.0000.0000.000
157D177PHE0-0.043-0.01716.9090.0190.0190.0000.0000.0000.000
158D178SER00.0460.02820.5840.0100.0100.0000.0000.0000.000
159D179SER00.018-0.01823.5180.0030.0030.0000.0000.0000.000
160D180GLU-1-0.935-0.96326.208-0.176-0.1760.0000.0000.0000.000
161D181GLU-1-0.769-0.86722.924-0.316-0.3160.0000.0000.0000.000
162D182ALA0-0.025-0.01724.4040.0010.0010.0000.0000.0000.000
163D183GLU-1-0.903-0.94025.657-0.170-0.1700.0000.0000.0000.000
164D184SER00.0180.01328.7050.0110.0110.0000.0000.0000.000
165D185VAL00.004-0.00223.8320.0070.0070.0000.0000.0000.000
166D186SER00.0050.00127.0900.0000.0000.0000.0000.0000.000
167D187ALA0-0.015-0.00428.2980.0080.0080.0000.0000.0000.000
168D188ALA00.0670.04628.8630.0070.0070.0000.0000.0000.000
169D189CYS0-0.097-0.05725.838-0.005-0.0050.0000.0000.0000.000
170D190ASN0-0.006-0.03028.4780.0020.0020.0000.0000.0000.000
171D191ASP-1-0.886-0.92731.521-0.137-0.1370.0000.0000.0000.000
172D192TRP0-0.068-0.03328.0620.0100.0100.0000.0000.0000.000
173D193ARG10.7810.87627.9350.1790.1790.0000.0000.0000.000
174D194ASP-1-0.855-0.92832.019-0.124-0.1240.0000.0000.0000.000
175D195SER0-0.057-0.01035.2910.0120.0120.0000.0000.0000.000
176D196ASP-1-0.874-0.95435.320-0.099-0.0990.0000.0000.0000.000
177D197LEU0-0.053-0.02036.4620.0000.0000.0000.0000.0000.000
178D198THR0-0.040-0.02232.1390.0010.0010.0000.0000.0000.000
179D199THR00.0020.03231.147-0.009-0.0090.0000.0000.0000.000
180D200ASP-1-0.907-0.96329.898-0.128-0.1280.0000.0000.0000.000
181D201VAL00.0360.03127.8130.0030.0030.0000.0000.0000.000
182D202PRO0-0.034-0.02723.885-0.013-0.0130.0000.0000.0000.000
183D203PHE0-0.016-0.02219.656-0.029-0.0290.0000.0000.0000.000
184D204PHE00.0110.00323.0780.0130.0130.0000.0000.0000.000
185D205LEU00.0380.01622.364-0.030-0.0300.0000.0000.0000.000
186D206VAL0-0.002-0.01221.8670.0180.0180.0000.0000.0000.000
187D207SER00.001-0.00123.241-0.016-0.0160.0000.0000.0000.000
188D208VAL0-0.003-0.01023.5060.0160.0160.0000.0000.0000.000
189D209SER00.1150.07426.203-0.001-0.0010.0000.0000.0000.000
190D210SER0-0.0170.02126.470-0.013-0.0130.0000.0000.0000.000
191D211ASP-1-0.952-1.01228.301-0.146-0.1460.0000.0000.0000.000
192D212SER0-0.025-0.02927.478-0.001-0.0010.0000.0000.0000.000
193D213LYS10.8690.94128.5410.1590.1590.0000.0000.0000.000
194D214ALA0-0.020-0.00326.597-0.006-0.0060.0000.0000.0000.000
195D215SER0-0.030-0.02228.3940.0150.0150.0000.0000.0000.000
196D216ILE00.0020.00725.779-0.008-0.0080.0000.0000.0000.000
197D217ARG10.8840.95427.6430.1810.1810.0000.0000.0000.000
198D218HIS00.0680.02827.625-0.019-0.0190.0000.0000.0000.000
199D219LEU00.003-0.00923.055-0.006-0.0060.0000.0000.0000.000
200D220LYS10.8430.90126.9840.1070.1070.0000.0000.0000.000
201D221ASP-1-0.873-0.93029.744-0.137-0.1370.0000.0000.0000.000
202D222LEU00.0200.01823.042-0.009-0.0090.0000.0000.0000.000
203D223GLU-1-0.821-0.91127.021-0.140-0.1400.0000.0000.0000.000
204D224ALA0-0.050-0.01228.6860.0110.0110.0000.0000.0000.000
205D225CYS0-0.082-0.04027.958-0.003-0.0030.0000.0000.0000.000
206D226GLN00.0250.02222.780-0.002-0.0020.0000.0000.0000.000
207D227GLY00.018-0.00326.4970.0170.0170.0000.0000.0000.000
208D228ASP-1-0.946-0.96326.419-0.174-0.1740.0000.0000.0000.000
209D229HIS0-0.069-0.04326.925-0.005-0.0050.0000.0000.0000.000
210D230GLN0-0.001-0.00225.9790.0100.0100.0000.0000.0000.000
211D231LYS10.8380.92119.8610.3530.3530.0000.0000.0000.000
212D232LEU00.0360.01121.0310.0180.0180.0000.0000.0000.000
213D233LEU0-0.045-0.01416.338-0.050-0.0500.0000.0000.0000.000
214D234PHE00.0360.01417.5630.0430.0430.0000.0000.0000.000
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216D236PHE00.006-0.00614.9240.0250.0250.0000.0000.0000.000
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