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: MVQ9Z

Calculation Name: 2O8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CYG0

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2705090.294151
FMO2-HF: Nuclear repulsion 2612862.941905
FMO2-HF: Total energy -92227.352246
FMO2-MP2: Total energy -92493.635205


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:8:MET)


Summations of interaction energy for fragment #1(A:8: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.
-7.552-2.24211.365-4.11-12.562-0.014
Interaction energy analysis for fragmet #1(A:8:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : 0.002
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].
3A10GLU-1-0.796-0.8822.653-4.850-1.6870.815-1.895-2.082-0.006
4A11ARG10.8240.8665.1331.5071.687-0.001-0.008-0.1700.000
5A12LEU0-0.002-0.0102.157-0.9470.3673.146-1.676-2.783-0.007
6A13LEU00.014-0.0012.3630.4182.1105.152-1.969-4.875-0.003
7A14GLN0-0.023-0.0273.6462.1500.4130.0542.043-0.360-0.001
8A15LYS10.7960.8816.243-0.620-0.6200.0000.0000.0000.000
9A16TYR00.004-0.0022.989-2.751-2.0532.199-0.605-2.2920.003
10A17ARG10.8840.9276.538-1.056-1.0560.0000.0000.0000.000
11A18ALA00.0150.0118.645-0.259-0.2590.0000.0000.0000.000
12A19GLN0-0.007-0.01010.613-0.170-0.1700.0000.0000.0000.000
13A20VAL00.0040.0059.237-0.147-0.1470.0000.0000.0000.000
14A21PHE0-0.043-0.03511.899-0.167-0.1670.0000.0000.0000.000
15A22GLU-1-0.871-0.92114.3550.4350.4350.0000.0000.0000.000
16A23TRP00.006-0.00911.889-0.002-0.0020.0000.0000.0000.000
17A24GLY0-0.0100.00716.056-0.049-0.0490.0000.0000.0000.000
18A25GLY0-0.0020.00017.556-0.058-0.0580.0000.0000.0000.000
19A26CYS0-0.043-0.01716.864-0.069-0.0690.0000.0000.0000.000
20A27PHE00.0490.00117.8270.0030.0030.0000.0000.0000.000
21A28ASP-1-0.783-0.87019.1950.1140.1140.0000.0000.0000.000
22A29LYS10.9240.96315.149-0.105-0.1050.0000.0000.0000.000
23A30MET0-0.0310.01114.354-0.006-0.0060.0000.0000.0000.000
24A31PHE00.0460.00915.062-0.015-0.0150.0000.0000.0000.000
25A32GLU-1-0.881-0.93615.248-0.078-0.0780.0000.0000.0000.000
26A33ALA0-0.026-0.00210.879-0.083-0.0830.0000.0000.0000.000
27A34LEU0-0.008-0.01111.980-0.090-0.0900.0000.0000.0000.000
28A35LYS10.8520.91614.143-0.026-0.0260.0000.0000.0000.000
29A36SER0-0.046-0.02410.359-0.052-0.0520.0000.0000.0000.000
30A37LEU0-0.015-0.0068.376-0.110-0.1100.0000.0000.0000.000
31A38ILE0-0.032-0.01611.745-0.067-0.0670.0000.0000.0000.000
32A39TYR00.0160.01913.7230.0080.0080.0000.0000.0000.000
33A40LEU00.002-0.0078.617-0.051-0.0510.0000.0000.0000.000
34A41SER0-0.084-0.05212.783-0.014-0.0140.0000.0000.0000.000
35A42GLU-1-0.824-0.91714.471-0.276-0.2760.0000.0000.0000.000
36A43PHE0-0.075-0.02914.6260.0360.0360.0000.0000.0000.000
37A44GLU-1-0.914-0.95911.879-1.059-1.0590.0000.0000.0000.000
38A45ASN0-0.069-0.03415.3080.0770.0770.0000.0000.0000.000
39A46SER0-0.022-0.00113.2820.0670.0670.0000.0000.0000.000
40A47GLU-1-0.734-0.81214.839-0.018-0.0180.0000.0000.0000.000
41A48PHE00.0520.03313.8380.0080.0080.0000.0000.0000.000
42A49ASP-1-0.774-0.87010.9960.4020.4020.0000.0000.0000.000
43A50ASP-1-0.798-0.92114.4620.2430.2430.0000.0000.0000.000
44A51GLU-1-0.865-0.90710.7491.1021.1020.0000.0000.0000.000
45A52GLU-1-0.747-0.83910.050-0.055-0.0550.0000.0000.0000.000
46A53ARG10.7780.88413.274-0.153-0.1530.0000.0000.0000.000
47A54HIS00.0070.01316.155-0.062-0.0620.0000.0000.0000.000
48A55LEU00.0150.00511.336-0.025-0.0250.0000.0000.0000.000
49A56LEU00.0180.00815.637-0.027-0.0270.0000.0000.0000.000
50A57THR0-0.030-0.03717.649-0.016-0.0160.0000.0000.0000.000
51A58LEU0-0.003-0.00117.319-0.027-0.0270.0000.0000.0000.000
52A59CYS0-0.0380.00518.027-0.029-0.0290.0000.0000.0000.000
53A60ILE00.0060.01120.008-0.017-0.0170.0000.0000.0000.000
54A61LYS10.9310.96823.270-0.235-0.2350.0000.0000.0000.000
55A62HIS10.8190.90920.759-0.341-0.3410.0000.0000.0000.000
56A63LYS10.8660.92422.723-0.139-0.1390.0000.0000.0000.000
57A64ILE00.0130.00325.353-0.017-0.0170.0000.0000.0000.000
58A65SER0-0.002-0.00227.491-0.010-0.0100.0000.0000.0000.000
59A66ASP-1-0.860-0.93625.5350.2070.2070.0000.0000.0000.000
60A67TYR00.0520.03028.333-0.012-0.0120.0000.0000.0000.000
61A68ARG10.8300.89930.718-0.103-0.1030.0000.0000.0000.000
62A69THR0-0.0100.01130.903-0.005-0.0050.0000.0000.0000.000
63A70MET0-0.007-0.00429.935-0.004-0.0040.0000.0000.0000.000
64A71THR0-0.032-0.02133.347-0.011-0.0110.0000.0000.0000.000
65A72SER0-0.039-0.04035.946-0.004-0.0040.0000.0000.0000.000
66A73GLN00.001-0.00233.9280.0030.0030.0000.0000.0000.000
67A74VAL00.0160.01436.577-0.004-0.0040.0000.0000.0000.000
68A75LEU0-0.001-0.00439.163-0.005-0.0050.0000.0000.0000.000
69A76GLN00.0160.02240.859-0.005-0.0050.0000.0000.0000.000
70A77GLU-1-0.807-0.89040.5360.0770.0770.0000.0000.0000.000
71A78GLN00.0350.02343.232-0.006-0.0060.0000.0000.0000.000
72A79THR0-0.091-0.05845.120-0.003-0.0030.0000.0000.0000.000
73A80LYS10.7960.88243.514-0.080-0.0800.0000.0000.0000.000
74A81GLN0-0.080-0.03445.882-0.003-0.0030.0000.0000.0000.000
75A82LEU00.000-0.00449.532-0.003-0.0030.0000.0000.0000.000
76A83ASN0-0.045-0.02653.363-0.001-0.0010.0000.0000.0000.000
77A84ASN00.0410.02049.226-0.003-0.0030.0000.0000.0000.000
78A85ASP-1-0.823-0.91649.7600.0270.0270.0000.0000.0000.000
79A86GLU-1-0.833-0.89948.8850.0170.0170.0000.0000.0000.000
80A87LEU00.0120.01143.5240.0000.0000.0000.0000.0000.000
81A88VAL00.0260.00944.9810.0030.0030.0000.0000.0000.000
82A89LYS10.8270.89845.576-0.017-0.0170.0000.0000.0000.000
83A90ILE00.0340.02741.1220.0000.0000.0000.0000.0000.000
84A91CYS0-0.079-0.03841.0100.0040.0040.0000.0000.0000.000
85A92SER0-0.006-0.01940.7890.0020.0020.0000.0000.0000.000
86A93GLU-1-0.956-0.97140.0940.0150.0150.0000.0000.0000.000
87A94TYR00.004-0.00431.9630.0020.0020.0000.0000.0000.000
88A95VAL00.012-0.00536.5060.0030.0030.0000.0000.0000.000
89A96PHE0-0.022-0.00737.3360.0010.0010.0000.0000.0000.000
90A97SER0-0.020-0.01833.775-0.005-0.0050.0000.0000.0000.000
91A98LEU00.0040.00631.6210.0000.0000.0000.0000.0000.000
92A99ARG10.8090.87932.724-0.047-0.0470.0000.0000.0000.000
93A100LYS10.8970.93332.798-0.001-0.0010.0000.0000.0000.000
94A101ASP-1-0.828-0.89629.7850.0120.0120.0000.0000.0000.000
95A102ILE0-0.038-0.01027.8590.0010.0010.0000.0000.0000.000
96A103LYS10.8330.92129.445-0.011-0.0110.0000.0000.0000.000
97A104ALA00.0300.01729.112-0.006-0.0060.0000.0000.0000.000
98A105PHE0-0.021-0.01021.717-0.009-0.0090.0000.0000.0000.000
99A106LEU00.001-0.00925.559-0.005-0.0050.0000.0000.0000.000
100A107GLN00.000-0.00427.2580.0000.0000.0000.0000.0000.000
101A108SER00.0040.01423.212-0.011-0.0110.0000.0000.0000.000
102A109PHE0-0.006-0.01720.192-0.013-0.0130.0000.0000.0000.000
103A110GLU-1-0.825-0.90223.281-0.012-0.0120.0000.0000.0000.000
104A111ASP-1-0.787-0.86622.980-0.137-0.1370.0000.0000.0000.000
105A112CYS0-0.052-0.01719.547-0.020-0.0200.0000.0000.0000.000
106A113VAL0-0.006-0.00820.698-0.008-0.0080.0000.0000.0000.000
107A114ASP-1-0.811-0.91022.591-0.052-0.0520.0000.0000.0000.000
108A115ARG10.7570.84019.0110.1950.1950.0000.0000.0000.000
109A116LEU0-0.0380.00417.938-0.026-0.0260.0000.0000.0000.000
110A117VAL00.0270.03217.9480.0160.0160.0000.0000.0000.000
111A118GLU-1-0.847-0.92420.262-0.033-0.0330.0000.0000.0000.000
112A119LYS10.9480.98919.8120.1420.1420.0000.0000.0000.000
113A120SER0-0.076-0.08221.2860.0140.0140.0000.0000.0000.000
114A121PHE00.0330.01123.455-0.010-0.0100.0000.0000.0000.000
115A122PHE00.0260.00421.523-0.004-0.0040.0000.0000.0000.000
116A123SER0-0.030-0.02620.9760.0070.0070.0000.0000.0000.000
117A124LYS10.8780.93822.8130.0540.0540.0000.0000.0000.000
118A125PHE00.0110.00326.1950.0060.0060.0000.0000.0000.000
119A126PHE0-0.017-0.01420.0930.0100.0100.0000.0000.0000.000
120A127LYS10.8100.91023.6730.1000.1000.0000.0000.0000.000
121A128LEU00.0350.01724.8700.0030.0030.0000.0000.0000.000
122A129LYS10.8240.90926.853-0.104-0.1040.0000.0000.0000.000
123A130VAL00.012-0.00622.8100.0090.0090.0000.0000.0000.000
124A131LYS10.8320.89326.1720.0250.0250.0000.0000.0000.000
125A132SER00.0030.00028.547-0.003-0.0030.0000.0000.0000.000
126A133ASP-1-0.823-0.88827.9610.1080.1080.0000.0000.0000.000
127A134ILE00.0080.00625.1240.0020.0020.0000.0000.0000.000
128A135SER00.0240.00229.487-0.003-0.0030.0000.0000.0000.000
129A136ARG10.8150.91631.492-0.089-0.0890.0000.0000.0000.000
130A137TYR00.013-0.00527.9200.0020.0020.0000.0000.0000.000
131A138LYS10.8200.88831.2220.0030.0030.0000.0000.0000.000
132A139LEU00.0180.02334.255-0.005-0.0050.0000.0000.0000.000
133A140GLU-1-0.798-0.85135.9780.0680.0680.0000.0000.0000.000
134A141PHE0-0.010-0.01332.361-0.001-0.0010.0000.0000.0000.000
135A142GLY00.0230.03336.534-0.006-0.0060.0000.0000.0000.000
136A143LEU0-0.066-0.04532.447-0.005-0.0050.0000.0000.0000.000
137A144CYS0-0.056-0.02535.997-0.004-0.0040.0000.0000.0000.000
138A145SER0-0.020-0.02337.9030.0060.0060.0000.0000.0000.000
139A146LEU00.048-0.00139.5750.0020.0020.0000.0000.0000.000
140A147GLU-1-0.870-0.93940.7180.0130.0130.0000.0000.0000.000
141A148ASP-1-0.793-0.86837.282-0.007-0.0070.0000.0000.0000.000
142A149SER0-0.001-0.00836.0670.0030.0030.0000.0000.0000.000
143A150LYS10.8260.91936.606-0.018-0.0180.0000.0000.0000.000
144A151LYS10.8290.89337.3140.0140.0140.0000.0000.0000.000
145A152ILE00.0250.01731.8990.0000.0000.0000.0000.0000.000
146A153HIS0-0.001-0.01634.0830.0120.0120.0000.0000.0000.000
147A154GLN00.0440.00835.4850.0050.0050.0000.0000.0000.000
148A155ASP-1-0.806-0.85234.536-0.006-0.0060.0000.0000.0000.000
149A156ALA00.0140.00531.7680.0000.0000.0000.0000.0000.000
150A157PHE0-0.010-0.02133.1690.0060.0060.0000.0000.0000.000
151A158THR00.008-0.00536.1030.0020.0020.0000.0000.0000.000
152A159LEU0-0.0030.00929.7110.0010.0010.0000.0000.0000.000
153A160LEU0-0.025-0.02233.3110.0030.0030.0000.0000.0000.000
154A161CYS0-0.078-0.04034.4330.0030.0030.0000.0000.0000.000
155A162GLU-1-0.898-0.94536.498-0.003-0.0030.0000.0000.0000.000
156A163HIS0-0.077-0.02733.347-0.002-0.0020.0000.0000.0000.000
157A164PRO00.0410.01634.3330.0080.0080.0000.0000.0000.000
158A165ASP-1-0.835-0.90334.3440.0330.0330.0000.0000.0000.000
159A166LYS10.8070.89530.170-0.013-0.0130.0000.0000.0000.000
160A167ILE00.0140.01030.4100.0080.0080.0000.0000.0000.000
161A168GLU-1-0.768-0.85430.2020.1130.1130.0000.0000.0000.000
162A169GLN0-0.044-0.01326.1690.0080.0080.0000.0000.0000.000
163A170LEU0-0.0080.00725.9780.0040.0040.0000.0000.0000.000
164A171PRO00.0370.02824.9170.0030.0030.0000.0000.0000.000
165A172LEU00.0430.03727.731-0.010-0.0100.0000.0000.0000.000
166A173GLY00.0350.01830.295-0.009-0.0090.0000.0000.0000.000
167A174PHE0-0.027-0.03323.989-0.006-0.0060.0000.0000.0000.000
168A175ILE00.0350.03330.127-0.011-0.0110.0000.0000.0000.000
169A176GLN0-0.013-0.01433.2580.0000.0000.0000.0000.0000.000
170A177ASN0-0.031-0.01131.612-0.007-0.0070.0000.0000.0000.000
171A178LEU00.0250.01832.645-0.005-0.0050.0000.0000.0000.000
172A179ALA00.0530.02934.700-0.008-0.0080.0000.0000.0000.000
173A180TYR00.0200.02637.288-0.006-0.0060.0000.0000.0000.000
174A181ILE0-0.032-0.01234.929-0.004-0.0040.0000.0000.0000.000
175A182LEU00.0260.00737.842-0.005-0.0050.0000.0000.0000.000
176A183SER0-0.071-0.05540.046-0.003-0.0030.0000.0000.0000.000
177A184GLU-1-0.833-0.90642.0670.0560.0560.0000.0000.0000.000
178A185LYS10.8100.90539.453-0.071-0.0710.0000.0000.0000.000
179A186TYR00.0130.00737.309-0.001-0.0010.0000.0000.0000.000
180A187GLY00.0280.02742.819-0.005-0.0050.0000.0000.0000.000
181A188GLU-1-0.795-0.87542.9530.0240.0240.0000.0000.0000.000
182A189LYS10.8420.90045.053-0.055-0.0550.0000.0000.0000.000
183A190LYS10.8840.94746.343-0.027-0.0270.0000.0000.0000.000
184A191GLN0-0.030-0.02242.2740.0000.0000.0000.0000.0000.000
185A192VAL00.0340.00041.0400.0000.0000.0000.0000.0000.000
186A193PHE00.0270.01543.3130.0010.0010.0000.0000.0000.000
187A194ASN0-0.018-0.01045.802-0.001-0.0010.0000.0000.0000.000
188A195MET00.0210.01940.483-0.001-0.0010.0000.0000.0000.000
189A196LEU00.0560.02438.8780.0010.0010.0000.0000.0000.000
190A197ASN0-0.055-0.01742.3940.0020.0020.0000.0000.0000.000
191A198SER0-0.013-0.02344.2930.0000.0000.0000.0000.0000.000
192A199LEU00.0210.01537.1900.0000.0000.0000.0000.0000.000
193A200GLY00.0390.00841.4570.0030.0030.0000.0000.0000.000
194A201LYS10.8520.91742.882-0.045-0.0450.0000.0000.0000.000
195A202ILE00.0220.01940.538-0.001-0.0010.0000.0000.0000.000
196A203LEU00.0150.00937.5320.0010.0010.0000.0000.0000.000
197A204GLU-1-0.813-0.90641.0770.0580.0580.0000.0000.0000.000
198A205LEU0-0.047-0.00744.1970.0000.0000.0000.0000.0000.000
199A206GLN00.0350.00337.5300.0060.0060.0000.0000.0000.000
200A207ILE0-0.015-0.00540.6210.0020.0020.0000.0000.0000.000
201A208LYS10.8440.92542.164-0.050-0.0500.0000.0000.0000.000
202A209GLU-1-0.887-0.95342.7090.0390.0390.0000.0000.0000.000
203A210GLN0-0.0180.00636.7820.0020.0020.0000.0000.0000.000
204A211GLU-1-0.877-0.93540.6060.0610.0610.0000.0000.0000.000
205A212ASN0-0.044-0.02236.5780.0060.0060.0000.0000.0000.000
206A213MET00.0680.01638.9920.0000.0000.0000.0000.0000.000
207A214ASP-1-0.852-0.91135.1840.1280.1280.0000.0000.0000.000
208A215ARG10.7480.81332.611-0.105-0.1050.0000.0000.0000.000
209A216LYS10.8450.92335.987-0.071-0.0710.0000.0000.0000.000
210A217ALA0-0.0050.01337.647-0.002-0.0020.0000.0000.0000.000
211A218GLN00.0090.01032.2220.0000.0000.0000.0000.0000.000
212A219ILE00.0690.03435.1130.0010.0010.0000.0000.0000.000
213A220THR0-0.031-0.03636.773-0.006-0.0060.0000.0000.0000.000
214A221VAL0-0.028-0.00534.192-0.002-0.0020.0000.0000.0000.000
215A222TYR0-0.003-0.01929.6710.0020.0020.0000.0000.0000.000
216A223LEU0-0.052-0.01836.314-0.005-0.0050.0000.0000.0000.000
217A224GLN0-0.022-0.01539.772-0.008-0.0080.0000.0000.0000.000
218A225GLY0-0.014-0.00637.035-0.001-0.0010.0000.0000.0000.000
219A226ILE0-0.017-0.00736.123-0.001-0.0010.0000.0000.0000.000
220A227LYS10.8070.91439.482-0.072-0.0720.0000.0000.0000.000