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: JQ2R9

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 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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2345664.540991
FMO2-HF: Nuclear repulsion 2265047.828557
FMO2-HF: Total energy -80616.712434
FMO2-MP2: Total energy -80851.468043


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.
-12.181-4.9869.12-6.066-10.249-0.031
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 : 0.033 / 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].
3A3MET0-0.038-0.0133.789-1.0132.290-0.008-1.800-1.4950.003
4A4ILE0-0.0210.0033.019-1.749-1.3340.034-0.132-0.317-0.001
5A5ILE00.0200.0045.6570.4530.4530.0000.0000.0000.000
6A6GLY00.0150.0089.3790.1080.1080.0000.0000.0000.000
7A7VAL0-0.017-0.01812.013-0.035-0.0350.0000.0000.0000.000
8A8TYR0-0.007-0.03015.5520.0450.0450.0000.0000.0000.000
9A9GLY0-0.022-0.01217.822-0.021-0.0210.0000.0000.0000.000
10A10ALA00.0100.01118.846-0.027-0.0270.0000.0000.0000.000
11A11SER0-0.045-0.03420.136-0.018-0.0180.0000.0000.0000.000
12A12GLY0-0.020-0.01523.532-0.012-0.0120.0000.0000.0000.000
13A13PHE00.012-0.00224.6370.0030.0030.0000.0000.0000.000
14A14GLY00.0820.05720.503-0.020-0.0200.0000.0000.0000.000
15A15LYS10.8640.91619.878-0.031-0.0310.0000.0000.0000.000
16A16GLU-1-0.813-0.88221.666-0.105-0.1050.0000.0000.0000.000
17A17VAL00.0480.00318.348-0.021-0.0210.0000.0000.0000.000
18A18MET0-0.0010.02613.331-0.065-0.0650.0000.0000.0000.000
19A19PRO0-0.021-0.02116.754-0.053-0.0530.0000.0000.0000.000
20A20LEU0-0.0050.02419.044-0.024-0.0240.0000.0000.0000.000
21A21VAL00.0500.01514.088-0.036-0.0360.0000.0000.0000.000
22A22ARG10.8290.91512.2670.5050.5050.0000.0000.0000.000
23A23GLN0-0.044-0.04115.433-0.035-0.0350.0000.0000.0000.000
24A24GLN00.0010.01616.5510.0250.0250.0000.0000.0000.000
25A25PHE0-0.003-0.00812.593-0.030-0.0300.0000.0000.0000.000
26A26PRO00.0220.01312.835-0.107-0.1070.0000.0000.0000.000
27A27THR0-0.053-0.03212.4400.0140.0140.0000.0000.0000.000
28A28LEU0-0.0020.0277.536-0.138-0.1380.0000.0000.0000.000
29A29SER0-0.004-0.0257.3250.1360.1360.0000.0000.0000.000
30A30LYS10.8030.8978.8680.0400.0400.0000.0000.0000.000
31A31GLU-1-0.840-0.9216.798-0.414-0.4140.0000.0000.0000.000
32A32GLN0-0.0200.0054.0980.7290.913-0.001-0.025-0.1580.000
33A33PHE00.0010.0036.0940.0550.0550.0000.0000.0000.000
34A34ALA00.013-0.0029.4030.1660.1660.0000.0000.0000.000
35A35PHE0-0.038-0.02311.398-0.065-0.0650.0000.0000.0000.000
36A36ILE00.0080.01512.7940.0710.0710.0000.0000.0000.000
37A37ASP-1-0.780-0.92315.7120.0620.0620.0000.0000.0000.000
38A38ASP-1-0.757-0.86619.1480.2860.2860.0000.0000.0000.000
39A39GLY0-0.0300.00020.2990.0180.0180.0000.0000.0000.000
40A40LEU0-0.041-0.03020.619-0.009-0.0090.0000.0000.0000.000
41A41SER0-0.018-0.00517.3360.0200.0200.0000.0000.0000.000
42A42GLY00.0240.01616.777-0.001-0.0010.0000.0000.0000.000
43A43THR0-0.027-0.00117.711-0.006-0.0060.0000.0000.0000.000
44A44THR0-0.039-0.02515.7020.0140.0140.0000.0000.0000.000
45A45LEU00.0090.00317.350-0.018-0.0180.0000.0000.0000.000
46A46ASN00.010-0.00817.726-0.003-0.0030.0000.0000.0000.000
47A47GLY00.0550.03017.394-0.035-0.0350.0000.0000.0000.000
48A48TYR00.0130.01212.199-0.039-0.0390.0000.0000.0000.000
49A49PRO00.0690.02010.1340.0210.0210.0000.0000.0000.000
50A50VAL0-0.0240.00213.377-0.082-0.0820.0000.0000.0000.000
51A51LEU0-0.0200.0029.9250.0800.0800.0000.0000.0000.000
52A52SER00.032-0.00614.601-0.070-0.0700.0000.0000.0000.000
53A53TYR0-0.013-0.05214.5140.0530.0530.0000.0000.0000.000
54A54LEU00.0160.00214.2380.0580.0580.0000.0000.0000.000
55A55ASP-1-0.809-0.86812.5860.9350.9350.0000.0000.0000.000
56A56PHE00.0150.0098.8700.3260.3260.0000.0000.0000.000
57A57ILE00.0190.0079.3230.1890.1890.0000.0000.0000.000
58A58SER0-0.073-0.05410.0110.2710.2710.0000.0000.0000.000
59A59LYS10.7990.9036.050-1.042-1.0420.0000.0000.0000.000
60A60PRO00.0080.0043.007-2.029-1.4031.366-0.505-1.4860.006
61A61ALA00.026-0.0132.1290.1322.2355.062-3.521-3.645-0.014
62A62ASP-1-0.883-0.9302.502-7.610-7.1862.668-0.066-3.026-0.025
63A63HIS0-0.032-0.0094.9030.2090.349-0.001-0.017-0.1220.000
64A64LYS10.8330.9236.156-2.035-2.0350.0000.0000.0000.000
65A65ALA00.0350.0228.7550.0410.0410.0000.0000.0000.000
66A66VAL00.000-0.00411.2180.0160.0160.0000.0000.0000.000
67A67THR00.0130.02913.9940.0020.0020.0000.0000.0000.000
68A68ILE00.011-0.00217.0260.0360.0360.0000.0000.0000.000
69A69ALA00.0200.01719.857-0.008-0.0080.0000.0000.0000.000
70A70ILE0-0.020-0.02021.7810.0060.0060.0000.0000.0000.000
71A71ALA00.0810.04024.294-0.002-0.0020.0000.0000.0000.000
72A72ASN0-0.058-0.01627.460-0.004-0.0040.0000.0000.0000.000
73A73SER00.0650.04227.8020.0060.0060.0000.0000.0000.000
74A74VAL00.0460.01728.7210.0020.0020.0000.0000.0000.000
75A75VAL0-0.009-0.00925.0860.0070.0070.0000.0000.0000.000
76A76ARG10.8110.90723.4650.0630.0630.0000.0000.0000.000
77A77GLU-1-0.760-0.85924.0910.0040.0040.0000.0000.0000.000
78A78LYS10.7690.87525.493-0.027-0.0270.0000.0000.0000.000
79A79LEU0-0.009-0.00220.7000.0130.0130.0000.0000.0000.000
80A80VAL00.0290.02020.5330.0100.0100.0000.0000.0000.000
81A81SER0-0.037-0.03521.3910.0020.0020.0000.0000.0000.000
82A82LEU0-0.067-0.02419.1580.0120.0120.0000.0000.0000.000
83A83LEU00.0230.00215.5100.0280.0280.0000.0000.0000.000
84A84GLU-1-0.854-0.91517.264-0.051-0.0510.0000.0000.0000.000
85A85LYS10.7450.86617.812-0.273-0.2730.0000.0000.0000.000
86A86ASP-1-0.834-0.88914.3230.3900.3900.0000.0000.0000.000
87A87GLY00.0120.01814.1400.0230.0230.0000.0000.0000.000
88A88VAL0-0.062-0.02112.216-0.053-0.0530.0000.0000.0000.000
89A89GLN00.0230.01212.896-0.082-0.0820.0000.0000.0000.000
90A90HIS00.006-0.01914.615-0.032-0.0320.0000.0000.0000.000
91A91LEU0-0.053-0.02812.424-0.042-0.0420.0000.0000.0000.000
92A92ALA0-0.018-0.00416.8990.0420.0420.0000.0000.0000.000
93A93VAL0-0.056-0.03617.912-0.042-0.0420.0000.0000.0000.000
94A94GLN00.0130.01320.6100.0200.0200.0000.0000.0000.000
95A95SER00.0330.00022.551-0.010-0.0100.0000.0000.0000.000
96A96THR0-0.021-0.01524.178-0.001-0.0010.0000.0000.0000.000
97A97ASN0-0.015-0.00426.0230.0000.0000.0000.0000.0000.000
98A98THR0-0.0170.00327.6110.0080.0080.0000.0000.0000.000
99A99VAL0-0.024-0.01129.488-0.007-0.0070.0000.0000.0000.000
100A100ILE00.012-0.00628.0320.0050.0050.0000.0000.0000.000
101A101LEU0-0.038-0.00132.494-0.004-0.0040.0000.0000.0000.000
102A102ASP-1-0.823-0.88934.510-0.122-0.1220.0000.0000.0000.000
103A103GLU-1-0.926-0.96236.091-0.115-0.1150.0000.0000.0000.000
104A104VAL0-0.036-0.01331.9300.0080.0080.0000.0000.0000.000
105A105GLU-1-0.905-0.95131.418-0.122-0.1220.0000.0000.0000.000
106A106ILE0-0.021-0.02827.3100.0100.0100.0000.0000.0000.000
107A107GLY00.0230.02826.999-0.010-0.0100.0000.0000.0000.000
108A108GLU-1-0.880-0.95121.471-0.166-0.1660.0000.0000.0000.000
109A109GLY00.0300.00020.3780.0240.0240.0000.0000.0000.000
110A110SER0-0.043-0.01321.3740.0130.0130.0000.0000.0000.000
111A111LEU0-0.021-0.00921.576-0.023-0.0230.0000.0000.0000.000
112A112LEU0-0.007-0.00224.0820.0200.0200.0000.0000.0000.000
113A113CYS0-0.0170.01625.741-0.015-0.0150.0000.0000.0000.000
114A114PRO00.0470.02725.8810.0020.0020.0000.0000.0000.000
115A115PHE0-0.017-0.03328.6970.0130.0130.0000.0000.0000.000
116A116THR0-0.044-0.01429.0520.0050.0050.0000.0000.0000.000
117A117CYS0-0.024-0.01331.799-0.008-0.0080.0000.0000.0000.000
118A118LEU0-0.014-0.00130.5760.0090.0090.0000.0000.0000.000
119A119THR0-0.003-0.01734.447-0.002-0.0020.0000.0000.0000.000
120A120SER00.053-0.01036.409-0.006-0.0060.0000.0000.0000.000
121A121ASN0-0.055-0.03738.3390.0070.0070.0000.0000.0000.000
122A122ILE0-0.055-0.01334.5950.0070.0070.0000.0000.0000.000
123A123LYS10.8700.95332.8040.0830.0830.0000.0000.0000.000
124A124ILE0-0.002-0.00429.8470.0090.0090.0000.0000.0000.000
125A125GLY0-0.0030.01330.603-0.004-0.0040.0000.0000.0000.000
126A126LYS10.8720.91725.5580.0700.0700.0000.0000.0000.000
127A127PHE0-0.011-0.01320.9290.0190.0190.0000.0000.0000.000
128A128PHE00.0540.03725.3210.0140.0140.0000.0000.0000.000
129A129HIS0-0.012-0.01123.323-0.005-0.0050.0000.0000.0000.000
130A130ALA00.0280.02427.7970.0110.0110.0000.0000.0000.000
131A131ASN00.017-0.02127.415-0.006-0.0060.0000.0000.0000.000
132A132ILE00.0290.02229.2250.0000.0000.0000.0000.0000.000
133A133TYR0-0.021-0.01831.2640.0110.0110.0000.0000.0000.000
134A134SER0-0.087-0.03632.2540.0050.0050.0000.0000.0000.000
135A135TYR0-0.024-0.04834.192-0.006-0.0060.0000.0000.0000.000
136A136VAL0-0.010-0.00734.2790.0080.0080.0000.0000.0000.000
137A137ALA00.0100.00536.950-0.006-0.0060.0000.0000.0000.000
138A138HIS00.032-0.00539.5840.0010.0010.0000.0000.0000.000
139A139ASP-1-0.781-0.86541.386-0.064-0.0640.0000.0000.0000.000
140A140CYS0-0.084-0.01038.6950.0060.0060.0000.0000.0000.000
141A141VAL00.0150.00537.647-0.006-0.0060.0000.0000.0000.000
142A142ILE0-0.039-0.02133.5410.0070.0070.0000.0000.0000.000
143A143GLY00.0410.01634.224-0.006-0.0060.0000.0000.0000.000
144A144ASP-1-0.799-0.88329.713-0.077-0.0770.0000.0000.0000.000
145A145TYR0-0.016-0.01925.3750.0080.0080.0000.0000.0000.000
146A146VAL0-0.0280.00629.4220.0060.0060.0000.0000.0000.000
147A147THR0-0.033-0.02529.960-0.010-0.0100.0000.0000.0000.000
148A148PHE0-0.018-0.01331.4510.0080.0080.0000.0000.0000.000
149A149ALA00.0180.00831.685-0.005-0.0050.0000.0000.0000.000
150A150PRO00.0270.00831.860-0.003-0.0030.0000.0000.0000.000
151A151GLY00.0200.02233.8580.0080.0080.0000.0000.0000.000
152A152ALA0-0.0320.00935.7290.0010.0010.0000.0000.0000.000
153A153LYS10.8950.93737.2670.0540.0540.0000.0000.0000.000
154A154CYS00.0000.01938.2590.0060.0060.0000.0000.0000.000
155A155ASN0-0.019-0.00540.154-0.007-0.0070.0000.0000.0000.000
156A156GLY00.1180.05542.391-0.001-0.0010.0000.0000.0000.000
157A157ASN0-0.074-0.05143.6200.0060.0060.0000.0000.0000.000
158A158ILE0-0.049-0.04541.6930.0060.0060.0000.0000.0000.000
159A159HIS00.0330.01740.497-0.005-0.0050.0000.0000.0000.000
160A160ILE0-0.045-0.03136.9330.0050.0050.0000.0000.0000.000
161A161GLU-1-0.786-0.89337.049-0.033-0.0330.0000.0000.0000.000
162A162ASP-1-0.802-0.90233.450-0.040-0.0400.0000.0000.0000.000
163A163HIS0-0.050-0.05330.2790.0050.0050.0000.0000.0000.000
164A164ALA0-0.0220.02233.6670.0040.0040.0000.0000.0000.000
165A165TYR00.0030.00033.046-0.005-0.0050.0000.0000.0000.000
166A166ILE0-0.019-0.00835.5200.0030.0030.0000.0000.0000.000
167A167GLY00.0550.01536.032-0.003-0.0030.0000.0000.0000.000
168A168THR0-0.047-0.03836.080-0.002-0.0020.0000.0000.0000.000
169A169GLY00.021-0.01137.5920.0040.0040.0000.0000.0000.000
170A170ALA0-0.0520.00039.8890.0010.0010.0000.0000.0000.000
171A171VAL0-0.020-0.01740.921-0.005-0.0050.0000.0000.0000.000
172A172ILE00.0000.00539.8630.0050.0050.0000.0000.0000.000
173A173LYS10.9150.96844.1920.0300.0300.0000.0000.0000.000
174A174GLN0-0.005-0.00346.1430.0000.0000.0000.0000.0000.000
175A175GLY0-0.035-0.01046.8410.0040.0040.0000.0000.0000.000
176A176THR0-0.072-0.04748.563-0.001-0.0010.0000.0000.0000.000
177A177PRO00.0990.03248.4200.0010.0010.0000.0000.0000.000
178A178ASP-1-0.911-0.94149.394-0.042-0.0420.0000.0000.0000.000
179A179LYS10.7980.89349.4160.0360.0360.0000.0000.0000.000
180A180PRO00.0740.07045.4210.0000.0000.0000.0000.0000.000
181A181LEU0-0.078-0.02744.9190.0040.0040.0000.0000.0000.000
182A182ILE00.008-0.00243.534-0.002-0.0020.0000.0000.0000.000
183A183ILE0-0.024-0.01240.4560.0040.0040.0000.0000.0000.000
184A184GLY00.0700.03640.970-0.003-0.0030.0000.0000.0000.000
185A185LYS10.9000.92035.6600.0220.0220.0000.0000.0000.000
186A186GLY0-0.004-0.01236.8330.0050.0050.0000.0000.0000.000
187A187ALA0-0.069-0.00437.8450.0040.0040.0000.0000.0000.000
188A188ILE0-0.008-0.01338.106-0.003-0.0030.0000.0000.0000.000
189A189VAL0-0.003-0.00339.9440.0030.0030.0000.0000.0000.000
190A190GLY00.0340.01439.921-0.001-0.0010.0000.0000.0000.000
191A191MET00.005-0.01439.699-0.002-0.0020.0000.0000.0000.000
192A192GLY0-0.020-0.00541.2050.0030.0030.0000.0000.0000.000
193A193ALA0-0.064-0.01343.5600.0010.0010.0000.0000.0000.000
194A194VAL00.0130.00744.763-0.003-0.0030.0000.0000.0000.000
195A195VAL00.0270.00444.2390.0030.0030.0000.0000.0000.000
196A196THR00.011-0.00147.234-0.002-0.0020.0000.0000.0000.000
197A197LYS10.9380.96249.4010.0180.0180.0000.0000.0000.000
198A198SER00.0710.02347.301-0.001-0.0010.0000.0000.0000.000
199A199VAL0-0.051-0.01644.7050.0030.0030.0000.0000.0000.000
200A200PRO00.010-0.00245.279-0.002-0.0020.0000.0000.0000.000
201A201ALA00.0720.03742.477-0.001-0.0010.0000.0000.0000.000
202A202GLY0-0.0040.00541.6350.0020.0020.0000.0000.0000.000
203A203VAL0-0.093-0.02742.6490.0030.0030.0000.0000.0000.000
204A204THR00.038-0.00942.194-0.003-0.0030.0000.0000.0000.000
205A205VAL0-0.018-0.01344.0590.0000.0000.0000.0000.0000.000
206A206VAL00.0410.02244.642-0.001-0.0010.0000.0000.0000.000
207A207GLY00.0430.02046.8390.0000.0000.0000.0000.0000.000
208A208ASN00.0440.03648.690-0.002-0.0020.0000.0000.0000.000
209A209PRO00.0400.00350.9980.0010.0010.0000.0000.0000.000
210A210ALA0-0.0040.01047.5920.0020.0020.0000.0000.0000.000
211A211ARG10.8010.89849.4600.0140.0140.0000.0000.0000.000
212A212ILE00.0310.00648.4260.0000.0000.0000.0000.0000.000
213A213LEU0-0.0190.00746.0300.0010.0010.0000.0000.0000.000
214A214GLU-1-0.821-0.87444.4500.0060.0060.0000.0000.0000.000
215A215ARG10.8640.90846.659-0.001-0.0010.0000.0000.0000.000
216A216LYS10.9871.00546.732-0.009-0.0090.0000.0000.0000.000