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: JQQ69

Calculation Name: 3OBF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OBF

Chain ID: A

ChEMBL ID:

UniProt ID: A1RB88

Base Structure: X-ray

Registration Date: 2023-09-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1806150.677875
FMO2-HF: Nuclear repulsion 1738357.913165
FMO2-HF: Total energy -67792.764711
FMO2-MP2: Total energy -67989.483752


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:126:SER)


Summations of interaction energy for fragment #1(A:126:SER)
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.
-6.175-3.4370.001-1.134-1.6050.003
Interaction energy analysis for fragmet #1(A:126:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.001
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].
3A128ALA00.0080.0073.870-0.8260.887-0.002-0.824-0.8880.002
4A129GLU-1-0.944-0.9625.4040.1260.316-0.001-0.012-0.1760.000
5A130GLU-1-0.762-0.8956.494-0.850-0.8500.0000.0000.0000.000
6A131ARG10.8400.9223.127-1.774-1.0770.006-0.287-0.4160.001
7A132ARG10.9230.9768.859-1.214-1.2140.0000.0000.0000.000
8A133VAL0-0.029-0.00610.838-0.062-0.0620.0000.0000.0000.000
9A134ALA00.0700.03711.523-0.033-0.0330.0000.0000.0000.000
10A135TYR00.0370.02612.414-0.015-0.0150.0000.0000.0000.000
11A136PRO0-0.065-0.04814.088-0.036-0.0360.0000.0000.0000.000
12A137VAL00.0050.00816.820-0.012-0.0120.0000.0000.0000.000
13A138LEU0-0.0050.00612.490-0.021-0.0210.0000.0000.0000.000
14A139ARG10.9550.97917.136-0.124-0.1240.0000.0000.0000.000
15A140GLU-1-0.836-0.90119.541-0.001-0.0010.0000.0000.0000.000
16A141LEU00.0430.01319.001-0.002-0.0020.0000.0000.0000.000
17A142THR0-0.0070.01520.408-0.009-0.0090.0000.0000.0000.000
18A143GLU-1-0.919-0.94522.3730.0210.0210.0000.0000.0000.000
19A144ARG10.7760.87225.0970.0080.0080.0000.0000.0000.000
20A145THR00.0120.00323.868-0.006-0.0060.0000.0000.0000.000
21A146GLY0-0.074-0.03625.9250.0000.0000.0000.0000.0000.000
22A147GLU-1-0.763-0.83923.610-0.152-0.1520.0000.0000.0000.000
23A148THR00.0020.00617.7050.0290.0290.0000.0000.0000.000
24A149SER00.0100.01017.835-0.016-0.0160.0000.0000.0000.000
25A150ALA0-0.006-0.02313.0060.0220.0220.0000.0000.0000.000
26A151LEU0-0.018-0.0098.2000.0610.0610.0000.0000.0000.000
27A152MET0-0.0260.0049.703-0.144-0.1440.0000.0000.0000.000
28A153VAL00.025-0.0034.7140.0330.063-0.001-0.003-0.0260.000
29A154TRP00.0190.0008.077-0.025-0.0250.0000.0000.0000.000
30A155ASN0-0.043-0.0478.443-0.098-0.0980.0000.0000.0000.000
31A156GLY00.0310.0309.8190.1150.1150.0000.0000.0000.000
32A157ASN0-0.028-0.01813.4000.1130.1130.0000.0000.0000.000
33A158GLU-1-0.801-0.88112.043-1.069-1.0690.0000.0000.0000.000
34A159SER0-0.012-0.00611.435-0.199-0.1990.0000.0000.0000.000
35A160MET0-0.026-0.0186.141-0.064-0.0640.0000.0000.0000.000
36A161CYS0-0.031-0.0218.778-0.129-0.1290.0000.0000.0000.000
37A162VAL0-0.039-0.0214.548-0.313-0.205-0.001-0.008-0.0990.000
38A163GLU-1-0.841-0.9436.8140.7590.7590.0000.0000.0000.000
39A164GLN0-0.051-0.0369.627-0.012-0.0120.0000.0000.0000.000
40A165ILE0-0.0210.00513.3590.0910.0910.0000.0000.0000.000
41A166PRO00.0310.02716.909-0.030-0.0300.0000.0000.0000.000
42A167SER00.022-0.01419.4590.0350.0350.0000.0000.0000.000
43A168ARG10.9040.95822.9330.0760.0760.0000.0000.0000.000
44A169HIS0-0.023-0.02625.7100.0200.0200.0000.0000.0000.000
45A170GLN00.0340.03820.507-0.027-0.0270.0000.0000.0000.000
46A171VAL0-0.011-0.00725.0810.0140.0140.0000.0000.0000.000
47A172LYS10.8410.89723.5350.1900.1900.0000.0000.0000.000
48A173HIS0-0.008-0.01119.268-0.006-0.0060.0000.0000.0000.000
49A174LEU00.0130.01819.284-0.033-0.0330.0000.0000.0000.000
50A175ALA00.0520.02614.7490.0090.0090.0000.0000.0000.000
51A176PRO00.0260.03514.365-0.013-0.0130.0000.0000.0000.000
52A177LEU00.014-0.0159.380-0.099-0.0990.0000.0000.0000.000
53A178GLY0-0.019-0.0068.2430.0670.0670.0000.0000.0000.000
54A179ALA0-0.0240.0009.244-0.052-0.0520.0000.0000.0000.000
55A180ARG10.8430.8998.6971.2911.2910.0000.0000.0000.000
56A181TYR00.0260.01713.0620.1180.1180.0000.0000.0000.000
57A182ASN00.035-0.00115.493-0.066-0.0660.0000.0000.0000.000
58A183GLU-1-0.863-0.92417.903-0.352-0.3520.0000.0000.0000.000
59A184ALA00.0370.00920.538-0.019-0.0190.0000.0000.0000.000
60A185LEU00.0240.01922.2520.0000.0000.0000.0000.0000.000
61A186SER0-0.0050.00818.5870.0150.0150.0000.0000.0000.000
62A187SER0-0.023-0.02519.730-0.019-0.0190.0000.0000.0000.000
63A188SER00.0230.00814.117-0.037-0.0370.0000.0000.0000.000
64A189VAL0-0.0010.01215.950-0.049-0.0490.0000.0000.0000.000
65A190GLN00.0130.00417.3690.0340.0340.0000.0000.0000.000
66A191VAL0-0.001-0.00215.8850.0110.0110.0000.0000.0000.000
67A192PHE00.0190.01310.738-0.023-0.0230.0000.0000.0000.000
68A193LEU00.0170.02515.8410.0170.0170.0000.0000.0000.000
69A194ALA0-0.0020.00118.9230.0360.0360.0000.0000.0000.000
70A195SER0-0.103-0.06615.9570.0110.0110.0000.0000.0000.000
71A196GLU-1-0.782-0.85116.292-0.570-0.5700.0000.0000.0000.000
72A197ASN0-0.027-0.03019.3230.0270.0270.0000.0000.0000.000
73A198GLU-1-0.748-0.86422.865-0.212-0.2120.0000.0000.0000.000
74A199ASP-1-0.820-0.89325.490-0.214-0.2140.0000.0000.0000.000
75A200ARG10.7570.86316.4080.5270.5270.0000.0000.0000.000
76A201VAL00.0230.00921.020-0.029-0.0290.0000.0000.0000.000
77A202ARG10.7530.83222.9770.1960.1960.0000.0000.0000.000
78A203GLN0-0.024-0.01723.879-0.014-0.0140.0000.0000.0000.000
79A204LEU0-0.0240.00618.226-0.003-0.0030.0000.0000.0000.000
80A205LEU00.0030.00522.363-0.007-0.0070.0000.0000.0000.000
81A206ARG10.7240.82925.0120.2080.2080.0000.0000.0000.000
82A207SER0-0.056-0.02923.7020.0010.0010.0000.0000.0000.000
83A208GLY0-0.016-0.00124.907-0.002-0.0020.0000.0000.0000.000
84A209SER0-0.057-0.03419.603-0.026-0.0260.0000.0000.0000.000
85A210ILE0-0.0300.00217.370-0.062-0.0620.0000.0000.0000.000
86A211THR00.0150.01021.0990.0360.0360.0000.0000.0000.000
87A212LEU00.0320.00023.864-0.011-0.0110.0000.0000.0000.000
88A213THR0-0.013-0.01326.7010.0050.0050.0000.0000.0000.000
89A214GLY00.0070.01230.3860.0040.0040.0000.0000.0000.000
90A215VAL00.0190.02027.7800.0050.0050.0000.0000.0000.000
91A216ASP-1-0.820-0.90231.176-0.165-0.1650.0000.0000.0000.000
92A217GLU-1-0.813-0.91232.855-0.182-0.1820.0000.0000.0000.000
93A218ASP-1-0.914-0.95033.520-0.151-0.1510.0000.0000.0000.000
94A219ALA00.0330.02632.331-0.005-0.0050.0000.0000.0000.000
95A220VAL0-0.042-0.01928.186-0.017-0.0170.0000.0000.0000.000
96A221GLU-1-0.804-0.89629.327-0.201-0.2010.0000.0000.0000.000
97A222ALA0-0.0160.00131.1560.0000.0000.0000.0000.0000.000
98A223TYR0-0.037-0.04222.112-0.011-0.0110.0000.0000.0000.000
99A224LEU00.009-0.01325.470-0.015-0.0150.0000.0000.0000.000
100A225LEU0-0.044-0.01427.6190.0010.0010.0000.0000.0000.000
101A226ARG10.8140.85525.9110.2470.2470.0000.0000.0000.000
102A227LEU0-0.051-0.01521.903-0.008-0.0080.0000.0000.0000.000
103A228LYS10.8760.94424.4690.1890.1890.0000.0000.0000.000
104A229GLU-1-0.865-0.92626.829-0.170-0.1700.0000.0000.0000.000
105A230SER0-0.116-0.06922.946-0.004-0.0040.0000.0000.0000.000
106A231MET0-0.044-0.01619.817-0.011-0.0110.0000.0000.0000.000
107A232GLU-1-0.935-0.96224.117-0.134-0.1340.0000.0000.0000.000
108A233ARG10.7960.89326.0890.2110.2110.0000.0000.0000.000
109A234GLY00.0020.01723.8090.0090.0090.0000.0000.0000.000
110A235TRP0-0.023-0.00122.142-0.022-0.0220.0000.0000.0000.000
111A236ALA00.0330.02920.8750.0160.0160.0000.0000.0000.000
112A237VAL0-0.006-0.02122.9260.0060.0060.0000.0000.0000.000
113A238ASN00.0760.05422.3310.0110.0110.0000.0000.0000.000
114A239PHE00.0270.00225.0340.0060.0060.0000.0000.0000.000
115A240GLY00.0110.01327.1010.0180.0180.0000.0000.0000.000
116A241GLU-1-0.853-0.89526.896-0.218-0.2180.0000.0000.0000.000
117A242THR00.0220.04422.2970.0040.0040.0000.0000.0000.000
118A243SER00.0220.00525.3070.0160.0160.0000.0000.0000.000
119A244ILE00.0170.00227.0470.0050.0050.0000.0000.0000.000
120A245GLU-1-0.834-0.89027.277-0.175-0.1750.0000.0000.0000.000
121A246GLU-1-0.942-0.96622.334-0.319-0.3190.0000.0000.0000.000
122A247VAL0-0.019-0.01225.3250.0110.0110.0000.0000.0000.000
123A248GLY00.0330.01222.064-0.014-0.0140.0000.0000.0000.000
124A249VAL0-0.0490.00321.7500.0060.0060.0000.0000.0000.000
125A250ALA00.034-0.00717.171-0.030-0.0300.0000.0000.0000.000
126A251SER00.010-0.00517.7040.0310.0310.0000.0000.0000.000
127A252PRO00.0100.00215.884-0.055-0.0550.0000.0000.0000.000
128A253VAL0-0.047-0.01912.7690.0600.0600.0000.0000.0000.000
129A254TYR00.0300.00113.818-0.081-0.0810.0000.0000.0000.000
130A255ASP-1-0.734-0.85412.703-0.092-0.0920.0000.0000.0000.000
131A256HIS00.0500.01314.163-0.040-0.0400.0000.0000.0000.000
132A257ARG10.8970.94414.973-0.042-0.0420.0000.0000.0000.000
133A258GLY00.0040.00117.0230.0050.0050.0000.0000.0000.000
134A259ASN0-0.089-0.04613.442-0.043-0.0430.0000.0000.0000.000
135A260MET0-0.0020.00614.0030.0040.0040.0000.0000.0000.000
136A261VAL0-0.030-0.0129.371-0.092-0.0920.0000.0000.0000.000
137A262ALA0-0.012-0.0058.806-0.332-0.3320.0000.0000.0000.000
138A263SER00.0200.00810.4850.1660.1660.0000.0000.0000.000
139A264VAL0-0.0190.00712.550-0.078-0.0780.0000.0000.0000.000
140A265LEU00.006-0.01015.1090.0020.0020.0000.0000.0000.000
141A266ILE00.0170.01116.8010.0170.0170.0000.0000.0000.000
142A267PRO0-0.051-0.00518.0840.0070.0070.0000.0000.0000.000
143A268ALA00.026-0.01521.0600.0210.0210.0000.0000.0000.000
144A269PRO0-0.0120.00124.431-0.009-0.0090.0000.0000.0000.000
145A270LYS10.8750.91327.2420.1900.1900.0000.0000.0000.000
146A271PHE0-0.034-0.02129.8890.0090.0090.0000.0000.0000.000
147A272ARG10.7540.84626.7060.1420.1420.0000.0000.0000.000
148A273VAL0-0.030-0.01327.6980.0050.0050.0000.0000.0000.000
149A274SER00.021-0.01231.029-0.008-0.0080.0000.0000.0000.000
150A275GLN00.0360.00331.899-0.013-0.0130.0000.0000.0000.000
151A276ASP-1-0.820-0.88132.357-0.106-0.1060.0000.0000.0000.000
152A277THR0-0.004-0.00329.5160.0020.0020.0000.0000.0000.000
153A278LEU0-0.0120.00126.624-0.005-0.0050.0000.0000.0000.000
154A279ASN0-0.011-0.01727.502-0.014-0.0140.0000.0000.0000.000
155A280SER0-0.0100.01728.6500.0000.0000.0000.0000.0000.000
156A281LEU00.028-0.00424.7930.0020.0020.0000.0000.0000.000
157A282GLY00.0100.00224.219-0.014-0.0140.0000.0000.0000.000
158A283GLU-1-0.927-0.95924.281-0.100-0.1000.0000.0000.0000.000
159A284ALA00.0040.00024.7260.0040.0040.0000.0000.0000.000
160A285CYS0-0.056-0.01519.801-0.011-0.0110.0000.0000.0000.000
161A286ALA00.0480.02720.173-0.015-0.0150.0000.0000.0000.000
162A287ALA0-0.009-0.00321.7030.0080.0080.0000.0000.0000.000
163A288ALA0-0.012-0.01018.7300.0210.0210.0000.0000.0000.000
164A289ALA00.021-0.00116.9530.0130.0130.0000.0000.0000.000
165A290ALA00.0460.03617.7520.0070.0070.0000.0000.0000.000
166A291LYS10.8250.90219.7470.0260.0260.0000.0000.0000.000
167A292VAL0-0.031-0.01712.9950.0450.0450.0000.0000.0000.000
168A293THR00.000-0.00315.7150.0180.0180.0000.0000.0000.000
169A294THR0-0.037-0.03017.0640.0390.0390.0000.0000.0000.000
170A295ARG10.8110.88916.341-0.099-0.0990.0000.0000.0000.000
171A296LEU0-0.0040.01711.1050.0550.0550.0000.0000.0000.000
172A297GLY0-0.038-0.00615.1130.0180.0180.0000.0000.0000.000
173A298GLY0-0.028-0.01617.055-0.005-0.0050.0000.0000.0000.000
174A299ARG10.8150.90617.9200.1020.1020.0000.0000.0000.000
175A300ALA00.0450.02920.180-0.023-0.0230.0000.0000.0000.000
176A301PRO00.0000.00720.6510.0290.0290.0000.0000.0000.000