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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: 3JK3L

Calculation Name: 3M3I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M3I

Chain ID: A

ChEMBL ID:

UniProt ID: E9AES8

Base Structure: X-ray

Registration Date: 2023-09-22

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1933966.654098
FMO2-HF: Nuclear repulsion 1862723.929573
FMO2-HF: Total energy -71242.724525
FMO2-MP2: Total energy -71450.505046


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:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-13.329-8.4821.543-2.442-3.95-0.002
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / 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].
3A12THR00.033-0.0022.833-5.080-1.7130.597-1.908-2.057-0.003
4A13ALA00.0760.0304.9351.0761.158-0.001-0.004-0.0770.000
5A14GLU-1-0.817-0.9048.536-1.690-1.6900.0000.0000.0000.000
6A15PHE0-0.042-0.0217.4530.3460.3460.0000.0000.0000.000
7A16TRP00.039-0.0055.7420.2340.2340.0000.0000.0000.000
8A17ILE00.0310.02310.8560.0990.0990.0000.0000.0000.000
9A18LYS10.9390.97212.9370.2830.2830.0000.0000.0000.000
10A19ARG10.8320.9149.999-0.361-0.3610.0000.0000.0000.000
11A20LEU0-0.0080.01013.0000.0780.0780.0000.0000.0000.000
12A21GLN0-0.049-0.02216.135-0.011-0.0110.0000.0000.0000.000
13A22LEU0-0.0480.00714.091-0.009-0.0090.0000.0000.0000.000
14A23VAL00.008-0.00217.997-0.051-0.0510.0000.0000.0000.000
15A24PRO00.002-0.01320.111-0.002-0.0020.0000.0000.0000.000
16A25HIS00.0440.04520.8320.0300.0300.0000.0000.0000.000
17A26PRO00.0180.00822.599-0.034-0.0340.0000.0000.0000.000
18A27GLU-1-0.771-0.85221.600-0.289-0.2890.0000.0000.0000.000
19A28GLY0-0.0110.02221.028-0.028-0.0280.0000.0000.0000.000
20A29GLY00.0590.03116.7380.0300.0300.0000.0000.0000.000
21A30TYR0-0.060-0.04414.6390.0600.0600.0000.0000.0000.000
22A31TYR0-0.025-0.01916.9160.0170.0170.0000.0000.0000.000
23A32SER00.0270.01418.9280.0010.0010.0000.0000.0000.000
24A33GLU-1-0.816-0.89821.054-0.041-0.0410.0000.0000.0000.000
25A34VAL0-0.033-0.00320.3190.0140.0140.0000.0000.0000.000
26A35VAL0-0.022-0.01323.5850.0100.0100.0000.0000.0000.000
27A36ARG10.8590.90126.8850.0140.0140.0000.0000.0000.000
28A37SER0-0.065-0.01530.0000.0100.0100.0000.0000.0000.000
29A38ALA00.0280.01632.747-0.011-0.0110.0000.0000.0000.000
30A39HIS00.0390.02235.942-0.010-0.0100.0000.0000.0000.000
31A40LYS10.8950.94636.246-0.017-0.0170.0000.0000.0000.000
32A41VAL00.0140.00836.2920.0050.0050.0000.0000.0000.000
33A42ASP-1-0.829-0.90539.231-0.009-0.0090.0000.0000.0000.000
34A43ASN0-0.003-0.02236.0410.0080.0080.0000.0000.0000.000
35A44GLU-1-0.792-0.88835.179-0.032-0.0320.0000.0000.0000.000
36A45GLU-1-0.915-0.94437.867-0.073-0.0730.0000.0000.0000.000
37A46GLY0-0.030-0.00641.0980.0000.0000.0000.0000.0000.000
38A47ASN0-0.045-0.01839.0540.0050.0050.0000.0000.0000.000
39A48ARG10.7970.88939.4580.0050.0050.0000.0000.0000.000
40A49ARG10.8060.87334.7480.0460.0460.0000.0000.0000.000
41A50HIS0-0.004-0.01132.577-0.001-0.0010.0000.0000.0000.000
42A51ALA00.0080.00434.050-0.005-0.0050.0000.0000.0000.000
43A52TYR00.0470.02628.2560.0020.0020.0000.0000.0000.000
44A53THR0-0.018-0.00927.295-0.001-0.0010.0000.0000.0000.000
45A54THR0-0.0190.00122.985-0.011-0.0110.0000.0000.0000.000
46A55ILE00.0360.01919.919-0.002-0.0020.0000.0000.0000.000
47A56TYR0-0.0070.00915.7830.0690.0690.0000.0000.0000.000
48A57PHE00.032-0.00715.749-0.046-0.0460.0000.0000.0000.000
49A58LEU0-0.031-0.0089.9070.0360.0360.0000.0000.0000.000
50A59CYS0-0.0320.02612.127-0.015-0.0150.0000.0000.0000.000
51A60THR00.037-0.00610.651-0.152-0.1520.0000.0000.0000.000
52A61PRO00.0080.00810.5810.1890.1890.0000.0000.0000.000
53A62GLU-1-0.956-0.96513.636-1.133-1.1330.0000.0000.0000.000
54A63SER0-0.076-0.02915.2040.1630.1630.0000.0000.0000.000
55A64PRO00.0540.00916.207-0.005-0.0050.0000.0000.0000.000
56A65SER0-0.113-0.07317.7710.0570.0570.0000.0000.0000.000
57A66HIS10.8850.91020.0780.4700.4700.0000.0000.0000.000
58A67LEU0-0.038-0.02123.4500.0270.0270.0000.0000.0000.000
59A68HIS10.8360.92022.7980.2720.2720.0000.0000.0000.000
60A69ARG10.8370.91427.8030.1460.1460.0000.0000.0000.000
61A70LEU00.0390.02826.347-0.001-0.0010.0000.0000.0000.000
62A71CYS0-0.0530.00230.6370.0010.0010.0000.0000.0000.000
63A72SER0-0.008-0.04131.3370.0030.0030.0000.0000.0000.000
64A73ASP-1-0.810-0.91128.752-0.058-0.0580.0000.0000.0000.000
65A74GLU-1-0.859-0.94223.196-0.126-0.1260.0000.0000.0000.000
66A75THR0-0.059-0.03322.043-0.013-0.0130.0000.0000.0000.000
67A76TRP0-0.027-0.02816.937-0.010-0.0100.0000.0000.0000.000
68A77MET0-0.020-0.02317.1210.0050.0050.0000.0000.0000.000
69A78TYR0-0.040-0.0317.0400.3120.3120.0000.0000.0000.000
70A79HIS0-0.062-0.02711.6310.1710.1710.0000.0000.0000.000
71A80ALA0-0.018-0.0186.6010.5200.5200.0000.0000.0000.000
72A81GLY00.0090.0184.171-0.469-0.406-0.001-0.005-0.0570.000
73A82ASP-1-0.729-0.8365.225-4.484-4.437-0.0010.000-0.0460.000
74A83PRO0-0.0150.0067.0430.4870.4870.0000.0000.0000.000
75A84LEU00.0030.00210.713-0.151-0.1510.0000.0000.0000.000
76A85GLN00.0300.02213.0220.1640.1640.0000.0000.0000.000
77A86LEU0-0.0050.00315.913-0.010-0.0100.0000.0000.0000.000
78A87HIS0-0.0160.00618.9900.0550.0550.0000.0000.0000.000
79A88VAL00.0390.00822.1890.0120.0120.0000.0000.0000.000
80A89ILE0-0.013-0.00425.3370.0030.0030.0000.0000.0000.000
81A90LEU00.0200.01327.9230.0070.0070.0000.0000.0000.000
82A91LYS10.9630.98730.9920.0910.0910.0000.0000.0000.000
83A92ASP-1-0.777-0.87234.399-0.081-0.0810.0000.0000.0000.000
84A93PRO00.022-0.00633.254-0.005-0.0050.0000.0000.0000.000
85A94GLN00.0270.00832.969-0.003-0.0030.0000.0000.0000.000
86A95ASP-1-0.761-0.84527.692-0.107-0.1070.0000.0000.0000.000
87A96GLU-1-0.906-0.95130.242-0.048-0.0480.0000.0000.0000.000
88A97ASP-1-0.948-0.96932.844-0.028-0.0280.0000.0000.0000.000
89A98ARG10.8300.94025.9700.0560.0560.0000.0000.0000.000
90A117ARG10.9810.98942.7430.0600.0600.0000.0000.0000.000
91A118PRO0-0.018-0.01741.2380.0000.0000.0000.0000.0000.000
92A119LYS10.8280.89437.5430.0820.0820.0000.0000.0000.000
93A120TYR0-0.057-0.04332.649-0.001-0.0010.0000.0000.0000.000
94A121GLN0-0.012-0.00734.150-0.013-0.0130.0000.0000.0000.000
95A122VAL0-0.014-0.00630.423-0.008-0.0080.0000.0000.0000.000
96A123TYR0-0.011-0.01222.8990.0030.0030.0000.0000.0000.000
97A124ARG10.7890.86325.2820.1310.1310.0000.0000.0000.000
98A125ARG10.8660.93916.1740.5540.5540.0000.0000.0000.000
99A126VAL0-0.002-0.01018.9510.0340.0340.0000.0000.0000.000
100A127LEU0-0.0130.00714.363-0.057-0.0570.0000.0000.0000.000
101A128VAL00.0170.01214.3870.0780.0780.0000.0000.0000.000
102A129GLY00.015-0.01211.734-0.131-0.1310.0000.0000.0000.000
103A130ALA00.008-0.00210.6390.1240.1240.0000.0000.0000.000
104A131ARG10.7820.9037.9361.0351.0350.0000.0000.0000.000
105A132VAL00.0230.00513.519-0.086-0.0860.0000.0000.0000.000
106A133GLU-1-0.851-0.91214.7860.0570.0570.0000.0000.0000.000
107A134ARG10.7920.87612.0930.2020.2020.0000.0000.0000.000
108A135GLY00.0000.00817.592-0.050-0.0500.0000.0000.0000.000
109A136GLU-1-0.817-0.91011.820-0.447-0.4470.0000.0000.0000.000
110A137LEU0-0.030-0.02016.0440.0860.0860.0000.0000.0000.000
111A138LEU00.0220.00913.971-0.024-0.0240.0000.0000.0000.000
112A139GLN0-0.044-0.02916.5110.0060.0060.0000.0000.0000.000
113A140TYR0-0.017-0.03219.468-0.022-0.0220.0000.0000.0000.000
114A141THR00.0020.00821.7090.0090.0090.0000.0000.0000.000
115A142VAL00.0020.01223.071-0.008-0.0080.0000.0000.0000.000
116A143PRO00.0130.00725.7480.0110.0110.0000.0000.0000.000
117A144GLY00.0400.02329.607-0.016-0.0160.0000.0000.0000.000
118A145GLY0-0.049-0.02831.7470.0010.0010.0000.0000.0000.000
119A146ALA0-0.028-0.00128.624-0.007-0.0070.0000.0000.0000.000
120A147ILE0-0.021-0.00528.565-0.001-0.0010.0000.0000.0000.000
121A148PHE0-0.037-0.02222.762-0.011-0.0110.0000.0000.0000.000
122A149GLY00.0750.04222.1150.0050.0050.0000.0000.0000.000
123A150SER0-0.006-0.00616.845-0.012-0.0120.0000.0000.0000.000
124A151SER00.0370.00315.806-0.024-0.0240.0000.0000.0000.000
125A152VAL00.015-0.0019.2170.0580.0580.0000.0000.0000.000
126A153ALA00.0100.01811.7450.0730.0730.0000.0000.0000.000
127A154ALA0-0.003-0.01710.466-0.317-0.3170.0000.0000.0000.000
128A155ASP-1-0.925-0.95810.375-1.569-1.5690.0000.0000.0000.000
129A156GLY00.0340.01911.3230.1070.1070.0000.0000.0000.000
130A157ALA0-0.047-0.03810.118-0.267-0.2670.0000.0000.0000.000
131A158ASP-1-0.840-0.9229.803-0.975-0.9750.0000.0000.0000.000
132A159GLY00.0040.0068.4640.0500.0500.0000.0000.0000.000
133A160GLN0-0.061-0.0345.2510.6950.6950.0000.0000.0000.000
134A161ALA0-0.084-0.0472.339-4.873-3.8870.926-0.647-1.2660.000
135A162GLY00.0240.0193.2561.3481.1290.0150.325-0.1210.000
136A163TYR0-0.066-0.0473.6360.6501.1710.008-0.203-0.3260.001
137A164SER0-0.012-0.0066.840-0.248-0.2480.0000.0000.0000.000
138A165LEU0-0.030-0.0149.0490.0610.0610.0000.0000.0000.000
139A166VAL00.0500.01510.6490.1520.1520.0000.0000.0000.000
140A167SER0-0.002-0.00813.8540.0430.0430.0000.0000.0000.000
141A168CYS0-0.0300.00817.406-0.013-0.0130.0000.0000.0000.000
142A169ILE00.001-0.01820.5680.0260.0260.0000.0000.0000.000
143A170VAL00.0160.02824.084-0.006-0.0060.0000.0000.0000.000
144A171SER0-0.043-0.04927.2060.0200.0200.0000.0000.0000.000
145A172PRO00.0300.01230.3530.0000.0000.0000.0000.0000.000
146A173GLY0-0.061-0.01430.442-0.006-0.0060.0000.0000.0000.000
147A174PHE00.0310.00428.076-0.006-0.0060.0000.0000.0000.000
148A175ASP-1-0.822-0.90430.212-0.057-0.0570.0000.0000.0000.000
149A176TYR00.0240.00726.545-0.011-0.0110.0000.0000.0000.000
150A177ARG10.7700.86132.1920.0530.0530.0000.0000.0000.000
151A178ASP-1-0.756-0.83233.166-0.070-0.0700.0000.0000.0000.000
152A179PHE0-0.045-0.02026.001-0.005-0.0050.0000.0000.0000.000
153A180GLU-1-0.836-0.89431.213-0.147-0.1470.0000.0000.0000.000
154A181ILE0-0.019-0.01726.638-0.012-0.0120.0000.0000.0000.000
155A182PHE0-0.026-0.01129.3730.0110.0110.0000.0000.0000.000
156A183THR0-0.002-0.01329.740-0.019-0.0190.0000.0000.0000.000
157A184GLN0-0.010-0.01727.6900.0260.0260.0000.0000.0000.000
158A185ALA00.0330.01032.0700.0120.0120.0000.0000.0000.000
159A186GLN00.0230.01834.3800.0000.0000.0000.0000.0000.000
160A187LEU00.0080.00130.4950.0110.0110.0000.0000.0000.000
161A188MET0-0.039-0.00634.2110.0030.0030.0000.0000.0000.000
162A189GLU-1-0.927-0.95336.346-0.150-0.1500.0000.0000.0000.000
163A190LEU0-0.095-0.04037.3110.0120.0120.0000.0000.0000.000
164A191TYR0-0.046-0.03434.1760.0090.0090.0000.0000.0000.000
165A192PRO00.0870.04034.717-0.014-0.0140.0000.0000.0000.000
166A193GLN0-0.023-0.01334.507-0.009-0.0090.0000.0000.0000.000
167A194HIS0-0.035-0.01930.448-0.017-0.0170.0000.0000.0000.000
168A195GLU-1-0.791-0.89230.252-0.274-0.2740.0000.0000.0000.000
169A196ALA0-0.016-0.01027.786-0.018-0.0180.0000.0000.0000.000
170A197VAL00.0040.00324.436-0.034-0.0340.0000.0000.0000.000
171A198ILE00.002-0.00726.268-0.021-0.0210.0000.0000.0000.000
172A199LYS10.8420.89727.9680.2550.2550.0000.0000.0000.000
173A200GLN0-0.067-0.00621.293-0.057-0.0570.0000.0000.0000.000
174A201MET0-0.0130.00519.697-0.059-0.0590.0000.0000.0000.000
175A202ALA0-0.0140.00824.1620.0070.0070.0000.0000.0000.000
176A203TYR0-0.037-0.02624.606-0.037-0.0370.0000.0000.0000.000
177A204GLU-1-0.917-0.95828.063-0.256-0.2560.0000.0000.0000.000