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: 941M2

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2694615.465964
FMO2-HF: Nuclear repulsion 2602388.549902
FMO2-HF: Total energy -92226.916062
FMO2-MP2: Total energy -92493.254076


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.
-6.991-1.87910.85-3.922-12.041-0.012
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-1-0.804-0.9032.785-4.317-1.1730.504-1.759-1.889-0.003
4A11ARG10.8370.8745.1411.5071.686-0.001-0.007-0.1710.000
5A12LEU0-0.004-0.0052.166-0.8620.3183.371-1.645-2.906-0.007
6A13LEU00.009-0.0052.4440.4742.0905.053-1.975-4.694-0.002
7A14GLN0-0.023-0.0253.6382.3260.5710.0462.066-0.357-0.001
8A15LYS10.8250.9006.285-0.703-0.7030.0000.0000.0000.000
9A16TYR00.005-0.0072.905-2.607-1.8591.877-0.602-2.0240.001
10A17ARG10.8660.9206.352-1.262-1.2620.0000.0000.0000.000
11A18ALA00.0120.0088.402-0.291-0.2910.0000.0000.0000.000
12A19GLN0-0.017-0.01610.302-0.192-0.1920.0000.0000.0000.000
13A20VAL00.0180.0169.175-0.190-0.1900.0000.0000.0000.000
14A21PHE0-0.054-0.04211.643-0.181-0.1810.0000.0000.0000.000
15A22GLU-1-0.842-0.90214.1890.4680.4680.0000.0000.0000.000
16A23TRP0-0.007-0.00811.854-0.001-0.0010.0000.0000.0000.000
17A24GLY0-0.032-0.00915.941-0.061-0.0610.0000.0000.0000.000
18A25GLY0-0.008-0.00217.686-0.062-0.0620.0000.0000.0000.000
19A26CYS0-0.042-0.01116.859-0.072-0.0720.0000.0000.0000.000
20A27PHE00.0580.00017.5250.0280.0280.0000.0000.0000.000
21A28ASP-1-0.777-0.87119.0580.1400.1400.0000.0000.0000.000
22A29LYS10.9380.96814.756-0.173-0.1730.0000.0000.0000.000
23A30MET0-0.0330.00314.2450.0000.0000.0000.0000.0000.000
24A31PHE00.0340.00614.943-0.006-0.0060.0000.0000.0000.000
25A32GLU-1-0.871-0.92615.247-0.040-0.0400.0000.0000.0000.000
26A33ALA0-0.035-0.00610.773-0.084-0.0840.0000.0000.0000.000
27A34LEU00.003-0.00511.946-0.087-0.0870.0000.0000.0000.000
28A35LYS10.8510.91014.033-0.058-0.0580.0000.0000.0000.000
29A36SER0-0.043-0.00810.430-0.067-0.0670.0000.0000.0000.000
30A37LEU0-0.007-0.0078.368-0.120-0.1200.0000.0000.0000.000
31A38ILE0-0.035-0.01711.789-0.073-0.0730.0000.0000.0000.000
32A39TYR00.0160.02113.7310.0040.0040.0000.0000.0000.000
33A40LEU0-0.003-0.0038.678-0.045-0.0450.0000.0000.0000.000
34A41SER0-0.064-0.04212.858-0.022-0.0220.0000.0000.0000.000
35A42GLU-1-0.828-0.91714.253-0.247-0.2470.0000.0000.0000.000
36A43PHE0-0.090-0.03814.7090.0310.0310.0000.0000.0000.000
37A44GLU-1-0.913-0.96312.026-1.020-1.0200.0000.0000.0000.000
38A45ASN0-0.077-0.02715.4650.0730.0730.0000.0000.0000.000
39A46SER0-0.034-0.00713.4030.0380.0380.0000.0000.0000.000
40A47GLU-1-0.759-0.83915.0160.0010.0010.0000.0000.0000.000
41A48PHE00.0200.01014.0050.0040.0040.0000.0000.0000.000
42A49ASP-1-0.778-0.86610.9370.4320.4320.0000.0000.0000.000
43A50ASP-1-0.804-0.92914.4030.2510.2510.0000.0000.0000.000
44A51GLU-1-0.879-0.91310.7821.0841.0840.0000.0000.0000.000
45A52GLU-1-0.757-0.85710.007-0.027-0.0270.0000.0000.0000.000
46A53ARG10.8080.89113.096-0.152-0.1520.0000.0000.0000.000
47A54HIS0-0.010-0.00416.189-0.058-0.0580.0000.0000.0000.000
48A55LEU00.0210.01011.339-0.022-0.0220.0000.0000.0000.000
49A56LEU00.0320.02015.611-0.025-0.0250.0000.0000.0000.000
50A57THR0-0.023-0.02917.589-0.017-0.0170.0000.0000.0000.000
51A58LEU0-0.018-0.00617.306-0.029-0.0290.0000.0000.0000.000
52A59CYS0-0.0310.00617.917-0.028-0.0280.0000.0000.0000.000
53A60ILE00.0260.01919.895-0.018-0.0180.0000.0000.0000.000
54A61LYS10.9360.97623.291-0.255-0.2550.0000.0000.0000.000
55A62HIS10.8380.89320.527-0.383-0.3830.0000.0000.0000.000
56A63LYS10.8740.93822.419-0.158-0.1580.0000.0000.0000.000
57A64ILE0-0.0060.00024.977-0.017-0.0170.0000.0000.0000.000
58A65SER0-0.011-0.01227.139-0.011-0.0110.0000.0000.0000.000
59A66ASP-1-0.870-0.93225.4860.2190.2190.0000.0000.0000.000
60A67TYR00.0470.02628.257-0.014-0.0140.0000.0000.0000.000
61A68ARG10.7620.83530.608-0.117-0.1170.0000.0000.0000.000
62A69THR00.0070.01830.852-0.008-0.0080.0000.0000.0000.000
63A70MET00.0010.00229.614-0.004-0.0040.0000.0000.0000.000
64A71THR0-0.031-0.01733.150-0.012-0.0120.0000.0000.0000.000
65A72SER0-0.034-0.03835.852-0.004-0.0040.0000.0000.0000.000
66A73GLN0-0.010-0.00933.5400.0030.0030.0000.0000.0000.000
67A74VAL00.0230.01936.519-0.005-0.0050.0000.0000.0000.000
68A75LEU0-0.011-0.01039.082-0.006-0.0060.0000.0000.0000.000
69A76GLN00.0190.00940.645-0.005-0.0050.0000.0000.0000.000
70A77GLU-1-0.815-0.89340.5970.0840.0840.0000.0000.0000.000
71A78GLN0-0.002-0.01043.173-0.006-0.0060.0000.0000.0000.000
72A79THR0-0.087-0.05145.013-0.003-0.0030.0000.0000.0000.000
73A80LYS10.8030.89843.362-0.088-0.0880.0000.0000.0000.000
74A81GLN0-0.063-0.01245.880-0.003-0.0030.0000.0000.0000.000
75A82LEU00.0150.00749.387-0.002-0.0020.0000.0000.0000.000
76A83ASN0-0.049-0.02953.136-0.002-0.0020.0000.0000.0000.000
77A84ASN00.0550.02049.246-0.003-0.0030.0000.0000.0000.000
78A85ASP-1-0.837-0.92049.9270.0320.0320.0000.0000.0000.000
79A86GLU-1-0.847-0.91848.8870.0230.0230.0000.0000.0000.000
80A87LEU00.0070.00843.5380.0000.0000.0000.0000.0000.000
81A88VAL00.0360.01345.0270.0030.0030.0000.0000.0000.000
82A89LYS10.8420.90845.451-0.022-0.0220.0000.0000.0000.000
83A90ILE00.0400.03441.0710.0000.0000.0000.0000.0000.000
84A91CYS0-0.075-0.03540.9670.0040.0040.0000.0000.0000.000
85A92SER0-0.014-0.01640.7730.0020.0020.0000.0000.0000.000
86A93GLU-1-0.948-0.96439.8370.0240.0240.0000.0000.0000.000
87A94TYR00.007-0.00631.8740.0030.0030.0000.0000.0000.000
88A95VAL00.0330.00536.4580.0030.0030.0000.0000.0000.000
89A96PHE0-0.043-0.02237.1360.0010.0010.0000.0000.0000.000
90A97SER00.006-0.00133.726-0.004-0.0040.0000.0000.0000.000
91A98LEU00.0100.02031.4710.0010.0010.0000.0000.0000.000
92A99ARG10.9020.95232.368-0.053-0.0530.0000.0000.0000.000
93A100LYS10.9460.97733.778-0.004-0.0040.0000.0000.0000.000
94A101ASP-1-0.859-0.93429.2050.0370.0370.0000.0000.0000.000
95A102ILE0-0.057-0.02327.7740.0020.0020.0000.0000.0000.000
96A103LYS10.8420.91829.539-0.024-0.0240.0000.0000.0000.000
97A104ALA00.0290.01729.019-0.006-0.0060.0000.0000.0000.000
98A105PHE0-0.015-0.01021.754-0.008-0.0080.0000.0000.0000.000
99A106LEU0-0.022-0.01825.636-0.002-0.0020.0000.0000.0000.000
100A107GLN0-0.0020.00027.348-0.002-0.0020.0000.0000.0000.000
101A108SER0-0.0040.01223.208-0.009-0.0090.0000.0000.0000.000
102A109PHE00.000-0.01820.153-0.014-0.0140.0000.0000.0000.000
103A110GLU-1-0.827-0.90723.150-0.001-0.0010.0000.0000.0000.000
104A111ASP-1-0.801-0.87422.919-0.119-0.1190.0000.0000.0000.000
105A112CYS0-0.048-0.01819.498-0.019-0.0190.0000.0000.0000.000
106A113VAL0-0.006-0.00820.954-0.010-0.0100.0000.0000.0000.000
107A114ASP-1-0.805-0.89922.562-0.040-0.0400.0000.0000.0000.000
108A115ARG10.7460.83919.0280.1730.1730.0000.0000.0000.000
109A116LEU0-0.053-0.00718.098-0.023-0.0230.0000.0000.0000.000
110A117VAL00.0400.03717.8340.0100.0100.0000.0000.0000.000
111A118GLU-1-0.891-0.94720.415-0.024-0.0240.0000.0000.0000.000
112A119LYS10.9300.95920.3840.1170.1170.0000.0000.0000.000
113A120SER0-0.043-0.04521.3030.0140.0140.0000.0000.0000.000
114A121PHE00.0490.02123.708-0.005-0.0050.0000.0000.0000.000
115A122PHE00.0410.01721.044-0.004-0.0040.0000.0000.0000.000
116A123SER0-0.042-0.01921.336-0.004-0.0040.0000.0000.0000.000
117A124LYS10.9440.97322.9580.0440.0440.0000.0000.0000.000
118A125PHE00.0080.00126.3700.0050.0050.0000.0000.0000.000
119A126PHE0-0.022-0.01420.0140.0090.0090.0000.0000.0000.000
120A127LYS10.8340.92223.8110.0880.0880.0000.0000.0000.000
121A128LEU00.0330.01825.0170.0030.0030.0000.0000.0000.000
122A129LYS10.8280.91726.440-0.116-0.1160.0000.0000.0000.000
123A130VAL00.017-0.00122.7160.0070.0070.0000.0000.0000.000
124A131LYS10.8650.91826.0740.0150.0150.0000.0000.0000.000
125A132SER00.000-0.00528.381-0.003-0.0030.0000.0000.0000.000
126A133ASP-1-0.872-0.90927.6780.1180.1180.0000.0000.0000.000
127A134ILE00.011-0.00525.0320.0030.0030.0000.0000.0000.000
128A135SER0-0.027-0.01229.289-0.004-0.0040.0000.0000.0000.000
129A136ARG10.9450.97832.519-0.093-0.0930.0000.0000.0000.000
130A137TYR00.0310.00928.0350.0020.0020.0000.0000.0000.000
131A138LYS10.8180.88730.993-0.010-0.0100.0000.0000.0000.000
132A139LEU00.0000.01134.047-0.005-0.0050.0000.0000.0000.000
133A140GLU-1-0.829-0.85635.5520.0810.0810.0000.0000.0000.000
134A141PHE0-0.058-0.03632.483-0.002-0.0020.0000.0000.0000.000
135A142GLY00.0180.01236.736-0.005-0.0050.0000.0000.0000.000
136A143LEU0-0.071-0.03932.529-0.005-0.0050.0000.0000.0000.000
137A144CYS0-0.036-0.01335.858-0.005-0.0050.0000.0000.0000.000
138A145SER0-0.011-0.01737.8030.0060.0060.0000.0000.0000.000
139A146LEU00.036-0.00539.6040.0020.0020.0000.0000.0000.000
140A147GLU-1-0.895-0.94940.8540.0160.0160.0000.0000.0000.000
141A148ASP-1-0.812-0.88037.4970.0000.0000.0000.0000.0000.000
142A149SER0-0.013-0.01935.6210.0030.0030.0000.0000.0000.000
143A150LYS10.8340.91336.637-0.024-0.0240.0000.0000.0000.000
144A151LYS10.8510.90337.4890.0070.0070.0000.0000.0000.000
145A152ILE00.0070.01531.870-0.001-0.0010.0000.0000.0000.000
146A153HIS0-0.015-0.02634.1010.0120.0120.0000.0000.0000.000
147A154GLN00.025-0.00835.5190.0050.0050.0000.0000.0000.000
148A155ASP-1-0.799-0.85434.4200.0000.0000.0000.0000.0000.000
149A156ALA00.0070.00831.808-0.001-0.0010.0000.0000.0000.000
150A157PHE0-0.003-0.02133.2140.0050.0050.0000.0000.0000.000
151A158THR00.026-0.00236.1690.0020.0020.0000.0000.0000.000
152A159LEU00.0020.02130.0270.0000.0000.0000.0000.0000.000
153A160LEU0-0.032-0.02933.3720.0020.0020.0000.0000.0000.000
154A161CYS0-0.074-0.03734.4430.0030.0030.0000.0000.0000.000
155A162GLU-1-0.941-0.96636.7270.0000.0000.0000.0000.0000.000
156A163HIS0-0.054-0.01433.736-0.003-0.0030.0000.0000.0000.000
157A164PRO00.0400.02134.5930.0070.0070.0000.0000.0000.000
158A165ASP-1-0.847-0.90734.5950.0340.0340.0000.0000.0000.000
159A166LYS10.8270.89630.383-0.013-0.0130.0000.0000.0000.000
160A167ILE00.0120.00730.6920.0090.0090.0000.0000.0000.000
161A168GLU-1-0.780-0.86230.5750.1090.1090.0000.0000.0000.000
162A169GLN0-0.061-0.02126.4590.0070.0070.0000.0000.0000.000
163A170LEU0-0.0140.00426.1280.0060.0060.0000.0000.0000.000
164A171PRO00.0420.03425.0510.0030.0030.0000.0000.0000.000
165A172LEU00.0510.03127.903-0.011-0.0110.0000.0000.0000.000
166A173GLY00.0300.01330.218-0.009-0.0090.0000.0000.0000.000
167A174PHE0-0.028-0.03023.924-0.006-0.0060.0000.0000.0000.000
168A175ILE00.0350.03330.059-0.011-0.0110.0000.0000.0000.000
169A176GLN0-0.018-0.02233.2500.0000.0000.0000.0000.0000.000
170A177ASN0-0.019-0.01031.828-0.007-0.0070.0000.0000.0000.000
171A178LEU00.0290.02332.711-0.005-0.0050.0000.0000.0000.000
172A179ALA00.0520.03334.870-0.008-0.0080.0000.0000.0000.000
173A180TYR00.0170.01937.107-0.005-0.0050.0000.0000.0000.000
174A181ILE0-0.039-0.02334.998-0.004-0.0040.0000.0000.0000.000
175A182LEU00.0280.01337.873-0.005-0.0050.0000.0000.0000.000
176A183SER0-0.064-0.04940.084-0.004-0.0040.0000.0000.0000.000
177A184GLU-1-0.844-0.91141.8950.0610.0610.0000.0000.0000.000
178A185LYS10.8110.90639.521-0.079-0.0790.0000.0000.0000.000
179A186TYR00.013-0.00137.432-0.001-0.0010.0000.0000.0000.000
180A187GLY00.0100.02042.978-0.005-0.0050.0000.0000.0000.000
181A188GLU-1-0.784-0.86543.2080.0250.0250.0000.0000.0000.000
182A189LYS10.8470.89545.029-0.059-0.0590.0000.0000.0000.000
183A190LYS10.9470.98246.514-0.029-0.0290.0000.0000.0000.000
184A191GLN0-0.024-0.02242.7280.0010.0010.0000.0000.0000.000
185A192VAL00.0500.01941.1690.0000.0000.0000.0000.0000.000
186A193PHE00.0010.00843.5330.0010.0010.0000.0000.0000.000
187A194ASN0-0.050-0.03346.017-0.001-0.0010.0000.0000.0000.000
188A195MET00.0370.01440.776-0.001-0.0010.0000.0000.0000.000
189A196LEU00.0560.01939.0060.0010.0010.0000.0000.0000.000
190A197ASN0-0.073-0.01942.7360.0010.0010.0000.0000.0000.000
191A198SER0-0.014-0.02044.6600.0000.0000.0000.0000.0000.000
192A199LEU00.0100.01637.5340.0000.0000.0000.0000.0000.000
193A200GLY00.0470.01641.8500.0020.0020.0000.0000.0000.000
194A201LYS10.9200.96043.415-0.043-0.0430.0000.0000.0000.000
195A202ILE00.0180.01840.7400.0000.0000.0000.0000.0000.000
196A203LEU00.0130.00837.8940.0010.0010.0000.0000.0000.000
197A204GLU-1-0.865-0.93941.3210.0590.0590.0000.0000.0000.000
198A205LEU0-0.046-0.01344.4330.0010.0010.0000.0000.0000.000
199A206GLN00.0340.00937.5560.0050.0050.0000.0000.0000.000
200A207ILE0-0.020-0.00940.7060.0020.0020.0000.0000.0000.000
201A208LYS10.8660.91842.258-0.049-0.0490.0000.0000.0000.000
202A209GLU-1-0.909-0.95443.1690.0360.0360.0000.0000.0000.000
203A210GLN0-0.0450.01037.3220.0010.0010.0000.0000.0000.000
204A211GLU-1-0.865-0.93941.2130.0560.0560.0000.0000.0000.000
205A212ASN0-0.022-0.00536.9420.0080.0080.0000.0000.0000.000
206A213MET00.0640.00939.616-0.001-0.0010.0000.0000.0000.000
207A214ASP-1-0.876-0.92735.3560.1290.1290.0000.0000.0000.000
208A215ARG10.7160.79233.040-0.100-0.1000.0000.0000.0000.000
209A216LYS10.8900.95136.358-0.067-0.0670.0000.0000.0000.000
210A217ALA0-0.0050.01437.818-0.001-0.0010.0000.0000.0000.000
211A218GLN00.0210.01332.544-0.001-0.0010.0000.0000.0000.000
212A219ILE00.0640.03635.2120.0020.0020.0000.0000.0000.000
213A220THR0-0.037-0.03936.876-0.004-0.0040.0000.0000.0000.000
214A221VAL0-0.0220.00533.899-0.002-0.0020.0000.0000.0000.000
215A222TYR0-0.005-0.01829.7110.0020.0020.0000.0000.0000.000
216A223LEU0-0.038-0.01236.428-0.004-0.0040.0000.0000.0000.000
217A224GLN0-0.024-0.02239.758-0.007-0.0070.0000.0000.0000.000
218A225GLY0-0.022-0.01337.107-0.001-0.0010.0000.0000.0000.000
219A226ILE0-0.026-0.01036.3410.0000.0000.0000.0000.0000.000
220A227LYS10.8220.93139.637-0.072-0.0720.0000.0000.0000.000