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

tag_button

FMODB ID: L7L79

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1795272.325032
FMO2-HF: Nuclear repulsion 1722839.564192
FMO2-HF: Total energy -72432.760839
FMO2-MP2: Total energy -72645.903416


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.
-35.261-29.83228.088-14.439-19.075-0.108
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 : -0.047 / q_NPA : -0.036
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].
3E3LYS10.8150.9022.4862.9505.8070.807-1.317-2.3460.007
4E4ILE00.0280.0205.6380.2000.2000.0000.0000.0000.000
5E5LEU0-0.041-0.0198.509-0.189-0.1890.0000.0000.0000.000
6E6GLU-1-0.771-0.87611.4080.0420.0420.0000.0000.0000.000
7E7ILE0-0.046-0.02513.620-0.080-0.0800.0000.0000.0000.000
8E8ALA00.0070.01217.1130.0470.0470.0000.0000.0000.000
9E9ASP-1-0.766-0.84520.845-0.155-0.1550.0000.0000.0000.000
10E10VAL0-0.067-0.04922.8900.0140.0140.0000.0000.0000.000
11E11VAL0-0.007-0.00625.005-0.004-0.0040.0000.0000.0000.000
12E12LYS10.8010.89927.4860.0480.0480.0000.0000.0000.000
13E13VAL00.0320.02130.5680.0060.0060.0000.0000.0000.000
14E14PRO00.0240.00532.066-0.004-0.0040.0000.0000.0000.000
15E15PRO00.0320.01235.3000.0040.0040.0000.0000.0000.000
16E16GLU-1-0.927-0.97337.4460.0020.0020.0000.0000.0000.000
17E17GLU-1-0.831-0.90333.1830.0390.0390.0000.0000.0000.000
18E18PHE0-0.051-0.02235.9090.0030.0030.0000.0000.0000.000
19E19GLY0-0.0180.00737.9790.0000.0000.0000.0000.0000.000
20E20LYS10.7720.87334.141-0.034-0.0340.0000.0000.0000.000
21E21ASP-1-0.809-0.90530.8320.0500.0500.0000.0000.0000.000
22E22LEU00.0340.03830.8240.0020.0020.0000.0000.0000.000
23E23LYS10.8330.89624.129-0.076-0.0760.0000.0000.0000.000
24E24GLU-1-0.848-0.93426.4430.1080.1080.0000.0000.0000.000
25E25THR0-0.027-0.02127.6810.0020.0020.0000.0000.0000.000
26E26VAL0-0.019-0.01625.087-0.005-0.0050.0000.0000.0000.000
27E27LYS10.8430.91220.965-0.160-0.1600.0000.0000.0000.000
28E28LYS10.8120.89523.337-0.106-0.1060.0000.0000.0000.000
29E29ILE00.0340.01524.794-0.001-0.0010.0000.0000.0000.000
30E30LEU0-0.027-0.01820.898-0.013-0.0130.0000.0000.0000.000
31E31MET0-0.0080.00820.118-0.015-0.0150.0000.0000.0000.000
32E32GLU-1-0.903-0.94820.4910.0550.0550.0000.0000.0000.000
33E33LYS10.7560.90121.6590.0950.0950.0000.0000.0000.000
34E34TYR0-0.048-0.06616.927-0.054-0.0540.0000.0000.0000.000
35E35GLU-1-0.757-0.86716.0540.1920.1920.0000.0000.0000.000
36E36GLY00.0070.01514.899-0.007-0.0070.0000.0000.0000.000
37E37ARG10.8320.91815.1020.1090.1090.0000.0000.0000.000
38E38LEU0-0.052-0.0179.5410.0350.0350.0000.0000.0000.000
39E39ASP-1-0.843-0.92111.213-0.668-0.6680.0000.0000.0000.000
40E40LYS10.7770.87010.4121.2091.2090.0000.0000.0000.000
41E41ASP-1-0.868-0.9319.977-1.354-1.3540.0000.0000.0000.000
42E42VAL00.0000.0009.035-0.262-0.2620.0000.0000.0000.000
43E43GLY00.0110.0167.260-0.173-0.1730.0000.0000.0000.000
44E44PHE0-0.015-0.0357.5570.1760.1760.0000.0000.0000.000
45E45VAL00.0230.0109.2160.0870.0870.0000.0000.0000.000
46E46LEU0-0.046-0.0288.3230.0890.0890.0000.0000.0000.000
47E47SER0-0.034-0.02412.1410.0120.0120.0000.0000.0000.000
48E48ILE0-0.032-0.00414.423-0.047-0.0470.0000.0000.0000.000
49E49VAL00.0330.02513.8620.0130.0130.0000.0000.0000.000
50E50ASP-1-0.795-0.89417.0330.1140.1140.0000.0000.0000.000
51E51VAL00.0100.01219.477-0.029-0.0290.0000.0000.0000.000
52E52LYS10.7350.84816.690-0.014-0.0140.0000.0000.0000.000
53E53ASP-1-0.887-0.94622.487-0.043-0.0430.0000.0000.0000.000
54E54ILE0-0.034-0.02125.199-0.004-0.0040.0000.0000.0000.000
55E55GLY00.0220.03128.0750.0040.0040.0000.0000.0000.000
56E56GLU-1-0.854-0.93130.610-0.018-0.0180.0000.0000.0000.000
57E57GLY0-0.009-0.02033.424-0.008-0.0080.0000.0000.0000.000
58E58LYS10.8700.95330.2630.0870.0870.0000.0000.0000.000
59E59VAL00.0330.01935.6900.0010.0010.0000.0000.0000.000
60E60VAL0-0.025-0.01036.929-0.004-0.0040.0000.0000.0000.000
61E61HIS00.0250.00639.5850.0050.0050.0000.0000.0000.000
62E62GLY0-0.010-0.01441.372-0.004-0.0040.0000.0000.0000.000
63E63ASP-1-0.790-0.85636.212-0.043-0.0430.0000.0000.0000.000
64E64GLY00.0300.01839.4200.0000.0000.0000.0000.0000.000
65E65SER0-0.052-0.03634.4320.0050.0050.0000.0000.0000.000
66E66ALA00.0110.02634.777-0.005-0.0050.0000.0000.0000.000
67E67TYR0-0.050-0.06230.874-0.002-0.0020.0000.0000.0000.000
68E68HIS00.0320.00129.626-0.003-0.0030.0000.0000.0000.000
69E69PRO0-0.057-0.02527.560-0.010-0.0100.0000.0000.0000.000
70E70VAL00.0020.00322.8850.0140.0140.0000.0000.0000.000
71E71VAL00.0060.00019.927-0.027-0.0270.0000.0000.0000.000
72E72PHE0-0.023-0.01416.3170.0290.0290.0000.0000.0000.000
73E73GLU-1-0.810-0.89014.1710.1260.1260.0000.0000.0000.000
74E74THR0-0.082-0.06112.1600.0260.0260.0000.0000.0000.000
75E75LEU00.0270.0258.581-0.061-0.0610.0000.0000.0000.000
76E76VAL00.003-0.0066.5920.0060.0060.0000.0000.0000.000
77E77TYR00.017-0.0012.642-4.248-3.9614.033-1.487-2.8330.012
78E78ILE00.006-0.0073.141-0.7370.6520.051-0.537-0.9030.000
79E79PRO0-0.0150.0242.000-8.346-9.6298.201-3.523-3.393-0.034
80E80GLU-1-0.822-0.9192.263-11.078-8.2382.307-1.757-3.390-0.023
81E81MET0-0.026-0.0275.0630.7750.866-0.001-0.002-0.0880.000
82E82TYR0-0.023-0.0217.718-0.036-0.0360.0000.0000.0000.000
83E83GLU-1-0.769-0.8671.881-18.100-19.15612.692-5.788-5.848-0.070
84E84LEU0-0.050-0.0285.6360.3590.3590.0000.0000.0000.000
85E85ILE0-0.0070.0014.2830.1360.364-0.001-0.024-0.2030.000
86E86GLU-1-0.791-0.8976.9040.7790.7790.0000.0000.0000.000
87E87GLY00.0150.0128.5590.3880.3880.0000.0000.0000.000
88E88GLU-1-0.840-0.89510.8770.5710.5710.0000.0000.0000.000
89E89VAL0-0.027-0.01614.2000.0030.0030.0000.0000.0000.000
90E90VAL0-0.024-0.01715.291-0.014-0.0140.0000.0000.0000.000
91E91ASP-1-0.862-0.94017.7810.1420.1420.0000.0000.0000.000
92E92VAL0-0.045-0.02319.3200.0020.0020.0000.0000.0000.000
93E93VAL00.0250.02921.871-0.013-0.0130.0000.0000.0000.000
94E94GLU-1-0.921-0.97423.8990.0230.0230.0000.0000.0000.000
95E95PHE0-0.024-0.00820.202-0.012-0.0120.0000.0000.0000.000
96E96GLY0-0.033-0.03219.927-0.029-0.0290.0000.0000.0000.000
97E97SER00.0240.02717.0330.0110.0110.0000.0000.0000.000
98E98PHE0-0.014-0.01515.249-0.039-0.0390.0000.0000.0000.000
99E99VAL00.001-0.00610.8270.0150.0150.0000.0000.0000.000
100E100ARG10.9080.95911.009-0.682-0.6820.0000.0000.0000.000
101E101LEU0-0.016-0.0165.811-0.055-0.0550.0000.0000.0000.000
102E102GLY00.0630.0276.8081.0331.0330.0000.0000.0000.000
103E103PRO0-0.066-0.0017.589-0.342-0.3420.0000.0000.0000.000
104E104LEU0-0.061-0.0357.928-0.354-0.3540.0000.0000.0000.000
105E105ASP-1-0.793-0.9049.5550.9650.9650.0000.0000.0000.000
106E106GLY0-0.058-0.02710.400-0.173-0.1730.0000.0000.0000.000
107E107LEU0-0.072-0.03511.1580.0470.0470.0000.0000.0000.000
108E108ILE00.0010.01713.873-0.097-0.0970.0000.0000.0000.000
109E109HIS00.0340.00715.6800.0200.0200.0000.0000.0000.000
110E110VAL00.0730.02319.0380.0000.0000.0000.0000.0000.000
111E111SER0-0.0080.00022.0370.0100.0100.0000.0000.0000.000
112E112GLN0-0.040-0.02417.477-0.013-0.0130.0000.0000.0000.000
113E113ILE00.0430.02917.933-0.001-0.0010.0000.0000.0000.000
114E114MET0-0.015-0.00919.4120.0230.0230.0000.0000.0000.000
115E115ASP-1-0.893-0.93822.033-0.051-0.0510.0000.0000.0000.000
116E116ASP-1-0.711-0.82224.8080.0610.0610.0000.0000.0000.000
117E117TYR0-0.0170.00827.256-0.012-0.0120.0000.0000.0000.000
118E118VAL00.000-0.00624.5280.0070.0070.0000.0000.0000.000
119E119SER0-0.039-0.02727.870-0.014-0.0140.0000.0000.0000.000
120E120TYR0-0.026-0.02026.2730.0000.0000.0000.0000.0000.000
121E121ASP-1-0.814-0.90028.0830.0850.0850.0000.0000.0000.000
122E122PRO00.002-0.01629.6330.0110.0110.0000.0000.0000.000
123E123LYS10.8750.94331.059-0.071-0.0710.0000.0000.0000.000
124E124ARG10.7410.83827.446-0.167-0.1670.0000.0000.0000.000
125E125GLU-1-0.843-0.89726.3960.1620.1620.0000.0000.0000.000
126E126ALA0-0.003-0.00524.7390.0210.0210.0000.0000.0000.000
127E127ILE0-0.045-0.01922.549-0.022-0.0220.0000.0000.0000.000
128E128ILE00.001-0.01225.2210.0160.0160.0000.0000.0000.000
129E129GLY00.0120.00027.535-0.014-0.0140.0000.0000.0000.000
130E130LYS10.7730.87628.473-0.029-0.0290.0000.0000.0000.000
131E131GLU-1-0.897-0.96131.4170.0310.0310.0000.0000.0000.000
132E132THR0-0.098-0.08327.8990.0070.0070.0000.0000.0000.000
133E133GLY0-0.0030.00930.1540.0090.0090.0000.0000.0000.000
134E134LYS10.8300.92022.885-0.115-0.1150.0000.0000.0000.000
135E135VAL0-0.009-0.00925.464-0.013-0.0130.0000.0000.0000.000
136E136LEU0-0.051-0.02417.9260.0170.0170.0000.0000.0000.000
137E137GLU-1-0.819-0.88521.9240.1840.1840.0000.0000.0000.000
138E138ILE00.0100.00320.6770.0380.0380.0000.0000.0000.000
139E139GLY00.0040.00619.699-0.015-0.0150.0000.0000.0000.000
140E140ASP-1-0.774-0.86218.9500.3260.3260.0000.0000.0000.000
141E141TYR0-0.042-0.02315.3590.0780.0780.0000.0000.0000.000
142E142VAL0-0.022-0.01612.562-0.080-0.0800.0000.0000.0000.000
143E143ARG10.8090.90111.259-0.469-0.4690.0000.0000.0000.000
144E144ALA00.008-0.00210.497-0.109-0.1090.0000.0000.0000.000
145E145ARG10.8480.9199.0680.4430.4430.0000.0000.0000.000
146E146ILE00.0180.0154.3770.2110.287-0.001-0.004-0.0710.000
147E147VAL0-0.036-0.0328.677-0.142-0.1420.0000.0000.0000.000
148E148ALA00.0010.00311.4430.0410.0410.0000.0000.0000.000
149E149ILE00.0250.0236.5160.1650.1650.0000.0000.0000.000
150E150SER0-0.021-0.01310.5800.0200.0200.0000.0000.0000.000
151E151LEU00.0610.0287.3460.1960.1960.0000.0000.0000.000
152E152LYS10.7800.88911.7860.4280.4280.0000.0000.0000.000
153E153ALA00.1170.07215.1320.0530.0530.0000.0000.0000.000
154E154GLU-1-0.769-0.89116.316-0.066-0.0660.0000.0000.0000.000
155E155ARG10.9200.95419.2080.2060.2060.0000.0000.0000.000
156E156LYS10.7660.88518.6110.1650.1650.0000.0000.0000.000
157E157ARG10.8880.93915.025-0.079-0.0790.0000.0000.0000.000
158E158GLY00.0280.02516.4720.0100.0100.0000.0000.0000.000
159E159SER00.0180.00812.366-0.078-0.0780.0000.0000.0000.000
160E160LYS10.9040.95913.3160.0900.0900.0000.0000.0000.000
161E161ILE00.0740.0387.064-0.184-0.1840.0000.0000.0000.000
162E162ALA0-0.0070.00210.6230.1610.1610.0000.0000.0000.000
163E163LEU00.0270.0158.523-0.192-0.1920.0000.0000.0000.000
164E164THR0-0.024-0.01312.0880.0560.0560.0000.0000.0000.000
165E165MET00.0380.02313.3570.0290.0290.0000.0000.0000.000
166E166ARG10.7940.90715.9490.0950.0950.0000.0000.0000.000
167E167GLN0-0.001-0.01214.433-0.058-0.0580.0000.0000.0000.000
168E168PRO00.0280.01818.1590.0360.0360.0000.0000.0000.000
169E169TYR0-0.032-0.03315.860-0.010-0.0100.0000.0000.0000.000
170E170LEU0-0.0530.00212.4460.0620.0620.0000.0000.0000.000
171E171GLY00.0460.00015.440-0.027-0.0270.0000.0000.0000.000
172E172LYS10.8930.94416.185-0.203-0.2030.0000.0000.0000.000
173E173LEU00.0160.00514.496-0.040-0.0400.0000.0000.0000.000
174E174GLU-1-0.842-0.93918.4010.3180.3180.0000.0000.0000.000
175E175TRP0-0.033-0.01619.871-0.029-0.0290.0000.0000.0000.000
176E176ILE00.0100.01516.283-0.019-0.0190.0000.0000.0000.000
177E177GLU-1-0.817-0.88920.5580.3190.3190.0000.0000.0000.000
178E178GLU-1-0.809-0.89422.6530.1330.1330.0000.0000.0000.000
179E179GLU-1-0.900-0.94722.4530.1220.1220.0000.0000.0000.000
180E180LYS10.7510.84919.883-0.341-0.3410.0000.0000.0000.000
181E181ALA0-0.0090.00424.305-0.013-0.0130.0000.0000.0000.000
182E182LYS10.8330.91427.645-0.141-0.1410.0000.0000.0000.000
183E183LYS10.9170.96623.353-0.116-0.1160.0000.0000.0000.000
184E184GLN0-0.078-0.03127.244-0.011-0.0110.0000.0000.0000.000