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: 37N7L

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 OptHSide
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 -1793950.259289
FMO2-HF: Nuclear repulsion 1721517.71105
FMO2-HF: Total energy -72432.548239
FMO2-MP2: Total energy -72645.708683


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.
-35.527-34.14829.528-14.86-16.046-0.105
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 : -0.056 / q_NPA : -0.043
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].
3E3LYS10.8350.9123.1301.8314.5670.060-1.176-1.6200.005
4E4ILE00.0370.0285.7070.0930.0930.0000.0000.0000.000
5E5LEU0-0.055-0.0278.328-0.131-0.1310.0000.0000.0000.000
6E6GLU-1-0.799-0.89411.3850.0420.0420.0000.0000.0000.000
7E7ILE0-0.039-0.02413.697-0.065-0.0650.0000.0000.0000.000
8E8ALA00.0110.01817.1270.0430.0430.0000.0000.0000.000
9E9ASP-1-0.768-0.86520.801-0.174-0.1740.0000.0000.0000.000
10E10VAL0-0.059-0.04222.9430.0170.0170.0000.0000.0000.000
11E11VAL0-0.0080.00224.788-0.006-0.0060.0000.0000.0000.000
12E12LYS10.8290.92627.2970.0660.0660.0000.0000.0000.000
13E13VAL00.0410.01730.4400.0040.0040.0000.0000.0000.000
14E14PRO00.0240.01132.177-0.002-0.0020.0000.0000.0000.000
15E15PRO00.0600.02035.4130.0040.0040.0000.0000.0000.000
16E16GLU-1-0.944-0.97337.573-0.013-0.0130.0000.0000.0000.000
17E17GLU-1-0.839-0.91633.3460.0170.0170.0000.0000.0000.000
18E18PHE0-0.035-0.01436.0150.0030.0030.0000.0000.0000.000
19E19GLY0-0.0240.00537.9790.0010.0010.0000.0000.0000.000
20E20LYS10.7700.87434.279-0.013-0.0130.0000.0000.0000.000
21E21ASP-1-0.829-0.91230.9530.0340.0340.0000.0000.0000.000
22E22LEU00.0420.03730.7290.0000.0000.0000.0000.0000.000
23E23LYS10.8560.90923.691-0.064-0.0640.0000.0000.0000.000
24E24GLU-1-0.885-0.95026.8380.0740.0740.0000.0000.0000.000
25E25THR0-0.015-0.02027.7160.0010.0010.0000.0000.0000.000
26E26VAL0-0.016-0.01524.934-0.006-0.0060.0000.0000.0000.000
27E27LYS10.8890.94720.387-0.132-0.1320.0000.0000.0000.000
28E28LYS10.8580.93323.333-0.067-0.0670.0000.0000.0000.000
29E29ILE00.0280.01524.933-0.005-0.0050.0000.0000.0000.000
30E30LEU0-0.030-0.01720.798-0.014-0.0140.0000.0000.0000.000
31E31MET0-0.052-0.02220.116-0.016-0.0160.0000.0000.0000.000
32E32GLU-1-0.919-0.95420.6420.0110.0110.0000.0000.0000.000
33E33LYS10.7790.91621.7220.1180.1180.0000.0000.0000.000
34E34TYR0-0.053-0.07517.043-0.045-0.0450.0000.0000.0000.000
35E35GLU-1-0.762-0.87516.0170.0860.0860.0000.0000.0000.000
36E36GLY0-0.0080.01015.0550.0000.0000.0000.0000.0000.000
37E37ARG10.8540.92815.5770.1510.1510.0000.0000.0000.000
38E38LEU0-0.056-0.0219.988-0.005-0.0050.0000.0000.0000.000
39E39ASP-1-0.868-0.93811.762-0.661-0.6610.0000.0000.0000.000
40E40LYS10.7950.87310.7801.1671.1670.0000.0000.0000.000
41E41ASP-1-0.863-0.92410.416-1.255-1.2550.0000.0000.0000.000
42E42VAL0-0.026-0.0049.216-0.236-0.2360.0000.0000.0000.000
43E43GLY00.0210.0177.548-0.262-0.2620.0000.0000.0000.000
44E44PHE0-0.023-0.0367.8310.2140.2140.0000.0000.0000.000
45E45VAL00.0140.0069.5580.0770.0770.0000.0000.0000.000
46E46LEU0-0.041-0.0278.6590.0770.0770.0000.0000.0000.000
47E47SER0-0.021-0.00112.5270.0310.0310.0000.0000.0000.000
48E48ILE00.0020.02914.531-0.040-0.0400.0000.0000.0000.000
49E49VAL00.015-0.00513.7020.0210.0210.0000.0000.0000.000
50E50ASP-1-0.824-0.91316.9370.0960.0960.0000.0000.0000.000
51E51VAL0-0.020-0.00219.312-0.028-0.0280.0000.0000.0000.000
52E52LYS10.7640.85916.564-0.010-0.0100.0000.0000.0000.000
53E53ASP-1-0.902-0.95322.439-0.044-0.0440.0000.0000.0000.000
54E54ILE0-0.021-0.00625.176-0.009-0.0090.0000.0000.0000.000
55E55GLY00.0050.01327.9190.0050.0050.0000.0000.0000.000
56E56GLU-1-0.865-0.93430.549-0.023-0.0230.0000.0000.0000.000
57E57GLY0-0.042-0.02033.344-0.008-0.0080.0000.0000.0000.000
58E58LYS10.8760.93830.4920.0870.0870.0000.0000.0000.000
59E59VAL00.0470.01635.856-0.001-0.0010.0000.0000.0000.000
60E60VAL0-0.021-0.00236.628-0.002-0.0020.0000.0000.0000.000
61E61HIS00.0410.00639.2800.0040.0040.0000.0000.0000.000
62E62GLY0-0.024-0.01941.083-0.003-0.0030.0000.0000.0000.000
63E63ASP-1-0.798-0.87835.991-0.059-0.0590.0000.0000.0000.000
64E64GLY00.0150.01339.5990.0010.0010.0000.0000.0000.000
65E65SER0-0.062-0.03634.4740.0040.0040.0000.0000.0000.000
66E66ALA0-0.0100.01234.999-0.004-0.0040.0000.0000.0000.000
67E67TYR0-0.052-0.06230.597-0.003-0.0030.0000.0000.0000.000
68E68HIS00.0330.00529.5290.0010.0010.0000.0000.0000.000
69E69PRO0-0.065-0.01327.421-0.009-0.0090.0000.0000.0000.000
70E70VAL00.0210.00422.9270.0140.0140.0000.0000.0000.000
71E71VAL00.0220.01519.707-0.026-0.0260.0000.0000.0000.000
72E72PHE0-0.026-0.01516.4790.0280.0280.0000.0000.0000.000
73E73GLU-1-0.812-0.89714.0870.1080.1080.0000.0000.0000.000
74E74THR0-0.068-0.05912.3140.0200.0200.0000.0000.0000.000
75E75LEU00.0360.0368.268-0.053-0.0530.0000.0000.0000.000
76E76VAL0-0.006-0.0146.6130.0040.0040.0000.0000.0000.000
77E77TYR00.0290.0112.809-4.477-3.1771.145-0.921-1.5250.011
78E78ILE0-0.017-0.0282.559-1.1810.3900.336-0.680-1.2270.001
79E79PRO0-0.0060.0291.866-7.941-11.0449.992-3.734-3.154-0.034
80E80GLU-1-0.836-0.9192.617-10.377-7.5560.841-1.399-2.262-0.019
81E81MET0-0.015-0.0265.3300.6590.744-0.0010.000-0.0830.000
82E82TYR0-0.037-0.0287.725-0.063-0.0630.0000.0000.0000.000
83E83GLU-1-0.771-0.8651.766-17.271-21.56917.156-6.921-5.938-0.069
84E84LEU0-0.069-0.0365.6860.2300.2300.0000.0000.0000.000
85E85ILE0-0.0010.0014.1340.1990.466-0.001-0.029-0.2370.000
86E86GLU-1-0.780-0.8996.8010.8000.8000.0000.0000.0000.000
87E87GLY00.0080.0118.7530.3130.3130.0000.0000.0000.000
88E88GLU-1-0.887-0.93210.9840.4460.4460.0000.0000.0000.000
89E89VAL0-0.030-0.01314.470-0.015-0.0150.0000.0000.0000.000
90E90VAL0-0.012-0.01715.773-0.001-0.0010.0000.0000.0000.000
91E91ASP-1-0.872-0.94918.2100.0850.0850.0000.0000.0000.000
92E92VAL0-0.037-0.00119.729-0.004-0.0040.0000.0000.0000.000
93E93VAL00.0190.02421.995-0.011-0.0110.0000.0000.0000.000
94E94GLU-1-0.911-0.97424.3590.0050.0050.0000.0000.0000.000
95E95PHE0-0.031-0.02220.891-0.009-0.0090.0000.0000.0000.000
96E96GLY0-0.005-0.01720.185-0.027-0.0270.0000.0000.0000.000
97E97SER00.0050.02517.1340.0130.0130.0000.0000.0000.000
98E98PHE0-0.011-0.01615.693-0.044-0.0440.0000.0000.0000.000
99E99VAL00.001-0.00311.2770.0300.0300.0000.0000.0000.000
100E100ARG10.9520.98811.594-0.546-0.5460.0000.0000.0000.000
101E101LEU0-0.015-0.0236.3020.0110.0110.0000.0000.0000.000
102E102GLY00.0590.0296.7560.9740.9740.0000.0000.0000.000
103E103PRO0-0.075-0.0137.871-0.249-0.2490.0000.0000.0000.000
104E104LEU0-0.058-0.0308.152-0.279-0.2790.0000.0000.0000.000
105E105ASP-1-0.814-0.9139.8980.6120.6120.0000.0000.0000.000
106E106GLY0-0.057-0.03310.698-0.163-0.1630.0000.0000.0000.000
107E107LEU0-0.077-0.04111.4750.0640.0640.0000.0000.0000.000
108E108ILE0-0.0010.01614.106-0.082-0.0820.0000.0000.0000.000
109E109HIS00.0230.00216.0520.0230.0230.0000.0000.0000.000
110E110VAL00.0750.02819.3550.0040.0040.0000.0000.0000.000
111E111SER0-0.0160.00222.2740.0090.0090.0000.0000.0000.000
112E112GLN0-0.071-0.05017.768-0.004-0.0040.0000.0000.0000.000
113E113ILE00.0420.02818.2130.0030.0030.0000.0000.0000.000
114E114MET0-0.017-0.00819.8500.0230.0230.0000.0000.0000.000
115E115ASP-1-0.907-0.94222.385-0.039-0.0390.0000.0000.0000.000
116E116ASP-1-0.712-0.82525.0890.0570.0570.0000.0000.0000.000
117E117TYR0-0.030-0.00827.357-0.012-0.0120.0000.0000.0000.000
118E118VAL00.0320.01824.9360.0090.0090.0000.0000.0000.000
119E119SER0-0.036-0.01828.222-0.013-0.0130.0000.0000.0000.000
120E120TYR0-0.021-0.01526.4840.0000.0000.0000.0000.0000.000
121E121ASP-1-0.836-0.90828.6990.0660.0660.0000.0000.0000.000
122E122PRO00.003-0.01329.8660.0090.0090.0000.0000.0000.000
123E123LYS10.9230.97331.168-0.053-0.0530.0000.0000.0000.000
124E124ARG10.6990.80027.874-0.138-0.1380.0000.0000.0000.000
125E125GLU-1-0.847-0.91126.7920.1280.1280.0000.0000.0000.000
126E126ALA00.0130.01225.0520.0150.0150.0000.0000.0000.000
127E127ILE0-0.052-0.02222.897-0.019-0.0190.0000.0000.0000.000
128E128ILE0-0.002-0.01525.5170.0140.0140.0000.0000.0000.000
129E129GLY00.0210.00627.873-0.014-0.0140.0000.0000.0000.000
130E130LYS10.7900.87228.592-0.019-0.0190.0000.0000.0000.000
131E131GLU-1-0.925-0.96631.5130.0300.0300.0000.0000.0000.000
132E132THR0-0.111-0.08527.6870.0090.0090.0000.0000.0000.000
133E133GLY0-0.0120.00830.2510.0080.0080.0000.0000.0000.000
134E134LYS10.8240.91822.939-0.123-0.1230.0000.0000.0000.000
135E135VAL00.008-0.00525.662-0.014-0.0140.0000.0000.0000.000
136E136LEU0-0.049-0.01918.2530.0190.0190.0000.0000.0000.000
137E137GLU-1-0.817-0.87922.1740.1510.1510.0000.0000.0000.000
138E138ILE00.0370.01020.6250.0340.0340.0000.0000.0000.000
139E139GLY0-0.013-0.00119.603-0.010-0.0100.0000.0000.0000.000
140E140ASP-1-0.781-0.86319.2190.2950.2950.0000.0000.0000.000
141E141TYR0-0.010-0.00615.3630.0630.0630.0000.0000.0000.000
142E142VAL0-0.013-0.01712.561-0.071-0.0710.0000.0000.0000.000
143E143ARG10.8400.92911.278-0.537-0.5370.0000.0000.0000.000
144E144ALA0-0.019-0.01910.385-0.115-0.1150.0000.0000.0000.000
145E145ARG10.8810.9439.0960.3120.3120.0000.0000.0000.000
146E146ILE0-0.0100.0064.8300.2320.2320.0000.0000.0000.000
147E147VAL0-0.028-0.0249.069-0.102-0.1020.0000.0000.0000.000
148E148ALA0-0.006-0.00811.5550.0390.0390.0000.0000.0000.000
149E149ILE00.0490.0376.9310.0970.0970.0000.0000.0000.000
150E150SER0-0.036-0.01311.0530.0380.0380.0000.0000.0000.000
151E151LEU00.0490.0287.8640.1630.1630.0000.0000.0000.000
152E152LYS10.8180.90312.4250.5140.5140.0000.0000.0000.000
153E153ALA00.1160.06915.7920.0440.0440.0000.0000.0000.000
154E154GLU-1-0.759-0.89816.610-0.161-0.1610.0000.0000.0000.000
155E155ARG10.9230.95519.4300.2380.2380.0000.0000.0000.000
156E156LYS10.7630.88819.0650.2360.2360.0000.0000.0000.000
157E157ARG10.9020.96215.2580.0600.0600.0000.0000.0000.000
158E158GLY00.0160.01016.8570.0210.0210.0000.0000.0000.000
159E159SER00.0130.00412.513-0.056-0.0560.0000.0000.0000.000
160E160LYS10.9150.96113.6180.2130.2130.0000.0000.0000.000
161E161ILE00.0720.0437.441-0.163-0.1630.0000.0000.0000.000
162E162ALA0-0.0150.00411.1690.1470.1470.0000.0000.0000.000
163E163LEU00.0270.0148.713-0.170-0.1700.0000.0000.0000.000
164E164THR0-0.003-0.00112.3970.0610.0610.0000.0000.0000.000
165E165MET00.0380.02213.6260.0310.0310.0000.0000.0000.000
166E166ARG10.8040.90916.0910.0910.0910.0000.0000.0000.000
167E167GLN00.002-0.01014.380-0.041-0.0410.0000.0000.0000.000
168E168PRO00.0310.02318.2090.0330.0330.0000.0000.0000.000
169E169TYR0-0.037-0.03815.932-0.004-0.0040.0000.0000.0000.000
170E170LEU0-0.0540.00212.5520.0670.0670.0000.0000.0000.000
171E171GLY00.0410.00415.269-0.029-0.0290.0000.0000.0000.000
172E172LYS10.8680.94116.102-0.187-0.1870.0000.0000.0000.000
173E173LEU00.024-0.00214.166-0.026-0.0260.0000.0000.0000.000
174E174GLU-1-0.833-0.93518.0720.3140.3140.0000.0000.0000.000
175E175TRP0-0.036-0.02319.967-0.024-0.0240.0000.0000.0000.000
176E176ILE00.0190.01616.211-0.014-0.0140.0000.0000.0000.000
177E177GLU-1-0.826-0.89320.4660.3390.3390.0000.0000.0000.000
178E178GLU-1-0.826-0.90822.5580.1410.1410.0000.0000.0000.000
179E179GLU-1-0.915-0.96422.1840.1460.1460.0000.0000.0000.000
180E180LYS10.7690.85919.752-0.363-0.3630.0000.0000.0000.000
181E181ALA00.0150.02624.272-0.013-0.0130.0000.0000.0000.000
182E182LYS10.8500.92027.606-0.146-0.1460.0000.0000.0000.000
183E183LYS10.9050.96123.492-0.148-0.1480.0000.0000.0000.000
184E184GLN0-0.084-0.03426.984-0.007-0.0070.0000.0000.0000.000