FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8NJZY

Calculation Name: 2GDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GDQ

Chain ID: A

ChEMBL ID:

UniProt ID: O06741

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 373
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6528454.568563
FMO2-HF: Nuclear repulsion 6379564.368744
FMO2-HF: Total energy -148890.199819
FMO2-MP2: Total energy -149322.778765


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-13.373-5.7933.143-4.417-6.302-0.018
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.017
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].
3A5LYS10.8170.9163.132-4.003-0.968-0.011-1.593-1.4300.001
4A6ILE00.0120.0015.130-0.972-0.953-0.001-0.006-0.0110.000
5A7VAL0-0.020-0.0126.6900.0940.0940.0000.0000.0000.000
6A8ARG10.8330.8889.4110.3250.3250.0000.0000.0000.000
7A9ILE0-0.011-0.00512.603-0.007-0.0070.0000.0000.0000.000
8A10GLU-1-0.809-0.85315.415-0.228-0.2280.0000.0000.0000.000
9A11THR0-0.032-0.03118.5640.0070.0070.0000.0000.0000.000
10A12PHE00.0210.00519.168-0.004-0.0040.0000.0000.0000.000
11A13PRO0-0.0060.01224.2700.0040.0040.0000.0000.0000.000
12A14LEU0-0.0190.00226.235-0.005-0.0050.0000.0000.0000.000
13A15PHE00.004-0.01729.6800.0060.0060.0000.0000.0000.000
14A16HIS00.0080.00233.449-0.006-0.0060.0000.0000.0000.000
15A17ARG10.9570.98036.1680.0230.0230.0000.0000.0000.000
16A18LEU0-0.052-0.00639.292-0.002-0.0020.0000.0000.0000.000
17A19GLU-1-0.907-0.94841.590-0.029-0.0290.0000.0000.0000.000
18A20LYS10.7470.85144.1090.0280.0280.0000.0000.0000.000
19A21PRO0-0.035-0.01744.2570.0000.0000.0000.0000.0000.000
20A22TYR0-0.005-0.00238.9020.0010.0010.0000.0000.0000.000
21A23GLY00.006-0.00244.0230.0000.0000.0000.0000.0000.000
22A24ASP-1-0.781-0.88142.091-0.002-0.0020.0000.0000.0000.000
23A25ALA00.0520.02345.5320.0000.0000.0000.0000.0000.000
24A26ASN0-0.064-0.01843.3660.0020.0020.0000.0000.0000.000
25A27GLY00.0030.00845.4720.0000.0000.0000.0000.0000.000
26A28PHE0-0.089-0.05944.874-0.001-0.0010.0000.0000.0000.000
27A29LYS10.8770.93539.1630.0060.0060.0000.0000.0000.000
28A30ARG10.8260.87341.7460.0080.0080.0000.0000.0000.000
29A31TYR0-0.055-0.05536.286-0.002-0.0020.0000.0000.0000.000
30A32ARG10.7760.86534.2240.0230.0230.0000.0000.0000.000
31A33THR0-0.010-0.01131.561-0.002-0.0020.0000.0000.0000.000
32A34CYS0-0.0150.00926.518-0.001-0.0010.0000.0000.0000.000
33A35TYR00.016-0.02322.8530.0000.0000.0000.0000.0000.000
34A36LEU00.0570.03421.3140.0060.0060.0000.0000.0000.000
35A37ILE0-0.067-0.03817.4580.0050.0050.0000.0000.0000.000
36A38ARG10.8460.90413.8930.2990.2990.0000.0000.0000.000
37A39ILE0-0.0040.00010.6600.0150.0150.0000.0000.0000.000
38A40ILE00.0190.0029.544-0.051-0.0510.0000.0000.0000.000
39A41THR0-0.040-0.0325.219-0.213-0.090-0.001-0.021-0.1000.000
40A42GLU-1-0.816-0.9132.562-4.844-2.3330.747-1.375-1.883-0.018
41A43SER0-0.041-0.0192.133-0.4480.3392.376-1.201-1.962-0.001
42A44GLY0-0.0040.0084.1140.0660.2910.004-0.061-0.1690.000
43A45ILE0-0.0070.0083.279-0.2740.2240.027-0.091-0.4330.000
44A46ASP-1-0.772-0.8706.791-0.419-0.4190.0000.0000.0000.000
45A47GLY0-0.027-0.0059.799-0.007-0.0070.0000.0000.0000.000
46A48TRP00.0430.01012.2160.0480.0480.0000.0000.0000.000
47A49GLY0-0.005-0.00515.9830.0180.0180.0000.0000.0000.000
48A50GLU-1-0.745-0.84518.489-0.054-0.0540.0000.0000.0000.000
49A51CYS0-0.066-0.02722.2990.0150.0150.0000.0000.0000.000
50A52VAL00.0740.02125.283-0.008-0.0080.0000.0000.0000.000
51A53ASP-1-0.829-0.89929.0030.0230.0230.0000.0000.0000.000
52A54TRP00.0260.00631.351-0.004-0.0040.0000.0000.0000.000
53A55LEU00.0150.00629.4680.0030.0030.0000.0000.0000.000
54A56PRO00.0030.00630.5840.0010.0010.0000.0000.0000.000
55A57ALA00.0090.00731.1100.0020.0020.0000.0000.0000.000
56A58LEU0-0.0140.00026.1150.0070.0070.0000.0000.0000.000
57A59HIS00.0920.05925.1080.0060.0060.0000.0000.0000.000
58A60VAL0-0.0260.00225.9920.0010.0010.0000.0000.0000.000
59A61GLY00.0100.00326.5170.0060.0060.0000.0000.0000.000
60A62PHE00.035-0.00319.8660.0130.0130.0000.0000.0000.000
61A63THR0-0.035-0.03421.7480.0090.0090.0000.0000.0000.000
62A64LYS10.9020.96222.837-0.010-0.0100.0000.0000.0000.000
63A65ARG10.9010.96122.774-0.064-0.0640.0000.0000.0000.000
64A66ILE00.0060.01418.8290.0160.0160.0000.0000.0000.000
65A67ILE00.0370.01316.6130.0230.0230.0000.0000.0000.000
66A68PRO0-0.006-0.00916.4380.0160.0160.0000.0000.0000.000
67A69PHE0-0.0160.00617.0030.0280.0280.0000.0000.0000.000
68A70LEU00.0310.01413.6210.0590.0590.0000.0000.0000.000
69A71LEU00.0100.01612.0080.0560.0560.0000.0000.0000.000
70A72GLY00.0130.0039.2010.0300.0300.0000.0000.0000.000
71A73LYS10.8160.9089.425-0.157-0.1570.0000.0000.0000.000
72A74GLN00.0290.0044.483-1.039-0.943-0.001-0.033-0.0620.000
73A75ALA00.0690.0227.173-0.215-0.2150.0000.0000.0000.000
74A76GLY00.0240.0167.276-0.180-0.1800.0000.0000.0000.000
75A77SER0-0.017-0.0068.147-0.092-0.0920.0000.0000.0000.000
76A78ARG10.8330.88511.488-0.272-0.2720.0000.0000.0000.000
77A79LEU00.0540.02413.384-0.035-0.0350.0000.0000.0000.000
78A80SER00.0240.01115.617-0.036-0.0360.0000.0000.0000.000
79A81LEU0-0.039-0.00811.923-0.042-0.0420.0000.0000.0000.000
80A82VAL00.0320.01816.390-0.040-0.0400.0000.0000.0000.000
81A83ARG10.9490.97918.806-0.186-0.1860.0000.0000.0000.000
82A84THR0-0.075-0.04119.261-0.014-0.0140.0000.0000.0000.000
83A85ILE00.0290.01117.805-0.022-0.0220.0000.0000.0000.000
84A86GLN0-0.030-0.03222.046-0.005-0.0050.0000.0000.0000.000
85A87LYS10.8420.93723.774-0.181-0.1810.0000.0000.0000.000
86A88TRP0-0.073-0.03220.390-0.007-0.0070.0000.0000.0000.000
87A89HIS00.0660.00725.554-0.006-0.0060.0000.0000.0000.000
88A90GLN00.0490.02025.0210.0020.0020.0000.0000.0000.000
89A91ARG10.8150.90425.056-0.020-0.0200.0000.0000.0000.000
90A92ALA00.0380.01222.331-0.005-0.0050.0000.0000.0000.000
91A93ALA0-0.031-0.01320.7960.0030.0030.0000.0000.0000.000
92A94SER00.0470.00720.0330.0090.0090.0000.0000.0000.000
93A95ALA00.0310.03220.064-0.004-0.0040.0000.0000.0000.000
94A96VAL00.018-0.00815.465-0.013-0.0130.0000.0000.0000.000
95A97SER0-0.051-0.03415.5150.0060.0060.0000.0000.0000.000
96A98MET0-0.0060.03015.804-0.003-0.0030.0000.0000.0000.000
97A99ALA00.0400.03113.951-0.019-0.0190.0000.0000.0000.000
98A100LEU0-0.034-0.03410.885-0.032-0.0320.0000.0000.0000.000
99A101THR0-0.044-0.03010.8290.0310.0310.0000.0000.0000.000
100A102GLU-1-0.775-0.87911.942-0.273-0.2730.0000.0000.0000.000
101A103ILE0-0.016-0.0066.179-0.051-0.0510.0000.0000.0000.000
102A104ALA0-0.024-0.0157.296-0.117-0.1170.0000.0000.0000.000
103A105ALA00.0000.0088.166-0.048-0.0480.0000.0000.0000.000
104A106LYS10.8090.8867.9280.3960.3960.0000.0000.0000.000
105A107ALA0-0.048-0.0243.709-0.357-0.1620.004-0.035-0.1630.000
106A108ALA0-0.045-0.0144.946-0.151-0.060-0.001-0.001-0.0890.000
107A109ASP-1-0.824-0.8827.520-0.424-0.4240.0000.0000.0000.000
108A110CYS0-0.036-0.0229.2230.0800.0800.0000.0000.0000.000
109A111SER00.022-0.01012.352-0.020-0.0200.0000.0000.0000.000
110A112VAL00.013-0.00814.5100.0170.0170.0000.0000.0000.000
111A113CYS0-0.024-0.00415.7230.0260.0260.0000.0000.0000.000
112A114GLU-1-0.817-0.87115.225-0.106-0.1060.0000.0000.0000.000
113A115LEU0-0.009-0.00710.7870.0280.0280.0000.0000.0000.000
114A116TRP0-0.070-0.05514.2690.0330.0330.0000.0000.0000.000
115A117GLY00.0020.00617.5990.0140.0140.0000.0000.0000.000
116A118GLY0-0.0020.01519.300-0.004-0.0040.0000.0000.0000.000
117A119ARG10.7910.85520.2070.0820.0820.0000.0000.0000.000
118A120TYR0-0.027-0.01723.739-0.002-0.0020.0000.0000.0000.000
119A121ARG10.8010.90626.9320.0110.0110.0000.0000.0000.000
120A122GLU-1-0.727-0.83325.278-0.068-0.0680.0000.0000.0000.000
121A123GLU-1-0.883-0.93727.820-0.047-0.0470.0000.0000.0000.000
122A124ILE0-0.034-0.02128.2730.0050.0050.0000.0000.0000.000
123A125PRO00.0460.02831.217-0.003-0.0030.0000.0000.0000.000
124A126VAL0-0.035-0.02532.3130.0010.0010.0000.0000.0000.000
125A127TYR00.0260.02735.2580.0000.0000.0000.0000.0000.000
126A128ALA00.0010.01037.542-0.001-0.0010.0000.0000.0000.000
127A129SER0-0.056-0.05737.6500.0030.0030.0000.0000.0000.000
128A130PHE00.009-0.01439.570-0.003-0.0030.0000.0000.0000.000
129A131GLN0-0.002-0.01740.1680.0030.0030.0000.0000.0000.000
130A132SER00.0480.01143.5100.0000.0000.0000.0000.0000.000
131A133TYR0-0.0290.02047.1090.0000.0000.0000.0000.0000.000
132A134SER00.039-0.00947.547-0.001-0.0010.0000.0000.0000.000
133A135ASP-1-0.770-0.86549.636-0.008-0.0080.0000.0000.0000.000
134A136SER0-0.087-0.05052.123-0.001-0.0010.0000.0000.0000.000
135A137PRO00.0680.02055.2300.0000.0000.0000.0000.0000.000
136A138GLN0-0.014-0.00156.4360.0010.0010.0000.0000.0000.000
137A139TRP00.0170.02251.248-0.001-0.0010.0000.0000.0000.000
138A140ILE00.0650.04152.296-0.001-0.0010.0000.0000.0000.000
139A141SER00.007-0.00753.4540.0000.0000.0000.0000.0000.000
140A142ARG10.9000.96550.4960.0130.0130.0000.0000.0000.000
141A143SER0-0.013-0.01748.865-0.002-0.0020.0000.0000.0000.000
142A144VAL00.0430.01149.138-0.001-0.0010.0000.0000.0000.000
143A145SER0-0.010-0.01350.649-0.001-0.0010.0000.0000.0000.000
144A146ASN0-0.008-0.00743.600-0.003-0.0030.0000.0000.0000.000
145A147VAL00.0580.01945.976-0.001-0.0010.0000.0000.0000.000
146A148GLU-1-0.829-0.90046.640-0.019-0.0190.0000.0000.0000.000
147A149ALA0-0.061-0.02945.801-0.001-0.0010.0000.0000.0000.000
148A150GLN00.0350.01941.661-0.005-0.0050.0000.0000.0000.000
149A151LEU00.0360.01843.421-0.001-0.0010.0000.0000.0000.000
150A152LYS10.8160.89345.6920.0200.0200.0000.0000.0000.000
151A153LYS10.8390.92540.0760.0320.0320.0000.0000.0000.000
152A154GLY0-0.001-0.00341.068-0.002-0.0020.0000.0000.0000.000
153A155PHE0-0.030-0.02437.067-0.001-0.0010.0000.0000.0000.000
154A156GLU-1-0.908-0.95341.914-0.019-0.0190.0000.0000.0000.000
155A157GLN0-0.020-0.01340.4540.0030.0030.0000.0000.0000.000
156A158ILE0-0.011-0.00541.476-0.002-0.0020.0000.0000.0000.000
157A159LYS10.7950.89438.0950.0050.0050.0000.0000.0000.000
158A160VAL0-0.028-0.01142.989-0.002-0.0020.0000.0000.0000.000
159A161LYS10.7590.85940.9880.0050.0050.0000.0000.0000.000
160A162ILE0-0.045-0.02746.863-0.001-0.0010.0000.0000.0000.000
161A163GLY00.026-0.00148.6660.0010.0010.0000.0000.0000.000
162A164GLY00.0530.03150.4200.0010.0010.0000.0000.0000.000
163A165THR0-0.067-0.03751.0760.0000.0000.0000.0000.0000.000
164A166SER0-0.0230.00154.8410.0010.0010.0000.0000.0000.000
165A167PHE00.1040.03156.165-0.001-0.0010.0000.0000.0000.000
166A168LYS10.9280.95157.5000.0000.0000.0000.0000.0000.000
167A169GLU-1-0.888-0.90656.701-0.004-0.0040.0000.0000.0000.000
168A170ASP-1-0.699-0.83552.976-0.002-0.0020.0000.0000.0000.000
169A171VAL00.0260.01654.823-0.001-0.0010.0000.0000.0000.000
170A172ARG10.8400.91257.2310.0040.0040.0000.0000.0000.000
171A173HIS00.0100.02349.234-0.002-0.0020.0000.0000.0000.000
172A174ILE00.0610.02850.292-0.001-0.0010.0000.0000.0000.000
173A175ASN0-0.036-0.02353.708-0.001-0.0010.0000.0000.0000.000
174A176ALA0-0.011-0.00655.770-0.001-0.0010.0000.0000.0000.000
175A177LEU00.0050.00649.550-0.001-0.0010.0000.0000.0000.000
176A178GLN00.0160.00752.541-0.002-0.0020.0000.0000.0000.000
177A179HIS0-0.093-0.05354.3900.0000.0000.0000.0000.0000.000
178A180THR0-0.022-0.00353.3160.0000.0000.0000.0000.0000.000
179A181ALA0-0.020-0.00749.888-0.001-0.0010.0000.0000.0000.000
180A182GLY00.0280.02151.635-0.001-0.0010.0000.0000.0000.000
181A183SER0-0.003-0.01951.7880.0000.0000.0000.0000.0000.000
182A184SER0-0.019-0.00550.0390.0010.0010.0000.0000.0000.000
183A185ILE0-0.058-0.00746.141-0.001-0.0010.0000.0000.0000.000
184A186THR00.0020.01343.8800.0020.0020.0000.0000.0000.000
185A187MET0-0.017-0.01845.331-0.001-0.0010.0000.0000.0000.000
186A188ILE0-0.0210.00540.7350.0010.0010.0000.0000.0000.000
187A189LEU00.0020.00044.999-0.001-0.0010.0000.0000.0000.000
188A190ASP-1-0.753-0.87141.8300.0020.0020.0000.0000.0000.000
189A191ALA00.0210.00945.043-0.001-0.0010.0000.0000.0000.000
190A192ASN0-0.044-0.01841.106-0.001-0.0010.0000.0000.0000.000
191A193GLN0-0.007-0.02840.7880.0020.0020.0000.0000.0000.000
192A194SER0-0.062-0.02645.7580.0010.0010.0000.0000.0000.000
193A195TYR0-0.043-0.01249.1390.0000.0000.0000.0000.0000.000
194A196ASP-1-0.756-0.88250.6740.0110.0110.0000.0000.0000.000
195A197ALA00.0570.00452.781-0.001-0.0010.0000.0000.0000.000
196A198ALA0-0.016-0.00953.662-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.076-0.05154.917-0.001-0.0010.0000.0000.0000.000
198A200ALA00.0150.01051.517-0.001-0.0010.0000.0000.0000.000
199A201PHE00.0430.01053.435-0.001-0.0010.0000.0000.0000.000
200A202LYS10.8990.96255.701-0.005-0.0050.0000.0000.0000.000
201A203TRP00.013-0.00453.334-0.001-0.0010.0000.0000.0000.000
202A204GLU-1-0.700-0.79855.0120.0040.0040.0000.0000.0000.000
203A205ARG10.8240.91056.692-0.001-0.0010.0000.0000.0000.000
204A206TYR00.0190.00856.7920.0000.0000.0000.0000.0000.000
205A207PHE00.0320.00651.088-0.001-0.0010.0000.0000.0000.000
206A208SER0-0.034-0.02755.0810.0000.0000.0000.0000.0000.000
207A209GLU-1-0.977-0.97757.772-0.002-0.0020.0000.0000.0000.000
208A210TRP0-0.083-0.04253.758-0.001-0.0010.0000.0000.0000.000
209A211THR00.007-0.00653.2510.0000.0000.0000.0000.0000.000
210A212ASN0-0.0010.00149.9080.0010.0010.0000.0000.0000.000
211A213ILE0-0.022-0.00548.570-0.001-0.0010.0000.0000.0000.000
212A214GLY00.0000.00344.6890.0010.0010.0000.0000.0000.000
213A215TRP0-0.077-0.07038.2580.0010.0010.0000.0000.0000.000
214A216LEU00.0080.01645.262-0.001-0.0010.0000.0000.0000.000
215A217GLU-1-0.770-0.87839.1460.0030.0030.0000.0000.0000.000
216A218GLU-1-0.770-0.88539.3790.0150.0150.0000.0000.0000.000
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