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: JL2G9

Calculation Name: 4J1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J1J

Chain ID: A

ChEMBL ID:

UniProt ID: F2WAD7

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2739888.203981
FMO2-HF: Nuclear repulsion 2649110.17391
FMO2-HF: Total energy -90778.030071
FMO2-MP2: Total energy -91044.536449


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:3:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
4.591-4.8890.40410.24-1.1640.001
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.015
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].
3A5PRO0-0.051-0.0192.9634.839-4.6690.40510.241-1.1390.001
4A6ASP-1-0.898-0.9405.110-0.207-0.179-0.001-0.001-0.0250.000
5A7PHE0-0.053-0.0358.5940.1070.1070.0000.0000.0000.000
6A8ILE0-0.001-0.0089.1440.0790.0790.0000.0000.0000.000
7A9TYR0-0.053-0.04210.801-0.101-0.1010.0000.0000.0000.000
8A10ASP-1-0.933-0.95313.8010.6330.6330.0000.0000.0000.000
9A11ASP-1-0.928-0.94816.4690.2240.2240.0000.0000.0000.000
10A12ARG10.9480.95018.017-0.303-0.3030.0000.0000.0000.000
11A13PRO00.0440.04221.6990.0010.0010.0000.0000.0000.000
12A14ALA0-0.070-0.04325.3330.0030.0030.0000.0000.0000.000
13A15ALA0-0.0090.00327.669-0.008-0.0080.0000.0000.0000.000
14A16VAL00.005-0.01928.742-0.013-0.0130.0000.0000.0000.000
15A17SER0-0.034-0.01532.4260.0070.0070.0000.0000.0000.000
16A18SER00.0360.02634.1930.0040.0040.0000.0000.0000.000
17A19THR0-0.047-0.02336.483-0.007-0.0070.0000.0000.0000.000
18A20PHE00.0250.02039.0040.0000.0000.0000.0000.0000.000
19A21ASN0-0.004-0.01040.796-0.007-0.0070.0000.0000.0000.000
20A22PRO00.0260.00344.4050.0030.0030.0000.0000.0000.000
21A23GLU-1-0.847-0.92545.5400.0620.0620.0000.0000.0000.000
22A24LYS10.9030.96443.246-0.091-0.0910.0000.0000.0000.000
23A25GLY00.0120.00643.2400.0020.0020.0000.0000.0000.000
24A26TYR0-0.009-0.00243.9630.0040.0040.0000.0000.0000.000
25A27MET00.0540.02746.9370.0000.0000.0000.0000.0000.000
26A28ASP-1-0.869-0.89543.3450.0940.0940.0000.0000.0000.000
27A29PHE0-0.034-0.01943.0380.0020.0020.0000.0000.0000.000
28A30ILE00.0240.00844.7990.0010.0010.0000.0000.0000.000
29A31THR0-0.079-0.09247.045-0.002-0.0020.0000.0000.0000.000
30A32ALA0-0.069-0.03043.1910.0000.0000.0000.0000.0000.000
31A33TYR0-0.030-0.02539.4880.0040.0040.0000.0000.0000.000
32A34GLY00.0390.02246.223-0.002-0.0020.0000.0000.0000.000
33A35LYS10.9280.96249.543-0.076-0.0760.0000.0000.0000.000
34A36ASN0-0.020-0.00447.086-0.005-0.0050.0000.0000.0000.000
35A37ILE0-0.0420.00447.6870.0010.0010.0000.0000.0000.000
36A38ASN00.0740.04250.600-0.003-0.0030.0000.0000.0000.000
37A39ALA00.0980.03552.5190.0020.0020.0000.0000.0000.000
38A40ASP-1-0.839-0.90153.2960.0510.0510.0000.0000.0000.000
39A41ASN0-0.016-0.04248.2920.0000.0000.0000.0000.0000.000
40A42VAL0-0.0010.01548.5300.0030.0030.0000.0000.0000.000
41A43ARG10.9090.93849.684-0.047-0.0470.0000.0000.0000.000
42A44ILE0-0.032-0.01246.3540.0000.0000.0000.0000.0000.000
43A45PHE00.004-0.00142.0260.0020.0020.0000.0000.0000.000
44A46PHE0-0.004-0.01345.7440.0010.0010.0000.0000.0000.000
45A47LEU0-0.046-0.01447.941-0.002-0.0020.0000.0000.0000.000
46A48ASN0-0.112-0.06343.396-0.001-0.0010.0000.0000.0000.000
47A49HIS00.0730.05341.1060.0060.0060.0000.0000.0000.000
48A50LYS10.9500.95540.486-0.058-0.0580.0000.0000.0000.000
49A51LYS10.9890.99239.797-0.056-0.0560.0000.0000.0000.000
50A52ALA00.0640.04938.4950.0050.0050.0000.0000.0000.000
51A53LYS10.9260.96236.365-0.075-0.0750.0000.0000.0000.000
52A54ASP-1-0.912-0.96535.0720.0880.0880.0000.0000.0000.000
53A55SER00.0490.01533.9550.0060.0060.0000.0000.0000.000
54A56LEU0-0.065-0.02832.4250.0110.0110.0000.0000.0000.000
55A57LYS10.7780.90729.377-0.102-0.1020.0000.0000.0000.000
56A58GLY00.0200.01529.4450.0060.0060.0000.0000.0000.000
57A59SER0-0.0130.01128.4840.0150.0150.0000.0000.0000.000
58A60PRO0-0.013-0.00523.2800.0040.0040.0000.0000.0000.000
59A61LYS10.9510.96224.237-0.190-0.1900.0000.0000.0000.000
60A62VAL00.0950.04424.230-0.013-0.0130.0000.0000.0000.000
61A63GLU-1-0.937-0.95726.7870.1840.1840.0000.0000.0000.000
62A64VAL0-0.064-0.04630.0690.0060.0060.0000.0000.0000.000
63A65ASP-1-0.915-0.95932.3180.1220.1220.0000.0000.0000.000
64A66LEU0-0.021-0.00935.362-0.003-0.0030.0000.0000.0000.000
65A67GLN0-0.010-0.03438.2890.0030.0030.0000.0000.0000.000
66A68PHE0-0.043-0.00641.113-0.002-0.0020.0000.0000.0000.000
67A69GLY00.0780.03944.923-0.002-0.0020.0000.0000.0000.000
68A70THR0-0.0020.01346.0920.0030.0030.0000.0000.0000.000
69A71LEU0-0.0020.00944.2850.0030.0030.0000.0000.0000.000
70A72ARG10.9210.98037.576-0.112-0.1120.0000.0000.0000.000
71A73VAL00.0300.00338.9340.0000.0000.0000.0000.0000.000
72A74LYS10.9630.98934.049-0.150-0.1500.0000.0000.0000.000
73A75VAL0-0.022-0.00534.654-0.003-0.0030.0000.0000.0000.000
74A76VAL00.0240.00630.3260.0080.0080.0000.0000.0000.000
75A77ASN0-0.046-0.03928.786-0.023-0.0230.0000.0000.0000.000
76A78ASN00.0270.00729.1610.0130.0130.0000.0000.0000.000
77A79HIS00.010-0.00330.559-0.019-0.0190.0000.0000.0000.000
78A80ASN00.0170.00426.230-0.018-0.0180.0000.0000.0000.000
79A81PRO0-0.006-0.00525.7800.0010.0010.0000.0000.0000.000
80A82ARG10.9100.98620.563-0.293-0.2930.0000.0000.0000.000
81A83ASN00.002-0.03922.162-0.023-0.0230.0000.0000.0000.000
82A84ARG10.9341.02523.497-0.132-0.1320.0000.0000.0000.000
83A85ASP-1-0.719-0.78323.4340.2230.2230.0000.0000.0000.000
84A86ASN0-0.067-0.15624.865-0.008-0.0080.0000.0000.0000.000
85A87PRO0-0.0890.00126.310-0.022-0.0220.0000.0000.0000.000
86A88VAL0-0.023-0.02929.3290.0030.0030.0000.0000.0000.000
87A89ALA00.0490.02232.565-0.008-0.0080.0000.0000.0000.000
88A90ASP-1-0.858-0.95234.1390.1090.1090.0000.0000.0000.000
89A91ASN0-0.031-0.01835.695-0.002-0.0020.0000.0000.0000.000
90A92ALA00.0030.01934.2700.0010.0010.0000.0000.0000.000
91A93ILE00.0300.01936.284-0.009-0.0090.0000.0000.0000.000
92A94THR00.0280.01034.8510.0040.0040.0000.0000.0000.000
93A95LEU00.0670.01537.111-0.005-0.0050.0000.0000.0000.000
94A96HIS0-0.083-0.04638.940-0.004-0.0040.0000.0000.0000.000
95A97ARG10.8700.93137.406-0.115-0.1150.0000.0000.0000.000
96A98LEU00.0140.02540.916-0.003-0.0030.0000.0000.0000.000
97A99SER0-0.003-0.04842.806-0.005-0.0050.0000.0000.0000.000
98A100GLY00.0240.00344.774-0.004-0.0040.0000.0000.0000.000
99A101TYR00.002-0.01242.041-0.003-0.0030.0000.0000.0000.000
100A102LEU00.0240.00846.003-0.002-0.0020.0000.0000.0000.000
101A103ALA00.0060.01548.878-0.003-0.0030.0000.0000.0000.000
102A104LYS10.8300.90550.446-0.059-0.0590.0000.0000.0000.000
103A105TRP00.0720.02550.843-0.001-0.0010.0000.0000.0000.000
104A106CYS0-0.049-0.02952.550-0.002-0.0020.0000.0000.0000.000
105A107PHE0-0.058-0.03154.772-0.002-0.0020.0000.0000.0000.000
106A108ASP-1-0.757-0.87255.0830.0530.0530.0000.0000.0000.000
107A109GLU-1-0.928-0.96056.4320.0500.0500.0000.0000.0000.000
108A110ILE0-0.073-0.06058.333-0.002-0.0020.0000.0000.0000.000
109A111ASP-1-0.948-0.97860.6450.0400.0400.0000.0000.0000.000
110A112HIS0-0.067-0.02057.9610.0000.0000.0000.0000.0000.000
111A113GLY00.0370.03162.862-0.001-0.0010.0000.0000.0000.000
112A114GLN00.011-0.00665.1960.0010.0010.0000.0000.0000.000
113A115ILE0-0.015-0.00364.5180.0000.0000.0000.0000.0000.000
114A116GLU-1-0.833-0.91861.1360.0420.0420.0000.0000.0000.000
115A117GLU-1-0.889-0.94061.4150.0370.0370.0000.0000.0000.000
116A118ALA0-0.064-0.03462.6420.0000.0000.0000.0000.0000.000
117A119GLU-1-0.840-0.93158.9860.0460.0460.0000.0000.0000.000
118A120VAL0-0.003-0.01356.9240.0010.0010.0000.0000.0000.000
119A121LYS10.8510.92658.447-0.036-0.0360.0000.0000.0000.000
120A122SER0-0.065-0.00860.926-0.001-0.0010.0000.0000.0000.000
121A123LYS10.7950.90456.555-0.047-0.0470.0000.0000.0000.000
122A124VAL0-0.0240.00753.2370.0010.0010.0000.0000.0000.000
123A125VAL00.0030.00553.860-0.002-0.0020.0000.0000.0000.000
124A126ILE00.0130.00650.6100.0030.0030.0000.0000.0000.000
125A127PRO00.004-0.00449.408-0.002-0.0020.0000.0000.0000.000
126A128LEU0-0.036-0.02846.800-0.002-0.0020.0000.0000.0000.000
127A129ALA00.0590.03551.291-0.002-0.0020.0000.0000.0000.000
128A130GLU-1-0.834-0.91654.7400.0360.0360.0000.0000.0000.000
129A131ALA0-0.079-0.02552.926-0.002-0.0020.0000.0000.0000.000
130A132LYS10.8360.93752.398-0.035-0.0350.0000.0000.0000.000
131A133GLY0-0.026-0.02656.897-0.001-0.0010.0000.0000.0000.000
132A134CYS0-0.0710.00957.6700.0000.0000.0000.0000.0000.000
133A135LYS11.0010.97058.979-0.032-0.0320.0000.0000.0000.000
134A136TRP00.0760.01556.739-0.001-0.0010.0000.0000.0000.000
135A137GLY0-0.083-0.03161.8120.0000.0000.0000.0000.0000.000
136A138ASP-1-0.849-0.92462.0370.0290.0290.0000.0000.0000.000
137A139GLY00.0000.00262.9900.0000.0000.0000.0000.0000.000
138A140VAL00.0180.00258.9030.0010.0010.0000.0000.0000.000
139A141ALA00.0620.04357.8300.0020.0020.0000.0000.0000.000
140A142LEU0-0.007-0.01056.7930.0010.0010.0000.0000.0000.000
141A143TYR0-0.015-0.02556.0890.0020.0020.0000.0000.0000.000
142A144LEU0-0.009-0.01353.6690.0010.0010.0000.0000.0000.000
143A145ALA0-0.0020.00652.5570.0030.0030.0000.0000.0000.000
144A146PHE0-0.028-0.02151.5360.0010.0010.0000.0000.0000.000
145A147ALA0-0.0280.00448.8850.0010.0010.0000.0000.0000.000
146A148PRO0-0.002-0.00844.0250.0000.0000.0000.0000.0000.000
147A149GLY00.0340.03944.5850.0030.0030.0000.0000.0000.000
148A150ALA00.0490.02845.3030.0010.0010.0000.0000.0000.000
149A151GLU-1-0.700-0.84544.2710.0660.0660.0000.0000.0000.000
150A152MET0-0.152-0.05744.0110.0020.0020.0000.0000.0000.000
151A153PHE00.0180.01147.3120.0020.0020.0000.0000.0000.000
152A154LEU00.0330.01850.434-0.002-0.0020.0000.0000.0000.000
153A155LYS10.9560.96852.889-0.044-0.0440.0000.0000.0000.000
154A156ASP-1-0.881-0.92554.7600.0490.0490.0000.0000.0000.000
155A157PHE0-0.027-0.01951.440-0.001-0.0010.0000.0000.0000.000
156A158GLU-1-0.909-0.96256.1730.0350.0350.0000.0000.0000.000
157A159PHE0-0.023-0.03054.244-0.002-0.0020.0000.0000.0000.000
158A160TYR00.0050.00855.566-0.001-0.0010.0000.0000.0000.000
159A161PRO00.0040.00750.339-0.001-0.0010.0000.0000.0000.000
160A162LEU00.0190.01951.1490.0000.0000.0000.0000.0000.000
161A163ALA00.0080.00652.351-0.001-0.0010.0000.0000.0000.000
162A164ILE0-0.006-0.00151.511-0.002-0.0020.0000.0000.0000.000
163A165ASP-1-0.875-0.94448.2140.0470.0470.0000.0000.0000.000
164A166ILE0-0.003-0.01050.560-0.002-0.0020.0000.0000.0000.000
165A167GLN0-0.009-0.00852.878-0.003-0.0030.0000.0000.0000.000
166A168ARG10.8610.92347.834-0.038-0.0380.0000.0000.0000.000
167A169VAL0-0.038-0.00548.384-0.001-0.0010.0000.0000.0000.000
168A170VAL0-0.019-0.01650.774-0.002-0.0020.0000.0000.0000.000
169A171LYS10.8620.94154.320-0.025-0.0250.0000.0000.0000.000
170A172ASP-1-0.867-0.90951.2160.0280.0280.0000.0000.0000.000
171A173GLY00.0260.02950.1360.0000.0000.0000.0000.0000.000
172A174MET0-0.085-0.03045.6950.0020.0020.0000.0000.0000.000
173A175ASP-1-0.770-0.83042.0050.0350.0350.0000.0000.0000.000
174A176ILE00.0680.01044.8410.0030.0030.0000.0000.0000.000
175A177THR0-0.102-0.10939.9600.0030.0030.0000.0000.0000.000
176A178PHE0-0.037-0.02539.7940.0050.0050.0000.0000.0000.000
177A179MET00.0090.01142.8500.0010.0010.0000.0000.0000.000
178A180ARG10.9470.96737.074-0.050-0.0500.0000.0000.0000.000
179A181LYS10.7900.90140.277-0.073-0.0730.0000.0000.0000.000
180A182VAL00.0520.01942.9430.0020.0020.0000.0000.0000.000
181A183LEU0-0.017-0.00346.146-0.001-0.0010.0000.0000.0000.000
182A184LYS10.9560.98639.620-0.075-0.0750.0000.0000.0000.000
183A185GLN0-0.053-0.01543.5570.0030.0030.0000.0000.0000.000
184A186ARG10.9120.94347.279-0.060-0.0600.0000.0000.0000.000
185A187TYR00.0370.03150.1130.0010.0010.0000.0000.0000.000
186A188GLY00.0470.01753.652-0.002-0.0020.0000.0000.0000.000
187A189THR0-0.017-0.01152.9620.0020.0020.0000.0000.0000.000
188A190LYS10.8950.95453.395-0.035-0.0350.0000.0000.0000.000
189A191THR00.0380.00549.8840.0020.0020.0000.0000.0000.000
190A192ALA00.0630.01648.722-0.002-0.0020.0000.0000.0000.000
191A193ASP-1-0.894-0.95749.5680.0400.0400.0000.0000.0000.000
192A194ASP-1-0.936-0.93852.0230.0350.0350.0000.0000.0000.000
193A195TRP0-0.036-0.02850.268-0.003-0.0030.0000.0000.0000.000
194A196MET0-0.028-0.02249.742-0.001-0.0010.0000.0000.0000.000
195A197ILE0-0.0260.00055.215-0.002-0.0020.0000.0000.0000.000
196A198SER0-0.033-0.03858.296-0.002-0.0020.0000.0000.0000.000
197A199GLU-1-0.884-0.91758.0590.0340.0340.0000.0000.0000.000
198A200VAL00.0410.02259.2130.0000.0000.0000.0000.0000.000
199A201THR00.0460.02360.874-0.001-0.0010.0000.0000.0000.000
200A202ALA00.0510.04060.6480.0000.0000.0000.0000.0000.000
201A203ILE00.0190.01756.0620.0000.0000.0000.0000.0000.000
202A204GLN0-0.013-0.01359.4050.0000.0000.0000.0000.0000.000
203A205SER0-0.040-0.03162.024-0.001-0.0010.0000.0000.0000.000
204A206ALA00.0460.02458.617-0.001-0.0010.0000.0000.0000.000
205A207VAL00.012-0.00757.7700.0000.0000.0000.0000.0000.000
206A208LYS10.8910.95260.017-0.023-0.0230.0000.0000.0000.000
207A209VAL0-0.002-0.00661.946-0.001-0.0010.0000.0000.0000.000
208A210VAL00.0270.00256.7290.0000.0000.0000.0000.0000.000
209A211ALA0-0.064-0.03160.1080.0000.0000.0000.0000.0000.000
210A212LYS10.8610.93361.858-0.024-0.0240.0000.0000.0000.000
211A213LEU00.0260.03658.8610.0000.0000.0000.0000.0000.000
212A214PRO0-0.015-0.00961.673-0.001-0.0010.0000.0000.0000.000
213A215TRP00.036-0.01953.763-0.001-0.0010.0000.0000.0000.000
214A216ALA00.0290.01257.1520.0010.0010.0000.0000.0000.000
215A217LYS10.8300.92358.218-0.019-0.0190.0000.0000.0000.000
216A218ALA00.0390.02758.641-0.001-0.0010.0000.0000.0000.000
217A219GLY00.0620.03459.0690.0010.0010.0000.0000.0000.000
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