FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 89N6Y

Calculation Name: 4M9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M9C

Chain ID: A

ChEMBL ID:

UniProt ID: B0V6J7

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:

Apendix: None


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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2342513.718414
FMO2-HF: Nuclear repulsion 2261898.051037
FMO2-HF: Total energy -80615.667377
FMO2-MP2: Total energy -80850.36318


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.
-9.414-2.2472.492-3.74-5.918-0.023
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 : 0.003 / q_NPA : -0.016
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].
3A3MET0-0.013-0.0013.838-0.1322.238-0.010-1.145-1.214-0.003
4A4ILE0-0.0160.0034.2980.3340.5440.001-0.054-0.1570.000
5A5ILE00.0250.0036.557-0.431-0.4310.0000.0000.0000.000
6A6GLY0-0.003-0.00610.1320.0920.0920.0000.0000.0000.000
7A7VAL0-0.010-0.01712.824-0.130-0.1300.0000.0000.0000.000
8A8TYR00.0210.00116.2280.0190.0190.0000.0000.0000.000
9A9GLY00.0140.00418.705-0.061-0.0610.0000.0000.0000.000
10A10ALA00.0150.02220.237-0.009-0.0090.0000.0000.0000.000
11A11SER0-0.015-0.01921.377-0.037-0.0370.0000.0000.0000.000
12A12GLY0-0.017-0.01424.6280.0050.0050.0000.0000.0000.000
13A13PHE00.007-0.00225.484-0.005-0.0050.0000.0000.0000.000
14A14GLY00.1060.06621.349-0.005-0.0050.0000.0000.0000.000
15A15LYS10.8840.92520.541-0.191-0.1910.0000.0000.0000.000
16A16GLU-1-0.875-0.93422.0930.0990.0990.0000.0000.0000.000
17A17VAL00.0440.00518.909-0.014-0.0140.0000.0000.0000.000
18A18MET0-0.0160.01713.864-0.030-0.0300.0000.0000.0000.000
19A19PRO0-0.039-0.02716.982-0.016-0.0160.0000.0000.0000.000
20A20LEU00.0170.01618.953-0.032-0.0320.0000.0000.0000.000
21A21VAL00.0590.02514.468-0.027-0.0270.0000.0000.0000.000
22A22ARG10.8510.92112.936-0.039-0.0390.0000.0000.0000.000
23A23GLN0-0.031-0.02415.329-0.067-0.0670.0000.0000.0000.000
24A24GLN00.0120.02516.720-0.012-0.0120.0000.0000.0000.000
25A25PHE0-0.039-0.02312.406-0.027-0.0270.0000.0000.0000.000
26A26PRO00.0300.01612.847-0.024-0.0240.0000.0000.0000.000
27A27THR0-0.066-0.03912.154-0.008-0.0080.0000.0000.0000.000
28A28LEU0-0.0100.0197.242-0.156-0.1560.0000.0000.0000.000
29A29SER00.008-0.0027.3080.1110.1110.0000.0000.0000.000
30A30LYS10.8600.9328.423-0.005-0.0050.0000.0000.0000.000
31A31GLU-1-0.879-0.9486.702-0.023-0.0230.0000.0000.0000.000
32A32GLN0-0.027-0.0033.8080.1330.3350.000-0.026-0.1760.000
33A33PHE0-0.011-0.0026.1940.2860.2860.0000.0000.0000.000
34A34ALA00.011-0.0049.7610.0090.0090.0000.0000.0000.000
35A35PHE0-0.049-0.01412.085-0.070-0.0700.0000.0000.0000.000
36A36ILE00.0160.02013.7550.0720.0720.0000.0000.0000.000
37A37ASP-1-0.873-0.97916.5400.2810.2810.0000.0000.0000.000
38A38ASP-1-0.803-0.91019.9030.5360.5360.0000.0000.0000.000
39A39GLY0-0.041-0.00821.403-0.005-0.0050.0000.0000.0000.000
40A40LEU0-0.079-0.04521.583-0.020-0.0200.0000.0000.0000.000
41A41SER00.0200.00618.4580.0390.0390.0000.0000.0000.000
42A42GLY00.0060.01117.429-0.043-0.0430.0000.0000.0000.000
43A43THR0-0.0330.00518.355-0.039-0.0390.0000.0000.0000.000
44A44THR0-0.039-0.02916.5680.0450.0450.0000.0000.0000.000
45A45LEU00.013-0.00417.803-0.051-0.0510.0000.0000.0000.000
46A46ASN00.004-0.00418.0680.0100.0100.0000.0000.0000.000
47A47GLY00.0240.00417.358-0.022-0.0220.0000.0000.0000.000
48A48TYR0-0.0090.00612.604-0.038-0.0380.0000.0000.0000.000
49A49PRO00.0670.03310.755-0.066-0.0660.0000.0000.0000.000
50A50VAL0-0.019-0.00214.0200.0240.0240.0000.0000.0000.000
51A51LEU0-0.024-0.01610.4080.0400.0400.0000.0000.0000.000
52A52SER00.0510.03515.088-0.055-0.0550.0000.0000.0000.000
53A53TYR00.001-0.02415.4700.1410.1410.0000.0000.0000.000
54A54LEU00.0250.00514.9350.1110.1110.0000.0000.0000.000
55A55ASP-1-0.847-0.92013.1441.0501.0500.0000.0000.0000.000
56A56PHE0-0.041-0.03010.2150.3680.3680.0000.0000.0000.000
57A57ILE00.010-0.00410.0460.4140.4140.0000.0000.0000.000
58A58SER0-0.081-0.03710.6460.1590.1590.0000.0000.0000.000
59A59LYS10.9110.9666.313-1.941-1.9410.0000.0000.0000.000
60A60PRO0-0.0150.0043.671-1.225-0.6090.105-0.170-0.5500.001
61A61ALA00.016-0.0332.6051.5413.7910.870-1.315-1.805-0.005
62A62ASP-1-0.931-0.9412.703-8.582-7.1631.527-1.022-1.924-0.016
63A63HIS0-0.019-0.0055.1490.1750.275-0.001-0.008-0.0920.000
64A64LYS10.9060.9696.771-1.823-1.8230.0000.0000.0000.000
65A65ALA00.0390.0249.185-0.280-0.2800.0000.0000.0000.000
66A66VAL00.0080.00412.2740.1300.1300.0000.0000.0000.000
67A67THR0-0.0060.02114.994-0.092-0.0920.0000.0000.0000.000
68A68ILE00.018-0.00417.8570.0440.0440.0000.0000.0000.000
69A69ALA00.0320.01920.643-0.037-0.0370.0000.0000.0000.000
70A70ILE0-0.049-0.02522.325-0.032-0.0320.0000.0000.0000.000
71A71ALA00.0930.04525.167-0.008-0.0080.0000.0000.0000.000
72A72ASN0-0.031-0.01528.506-0.014-0.0140.0000.0000.0000.000
73A73SER00.0880.02128.9040.0150.0150.0000.0000.0000.000
74A74VAL00.0300.02629.8820.0060.0060.0000.0000.0000.000
75A75VAL0-0.027-0.02325.9800.0080.0080.0000.0000.0000.000
76A76ARG10.8050.90424.732-0.139-0.1390.0000.0000.0000.000
77A77GLU-1-0.854-0.93725.1000.1630.1630.0000.0000.0000.000
78A78LYS10.8870.94126.271-0.173-0.1730.0000.0000.0000.000
79A79LEU0-0.0010.00021.7340.0150.0150.0000.0000.0000.000
80A80VAL00.0150.02221.4170.0360.0360.0000.0000.0000.000
81A81SER0-0.015-0.00321.8330.0050.0050.0000.0000.0000.000
82A82LEU0-0.068-0.03219.8950.0030.0030.0000.0000.0000.000
83A83LEU0-0.002-0.01716.1190.0370.0370.0000.0000.0000.000
84A84GLU-1-0.840-0.91517.6550.2430.2430.0000.0000.0000.000
85A85LYS10.8040.91818.239-0.510-0.5100.0000.0000.0000.000
86A86ASP-1-0.880-0.94114.8430.6310.6310.0000.0000.0000.000
87A87GLY00.0050.01414.6490.0680.0680.0000.0000.0000.000
88A88VAL0-0.071-0.02912.8130.0290.0290.0000.0000.0000.000
89A89GLN00.0310.02413.279-0.073-0.0730.0000.0000.0000.000
90A90HIS0-0.023-0.02515.1610.0880.0880.0000.0000.0000.000
91A91LEU0-0.056-0.03013.277-0.059-0.0590.0000.0000.0000.000
92A92ALA0-0.0140.00117.6110.0100.0100.0000.0000.0000.000
93A93VAL0-0.048-0.02818.294-0.011-0.0110.0000.0000.0000.000
94A94GLN00.0370.02520.872-0.011-0.0110.0000.0000.0000.000
95A95SER00.007-0.00122.6010.0070.0070.0000.0000.0000.000
96A96THR00.020-0.00224.344-0.008-0.0080.0000.0000.0000.000
97A97ASN0-0.0230.00225.887-0.001-0.0010.0000.0000.0000.000
98A98THR0-0.0060.00927.7390.0040.0040.0000.0000.0000.000
99A99VAL0-0.0140.00029.629-0.009-0.0090.0000.0000.0000.000
100A100ILE0-0.007-0.01828.4610.0100.0100.0000.0000.0000.000
101A101LEU0-0.067-0.02332.725-0.007-0.0070.0000.0000.0000.000
102A102ASP-1-0.878-0.92534.835-0.035-0.0350.0000.0000.0000.000
103A103GLU-1-0.957-0.97436.220-0.021-0.0210.0000.0000.0000.000
104A104VAL0-0.028-0.01132.2120.0070.0070.0000.0000.0000.000
105A105GLU-1-0.923-0.95831.9260.0050.0050.0000.0000.0000.000
106A106ILE0-0.033-0.03027.5290.0090.0090.0000.0000.0000.000
107A107GLY0-0.0190.00127.869-0.006-0.0060.0000.0000.0000.000
108A108GLU-1-0.884-0.95622.1070.1250.1250.0000.0000.0000.000
109A109GLY00.0270.00721.6220.0100.0100.0000.0000.0000.000
110A110SER0-0.032-0.00422.6660.0100.0100.0000.0000.0000.000
111A111LEU00.0130.00121.8960.0070.0070.0000.0000.0000.000
112A112LEU0-0.022-0.01324.442-0.002-0.0020.0000.0000.0000.000
113A113CYS0-0.0120.01425.787-0.004-0.0040.0000.0000.0000.000
114A114PRO00.0300.02826.102-0.011-0.0110.0000.0000.0000.000
115A115PHE0-0.020-0.04228.8150.0040.0040.0000.0000.0000.000
116A116THR0-0.018-0.01129.407-0.001-0.0010.0000.0000.0000.000
117A117CYS0-0.059-0.03232.168-0.009-0.0090.0000.0000.0000.000
118A118LEU00.0100.00830.9010.0070.0070.0000.0000.0000.000
119A119THR00.0310.00034.728-0.005-0.0050.0000.0000.0000.000
120A120SER00.0890.02636.850-0.003-0.0030.0000.0000.0000.000
121A121ASN0-0.009-0.00938.4880.0030.0030.0000.0000.0000.000
122A122ILE0-0.0450.00035.0230.0050.0050.0000.0000.0000.000
123A123LYS10.9330.99533.620-0.046-0.0460.0000.0000.0000.000
124A124ILE0-0.012-0.02330.4860.0060.0060.0000.0000.0000.000
125A125GLY0-0.032-0.00531.488-0.004-0.0040.0000.0000.0000.000
126A126LYS10.9130.95926.140-0.103-0.1030.0000.0000.0000.000
127A127PHE00.004-0.01021.6210.0010.0010.0000.0000.0000.000
128A128PHE00.0490.03126.4270.0060.0060.0000.0000.0000.000
129A129HIS0-0.004-0.00724.042-0.004-0.0040.0000.0000.0000.000
130A130ALA00.0290.02728.310-0.005-0.0050.0000.0000.0000.000
131A131ASN00.0550.01628.684-0.008-0.0080.0000.0000.0000.000
132A132ILE00.0250.00729.434-0.010-0.0100.0000.0000.0000.000
133A133TYR0-0.021-0.02131.5850.0030.0030.0000.0000.0000.000
134A134SER0-0.096-0.02932.541-0.003-0.0030.0000.0000.0000.000
135A135TYR0-0.025-0.05134.334-0.003-0.0030.0000.0000.0000.000
136A136VAL00.011-0.00234.7960.0050.0050.0000.0000.0000.000
137A137ALA0-0.013-0.00737.347-0.005-0.0050.0000.0000.0000.000
138A138HIS0-0.038-0.05140.0050.0030.0030.0000.0000.0000.000
139A139ASP-1-0.806-0.88241.4050.0070.0070.0000.0000.0000.000
140A140CYS0-0.098-0.01539.0980.0040.0040.0000.0000.0000.000
141A141VAL00.0200.00938.224-0.002-0.0020.0000.0000.0000.000
142A142ILE0-0.030-0.02334.0600.0040.0040.0000.0000.0000.000
143A143GLY00.0050.00234.859-0.002-0.0020.0000.0000.0000.000
144A144ASP-1-0.823-0.91930.5790.0870.0870.0000.0000.0000.000
145A145TYR0-0.009-0.01225.857-0.002-0.0020.0000.0000.0000.000
146A146VAL00.0100.02430.6680.0010.0010.0000.0000.0000.000
147A147THR0-0.035-0.02530.8400.0060.0060.0000.0000.0000.000
148A148PHE0-0.017-0.01132.041-0.006-0.0060.0000.0000.0000.000
149A149ALA0-0.005-0.00532.3500.0050.0050.0000.0000.0000.000
150A150PRO00.0370.00532.246-0.006-0.0060.0000.0000.0000.000
151A151GLY00.0060.00034.407-0.001-0.0010.0000.0000.0000.000
152A152ALA0-0.058-0.00536.318-0.004-0.0040.0000.0000.0000.000
153A153LYS10.9490.97237.702-0.033-0.0330.0000.0000.0000.000
154A154CYS00.0000.01638.7640.0010.0010.0000.0000.0000.000
155A155ASN0-0.0160.00040.631-0.006-0.0060.0000.0000.0000.000
156A156GLY00.1050.05042.8190.0010.0010.0000.0000.0000.000
157A157ASN0-0.0090.00244.1680.0020.0020.0000.0000.0000.000
158A158ILE0-0.017-0.02942.0260.0020.0020.0000.0000.0000.000
159A159HIS00.0430.02041.3670.0010.0010.0000.0000.0000.000
160A160ILE0-0.037-0.02837.6940.0020.0020.0000.0000.0000.000
161A161GLU-1-0.861-0.94438.1410.0560.0560.0000.0000.0000.000
162A162ASP-1-0.828-0.93135.1860.0860.0860.0000.0000.0000.000
163A163HIS0-0.056-0.03131.393-0.006-0.0060.0000.0000.0000.000
164A164ALA0-0.0090.03135.1270.0020.0020.0000.0000.0000.000
165A165TYR00.0020.00133.5650.0020.0020.0000.0000.0000.000
166A166ILE0-0.020-0.01536.306-0.006-0.0060.0000.0000.0000.000
167A167GLY00.0460.01636.8740.0030.0030.0000.0000.0000.000
168A168THR0-0.042-0.02536.770-0.005-0.0050.0000.0000.0000.000
169A169GLY00.0360.00238.324-0.002-0.0020.0000.0000.0000.000
170A170ALA0-0.0470.00140.562-0.004-0.0040.0000.0000.0000.000
171A171VAL0-0.001-0.00741.734-0.002-0.0020.0000.0000.0000.000
172A172ILE0-0.0060.00041.2200.0010.0010.0000.0000.0000.000
173A173LYS10.9290.96445.034-0.025-0.0250.0000.0000.0000.000
174A174GLN00.0050.01246.7790.0020.0020.0000.0000.0000.000
175A175GLY00.0040.00447.3540.0010.0010.0000.0000.0000.000
176A176THR0-0.076-0.04949.177-0.002-0.0020.0000.0000.0000.000
177A177PRO00.0620.01249.0130.0020.0020.0000.0000.0000.000
178A178ASP-1-0.873-0.91350.1010.0110.0110.0000.0000.0000.000
179A179LYS10.8090.90950.537-0.026-0.0260.0000.0000.0000.000
180A180PRO00.0710.05346.3950.0000.0000.0000.0000.0000.000
181A181LEU0-0.096-0.04045.7370.0020.0020.0000.0000.0000.000
182A182ILE00.002-0.00844.3420.0010.0010.0000.0000.0000.000
183A183ILE0-0.028-0.01041.1220.0000.0000.0000.0000.0000.000
184A184GLY00.0450.01542.1210.0020.0020.0000.0000.0000.000
185A185LYS10.9990.99836.770-0.090-0.0900.0000.0000.0000.000
186A186GLY0-0.016-0.01338.2880.0000.0000.0000.0000.0000.000
187A187ALA0-0.068-0.00739.2990.0010.0010.0000.0000.0000.000
188A188ILE00.007-0.00139.2370.0040.0040.0000.0000.0000.000
189A189VAL0-0.020-0.01240.636-0.005-0.0050.0000.0000.0000.000
190A190GLY00.0150.00540.9850.0030.0030.0000.0000.0000.000
191A191MET00.009-0.01340.549-0.002-0.0020.0000.0000.0000.000
192A192GLY0-0.027-0.00841.972-0.002-0.0020.0000.0000.0000.000
193A193ALA0-0.071-0.01944.343-0.003-0.0030.0000.0000.0000.000
194A194VAL00.0150.00945.598-0.001-0.0010.0000.0000.0000.000
195A195VAL00.016-0.00245.007-0.001-0.0010.0000.0000.0000.000
196A196THR0-0.020-0.01748.054-0.002-0.0020.0000.0000.0000.000
197A197LYS10.9580.97150.150-0.038-0.0380.0000.0000.0000.000
198A198SER00.0580.02048.0710.0010.0010.0000.0000.0000.000
199A199VAL0-0.043-0.00345.401-0.001-0.0010.0000.0000.0000.000
200A200PRO0-0.005-0.00646.3440.0010.0010.0000.0000.0000.000
201A201ALA00.0670.02543.6780.0020.0020.0000.0000.0000.000
202A202GLY0-0.0080.00342.754-0.001-0.0010.0000.0000.0000.000
203A203VAL0-0.078-0.01143.7840.0000.0000.0000.0000.0000.000
204A204THR00.0920.04643.4330.0000.0000.0000.0000.0000.000
205A205VAL0-0.018-0.01345.178-0.004-0.0040.0000.0000.0000.000
206A206VAL00.0570.02345.7070.0020.0020.0000.0000.0000.000
207A207GLY00.0200.01047.771-0.002-0.0020.0000.0000.0000.000
208A208ASN00.0150.03349.561-0.001-0.0010.0000.0000.0000.000
209A209PRO00.0510.00751.857-0.001-0.0010.0000.0000.0000.000
210A210ALA00.0030.00848.5200.0010.0010.0000.0000.0000.000
211A211ARG10.8260.90750.391-0.043-0.0430.0000.0000.0000.000
212A212ILE00.020-0.00249.7800.0020.0020.0000.0000.0000.000
213A213LEU0-0.037-0.00847.491-0.003-0.0030.0000.0000.0000.000
214A214GLU-1-0.929-0.95845.1630.0780.0780.0000.0000.0000.000
215A215ARG10.9280.95047.724-0.052-0.0520.0000.0000.0000.000
216A216LYS10.9861.00248.006-0.060-0.0600.0000.0000.0000.000