FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 72NGK

Calculation Name: 1VHK-D-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VHK

Chain ID: D

ChEMBL ID:
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UniProt ID: P54461

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 178
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1900036.609686
FMO2-HF: Nuclear repulsion 1829621.831197
FMO2-HF: Total energy -70414.778489
FMO2-MP2: Total energy -70619.896859


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:2:GLN)


Summations of interaction energy for fragment #1(D:2: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.
-11.497-6.6961.485-2.32-3.966-0.007
Interaction energy analysis for fragmet #1(D:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.021
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].
3D4TYR00.0060.0032.838-3.9820.7391.486-2.318-3.889-0.007
4D5PHE0-0.032-0.0136.062-0.305-0.3050.0000.0000.0000.000
5D6ILE0-0.074-0.0519.5640.3410.3410.0000.0000.0000.000
6D43CYM-1-0.935-0.9616.648-3.499-3.4990.0000.0000.0000.000
7D44CYS0-0.042-0.0178.1370.2840.2840.0000.0000.0000.000
8D45SER0-0.004-0.02910.9420.2030.2030.0000.0000.0000.000
9D46GLN00.0460.02514.2890.0300.0300.0000.0000.0000.000
10D47ASP-1-0.899-0.92016.470-0.610-0.6100.0000.0000.0000.000
11D48GLY0-0.031-0.00415.2860.0330.0330.0000.0000.0000.000
12D49PHE0-0.060-0.03115.4730.0010.0010.0000.0000.0000.000
13D50GLU-1-0.773-0.8448.451-2.897-2.8970.0000.0000.0000.000
14D51ALA0-0.031-0.0108.7580.0730.0730.0000.0000.0000.000
15D73GLU-1-0.886-0.93411.573-1.602-1.6020.0000.0000.0000.000
16D74ASN0-0.031-0.02214.195-0.037-0.0370.0000.0000.0000.000
17D75ARG10.8310.87910.2081.8461.8460.0000.0000.0000.000
18D76GLU-1-0.793-0.85415.591-0.563-0.5630.0000.0000.0000.000
19D77LEU00.0310.03218.2080.0230.0230.0000.0000.0000.000
20D78PRO0-0.055-0.02921.5680.0100.0100.0000.0000.0000.000
21D79ILE0-0.067-0.02624.5160.0060.0060.0000.0000.0000.000
22D80LYS10.9380.97624.4820.2700.2700.0000.0000.0000.000
23D81VAL00.0510.01324.5020.0250.0250.0000.0000.0000.000
24D82TYR00.012-0.00624.7820.0040.0040.0000.0000.0000.000
25D83ILE00.008-0.00724.4130.0100.0100.0000.0000.0000.000
26D84ALA00.0370.03227.0450.0180.0180.0000.0000.0000.000
27D85SER0-0.017-0.02528.1870.0010.0010.0000.0000.0000.000
28D86GLY00.0450.03030.3430.0080.0080.0000.0000.0000.000
29D87LEU0-0.033-0.03730.5960.0120.0120.0000.0000.0000.000
30D88PRO0-0.0140.01228.837-0.003-0.0030.0000.0000.0000.000
31D89LYS10.8880.93331.612-0.139-0.1390.0000.0000.0000.000
32D90GLY0-0.003-0.00629.7340.0070.0070.0000.0000.0000.000
33D91ASP-1-0.857-0.93824.1330.3690.3690.0000.0000.0000.000
34D92LYS10.7770.88324.705-0.150-0.1500.0000.0000.0000.000
35D93LEU00.028-0.00225.127-0.006-0.0060.0000.0000.0000.000
36D94GLU-1-0.791-0.89420.9060.4760.4760.0000.0000.0000.000
37D95TRP0-0.018-0.01320.698-0.012-0.0120.0000.0000.0000.000
38D96ILE0-0.0140.00321.266-0.018-0.0180.0000.0000.0000.000
39D97ILE0-0.0140.00518.447-0.035-0.0350.0000.0000.0000.000
40D98GLN0-0.0210.00214.354-0.140-0.1400.0000.0000.0000.000
41D99LYS10.8400.90616.591-0.345-0.3450.0000.0000.0000.000
42D100GLY00.0430.01019.121-0.058-0.0580.0000.0000.0000.000
43D101THR0-0.045-0.03814.338-0.067-0.0670.0000.0000.0000.000
44D102GLU-1-0.847-0.89614.5290.0970.0970.0000.0000.0000.000
45D103LEU0-0.047-0.02715.593-0.083-0.0830.0000.0000.0000.000
46D104GLY00.0700.03718.070-0.016-0.0160.0000.0000.0000.000
47D105ALA0-0.064-0.02319.389-0.008-0.0080.0000.0000.0000.000
48D106HIS0-0.038-0.02919.7530.0090.0090.0000.0000.0000.000
49D107ALA0-0.010-0.01021.3100.0020.0020.0000.0000.0000.000
50D108PHE00.0240.01919.5530.0120.0120.0000.0000.0000.000
51D109ILE0-0.024-0.03024.7010.0090.0090.0000.0000.0000.000
52D110PRO00.0100.01626.896-0.001-0.0010.0000.0000.0000.000
53D111PHE00.0300.00629.668-0.004-0.0040.0000.0000.0000.000
54D112GLN0-0.026-0.01433.4660.0180.0180.0000.0000.0000.000
55D113ALA00.0260.01736.450-0.010-0.0100.0000.0000.0000.000
56D114ALA0-0.023-0.01638.1390.0080.0080.0000.0000.0000.000
57D115ARG10.8590.92339.592-0.046-0.0460.0000.0000.0000.000
58D116SER0-0.049-0.01235.1220.0040.0040.0000.0000.0000.000
59D117VAL0-0.028-0.00736.3850.0000.0000.0000.0000.0000.000
60D128LYS11.0000.99524.767-0.198-0.1980.0000.0000.0000.000
61D129ARG10.8740.94023.454-0.079-0.0790.0000.0000.0000.000
62D130GLU-1-0.890-0.93420.8510.3970.3970.0000.0000.0000.000
63D131ARG10.8440.91119.445-0.469-0.4690.0000.0000.0000.000
64D132TRP00.023-0.01419.0130.0180.0180.0000.0000.0000.000
65D133THR0-0.006-0.00917.299-0.032-0.0320.0000.0000.0000.000
66D134LYS10.9340.96214.495-0.977-0.9770.0000.0000.0000.000
67D135ILE0-0.036-0.00514.3420.1360.1360.0000.0000.0000.000
68D136ALA00.0490.03314.7400.0170.0170.0000.0000.0000.000
69D137LYS10.9510.9829.453-0.436-0.4360.0000.0000.0000.000
70D138GLU-1-0.908-0.9489.8191.1951.1950.0000.0000.0000.000
71D139ALA00.0410.00610.0130.0310.0310.0000.0000.0000.000
72D140ALA0-0.0150.00711.454-0.166-0.1660.0000.0000.0000.000
73D141GLU-1-0.879-0.9586.1330.3580.3580.0000.0000.0000.000
74D142GLN0-0.008-0.0085.609-0.278-0.2780.0000.0000.0000.000
75D143SER0-0.055-0.0477.870-0.258-0.2580.0000.0000.0000.000
76D144TYR0-0.086-0.0404.672-0.354-0.274-0.001-0.002-0.0770.000
77D145ARG10.8020.8829.4600.4580.4580.0000.0000.0000.000
78D146ASN0-0.028-0.02611.224-0.250-0.2500.0000.0000.0000.000
79D147GLU-1-0.853-0.91813.708-0.326-0.3260.0000.0000.0000.000
80D148VAL0-0.008-0.00912.8210.0290.0290.0000.0000.0000.000
81D149PRO0-0.0020.01415.4130.0510.0510.0000.0000.0000.000
82D150ARG10.9070.96118.6290.2020.2020.0000.0000.0000.000
83D151VAL00.015-0.00220.4300.0010.0010.0000.0000.0000.000
84D152MET0-0.061-0.02522.9920.0150.0150.0000.0000.0000.000
85D153ASP-1-0.836-0.91626.5060.1120.1120.0000.0000.0000.000
86D154VAL0-0.036-0.01729.055-0.009-0.0090.0000.0000.0000.000
87D155HIS0-0.016-0.00130.806-0.017-0.0170.0000.0000.0000.000
88D156SER00.007-0.01334.0960.0050.0050.0000.0000.0000.000
89D157PHE00.0600.01437.527-0.006-0.0060.0000.0000.0000.000
90D158GLN00.0430.01139.237-0.005-0.0050.0000.0000.0000.000
91D159GLN00.0300.03236.2320.0000.0000.0000.0000.0000.000
92D160LEU0-0.012-0.00233.468-0.007-0.0070.0000.0000.0000.000
93D161LEU00.0500.01036.426-0.009-0.0090.0000.0000.0000.000
94D162GLN0-0.073-0.01639.496-0.002-0.0020.0000.0000.0000.000
95D163ARG10.8970.95031.7990.0350.0350.0000.0000.0000.000
96D164MET0-0.040-0.00935.424-0.005-0.0050.0000.0000.0000.000
97D165GLN00.0400.00437.014-0.004-0.0040.0000.0000.0000.000
98D166ASP-1-0.942-0.95134.214-0.074-0.0740.0000.0000.0000.000
99D167PHE0-0.063-0.04829.992-0.011-0.0110.0000.0000.0000.000
100D168ASP-1-0.826-0.89532.928-0.151-0.1510.0000.0000.0000.000
101D169LYS10.9570.96534.3380.1030.1030.0000.0000.0000.000
102D170CYS00.0180.02534.231-0.001-0.0010.0000.0000.0000.000
103D171VAL0-0.0110.00333.7290.0030.0030.0000.0000.0000.000
104D172VAL00.0200.00034.8790.0060.0060.0000.0000.0000.000
105D173ALA0-0.044-0.02933.664-0.002-0.0020.0000.0000.0000.000
106D174TYR0-0.032-0.03135.8260.0110.0110.0000.0000.0000.000
107D175GLU-1-0.920-0.95239.296-0.027-0.0270.0000.0000.0000.000
108D176GLU-1-0.910-0.92841.994-0.011-0.0110.0000.0000.0000.000
109D184SER00.008-0.00538.881-0.001-0.0010.0000.0000.0000.000
110D185ALA00.0810.02740.193-0.006-0.0060.0000.0000.0000.000
111D186PHE00.0450.02730.482-0.007-0.0070.0000.0000.0000.000
112D187SER00.0200.01135.153-0.008-0.0080.0000.0000.0000.000
113D188ALA00.0310.02536.226-0.010-0.0100.0000.0000.0000.000
114D189ILE0-0.007-0.01634.816-0.010-0.0100.0000.0000.0000.000
115D190VAL00.016-0.00630.570-0.010-0.0100.0000.0000.0000.000
116D191SER0-0.056-0.03932.759-0.012-0.0120.0000.0000.0000.000
117D192SER0-0.077-0.03934.470-0.013-0.0130.0000.0000.0000.000
118D193LEU0-0.0240.01231.4430.0030.0030.0000.0000.0000.000
119D194PRO00.0130.00432.025-0.018-0.0180.0000.0000.0000.000
120D195LYS10.9911.00027.5230.2990.2990.0000.0000.0000.000
121D196GLY0-0.0140.00227.4310.0080.0080.0000.0000.0000.000
122D197SER0-0.065-0.03928.4370.0120.0120.0000.0000.0000.000
123D198SER0-0.009-0.01528.831-0.020-0.0200.0000.0000.0000.000
124D199LEU0-0.038-0.01729.2350.0090.0090.0000.0000.0000.000
125D200LEU0-0.0100.02329.309-0.002-0.0020.0000.0000.0000.000
126D201ILE0-0.019-0.01328.802-0.001-0.0010.0000.0000.0000.000
127D202VAL00.0260.02430.8890.0090.0090.0000.0000.0000.000
128D203PHE00.0250.00628.9390.0000.0000.0000.0000.0000.000
129D204GLY00.0320.01133.2590.0070.0070.0000.0000.0000.000
130D205PRO00.0160.02233.6830.0050.0050.0000.0000.0000.000
131D206GLU-1-0.797-0.91833.6110.1430.1430.0000.0000.0000.000
132D207GLY0-0.035-0.01436.2290.0000.0000.0000.0000.0000.000
133D208GLY00.0070.01037.538-0.007-0.0070.0000.0000.0000.000
134D209LEU00.0380.02136.7840.0060.0060.0000.0000.0000.000
135D210THR0-0.086-0.08439.925-0.002-0.0020.0000.0000.0000.000
136D211GLU-1-0.823-0.91743.6670.0250.0250.0000.0000.0000.000
137D212ALA00.0170.01546.277-0.004-0.0040.0000.0000.0000.000
138D213GLU-1-0.827-0.88840.2750.0390.0390.0000.0000.0000.000
139D214VAL00.007-0.01441.194-0.004-0.0040.0000.0000.0000.000
140D215GLU-1-0.948-0.95243.237-0.004-0.0040.0000.0000.0000.000
141D216ARG10.9400.96643.954-0.016-0.0160.0000.0000.0000.000
142D217LEU0-0.033-0.02738.475-0.004-0.0040.0000.0000.0000.000
143D218THR0-0.0020.00742.109-0.007-0.0070.0000.0000.0000.000
144D219GLU-1-0.944-0.96844.190-0.015-0.0150.0000.0000.0000.000
145D220GLN0-0.101-0.05141.005-0.002-0.0020.0000.0000.0000.000
146D221ASP-1-0.929-0.96341.374-0.057-0.0570.0000.0000.0000.000
147D222GLY0-0.060-0.02639.303-0.007-0.0070.0000.0000.0000.000
148D223VAL0-0.028-0.02939.2270.0020.0020.0000.0000.0000.000
149D224THR0-0.017-0.02338.912-0.003-0.0030.0000.0000.0000.000
150D225CYS0-0.100-0.03736.903-0.011-0.0110.0000.0000.0000.000
151D226GLY00.1030.07137.6110.0060.0060.0000.0000.0000.000
152D227LEU0-0.075-0.04832.394-0.009-0.0090.0000.0000.0000.000
153D228GLY0-0.0010.00134.7060.0030.0030.0000.0000.0000.000
154D229PRO00.0160.00136.9790.0050.0050.0000.0000.0000.000
155D230ARG10.9290.96734.3910.0110.0110.0000.0000.0000.000
156D231ILE00.0510.02236.989-0.002-0.0020.0000.0000.0000.000
157D232LEU00.0090.00531.0920.0090.0090.0000.0000.0000.000
158D233ARG10.9320.97530.864-0.119-0.1190.0000.0000.0000.000
159D234THR0-0.0080.00330.616-0.002-0.0020.0000.0000.0000.000
160D235GLU-1-0.751-0.89126.5260.1380.1380.0000.0000.0000.000
161D236THR0-0.028-0.02926.5000.0000.0000.0000.0000.0000.000
162D237ALA00.0000.01328.077-0.017-0.0170.0000.0000.0000.000
163D238PRO00.0470.01125.662-0.019-0.0190.0000.0000.0000.000
164D239LEU00.0180.01722.482-0.021-0.0210.0000.0000.0000.000
165D240TYR00.0150.02025.090-0.028-0.0280.0000.0000.0000.000
166D241ALA00.0080.00827.907-0.019-0.0190.0000.0000.0000.000
167D242LEU00.0140.01321.907-0.016-0.0160.0000.0000.0000.000
168D243SER00.003-0.01223.910-0.031-0.0310.0000.0000.0000.000
169D244ALA0-0.038-0.02124.883-0.021-0.0210.0000.0000.0000.000
170D245ILE0-0.009-0.00725.674-0.012-0.0120.0000.0000.0000.000
171D246SER00.003-0.01422.053-0.008-0.0080.0000.0000.0000.000
172D247TYR00.0130.00524.553-0.011-0.0110.0000.0000.0000.000
173D248GLN00.008-0.00626.731-0.020-0.0200.0000.0000.0000.000
174D249THR0-0.077-0.07226.082-0.013-0.0130.0000.0000.0000.000
175D250GLU-1-0.796-0.87420.916-0.435-0.4350.0000.0000.0000.000
176D251LEU0-0.050-0.01722.086-0.014-0.0140.0000.0000.0000.000
177D252LEU0-0.070-0.01925.7620.0150.0150.0000.0000.0000.000
178D253ARG10.8530.97025.6240.2350.2350.0000.0000.0000.000