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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: 89M1Y

Calculation Name: 4JG2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JG2

Chain ID: A

ChEMBL ID:

UniProt ID: Q73EI2

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1811842.176879
FMO2-HF: Nuclear repulsion 1741901.653181
FMO2-HF: Total energy -69940.523697
FMO2-MP2: Total energy -70147.793384


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:-11:LYS)


Summations of interaction energy for fragment #1(A:-11:LYS)
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.
-101.173-92.47342.024-24.083-26.643-0.225
Interaction energy analysis for fragmet #1(A:-11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.916
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].
3A-9THR00.018-0.0033.8171.0403.559-0.014-1.266-1.2400.008
4A-8GLU-1-0.800-0.8431.658-141.525-142.14022.865-12.376-9.875-0.144
5A-7ASN00.0540.0164.5993.7843.906-0.001-0.012-0.1090.000
6A-6LEU00.0460.0134.780-2.696-2.616-0.001-0.002-0.0770.000
7A-5TYR0-0.0170.0006.122-0.133-0.1330.0000.0000.0000.000
8A-4PHE0-0.034-0.0267.6310.9080.9080.0000.0000.0000.000
9A-3GLN0-0.063-0.0062.555-4.592-3.6220.979-0.674-1.2750.001
10A-2SER0-0.007-0.0291.828-17.974-19.25812.439-5.816-5.339-0.061
11A-1ASN0-0.004-0.0034.0602.7573.313-0.001-0.179-0.376-0.001
12A0ALA00.0080.0114.7004.9235.064-0.001-0.031-0.1090.000
13A4GLN00.0560.0162.498-22.389-17.1274.011-3.421-5.853-0.025
14A5ASN0-0.030-0.0162.4823.0294.0371.733-0.512-2.229-0.003
15A6ARG10.8840.9113.43625.29125.2320.0150.206-0.1610.000
16A7THR00.0650.0446.8502.0522.0520.0000.0000.0000.000
17A8LYS10.9150.9735.01742.49442.4940.0000.0000.0000.000
18A9VAL0-0.008-0.0036.889-0.738-0.7380.0000.0000.0000.000
19A10VAL0-0.034-0.0217.9360.3720.3720.0000.0000.0000.000
20A11THR00.0500.01910.4090.1670.1670.0000.0000.0000.000
21A12SER00.0510.00913.791-0.523-0.5230.0000.0000.0000.000
22A13VAL00.000-0.02415.5370.1980.1980.0000.0000.0000.000
23A14ASN0-0.014-0.00218.0660.9450.9450.0000.0000.0000.000
24A15THR0-0.0340.01118.0410.1420.1420.0000.0000.0000.000
25A16ARG10.8800.94220.27010.36010.3600.0000.0000.0000.000
26A17LEU0-0.0070.00420.503-0.323-0.3230.0000.0000.0000.000
27A18SER00.0980.04024.0550.7070.7070.0000.0000.0000.000
28A19TYR0-0.034-0.01925.848-0.415-0.4150.0000.0000.0000.000
29A20PHE0-0.024-0.02022.137-0.464-0.4640.0000.0000.0000.000
30A21HIS00.0230.01624.6280.4570.4570.0000.0000.0000.000
31A22GLY00.0360.00222.187-0.404-0.4040.0000.0000.0000.000
32A23TRP0-0.004-0.00822.632-0.521-0.5210.0000.0000.0000.000
33A24GLU-1-0.827-0.88725.242-10.215-10.2150.0000.0000.0000.000
34A25PRO0-0.049-0.00724.897-0.191-0.1910.0000.0000.0000.000
35A26VAL00.0850.02626.4880.3710.3710.0000.0000.0000.000
36A27SER0-0.008-0.00927.943-0.297-0.2970.0000.0000.0000.000
37A28ILE0-0.014-0.01426.6240.1730.1730.0000.0000.0000.000
38A29ASN0-0.027-0.02630.569-0.163-0.1630.0000.0000.0000.000
39A30GLY00.0930.05833.5610.0940.0940.0000.0000.0000.000
40A31GLY0-0.049-0.01229.550-0.067-0.0670.0000.0000.0000.000
41A32ALA0-0.031-0.01326.8240.0350.0350.0000.0000.0000.000
42A33GLU-1-0.893-0.93927.234-10.693-10.6930.0000.0000.0000.000
43A34LYS10.7980.88722.15211.73611.7360.0000.0000.0000.000
44A35TYR00.1000.07120.7110.2650.2650.0000.0000.0000.000
45A36SER0-0.057-0.05521.481-0.307-0.3070.0000.0000.0000.000
46A37VAL00.0120.01020.1210.1710.1710.0000.0000.0000.000
47A38SER0-0.016-0.00321.859-0.293-0.2930.0000.0000.0000.000
48A39VAL0-0.023-0.01317.6340.1650.1650.0000.0000.0000.000
49A40LEU00.0240.01721.039-0.044-0.0440.0000.0000.0000.000
50A41ILE0-0.017-0.02617.564-0.372-0.3720.0000.0000.0000.000
51A42PRO00.0690.04020.4610.3460.3460.0000.0000.0000.000
52A43LYS10.8190.88321.4289.9489.9480.0000.0000.0000.000
53A44THR0-0.009-0.01222.792-0.113-0.1130.0000.0000.0000.000
54A45ASP-1-0.811-0.85116.456-15.902-15.9020.0000.0000.0000.000
55A46LYS10.9250.93017.74811.44511.4450.0000.0000.0000.000
56A47GLU-1-0.919-0.93611.571-18.800-18.8000.0000.0000.0000.000
57A48THR00.012-0.02313.217-1.343-1.3430.0000.0000.0000.000
58A49ILE0-0.038-0.01414.175-0.481-0.4810.0000.0000.0000.000
59A50ASN0-0.030-0.02214.5850.2640.2640.0000.0000.0000.000
60A51ALA00.0120.0159.983-0.371-0.3710.0000.0000.0000.000
61A52ILE00.0120.00411.550-0.813-0.8130.0000.0000.0000.000
62A53ASN0-0.017-0.00813.7670.1100.1100.0000.0000.0000.000
63A54ALA0-0.0010.00511.5050.2180.2180.0000.0000.0000.000
64A55ALA00.0190.01510.341-0.380-0.3800.0000.0000.0000.000
65A56VAL0-0.039-0.02711.7540.0680.0680.0000.0000.0000.000
66A57ASP-1-0.800-0.88915.262-14.438-14.4380.0000.0000.0000.000
67A58ALA0-0.0240.00010.6210.3050.3050.0000.0000.0000.000
68A59ALA00.0170.01112.701-0.061-0.0610.0000.0000.0000.000
69A60ILE0-0.042-0.02613.9140.7540.7540.0000.0000.0000.000
70A61GLU-1-0.829-0.89714.573-16.816-16.8160.0000.0000.0000.000
71A62GLU-1-0.889-0.9449.758-25.830-25.8300.0000.0000.0000.000
72A63GLY0-0.017-0.00914.5110.3800.3800.0000.0000.0000.000
73A64ILE0-0.066-0.03617.7300.6020.6020.0000.0000.0000.000
74A65ALA0-0.008-0.00115.6290.5230.5230.0000.0000.0000.000
75A66LYS10.8860.96116.57816.53116.5310.0000.0000.0000.000
76A67PHE0-0.023-0.03018.2630.3410.3410.0000.0000.0000.000
77A68GLY00.0190.03721.3920.6330.6330.0000.0000.0000.000
78A69GLY00.0260.00923.3220.1000.1000.0000.0000.0000.000
79A70LYS10.9310.96024.5899.3889.3880.0000.0000.0000.000
80A71LYS10.9340.95018.65914.39214.3920.0000.0000.0000.000
81A72PRO0-0.0110.00322.2390.4930.4930.0000.0000.0000.000
82A73ASN00.0360.01724.599-0.421-0.4210.0000.0000.0000.000
83A74LYS10.9060.91019.54813.90813.9080.0000.0000.0000.000
84A75ALA00.0300.02025.085-0.069-0.0690.0000.0000.0000.000
85A76ALA0-0.059-0.02027.8960.2330.2330.0000.0000.0000.000
86A77ILE0-0.073-0.03922.0780.0160.0160.0000.0000.0000.000
87A78LYS10.9110.96424.33411.23311.2330.0000.0000.0000.000
88A79LEU00.040-0.00120.812-0.614-0.6140.0000.0000.0000.000
89A80PRO00.005-0.00517.6960.5120.5120.0000.0000.0000.000
90A81LEU0-0.0110.00918.4050.0410.0410.0000.0000.0000.000
91A82ARG10.7840.88420.84711.65711.6570.0000.0000.0000.000
92A83ASP-1-0.779-0.89424.246-10.584-10.5840.0000.0000.0000.000
93A84GLY0-0.006-0.01626.5850.2830.2830.0000.0000.0000.000
94A85ASP-1-0.775-0.86628.329-9.442-9.4420.0000.0000.0000.000
95A86VAL0-0.015-0.01530.3800.3040.3040.0000.0000.0000.000
96A87GLU-1-0.836-0.88727.574-10.520-10.5200.0000.0000.0000.000
97A88ARG10.8360.92029.5709.8019.8010.0000.0000.0000.000
98A89ASP-1-0.876-0.92032.697-8.116-8.1160.0000.0000.0000.000
99A90ASP-1-0.870-0.94332.248-8.984-8.9840.0000.0000.0000.000
100A91GLU-1-0.875-0.96432.839-8.489-8.4890.0000.0000.0000.000
101A92ALA0-0.065-0.02329.623-0.170-0.1700.0000.0000.0000.000
102A93TYR0-0.054-0.04727.058-0.546-0.5460.0000.0000.0000.000
103A94LYS10.9220.98128.6318.5648.5640.0000.0000.0000.000
104A95GLY0-0.0030.00928.522-0.166-0.1660.0000.0000.0000.000
105A96HIS0-0.090-0.06123.702-0.731-0.7310.0000.0000.0000.000
106A97TYR00.0190.01321.4540.2310.2310.0000.0000.0000.000
107A98PHE0-0.001-0.01122.099-0.161-0.1610.0000.0000.0000.000
108A99VAL0-0.0060.00917.358-0.087-0.0870.0000.0000.0000.000
109A100ASN0-0.0110.00520.7490.2290.2290.0000.0000.0000.000
110A101ALA00.0090.01317.351-0.240-0.2400.0000.0000.0000.000
111A102ASN0-0.019-0.02718.6160.6840.6840.0000.0000.0000.000
112A103SER00.0300.01516.433-0.790-0.7900.0000.0000.0000.000
113A104LYS10.9720.98218.88713.18513.1850.0000.0000.0000.000
114A105THR00.0110.02317.0070.5390.5390.0000.0000.0000.000
115A106PRO00.0110.00518.893-0.351-0.3510.0000.0000.0000.000
116A107PRO0-0.0280.01116.447-0.887-0.8870.0000.0000.0000.000
117A108GLN00.0180.00213.518-0.477-0.4770.0000.0000.0000.000
118A109ILE0-0.0080.00016.639-0.741-0.7410.0000.0000.0000.000
119A110VAL0-0.0050.00315.6770.4300.4300.0000.0000.0000.000
120A111ASP-1-0.692-0.83019.035-14.249-14.2490.0000.0000.0000.000
121A112LYS10.9150.94418.58112.50412.5040.0000.0000.0000.000
122A113ALA0-0.043-0.00918.444-0.536-0.5360.0000.0000.0000.000
123A114VAL0-0.057-0.02913.732-0.642-0.6420.0000.0000.0000.000
124A115ARG10.8850.92817.05812.92712.9270.0000.0000.0000.000
125A116PRO0-0.003-0.01319.6270.0710.0710.0000.0000.0000.000
126A117ILE0-0.0100.00321.2090.5040.5040.0000.0000.0000.000
127A118LEU0-0.029-0.02023.853-0.024-0.0240.0000.0000.0000.000
128A119ASP-1-0.789-0.88027.096-9.607-9.6070.0000.0000.0000.000
129A120ARG10.8420.88527.56210.47910.4790.0000.0000.0000.000
130A121ASN0-0.050-0.04428.646-0.039-0.0390.0000.0000.0000.000
131A122GLU-1-0.877-0.92026.354-11.004-11.0040.0000.0000.0000.000
132A123VAL0-0.081-0.04922.879-0.427-0.4270.0000.0000.0000.000
133A124TYR00.028-0.01026.0650.1290.1290.0000.0000.0000.000
134A125SER00.0230.00327.222-0.487-0.4870.0000.0000.0000.000
135A126GLY00.0620.03927.4440.4000.4000.0000.0000.0000.000
136A127CYS0-0.0740.00725.173-0.129-0.1290.0000.0000.0000.000
137A128TYR00.031-0.00522.596-0.091-0.0910.0000.0000.0000.000
138A129ALA00.0490.00219.677-0.026-0.0260.0000.0000.0000.000
139A130ARG10.8360.93110.61521.12321.1230.0000.0000.0000.000
140A131VAL00.0370.01115.238-0.031-0.0310.0000.0000.0000.000
141A132SER0-0.029-0.0119.887-2.004-2.0040.0000.0000.0000.000
142A133LEU0-0.023-0.00511.3251.2931.2930.0000.0000.0000.000
143A134ASN00.0110.0058.660-4.518-4.5180.0000.0000.0000.000
144A135PHE00.0090.00411.2432.1472.1470.0000.0000.0000.000
145A136TYR00.0230.00412.319-0.952-0.9520.0000.0000.0000.000
146A137ALA00.0280.02014.8531.0251.0250.0000.0000.0000.000
147A138PHE0-0.043-0.02118.064-0.062-0.0620.0000.0000.0000.000
148A139ASN0-0.005-0.02421.0130.5760.5760.0000.0000.0000.000
149A140SER00.0420.02824.679-0.025-0.0250.0000.0000.0000.000
150A141ASN00.0310.00826.8280.2660.2660.0000.0000.0000.000
151A142GLY00.0440.03529.8510.1340.1340.0000.0000.0000.000
152A143ASN0-0.047-0.01126.856-0.021-0.0210.0000.0000.0000.000
153A144LYS11.0130.99524.82510.09410.0940.0000.0000.0000.000
154A145GLY00.0060.01322.4750.3910.3910.0000.0000.0000.000
155A146VAL0-0.044-0.01016.364-0.415-0.4150.0000.0000.0000.000
156A147ALA0-0.0040.01318.1920.5830.5830.0000.0000.0000.000
157A148CYS0-0.008-0.02015.281-0.937-0.9370.0000.0000.0000.000
158A149GLY00.0080.01214.5730.8650.8650.0000.0000.0000.000
159A150LEU0-0.029-0.02014.048-1.099-1.0990.0000.0000.0000.000
160A151GLY00.0090.00412.152-0.462-0.4620.0000.0000.0000.000
161A152ASN0-0.014-0.02512.0022.0642.0640.0000.0000.0000.000
162A153ILE00.0290.01114.235-0.177-0.1770.0000.0000.0000.000
163A154GLN0-0.050-0.02015.496-0.519-0.5190.0000.0000.0000.000
164A155LYS10.8150.89817.41011.81511.8150.0000.0000.0000.000
165A156ILE0-0.112-0.05817.640-0.176-0.1760.0000.0000.0000.000
166A157ARG10.9180.95221.70411.90811.9080.0000.0000.0000.000
167A158ASP-1-0.756-0.84625.296-11.032-11.0320.0000.0000.0000.000
168A159GLY0-0.015-0.01628.382-0.102-0.1020.0000.0000.0000.000
169A160GLU-1-0.914-0.94129.707-8.609-8.6090.0000.0000.0000.000
170A161PRO00.0470.01931.663-0.304-0.3040.0000.0000.0000.000
171A162LEU0-0.066-0.02628.9650.1890.1890.0000.0000.0000.000
172A163GLY00.0290.01732.843-0.050-0.0500.0000.0000.0000.000
173A164GLY0-0.023-0.01832.865-0.286-0.2860.0000.0000.0000.000
174A165ARG10.9400.96527.30910.67310.6730.0000.0000.0000.000
175A166THR0-0.009-0.01234.6710.0020.0020.0000.0000.0000.000
176A167ASN0-0.071-0.04635.2910.1840.1840.0000.0000.0000.000
177A168ALA00.0920.06037.696-0.018-0.0180.0000.0000.0000.000
178A169ALA0-0.022-0.01940.7450.0920.0920.0000.0000.0000.000
179A170ASP-1-0.898-0.93635.835-8.573-8.5730.0000.0000.0000.000
180A171ASP-1-0.975-0.97038.646-8.228-8.2280.0000.0000.0000.000
181A172PHE0-0.100-0.05640.9940.1640.1640.0000.0000.0000.000
182A173THR00.0240.01444.637-0.073-0.0730.0000.0000.0000.000
183A174THR0-0.056-0.04347.258-0.012-0.0120.0000.0000.0000.000
184A175ILE0-0.035-0.01550.3590.0220.0220.0000.0000.0000.000
185A176GLU-1-0.913-0.94052.726-5.905-5.9050.0000.0000.0000.000