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: QV5YY

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2434327.514694
FMO2-HF: Nuclear repulsion 2352990.077595
FMO2-HF: Total energy -81337.437099
FMO2-MP2: Total energy -81576.185714


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.
-34.504-27.28231.281-13.593-24.913-0.08
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 : 0.017 / q_NPA : 0.004
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].
3A3LEU0-0.025-0.0143.7610.2502.447-0.029-1.031-1.1370.004
4A4PHE0-0.012-0.0075.801-0.395-0.3950.0000.0000.0000.000
5A5VAL00.027-0.0089.3160.2900.2900.0000.0000.0000.000
6A6SER0-0.025-0.08111.915-0.090-0.0900.0000.0000.0000.000
7A7ASP-1-0.819-0.90815.736-0.107-0.1070.0000.0000.0000.000
8A8GLY0-0.0100.00418.6410.0130.0130.0000.0000.0000.000
9A9VAL0-0.024-0.01316.4710.0210.0210.0000.0000.0000.000
10A10PRO00.0690.03316.8570.0160.0160.0000.0000.0000.000
11A11GLY00.0390.01815.3840.0300.0300.0000.0000.0000.000
12A12CYS0-0.040-0.02112.3320.0920.0920.0000.0000.0000.000
13A13LEU00.0220.01312.5780.0070.0070.0000.0000.0000.000
14A14PRO00.0410.03213.3770.0090.0090.0000.0000.0000.000
15A15VAL0-0.052-0.0488.2450.0740.0740.0000.0000.0000.000
16A16LEU0-0.0090.0028.7470.0370.0370.0000.0000.0000.000
17A17ALA00.0200.03110.484-0.036-0.0360.0000.0000.0000.000
18A18ALA0-0.009-0.0018.9370.0010.0010.0000.0000.0000.000
19A19ALA00.0310.0075.7980.1530.1530.0000.0000.0000.000
20A20GLY0-0.044-0.0225.981-0.029-0.0290.0000.0000.0000.000
21A21ARG10.9260.9667.787-0.783-0.7830.0000.0000.0000.000
22A22ALA00.0390.0273.640-0.0520.1610.007-0.041-0.1800.000
23A23ARG10.9260.9615.5560.0620.0620.0000.0000.0000.000
24A24GLY00.0090.0078.5020.0810.0810.0000.0000.0000.000
25A25ARG10.8580.9427.142-1.634-1.6340.0000.0000.0000.000
26A26ALA00.0130.0002.896-0.3890.3050.211-0.186-0.7190.000
27A27GLU-1-0.954-0.9643.900-3.549-2.9370.000-0.100-0.5130.000
28A28VAL0-0.013-0.0112.194-0.2860.0656.171-2.178-4.344-0.016
29A29LEU0-0.0070.0013.3660.5181.3320.040-0.022-0.8320.000
30A30ILE0-0.004-0.0055.4960.1210.1210.0000.0000.0000.000
31A31SER0-0.021-0.0098.184-0.047-0.0470.0000.0000.0000.000
32A32THR0-0.009-0.00510.4720.1430.1430.0000.0000.0000.000
33A33VAL0-0.0140.00312.946-0.054-0.0540.0000.0000.0000.000
34A34GLY00.0600.05915.4890.0630.0630.0000.0000.0000.000
35A35PRO0-0.021-0.02017.7290.0200.0200.0000.0000.0000.000
36A36GLN0-0.008-0.03219.8000.0510.0510.0000.0000.0000.000
37A37ASP-1-0.820-0.88316.591-0.247-0.2470.0000.0000.0000.000
38A38CYS0-0.055-0.03116.6190.0610.0610.0000.0000.0000.000
39A39VAL00.0280.01111.122-0.037-0.0370.0000.0000.0000.000
40A40VAL0-0.047-0.01111.259-0.031-0.0310.0000.0000.0000.000
41A41PRO00.0250.01512.0430.0110.0110.0000.0000.0000.000
42A42PHE00.008-0.00112.699-0.005-0.0050.0000.0000.0000.000
43A43LEU0-0.054-0.02214.8450.0340.0340.0000.0000.0000.000
44A44THR00.0070.00317.933-0.030-0.0300.0000.0000.0000.000
45A45ARG10.9280.96320.336-0.150-0.1500.0000.0000.0000.000
46A46PRO00.0520.03717.6790.0340.0340.0000.0000.0000.000
47A47LYS10.9330.95714.596-0.371-0.3710.0000.0000.0000.000
48A48VAL0-0.0150.02212.541-0.014-0.0140.0000.0000.0000.000
49A49PRO00.012-0.0099.606-0.017-0.0170.0000.0000.0000.000
50A50VAL0-0.060-0.0258.1750.1260.1260.0000.0000.0000.000
51A51LEU00.0100.0112.025-1.953-1.7693.308-0.724-2.7680.001
52A52GLN0-0.012-0.0094.391-0.2030.066-0.001-0.042-0.2260.000
53A53LEU00.016-0.0152.694-3.001-0.0151.695-1.778-2.904-0.014
54A54ASP-1-0.783-0.8821.870-22.174-20.8919.977-5.405-5.855-0.064
55A55SER0-0.070-0.0263.8400.2030.3900.007-0.056-0.1380.000
56A56GLY00.011-0.0016.1080.0370.0370.0000.0000.0000.000
57A57ASN0-0.047-0.0147.670-0.124-0.1240.0000.0000.0000.000
58A58TYR00.034-0.0077.1750.1830.1830.0000.0000.0000.000
59A59LEU0-0.0200.0126.705-0.065-0.0650.0000.0000.0000.000
60A60PHE00.0510.0029.089-0.140-0.1400.0000.0000.0000.000
61A61SER0-0.0080.01011.894-0.154-0.1540.0000.0000.0000.000
62A62THR00.0920.02811.3200.2340.2340.0000.0000.0000.000
63A63SER00.1080.04611.3590.1610.1610.0000.0000.0000.000
64A64ALA0-0.026-0.00711.6190.0870.0870.0000.0000.0000.000
65A65ILE0-0.018-0.0065.9230.4330.4330.0000.0000.0000.000
66A66CYS0-0.023-0.0037.1410.3550.3550.0000.0000.0000.000
67A67ARG10.8870.9419.157-1.053-1.0530.0000.0000.0000.000
68A68TYR00.0120.0032.516-3.328-5.6236.936-1.537-3.1040.007
69A69PHE00.005-0.0041.9870.248-0.5192.882-0.356-1.7590.002
70A70PHE00.0350.0126.001-0.236-0.2360.0000.0000.0000.000
71A71LEU00.0000.0179.225-0.132-0.1320.0000.0000.0000.000
72A72LEU0-0.069-0.0243.798-0.783-0.2890.077-0.137-0.4340.000
73A73SER0-0.092-0.0588.016-0.414-0.4140.0000.0000.0000.000
74A74GLY0-0.001-0.00310.316-0.214-0.2140.0000.0000.0000.000
75A75TRP0-0.031-0.01412.470-0.048-0.0480.0000.0000.0000.000
76A76GLU-1-0.873-0.94014.1520.9320.9320.0000.0000.0000.000
77A77GLN0-0.034-0.03515.0890.0830.0830.0000.0000.0000.000
78A78ASP-1-0.781-0.85817.7040.5290.5290.0000.0000.0000.000
79A79ASP-1-0.885-0.96020.9050.4740.4740.0000.0000.0000.000
80A80LEU0-0.033-0.00123.531-0.001-0.0010.0000.0000.0000.000
81A81THR0-0.005-0.02417.017-0.003-0.0030.0000.0000.0000.000
82A82ASN0-0.008-0.01718.8040.1000.1000.0000.0000.0000.000
83A83GLN00.0050.01420.516-0.014-0.0140.0000.0000.0000.000
84A84TRP00.0230.00521.270-0.020-0.0200.0000.0000.0000.000
85A85LEU0-0.035-0.03215.1780.0040.0040.0000.0000.0000.000
86A86GLU-1-0.951-0.95619.6690.4450.4450.0000.0000.0000.000
87A87TRP00.0460.02922.297-0.032-0.0320.0000.0000.0000.000
88A88GLU-1-0.870-0.93819.4850.4780.4780.0000.0000.0000.000
89A89ALA00.003-0.00720.089-0.026-0.0260.0000.0000.0000.000
90A90THR0-0.103-0.07021.802-0.039-0.0390.0000.0000.0000.000
91A91GLU-1-0.935-0.96325.4000.2210.2210.0000.0000.0000.000
92A92LEU0-0.075-0.03123.073-0.025-0.0250.0000.0000.0000.000
93A93GLN00.000-0.00919.854-0.060-0.0600.0000.0000.0000.000
94A94PRO0-0.0150.01424.197-0.027-0.0270.0000.0000.0000.000
95A95ALA00.0430.02227.346-0.022-0.0220.0000.0000.0000.000
96A96LEU00.008-0.01623.403-0.022-0.0220.0000.0000.0000.000
97A97SER0-0.034-0.02124.963-0.019-0.0190.0000.0000.0000.000
98A98ALA0-0.027-0.01226.965-0.020-0.0200.0000.0000.0000.000
99A99ALA00.0240.01829.823-0.015-0.0150.0000.0000.0000.000
100A100LEU00.0220.00024.797-0.017-0.0170.0000.0000.0000.000
101A101TYR0-0.073-0.08929.025-0.018-0.0180.0000.0000.0000.000
102A102TYR00.012-0.01230.950-0.013-0.0130.0000.0000.0000.000
103A103LEU00.0020.01529.986-0.010-0.0100.0000.0000.0000.000
104A104VAL0-0.041-0.02528.142-0.011-0.0110.0000.0000.0000.000
105A105VAL0-0.109-0.05130.360-0.011-0.0110.0000.0000.0000.000
106A106GLN0-0.041-0.02932.754-0.006-0.0060.0000.0000.0000.000
107A107GLY0-0.027-0.00135.150-0.003-0.0030.0000.0000.0000.000
108A108LYS10.9340.98136.596-0.085-0.0850.0000.0000.0000.000
109A109LYS10.9780.96836.558-0.052-0.0520.0000.0000.0000.000
110A110GLY00.0670.04437.9230.0000.0000.0000.0000.0000.000
111A111GLU-1-0.818-0.93737.5850.1090.1090.0000.0000.0000.000
112A112ASP-1-0.951-0.95838.8510.0840.0840.0000.0000.0000.000
113A113VAL0-0.101-0.04532.7230.0040.0040.0000.0000.0000.000
114A114LEU00.022-0.00133.6300.0110.0110.0000.0000.0000.000
115A115GLY0-0.0060.00535.1460.0090.0090.0000.0000.0000.000
116A116SER0-0.028-0.01632.7210.0010.0010.0000.0000.0000.000
117A117VAL00.0200.00929.5930.0130.0130.0000.0000.0000.000
118A118ARG10.9160.99031.991-0.110-0.1100.0000.0000.0000.000
119A119ARG10.9370.98134.137-0.182-0.1820.0000.0000.0000.000
120A120ALA00.0530.02228.7540.0050.0050.0000.0000.0000.000
121A121LEU00.0430.01128.7080.0120.0120.0000.0000.0000.000
122A122THR00.000-0.02030.8140.0000.0000.0000.0000.0000.000
123A123HIS0-0.079-0.02628.353-0.010-0.0100.0000.0000.0000.000
124A124ILE00.0410.03125.8900.0070.0070.0000.0000.0000.000
125A125ASP-1-0.781-0.89429.0080.1750.1750.0000.0000.0000.000
126A126HIS0-0.076-0.06231.620-0.009-0.0090.0000.0000.0000.000
127A127SER0-0.016-0.01928.840-0.001-0.0010.0000.0000.0000.000
128A128LEU0-0.016-0.01626.0360.0020.0020.0000.0000.0000.000
129A129SER0-0.025-0.00529.902-0.008-0.0080.0000.0000.0000.000
130A130ARG10.8550.93633.347-0.187-0.1870.0000.0000.0000.000
131A131GLN0-0.0200.00426.6150.0110.0110.0000.0000.0000.000
132A132ASN00.0190.00131.795-0.012-0.0120.0000.0000.0000.000
133A133CYS0-0.058-0.01226.944-0.012-0.0120.0000.0000.0000.000
134A134PRO0-0.0130.00226.209-0.003-0.0030.0000.0000.0000.000
135A135PHE0-0.033-0.02122.210-0.004-0.0040.0000.0000.0000.000
136A136LEU0-0.003-0.02721.717-0.005-0.0050.0000.0000.0000.000
137A137ALA0-0.033-0.01021.402-0.003-0.0030.0000.0000.0000.000
138A138GLY0-0.0030.00322.4530.0030.0030.0000.0000.0000.000
139A139GLU-1-0.889-0.95823.3720.2720.2720.0000.0000.0000.000
140A140THR0-0.093-0.02619.985-0.009-0.0090.0000.0000.0000.000
141A141GLU-1-0.843-0.90516.8490.4080.4080.0000.0000.0000.000
142A142SER00.000-0.02916.1260.0770.0770.0000.0000.0000.000
143A143LEU0-0.033-0.00811.950-0.002-0.0020.0000.0000.0000.000
144A144ALA00.0490.00614.885-0.010-0.0100.0000.0000.0000.000
145A145ASP-1-0.705-0.83418.1870.3920.3920.0000.0000.0000.000
146A146ILE00.0200.01512.689-0.033-0.0330.0000.0000.0000.000
147A147VAL0-0.005-0.01214.357-0.026-0.0260.0000.0000.0000.000
148A148LEU00.0100.00616.334-0.046-0.0460.0000.0000.0000.000
149A149TRP0-0.029-0.01916.191-0.029-0.0290.0000.0000.0000.000
150A150GLY0-0.040-0.03716.941-0.040-0.0400.0000.0000.0000.000
151A151ALA0-0.026-0.00917.936-0.039-0.0390.0000.0000.0000.000
152A152LEU00.010-0.00420.344-0.039-0.0390.0000.0000.0000.000
153A153TYR0-0.0280.00420.774-0.043-0.0430.0000.0000.0000.000
154A154PRO0-0.046-0.03721.077-0.029-0.0290.0000.0000.0000.000
155A155LEU00.0010.00323.904-0.020-0.0200.0000.0000.0000.000
156A156LEU00.012-0.00926.303-0.014-0.0140.0000.0000.0000.000
157A157GLN0-0.051-0.01125.126-0.011-0.0110.0000.0000.0000.000
158A158ASP-1-0.907-0.94227.1540.0670.0670.0000.0000.0000.000
159A159PRO00.021-0.00830.7390.0080.0080.0000.0000.0000.000
160A160ALA0-0.0200.00433.1180.0020.0020.0000.0000.0000.000
161A161TYR0-0.072-0.05031.421-0.001-0.0010.0000.0000.0000.000
162A162LEU0-0.019-0.00529.1270.0150.0150.0000.0000.0000.000
163A163PRO0-0.014-0.01132.578-0.006-0.0060.0000.0000.0000.000
164A164GLU-1-0.880-0.94235.3050.0980.0980.0000.0000.0000.000
165A165GLU-1-0.911-0.96036.9880.1160.1160.0000.0000.0000.000
166A166LEU0-0.110-0.03433.3970.0050.0050.0000.0000.0000.000
167A167SER00.0510.00733.3080.0080.0080.0000.0000.0000.000
168A168ALA00.0230.01931.4430.0020.0020.0000.0000.0000.000
169A169LEU0-0.035-0.02527.6390.0120.0120.0000.0000.0000.000
170A170HIS00.0350.02128.5520.0130.0130.0000.0000.0000.000
171A171SER00.0220.00929.4490.0000.0000.0000.0000.0000.000
172A172TRP0-0.028-0.00521.538-0.008-0.0080.0000.0000.0000.000
173A173PHE00.007-0.01023.3240.0120.0120.0000.0000.0000.000
174A174GLN0-0.024-0.01624.608-0.003-0.0030.0000.0000.0000.000
175A175THR0-0.014-0.01423.783-0.011-0.0110.0000.0000.0000.000
176A176LEU0-0.007-0.00818.8830.0040.0040.0000.0000.0000.000
177A177SER0-0.0090.00420.6120.0020.0020.0000.0000.0000.000
178A178THR0-0.090-0.03921.999-0.020-0.0200.0000.0000.0000.000
179A179GLN00.0020.01018.6570.0070.0070.0000.0000.0000.000
180A180GLU-1-0.876-0.94517.2700.0290.0290.0000.0000.0000.000
181A181PRO0-0.004-0.01113.127-0.030-0.0300.0000.0000.0000.000
182A182CYS00.0060.01215.0890.0110.0110.0000.0000.0000.000
183A183GLN00.0250.01617.230-0.032-0.0320.0000.0000.0000.000
184A184ARG10.9200.95612.6070.0540.0540.0000.0000.0000.000
185A185ALA0-0.0010.00714.121-0.044-0.0440.0000.0000.0000.000
186A186ALA00.0560.01415.544-0.021-0.0210.0000.0000.0000.000
187A187GLN0-0.014-0.00419.080-0.040-0.0400.0000.0000.0000.000
188A188THR0-0.045-0.00614.019-0.046-0.0460.0000.0000.0000.000
189A189VAL0-0.026-0.01815.361-0.028-0.0280.0000.0000.0000.000
190A190LEU0-0.018-0.01417.807-0.010-0.0100.0000.0000.0000.000
191A191LYS10.8090.92318.7080.1050.1050.0000.0000.0000.000
192A192GLN00.041-0.01822.4000.0140.0140.0000.0000.0000.000
193A193GLN0-0.114-0.04225.346-0.007-0.0070.0000.0000.0000.000
194A194GLY00.0400.04226.1070.0040.0040.0000.0000.0000.000
195A195VAL00.1180.03425.830-0.006-0.0060.0000.0000.0000.000
196A196LEU0-0.020-0.01026.8890.0020.0020.0000.0000.0000.000
197A197ALA0-0.047-0.01523.432-0.006-0.0060.0000.0000.0000.000
198A198LEU00.0390.01421.571-0.006-0.0060.0000.0000.0000.000
199A199ARG10.9440.99224.350-0.011-0.0110.0000.0000.0000.000
200A200PRO0-0.035-0.03624.8710.0060.0060.0000.0000.0000.000
201A201TYR00.0870.04920.0900.0030.0030.0000.0000.0000.000
202A202LEU00.0520.01323.8540.0130.0130.0000.0000.0000.000
203A203GLN0-0.026-0.01626.347-0.002-0.0020.0000.0000.0000.000
204A204LYS10.8580.93823.747-0.022-0.0220.0000.0000.0000.000
205A205GLN0-0.080-0.01323.1230.0250.0250.0000.0000.0000.000
206A206PRO0-0.0080.00126.611-0.013-0.0130.0000.0000.0000.000
207A207GLN00.0360.07229.711-0.008-0.0080.0000.0000.0000.000
208A208PRO00.0240.02031.7920.0060.0060.0000.0000.0000.000
209A209SER00.0590.02133.035-0.004-0.0040.0000.0000.0000.000
210A210PRO0-0.083-0.03936.119-0.006-0.0060.0000.0000.0000.000
211A211ALA00.0250.03238.8020.0060.0060.0000.0000.0000.000