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: 7GR4K

Calculation Name: 4XPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XPU

Chain ID: A

ChEMBL ID:

UniProt ID: P68739

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptHSide
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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2428414.426251
FMO2-HF: Nuclear repulsion 2347599.259745
FMO2-HF: Total energy -80815.166506
FMO2-MP2: Total energy -81049.815712


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.
0.2340.83411.444-3.896-8.147-0.01
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 : 0.021 / q_NPA : 0.010
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].
3A3LEU00.0180.0002.165-3.0290.4421.789-1.835-3.425-0.007
4A4ALA00.004-0.0111.8031.822-1.3639.622-2.259-4.178-0.004
5A5SER0-0.005-0.0153.5070.8721.1860.0330.198-0.5440.001
6A6LEU00.0330.0295.4430.5970.5970.0000.0000.0000.000
7A7ARG10.8820.9406.3620.3430.3430.0000.0000.0000.000
8A8ALA0-0.0020.0047.4110.1430.1430.0000.0000.0000.000
9A9GLN00.0990.0379.0800.2890.2890.0000.0000.0000.000
10A10GLN0-0.0010.02110.9540.1670.1670.0000.0000.0000.000
11A11ILE0-0.049-0.03812.0350.0750.0750.0000.0000.0000.000
12A12GLU-1-0.900-0.92613.534-0.526-0.5260.0000.0000.0000.000
13A13LEU00.0390.01215.3030.0510.0510.0000.0000.0000.000
14A14ALA0-0.033-0.03016.8110.0370.0370.0000.0000.0000.000
15A15SER0-0.081-0.05517.5240.0360.0360.0000.0000.0000.000
16A16SER0-0.025-0.00319.2160.0100.0100.0000.0000.0000.000
17A17VAL0-0.052-0.00821.3250.0120.0120.0000.0000.0000.000
18A18ILE0-0.0010.02023.6780.0070.0070.0000.0000.0000.000
19A19ARG10.8300.88223.0830.0870.0870.0000.0000.0000.000
20A20GLU-1-0.808-0.88329.280-0.081-0.0810.0000.0000.0000.000
21A21ASP-1-0.743-0.83632.437-0.060-0.0600.0000.0000.0000.000
22A22ARG10.8330.89729.6770.1090.1090.0000.0000.0000.000
23A23LEU00.0110.01234.250-0.006-0.0060.0000.0000.0000.000
24A24ASP-1-0.828-0.90335.039-0.095-0.0950.0000.0000.0000.000
25A25LYS10.7640.87138.0260.0620.0620.0000.0000.0000.000
26A26ASP-1-0.885-0.91940.509-0.048-0.0480.0000.0000.0000.000
27A27PRO0-0.028-0.03842.3030.0010.0010.0000.0000.0000.000
28A28PRO0-0.023-0.01039.456-0.001-0.0010.0000.0000.0000.000
29A29ASP-1-0.813-0.90541.548-0.046-0.0460.0000.0000.0000.000
30A30LEU0-0.083-0.04939.3470.0040.0040.0000.0000.0000.000
31A31ILE0-0.0170.00137.448-0.003-0.0030.0000.0000.0000.000
32A32ALA00.0560.00933.9060.0010.0010.0000.0000.0000.000
33A33GLY0-0.054-0.01533.7390.0010.0010.0000.0000.0000.000
34A34ALA0-0.001-0.00928.988-0.003-0.0030.0000.0000.0000.000
35A35ASP-1-0.812-0.89529.1030.0040.0040.0000.0000.0000.000
36A36VAL00.0010.00423.895-0.008-0.0080.0000.0000.0000.000
37A37GLY0-0.0100.00225.0470.0100.0100.0000.0000.0000.000
38A38PHE0-0.055-0.03219.7270.0000.0000.0000.0000.0000.000
39A39GLU-1-0.745-0.84225.0070.0180.0180.0000.0000.0000.000
40A40GLN00.021-0.00225.6710.0100.0100.0000.0000.0000.000
41A41GLY00.0040.00325.1470.0080.0080.0000.0000.0000.000
42A42GLY0-0.032-0.01121.4610.0210.0210.0000.0000.0000.000
43A43GLU-1-0.892-0.93220.6870.1130.1130.0000.0000.0000.000
44A44VAL0-0.017-0.00122.595-0.020-0.0200.0000.0000.0000.000
45A45THR0-0.037-0.01121.5370.0110.0110.0000.0000.0000.000
46A46ARG10.8160.89223.959-0.011-0.0110.0000.0000.0000.000
47A47ALA00.0160.00126.2210.0040.0040.0000.0000.0000.000
48A48ALA0-0.0210.00228.157-0.003-0.0030.0000.0000.0000.000
49A49MET0-0.019-0.00728.3750.0000.0000.0000.0000.0000.000
50A50VAL0-0.001-0.00932.9820.0030.0030.0000.0000.0000.000
51A51LEU00.0260.02136.091-0.003-0.0030.0000.0000.0000.000
52A52LEU0-0.023-0.02538.5820.0050.0050.0000.0000.0000.000
53A53LYS10.8920.94341.3090.0260.0260.0000.0000.0000.000
54A54TYR0-0.0410.00942.2100.0030.0030.0000.0000.0000.000
55A55PRO00.0610.01344.291-0.001-0.0010.0000.0000.0000.000
56A56SER0-0.064-0.06546.4560.0020.0020.0000.0000.0000.000
57A57LEU0-0.032-0.03342.1450.0030.0030.0000.0000.0000.000
58A58GLU-1-0.817-0.85444.328-0.024-0.0240.0000.0000.0000.000
59A59LEU00.0090.00740.793-0.003-0.0030.0000.0000.0000.000
60A60VAL0-0.016-0.00942.1070.0010.0010.0000.0000.0000.000
61A61GLU-1-0.774-0.84738.307-0.053-0.0530.0000.0000.0000.000
62A62TYR00.008-0.00237.3480.0010.0010.0000.0000.0000.000
63A63LYS10.8170.91834.2870.0520.0520.0000.0000.0000.000
64A64VAL00.0060.00031.8720.0010.0010.0000.0000.0000.000
65A65ALA00.0290.03028.473-0.002-0.0020.0000.0000.0000.000
66A66ARG10.8000.84827.7530.0060.0060.0000.0000.0000.000
67A67ILE0-0.0060.00422.026-0.006-0.0060.0000.0000.0000.000
68A68ALA00.0340.01922.0150.0140.0140.0000.0000.0000.000
69A69THR0-0.061-0.05317.760-0.032-0.0320.0000.0000.0000.000
70A70THR00.0260.01715.6800.0190.0190.0000.0000.0000.000
71A71MET00.0140.02310.121-0.037-0.0370.0000.0000.0000.000
72A72PRO00.0760.05011.640-0.001-0.0010.0000.0000.0000.000
73A73TYR0-0.005-0.02713.107-0.017-0.0170.0000.0000.0000.000
74A74ILE00.0550.0368.0310.1000.1000.0000.0000.0000.000
75A75PRO00.0330.00711.801-0.111-0.1110.0000.0000.0000.000
76A76GLY0-0.039-0.02811.7080.0510.0510.0000.0000.0000.000
77A77PHE00.022-0.0028.250-0.066-0.0660.0000.0000.0000.000
78A78LEU0-0.0160.00512.894-0.032-0.0320.0000.0000.0000.000
79A79SER00.0340.00916.278-0.006-0.0060.0000.0000.0000.000
80A80PHE00.002-0.01212.455-0.011-0.0110.0000.0000.0000.000
81A81ARG10.8320.92514.757-0.121-0.1210.0000.0000.0000.000
82A82GLU-1-0.863-0.94517.019-0.005-0.0050.0000.0000.0000.000
83A83TYR00.0410.00818.4380.0030.0030.0000.0000.0000.000
84A84PRO00.0120.00018.1280.0020.0020.0000.0000.0000.000
85A85ALA00.0350.02621.0830.0040.0040.0000.0000.0000.000
86A86LEU0-0.005-0.00723.2760.0050.0050.0000.0000.0000.000
87A87LEU0-0.0080.00722.5270.0030.0030.0000.0000.0000.000
88A88ALA00.0210.00625.2800.0040.0040.0000.0000.0000.000
89A89ALA00.006-0.01127.0860.0050.0050.0000.0000.0000.000
90A90TRP00.0320.00728.3240.0100.0100.0000.0000.0000.000
91A91GLU-1-0.906-0.95427.784-0.130-0.1300.0000.0000.0000.000
92A92MET0-0.069-0.01830.8860.0050.0050.0000.0000.0000.000
93A93LEU0-0.082-0.02832.9550.0080.0080.0000.0000.0000.000
94A94SER0-0.052-0.06335.551-0.006-0.0060.0000.0000.0000.000
95A95GLN0-0.025-0.01338.181-0.001-0.0010.0000.0000.0000.000
96A96LYS10.8470.92132.4990.0930.0930.0000.0000.0000.000
97A97PRO0-0.036-0.00333.8130.0030.0030.0000.0000.0000.000
98A98ASP-1-0.733-0.87035.280-0.068-0.0680.0000.0000.0000.000
99A99LEU0-0.031-0.01233.716-0.002-0.0020.0000.0000.0000.000
100A100VAL00.0050.00329.9640.0050.0050.0000.0000.0000.000
101A101PHE0-0.026-0.02031.8550.0010.0010.0000.0000.0000.000
102A102VAL00.034-0.00625.9340.0010.0010.0000.0000.0000.000
103A103ASP-1-0.820-0.90329.3570.0100.0100.0000.0000.0000.000
104A104GLY00.0250.01125.8440.0070.0070.0000.0000.0000.000
105A105HIS10.7600.86423.399-0.019-0.0190.0000.0000.0000.000
106A106GLY00.0860.05923.977-0.008-0.0080.0000.0000.0000.000
107A107ILE00.0750.03422.8220.0070.0070.0000.0000.0000.000
108A108SER0-0.0130.02523.2990.0100.0100.0000.0000.0000.000
109A109HIS00.029-0.01316.3460.0100.0100.0000.0000.0000.000
110A110PRO0-0.031-0.01617.594-0.010-0.0100.0000.0000.0000.000
111A111ARG10.8000.89210.796-0.202-0.2020.0000.0000.0000.000
112A112ARG10.7540.87316.985-0.019-0.0190.0000.0000.0000.000
113A113LEU00.0560.02715.659-0.015-0.0150.0000.0000.0000.000
114A114GLY0-0.052-0.01718.2530.0120.0120.0000.0000.0000.000
115A115VAL00.0470.01120.644-0.023-0.0230.0000.0000.0000.000
116A116ALA00.0040.01221.550-0.015-0.0150.0000.0000.0000.000
117A117SER00.010-0.01421.7490.0000.0000.0000.0000.0000.000
118A118HIS0-0.0160.01415.1670.0170.0170.0000.0000.0000.000
119A119PHE00.016-0.01220.425-0.021-0.0210.0000.0000.0000.000
120A120GLY00.0280.01323.218-0.008-0.0080.0000.0000.0000.000
121A121LEU0-0.023-0.00920.092-0.004-0.0040.0000.0000.0000.000
122A122LEU0-0.058-0.03418.224-0.015-0.0150.0000.0000.0000.000
123A123VAL0-0.016-0.00422.512-0.005-0.0050.0000.0000.0000.000
124A124ASP-1-0.848-0.89825.973-0.138-0.1380.0000.0000.0000.000
125A125VAL00.0120.00627.5550.0100.0100.0000.0000.0000.000
126A126PRO00.0190.03629.4660.0000.0000.0000.0000.0000.000
127A127THR0-0.016-0.02427.3740.0050.0050.0000.0000.0000.000
128A128ILE0-0.037-0.00829.6630.0000.0000.0000.0000.0000.000
129A129GLY00.0120.00827.9220.0000.0000.0000.0000.0000.000
130A130VAL0-0.024-0.01328.7500.0050.0050.0000.0000.0000.000
131A131ALA00.0160.01427.8120.0040.0040.0000.0000.0000.000
132A132LYS10.7830.85929.774-0.008-0.0080.0000.0000.0000.000
133A133LYS10.9650.97328.428-0.047-0.0470.0000.0000.0000.000
134A134ARG10.9390.98027.021-0.073-0.0730.0000.0000.0000.000
135A135LEU0-0.038-0.00920.8230.0060.0060.0000.0000.0000.000
136A136CYS0-0.006-0.00622.6220.0140.0140.0000.0000.0000.000
137A137GLY00.0610.04524.778-0.011-0.0110.0000.0000.0000.000
138A138LYS10.8990.93227.348-0.038-0.0380.0000.0000.0000.000
139A139PHE00.0470.01630.989-0.004-0.0040.0000.0000.0000.000
140A140GLU-1-0.887-0.93134.4290.0190.0190.0000.0000.0000.000
141A141PRO0-0.055-0.03437.646-0.002-0.0020.0000.0000.0000.000
142A142LEU00.0000.01338.360-0.002-0.0020.0000.0000.0000.000
143A143SER00.024-0.00641.2290.0030.0030.0000.0000.0000.000
144A144SER0-0.004-0.01043.9810.0000.0000.0000.0000.0000.000
145A145GLU-1-0.809-0.87845.8190.0110.0110.0000.0000.0000.000
146A146PRO0-0.048-0.04145.0580.0010.0010.0000.0000.0000.000
147A147GLY00.005-0.00344.060-0.001-0.0010.0000.0000.0000.000
148A148ALA0-0.0030.02342.797-0.001-0.0010.0000.0000.0000.000
149A149LEU0-0.005-0.02238.7750.0000.0000.0000.0000.0000.000
150A150ALA00.0250.02637.6030.0000.0000.0000.0000.0000.000
151A151PRO00.0230.02834.788-0.001-0.0010.0000.0000.0000.000
152A152LEU0-0.083-0.04028.1330.0060.0060.0000.0000.0000.000
153A153MET00.0220.00930.658-0.006-0.0060.0000.0000.0000.000
154A154ASP-1-0.785-0.90723.9390.0460.0460.0000.0000.0000.000
155A155LYS10.8170.90621.294-0.051-0.0510.0000.0000.0000.000
156A156GLY00.0370.02527.058-0.005-0.0050.0000.0000.0000.000
157A157GLU-1-0.775-0.85225.268-0.045-0.0450.0000.0000.0000.000
158A158GLN00.024-0.00329.4360.0080.0080.0000.0000.0000.000
159A159LEU0-0.059-0.02524.636-0.005-0.0050.0000.0000.0000.000
160A160ALA0-0.024-0.03428.357-0.004-0.0040.0000.0000.0000.000
161A161TRP00.007-0.00230.8970.0060.0060.0000.0000.0000.000
162A162VAL0-0.055-0.01832.9820.0010.0010.0000.0000.0000.000
163A163TRP00.0890.03935.341-0.001-0.0010.0000.0000.0000.000
164A164ARG10.7960.89238.390-0.017-0.0170.0000.0000.0000.000
165A165SER0-0.012-0.01339.9950.0000.0000.0000.0000.0000.000
166A166LYS10.9060.93241.774-0.007-0.0070.0000.0000.0000.000
167A167ALA00.0440.02143.6790.0020.0020.0000.0000.0000.000
168A168ARG10.9500.96044.859-0.015-0.0150.0000.0000.0000.000
169A169CYS0-0.0180.02340.5420.0010.0010.0000.0000.0000.000
170A170ASN00.018-0.00636.420-0.001-0.0010.0000.0000.0000.000
171A171PRO00.0220.02835.689-0.003-0.0030.0000.0000.0000.000
172A172LEU0-0.0300.00334.2270.0040.0040.0000.0000.0000.000
173A173PHE0-0.016-0.02230.0960.0020.0020.0000.0000.0000.000
174A174ILE00.0200.02030.652-0.002-0.0020.0000.0000.0000.000
175A175ALA0-0.001-0.00427.9020.0020.0020.0000.0000.0000.000
176A176THR00.0410.03627.6690.0000.0000.0000.0000.0000.000
177A177GLY00.0110.00126.0720.0040.0040.0000.0000.0000.000
178A178HIS00.007-0.02025.439-0.007-0.0070.0000.0000.0000.000
179A179ARG10.8020.89827.3870.1190.1190.0000.0000.0000.000
180A180VAL00.0170.01330.5530.0060.0060.0000.0000.0000.000
181A181SER0-0.008-0.01731.2050.0010.0010.0000.0000.0000.000
182A182VAL00.002-0.02431.6120.0020.0020.0000.0000.0000.000
183A183ASP-1-0.831-0.91133.139-0.025-0.0250.0000.0000.0000.000
184A184SER0-0.009-0.04036.2470.0040.0040.0000.0000.0000.000
185A185ALA0-0.049-0.01632.8760.0010.0010.0000.0000.0000.000
186A186LEU0-0.022-0.01534.8960.0030.0030.0000.0000.0000.000
187A187ALA00.0220.01737.3210.0020.0020.0000.0000.0000.000
188A188TRP00.0410.00936.9520.0040.0040.0000.0000.0000.000
189A189VAL00.016-0.00235.2250.0020.0020.0000.0000.0000.000
190A190GLN0-0.036-0.02938.3450.0010.0010.0000.0000.0000.000
191A191ARG10.8860.96841.7520.0350.0350.0000.0000.0000.000
192A192CYS0-0.024-0.00439.706-0.001-0.0010.0000.0000.0000.000
193A193MET0-0.052-0.01039.4460.0030.0030.0000.0000.0000.000
194A194LYS10.9770.99443.3360.0160.0160.0000.0000.0000.000
195A195GLY00.0100.01145.9930.0010.0010.0000.0000.0000.000
196A196TYR0-0.050-0.02042.4310.0030.0030.0000.0000.0000.000
197A197ARG10.8360.90034.355-0.020-0.0200.0000.0000.0000.000
198A198LEU00.0100.02834.8740.0000.0000.0000.0000.0000.000
199A199PRO00.0350.03136.4850.0000.0000.0000.0000.0000.000
200A200GLU-1-0.741-0.87138.321-0.011-0.0110.0000.0000.0000.000
201A201PRO00.0470.03535.9150.0010.0010.0000.0000.0000.000
202A202THR00.0410.00132.508-0.001-0.0010.0000.0000.0000.000
203A203ARG10.7780.88135.0270.0110.0110.0000.0000.0000.000
204A204TRP00.012-0.01337.8880.0030.0030.0000.0000.0000.000
205A205ALA0-0.006-0.00133.0050.0010.0010.0000.0000.0000.000
206A206ASP-1-0.831-0.90132.9760.0070.0070.0000.0000.0000.000
207A207ALA0-0.098-0.03434.8280.0030.0030.0000.0000.0000.000
208A208VAL0-0.048-0.00535.1700.0030.0030.0000.0000.0000.000