Manual

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: J2M29

Calculation Name: 1GO3-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GO3

Chain ID: E

ChEMBL ID:

UniProt ID: Q57840

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1792538.320234
FMO2-HF: Nuclear repulsion 1720106.65693
FMO2-HF: Total energy -72431.663304
FMO2-MP2: Total energy -72644.800152


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:1:MET)


Summations of interaction energy for fragment #1(E: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.
-35.916-36.23534.018-16.005-17.694-0.131
Interaction energy analysis for fragmet #1(E:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.035
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].
3E3LYS10.9320.9683.7220.5923.049-0.004-1.152-1.3020.005
4E4ILE00.0420.0375.7110.1450.1450.0000.0000.0000.000
5E5LEU0-0.074-0.0398.220-0.136-0.1360.0000.0000.0000.000
6E6GLU-1-0.808-0.90911.432-0.047-0.0470.0000.0000.0000.000
7E7ILE0-0.042-0.02813.545-0.060-0.0600.0000.0000.0000.000
8E8ALA00.0010.01117.0990.0430.0430.0000.0000.0000.000
9E9ASP-1-0.815-0.89920.546-0.186-0.1860.0000.0000.0000.000
10E10VAL0-0.070-0.04022.6880.0170.0170.0000.0000.0000.000
11E11VAL0-0.0020.00224.537-0.004-0.0040.0000.0000.0000.000
12E12LYS10.9260.97227.0090.0670.0670.0000.0000.0000.000
13E13VAL00.0310.01130.1560.0040.0040.0000.0000.0000.000
14E14PRO00.0210.00931.839-0.002-0.0020.0000.0000.0000.000
15E15PRO00.0600.01935.1280.0030.0030.0000.0000.0000.000
16E16GLU-1-0.950-0.97437.380-0.016-0.0160.0000.0000.0000.000
17E17GLU-1-0.849-0.92033.1650.0090.0090.0000.0000.0000.000
18E18PHE0-0.038-0.01035.9040.0020.0020.0000.0000.0000.000
19E19GLY0-0.0310.00237.9190.0000.0000.0000.0000.0000.000
20E20LYS10.7880.87934.500-0.008-0.0080.0000.0000.0000.000
21E21ASP-1-0.849-0.92131.0190.0170.0170.0000.0000.0000.000
22E22LEU00.0590.03430.6520.0010.0010.0000.0000.0000.000
23E23LYS10.8880.93824.005-0.033-0.0330.0000.0000.0000.000
24E24GLU-1-0.911-0.95826.9440.0510.0510.0000.0000.0000.000
25E25THR00.003-0.00927.7340.0020.0020.0000.0000.0000.000
26E26VAL0-0.010-0.01024.894-0.005-0.0050.0000.0000.0000.000
27E27LYS10.9440.97320.796-0.096-0.0960.0000.0000.0000.000
28E28LYS10.8740.94823.262-0.049-0.0490.0000.0000.0000.000
29E29ILE00.0320.01624.881-0.002-0.0020.0000.0000.0000.000
30E30LEU0-0.029-0.01820.583-0.011-0.0110.0000.0000.0000.000
31E31MET0-0.062-0.02820.080-0.013-0.0130.0000.0000.0000.000
32E32GLU-1-0.920-0.95620.6480.0070.0070.0000.0000.0000.000
33E33LYS10.8680.95821.4990.1240.1240.0000.0000.0000.000
34E34TYR0-0.103-0.10216.793-0.038-0.0380.0000.0000.0000.000
35E35GLU-1-0.774-0.88616.0250.0800.0800.0000.0000.0000.000
36E36GLY0-0.0120.00915.0630.0010.0010.0000.0000.0000.000
37E37ARG10.9050.96315.5840.1630.1630.0000.0000.0000.000
38E38LEU0-0.051-0.01310.0030.0010.0010.0000.0000.0000.000
39E39ASP-1-0.877-0.93811.769-0.636-0.6360.0000.0000.0000.000
40E40LYS10.8040.88410.7841.0861.0860.0000.0000.0000.000
41E41ASP-1-0.877-0.94410.418-1.156-1.1560.0000.0000.0000.000
42E42VAL0-0.0210.0019.116-0.248-0.2480.0000.0000.0000.000
43E43GLY00.0230.0167.550-0.262-0.2620.0000.0000.0000.000
44E44PHE0-0.028-0.0367.8370.1990.1990.0000.0000.0000.000
45E45VAL00.0130.0089.5630.0710.0710.0000.0000.0000.000
46E46LEU0-0.042-0.0318.7640.0840.0840.0000.0000.0000.000
47E47SER0-0.0120.00612.5270.0260.0260.0000.0000.0000.000
48E48ILE0-0.0110.02614.531-0.047-0.0470.0000.0000.0000.000
49E49VAL0-0.001-0.01313.7110.0240.0240.0000.0000.0000.000
50E50ASP-1-0.846-0.93816.9230.0500.0500.0000.0000.0000.000
51E51VAL0-0.037-0.01019.322-0.028-0.0280.0000.0000.0000.000
52E52LYS10.7880.86116.7450.0510.0510.0000.0000.0000.000
53E53ASP-1-0.924-0.95922.444-0.067-0.0670.0000.0000.0000.000
54E54ILE0-0.010-0.00425.211-0.008-0.0080.0000.0000.0000.000
55E55GLY00.0010.01127.9530.0050.0050.0000.0000.0000.000
56E56GLU-1-0.876-0.93930.594-0.035-0.0350.0000.0000.0000.000
57E57GLY0-0.040-0.02233.344-0.008-0.0080.0000.0000.0000.000
58E58LYS10.8810.94130.3650.0970.0970.0000.0000.0000.000
59E59VAL00.0510.02035.589-0.001-0.0010.0000.0000.0000.000
60E60VAL0-0.027-0.00336.276-0.002-0.0020.0000.0000.0000.000
61E61HIS00.0380.00039.0170.0030.0030.0000.0000.0000.000
62E62GLY0-0.031-0.02140.837-0.003-0.0030.0000.0000.0000.000
63E63ASP-1-0.849-0.91136.004-0.061-0.0610.0000.0000.0000.000
64E64GLY00.0050.00439.3150.0010.0010.0000.0000.0000.000
65E65SER0-0.051-0.02134.1270.0040.0040.0000.0000.0000.000
66E66ALA0-0.0070.01334.753-0.003-0.0030.0000.0000.0000.000
67E67TYR0-0.087-0.07830.423-0.004-0.0040.0000.0000.0000.000
68E68HIS00.0390.00929.3940.0020.0020.0000.0000.0000.000
69E69PRO0-0.067-0.02027.323-0.009-0.0090.0000.0000.0000.000
70E70VAL00.0220.01022.7900.0130.0130.0000.0000.0000.000
71E71VAL00.0310.02119.693-0.024-0.0240.0000.0000.0000.000
72E72PHE0-0.040-0.02116.1830.0280.0280.0000.0000.0000.000
73E73GLU-1-0.817-0.88013.996-0.013-0.0130.0000.0000.0000.000
74E74THR0-0.072-0.05411.9850.0300.0300.0000.0000.0000.000
75E75LEU00.0370.0328.237-0.069-0.0690.0000.0000.0000.000
76E76VAL0-0.006-0.0146.2190.0330.0330.0000.0000.0000.000
77E77TYR00.0270.0113.148-3.094-1.8010.296-0.619-0.9690.006
78E78ILE0-0.024-0.0282.331-1.0480.4180.947-0.850-1.564-0.001
79E79PRO0-0.0060.0191.868-7.287-10.55810.075-3.761-3.043-0.033
80E80GLU-1-0.900-0.9542.649-9.752-7.2861.619-1.292-2.793-0.016
81E81MET0-0.023-0.0314.8490.8180.912-0.001-0.001-0.0910.000
82E82TYR0-0.046-0.0287.423-0.009-0.0090.0000.0000.0000.000
83E83GLU-1-0.759-0.8611.763-19.039-24.13421.087-8.312-7.680-0.092
84E84LEU0-0.083-0.0415.7550.0430.0430.0000.0000.0000.000
85E85ILE0-0.0050.0014.2870.3330.604-0.001-0.018-0.2520.000
86E86GLU-1-0.878-0.9676.8480.7760.7760.0000.0000.0000.000
87E87GLY0-0.0030.0028.8240.3510.3510.0000.0000.0000.000
88E88GLU-1-0.929-0.96011.0610.4410.4410.0000.0000.0000.000
89E89VAL0-0.043-0.01414.551-0.002-0.0020.0000.0000.0000.000
90E90VAL0-0.013-0.01615.863-0.011-0.0110.0000.0000.0000.000
91E91ASP-1-0.895-0.95718.2940.1320.1320.0000.0000.0000.000
92E92VAL0-0.0250.00919.8090.0060.0060.0000.0000.0000.000
93E93VAL00.0150.02422.091-0.016-0.0160.0000.0000.0000.000
94E94GLU-1-0.909-0.97424.4310.0390.0390.0000.0000.0000.000
95E95PHE0-0.032-0.02420.922-0.008-0.0080.0000.0000.0000.000
96E96GLY0-0.003-0.01820.252-0.021-0.0210.0000.0000.0000.000
97E97SER00.0110.02317.0180.0090.0090.0000.0000.0000.000
98E98PHE0-0.009-0.01315.771-0.028-0.0280.0000.0000.0000.000
99E99VAL00.0140.00611.1580.0190.0190.0000.0000.0000.000
100E100ARG11.0061.01711.497-0.595-0.5950.0000.0000.0000.000
101E101LEU0-0.031-0.0326.3860.0050.0050.0000.0000.0000.000
102E102GLY00.0570.0276.7561.0111.0110.0000.0000.0000.000
103E103PRO0-0.074-0.0167.851-0.282-0.2820.0000.0000.0000.000
104E104LEU0-0.048-0.0267.995-0.295-0.2950.0000.0000.0000.000
105E105ASP-1-0.817-0.9139.8980.7410.7410.0000.0000.0000.000
106E106GLY0-0.061-0.03310.768-0.157-0.1570.0000.0000.0000.000
107E107LEU0-0.080-0.04111.5450.0430.0430.0000.0000.0000.000
108E108ILE0-0.0070.01514.204-0.075-0.0750.0000.0000.0000.000
109E109HIS00.018-0.00316.1130.0220.0220.0000.0000.0000.000
110E110VAL00.0860.03319.4110.0060.0060.0000.0000.0000.000
111E111SER0-0.034-0.00722.3330.0080.0080.0000.0000.0000.000
112E112GLN0-0.072-0.06717.764-0.015-0.0150.0000.0000.0000.000
113E113ILE00.0450.02918.2600.0120.0120.0000.0000.0000.000
114E114MET0-0.027-0.01619.9050.0240.0240.0000.0000.0000.000
115E115ASP-1-0.993-0.98922.4330.0200.0200.0000.0000.0000.000
116E116ASP-1-0.706-0.84125.1280.0800.0800.0000.0000.0000.000
117E117TYR0-0.021-0.00927.406-0.009-0.0090.0000.0000.0000.000
118E118VAL00.0200.01324.9730.0070.0070.0000.0000.0000.000
119E119SER0-0.040-0.02628.281-0.014-0.0140.0000.0000.0000.000
120E120TYR0-0.019-0.00926.5190.0000.0000.0000.0000.0000.000
121E121ASP-1-0.842-0.90728.7700.0890.0890.0000.0000.0000.000
122E122PRO00.001-0.02129.9430.0090.0090.0000.0000.0000.000
123E123LYS10.9370.98731.249-0.071-0.0710.0000.0000.0000.000
124E124ARG10.7090.80628.154-0.158-0.1580.0000.0000.0000.000
125E125GLU-1-0.854-0.91526.7400.1610.1610.0000.0000.0000.000
126E126ALA00.0230.01925.1300.0180.0180.0000.0000.0000.000
127E127ILE0-0.060-0.02322.881-0.022-0.0220.0000.0000.0000.000
128E128ILE00.005-0.01225.5870.0140.0140.0000.0000.0000.000
129E129GLY00.0040.00027.944-0.013-0.0130.0000.0000.0000.000
130E130LYS10.8070.87828.651-0.050-0.0500.0000.0000.0000.000
131E131GLU-1-0.916-0.95631.5550.0510.0510.0000.0000.0000.000
132E132THR0-0.129-0.07327.7590.0090.0090.0000.0000.0000.000
133E133GLY0-0.0010.01030.3020.0060.0060.0000.0000.0000.000
134E134LYS10.9040.95523.323-0.145-0.1450.0000.0000.0000.000
135E135VAL00.0180.00025.721-0.013-0.0130.0000.0000.0000.000
136E136LEU0-0.065-0.02618.4010.0200.0200.0000.0000.0000.000
137E137GLU-1-0.826-0.89922.2780.1710.1710.0000.0000.0000.000
138E138ILE00.0300.00520.7130.0370.0370.0000.0000.0000.000
139E139GLY0-0.0160.00319.687-0.018-0.0180.0000.0000.0000.000
140E140ASP-1-0.818-0.89819.4040.3310.3310.0000.0000.0000.000
141E141TYR00.0080.00615.4720.0710.0710.0000.0000.0000.000
142E142VAL0-0.019-0.02312.584-0.080-0.0800.0000.0000.0000.000
143E143ARG10.9280.99011.414-0.479-0.4790.0000.0000.0000.000
144E144ALA0-0.022-0.02010.434-0.142-0.1420.0000.0000.0000.000
145E145ARG10.8820.9449.1250.1090.1090.0000.0000.0000.000
146E146ILE00.0100.0125.1270.1590.1590.0000.0000.0000.000
147E147VAL0-0.040-0.0279.095-0.111-0.1110.0000.0000.0000.000
148E148ALA00.003-0.01011.5740.0160.0160.0000.0000.0000.000
149E149ILE00.0460.0367.0310.1050.1050.0000.0000.0000.000
150E150SER0-0.046-0.01811.0600.0180.0180.0000.0000.0000.000
151E151LEU00.0520.0247.9280.1620.1620.0000.0000.0000.000
152E152LYS10.8250.91612.4330.4240.4240.0000.0000.0000.000
153E153ALA00.1160.06515.8000.0440.0440.0000.0000.0000.000
154E154GLU-1-0.770-0.90316.617-0.126-0.1260.0000.0000.0000.000
155E155ARG10.9230.95419.4410.2110.2110.0000.0000.0000.000
156E156LYS10.7700.89319.1850.1800.1800.0000.0000.0000.000
157E157ARG10.8940.95315.2690.0270.0270.0000.0000.0000.000
158E158GLY00.0210.01616.8800.0180.0180.0000.0000.0000.000
159E159SER00.0180.00012.515-0.062-0.0620.0000.0000.0000.000
160E160LYS10.9220.96813.6260.1340.1340.0000.0000.0000.000
161E161ILE00.0770.0427.304-0.160-0.1600.0000.0000.0000.000
162E162ALA0-0.024-0.00311.1790.1410.1410.0000.0000.0000.000
163E163LEU00.0370.0148.684-0.147-0.1470.0000.0000.0000.000
164E164THR0-0.0070.00712.4450.0260.0260.0000.0000.0000.000
165E165MET00.0400.03513.6660.0510.0510.0000.0000.0000.000
166E166ARG10.8820.96616.1320.0300.0300.0000.0000.0000.000
167E167GLN00.008-0.01114.499-0.018-0.0180.0000.0000.0000.000
168E168PRO00.0310.02618.3350.0320.0320.0000.0000.0000.000
169E169TYR0-0.021-0.03015.6330.0000.0000.0000.0000.0000.000
170E170LEU0-0.0510.00112.6760.0780.0780.0000.0000.0000.000
171E171GLY00.0560.00415.315-0.042-0.0420.0000.0000.0000.000
172E172LYS10.9430.98616.154-0.206-0.2060.0000.0000.0000.000
173E173LEU00.025-0.00114.296-0.032-0.0320.0000.0000.0000.000
174E174GLU-1-0.853-0.94118.1240.3430.3430.0000.0000.0000.000
175E175TRP0-0.058-0.02820.199-0.026-0.0260.0000.0000.0000.000
176E176ILE00.0270.02316.194-0.015-0.0150.0000.0000.0000.000
177E177GLU-1-0.852-0.90720.4970.3160.3160.0000.0000.0000.000
178E178GLU-1-0.860-0.93222.3910.1540.1540.0000.0000.0000.000
179E179GLU-1-0.973-1.00321.5680.1980.1980.0000.0000.0000.000
180E180LYS10.7620.86119.582-0.345-0.3450.0000.0000.0000.000
181E181ALA00.0210.02824.108-0.015-0.0150.0000.0000.0000.000
182E182LYS10.8860.94727.457-0.154-0.1540.0000.0000.0000.000
183E183LYS10.8950.95822.942-0.159-0.1590.0000.0000.0000.000
184E184GLN0-0.068-0.02926.350-0.005-0.0050.0000.0000.0000.000