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: R92R8

Calculation Name: 1OGH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OGH

Chain ID: A

ChEMBL ID:

UniProt ID: Q57872

Base Structure: X-ray

Registration Date: 2023-09-20

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1802388.730588
FMO2-HF: Nuclear repulsion 1733186.969824
FMO2-HF: Total energy -69201.760765
FMO2-MP2: Total energy -69406.985244


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:1:MET)


Summations of interaction energy for fragment #1(A: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.
-4.1971.0842.118-3.015-4.386-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.013
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].
3A3LEU0-0.051-0.0133.839-0.7271.287-0.008-0.952-1.0550.004
4A4SER0-0.020-0.0405.8980.4400.4400.0000.0000.0000.000
5A5ASP-1-0.809-0.9048.176-0.099-0.0990.0000.0000.0000.000
6A6LYS10.8740.8999.978-0.232-0.2320.0000.0000.0000.000
7A7ASP-1-0.791-0.8506.914-0.396-0.3960.0000.0000.0000.000
8A8ILE0-0.024-0.0129.507-0.108-0.1080.0000.0000.0000.000
9A9ILE0-0.0050.00011.4390.0260.0260.0000.0000.0000.000
10A10ASP-1-0.842-0.90612.142-0.284-0.2840.0000.0000.0000.000
11A11TYR0-0.0180.0017.630-0.096-0.0960.0000.0000.0000.000
12A12VAL00.0350.03612.9880.0320.0320.0000.0000.0000.000
13A13THR0-0.065-0.03816.2110.0670.0670.0000.0000.0000.000
14A14SER0-0.075-0.07114.9050.0150.0150.0000.0000.0000.000
15A15LYS10.7950.88717.5240.3130.3130.0000.0000.0000.000
16A16ARG10.8950.96110.4720.7580.7580.0000.0000.0000.000
17A17ILE00.0170.01410.394-0.049-0.0490.0000.0000.0000.000
18A18ILE0-0.059-0.02514.9230.0860.0860.0000.0000.0000.000
19A19ILE00.0100.00115.775-0.025-0.0250.0000.0000.0000.000
20A20LYS10.8180.93919.7760.3030.3030.0000.0000.0000.000
21A21PRO00.0290.00723.6220.0030.0030.0000.0000.0000.000
22A22PHE00.0380.00217.331-0.018-0.0180.0000.0000.0000.000
23A23ASN0-0.005-0.02121.4090.0250.0250.0000.0000.0000.000
24A24LYS11.0201.01819.5670.0780.0780.0000.0000.0000.000
25A25ASP-1-0.867-0.92319.535-0.108-0.1080.0000.0000.0000.000
26A26PHE0-0.075-0.03619.8930.0300.0300.0000.0000.0000.000
27A27VAL0-0.0160.01114.071-0.031-0.0310.0000.0000.0000.000
28A28GLY00.0190.01714.7570.0560.0560.0000.0000.0000.000
29A29PRO0-0.009-0.02712.792-0.061-0.0610.0000.0000.0000.000
30A30CYS0-0.024-0.0078.2670.1310.1310.0000.0000.0000.000
31A31SER00.0070.0139.818-0.143-0.1430.0000.0000.0000.000
32A32TYR00.0200.01312.3880.0510.0510.0000.0000.0000.000
33A33ASP-1-0.751-0.83315.426-0.169-0.1690.0000.0000.0000.000
34A34VAL0-0.008-0.00318.408-0.015-0.0150.0000.0000.0000.000
35A35THR0-0.041-0.05820.9130.0330.0330.0000.0000.0000.000
36A36LEU0-0.040-0.00624.638-0.014-0.0140.0000.0000.0000.000
37A37GLY00.0340.02427.1630.0090.0090.0000.0000.0000.000
38A38ASP-1-0.847-0.92529.049-0.098-0.0980.0000.0000.0000.000
39A39GLU-1-0.823-0.88431.635-0.103-0.1030.0000.0000.0000.000
40A40PHE00.000-0.01330.335-0.009-0.0090.0000.0000.0000.000
41A41ILE0-0.025-0.01031.7820.0040.0040.0000.0000.0000.000
42A42ILE00.0040.00533.047-0.001-0.0010.0000.0000.0000.000
43A43TYR00.0380.01230.4970.0000.0000.0000.0000.0000.000
44A44ASP-1-0.836-0.91736.924-0.059-0.0590.0000.0000.0000.000
45A45ASP-1-0.812-0.86738.579-0.061-0.0610.0000.0000.0000.000
46A46GLU-1-0.976-0.98439.778-0.038-0.0380.0000.0000.0000.000
47A47VAL0-0.013-0.01538.1140.0010.0010.0000.0000.0000.000
48A48TYR0-0.014-0.00833.031-0.002-0.0020.0000.0000.0000.000
49A49ASP-1-0.766-0.83134.420-0.062-0.0620.0000.0000.0000.000
50A50LEU00.001-0.01529.167-0.003-0.0030.0000.0000.0000.000
51A51SER0-0.111-0.06732.990-0.004-0.0040.0000.0000.0000.000
52A52LYS10.7750.86335.4790.0630.0630.0000.0000.0000.000
53A53GLU-1-0.905-0.94735.398-0.104-0.1040.0000.0000.0000.000
54A54LEU0-0.035-0.01232.5720.0040.0040.0000.0000.0000.000
55A55ASN0-0.066-0.05336.582-0.005-0.0050.0000.0000.0000.000
56A56TYR0-0.035-0.02435.278-0.002-0.0020.0000.0000.0000.000
57A57LYS10.8500.92137.9730.0630.0630.0000.0000.0000.000
58A58ARG10.8780.92132.5950.1120.1120.0000.0000.0000.000
59A59ILE0-0.0080.00336.2950.0060.0060.0000.0000.0000.000
60A60LYS10.8010.86734.9640.0960.0960.0000.0000.0000.000
61A61ILE0-0.0170.01933.7220.0060.0060.0000.0000.0000.000
62A62LYS10.9250.96837.2180.0480.0480.0000.0000.0000.000
63A63ASN0-0.104-0.09037.445-0.003-0.0030.0000.0000.0000.000
64A64SER00.015-0.00335.601-0.004-0.0040.0000.0000.0000.000
65A65ILE0-0.0050.01333.6510.0020.0020.0000.0000.0000.000
66A66LEU0-0.0060.00335.4780.0000.0000.0000.0000.0000.000
67A67VAL00.0200.00531.677-0.001-0.0010.0000.0000.0000.000
68A68CYS0-0.025-0.00834.7280.0050.0050.0000.0000.0000.000
69A69PRO00.0130.01134.530-0.004-0.0040.0000.0000.0000.000
70A70LEU00.0370.01235.3750.0000.0000.0000.0000.0000.000
71A71ASN0-0.063-0.02537.2000.0030.0030.0000.0000.0000.000
72A72TYR0-0.001-0.01938.6070.0040.0040.0000.0000.0000.000
73A73ASN0-0.050-0.01241.8190.0010.0010.0000.0000.0000.000
74A74LEU00.008-0.00540.5020.0020.0020.0000.0000.0000.000
75A75THR00.0370.02644.906-0.002-0.0020.0000.0000.0000.000
76A76GLU-1-0.862-0.95547.833-0.036-0.0360.0000.0000.0000.000
77A77GLU-1-0.973-0.96849.481-0.019-0.0190.0000.0000.0000.000
78A78LYS10.8790.95045.0480.0200.0200.0000.0000.0000.000
79A79ILE00.0340.01044.0090.0000.0000.0000.0000.0000.000
80A80ASN00.0570.02945.610-0.004-0.0040.0000.0000.0000.000
81A81TYR00.0690.03945.5780.0010.0010.0000.0000.0000.000
82A82PHE0-0.023-0.03042.3000.0010.0010.0000.0000.0000.000
83A83LYS10.9040.95043.7280.0380.0380.0000.0000.0000.000
84A84GLU-1-0.923-0.96644.825-0.027-0.0270.0000.0000.0000.000
85A85LYS10.8280.92144.8430.0170.0170.0000.0000.0000.000
86A86TYR0-0.018-0.02340.6650.0030.0030.0000.0000.0000.000
87A87ASN0-0.046-0.00541.198-0.003-0.0030.0000.0000.0000.000
88A88VAL0-0.029-0.00238.631-0.003-0.0030.0000.0000.0000.000
89A89ASP-1-0.753-0.86339.470-0.057-0.0570.0000.0000.0000.000
90A90TYR0-0.001-0.00938.3600.0000.0000.0000.0000.0000.000
91A91VAL0-0.005-0.00839.2990.0000.0000.0000.0000.0000.000
92A92VAL00.0010.01135.1170.0000.0000.0000.0000.0000.000
93A93GLU-1-0.788-0.90737.194-0.031-0.0310.0000.0000.0000.000
94A94GLY0-0.0020.00535.013-0.002-0.0020.0000.0000.0000.000
95A95GLY0-0.014-0.00731.826-0.001-0.0010.0000.0000.0000.000
96A96VAL0-0.047-0.01930.9000.0020.0020.0000.0000.0000.000
97A97LEU00.0260.02626.942-0.007-0.0070.0000.0000.0000.000
98A98GLY00.0470.01727.5500.0090.0090.0000.0000.0000.000
99A99THR0-0.015-0.01925.380-0.017-0.0170.0000.0000.0000.000
100A100THR00.0270.01820.6720.0140.0140.0000.0000.0000.000
101A101ASN0-0.036-0.03224.0990.0090.0090.0000.0000.0000.000
102A102GLU-1-0.804-0.87821.140-0.218-0.2180.0000.0000.0000.000
103A103TYR0-0.025-0.01422.023-0.009-0.0090.0000.0000.0000.000
104A104ILE0-0.013-0.01815.622-0.008-0.0080.0000.0000.0000.000
105A105GLU-1-0.760-0.87817.825-0.284-0.2840.0000.0000.0000.000
106A106LEU0-0.0120.00911.794-0.053-0.0530.0000.0000.0000.000
107A107PRO00.0070.01311.1000.0900.0900.0000.0000.0000.000
108A108ASN00.0370.00512.481-0.117-0.1170.0000.0000.0000.000
109A109ASP-1-0.777-0.8849.203-1.119-1.1190.0000.0000.0000.000
110A110ILE0-0.059-0.0356.472-0.470-0.4700.0000.0000.0000.000
111A111SER00.0080.0097.1920.4050.4050.0000.0000.0000.000
112A112ALA0-0.006-0.0238.055-0.445-0.4450.0000.0000.0000.000
113A113GLN0-0.024-0.0079.9170.1270.1270.0000.0000.0000.000
114A114TYR0-0.003-0.02111.4920.0110.0110.0000.0000.0000.000
115A115GLN00.0080.00913.4820.0510.0510.0000.0000.0000.000
116A116GLY00.0690.04116.2970.0050.0050.0000.0000.0000.000
117A117ARG10.8040.88119.3690.1320.1320.0000.0000.0000.000
118A118SER00.0420.00319.2540.0130.0130.0000.0000.0000.000
119A119SER0-0.058-0.03221.7970.0110.0110.0000.0000.0000.000
120A120LEU00.0290.02024.7470.0070.0070.0000.0000.0000.000
121A121GLY00.0770.04424.0040.0040.0040.0000.0000.0000.000
122A122ARG10.8780.93222.377-0.034-0.0340.0000.0000.0000.000
123A123VAL0-0.027-0.00227.1770.0060.0060.0000.0000.0000.000
124A124PHE0-0.0040.00028.140-0.002-0.0020.0000.0000.0000.000
125A125LEU00.0070.01827.067-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.025-0.01824.193-0.004-0.0040.0000.0000.0000.000
127A127SER00.0370.00222.625-0.003-0.0030.0000.0000.0000.000
128A128HIS0-0.044-0.03718.497-0.050-0.0500.0000.0000.0000.000
129A129GLN0-0.058-0.03621.8210.0280.0280.0000.0000.0000.000
130A130THR0-0.0070.00619.0080.0010.0010.0000.0000.0000.000
131A131ALA0-0.016-0.02714.609-0.003-0.0030.0000.0000.0000.000
132A132GLY00.0630.03214.344-0.040-0.0400.0000.0000.0000.000
133A133TRP0-0.054-0.0176.224-0.109-0.1090.0000.0000.0000.000
134A134ILE0-0.0230.00612.0900.0870.0870.0000.0000.0000.000
135A135ASP-1-0.851-0.91612.013-0.621-0.6210.0000.0000.0000.000
136A136ALA00.0140.00110.817-0.029-0.0290.0000.0000.0000.000
137A137GLY00.0030.01812.6080.1080.1080.0000.0000.0000.000
138A138PHE0-0.0280.00115.3870.0660.0660.0000.0000.0000.000
139A139LYS10.8710.90917.2680.3210.3210.0000.0000.0000.000
140A140GLY00.0450.03220.0890.0310.0310.0000.0000.0000.000
141A141LYS10.8090.90821.0010.1700.1700.0000.0000.0000.000
142A142ILE00.0210.01817.804-0.005-0.0050.0000.0000.0000.000
143A143THR00.0130.00520.9910.0290.0290.0000.0000.0000.000
144A144LEU0-0.055-0.02421.918-0.012-0.0120.0000.0000.0000.000
145A145GLU-1-0.732-0.86622.019-0.150-0.1500.0000.0000.0000.000
146A146ILE0-0.053-0.01525.3210.0060.0060.0000.0000.0000.000
147A147VAL00.0490.03227.6230.0060.0060.0000.0000.0000.000
148A148ALA00.0020.01828.708-0.001-0.0010.0000.0000.0000.000
149A149PHE0-0.004-0.01827.0590.0040.0040.0000.0000.0000.000
150A150ASP-1-0.818-0.88131.9490.0010.0010.0000.0000.0000.000
151A151LYS10.8110.88134.5510.0050.0050.0000.0000.0000.000
152A152PRO0-0.001-0.01034.907-0.003-0.0030.0000.0000.0000.000
153A153VAL0-0.0250.00730.9230.0030.0030.0000.0000.0000.000
154A154ILE0-0.034-0.01134.195-0.004-0.0040.0000.0000.0000.000
155A155LEU0-0.027-0.00628.993-0.002-0.0020.0000.0000.0000.000
156A156TYR00.028-0.01031.5030.0040.0040.0000.0000.0000.000
157A157LYS10.8380.90831.0300.0780.0780.0000.0000.0000.000
158A158ASN0-0.017-0.01328.8370.0000.0000.0000.0000.0000.000
159A159GLN00.0300.04227.2090.0030.0030.0000.0000.0000.000
160A160ARG10.8230.88321.4680.1110.1110.0000.0000.0000.000
161A161ILE0-0.026-0.02322.7990.0190.0190.0000.0000.0000.000
162A162GLY00.0190.00819.8520.0140.0140.0000.0000.0000.000
163A163GLN0-0.053-0.03115.2800.0260.0260.0000.0000.0000.000
164A164LEU00.0090.01313.5150.0010.0010.0000.0000.0000.000
165A165ILE00.010-0.0017.8040.0470.0470.0000.0000.0000.000
166A166PHE00.0420.0168.458-0.056-0.0560.0000.0000.0000.000
167A167SER00.0200.0022.838-3.023-1.8870.278-0.639-0.776-0.005
168A168LYS10.8090.9022.0262.5133.8941.821-1.052-2.1490.002
169A169LEU00.0060.0193.339-1.328-0.5780.027-0.372-0.406-0.003
170A170LEU0-0.017-0.0125.5110.0320.0320.0000.0000.0000.000
171A171SER0-0.030-0.0296.6380.1150.1150.0000.0000.0000.000
172A172PRO0-0.050-0.0189.682-0.130-0.1300.0000.0000.0000.000
173A173ALA00.0530.02311.7390.0830.0830.0000.0000.0000.000
174A174ASP-1-0.916-0.95213.648-0.267-0.2670.0000.0000.0000.000
175A175VAL0-0.075-0.05415.643-0.011-0.0110.0000.0000.0000.000