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: 8998Y

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1800469.568189
FMO2-HF: Nuclear repulsion 1732678.005908
FMO2-HF: Total energy -67791.562281
FMO2-MP2: Total energy -67988.35213


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.
-9.888-6.3040.138-1.672-2.050.005
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 : 0.016 / 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].
3A128ALA00.0260.0103.828-0.5951.204-0.006-0.861-0.9330.002
4A129GLU-1-0.902-0.9575.397-0.0750.093-0.001-0.011-0.1560.000
5A130GLU-1-0.842-0.9287.201-0.452-0.4520.0000.0000.0000.000
6A131ARG10.8730.9262.743-5.475-3.9420.146-0.794-0.8850.003
7A132ARG10.9330.9818.641-1.303-1.3030.0000.0000.0000.000
8A133VAL0-0.021-0.01510.782-0.105-0.1050.0000.0000.0000.000
9A134ALA00.0300.01211.970-0.053-0.0530.0000.0000.0000.000
10A135TYR00.0430.04112.396-0.037-0.0370.0000.0000.0000.000
11A136PRO0-0.101-0.06514.094-0.049-0.0490.0000.0000.0000.000
12A137VAL00.0010.00716.954-0.019-0.0190.0000.0000.0000.000
13A138LEU00.0070.00412.839-0.029-0.0290.0000.0000.0000.000
14A139ARG10.9370.97217.507-0.178-0.1780.0000.0000.0000.000
15A140GLU-1-0.931-0.96819.6580.0140.0140.0000.0000.0000.000
16A141LEU00.0190.00019.244-0.008-0.0080.0000.0000.0000.000
17A142THR0-0.0070.00520.326-0.015-0.0150.0000.0000.0000.000
18A143GLU-1-0.986-0.98322.3500.0500.0500.0000.0000.0000.000
19A144ARG10.8620.93725.1650.0050.0050.0000.0000.0000.000
20A145THR00.0220.02123.618-0.005-0.0050.0000.0000.0000.000
21A146GLY0-0.041-0.00725.779-0.002-0.0020.0000.0000.0000.000
22A147GLU-1-0.775-0.86423.350-0.148-0.1480.0000.0000.0000.000
23A148THR00.0290.01617.5410.0310.0310.0000.0000.0000.000
24A149SER00.0100.00117.473-0.014-0.0140.0000.0000.0000.000
25A150ALA0-0.018-0.02913.0400.0230.0230.0000.0000.0000.000
26A151LEU0-0.0050.0068.6170.0390.0390.0000.0000.0000.000
27A152MET0-0.055-0.0169.746-0.156-0.1560.0000.0000.0000.000
28A153VAL00.024-0.0014.9600.0060.0060.0000.0000.0000.000
29A154TRP00.0200.0158.1480.0250.0250.0000.0000.0000.000
30A155ASN0-0.064-0.0648.211-0.118-0.1180.0000.0000.0000.000
31A156GLY00.0140.0069.5160.1580.1580.0000.0000.0000.000
32A157ASN0-0.048-0.03813.0960.0590.0590.0000.0000.0000.000
33A158GLU-1-0.786-0.85911.742-1.161-1.1610.0000.0000.0000.000
34A159SER0-0.039-0.05011.519-0.253-0.2530.0000.0000.0000.000
35A160MET0-0.012-0.0136.565-0.149-0.1490.0000.0000.0000.000
36A161CYS0-0.037-0.0088.578-0.138-0.1380.0000.0000.0000.000
37A162VAL0-0.042-0.0154.500-0.208-0.124-0.001-0.006-0.0760.000
38A163GLU-1-0.882-0.9776.9270.8150.8150.0000.0000.0000.000
39A164GLN0-0.038-0.0249.919-0.032-0.0320.0000.0000.0000.000
40A165ILE0-0.0290.01013.5710.0940.0940.0000.0000.0000.000
41A166PRO00.0280.02017.143-0.035-0.0350.0000.0000.0000.000
42A167SER00.0400.00519.6330.0300.0300.0000.0000.0000.000
43A168ARG10.9610.97923.0380.0570.0570.0000.0000.0000.000
44A169HIS0-0.082-0.05525.9140.0140.0140.0000.0000.0000.000
45A170GLN00.0190.02121.021-0.030-0.0300.0000.0000.0000.000
46A171VAL00.0240.02225.2580.0120.0120.0000.0000.0000.000
47A172LYS10.9580.96623.8450.1650.1650.0000.0000.0000.000
48A173HIS0-0.0010.00319.383-0.005-0.0050.0000.0000.0000.000
49A174LEU00.0380.02419.387-0.030-0.0300.0000.0000.0000.000
50A175ALA00.0400.02114.6510.0150.0150.0000.0000.0000.000
51A176PRO00.0170.02814.4210.0040.0040.0000.0000.0000.000
52A177LEU00.038-0.0099.037-0.093-0.0930.0000.0000.0000.000
53A178GLY0-0.050-0.0298.5240.0780.0780.0000.0000.0000.000
54A179ALA0-0.0220.0069.527-0.041-0.0410.0000.0000.0000.000
55A180ARG10.8770.9228.6341.3031.3030.0000.0000.0000.000
56A181TYR0-0.007-0.00212.7890.1390.1390.0000.0000.0000.000
57A182ASN00.0590.00715.274-0.072-0.0720.0000.0000.0000.000
58A183GLU-1-0.894-0.92717.700-0.354-0.3540.0000.0000.0000.000
59A184ALA00.0530.00320.359-0.029-0.0290.0000.0000.0000.000
60A185LEU00.0300.01422.240-0.009-0.0090.0000.0000.0000.000
61A186SER00.0060.02318.3700.0100.0100.0000.0000.0000.000
62A187SER0-0.001-0.02520.020-0.021-0.0210.0000.0000.0000.000
63A188SER00.0470.05514.304-0.047-0.0470.0000.0000.0000.000
64A189VAL00.0170.01816.014-0.063-0.0630.0000.0000.0000.000
65A190GLN0-0.030-0.02417.3690.0210.0210.0000.0000.0000.000
66A191VAL0-0.004-0.00515.9970.0140.0140.0000.0000.0000.000
67A192PHE00.008-0.00311.077-0.026-0.0260.0000.0000.0000.000
68A193LEU00.0020.01715.8490.0160.0160.0000.0000.0000.000
69A194ALA00.0040.00918.7990.0400.0400.0000.0000.0000.000
70A195SER0-0.114-0.06816.0140.0160.0160.0000.0000.0000.000
71A196GLU-1-0.884-0.93415.703-0.670-0.6700.0000.0000.0000.000
72A197ASN00.0070.00119.3320.0430.0430.0000.0000.0000.000
73A198GLU-1-0.779-0.91222.633-0.246-0.2460.0000.0000.0000.000
74A199ASP-1-0.897-0.95225.388-0.254-0.2540.0000.0000.0000.000
75A200ARG10.9350.98616.3800.5770.5770.0000.0000.0000.000
76A201VAL00.0270.01221.051-0.026-0.0260.0000.0000.0000.000
77A202ARG10.8710.93322.8210.2290.2290.0000.0000.0000.000
78A203GLN0-0.047-0.02823.474-0.018-0.0180.0000.0000.0000.000
79A204LEU0-0.016-0.00818.059-0.002-0.0020.0000.0000.0000.000
80A205LEU00.0020.00322.169-0.002-0.0020.0000.0000.0000.000
81A206ARG10.8090.89124.9170.2340.2340.0000.0000.0000.000
82A207SER0-0.060-0.01523.2080.0020.0020.0000.0000.0000.000
83A208GLY00.0140.01424.6450.0040.0040.0000.0000.0000.000
84A209SER0-0.088-0.03919.110-0.030-0.0300.0000.0000.0000.000
85A210ILE0-0.0200.00417.165-0.052-0.0520.0000.0000.0000.000
86A211THR0-0.0010.00120.9620.0410.0410.0000.0000.0000.000
87A212LEU00.0420.00523.815-0.014-0.0140.0000.0000.0000.000
88A213THR0-0.021-0.01726.6990.0050.0050.0000.0000.0000.000
89A214GLY0-0.0170.00330.2010.0060.0060.0000.0000.0000.000
90A215VAL0-0.003-0.00127.9620.0010.0010.0000.0000.0000.000
91A216ASP-1-0.807-0.90631.361-0.174-0.1740.0000.0000.0000.000
92A217GLU-1-0.846-0.93132.979-0.198-0.1980.0000.0000.0000.000
93A218ASP-1-0.864-0.93833.634-0.168-0.1680.0000.0000.0000.000
94A219ALA00.0090.02731.936-0.005-0.0050.0000.0000.0000.000
95A220VAL0-0.089-0.05128.251-0.019-0.0190.0000.0000.0000.000
96A221GLU-1-0.902-0.95829.396-0.216-0.2160.0000.0000.0000.000
97A222ALA0-0.0070.00031.276-0.002-0.0020.0000.0000.0000.000
98A223TYR0-0.053-0.04322.138-0.015-0.0150.0000.0000.0000.000
99A224LEU00.021-0.00325.514-0.019-0.0190.0000.0000.0000.000
100A225LEU0-0.050-0.00727.430-0.004-0.0040.0000.0000.0000.000
101A226ARG10.8250.88426.3020.2630.2630.0000.0000.0000.000
102A227LEU0-0.024-0.00222.251-0.009-0.0090.0000.0000.0000.000
103A228LYS10.9170.98124.8070.2130.2130.0000.0000.0000.000
104A229GLU-1-0.912-0.96126.939-0.174-0.1740.0000.0000.0000.000
105A230SER0-0.122-0.07323.544-0.003-0.0030.0000.0000.0000.000
106A231MET0-0.045-0.02520.208-0.008-0.0080.0000.0000.0000.000
107A232GLU-1-0.950-0.96924.403-0.147-0.1470.0000.0000.0000.000
108A233ARG10.8410.94026.3300.2270.2270.0000.0000.0000.000
109A234GLY00.0210.01924.1030.0140.0140.0000.0000.0000.000
110A235TRP0-0.037-0.01822.274-0.020-0.0200.0000.0000.0000.000
111A236ALA00.0260.02521.4240.0190.0190.0000.0000.0000.000
112A237VAL00.018-0.00723.2900.0010.0010.0000.0000.0000.000
113A238ASN00.0360.03422.3810.0150.0150.0000.0000.0000.000
114A239PHE00.003-0.01925.1780.0100.0100.0000.0000.0000.000
115A240GLY0-0.013-0.02127.2840.0150.0150.0000.0000.0000.000
116A241GLU-1-0.842-0.91526.971-0.230-0.2300.0000.0000.0000.000
117A242THR00.0110.02222.490-0.002-0.0020.0000.0000.0000.000
118A243SER00.0500.02725.0640.0120.0120.0000.0000.0000.000
119A244ILE00.002-0.00126.8150.0050.0050.0000.0000.0000.000
120A245GLU-1-0.982-0.99227.319-0.170-0.1700.0000.0000.0000.000
121A246GLU-1-0.970-0.98722.664-0.315-0.3150.0000.0000.0000.000
122A247VAL0-0.018-0.00225.1090.0010.0010.0000.0000.0000.000
123A248GLY00.018-0.00121.882-0.017-0.0170.0000.0000.0000.000
124A249VAL0-0.0560.00921.8630.0080.0080.0000.0000.0000.000
125A250ALA00.027-0.00617.435-0.024-0.0240.0000.0000.0000.000
126A251SER00.0160.00218.0520.0300.0300.0000.0000.0000.000
127A252PRO00.0260.01115.909-0.059-0.0590.0000.0000.0000.000
128A253VAL0-0.038-0.00312.8710.0730.0730.0000.0000.0000.000
129A254TYR00.0450.00314.135-0.091-0.0910.0000.0000.0000.000
130A255ASP-1-0.686-0.85312.576-0.218-0.2180.0000.0000.0000.000
131A256HIS00.011-0.00514.635-0.003-0.0030.0000.0000.0000.000
132A257ARG10.8560.91215.4960.0450.0450.0000.0000.0000.000
133A258GLY0-0.038-0.00817.422-0.001-0.0010.0000.0000.0000.000
134A259ASN0-0.050-0.01113.868-0.023-0.0230.0000.0000.0000.000
135A260MET0-0.021-0.00613.9560.0040.0040.0000.0000.0000.000
136A261VAL0-0.034-0.0129.462-0.091-0.0910.0000.0000.0000.000
137A262ALA0-0.029-0.0218.897-0.349-0.3490.0000.0000.0000.000
138A263SER0-0.026-0.01010.7330.1710.1710.0000.0000.0000.000
139A264VAL00.0210.02313.024-0.071-0.0710.0000.0000.0000.000
140A265LEU00.011-0.00315.3720.0140.0140.0000.0000.0000.000
141A266ILE00.0180.00417.0250.0270.0270.0000.0000.0000.000
142A267PRO0-0.059-0.01817.8860.0000.0000.0000.0000.0000.000
143A268ALA00.0430.00620.8720.0250.0250.0000.0000.0000.000
144A269PRO0-0.014-0.00524.321-0.010-0.0100.0000.0000.0000.000
145A270LYS10.9420.97927.0710.1850.1850.0000.0000.0000.000
146A271PHE0-0.025-0.01929.6260.0090.0090.0000.0000.0000.000
147A272ARG10.7380.84126.1000.1350.1350.0000.0000.0000.000
148A273VAL0-0.0060.01227.6320.0070.0070.0000.0000.0000.000
149A274SER00.0430.02731.093-0.007-0.0070.0000.0000.0000.000
150A275GLN00.041-0.00332.118-0.014-0.0140.0000.0000.0000.000
151A276ASP-1-0.870-0.93632.538-0.107-0.1070.0000.0000.0000.000
152A277THR0-0.029-0.00529.6290.0030.0030.0000.0000.0000.000
153A278LEU0-0.012-0.01026.667-0.003-0.0030.0000.0000.0000.000
154A279ASN0-0.039-0.03028.062-0.013-0.0130.0000.0000.0000.000
155A280SER00.0220.02429.335-0.002-0.0020.0000.0000.0000.000
156A281LEU00.0160.00224.9410.0020.0020.0000.0000.0000.000
157A282GLY00.0180.00224.606-0.011-0.0110.0000.0000.0000.000
158A283GLU-1-0.907-0.94124.667-0.105-0.1050.0000.0000.0000.000
159A284ALA0-0.003-0.00425.1100.0050.0050.0000.0000.0000.000
160A285CYS0-0.079-0.03020.077-0.006-0.0060.0000.0000.0000.000
161A286ALA00.0420.02620.652-0.014-0.0140.0000.0000.0000.000
162A287ALA0-0.032-0.01222.0430.0070.0070.0000.0000.0000.000
163A288ALA0-0.002-0.00919.3890.0200.0200.0000.0000.0000.000
164A289ALA00.021-0.00617.3440.0170.0170.0000.0000.0000.000
165A290ALA00.0450.02617.9780.0040.0040.0000.0000.0000.000
166A291LYS10.9480.97220.1210.0230.0230.0000.0000.0000.000
167A292VAL00.003-0.00213.4140.0510.0510.0000.0000.0000.000
168A293THR00.0120.01716.0520.0160.0160.0000.0000.0000.000
169A294THR0-0.049-0.02217.2790.0360.0360.0000.0000.0000.000
170A295ARG10.8460.91816.981-0.128-0.1280.0000.0000.0000.000
171A296LEU0-0.0220.01111.6430.0550.0550.0000.0000.0000.000
172A297GLY0-0.0180.00715.2750.0170.0170.0000.0000.0000.000
173A298GLY0-0.027-0.01417.348-0.015-0.0150.0000.0000.0000.000
174A299ARG10.8720.92718.0370.1510.1510.0000.0000.0000.000
175A300ALA00.0230.02120.512-0.026-0.0260.0000.0000.0000.000
176A301PRO0-0.0020.01420.2390.0340.0340.0000.0000.0000.000