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: Z683N

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1802348.840122
FMO2-HF: Nuclear repulsion 1733147.454473
FMO2-HF: Total energy -69201.385649
FMO2-MP2: Total energy -69406.541165


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.
-2.4932.7790.579-2.33-3.5220.004
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 : 0.035 / q_NPA : 0.019
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].
3A3LEU0-0.048-0.0183.801-1.0921.413-0.019-1.172-1.3140.006
4A4SER0-0.034-0.0515.8660.3690.3690.0000.0000.0000.000
5A5ASP-1-0.827-0.9218.019-0.061-0.0610.0000.0000.0000.000
6A6LYS10.9430.94610.052-0.437-0.4370.0000.0000.0000.000
7A7ASP-1-0.794-0.8576.676-0.343-0.3430.0000.0000.0000.000
8A8ILE0-0.035-0.0189.615-0.094-0.0940.0000.0000.0000.000
9A9ILE0-0.001-0.00411.6360.0100.0100.0000.0000.0000.000
10A10ASP-1-0.867-0.91212.067-0.248-0.2480.0000.0000.0000.000
11A11TYR0-0.010-0.0197.662-0.119-0.1190.0000.0000.0000.000
12A12VAL00.0370.03613.1590.0230.0230.0000.0000.0000.000
13A13THR0-0.062-0.03916.3490.0550.0550.0000.0000.0000.000
14A14SER0-0.070-0.05215.3060.0130.0130.0000.0000.0000.000
15A15LYS10.7950.89117.8850.2930.2930.0000.0000.0000.000
16A16ARG10.9230.98010.4330.7720.7720.0000.0000.0000.000
17A17ILE00.0150.01110.424-0.055-0.0550.0000.0000.0000.000
18A18ILE0-0.059-0.01915.0100.0840.0840.0000.0000.0000.000
19A19ILE00.0270.00715.448-0.025-0.0250.0000.0000.0000.000
20A20LYS10.8620.98319.7240.3010.3010.0000.0000.0000.000
21A21PRO00.0540.00423.572-0.002-0.0020.0000.0000.0000.000
22A22PHE00.0540.01417.237-0.013-0.0130.0000.0000.0000.000
23A23ASN00.0110.00421.5180.0270.0270.0000.0000.0000.000
24A24LYS11.0161.00719.6400.0630.0630.0000.0000.0000.000
25A25ASP-1-0.896-0.95619.566-0.080-0.0800.0000.0000.0000.000
26A26PHE0-0.103-0.06019.8180.0280.0280.0000.0000.0000.000
27A27VAL0-0.0210.01214.013-0.039-0.0390.0000.0000.0000.000
28A28GLY00.0210.01915.1190.0530.0530.0000.0000.0000.000
29A29PRO00.003-0.01812.695-0.042-0.0420.0000.0000.0000.000
30A30CYS0-0.007-0.0088.2810.1300.1300.0000.0000.0000.000
31A31SER00.0020.01510.007-0.132-0.1320.0000.0000.0000.000
32A32TYR00.0120.01912.4590.0710.0710.0000.0000.0000.000
33A33ASP-1-0.765-0.84515.543-0.164-0.1640.0000.0000.0000.000
34A34VAL0-0.028-0.00918.458-0.008-0.0080.0000.0000.0000.000
35A35THR0-0.049-0.06720.9120.0330.0330.0000.0000.0000.000
36A36LEU0-0.0330.00324.641-0.016-0.0160.0000.0000.0000.000
37A37GLY00.0410.02327.2820.0090.0090.0000.0000.0000.000
38A38ASP-1-0.880-0.95129.557-0.103-0.1030.0000.0000.0000.000
39A39GLU-1-0.834-0.88632.080-0.111-0.1110.0000.0000.0000.000
40A40PHE0-0.001-0.02130.530-0.009-0.0090.0000.0000.0000.000
41A41ILE0-0.033-0.00932.0440.0050.0050.0000.0000.0000.000
42A42ILE0-0.007-0.01433.521-0.001-0.0010.0000.0000.0000.000
43A43TYR00.0300.01130.5200.0000.0000.0000.0000.0000.000
44A44ASP-1-0.844-0.91536.872-0.070-0.0700.0000.0000.0000.000
45A45ASP-1-0.806-0.86139.165-0.075-0.0750.0000.0000.0000.000
46A46GLU-1-1.002-0.99940.250-0.050-0.0500.0000.0000.0000.000
47A47VAL0-0.021-0.02238.5980.0010.0010.0000.0000.0000.000
48A48TYR0-0.026-0.00833.354-0.002-0.0020.0000.0000.0000.000
49A49ASP-1-0.764-0.83735.406-0.081-0.0810.0000.0000.0000.000
50A50LEU00.004-0.01529.344-0.001-0.0010.0000.0000.0000.000
51A51SER0-0.095-0.06333.469-0.003-0.0030.0000.0000.0000.000
52A52LYS10.7890.87535.8450.0800.0800.0000.0000.0000.000
53A53GLU-1-0.920-0.95435.798-0.123-0.1230.0000.0000.0000.000
54A54LEU0-0.035-0.01632.6840.0050.0050.0000.0000.0000.000
55A55ASN0-0.050-0.03636.712-0.005-0.0050.0000.0000.0000.000
56A56TYR0-0.022-0.01735.746-0.002-0.0020.0000.0000.0000.000
57A57LYS10.8680.92337.9220.0710.0710.0000.0000.0000.000
58A58ARG10.9030.93632.7950.1210.1210.0000.0000.0000.000
59A59ILE0-0.032-0.01036.6790.0060.0060.0000.0000.0000.000
60A60LYS10.8060.88235.5390.1000.1000.0000.0000.0000.000
61A61ILE0-0.0230.00734.1360.0060.0060.0000.0000.0000.000
62A62LYS10.9310.97037.5820.0500.0500.0000.0000.0000.000
63A63ASN0-0.062-0.05837.200-0.004-0.0040.0000.0000.0000.000
64A64SER00.003-0.00135.694-0.002-0.0020.0000.0000.0000.000
65A65ILE00.0040.01633.5700.0020.0020.0000.0000.0000.000
66A66LEU0-0.0070.00135.4690.0010.0010.0000.0000.0000.000
67A67VAL00.0160.00531.914-0.001-0.0010.0000.0000.0000.000
68A68CYS0-0.033-0.01735.0240.0060.0060.0000.0000.0000.000
69A69PRO00.0100.00334.867-0.005-0.0050.0000.0000.0000.000
70A70LEU00.0390.00935.4260.0000.0000.0000.0000.0000.000
71A71ASN0-0.047-0.01437.2280.0030.0030.0000.0000.0000.000
72A72TYR00.011-0.01139.0880.0050.0050.0000.0000.0000.000
73A73ASN0-0.055-0.01541.9080.0010.0010.0000.0000.0000.000
74A74LEU00.009-0.00240.8040.0020.0020.0000.0000.0000.000
75A75THR00.0190.01845.192-0.002-0.0020.0000.0000.0000.000
76A76GLU-1-0.854-0.94947.936-0.041-0.0410.0000.0000.0000.000
77A77GLU-1-0.981-0.98249.828-0.022-0.0220.0000.0000.0000.000
78A78LYS10.8850.95445.2590.0240.0240.0000.0000.0000.000
79A79ILE00.0620.02044.2160.0000.0000.0000.0000.0000.000
80A80ASN00.0470.01546.098-0.003-0.0030.0000.0000.0000.000
81A81TYR00.0530.03845.8990.0010.0010.0000.0000.0000.000
82A82PHE0-0.003-0.02442.5880.0020.0020.0000.0000.0000.000
83A83LYS10.9140.96444.1610.0420.0420.0000.0000.0000.000
84A84GLU-1-0.945-0.97245.229-0.027-0.0270.0000.0000.0000.000
85A85LYS10.8220.93245.0110.0190.0190.0000.0000.0000.000
86A86TYR0-0.026-0.03740.8330.0030.0030.0000.0000.0000.000
87A87ASN0-0.041-0.00341.447-0.002-0.0020.0000.0000.0000.000
88A88VAL0-0.0110.00938.781-0.003-0.0030.0000.0000.0000.000
89A89ASP-1-0.822-0.91239.934-0.058-0.0580.0000.0000.0000.000
90A90TYR00.010-0.00438.4800.0000.0000.0000.0000.0000.000
91A91VAL0-0.015-0.00639.3590.0000.0000.0000.0000.0000.000
92A92VAL00.0100.01335.3590.0000.0000.0000.0000.0000.000
93A93GLU-1-0.807-0.91537.305-0.041-0.0410.0000.0000.0000.000
94A94GLY0-0.0010.00434.803-0.002-0.0020.0000.0000.0000.000
95A95GLY0-0.035-0.00431.703-0.002-0.0020.0000.0000.0000.000
96A96VAL0-0.015-0.00431.1620.0020.0020.0000.0000.0000.000
97A97LEU00.0120.01627.451-0.007-0.0070.0000.0000.0000.000
98A98GLY00.0370.01827.8670.0110.0110.0000.0000.0000.000
99A99THR0-0.008-0.01725.692-0.018-0.0180.0000.0000.0000.000
100A100THR00.0090.02021.1100.0140.0140.0000.0000.0000.000
101A101ASN0-0.024-0.02924.5360.0070.0070.0000.0000.0000.000
102A102GLU-1-0.809-0.87321.292-0.225-0.2250.0000.0000.0000.000
103A103TYR0-0.066-0.05222.511-0.007-0.0070.0000.0000.0000.000
104A104ILE00.013-0.01215.693-0.005-0.0050.0000.0000.0000.000
105A105GLU-1-0.806-0.88818.037-0.306-0.3060.0000.0000.0000.000
106A106LEU0-0.034-0.00412.101-0.042-0.0420.0000.0000.0000.000
107A107PRO00.0150.02011.5250.0780.0780.0000.0000.0000.000
108A108ASN00.0430.00612.818-0.125-0.1250.0000.0000.0000.000
109A109ASP-1-0.768-0.8779.108-1.177-1.1770.0000.0000.0000.000
110A110ILE0-0.038-0.0216.814-0.488-0.4880.0000.0000.0000.000
111A111SER00.0240.0227.5020.3800.3800.0000.0000.0000.000
112A112ALA0-0.007-0.0178.262-0.420-0.4200.0000.0000.0000.000
113A113GLN0-0.026-0.01610.1910.0530.0530.0000.0000.0000.000
114A114TYR0-0.016-0.02511.8870.0170.0170.0000.0000.0000.000
115A115GLN0-0.0010.00513.6040.0620.0620.0000.0000.0000.000
116A116GLY00.0370.02316.5240.0050.0050.0000.0000.0000.000
117A117ARG10.8280.89819.4750.1240.1240.0000.0000.0000.000
118A118SER00.0430.00519.1980.0150.0150.0000.0000.0000.000
119A119SER0-0.058-0.03621.5810.0090.0090.0000.0000.0000.000
120A120LEU00.0230.01924.4970.0070.0070.0000.0000.0000.000
121A121GLY00.0640.03923.6950.0030.0030.0000.0000.0000.000
122A122ARG10.8870.93421.900-0.033-0.0330.0000.0000.0000.000
123A123VAL0-0.0260.00126.8080.0070.0070.0000.0000.0000.000
124A124PHE0-0.015-0.00727.850-0.003-0.0030.0000.0000.0000.000
125A125LEU00.0060.02326.874-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.022-0.00424.073-0.007-0.0070.0000.0000.0000.000
127A127SER00.0650.01922.849-0.004-0.0040.0000.0000.0000.000
128A128HIS0-0.012-0.01818.234-0.052-0.0520.0000.0000.0000.000
129A129GLN0-0.039-0.02321.8940.0270.0270.0000.0000.0000.000
130A130THR00.0050.01318.997-0.004-0.0040.0000.0000.0000.000
131A131ALA0-0.005-0.02014.388-0.004-0.0040.0000.0000.0000.000
132A132GLY00.0740.03414.674-0.041-0.0410.0000.0000.0000.000
133A133TRP0-0.066-0.0226.552-0.116-0.1160.0000.0000.0000.000
134A134ILE0-0.0160.00712.6170.0980.0980.0000.0000.0000.000
135A135ASP-1-0.856-0.91512.611-0.677-0.6770.0000.0000.0000.000
136A136ALA00.008-0.01311.133-0.015-0.0150.0000.0000.0000.000
137A137GLY0-0.007-0.00212.9430.0990.0990.0000.0000.0000.000
138A138PHE0-0.0320.00015.7820.0690.0690.0000.0000.0000.000
139A139LYS10.8600.91017.6490.3320.3320.0000.0000.0000.000
140A140GLY00.0430.02620.4500.0310.0310.0000.0000.0000.000
141A141LYS10.8000.90521.0430.1790.1790.0000.0000.0000.000
142A142ILE00.0150.00718.333-0.011-0.0110.0000.0000.0000.000
143A143THR00.0250.01321.5850.0310.0310.0000.0000.0000.000
144A144LEU0-0.066-0.02822.192-0.010-0.0100.0000.0000.0000.000
145A145GLU-1-0.801-0.90622.725-0.184-0.1840.0000.0000.0000.000
146A146ILE0-0.057-0.02925.6310.0030.0030.0000.0000.0000.000
147A147VAL00.0400.02327.9640.0070.0070.0000.0000.0000.000
148A148ALA00.0040.01728.835-0.001-0.0010.0000.0000.0000.000
149A149PHE00.004-0.02726.8900.0030.0030.0000.0000.0000.000
150A150ASP-1-0.827-0.89031.873-0.006-0.0060.0000.0000.0000.000
151A151LYS10.8010.88534.3430.0110.0110.0000.0000.0000.000
152A152PRO0-0.004-0.01434.860-0.004-0.0040.0000.0000.0000.000
153A153VAL0-0.0140.01130.8060.0040.0040.0000.0000.0000.000
154A154ILE0-0.024-0.00234.171-0.005-0.0050.0000.0000.0000.000
155A155LEU0-0.0240.00029.009-0.002-0.0020.0000.0000.0000.000
156A156TYR00.032-0.00731.5830.0030.0030.0000.0000.0000.000
157A157LYS10.9110.94231.0120.0770.0770.0000.0000.0000.000
158A158ASN0-0.033-0.02528.9230.0010.0010.0000.0000.0000.000
159A159GLN00.0090.03227.0600.0040.0040.0000.0000.0000.000
160A160ARG10.8540.90221.4730.0950.0950.0000.0000.0000.000
161A161ILE0-0.006-0.00822.6830.0190.0190.0000.0000.0000.000
162A162GLY00.0330.01420.0030.0150.0150.0000.0000.0000.000
163A163GLN0-0.031-0.01515.4090.0380.0380.0000.0000.0000.000
164A164LEU00.0020.01113.709-0.005-0.0050.0000.0000.0000.000
165A165ILE00.0090.0047.8820.0470.0470.0000.0000.0000.000
166A166PHE00.0390.0118.345-0.002-0.0020.0000.0000.0000.000
167A167SER0-0.005-0.0032.880-1.170-0.4390.067-0.332-0.4660.000
168A168LYS10.8350.9002.4102.6884.2820.527-0.614-1.507-0.001
169A169LEU0-0.0190.0033.631-0.880-0.4380.004-0.212-0.235-0.001
170A170LEU0-0.024-0.0126.1260.0330.0330.0000.0000.0000.000
171A171SER0-0.029-0.0247.1520.1680.1680.0000.0000.0000.000
172A172PRO0-0.052-0.01910.194-0.127-0.1270.0000.0000.0000.000
173A173ALA00.0450.01912.1960.0770.0770.0000.0000.0000.000
174A174ASP-1-0.919-0.96414.033-0.324-0.3240.0000.0000.0000.000
175A175VAL0-0.059-0.02216.490-0.004-0.0040.0000.0000.0000.000