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: MV83Z

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 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 178
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1899880.176841
FMO2-HF: Nuclear repulsion 1829466.815647
FMO2-HF: Total energy -70413.361193
FMO2-MP2: Total energy -70618.507245


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.
-7.264-2.8691.554-2.254-3.695-0.005
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 : -0.021 / q_NPA : -0.013
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].
3D4TYR00.0280.0092.530-2.4801.9151.554-2.254-3.695-0.005
4D5PHE0-0.014-0.0035.970-0.349-0.3490.0000.0000.0000.000
5D6ILE0-0.034-0.0159.6930.3310.3310.0000.0000.0000.000
6D43CYM-1-0.918-0.9556.744-2.796-2.7960.0000.0000.0000.000
7D44CYS0-0.052-0.0248.2470.2640.2640.0000.0000.0000.000
8D45SER00.0250.03310.9420.1870.1870.0000.0000.0000.000
9D46GLN0-0.012-0.02214.2900.0170.0170.0000.0000.0000.000
10D47ASP-1-0.891-0.95416.375-0.515-0.5150.0000.0000.0000.000
11D48GLY0-0.040-0.00615.2850.0280.0280.0000.0000.0000.000
12D49PHE0-0.081-0.04815.327-0.004-0.0040.0000.0000.0000.000
13D50GLU-1-0.792-0.8709.220-2.513-2.5130.0000.0000.0000.000
14D51ALA0-0.022-0.0018.7200.0350.0350.0000.0000.0000.000
15D73GLU-1-0.978-0.99812.249-1.399-1.3990.0000.0000.0000.000
16D74ASN0-0.032-0.03314.199-0.006-0.0060.0000.0000.0000.000
17D75ARG10.8890.9329.8881.7531.7530.0000.0000.0000.000
18D76GLU-1-0.804-0.85815.593-0.433-0.4330.0000.0000.0000.000
19D77LEU00.0440.03118.2100.0160.0160.0000.0000.0000.000
20D78PRO0-0.051-0.02821.5290.0080.0080.0000.0000.0000.000
21D79ILE0-0.068-0.02924.5170.0050.0050.0000.0000.0000.000
22D80LYS10.9810.99624.4470.2330.2330.0000.0000.0000.000
23D81VAL00.0450.01724.4610.0220.0220.0000.0000.0000.000
24D82TYR0-0.016-0.02024.7430.0100.0100.0000.0000.0000.000
25D83ILE00.026-0.00324.6070.0070.0070.0000.0000.0000.000
26D84ALA00.0220.02627.0100.0190.0190.0000.0000.0000.000
27D85SER00.001-0.01228.366-0.003-0.0030.0000.0000.0000.000
28D86GLY00.0220.01730.3130.0080.0080.0000.0000.0000.000
29D87LEU0-0.024-0.03529.8240.0130.0130.0000.0000.0000.000
30D88PRO00.0060.04328.485-0.005-0.0050.0000.0000.0000.000
31D89LYS10.8950.93331.167-0.163-0.1630.0000.0000.0000.000
32D90GLY0-0.033-0.02629.3300.0090.0090.0000.0000.0000.000
33D91ASP-1-0.826-0.91423.7440.3850.3850.0000.0000.0000.000
34D92LYS10.8610.94424.271-0.175-0.1750.0000.0000.0000.000
35D93LEU00.0420.01024.749-0.004-0.0040.0000.0000.0000.000
36D94GLU-1-0.873-0.95120.5000.5110.5110.0000.0000.0000.000
37D95TRP0-0.015-0.01220.320-0.006-0.0060.0000.0000.0000.000
38D96ILE0-0.0150.00221.205-0.013-0.0130.0000.0000.0000.000
39D97ILE0-0.028-0.00218.440-0.030-0.0300.0000.0000.0000.000
40D98GLN00.0240.01914.769-0.130-0.1300.0000.0000.0000.000
41D99LYS10.9540.97016.954-0.423-0.4230.0000.0000.0000.000
42D100GLY00.0450.02019.096-0.056-0.0560.0000.0000.0000.000
43D101THR0-0.047-0.03114.280-0.069-0.0690.0000.0000.0000.000
44D102GLU-1-0.960-0.96514.3570.1480.1480.0000.0000.0000.000
45D103LEU0-0.064-0.03215.563-0.085-0.0850.0000.0000.0000.000
46D104GLY00.0620.04118.026-0.023-0.0230.0000.0000.0000.000
47D105ALA0-0.074-0.02319.352-0.010-0.0100.0000.0000.0000.000
48D106HIS0-0.021-0.00819.7150.0090.0090.0000.0000.0000.000
49D107ALA00.000-0.00921.2710.0070.0070.0000.0000.0000.000
50D108PHE00.0260.02819.5360.0080.0080.0000.0000.0000.000
51D109ILE0-0.015-0.03324.6670.0090.0090.0000.0000.0000.000
52D110PRO00.0090.01627.009-0.003-0.0030.0000.0000.0000.000
53D111PHE00.0270.00529.638-0.006-0.0060.0000.0000.0000.000
54D112GLN0-0.029-0.01233.4370.0200.0200.0000.0000.0000.000
55D113ALA00.0260.01336.376-0.010-0.0100.0000.0000.0000.000
56D114ALA0-0.029-0.02338.1120.0070.0070.0000.0000.0000.000
57D115ARG10.8870.94539.496-0.064-0.0640.0000.0000.0000.000
58D116SER0-0.058-0.03734.6790.0050.0050.0000.0000.0000.000
59D117VAL0-0.035-0.00736.012-0.001-0.0010.0000.0000.0000.000
60D128LYS11.0091.00624.410-0.223-0.2230.0000.0000.0000.000
61D129ARG10.9430.98523.138-0.127-0.1270.0000.0000.0000.000
62D130GLU-1-0.883-0.92420.8240.4270.4270.0000.0000.0000.000
63D131ARG10.9210.96918.833-0.548-0.5480.0000.0000.0000.000
64D132TRP00.029-0.01118.6010.0310.0310.0000.0000.0000.000
65D133THR0-0.022-0.02617.159-0.026-0.0260.0000.0000.0000.000
66D134LYS10.9280.95914.265-1.086-1.0860.0000.0000.0000.000
67D135ILE0-0.034-0.01414.0020.1580.1580.0000.0000.0000.000
68D136ALA00.0500.03414.5860.0350.0350.0000.0000.0000.000
69D137LYS10.9660.98710.578-0.633-0.6330.0000.0000.0000.000
70D138GLU-1-0.942-0.9619.2101.6881.6880.0000.0000.0000.000
71D139ALA00.0480.0089.9910.0590.0590.0000.0000.0000.000
72D140ALA0-0.020-0.00511.424-0.170-0.1700.0000.0000.0000.000
73D141GLU-1-0.935-0.9876.0721.2691.2690.0000.0000.0000.000
74D142GLN0-0.013-0.0085.2230.4420.4420.0000.0000.0000.000
75D143SER0-0.033-0.0227.846-0.329-0.3290.0000.0000.0000.000
76D144TYR0-0.088-0.0384.872-0.573-0.5730.0000.0000.0000.000
77D145ARG10.8040.8749.4210.3220.3220.0000.0000.0000.000
78D146ASN0-0.027-0.02611.181-0.225-0.2250.0000.0000.0000.000
79D147GLU-1-0.917-0.96113.665-0.231-0.2310.0000.0000.0000.000
80D148VAL0-0.019-0.01712.8190.0410.0410.0000.0000.0000.000
81D149PRO00.0130.02215.3750.0400.0400.0000.0000.0000.000
82D150ARG10.9660.99018.5920.1260.1260.0000.0000.0000.000
83D151VAL0-0.003-0.01320.3820.0000.0000.0000.0000.0000.000
84D152MET0-0.085-0.04122.9160.0090.0090.0000.0000.0000.000
85D153ASP-1-0.858-0.93426.4150.1410.1410.0000.0000.0000.000
86D154VAL0-0.048-0.02428.982-0.009-0.0090.0000.0000.0000.000
87D155HIS0-0.045-0.02330.447-0.019-0.0190.0000.0000.0000.000
88D156SER00.0230.00534.0220.0050.0050.0000.0000.0000.000
89D157PHE00.0820.02537.471-0.005-0.0050.0000.0000.0000.000
90D158GLN00.0420.01139.205-0.005-0.0050.0000.0000.0000.000
91D159GLN0-0.003-0.00736.2880.0010.0010.0000.0000.0000.000
92D160LEU0-0.011-0.00433.469-0.007-0.0070.0000.0000.0000.000
93D161LEU00.0390.00536.391-0.008-0.0080.0000.0000.0000.000
94D162GLN0-0.058-0.00939.391-0.002-0.0020.0000.0000.0000.000
95D163ARG10.9400.97231.3610.0010.0010.0000.0000.0000.000
96D164MET0-0.037-0.01235.385-0.005-0.0050.0000.0000.0000.000
97D165GLN00.0450.01136.9770.0000.0000.0000.0000.0000.000
98D166ASP-1-0.956-0.95734.289-0.049-0.0490.0000.0000.0000.000
99D167PHE0-0.075-0.05329.680-0.009-0.0090.0000.0000.0000.000
100D168ASP-1-0.853-0.91633.586-0.120-0.1200.0000.0000.0000.000
101D169LYS10.9420.96134.3000.0750.0750.0000.0000.0000.000
102D170CYS00.0170.01734.1910.0010.0010.0000.0000.0000.000
103D171VAL0-0.0120.00633.6990.0010.0010.0000.0000.0000.000
104D172VAL00.0230.00134.8440.0070.0070.0000.0000.0000.000
105D173ALA0-0.046-0.02933.668-0.003-0.0030.0000.0000.0000.000
106D174TYR0-0.040-0.03835.7940.0110.0110.0000.0000.0000.000
107D175GLU-1-0.930-0.96539.266-0.008-0.0080.0000.0000.0000.000
108D176GLU-1-0.931-0.95841.9640.0020.0020.0000.0000.0000.000
109D184SER00.014-0.00238.879-0.001-0.0010.0000.0000.0000.000
110D185ALA00.0700.02640.158-0.006-0.0060.0000.0000.0000.000
111D186PHE00.0580.02930.521-0.007-0.0070.0000.0000.0000.000
112D187SER00.0270.01035.117-0.007-0.0070.0000.0000.0000.000
113D188ALA00.0220.02236.191-0.010-0.0100.0000.0000.0000.000
114D189ILE0-0.003-0.02334.615-0.009-0.0090.0000.0000.0000.000
115D190VAL00.011-0.00730.641-0.009-0.0090.0000.0000.0000.000
116D191SER0-0.055-0.03832.724-0.013-0.0130.0000.0000.0000.000
117D192SER0-0.062-0.02334.471-0.013-0.0130.0000.0000.0000.000
118D193LEU0-0.0110.01931.5570.0020.0020.0000.0000.0000.000
119D194PRO00.0100.00632.026-0.017-0.0170.0000.0000.0000.000
120D195LYS10.9730.99927.3170.2610.2610.0000.0000.0000.000
121D196GLY0-0.0240.00227.4290.0060.0060.0000.0000.0000.000
122D197SER0-0.042-0.03928.4400.0110.0110.0000.0000.0000.000
123D198SER00.000-0.00528.789-0.013-0.0130.0000.0000.0000.000
124D199LEU0-0.028-0.01229.1870.0060.0060.0000.0000.0000.000
125D200LEU0-0.0130.02329.2700.0010.0010.0000.0000.0000.000
126D201ILE0-0.011-0.01128.612-0.003-0.0030.0000.0000.0000.000
127D202VAL00.0190.02130.8550.0110.0110.0000.0000.0000.000
128D203PHE00.0150.00428.883-0.002-0.0020.0000.0000.0000.000
129D204GLY00.0180.01133.2290.0070.0070.0000.0000.0000.000
130D205PRO00.0220.03233.6120.0060.0060.0000.0000.0000.000
131D206GLU-1-0.790-0.93032.8680.1550.1550.0000.0000.0000.000
132D207GLY0-0.048-0.02535.974-0.001-0.0010.0000.0000.0000.000
133D208GLY00.0000.00637.513-0.008-0.0080.0000.0000.0000.000
134D209LEU00.0310.00636.8870.0050.0050.0000.0000.0000.000
135D210THR0-0.092-0.06439.897-0.003-0.0030.0000.0000.0000.000
136D211GLU-1-0.797-0.91143.6390.0360.0360.0000.0000.0000.000
137D212ALA00.0130.01546.247-0.004-0.0040.0000.0000.0000.000
138D213GLU-1-0.869-0.91440.5430.0570.0570.0000.0000.0000.000
139D214VAL00.031-0.00241.129-0.004-0.0040.0000.0000.0000.000
140D215GLU-1-0.938-0.94443.2050.0070.0070.0000.0000.0000.000
141D216ARG10.9560.96543.843-0.031-0.0310.0000.0000.0000.000
142D217LEU0-0.030-0.02538.533-0.004-0.0040.0000.0000.0000.000
143D218THR0-0.0130.00542.074-0.007-0.0070.0000.0000.0000.000
144D219GLU-1-0.983-0.98644.154-0.001-0.0010.0000.0000.0000.000
145D220GLN0-0.084-0.03941.185-0.003-0.0030.0000.0000.0000.000
146D221ASP-1-0.935-0.96241.336-0.039-0.0390.0000.0000.0000.000
147D222GLY0-0.066-0.03039.265-0.006-0.0060.0000.0000.0000.000
148D223VAL0-0.018-0.02739.1800.0010.0010.0000.0000.0000.000
149D224THR00.0020.01538.876-0.001-0.0010.0000.0000.0000.000
150D225CYS0-0.090-0.02636.911-0.011-0.0110.0000.0000.0000.000
151D226GLY00.0970.07037.5800.0070.0070.0000.0000.0000.000
152D227LEU0-0.065-0.04832.139-0.008-0.0080.0000.0000.0000.000
153D228GLY0-0.009-0.00234.6790.0040.0040.0000.0000.0000.000
154D229PRO00.0300.01236.9520.0050.0050.0000.0000.0000.000
155D230ARG10.9230.96034.574-0.006-0.0060.0000.0000.0000.000
156D231ILE00.0680.03236.831-0.001-0.0010.0000.0000.0000.000
157D232LEU0-0.0060.00031.7110.0090.0090.0000.0000.0000.000
158D233ARG10.9360.96830.826-0.133-0.1330.0000.0000.0000.000
159D234THR0-0.018-0.00330.352-0.001-0.0010.0000.0000.0000.000
160D235GLU-1-0.813-0.93226.1310.1640.1640.0000.0000.0000.000
161D236THR0-0.063-0.04126.4060.0030.0030.0000.0000.0000.000
162D237ALA00.0050.01628.052-0.015-0.0150.0000.0000.0000.000
163D238PRO00.0390.00625.710-0.019-0.0190.0000.0000.0000.000
164D239LEU00.0160.01522.355-0.017-0.0170.0000.0000.0000.000
165D240TYR00.0110.01225.063-0.029-0.0290.0000.0000.0000.000
166D241ALA00.0090.00127.880-0.020-0.0200.0000.0000.0000.000
167D242LEU00.0110.01322.022-0.017-0.0170.0000.0000.0000.000
168D243SER00.0210.00523.888-0.031-0.0310.0000.0000.0000.000
169D244ALA0-0.041-0.02024.853-0.021-0.0210.0000.0000.0000.000
170D245ILE0-0.004-0.00525.428-0.014-0.0140.0000.0000.0000.000
171D246SER00.0290.03122.308-0.005-0.0050.0000.0000.0000.000
172D247TYR00.0140.01024.530-0.017-0.0170.0000.0000.0000.000
173D248GLN0-0.026-0.02226.730-0.026-0.0260.0000.0000.0000.000
174D249THR0-0.084-0.07925.867-0.015-0.0150.0000.0000.0000.000
175D250GLU-1-0.819-0.92420.791-0.374-0.3740.0000.0000.0000.000
176D251LEU0-0.047-0.01922.136-0.016-0.0160.0000.0000.0000.000
177D252LEU0-0.052-0.00925.7610.0120.0120.0000.0000.0000.000
178D253ARG10.8490.96925.6790.2060.2060.0000.0000.0000.000