FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 9GN72

Calculation Name: 3VZH-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZH

Chain ID: A

ChEMBL ID:

UniProt ID: Q99YS3

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2418419.36451
FMO2-HF: Nuclear repulsion 2336235.387453
FMO2-HF: Total energy -82183.977057
FMO2-MP2: Total energy -82425.039527


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(A:-1:GLY )


Summations of interaction energy for fragment #1(A:-1:GLY )
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.
1.2982.774-0.005-0.773-0.6980.004
Interaction energy analysis for fragmet #1(A:-1:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / 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].
3A1MET 00.0010.0013.8200.3701.846-0.005-0.773-0.6980.004
4A2TYR 0-0.016-0.0116.1320.5980.5980.0000.0000.0000.000
5A3ARG 10.8250.8959.0290.7950.7950.0000.0000.0000.000
6A4SER 0-0.049-0.02112.3630.0490.0490.0000.0000.0000.000
7A5ARG 10.8880.90615.7760.2390.2390.0000.0000.0000.000
8A6ASP -1-0.857-0.90118.437-0.540-0.5400.0000.0000.0000.000
9A7PHE 0-0.050-0.02719.8620.0450.0450.0000.0000.0000.000
10A8TYR 00.0380.01423.651-0.020-0.0200.0000.0000.0000.000
11A9VAL 00.0060.00227.1040.0150.0150.0000.0000.0000.000
12A10ARG 11.0281.01829.9480.1310.1310.0000.0000.0000.000
13A11VAL 0-0.016-0.01431.3680.0070.0070.0000.0000.0000.000
14A12SER 0-0.040-0.02134.3400.0020.0020.0000.0000.0000.000
15A13GLY 00.0960.02837.9620.0010.0010.0000.0000.0000.000
16A14GLN 00.0230.02340.4490.0030.0030.0000.0000.0000.000
17A15ARG 10.9270.97542.3590.0900.0900.0000.0000.0000.000
18A16ALA 00.0320.01637.477-0.004-0.0040.0000.0000.0000.000
19A17LEU 00.000-0.00738.1640.0050.0050.0000.0000.0000.000
20A18PHE 0-0.0170.00133.677-0.005-0.0050.0000.0000.0000.000
21A19THR 00.0570.02435.5260.0000.0000.0000.0000.0000.000
22A20ASN 00.0400.00933.847-0.016-0.0160.0000.0000.0000.000
23A21PRO 0-0.055-0.02531.7480.0100.0100.0000.0000.0000.000
24A22ALA 00.0330.00833.366-0.003-0.0030.0000.0000.0000.000
25A23THR 00.0180.02235.9280.0010.0010.0000.0000.0000.000
26A24LYS 10.9790.97538.3460.0700.0700.0000.0000.0000.000
27A25GLY 00.0200.01740.7470.0010.0010.0000.0000.0000.000
28A26GLY 00.0440.03241.3280.0020.0020.0000.0000.0000.000
29A27SER 0-0.102-0.06241.539-0.007-0.0070.0000.0000.0000.000
30A28GLU -1-0.963-0.97542.522-0.073-0.0730.0000.0000.0000.000
31A29ARG 10.9460.98440.1690.0930.0930.0000.0000.0000.000
32A30SER 00.0120.00442.0480.0010.0010.0000.0000.0000.000
33A31SER 0-0.013-0.01038.538-0.005-0.0050.0000.0000.0000.000
34A32TYR 00.0180.01833.741-0.001-0.0010.0000.0000.0000.000
35A33SER 00.0310.01637.5170.0020.0020.0000.0000.0000.000
36A34VAL 00.0270.01632.751-0.001-0.0010.0000.0000.0000.000
37A35PRO 0-0.011-0.00430.7350.0020.0020.0000.0000.0000.000
38A36THR 00.0560.04229.361-0.011-0.0110.0000.0000.0000.000
39A37ARG 10.9150.94418.5810.4440.4440.0000.0000.0000.000
40A38GLN 00.0110.00624.574-0.003-0.0030.0000.0000.0000.000
41A39ALA 00.0070.01326.9020.0030.0030.0000.0000.0000.000
42A40LEU 00.0190.00526.4070.0030.0030.0000.0000.0000.000
43A41ASN 0-0.021-0.02422.486-0.021-0.0210.0000.0000.0000.000
44A42GLY 00.0060.00624.9300.0030.0030.0000.0000.0000.000
45A43ILE 00.0220.02427.9810.0080.0080.0000.0000.0000.000
46A44VAL 0-0.009-0.01123.1700.0070.0070.0000.0000.0000.000
47A45ASP -1-0.874-0.94423.195-0.266-0.2660.0000.0000.0000.000
48A46ALA 0-0.083-0.02725.6920.0150.0150.0000.0000.0000.000
49A47ILE 00.0030.01227.2510.0140.0140.0000.0000.0000.000
50A48TYR 0-0.050-0.07422.4350.0320.0320.0000.0000.0000.000
51A49TYR 00.0680.05221.587-0.008-0.0080.0000.0000.0000.000
52A50LYS 10.8810.93121.1200.1560.1560.0000.0000.0000.000
53A51PRO 00.0010.01920.576-0.023-0.0230.0000.0000.0000.000
54A52THR 0-0.026-0.05216.206-0.008-0.0080.0000.0000.0000.000
55A53PHE 0-0.032-0.01215.722-0.040-0.0400.0000.0000.0000.000
56A54THR 00.0120.01115.3440.0720.0720.0000.0000.0000.000
57A55ASN 0-0.026-0.02116.665-0.093-0.0930.0000.0000.0000.000
58A56ILE 0-0.027-0.01214.9550.0120.0120.0000.0000.0000.000
59A57VAL 00.0570.02418.472-0.009-0.0090.0000.0000.0000.000
60A58THR 0-0.069-0.04318.376-0.019-0.0190.0000.0000.0000.000
61A59GLU -1-0.815-0.88121.249-0.324-0.3240.0000.0000.0000.000
62A60VAL 0-0.019-0.00124.8570.0070.0070.0000.0000.0000.000
63A61LYS 10.9080.97428.4520.2180.2180.0000.0000.0000.000
64A62VAL 00.011-0.01831.6960.0070.0070.0000.0000.0000.000
65A63ILE 0-0.0190.01334.6870.0030.0030.0000.0000.0000.000
66A64ASN 00.0460.00937.4620.0030.0030.0000.0000.0000.000
67A65GLN 0-0.003-0.00340.197-0.004-0.0040.0000.0000.0000.000
68A66ILE 0-0.021-0.01638.3740.0000.0000.0000.0000.0000.000
69A67GLN 0-0.0160.00442.1970.0030.0030.0000.0000.0000.000
70A68THR 00.004-0.01943.559-0.004-0.0040.0000.0000.0000.000
71A69GLU -1-0.960-0.97145.913-0.075-0.0750.0000.0000.0000.000
72A70LEU 0-0.0170.00547.360-0.003-0.0030.0000.0000.0000.000
73A71GLN 00.0110.00248.7550.0010.0010.0000.0000.0000.000
74A72GLY 0-0.0010.00450.408-0.001-0.0010.0000.0000.0000.000
75A73VAL 0-0.040-0.02049.4950.0010.0010.0000.0000.0000.000
76A74ARG 10.9610.96252.8290.0470.0470.0000.0000.0000.000
77A75NME 00.0290.02455.7280.0000.0000.0000.0000.0000.000
78A84ACE 00.0480.01149.4160.0000.0000.0000.0000.0000.000
79A85SER 0-0.053-0.03550.4720.0030.0030.0000.0000.0000.000
80A86TYR 00.0250.02549.7730.0020.0020.0000.0000.0000.000
81A87VAL 00.0030.02144.205-0.002-0.0020.0000.0000.0000.000
82A88SER 0-0.044-0.02145.0110.0010.0010.0000.0000.0000.000
83A89TYR 0-0.073-0.10342.364-0.005-0.0050.0000.0000.0000.000
84A90LEU 00.0240.01338.0610.0020.0020.0000.0000.0000.000
85A91SER 0-0.013-0.03342.2400.0030.0030.0000.0000.0000.000
86A92ASP -1-0.935-0.95943.318-0.107-0.1070.0000.0000.0000.000
87A93VAL 00.0110.03037.985-0.005-0.0050.0000.0000.0000.000
88A94VAL 00.033-0.00436.4410.0020.0020.0000.0000.0000.000
89A95TYR 00.001-0.00932.143-0.004-0.0040.0000.0000.0000.000
90A96LEU 00.0290.03031.2290.0020.0020.0000.0000.0000.000
91A97ILE 0-0.048-0.02425.488-0.013-0.0130.0000.0000.0000.000
92A98LYS 11.0051.01921.3280.4360.4360.0000.0000.0000.000
93A99PHE 0-0.041-0.04121.142-0.018-0.0180.0000.0000.0000.000
94A100HIS 00.0310.03514.153-0.015-0.0150.0000.0000.0000.000
95A101PHE 00.0420.01215.7380.0240.0240.0000.0000.0000.000
96A102VAL 00.0530.03411.186-0.076-0.0760.0000.0000.0000.000
97A103TRP 00.023-0.0059.5950.1860.1860.0000.0000.0000.000
98A104ASN 00.0320.01711.849-0.125-0.1250.0000.0000.0000.000
99A105GLU -1-0.846-0.9328.525-0.349-0.3490.0000.0000.0000.000
100A106ASP -1-0.895-0.94011.858-0.139-0.1390.0000.0000.0000.000
101A107ARG 10.6910.81014.8720.1390.1390.0000.0000.0000.000
102A108LYS 10.9620.9719.659-0.107-0.1070.0000.0000.0000.000
103A109ASP -1-0.792-0.86514.6450.0180.0180.0000.0000.0000.000
104A110LEU 0-0.055-0.01717.1210.0060.0060.0000.0000.0000.000
105A111ASN 00.0410.01411.891-0.073-0.0730.0000.0000.0000.000
106A112SER 0-0.003-0.00514.906-0.025-0.0250.0000.0000.0000.000
107A113ASP -1-0.756-0.85617.518-0.139-0.1390.0000.0000.0000.000
108A114ARG 10.8450.9469.8260.2250.2250.0000.0000.0000.000
109A115LEU 0-0.032-0.01614.414-0.004-0.0040.0000.0000.0000.000
110A116PRO 00.0660.02013.6260.0010.0010.0000.0000.0000.000
111A117ALA 00.0640.03816.4390.0020.0020.0000.0000.0000.000
112A118LYS 10.8560.92619.8260.1200.1200.0000.0000.0000.000
113A119HIS 0-0.013-0.00617.8220.0020.0020.0000.0000.0000.000
114A120GLU -1-0.813-0.90617.837-0.408-0.4080.0000.0000.0000.000
115A121ALA 00.0420.03221.0770.0140.0140.0000.0000.0000.000
116A122ILE 0-0.092-0.04724.0560.0170.0170.0000.0000.0000.000
117A123MET 00.0050.04022.0470.0230.0230.0000.0000.0000.000
118A124GLU -1-0.800-0.87224.456-0.213-0.2130.0000.0000.0000.000
119A125ARG 10.9140.95326.7830.1420.1420.0000.0000.0000.000
120A126SER 0-0.089-0.06827.6720.0160.0160.0000.0000.0000.000
121A127ILE 00.0170.02325.8440.0080.0080.0000.0000.0000.000
122A128ARG 10.8790.95129.9650.1600.1600.0000.0000.0000.000
123A129LYS 10.8650.93632.4100.1270.1270.0000.0000.0000.000
124A130GLY 00.0730.05333.7210.0070.0070.0000.0000.0000.000
125A131GLY 0-0.048-0.01731.030-0.002-0.0020.0000.0000.0000.000
126A132ARG 10.8060.88428.4860.1480.1480.0000.0000.0000.000
127A133ARG 10.8920.95328.8690.1330.1330.0000.0000.0000.000
128A134ASP -1-0.848-0.91433.402-0.104-0.1040.0000.0000.0000.000
129A135VAL 0-0.011-0.00432.114-0.008-0.0080.0000.0000.0000.000
130A136PHE 0-0.012-0.00534.0330.0070.0070.0000.0000.0000.000
131A137LEU 00.0050.00634.074-0.013-0.0130.0000.0000.0000.000
132A138GLY 0-0.028-0.02034.0960.0050.0050.0000.0000.0000.000
133A139THR 0-0.061-0.04235.1110.0020.0020.0000.0000.0000.000
134A140ARG 10.9530.96335.5040.0970.0970.0000.0000.0000.000
135A141GLU -1-0.780-0.83339.417-0.091-0.0910.0000.0000.0000.000
136A142CYS 0-0.078-0.01139.2840.0040.0040.0000.0000.0000.000
137A143LEU 00.0170.00638.845-0.007-0.0070.0000.0000.0000.000
138A144GLY 0-0.007-0.01036.7390.0000.0000.0000.0000.0000.000
139A145LEU 0-0.0290.00537.6200.0030.0030.0000.0000.0000.000
140A146VAL 0-0.043-0.03031.417-0.009-0.0090.0000.0000.0000.000
141A147ASP -1-0.854-0.93334.241-0.121-0.1210.0000.0000.0000.000
142A148ASP -1-0.874-0.96630.506-0.196-0.1960.0000.0000.0000.000
143A149ILE 0-0.0060.01730.3630.0070.0070.0000.0000.0000.000
144A150SER 00.0390.01729.420-0.016-0.0160.0000.0000.0000.000
145A151GLN 0-0.052-0.05324.808-0.003-0.0030.0000.0000.0000.000
146A152GLU -1-0.892-0.94628.095-0.167-0.1670.0000.0000.0000.000
147A153GLU -1-0.887-0.93631.246-0.151-0.1510.0000.0000.0000.000
148A154TYR 0-0.088-0.07427.0120.0060.0060.0000.0000.0000.000
149A155GLU -1-0.913-0.94526.606-0.278-0.2780.0000.0000.0000.000
150A156THR 0-0.057-0.03530.9040.0100.0100.0000.0000.0000.000
151A157THR 0-0.046-0.01934.2900.0140.0140.0000.0000.0000.000
152A158VAL 0-0.039-0.02435.588-0.009-0.0090.0000.0000.0000.000
153A159SER 0-0.031-0.03535.9050.0050.0050.0000.0000.0000.000
154A160TYR 00.0260.00237.8770.0040.0040.0000.0000.0000.000
155A161TYR 00.0070.00237.8220.0050.0050.0000.0000.0000.000
156A162ASN 0-0.018-0.00937.362-0.013-0.0130.0000.0000.0000.000
157A163GLY 00.0080.00738.0520.0080.0080.0000.0000.0000.000
158A164VAL 0-0.0160.00439.0310.0050.0050.0000.0000.0000.000
159A165ASN 0-0.024-0.03234.968-0.013-0.0130.0000.0000.0000.000
160A166ILE 00.0130.00536.0900.0090.0090.0000.0000.0000.000
161A167ASP -1-0.869-0.93134.678-0.177-0.1770.0000.0000.0000.000
162A168LEU 0-0.018-0.01433.8680.0090.0090.0000.0000.0000.000
163A169GLY 00.0240.02434.9680.0060.0060.0000.0000.0000.000
164A170ILE 0-0.051-0.03331.292-0.012-0.0120.0000.0000.0000.000
165A171MET 0-0.022-0.00430.8330.0090.0090.0000.0000.0000.000
166A172PHE 0-0.017-0.02228.395-0.014-0.0140.0000.0000.0000.000
167A173HIS 0-0.0070.02621.2960.0140.0140.0000.0000.0000.000
168A174SER 0-0.055-0.08023.131-0.014-0.0140.0000.0000.0000.000
169A175PHE 00.0150.00625.2770.0090.0090.0000.0000.0000.000
170A176ALA 00.0030.03021.257-0.026-0.0260.0000.0000.0000.000
171A177TYR 0-0.007-0.01121.7540.0340.0340.0000.0000.0000.000
172A178PRO 00.0100.01521.270-0.010-0.0100.0000.0000.0000.000
173A179LYS 10.9350.93921.5700.0790.0790.0000.0000.0000.000
174A180ASP -1-0.755-0.84523.036-0.106-0.1060.0000.0000.0000.000
175A181LYS 10.8150.88724.6530.1090.1090.0000.0000.0000.000
176A182LYS 10.8930.95526.2460.0940.0940.0000.0000.0000.000
177A183THR 00.0530.02827.837-0.011-0.0110.0000.0000.0000.000
178A184PRO 00.0170.01426.5640.0020.0020.0000.0000.0000.000
179A185LEU 0-0.028-0.02322.7810.0130.0130.0000.0000.0000.000
180A186LYS 10.9790.98921.5570.1720.1720.0000.0000.0000.000
181A187SER 00.0160.01125.949-0.009-0.0090.0000.0000.0000.000
182A188TYR 00.0330.01820.7230.0040.0040.0000.0000.0000.000
183A189PHE 00.0080.00125.9820.0020.0020.0000.0000.0000.000
184A190THR 00.007-0.00325.369-0.014-0.0140.0000.0000.0000.000
185A191LYS 10.9401.00028.2060.1820.1820.0000.0000.0000.000
186A192THR 0-0.031-0.00828.776-0.026-0.0260.0000.0000.0000.000
187A193VAL 0-0.022-0.01829.9760.0130.0130.0000.0000.0000.000
188A194MET 0-0.0080.02730.685-0.016-0.0160.0000.0000.0000.000
189A195LYS 10.9470.96128.6900.2560.2560.0000.0000.0000.000
190A196ASN 00.0220.02232.791-0.001-0.0010.0000.0000.0000.000
191A197GLY 00.0620.02334.820-0.001-0.0010.0000.0000.0000.000
192A198VAL 0-0.0190.00428.288-0.003-0.0030.0000.0000.0000.000
193A199ILE 0-0.001-0.00427.4460.0040.0040.0000.0000.0000.000
194A200THR 0-0.012-0.01022.713-0.003-0.0030.0000.0000.0000.000
195A201PHE 0-0.064-0.05122.3380.0060.0060.0000.0000.0000.000
196A202LYS 11.0191.03320.8100.2680.2680.0000.0000.0000.000
197A203ALA 00.0270.01516.5500.0140.0140.0000.0000.0000.000
198A204GLN 0-0.008-0.03918.5270.0240.0240.0000.0000.0000.000
199A205SER 0-0.029-0.01916.4700.0170.0170.0000.0000.0000.000
200A206GLU -1-0.915-0.95116.863-0.565-0.5650.0000.0000.0000.000
201A207CYS 0-0.134-0.05620.3050.0300.0300.0000.0000.0000.000
202A208ASP -1-0.830-0.92423.706-0.215-0.2150.0000.0000.0000.000
203A209ILE 0-0.0110.00226.8740.0150.0150.0000.0000.0000.000
204A210VAL 00.0100.00223.372-0.014-0.0140.0000.0000.0000.000
205A211ASN 0-0.042-0.01726.5150.0210.0210.0000.0000.0000.000
206A212THR 0-0.017-0.01827.109-0.010-0.0100.0000.0000.0000.000
207A213NME 00.0230.02228.5790.0030.0030.0000.0000.0000.000