FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 5NK2Z

Calculation Name: 4ME7-E-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ME7

Chain ID: E

ChEMBL ID:

UniProt ID: P96621

Base Structure: X-ray

Registration Date: 2025-07-10

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 153
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -386686.493433
FMO2-HF: Nuclear repulsion 353878.937329
FMO2-HF: Total energy -32807.556104
FMO2-MP2: Total energy -32898.635723


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(E:6:ALA)


Summations of interaction energy for fragment #1(E:6:ALA)
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.
-1.7240.456-0.028-0.992-1.1610
Interaction energy analysis for fragmet #1(E:6:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.190 / q_NPA : 0.053
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].
4E7ARG10.8531.0243.4322.3272.464-0.0030.067-0.2020.000
5E8THR00.0990.0043.823-1.884-0.007-0.022-1.046-0.8100.000
6E8THR0-0.0640.0336.971-0.109-0.1090.0000.0000.0000.000
7E9GLU00.110-0.2384.6190.6910.691-0.002-0.0090.0110.000
8E9GLU-1-1.001-0.7215.291-0.229-0.2290.0000.0000.0000.000
9E10MET00.045-0.0796.807-0.181-0.1810.0000.0000.0000.000
10E10MET0-0.0860.0867.8330.1250.1250.0000.0000.0000.000
11E11LYS00.060-0.1469.6730.0590.0590.0000.0000.0000.000
12E11LYS10.9001.10612.500-0.224-0.2240.0000.0000.0000.000
13E12ILE00.033-0.09512.712-0.027-0.0270.0000.0000.0000.000
14E12ILE0-0.0550.10311.5000.0100.0100.0000.0000.0000.000
15E13SER00.069-0.10014.413-0.011-0.0110.0000.0000.0000.000
16E13SER0-0.0470.07018.695-0.014-0.0140.0000.0000.0000.000
17E14LEU00.025-0.10717.445-0.015-0.0150.0000.0000.0000.000
18E14LEU0-0.0490.11914.6520.0070.0070.0000.0000.0000.000
19E15PRO00.049-0.07518.521-0.017-0.0170.0000.0000.0000.000
20E16GLU00.173-0.02421.1290.0280.0280.0000.0000.0000.000
21E16GLU-1-0.996-0.80823.1790.1620.1620.0000.0000.0000.000
22E17ASN00.082-0.07922.8300.0040.0040.0000.0000.0000.000
23E17ASN0-0.0520.07725.068-0.001-0.0010.0000.0000.0000.000
24E18LEU00.138-0.08820.868-0.010-0.0100.0000.0000.0000.000
25E18LEU0-0.0960.11118.9290.0040.0040.0000.0000.0000.000
26E19VAL00.047-0.09518.1710.0230.0230.0000.0000.0000.000
27E19VAL0-0.1190.09417.2370.0060.0060.0000.0000.0000.000
28E20ALA00.148-0.12219.0250.0170.0170.0000.0000.0000.000
29E20ALA0-0.0540.13523.342-0.005-0.0050.0000.0000.0000.000
30E21GLU00.076-0.15521.950-0.012-0.0120.0000.0000.0000.000
31E21GLU-1-1.044-0.81421.8380.2230.2230.0000.0000.0000.000
32E22LEU00.044-0.12117.453-0.015-0.0150.0000.0000.0000.000
33E22LEU0-0.1410.09014.0570.0180.0180.0000.0000.0000.000
34E23ASP00.080-0.12417.6580.0240.0240.0000.0000.0000.000
35E23ASP-1-0.868-0.78117.0940.3150.3150.0000.0000.0000.000
36E24GLY00.016-0.08618.643-0.018-0.0180.0000.0000.0000.000
37E25VAL0-0.015-0.04919.386-0.027-0.0270.0000.0000.0000.000
38E25VAL0-0.0580.10217.3630.0000.0000.0000.0000.0000.000
39E26ALA00.132-0.09416.423-0.003-0.0030.0000.0000.0000.000
40E26ALA0-0.0920.11115.6320.0070.0070.0000.0000.0000.000
41E27MET00.105-0.10917.222-0.008-0.0080.0000.0000.0000.000
42E27MET0-0.0950.10120.794-0.002-0.0020.0000.0000.0000.000
43E28ARG00.015-0.09620.070-0.021-0.0210.0000.0000.0000.000
44E28ARG10.8611.05921.396-0.190-0.1900.0000.0000.0000.000
45E29GLU00.019-0.14018.122-0.033-0.0330.0000.0000.0000.000
46E29GLU-1-0.946-0.80917.3160.2940.2940.0000.0000.0000.000
47E30LYS00.026-0.08517.3830.0080.0080.0000.0000.0000.000
48E30LYS10.8431.05718.014-0.133-0.1330.0000.0000.0000.000
49E31ARG00.133-0.07313.366-0.029-0.0290.0000.0000.0000.000
50E31ARG10.7500.98812.308-0.385-0.3850.0000.0000.0000.000
51E32SER00.096-0.05610.937-0.043-0.0430.0000.0000.0000.000
52E32SER0-0.0180.0819.6820.0580.0580.0000.0000.0000.000
53E33ARG00.139-0.09411.6120.0400.0400.0000.0000.0000.000
54E33ARG10.7861.01111.547-0.354-0.3540.0000.0000.0000.000
55E34ASN00.080-0.0607.1840.0110.0110.0000.0000.0000.000
56E34ASN0-0.0600.0924.774-0.0360.130-0.001-0.004-0.1600.000
57E35GLU00.124-0.1097.3360.4830.4830.0000.0000.0000.000
58E35GLU-1-0.962-0.8218.4960.3920.3920.0000.0000.0000.000
59E36LEU00.027-0.1478.3050.0540.0540.0000.0000.0000.000
60E36LEU0-0.0710.13812.378-0.005-0.0050.0000.0000.0000.000
61E37ILE00.117-0.12010.369-0.072-0.0720.0000.0000.0000.000
62E37ILE0-0.1000.1089.3820.0080.0080.0000.0000.0000.000
63E38SER00.004-0.0856.545-0.145-0.1450.0000.0000.0000.000
64E38SER0-0.0260.0885.583-0.042-0.0420.0000.0000.0000.000
65E39GLN00.069-0.1447.936-0.020-0.0200.0000.0000.0000.000
66E39GLN0-0.0260.15510.581-0.006-0.0060.0000.0000.0000.000
67E40ALA00.058-0.12910.598-0.112-0.1120.0000.0000.0000.000
68E40ALA0-0.0540.12912.954-0.011-0.0110.0000.0000.0000.000
69E41VAL00.052-0.12211.148-0.197-0.1970.0000.0000.0000.000
70E41VAL0-0.0660.11510.1630.0200.0200.0000.0000.0000.000
71E42ARG00.089-0.09211.098-0.096-0.0960.0000.0000.0000.000
72E42ARG10.8701.0816.419-1.398-1.3980.0000.0000.0000.000
73E43ALA00.128-0.11312.151-0.099-0.0990.0000.0000.0000.000
74E43ALA0-0.0580.13915.459-0.005-0.0050.0000.0000.0000.000
75E44TYR00.112-0.07115.311-0.081-0.0810.0000.0000.0000.000
76E44TYR0-0.0810.10615.706-0.023-0.0230.0000.0000.0000.000
77E45VAL00.041-0.13514.799-0.086-0.0860.0000.0000.0000.000
78E45VAL0-0.0500.13513.4190.0040.0040.0000.0000.0000.000
79E46SER00.046-0.09015.834-0.059-0.0590.0000.0000.0000.000
80E46SER0-0.0140.09115.228-0.024-0.0240.0000.0000.0000.000
81E47GLU00.121-0.10917.431-0.052-0.0520.0000.0000.0000.000
82E47GLU-1-0.976-0.81220.0350.2170.2170.0000.0000.0000.000
83E48ARG0-0.003-0.14519.562-0.042-0.0420.0000.0000.0000.000
84E48ARG10.8351.05619.359-0.259-0.2590.0000.0000.0000.000
85E49THR00.037-0.06319.328-0.029-0.0290.0000.0000.0000.000
86E49THR0-0.0520.05718.025-0.004-0.0040.0000.0000.0000.000
87E50THR00.034-0.09220.652-0.028-0.0280.0000.0000.0000.000
88E50THR0-0.0240.07220.922-0.010-0.0100.0000.0000.0000.000
89E51ARG00.063-0.08022.821-0.023-0.0230.0000.0000.0000.000
90E51ARG10.8351.04324.518-0.186-0.1860.0000.0000.0000.000
91E52HIS00.102-0.08524.228-0.015-0.0150.0000.0000.0000.000
92E52HIS0-0.0770.10523.6330.0060.0060.0000.0000.0000.000
93E53ASN00.130-0.05924.530-0.013-0.0130.0000.0000.0000.000
94E53ASN0-0.1130.07021.816-0.002-0.0020.0000.0000.0000.000
95E54ARG00.069-0.12725.929-0.014-0.0140.0000.0000.0000.000
96E54ARG10.8701.06525.791-0.093-0.0930.0000.0000.0000.000
97E55ASP00.047-0.07728.520-0.011-0.0110.0000.0000.0000.000
98E55ASP-1-0.862-0.77529.3550.0890.0890.0000.0000.0000.000
99E56LEU00.043-0.12428.958-0.006-0.0060.0000.0000.0000.000
100E56LEU0-0.0700.12426.716-0.001-0.0010.0000.0000.0000.000
101E57MET00.084-0.08130.000-0.008-0.0080.0000.0000.0000.000
102E57MET0-0.0980.07129.0420.0030.0030.0000.0000.0000.000
103E58ARG00.119-0.06531.645-0.007-0.0070.0000.0000.0000.000
104E58ARG10.7750.99033.820-0.070-0.0700.0000.0000.0000.000
105E59ARG00.068-0.09933.789-0.005-0.0050.0000.0000.0000.000
106E59ARG10.7961.02532.164-0.071-0.0710.0000.0000.0000.000
107E60GLY00.059-0.07534.176-0.003-0.0030.0000.0000.0000.000
108E61TYR00.1230.01235.525-0.005-0.0050.0000.0000.0000.000
109E61TYR0-0.1070.07934.1910.0010.0010.0000.0000.0000.000
110E62MET00.061-0.09037.653-0.004-0.0040.0000.0000.0000.000
111E62MET0-0.1150.06138.7640.0030.0030.0000.0000.0000.000
112E63GLU00.011-0.12838.783-0.002-0.0020.0000.0000.0000.000
113E63GLU-1-0.991-0.84437.4270.0370.0370.0000.0000.0000.000
114E64MET00.048-0.11839.734-0.002-0.0020.0000.0000.0000.000
115E64MET0-0.0780.12938.173-0.002-0.0020.0000.0000.0000.000
116E65ALA00.135-0.11041.089-0.003-0.0030.0000.0000.0000.000
117E65ALA0-0.0820.12943.2110.0000.0000.0000.0000.0000.000
118E66LYS00.109-0.07943.769-0.001-0.0010.0000.0000.0000.000
119E66LYS10.8561.05446.385-0.015-0.0150.0000.0000.0000.000
120E67ILE00.044-0.11844.465-0.001-0.0010.0000.0000.0000.000
121E67ILE0-0.0450.10042.5300.0000.0000.0000.0000.0000.000
122E68ASN00.088-0.07043.209-0.002-0.0020.0000.0000.0000.000
123E68ASN0-0.0920.06640.8100.0020.0020.0000.0000.0000.000
124E69LEU00.154-0.07844.413-0.001-0.0010.0000.0000.0000.000
125E69LEU0-0.0980.11347.2420.0000.0000.0000.0000.0000.000
126E70ASN00.135-0.05647.599-0.001-0.0010.0000.0000.0000.000
127E70ASN0-0.1480.04348.959-0.001-0.0010.0000.0000.0000.000
128E71ILE00.070-0.07447.5210.0000.0000.0000.0000.0000.000
129E71ILE0-0.0680.08544.4170.0000.0000.0000.0000.0000.000
130E72SER00.099-0.05747.807-0.002-0.0020.0000.0000.0000.000
131E72SER0-0.0810.04946.7760.0000.0000.0000.0000.0000.000
132E73SER0-0.014-0.08448.4990.0000.0000.0000.0000.0000.000
133E73SER0-0.0790.04951.2530.0000.0000.0000.0000.0000.000
134E74GLU00.054-0.12351.8560.0000.0000.0000.0000.0000.000
135E74GLU-1-1.052-0.85651.2650.0030.0030.0000.0000.0000.000
136E75ALA00.091-0.10850.647-0.001-0.0010.0000.0000.0000.000
137E75ALA0-0.0790.11149.8680.0000.0000.0000.0000.0000.000
138E76HIS00.084-0.07452.004-0.001-0.0010.0000.0000.0000.000
139E76HIS0-0.1140.06252.7880.0000.0000.0000.0000.0000.000
140E77PHE00.118-0.08553.3510.0000.0000.0000.0000.0000.000
141E77PHE0-0.0840.08557.1810.0000.0000.0000.0000.0000.000
142E78ALA00.101-0.09153.5590.0000.0000.0000.0000.0000.000
143E78ALA0-0.1100.09152.7100.0000.0000.0000.0000.0000.000
144E79GLU00.035-0.13551.686-0.001-0.0010.0000.0000.0000.000
145E79GLU-1-1.012-0.87348.6220.0070.0070.0000.0000.0000.000
146E80CYS00.113-0.09252.4220.0000.0000.0000.0000.0000.000
147E80CYS0-0.1840.07155.9110.0000.0000.0000.0000.0000.000
148E81GLU00.189-0.04155.5370.0000.0000.0000.0000.0000.000
149E81GLU-1-1.075-0.89656.8490.0000.0000.0000.0000.0000.000
150E82ALA0-0.005-0.09553.100-0.001-0.0010.0000.0000.0000.000
151E82ALA0-0.1170.06552.4840.0000.0000.0000.0000.0000.000
152E83GLU0-0.159-0.18653.355-0.001-0.0010.0000.0000.0000.000
153E83GLU-1-0.903-0.93654.9810.0020.0020.0000.0000.0000.000