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: 6N29Z

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 OptH
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 -1800754.435902
FMO2-HF: Nuclear repulsion 1731554.30729
FMO2-HF: Total energy -69200.128612
FMO2-MP2: Total energy -69405.270055


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.
-3.5861.4040.292-2.136-3.1460.003
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 : 0.019 / q_NPA : 0.010
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].
3A3LEU0-0.046-0.0203.801-0.6711.760-0.018-1.127-1.2860.006
4A4SER0-0.029-0.0185.9610.2000.2000.0000.0000.0000.000
5A5ASP-1-0.826-0.9218.056-0.050-0.0500.0000.0000.0000.000
6A6LYS10.9330.94410.626-0.563-0.5630.0000.0000.0000.000
7A7ASP-1-0.798-0.8856.6470.1230.1230.0000.0000.0000.000
8A8ILE0-0.041-0.0239.687-0.103-0.1030.0000.0000.0000.000
9A9ILE0-0.002-0.00611.5410.0170.0170.0000.0000.0000.000
10A10ASP-1-0.882-0.92011.777-0.005-0.0050.0000.0000.0000.000
11A11TYR0-0.019-0.0387.355-0.127-0.1270.0000.0000.0000.000
12A12VAL00.0160.02112.9090.0120.0120.0000.0000.0000.000
13A13THR0-0.096-0.04516.0690.0470.0470.0000.0000.0000.000
14A14SER0-0.080-0.05115.1170.0090.0090.0000.0000.0000.000
15A15LYS10.8930.94017.7290.2380.2380.0000.0000.0000.000
16A16ARG10.9210.98610.2260.5130.5130.0000.0000.0000.000
17A17ILE00.0270.01610.268-0.070-0.0700.0000.0000.0000.000
18A18ILE0-0.067-0.01714.7870.0950.0950.0000.0000.0000.000
19A19ILE00.0300.00515.263-0.041-0.0410.0000.0000.0000.000
20A20LYS10.8710.97919.4430.3020.3020.0000.0000.0000.000
21A21PRO00.0530.00523.289-0.006-0.0060.0000.0000.0000.000
22A22PHE00.0560.01717.134-0.017-0.0170.0000.0000.0000.000
23A23ASN00.0130.00421.4200.0440.0440.0000.0000.0000.000
24A24LYS11.0281.00019.7280.0590.0590.0000.0000.0000.000
25A25ASP-1-0.917-0.95619.633-0.112-0.1120.0000.0000.0000.000
26A26PHE0-0.117-0.06319.7620.0200.0200.0000.0000.0000.000
27A27VAL0-0.0230.01014.059-0.061-0.0610.0000.0000.0000.000
28A28GLY00.0340.02715.1600.0680.0680.0000.0000.0000.000
29A29PRO0-0.004-0.02812.642-0.032-0.0320.0000.0000.0000.000
30A30CYS0-0.018-0.0108.3180.0970.0970.0000.0000.0000.000
31A31SER0-0.0180.00610.003-0.207-0.2070.0000.0000.0000.000
32A32TYR00.0430.03512.4590.1240.1240.0000.0000.0000.000
33A33ASP-1-0.824-0.90015.543-0.349-0.3490.0000.0000.0000.000
34A34VAL0-0.035-0.01518.4070.0080.0080.0000.0000.0000.000
35A35THR0-0.063-0.06420.9120.0340.0340.0000.0000.0000.000
36A36LEU0-0.044-0.00524.641-0.017-0.0170.0000.0000.0000.000
37A37GLY00.0420.02627.2450.0160.0160.0000.0000.0000.000
38A38ASP-1-0.952-0.99429.520-0.154-0.1540.0000.0000.0000.000
39A39GLU-1-0.927-0.96532.078-0.154-0.1540.0000.0000.0000.000
40A40PHE0-0.012-0.02530.555-0.014-0.0140.0000.0000.0000.000
41A41ILE0-0.0340.00131.9690.0110.0110.0000.0000.0000.000
42A42ILE0-0.014-0.03233.492-0.004-0.0040.0000.0000.0000.000
43A43TYR00.018-0.00130.3150.0030.0030.0000.0000.0000.000
44A44ASP-1-0.951-0.98136.847-0.114-0.1140.0000.0000.0000.000
45A45ASP-1-0.777-0.85739.305-0.119-0.1190.0000.0000.0000.000
46A46GLU-1-1.003-0.99840.229-0.096-0.0960.0000.0000.0000.000
47A47VAL0-0.019-0.02138.590-0.001-0.0010.0000.0000.0000.000
48A48TYR0-0.040-0.02433.730-0.002-0.0020.0000.0000.0000.000
49A49ASP-1-0.769-0.86335.392-0.134-0.1340.0000.0000.0000.000
50A50LEU00.003-0.01529.3000.0000.0000.0000.0000.0000.000
51A51SER0-0.115-0.06033.454-0.002-0.0020.0000.0000.0000.000
52A52LYS10.8210.90235.8310.1280.1280.0000.0000.0000.000
53A53GLU-1-0.932-0.95935.618-0.174-0.1740.0000.0000.0000.000
54A54LEU0-0.027-0.01332.5720.0050.0050.0000.0000.0000.000
55A55ASN0-0.036-0.01436.690-0.004-0.0040.0000.0000.0000.000
56A56TYR0-0.028-0.01735.860-0.005-0.0050.0000.0000.0000.000
57A57LYS10.9640.99337.8950.1160.1160.0000.0000.0000.000
58A58ARG10.9550.97032.5890.1680.1680.0000.0000.0000.000
59A59ILE0-0.039-0.00936.6430.0100.0100.0000.0000.0000.000
60A60LYS10.9570.98336.2310.1240.1240.0000.0000.0000.000
61A61ILE0-0.0370.00134.1730.0090.0090.0000.0000.0000.000
62A62LYS10.9360.96737.5450.0850.0850.0000.0000.0000.000
63A63ASN0-0.044-0.05137.174-0.005-0.0050.0000.0000.0000.000
64A64SER00.0080.00635.657-0.005-0.0050.0000.0000.0000.000
65A65ILE00.0030.01233.5010.0050.0050.0000.0000.0000.000
66A66LEU0-0.0080.00235.436-0.002-0.0020.0000.0000.0000.000
67A67VAL00.0170.00731.8790.0010.0010.0000.0000.0000.000
68A68CYS0-0.037-0.02034.9950.0040.0040.0000.0000.0000.000
69A69PRO00.0240.01134.834-0.006-0.0060.0000.0000.0000.000
70A70LEU00.0430.01335.4150.0040.0040.0000.0000.0000.000
71A71ASN0-0.037-0.00937.2070.0050.0050.0000.0000.0000.000
72A72TYR00.014-0.00539.3710.0050.0050.0000.0000.0000.000
73A73ASN0-0.045-0.01241.8850.0040.0040.0000.0000.0000.000
74A74LEU0-0.002-0.00940.8290.0040.0040.0000.0000.0000.000
75A75THR00.0290.02645.167-0.001-0.0010.0000.0000.0000.000
76A76GLU-1-0.873-0.95747.909-0.082-0.0820.0000.0000.0000.000
77A77GLU-1-0.963-0.97449.799-0.056-0.0560.0000.0000.0000.000
78A78LYS10.8880.95445.4190.0700.0700.0000.0000.0000.000
79A79ILE00.0650.02044.139-0.002-0.0020.0000.0000.0000.000
80A80ASN00.0290.00946.067-0.004-0.0040.0000.0000.0000.000
81A81TYR0-0.0080.00445.8920.0020.0020.0000.0000.0000.000
82A82PHE0-0.004-0.02442.7420.0010.0010.0000.0000.0000.000
83A83LYS10.9330.97144.1270.0850.0850.0000.0000.0000.000
84A84GLU-1-0.931-0.96245.197-0.060-0.0600.0000.0000.0000.000
85A85LYS10.8540.95745.0740.0640.0640.0000.0000.0000.000
86A86TYR0-0.046-0.05040.8370.0020.0020.0000.0000.0000.000
87A87ASN0-0.0280.00441.452-0.002-0.0020.0000.0000.0000.000
88A88VAL0-0.0130.00438.771-0.003-0.0030.0000.0000.0000.000
89A89ASP-1-0.828-0.92139.938-0.100-0.1000.0000.0000.0000.000
90A90TYR0-0.024-0.02338.3250.0040.0040.0000.0000.0000.000
91A91VAL0-0.002-0.00339.326-0.002-0.0020.0000.0000.0000.000
92A92VAL00.0010.01235.2710.0020.0020.0000.0000.0000.000
93A93GLU-1-0.831-0.92737.308-0.099-0.0990.0000.0000.0000.000
94A94GLY0-0.0020.00034.782-0.001-0.0010.0000.0000.0000.000
95A95GLY0-0.035-0.00331.674-0.005-0.0050.0000.0000.0000.000
96A96VAL0-0.023-0.00931.1280.0080.0080.0000.0000.0000.000
97A97LEU00.0210.01827.498-0.015-0.0150.0000.0000.0000.000
98A98GLY00.0370.01527.8320.0190.0190.0000.0000.0000.000
99A99THR0-0.025-0.02225.656-0.023-0.0230.0000.0000.0000.000
100A100THR00.0010.00921.0610.0120.0120.0000.0000.0000.000
101A101ASN0-0.037-0.03824.4990.0190.0190.0000.0000.0000.000
102A102GLU-1-0.840-0.90021.205-0.310-0.3100.0000.0000.0000.000
103A103TYR0-0.086-0.07522.489-0.016-0.0160.0000.0000.0000.000
104A104ILE00.008-0.01415.5060.0000.0000.0000.0000.0000.000
105A105GLU-1-0.858-0.90918.007-0.329-0.3290.0000.0000.0000.000
106A106LEU0-0.040-0.00812.124-0.040-0.0400.0000.0000.0000.000
107A107PRO00.0110.01911.5270.0880.0880.0000.0000.0000.000
108A108ASN00.0440.00312.813-0.152-0.1520.0000.0000.0000.000
109A109ASP-1-0.761-0.8728.972-1.006-1.0060.0000.0000.0000.000
110A110ILE0-0.037-0.0206.803-0.486-0.4860.0000.0000.0000.000
111A111SER00.0190.0217.5020.3980.3980.0000.0000.0000.000
112A112ALA0-0.001-0.0158.245-0.504-0.5040.0000.0000.0000.000
113A113GLN0-0.037-0.03210.3110.0010.0010.0000.0000.0000.000
114A114TYR0-0.012-0.02511.8560.0180.0180.0000.0000.0000.000
115A115GLN0-0.0050.00613.7680.0880.0880.0000.0000.0000.000
116A116GLY00.0210.01316.4950.0240.0240.0000.0000.0000.000
117A117ARG10.9290.97619.4460.2190.2190.0000.0000.0000.000
118A118SER00.0530.00919.5150.0190.0190.0000.0000.0000.000
119A119SER0-0.058-0.03921.5880.0150.0150.0000.0000.0000.000
120A120LEU00.0140.01124.4800.0160.0160.0000.0000.0000.000
121A121GLY00.0700.04523.6840.0070.0070.0000.0000.0000.000
122A122ARG10.8980.93621.6850.1430.1430.0000.0000.0000.000
123A123VAL0-0.036-0.00326.8170.0140.0140.0000.0000.0000.000
124A124PHE0-0.0010.00127.8430.0020.0020.0000.0000.0000.000
125A125LEU00.0080.02626.8310.0010.0010.0000.0000.0000.000
126A126THR0-0.020-0.00523.986-0.018-0.0180.0000.0000.0000.000
127A127SER00.0560.02222.641-0.001-0.0010.0000.0000.0000.000
128A128HIS0-0.024-0.03118.395-0.056-0.0560.0000.0000.0000.000
129A129GLN0-0.038-0.01721.8690.0210.0210.0000.0000.0000.000
130A130THR00.0020.01019.020-0.016-0.0160.0000.0000.0000.000
131A131ALA0-0.011-0.02014.359-0.009-0.0090.0000.0000.0000.000
132A132GLY00.0910.05214.653-0.078-0.0780.0000.0000.0000.000
133A133TRP0-0.052-0.0126.479-0.126-0.1260.0000.0000.0000.000
134A134ILE0-0.0230.00212.5950.1350.1350.0000.0000.0000.000
135A135ASP-1-0.860-0.92112.601-0.841-0.8410.0000.0000.0000.000
136A136ALA00.012-0.01111.193-0.011-0.0110.0000.0000.0000.000
137A137GLY0-0.009-0.00412.9390.1100.1100.0000.0000.0000.000
138A138PHE0-0.0370.00015.7750.0790.0790.0000.0000.0000.000
139A139LYS10.9230.95417.6390.3430.3430.0000.0000.0000.000
140A140GLY00.0410.02220.4370.0320.0320.0000.0000.0000.000
141A141LYS10.9020.96221.0250.2240.2240.0000.0000.0000.000
142A142ILE00.0270.01617.743-0.014-0.0140.0000.0000.0000.000
143A143THR00.0270.01321.5510.0400.0400.0000.0000.0000.000
144A144LEU0-0.057-0.02522.171-0.022-0.0220.0000.0000.0000.000
145A145GLU-1-0.803-0.90323.011-0.323-0.3230.0000.0000.0000.000
146A146ILE0-0.053-0.02725.605-0.006-0.0060.0000.0000.0000.000
147A147VAL00.0410.02527.9410.0150.0150.0000.0000.0000.000
148A148ALA0-0.0070.00928.811-0.009-0.0090.0000.0000.0000.000
149A149PHE0-0.011-0.03426.7620.0070.0070.0000.0000.0000.000
150A150ASP-1-0.936-0.95631.853-0.091-0.0910.0000.0000.0000.000
151A151LYS10.9440.97034.3230.0870.0870.0000.0000.0000.000
152A152PRO0-0.017-0.02234.836-0.007-0.0070.0000.0000.0000.000
153A153VAL0-0.0030.01830.7770.0040.0040.0000.0000.0000.000
154A154ILE0-0.021-0.00534.142-0.003-0.0030.0000.0000.0000.000
155A155LEU0-0.030-0.00329.066-0.007-0.0070.0000.0000.0000.000
156A156TYR00.020-0.01131.5680.0100.0100.0000.0000.0000.000
157A157LYS10.9360.96231.0120.1160.1160.0000.0000.0000.000
158A158ASN0-0.034-0.02328.9370.0010.0010.0000.0000.0000.000
159A159GLN0-0.0010.02327.0690.0090.0090.0000.0000.0000.000
160A160ARG10.8670.91521.7600.1860.1860.0000.0000.0000.000
161A161ILE0-0.009-0.01722.6180.0220.0220.0000.0000.0000.000
162A162GLY00.0210.01019.9640.0090.0090.0000.0000.0000.000
163A163GLN0-0.028-0.00915.2580.0790.0790.0000.0000.0000.000
164A164LEU0-0.0010.00413.609-0.015-0.0150.0000.0000.0000.000
165A165ILE00.0120.0057.8500.0620.0620.0000.0000.0000.000
166A166PHE00.0320.0088.3200.0160.0160.0000.0000.0000.000
167A167SER00.0080.0073.474-2.313-1.7340.021-0.294-0.306-0.002
168A168LYS10.8180.8872.6032.6074.1610.285-0.515-1.3240.000
169A169LEU0-0.0260.0013.636-1.159-0.7330.004-0.200-0.230-0.001
170A170LEU0-0.030-0.0166.1410.1460.1460.0000.0000.0000.000
171A171SER0-0.019-0.0207.1740.2570.2570.0000.0000.0000.000
172A172PRO0-0.051-0.01610.208-0.173-0.1730.0000.0000.0000.000
173A173ALA00.0410.01912.2070.0700.0700.0000.0000.0000.000
174A174ASP-1-0.918-0.96514.042-0.298-0.2980.0000.0000.0000.000
175A175VAL0-0.068-0.02516.490-0.011-0.0110.0000.0000.0000.000