Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4JG9N

Calculation Name: 4BVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BVY

Chain ID: A

ChEMBL ID:

UniProt ID: O43324

Base Structure: X-ray

Registration Date: 2023-09-23

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2445531.602369
FMO2-HF: Nuclear repulsion 2364191.89431
FMO2-HF: Total energy -81339.708059
FMO2-MP2: Total energy -81578.482136


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-44.896-40.93646.304-19.717-30.545-0.101
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / 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].
3A3LEU0-0.0090.0033.881-0.3301.545-0.015-0.916-0.9430.003
4A4PHE00.007-0.0065.996-0.135-0.1350.0000.0000.0000.000
5A5VAL00.015-0.0099.2310.1440.1440.0000.0000.0000.000
6A6SER0-0.042-0.05312.329-0.008-0.0080.0000.0000.0000.000
7A7ASP-1-0.778-0.88216.122-0.091-0.0910.0000.0000.0000.000
8A8GLY0-0.0010.00719.3580.0200.0200.0000.0000.0000.000
9A9VAL0-0.046-0.02516.6800.0190.0190.0000.0000.0000.000
10A10PRO00.0550.02717.757-0.007-0.0070.0000.0000.0000.000
11A11GLY00.0330.00616.1940.0000.0000.0000.0000.0000.000
12A12CYS0-0.032-0.02913.1370.0580.0580.0000.0000.0000.000
13A13LEU00.0130.02513.174-0.043-0.0430.0000.0000.0000.000
14A14PRO00.0250.02914.031-0.037-0.0370.0000.0000.0000.000
15A15VAL00.002-0.0178.906-0.002-0.0020.0000.0000.0000.000
16A16LEU0-0.031-0.0128.932-0.097-0.0970.0000.0000.0000.000
17A17ALA00.0190.01710.677-0.123-0.1230.0000.0000.0000.000
18A18ALA0-0.013-0.0029.298-0.033-0.0330.0000.0000.0000.000
19A19ALA00.0150.0016.177-0.027-0.0270.0000.0000.0000.000
20A20GLY0-0.037-0.0166.399-0.446-0.4460.0000.0000.0000.000
21A21ARG10.8310.8927.857-0.058-0.0580.0000.0000.0000.000
22A22ALA00.0500.0293.155-0.1440.1460.052-0.078-0.2640.000
23A23ARG10.9370.9665.1211.0991.149-0.0010.000-0.0480.000
24A24GLY00.0040.0058.0420.2720.2720.0000.0000.0000.000
25A25ARG10.8550.9336.4680.1350.1350.0000.0000.0000.000
26A26ALA00.0100.0062.346-0.098-0.2032.112-0.574-1.4320.000
27A27GLU-1-0.948-0.9663.243-1.527-0.3490.038-0.313-0.902-0.001
28A28VAL0-0.012-0.0192.182-11.705-9.4525.884-3.327-4.811-0.042
29A29LEU00.0040.0043.7201.0542.0140.006-0.284-0.6820.001
30A30ILE00.005-0.0035.7480.1340.1340.0000.0000.0000.000
31A31SER0-0.008-0.0078.4330.1450.1450.0000.0000.0000.000
32A32THR00.001-0.01010.2460.0730.0730.0000.0000.0000.000
33A33VAL0-0.0310.00512.9030.0090.0090.0000.0000.0000.000
34A34GLY00.0540.04215.410-0.003-0.0030.0000.0000.0000.000
35A35PRO0-0.009-0.01217.7600.0230.0230.0000.0000.0000.000
36A36GLN0-0.025-0.02719.9380.0160.0160.0000.0000.0000.000
37A37ASP-1-0.784-0.88116.3600.0500.0500.0000.0000.0000.000
38A38CYS0-0.041-0.02516.1570.0260.0260.0000.0000.0000.000
39A39VAL00.0090.00411.3090.0070.0070.0000.0000.0000.000
40A40VAL0-0.0100.00511.1330.0340.0340.0000.0000.0000.000
41A41PRO0-0.008-0.00812.270-0.020-0.0200.0000.0000.0000.000
42A42PHE00.0060.01212.511-0.031-0.0310.0000.0000.0000.000
43A43LEU0-0.026-0.00714.7330.0010.0010.0000.0000.0000.000
44A44THR0-0.011-0.00718.010-0.016-0.0160.0000.0000.0000.000
45A45ARG10.9370.96019.832-0.197-0.1970.0000.0000.0000.000
46A46PRO00.0380.03117.5980.0310.0310.0000.0000.0000.000
47A47LYS10.9080.95213.886-0.348-0.3480.0000.0000.0000.000
48A48VAL00.0100.03512.8580.0100.0100.0000.0000.0000.000
49A49PRO00.001-0.00710.351-0.022-0.0220.0000.0000.0000.000
50A50VAL0-0.051-0.0308.0150.1060.1060.0000.0000.0000.000
51A51LEU0-0.0160.0032.449-2.266-1.1531.654-0.527-2.2400.004
52A52GLN00.0240.0174.3730.1920.473-0.001-0.041-0.2400.000
53A53LEU00.0340.0052.402-3.469-1.0483.818-2.162-4.076-0.017
54A54ASP-1-0.824-0.9191.854-20.897-21.90314.379-5.817-7.558-0.074
55A55SER0-0.042-0.0093.8030.5660.7890.008-0.066-0.1650.000
56A56GLY00.0070.0076.2040.1380.1380.0000.0000.0000.000
57A57ASN0-0.045-0.0267.481-0.026-0.0260.0000.0000.0000.000
58A58TYR00.0320.0036.9760.1340.1340.0000.0000.0000.000
59A59LEU00.0040.0176.645-0.182-0.1820.0000.0000.0000.000
60A60PHE00.028-0.0058.882-0.143-0.1430.0000.0000.0000.000
61A61SER00.0160.00411.681-0.176-0.1760.0000.0000.0000.000
62A62THR00.0730.04412.0740.1870.1870.0000.0000.0000.000
63A63SER00.0610.00711.8580.1060.1060.0000.0000.0000.000
64A64ALA0-0.0100.00411.9380.0230.0230.0000.0000.0000.000
65A65ILE0-0.032-0.0156.6090.3020.3020.0000.0000.0000.000
66A66CYS0-0.039-0.0067.4380.1410.1410.0000.0000.0000.000
67A67ARG10.8680.9129.253-0.696-0.6960.0000.0000.0000.000
68A68TYR00.001-0.0242.179-5.686-12.44017.043-5.270-5.0190.026
69A69PHE00.020-0.0062.428-0.5950.0700.577-0.136-1.1050.002
70A70PHE00.0280.0135.857-0.363-0.3630.0000.0000.0000.000
71A71LEU00.0120.0238.681-0.122-0.1220.0000.0000.0000.000
72A72LEU0-0.062-0.0252.446-1.247-0.7310.750-0.206-1.060-0.003
73A73SER0-0.096-0.0596.873-0.299-0.2990.0000.0000.0000.000
74A74GLY00.0000.0069.503-0.087-0.0870.0000.0000.0000.000
75A75TRP0-0.013-0.00411.8910.0200.0200.0000.0000.0000.000
76A76GLU-1-0.873-0.93913.2150.5140.5140.0000.0000.0000.000
77A77GLN0-0.049-0.02914.9530.0370.0370.0000.0000.0000.000
78A78ASP-1-0.769-0.84617.2300.2220.2220.0000.0000.0000.000
79A79ASP-1-0.820-0.92920.3130.2930.2930.0000.0000.0000.000
80A80LEU0-0.0220.02122.9870.0010.0010.0000.0000.0000.000
81A81THR0-0.055-0.07416.662-0.002-0.0020.0000.0000.0000.000
82A82ASN0-0.048-0.02918.8650.0850.0850.0000.0000.0000.000
83A83GLN00.0250.02120.425-0.002-0.0020.0000.0000.0000.000
84A84TRP00.002-0.00721.026-0.006-0.0060.0000.0000.0000.000
85A85LEU0-0.009-0.01915.0450.0050.0050.0000.0000.0000.000
86A86GLU-1-0.960-0.96319.6530.2900.2900.0000.0000.0000.000
87A87TRP0-0.0070.00022.346-0.016-0.0160.0000.0000.0000.000
88A88GLU-1-0.825-0.90118.8000.3200.3200.0000.0000.0000.000
89A89ALA0-0.001-0.01120.194-0.017-0.0170.0000.0000.0000.000
90A90THR0-0.087-0.05922.117-0.016-0.0160.0000.0000.0000.000
91A91GLU-1-0.894-0.93425.8360.1270.1270.0000.0000.0000.000
92A92LEU0-0.044-0.01623.411-0.014-0.0140.0000.0000.0000.000
93A93GLN0-0.009-0.01720.172-0.035-0.0350.0000.0000.0000.000
94A94PRO0-0.0220.01224.620-0.016-0.0160.0000.0000.0000.000
95A95ALA00.0340.02227.921-0.014-0.0140.0000.0000.0000.000
96A96LEU00.009-0.01024.100-0.015-0.0150.0000.0000.0000.000
97A97SER0-0.037-0.02725.863-0.010-0.0100.0000.0000.0000.000
98A98ALA0-0.025-0.00927.785-0.011-0.0110.0000.0000.0000.000
99A99ALA00.0180.01830.354-0.009-0.0090.0000.0000.0000.000
100A100LEU00.0240.00125.319-0.011-0.0110.0000.0000.0000.000
101A101TYR0-0.019-0.03329.629-0.011-0.0110.0000.0000.0000.000
102A102TYR00.013-0.00831.559-0.009-0.0090.0000.0000.0000.000
103A103LEU00.0060.01530.683-0.006-0.0060.0000.0000.0000.000
104A104VAL0-0.071-0.03929.044-0.007-0.0070.0000.0000.0000.000
105A105VAL0-0.069-0.03330.678-0.003-0.0030.0000.0000.0000.000
106A106GLN0-0.016-0.01133.338-0.003-0.0030.0000.0000.0000.000
107A107GLY0-0.0180.01435.821-0.003-0.0030.0000.0000.0000.000
108A108LYS10.8430.93137.280-0.056-0.0560.0000.0000.0000.000
109A109LYS10.9120.92837.192-0.022-0.0220.0000.0000.0000.000
110A110GLY00.0680.04838.3190.0010.0010.0000.0000.0000.000
111A111GLU-1-0.739-0.86438.0050.0470.0470.0000.0000.0000.000
112A112ASP-1-0.881-0.92039.0980.0490.0490.0000.0000.0000.000
113A113VAL0-0.058-0.01533.4410.0030.0030.0000.0000.0000.000
114A114LEU00.0230.00833.6970.0080.0080.0000.0000.0000.000
115A115GLY00.0330.01535.2380.0050.0050.0000.0000.0000.000
116A116SER0-0.070-0.04533.2720.0030.0030.0000.0000.0000.000
117A117VAL00.0250.01629.7540.0090.0090.0000.0000.0000.000
118A118ARG10.7920.87932.541-0.041-0.0410.0000.0000.0000.000
119A119ARG10.9380.97533.867-0.096-0.0960.0000.0000.0000.000
120A120ALA00.0250.01529.4320.0020.0020.0000.0000.0000.000
121A121LEU00.0330.00529.0260.0040.0040.0000.0000.0000.000
122A122THR00.029-0.01131.126-0.004-0.0040.0000.0000.0000.000
123A123HIS0-0.074-0.02629.170-0.008-0.0080.0000.0000.0000.000
124A124ILE00.0410.03726.4030.0020.0020.0000.0000.0000.000
125A125ASP-1-0.753-0.87728.9710.0470.0470.0000.0000.0000.000
126A126HIS0-0.094-0.07031.648-0.004-0.0040.0000.0000.0000.000
127A127SER0-0.008-0.01728.9170.0010.0010.0000.0000.0000.000
128A128LEU0-0.025-0.00226.1710.0010.0010.0000.0000.0000.000
129A129SER0-0.025-0.02629.986-0.006-0.0060.0000.0000.0000.000
130A130ARG10.8620.93932.807-0.069-0.0690.0000.0000.0000.000
131A131GLN0-0.056-0.00426.6120.0060.0060.0000.0000.0000.000
132A132ASN0-0.043-0.04131.222-0.005-0.0050.0000.0000.0000.000
133A133CYS0-0.0210.02426.506-0.006-0.0060.0000.0000.0000.000
134A134PRO0-0.045-0.02026.0460.0030.0030.0000.0000.0000.000
135A135PHE0-0.019-0.00722.145-0.008-0.0080.0000.0000.0000.000
136A136LEU0-0.011-0.02621.4820.0040.0040.0000.0000.0000.000
137A137ALA00.003-0.00221.1550.0110.0110.0000.0000.0000.000
138A138GLY00.0380.03022.8320.0060.0060.0000.0000.0000.000
139A139GLU-1-0.873-0.96723.7100.0400.0400.0000.0000.0000.000
140A140THR0-0.064-0.02018.979-0.019-0.0190.0000.0000.0000.000
141A141GLU-1-0.800-0.85116.618-0.023-0.0230.0000.0000.0000.000
142A142SER00.014-0.00716.2780.0080.0080.0000.0000.0000.000
143A143LEU0-0.020-0.00311.9080.0010.0010.0000.0000.0000.000
144A144ALA00.0450.00814.8040.0080.0080.0000.0000.0000.000
145A145ASP-1-0.733-0.84918.2470.1000.1000.0000.0000.0000.000
146A146ILE00.0190.00612.963-0.016-0.0160.0000.0000.0000.000
147A147VAL0-0.023-0.01814.364-0.004-0.0040.0000.0000.0000.000
148A148LEU00.0200.00816.522-0.017-0.0170.0000.0000.0000.000
149A149TRP0-0.031-0.01316.668-0.017-0.0170.0000.0000.0000.000
150A150GLY0-0.018-0.02817.150-0.018-0.0180.0000.0000.0000.000
151A151ALA0-0.034-0.01918.208-0.007-0.0070.0000.0000.0000.000
152A152LEU00.0310.00720.465-0.014-0.0140.0000.0000.0000.000
153A153TYR0-0.0060.00821.244-0.018-0.0180.0000.0000.0000.000
154A154PRO0-0.047-0.04321.599-0.013-0.0130.0000.0000.0000.000
155A155LEU0-0.029-0.00524.497-0.004-0.0040.0000.0000.0000.000
156A156LEU00.019-0.00126.413-0.007-0.0070.0000.0000.0000.000
157A157GLN0-0.020-0.00725.752-0.009-0.0090.0000.0000.0000.000
158A158ASP-1-0.901-0.94027.6980.0020.0020.0000.0000.0000.000
159A159PRO00.0360.00231.4150.0070.0070.0000.0000.0000.000
160A160ALA0-0.042-0.00333.8500.0030.0030.0000.0000.0000.000
161A161TYR0-0.065-0.05331.8490.0060.0060.0000.0000.0000.000
162A162LEU0-0.020-0.00429.7700.0080.0080.0000.0000.0000.000
163A163PRO0-0.035-0.00133.002-0.004-0.0040.0000.0000.0000.000
164A164GLU-1-0.896-0.96735.9900.0100.0100.0000.0000.0000.000
165A165GLU-1-0.848-0.91437.5830.0340.0340.0000.0000.0000.000
166A166LEU0-0.084-0.01433.4830.0020.0020.0000.0000.0000.000
167A167SER00.030-0.00133.507-0.001-0.0010.0000.0000.0000.000
168A168ALA00.0110.01631.726-0.005-0.0050.0000.0000.0000.000
169A169LEU00.010-0.01227.7890.0000.0000.0000.0000.0000.000
170A170HIS00.0220.00828.736-0.003-0.0030.0000.0000.0000.000
171A171SER00.0170.00929.533-0.008-0.0080.0000.0000.0000.000
172A172TRP0-0.0160.00122.015-0.009-0.0090.0000.0000.0000.000
173A173PHE00.0270.00923.733-0.005-0.0050.0000.0000.0000.000
174A174GLN0-0.015-0.00325.049-0.016-0.0160.0000.0000.0000.000
175A175THR0-0.024-0.00724.012-0.016-0.0160.0000.0000.0000.000
176A176LEU0-0.012-0.00719.526-0.015-0.0150.0000.0000.0000.000
177A177SER0-0.012-0.01420.967-0.017-0.0170.0000.0000.0000.000
178A178THR0-0.097-0.05823.009-0.017-0.0170.0000.0000.0000.000
179A179GLN0-0.033-0.01618.190-0.026-0.0260.0000.0000.0000.000
180A180GLU-1-0.789-0.86716.583-0.375-0.3750.0000.0000.0000.000
181A181PRO00.0170.00013.508-0.011-0.0110.0000.0000.0000.000
182A182CYS0-0.0100.00415.4800.0020.0020.0000.0000.0000.000
183A183GLN00.0190.02017.554-0.005-0.0050.0000.0000.0000.000
184A184ARG10.8430.88412.9580.4540.4540.0000.0000.0000.000
185A185ALA0-0.0120.01814.538-0.010-0.0100.0000.0000.0000.000
186A186ALA00.0410.00515.9330.0180.0180.0000.0000.0000.000
187A187GLN0-0.008-0.00419.387-0.013-0.0130.0000.0000.0000.000
188A188THR0-0.051-0.03814.299-0.011-0.0110.0000.0000.0000.000
189A189VAL0-0.040-0.01916.2230.0110.0110.0000.0000.0000.000
190A190LEU0-0.020-0.01918.6530.0190.0190.0000.0000.0000.000
191A191LYS10.8070.90819.2690.1190.1190.0000.0000.0000.000
192A192GLN00.006-0.00423.3420.0000.0000.0000.0000.0000.000
193A193GLN0-0.026-0.01425.6960.0000.0000.0000.0000.0000.000
194A194GLY00.0580.04126.5160.0080.0080.0000.0000.0000.000
195A195VAL00.0600.01526.4060.0010.0010.0000.0000.0000.000
196A196LEU0-0.022-0.01527.5490.0080.0080.0000.0000.0000.000
197A197ALA0-0.031-0.00623.9680.0040.0040.0000.0000.0000.000
198A198LEU00.0350.01822.6680.0040.0040.0000.0000.0000.000
199A199ARG10.9260.98825.175-0.007-0.0070.0000.0000.0000.000
200A200PRO00.006-0.00724.7980.0080.0080.0000.0000.0000.000
201A201TYR00.0010.00119.9940.0130.0130.0000.0000.0000.000
202A202LEU00.029-0.00224.0070.0140.0140.0000.0000.0000.000
203A203GLN0-0.039-0.01826.8410.0030.0030.0000.0000.0000.000
204A204LYS10.8290.92022.816-0.085-0.0850.0000.0000.0000.000
205A205GLN0-0.042-0.00723.1080.0280.0280.0000.0000.0000.000
206A206PRO0-0.015-0.01526.825-0.009-0.0090.0000.0000.0000.000
207A207GLN00.0400.03529.959-0.006-0.0060.0000.0000.0000.000
208A208PRO0-0.0060.01533.0200.0070.0070.0000.0000.0000.000
209A209SER00.0270.01833.868-0.002-0.0020.0000.0000.0000.000
210A210PRO00.000-0.00236.608-0.003-0.0030.0000.0000.0000.000
211A211ALA0-0.021-0.01238.9650.0010.0010.0000.0000.0000.000