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: LZ749

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2747198.359362
FMO2-HF: Nuclear repulsion 2656417.627119
FMO2-HF: Total energy -90780.732243
FMO2-MP2: Total energy -91047.111739


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.
4.817-2.5960.3738.063-1.0230.001
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 : -0.029 / q_NPA : -0.022
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].
3A5PRO0-0.045-0.0102.8755.250-2.1950.3748.063-0.9920.001
4A6ASP-1-0.876-0.9385.330-0.463-0.431-0.0010.000-0.0310.000
5A7PHE0-0.057-0.0328.808-0.027-0.0270.0000.0000.0000.000
6A8ILE0-0.005-0.0078.7800.2100.2100.0000.0000.0000.000
7A9TYR0-0.021-0.02211.226-0.139-0.1390.0000.0000.0000.000
8A10ASP-1-0.836-0.90314.4820.5720.5720.0000.0000.0000.000
9A11ASP-1-0.925-0.95516.4870.1950.1950.0000.0000.0000.000
10A12ARG10.8180.89916.029-0.469-0.4690.0000.0000.0000.000
11A13PRO00.0270.01921.753-0.015-0.0150.0000.0000.0000.000
12A14ALA0-0.045-0.03425.5460.0070.0070.0000.0000.0000.000
13A15ALA00.0190.01726.834-0.001-0.0010.0000.0000.0000.000
14A16VAL0-0.013-0.01028.543-0.005-0.0050.0000.0000.0000.000
15A17SER0-0.032-0.02432.3790.0010.0010.0000.0000.0000.000
16A18SER00.0100.01933.9770.0010.0010.0000.0000.0000.000
17A19THR0-0.068-0.04036.062-0.002-0.0020.0000.0000.0000.000
18A20PHE0-0.027-0.00839.050-0.004-0.0040.0000.0000.0000.000
19A21ASN00.0120.00540.650-0.004-0.0040.0000.0000.0000.000
20A22PRO00.0020.00044.2330.0000.0000.0000.0000.0000.000
21A23GLU-1-0.797-0.90945.5440.0400.0400.0000.0000.0000.000
22A24LYS10.8270.90242.635-0.061-0.0610.0000.0000.0000.000
23A25GLY00.0150.00342.9420.0000.0000.0000.0000.0000.000
24A26TYR0-0.063-0.06543.680-0.001-0.0010.0000.0000.0000.000
25A27MET00.0580.03146.716-0.002-0.0020.0000.0000.0000.000
26A28ASP-1-0.850-0.88943.0260.0560.0560.0000.0000.0000.000
27A29PHE0-0.015-0.01242.966-0.002-0.0020.0000.0000.0000.000
28A30ILE00.0230.01144.731-0.002-0.0020.0000.0000.0000.000
29A31THR0-0.034-0.02446.876-0.003-0.0030.0000.0000.0000.000
30A32ALA0-0.065-0.03342.948-0.002-0.0020.0000.0000.0000.000
31A33TYR00.016-0.01338.956-0.002-0.0020.0000.0000.0000.000
32A34GLY00.0300.01445.790-0.003-0.0030.0000.0000.0000.000
33A35LYS10.8910.94648.675-0.032-0.0320.0000.0000.0000.000
34A36ASN00.0050.01647.339-0.004-0.0040.0000.0000.0000.000
35A37ILE0-0.0380.00647.441-0.001-0.0010.0000.0000.0000.000
36A38ASN00.0810.04850.317-0.001-0.0010.0000.0000.0000.000
37A39ALA00.0990.04752.2900.0000.0000.0000.0000.0000.000
38A40ASP-1-0.834-0.89553.3730.0090.0090.0000.0000.0000.000
39A41ASN0-0.025-0.03348.410-0.002-0.0020.0000.0000.0000.000
40A42VAL0-0.0100.00248.3510.0010.0010.0000.0000.0000.000
41A43ARG10.8980.94949.686-0.008-0.0080.0000.0000.0000.000
42A44ILE0-0.041-0.02246.2380.0000.0000.0000.0000.0000.000
43A45PHE00.0100.01341.9230.0000.0000.0000.0000.0000.000
44A46PHE00.0200.00345.7790.0000.0000.0000.0000.0000.000
45A47LEU0-0.0220.00547.9110.0000.0000.0000.0000.0000.000
46A48ASN0-0.081-0.06543.595-0.004-0.0040.0000.0000.0000.000
47A49HIS00.0570.04641.249-0.001-0.0010.0000.0000.0000.000
48A50LYS10.9000.92840.253-0.010-0.0100.0000.0000.0000.000
49A51LYS10.9140.95439.604-0.006-0.0060.0000.0000.0000.000
50A52ALA00.0420.04338.094-0.001-0.0010.0000.0000.0000.000
51A53LYS10.9340.96736.384-0.038-0.0380.0000.0000.0000.000
52A54ASP-1-0.866-0.93735.0610.0150.0150.0000.0000.0000.000
53A55SER00.0350.00433.865-0.003-0.0030.0000.0000.0000.000
54A56LEU0-0.056-0.03331.9960.0010.0010.0000.0000.0000.000
55A57LYS10.8240.91730.449-0.042-0.0420.0000.0000.0000.000
56A58GLY00.0300.02229.4430.0010.0010.0000.0000.0000.000
57A59SER0-0.0070.01328.121-0.005-0.0050.0000.0000.0000.000
58A60PRO00.0230.01823.0720.0100.0100.0000.0000.0000.000
59A61LYS10.8710.93723.685-0.026-0.0260.0000.0000.0000.000
60A62VAL00.1000.03423.957-0.005-0.0050.0000.0000.0000.000
61A63GLU-1-0.828-0.87726.7260.0680.0680.0000.0000.0000.000
62A64VAL0-0.063-0.05429.523-0.006-0.0060.0000.0000.0000.000
63A65ASP-1-0.828-0.88132.0640.0260.0260.0000.0000.0000.000
64A66LEU0-0.011-0.00434.989-0.005-0.0050.0000.0000.0000.000
65A67GLN00.007-0.01237.9710.0020.0020.0000.0000.0000.000
66A68PHE0-0.023-0.00440.458-0.002-0.0020.0000.0000.0000.000
67A69GLY00.0770.03744.8440.0010.0010.0000.0000.0000.000
68A70THR0-0.022-0.01846.179-0.001-0.0010.0000.0000.0000.000
69A71LEU0-0.0040.01144.2950.0010.0010.0000.0000.0000.000
70A72ARG10.8170.88536.887-0.015-0.0150.0000.0000.0000.000
71A73VAL0-0.002-0.01439.1930.0020.0020.0000.0000.0000.000
72A74LYS10.8670.92531.739-0.060-0.0600.0000.0000.0000.000
73A75VAL0-0.043-0.01934.8870.0030.0030.0000.0000.0000.000
74A76VAL00.0260.00630.157-0.001-0.0010.0000.0000.0000.000
75A77ASN0-0.016-0.01528.143-0.004-0.0040.0000.0000.0000.000
76A78ASN00.0070.00229.0190.0040.0040.0000.0000.0000.000
77A79HIS0-0.005-0.01030.670-0.001-0.0010.0000.0000.0000.000
78A80ASN00.0290.01225.606-0.001-0.0010.0000.0000.0000.000
79A81PRO0-0.020-0.02425.8510.0080.0080.0000.0000.0000.000
80A82ARG10.8900.94620.843-0.072-0.0720.0000.0000.0000.000
81A83ASN00.0540.02622.516-0.023-0.0230.0000.0000.0000.000
82A84ARG10.8890.95823.818-0.121-0.1210.0000.0000.0000.000
83A85ASP-1-0.739-0.85623.4560.1550.1550.0000.0000.0000.000
84A86ASN0-0.103-0.07125.320-0.011-0.0110.0000.0000.0000.000
85A87PRO00.0200.02726.108-0.009-0.0090.0000.0000.0000.000
86A88VAL0-0.020-0.01429.031-0.006-0.0060.0000.0000.0000.000
87A89ALA00.0470.01832.073-0.005-0.0050.0000.0000.0000.000
88A90ASP-1-0.815-0.91733.7530.0830.0830.0000.0000.0000.000
89A91ASN00.010-0.00335.822-0.002-0.0020.0000.0000.0000.000
90A92ALA00.0000.01934.272-0.004-0.0040.0000.0000.0000.000
91A93ILE00.0250.02236.213-0.002-0.0020.0000.0000.0000.000
92A94THR00.0360.02234.3090.0000.0000.0000.0000.0000.000
93A95LEU00.0250.00136.848-0.002-0.0020.0000.0000.0000.000
94A96HIS0-0.069-0.04238.983-0.003-0.0030.0000.0000.0000.000
95A97ARG10.8110.90136.588-0.076-0.0760.0000.0000.0000.000
96A98LEU00.0230.02140.911-0.002-0.0020.0000.0000.0000.000
97A99SER0-0.014-0.03142.798-0.003-0.0030.0000.0000.0000.000
98A100GLY00.0260.01244.811-0.002-0.0020.0000.0000.0000.000
99A101TYR0-0.008-0.01141.5920.0000.0000.0000.0000.0000.000
100A102LEU00.0260.01045.830-0.002-0.0020.0000.0000.0000.000
101A103ALA00.0220.02348.766-0.002-0.0020.0000.0000.0000.000
102A104LYS10.7850.88450.357-0.035-0.0350.0000.0000.0000.000
103A105TRP00.0600.01950.962-0.001-0.0010.0000.0000.0000.000
104A106CYS0-0.064-0.03152.404-0.002-0.0020.0000.0000.0000.000
105A107PHE0-0.046-0.02754.838-0.001-0.0010.0000.0000.0000.000
106A108ASP-1-0.725-0.83254.5840.0300.0300.0000.0000.0000.000
107A109GLU-1-0.888-0.93856.2980.0190.0190.0000.0000.0000.000
108A110ILE0-0.082-0.05558.207-0.001-0.0010.0000.0000.0000.000
109A111ASP-1-0.945-0.96760.5920.0220.0220.0000.0000.0000.000
110A112HIS0-0.097-0.04957.3930.0010.0010.0000.0000.0000.000
111A113GLY00.0340.02562.7650.0000.0000.0000.0000.0000.000
112A114GLN00.0270.00264.8310.0000.0000.0000.0000.0000.000
113A115ILE0-0.040-0.01064.653-0.001-0.0010.0000.0000.0000.000
114A116GLU-1-0.832-0.91561.1260.0150.0150.0000.0000.0000.000
115A117GLU-1-0.823-0.89861.0510.0160.0160.0000.0000.0000.000
116A118ALA0-0.046-0.02162.2380.0000.0000.0000.0000.0000.000
117A119GLU-1-0.820-0.89558.2040.0110.0110.0000.0000.0000.000
118A120VAL00.000-0.01456.6060.0000.0000.0000.0000.0000.000
119A121LYS10.8230.89158.260-0.017-0.0170.0000.0000.0000.000
120A122SER0-0.059-0.01260.733-0.001-0.0010.0000.0000.0000.000
121A123LYS10.7370.84556.194-0.011-0.0110.0000.0000.0000.000
122A124VAL0-0.0050.00152.991-0.001-0.0010.0000.0000.0000.000
123A125VAL0-0.0090.00153.6290.0000.0000.0000.0000.0000.000
124A126ILE00.0190.01050.6440.0010.0010.0000.0000.0000.000
125A127PRO0-0.007-0.01349.7650.0000.0000.0000.0000.0000.000
126A128LEU0-0.029-0.01447.327-0.001-0.0010.0000.0000.0000.000
127A129ALA00.0460.04051.7210.0000.0000.0000.0000.0000.000
128A130GLU-1-0.746-0.85155.3210.0120.0120.0000.0000.0000.000
129A131ALA0-0.078-0.02853.091-0.001-0.0010.0000.0000.0000.000
130A132LYS10.7730.88453.255-0.018-0.0180.0000.0000.0000.000
131A133GLY0-0.038-0.03557.1880.0000.0000.0000.0000.0000.000
132A134CYS0-0.089-0.02458.1290.0000.0000.0000.0000.0000.000
133A135LYS10.8760.90159.194-0.011-0.0110.0000.0000.0000.000
134A136TRP00.0600.00056.6540.0010.0010.0000.0000.0000.000
135A137GLY0-0.045-0.00761.6790.0000.0000.0000.0000.0000.000
136A138ASP-1-0.814-0.89162.4480.0150.0150.0000.0000.0000.000
137A139GLY00.0350.01162.9140.0010.0010.0000.0000.0000.000
138A140VAL00.0010.00759.5330.0000.0000.0000.0000.0000.000
139A141ALA00.0550.03457.8410.0010.0010.0000.0000.0000.000
140A142LEU0-0.006-0.01456.9580.0010.0010.0000.0000.0000.000
141A143TYR0-0.028-0.04156.1360.0010.0010.0000.0000.0000.000
142A144LEU00.005-0.00253.6620.0000.0000.0000.0000.0000.000
143A145ALA0-0.0100.00052.6660.0020.0020.0000.0000.0000.000
144A146PHE0-0.021-0.01351.9230.0010.0010.0000.0000.0000.000
145A147ALA0-0.0020.01148.8220.0000.0000.0000.0000.0000.000
146A148PRO0-0.047-0.03044.3170.0020.0020.0000.0000.0000.000
147A149GLY00.0420.02445.0410.0000.0000.0000.0000.0000.000
148A150ALA00.0420.02345.7360.0010.0010.0000.0000.0000.000
149A151GLU-1-0.727-0.85144.8130.0460.0460.0000.0000.0000.000
150A152MET0-0.123-0.04943.6120.0040.0040.0000.0000.0000.000
151A153PHE00.0350.01747.2420.0020.0020.0000.0000.0000.000
152A154LEU00.0030.00950.916-0.003-0.0030.0000.0000.0000.000
153A155LYS10.8830.92652.743-0.034-0.0340.0000.0000.0000.000
154A156ASP-1-0.843-0.89654.7600.0320.0320.0000.0000.0000.000
155A157PHE0-0.034-0.01851.553-0.002-0.0020.0000.0000.0000.000
156A158GLU-1-0.830-0.91355.9750.0240.0240.0000.0000.0000.000
157A159PHE00.029-0.00454.642-0.001-0.0010.0000.0000.0000.000
158A160TYR0-0.025-0.02955.5250.0000.0000.0000.0000.0000.000
159A161PRO00.0030.00550.6220.0000.0000.0000.0000.0000.000
160A162LEU00.0200.02051.4670.0000.0000.0000.0000.0000.000
161A163ALA00.0040.00552.7410.0000.0000.0000.0000.0000.000
162A164ILE0-0.014-0.00151.689-0.001-0.0010.0000.0000.0000.000
163A165ASP-1-0.867-0.94548.3290.0370.0370.0000.0000.0000.000
164A166ILE0-0.008-0.00950.9210.0000.0000.0000.0000.0000.000
165A167GLN00.0190.01653.500-0.001-0.0010.0000.0000.0000.000
166A168ARG10.8540.89846.896-0.027-0.0270.0000.0000.0000.000
167A169VAL0-0.029-0.00648.767-0.001-0.0010.0000.0000.0000.000
168A170VAL0-0.030-0.02151.151-0.001-0.0010.0000.0000.0000.000
169A171LYS10.8420.92354.580-0.022-0.0220.0000.0000.0000.000
170A172ASP-1-0.810-0.86751.1720.0180.0180.0000.0000.0000.000
171A173GLY00.0270.02650.417-0.001-0.0010.0000.0000.0000.000
172A174MET0-0.100-0.02545.8610.0000.0000.0000.0000.0000.000
173A175ASP-1-0.767-0.87942.3680.0450.0450.0000.0000.0000.000
174A176ILE00.0470.01545.2630.0010.0010.0000.0000.0000.000
175A177THR0-0.107-0.07340.4420.0040.0040.0000.0000.0000.000
176A178PHE00.003-0.00840.6400.0030.0030.0000.0000.0000.000
177A179MET00.0220.01343.1430.0010.0010.0000.0000.0000.000
178A180ARG10.9310.96637.983-0.065-0.0650.0000.0000.0000.000
179A181LYS10.7870.90341.049-0.053-0.0530.0000.0000.0000.000
180A182VAL00.0620.02543.4040.0010.0010.0000.0000.0000.000
181A183LEU0-0.010-0.00846.7880.0000.0000.0000.0000.0000.000
182A184LYS10.9600.98639.707-0.078-0.0780.0000.0000.0000.000
183A185GLN0-0.026-0.00943.3540.0020.0020.0000.0000.0000.000
184A186ARG10.9110.95047.227-0.056-0.0560.0000.0000.0000.000
185A187TYR0-0.013-0.01049.974-0.001-0.0010.0000.0000.0000.000
186A188GLY00.0510.02453.472-0.001-0.0010.0000.0000.0000.000
187A189THR0-0.002-0.01052.4560.0020.0020.0000.0000.0000.000
188A190LYS10.7990.91652.789-0.036-0.0360.0000.0000.0000.000
189A191THR0-0.016-0.04149.4180.0000.0000.0000.0000.0000.000
190A192ALA00.0570.01549.050-0.002-0.0020.0000.0000.0000.000
191A193ASP-1-0.843-0.91249.6960.0550.0550.0000.0000.0000.000
192A194ASP-1-0.809-0.86352.4590.0400.0400.0000.0000.0000.000
193A195TRP0-0.019-0.02650.179-0.003-0.0030.0000.0000.0000.000
194A196MET0-0.058-0.03749.578-0.002-0.0020.0000.0000.0000.000
195A197ILE0-0.036-0.00755.562-0.001-0.0010.0000.0000.0000.000
196A198SER0-0.032-0.04558.708-0.002-0.0020.0000.0000.0000.000
197A199GLU-1-0.823-0.88557.9580.0330.0330.0000.0000.0000.000
198A200VAL00.0080.01459.473-0.001-0.0010.0000.0000.0000.000
199A201THR00.0540.02660.994-0.001-0.0010.0000.0000.0000.000
200A202ALA00.0310.03060.737-0.001-0.0010.0000.0000.0000.000
201A203ILE00.0200.01556.318-0.001-0.0010.0000.0000.0000.000
202A204GLN0-0.022-0.02259.459-0.001-0.0010.0000.0000.0000.000
203A205SER0-0.037-0.02662.243-0.002-0.0020.0000.0000.0000.000
204A206ALA00.0570.03158.765-0.001-0.0010.0000.0000.0000.000
205A207VAL0-0.008-0.01457.743-0.001-0.0010.0000.0000.0000.000
206A208LYS10.8950.94860.162-0.020-0.0200.0000.0000.0000.000
207A209VAL00.0180.01362.097-0.001-0.0010.0000.0000.0000.000
208A210VAL00.0260.00556.962-0.001-0.0010.0000.0000.0000.000
209A211ALA0-0.073-0.03560.358-0.001-0.0010.0000.0000.0000.000
210A212LYS10.8840.94462.226-0.017-0.0170.0000.0000.0000.000
211A213LEU00.0170.02959.011-0.001-0.0010.0000.0000.0000.000
212A214PRO0-0.014-0.01361.9590.0000.0000.0000.0000.0000.000
213A215TRP00.0810.02353.947-0.001-0.0010.0000.0000.0000.000
214A216ALA0-0.005-0.00457.278-0.001-0.0010.0000.0000.0000.000
215A217LYS10.8740.93658.561-0.011-0.0110.0000.0000.0000.000
216A218ALA00.0340.03258.892-0.001-0.0010.0000.0000.0000.000
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