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: 2JR2R

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 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 178
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1906657.755064
FMO2-HF: Nuclear repulsion 1836242.235253
FMO2-HF: Total energy -70415.519811
FMO2-MP2: Total energy -70620.62084


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.
-15.761-10.7041.724-2.611-4.172-0.002
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 : -0.038 / q_NPA : -0.025
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].
3D4TYR0-0.029-0.0082.670-6.264-1.3231.725-2.600-4.067-0.002
4D5PHE0-0.020-0.0096.114-0.241-0.2410.0000.0000.0000.000
5D6ILE0-0.092-0.0669.0260.3850.3850.0000.0000.0000.000
6D43CYM-1-0.897-0.9475.922-3.242-3.2420.0000.0000.0000.000
7D44CYS0-0.039-0.0157.7730.1010.1010.0000.0000.0000.000
8D45SER0-0.029-0.03410.9020.2190.2190.0000.0000.0000.000
9D46GLN00.0160.00614.0850.0110.0110.0000.0000.0000.000
10D47ASP-1-0.891-0.91316.386-0.549-0.5490.0000.0000.0000.000
11D48GLY00.0070.02015.6550.0250.0250.0000.0000.0000.000
12D49PHE0-0.054-0.02615.588-0.091-0.0910.0000.0000.0000.000
13D50GLU-1-0.747-0.8278.677-3.064-3.0640.0000.0000.0000.000
14D51ALA0-0.041-0.0208.8870.0010.0010.0000.0000.0000.000
15D73GLU-1-0.878-0.92811.650-1.802-1.8020.0000.0000.0000.000
16D74ASN0-0.045-0.03214.6020.0140.0140.0000.0000.0000.000
17D75ARG10.8090.87310.1942.0702.0700.0000.0000.0000.000
18D76GLU-1-0.772-0.84615.406-0.702-0.7020.0000.0000.0000.000
19D77LEU00.0240.02718.1570.0270.0270.0000.0000.0000.000
20D78PRO0-0.051-0.02621.4550.0210.0210.0000.0000.0000.000
21D79ILE0-0.041-0.01624.3370.0280.0280.0000.0000.0000.000
22D80LYS10.9380.97224.6290.2750.2750.0000.0000.0000.000
23D81VAL00.0320.01324.3070.0350.0350.0000.0000.0000.000
24D82TYR00.0300.02024.5470.0010.0010.0000.0000.0000.000
25D83ILE00.0160.00924.1250.0100.0100.0000.0000.0000.000
26D84ALA00.0370.01826.9150.0190.0190.0000.0000.0000.000
27D85SER0-0.035-0.03028.245-0.004-0.0040.0000.0000.0000.000
28D86GLY00.0510.03130.4230.0130.0130.0000.0000.0000.000
29D87LEU0-0.033-0.02830.6330.0070.0070.0000.0000.0000.000
30D88PRO0-0.0180.00428.938-0.004-0.0040.0000.0000.0000.000
31D89LYS10.8690.91431.781-0.104-0.1040.0000.0000.0000.000
32D90GLY00.0200.00529.5070.0020.0020.0000.0000.0000.000
33D91ASP-1-0.866-0.93723.8360.3240.3240.0000.0000.0000.000
34D92LYS10.7870.88424.409-0.105-0.1050.0000.0000.0000.000
35D93LEU00.0280.00924.863-0.017-0.0170.0000.0000.0000.000
36D94GLU-1-0.789-0.90520.6430.4170.4170.0000.0000.0000.000
37D95TRP0-0.015-0.00420.373-0.020-0.0200.0000.0000.0000.000
38D96ILE00.0080.01221.049-0.030-0.0300.0000.0000.0000.000
39D97ILE0-0.028-0.00418.284-0.038-0.0380.0000.0000.0000.000
40D98GLN0-0.038-0.02413.886-0.139-0.1390.0000.0000.0000.000
41D99LYS10.8210.89416.129-0.152-0.1520.0000.0000.0000.000
42D100GLY00.0430.01018.994-0.058-0.0580.0000.0000.0000.000
43D101THR0-0.048-0.02714.234-0.057-0.0570.0000.0000.0000.000
44D102GLU-1-0.816-0.89314.360-0.135-0.1350.0000.0000.0000.000
45D103LEU0-0.060-0.02115.510-0.073-0.0730.0000.0000.0000.000
46D104GLY00.0630.02417.9700.0030.0030.0000.0000.0000.000
47D105ALA0-0.039-0.02019.0870.0020.0020.0000.0000.0000.000
48D106HIS0-0.024-0.01419.5230.0070.0070.0000.0000.0000.000
49D107ALA0-0.020-0.02021.2250.0120.0120.0000.0000.0000.000
50D108PHE00.0070.01019.4190.0070.0070.0000.0000.0000.000
51D109ILE00.004-0.01324.6520.0180.0180.0000.0000.0000.000
52D110PRO00.0070.01326.527-0.002-0.0020.0000.0000.0000.000
53D111PHE00.015-0.01229.2920.0010.0010.0000.0000.0000.000
54D112GLN0-0.008-0.01033.1060.0130.0130.0000.0000.0000.000
55D113ALA00.0370.02136.216-0.009-0.0090.0000.0000.0000.000
56D114ALA0-0.039-0.02437.8550.0090.0090.0000.0000.0000.000
57D115ARG10.8110.90039.509-0.021-0.0210.0000.0000.0000.000
58D116SER0-0.034-0.01235.0200.0020.0020.0000.0000.0000.000
59D117VAL0-0.051-0.01535.6640.0030.0030.0000.0000.0000.000
60D128LYS11.0090.99424.527-0.208-0.2080.0000.0000.0000.000
61D129ARG10.8350.91923.386-0.102-0.1020.0000.0000.0000.000
62D130GLU-1-0.887-0.93420.6310.4350.4350.0000.0000.0000.000
63D131ARG10.7820.88719.173-0.405-0.4050.0000.0000.0000.000
64D132TRP00.0400.00118.7130.0220.0220.0000.0000.0000.000
65D133THR00.013-0.00317.639-0.032-0.0320.0000.0000.0000.000
66D134LYS10.9460.97413.978-1.016-1.0160.0000.0000.0000.000
67D135ILE0-0.0150.00214.1200.1140.1140.0000.0000.0000.000
68D136ALA00.0380.02014.608-0.027-0.0270.0000.0000.0000.000
69D137LYS10.8700.9439.318-0.748-0.7480.0000.0000.0000.000
70D138GLU-1-0.873-0.9289.9930.6820.6820.0000.0000.0000.000
71D139ALA00.0470.0209.715-0.115-0.1150.0000.0000.0000.000
72D140ALA0-0.0010.02111.176-0.216-0.2160.0000.0000.0000.000
73D141GLU-1-0.825-0.9236.0910.4240.4240.0000.0000.0000.000
74D142GLN0-0.020-0.0175.578-0.871-0.8710.0000.0000.0000.000
75D143SER0-0.074-0.0607.694-0.344-0.3440.0000.0000.0000.000
76D144TYR0-0.056-0.0334.090-0.561-0.445-0.001-0.011-0.1050.000
77D145ARG10.8030.8889.0840.6150.6150.0000.0000.0000.000
78D146ASN0-0.029-0.03911.090-0.321-0.3210.0000.0000.0000.000
79D147GLU-1-0.842-0.89913.718-0.277-0.2770.0000.0000.0000.000
80D148VAL00.001-0.00112.703-0.003-0.0030.0000.0000.0000.000
81D149PRO0-0.0130.00115.1600.0590.0590.0000.0000.0000.000
82D150ARG10.8840.94018.4070.2330.2330.0000.0000.0000.000
83D151VAL00.0260.01320.343-0.011-0.0110.0000.0000.0000.000
84D152MET0-0.033-0.00722.9270.0220.0220.0000.0000.0000.000
85D153ASP-1-0.848-0.92826.5450.1400.1400.0000.0000.0000.000
86D154VAL0-0.043-0.02129.095-0.013-0.0130.0000.0000.0000.000
87D155HIS00.0030.01530.837-0.015-0.0150.0000.0000.0000.000
88D156SER00.013-0.02333.9920.0030.0030.0000.0000.0000.000
89D157PHE00.0500.01837.124-0.006-0.0060.0000.0000.0000.000
90D158GLN00.0380.02038.817-0.007-0.0070.0000.0000.0000.000
91D159GLN00.0260.03036.091-0.002-0.0020.0000.0000.0000.000
92D160LEU0-0.0110.00133.259-0.006-0.0060.0000.0000.0000.000
93D161LEU00.0710.02736.066-0.010-0.0100.0000.0000.0000.000
94D162GLN0-0.071-0.02339.312-0.003-0.0030.0000.0000.0000.000
95D163ARG10.8580.92631.5530.0360.0360.0000.0000.0000.000
96D164MET0-0.036-0.00235.314-0.007-0.0070.0000.0000.0000.000
97D165GLN00.024-0.00636.935-0.005-0.0050.0000.0000.0000.000
98D166ASP-1-0.899-0.93133.545-0.073-0.0730.0000.0000.0000.000
99D167PHE0-0.047-0.04230.029-0.013-0.0130.0000.0000.0000.000
100D168ASP-1-0.836-0.90232.667-0.173-0.1730.0000.0000.0000.000
101D169LYS10.9210.94934.1190.1310.1310.0000.0000.0000.000
102D170CYS00.0150.04433.907-0.003-0.0030.0000.0000.0000.000
103D171VAL0-0.015-0.00433.8160.0000.0000.0000.0000.0000.000
104D172VAL00.0130.00734.8430.0060.0060.0000.0000.0000.000
105D173ALA0-0.024-0.01233.385-0.003-0.0030.0000.0000.0000.000
106D174TYR0-0.040-0.03135.5360.0110.0110.0000.0000.0000.000
107D175GLU-1-0.861-0.91439.130-0.065-0.0650.0000.0000.0000.000
108D176GLU-1-0.927-0.95441.814-0.032-0.0320.0000.0000.0000.000
109D184SER00.0010.00138.969-0.002-0.0020.0000.0000.0000.000
110D185ALA00.0470.01239.619-0.008-0.0080.0000.0000.0000.000
111D186PHE00.0520.01830.149-0.008-0.0080.0000.0000.0000.000
112D187SER00.0040.00534.826-0.011-0.0110.0000.0000.0000.000
113D188ALA00.0540.02735.678-0.011-0.0110.0000.0000.0000.000
114D189ILE0-0.0120.00334.569-0.008-0.0080.0000.0000.0000.000
115D190VAL00.0240.00630.088-0.010-0.0100.0000.0000.0000.000
116D191SER0-0.042-0.04232.309-0.013-0.0130.0000.0000.0000.000
117D192SER0-0.058-0.03734.213-0.010-0.0100.0000.0000.0000.000
118D193LEU0-0.0250.00831.1360.0020.0020.0000.0000.0000.000
119D194PRO00.0120.00431.805-0.021-0.0210.0000.0000.0000.000
120D195LYS10.9740.98927.3370.3480.3480.0000.0000.0000.000
121D196GLY0-0.0090.00027.4450.0090.0090.0000.0000.0000.000
122D197SER0-0.062-0.03128.4260.0140.0140.0000.0000.0000.000
123D198SER0-0.011-0.02628.702-0.025-0.0250.0000.0000.0000.000
124D199LEU0-0.031-0.01629.1340.0110.0110.0000.0000.0000.000
125D200LEU0-0.0040.01629.188-0.003-0.0030.0000.0000.0000.000
126D201ILE0-0.026-0.01628.5070.0000.0000.0000.0000.0000.000
127D202VAL00.0170.01630.6210.0100.0100.0000.0000.0000.000
128D203PHE00.0300.00928.606-0.001-0.0010.0000.0000.0000.000
129D204GLY00.0500.01932.8040.0090.0090.0000.0000.0000.000
130D205PRO00.0250.04533.3690.0020.0020.0000.0000.0000.000
131D206GLU-1-0.812-0.91333.3040.1030.1030.0000.0000.0000.000
132D207GLY00.0050.00635.7010.0030.0030.0000.0000.0000.000
133D208GLY0-0.0110.00437.205-0.006-0.0060.0000.0000.0000.000
134D209LEU00.0220.00836.4090.0080.0080.0000.0000.0000.000
135D210THR0-0.065-0.05939.596-0.002-0.0020.0000.0000.0000.000
136D211GLU-1-0.791-0.90043.3220.0060.0060.0000.0000.0000.000
137D212ALA00.0460.02845.820-0.004-0.0040.0000.0000.0000.000
138D213GLU-1-0.817-0.88639.7440.0210.0210.0000.0000.0000.000
139D214VAL0-0.009-0.01640.972-0.005-0.0050.0000.0000.0000.000
140D215GLU-1-0.928-0.95442.830-0.016-0.0160.0000.0000.0000.000
141D216ARG10.9330.96643.973-0.005-0.0050.0000.0000.0000.000
142D217LEU0-0.041-0.03638.174-0.003-0.0030.0000.0000.0000.000
143D218THR00.0050.00441.758-0.007-0.0070.0000.0000.0000.000
144D219GLU-1-0.966-0.98044.060-0.023-0.0230.0000.0000.0000.000
145D220GLN0-0.084-0.04040.800-0.001-0.0010.0000.0000.0000.000
146D221ASP-1-0.918-0.96040.958-0.072-0.0720.0000.0000.0000.000
147D222GLY0-0.043-0.03238.801-0.009-0.0090.0000.0000.0000.000
148D223VAL0-0.031-0.02139.0020.0040.0040.0000.0000.0000.000
149D224THR0-0.017-0.03438.583-0.006-0.0060.0000.0000.0000.000
150D225CYS0-0.087-0.03036.831-0.012-0.0120.0000.0000.0000.000
151D226GLY00.0650.04637.2160.0040.0040.0000.0000.0000.000
152D227LEU0-0.041-0.02632.138-0.009-0.0090.0000.0000.0000.000
153D228GLY00.0180.00434.849-0.011-0.0110.0000.0000.0000.000
154D229PRO0-0.0090.00737.3530.0070.0070.0000.0000.0000.000
155D230ARG10.9320.95234.0560.0730.0730.0000.0000.0000.000
156D231ILE00.0490.02636.919-0.004-0.0040.0000.0000.0000.000
157D232LEU0-0.0220.00230.6970.0060.0060.0000.0000.0000.000
158D233ARG10.9330.97630.778-0.060-0.0600.0000.0000.0000.000
159D234THR00.002-0.01230.461-0.007-0.0070.0000.0000.0000.000
160D235GLU-1-0.785-0.91226.4010.0740.0740.0000.0000.0000.000
161D236THR0-0.049-0.03126.256-0.002-0.0020.0000.0000.0000.000
162D237ALA00.0170.00827.832-0.021-0.0210.0000.0000.0000.000
163D238PRO00.0390.01625.492-0.020-0.0200.0000.0000.0000.000
164D239LEU00.0320.02622.130-0.026-0.0260.0000.0000.0000.000
165D240TYR0-0.031-0.01024.747-0.035-0.0350.0000.0000.0000.000
166D241ALA00.0070.00327.595-0.020-0.0200.0000.0000.0000.000
167D242LEU0-0.0050.00921.814-0.010-0.0100.0000.0000.0000.000
168D243SER00.006-0.00723.712-0.039-0.0390.0000.0000.0000.000
169D244ALA0-0.042-0.02224.702-0.022-0.0220.0000.0000.0000.000
170D245ILE00.0080.00125.320-0.006-0.0060.0000.0000.0000.000
171D246SER00.0130.01121.538-0.009-0.0090.0000.0000.0000.000
172D247TYR00.012-0.01123.905-0.007-0.0070.0000.0000.0000.000
173D248GLN00.0110.00626.276-0.007-0.0070.0000.0000.0000.000
174D249THR0-0.082-0.07525.756-0.004-0.0040.0000.0000.0000.000
175D250GLU-1-0.801-0.88920.585-0.542-0.5420.0000.0000.0000.000
176D251LEU0-0.058-0.02121.686-0.017-0.0170.0000.0000.0000.000
177D252LEU0-0.037-0.00725.5060.0160.0160.0000.0000.0000.000
178D253ARG10.7920.94025.5700.2900.2900.0000.0000.0000.000