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: LZK79

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2692920.28964
FMO2-HF: Nuclear repulsion 2600694.410053
FMO2-HF: Total energy -92225.879586
FMO2-MP2: Total energy -92492.216214


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.
-6.144-2.43110.364-2.952-11.125-0.014
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 : -0.051 / q_NPA : -0.032
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-1-0.878-0.9612.805-4.269-1.8760.527-1.294-1.626-0.006
4A11ARG10.8600.8935.1240.8060.989-0.001-0.007-0.1740.000
5A12LEU00.0100.0052.150-0.905-0.1734.013-1.647-3.099-0.006
6A13LEU00.010-0.0032.5730.2411.9245.000-2.184-4.498-0.001
7A14GLN00.0240.0113.6122.4890.2620.0372.578-0.389-0.001
8A15LYS10.8160.9026.288-0.722-0.7220.0000.0000.0000.000
9A16TYR00.002-0.0073.172-1.955-1.0060.788-0.398-1.3390.000
10A17ARG10.8640.9176.265-1.220-1.2200.0000.0000.0000.000
11A18ALA00.0110.0108.353-0.283-0.2830.0000.0000.0000.000
12A19GLN0-0.0010.00310.133-0.155-0.1550.0000.0000.0000.000
13A20VAL00.0150.0059.129-0.179-0.1790.0000.0000.0000.000
14A21PHE0-0.049-0.04011.541-0.160-0.1600.0000.0000.0000.000
15A22GLU-1-0.841-0.90114.1470.3220.3220.0000.0000.0000.000
16A23TRP0-0.006-0.00911.776-0.015-0.0150.0000.0000.0000.000
17A24GLY0-0.033-0.00815.906-0.052-0.0520.0000.0000.0000.000
18A25GLY00.0000.00617.519-0.046-0.0460.0000.0000.0000.000
19A26CYS0-0.0360.00116.708-0.052-0.0520.0000.0000.0000.000
20A27PHE00.058-0.00717.4800.0280.0280.0000.0000.0000.000
21A28ASP-1-0.780-0.86919.0030.1150.1150.0000.0000.0000.000
22A29LYS10.9390.96214.088-0.120-0.1200.0000.0000.0000.000
23A30MET0-0.045-0.00714.1850.0060.0060.0000.0000.0000.000
24A31PHE00.0310.00214.8830.0090.0090.0000.0000.0000.000
25A32GLU-1-0.880-0.94315.315-0.008-0.0080.0000.0000.0000.000
26A33ALA0-0.041-0.01110.698-0.061-0.0610.0000.0000.0000.000
27A34LEU00.004-0.00711.905-0.052-0.0520.0000.0000.0000.000
28A35LYS10.8740.93814.008-0.054-0.0540.0000.0000.0000.000
29A36SER0-0.0160.01010.829-0.059-0.0590.0000.0000.0000.000
30A37LEU00.0160.0008.399-0.077-0.0770.0000.0000.0000.000
31A38ILE0-0.034-0.01411.729-0.032-0.0320.0000.0000.0000.000
32A39TYR00.0020.01213.7470.0100.0100.0000.0000.0000.000
33A40LEU0-0.009-0.0068.645-0.006-0.0060.0000.0000.0000.000
34A41SER0-0.073-0.05512.8830.0070.0070.0000.0000.0000.000
35A42GLU-1-0.832-0.92714.174-0.077-0.0770.0000.0000.0000.000
36A43PHE0-0.083-0.03314.7040.0150.0150.0000.0000.0000.000
37A44GLU-1-0.921-0.96812.056-0.367-0.3670.0000.0000.0000.000
38A45ASN0-0.062-0.01515.4860.0500.0500.0000.0000.0000.000
39A46SER0-0.039-0.00213.3160.0360.0360.0000.0000.0000.000
40A47GLU-1-0.752-0.83215.0480.1330.1330.0000.0000.0000.000
41A48PHE0-0.004-0.00313.6700.0240.0240.0000.0000.0000.000
42A49ASP-1-0.763-0.86311.0550.4960.4960.0000.0000.0000.000
43A50ASP-1-0.829-0.94214.4240.2600.2600.0000.0000.0000.000
44A51GLU-1-0.894-0.92811.0310.7800.7800.0000.0000.0000.000
45A52GLU-1-0.759-0.86810.0660.2040.2040.0000.0000.0000.000
46A53ARG10.8240.89813.125-0.236-0.2360.0000.0000.0000.000
47A54HIS0-0.005-0.00116.303-0.045-0.0450.0000.0000.0000.000
48A55LEU00.0210.00911.525-0.023-0.0230.0000.0000.0000.000
49A56LEU00.0260.01815.659-0.027-0.0270.0000.0000.0000.000
50A57THR0-0.041-0.03517.608-0.024-0.0240.0000.0000.0000.000
51A58LEU0-0.010-0.00417.467-0.029-0.0290.0000.0000.0000.000
52A59CYS0-0.0350.00818.000-0.027-0.0270.0000.0000.0000.000
53A60ILE00.0310.01919.926-0.019-0.0190.0000.0000.0000.000
54A61LYS10.9440.98523.341-0.205-0.2050.0000.0000.0000.000
55A62HIS10.8070.87020.093-0.290-0.2900.0000.0000.0000.000
56A63LYS10.9020.95122.395-0.125-0.1250.0000.0000.0000.000
57A64ILE0-0.0090.00324.914-0.015-0.0150.0000.0000.0000.000
58A65SER0-0.012-0.01927.007-0.010-0.0100.0000.0000.0000.000
59A66ASP-1-0.879-0.94826.1220.1430.1430.0000.0000.0000.000
60A67TYR00.0190.01728.202-0.011-0.0110.0000.0000.0000.000
61A68ARG10.7670.85530.552-0.095-0.0950.0000.0000.0000.000
62A69THR00.0280.02230.871-0.007-0.0070.0000.0000.0000.000
63A70MET00.0000.00329.546-0.005-0.0050.0000.0000.0000.000
64A71THR0-0.021-0.00933.086-0.009-0.0090.0000.0000.0000.000
65A72SER0-0.050-0.03035.778-0.005-0.0050.0000.0000.0000.000
66A73GLN00.005-0.00333.1380.0010.0010.0000.0000.0000.000
67A74VAL00.0370.02236.398-0.004-0.0040.0000.0000.0000.000
68A75LEU0-0.018-0.01639.010-0.004-0.0040.0000.0000.0000.000
69A76GLN0-0.013-0.01040.296-0.004-0.0040.0000.0000.0000.000
70A77GLU-1-0.917-0.96440.2110.0500.0500.0000.0000.0000.000
71A78GLN00.007-0.00543.066-0.006-0.0060.0000.0000.0000.000
72A79THR0-0.100-0.04844.903-0.003-0.0030.0000.0000.0000.000
73A80LYS10.9280.97643.669-0.053-0.0530.0000.0000.0000.000
74A81GLN0-0.046-0.00445.945-0.003-0.0030.0000.0000.0000.000
75A82LEU00.0110.00549.274-0.001-0.0010.0000.0000.0000.000
76A83ASN0-0.024-0.01253.025-0.001-0.0010.0000.0000.0000.000
77A84ASN00.0510.01649.282-0.002-0.0020.0000.0000.0000.000
78A85ASP-1-0.844-0.92449.8410.0190.0190.0000.0000.0000.000
79A86GLU-1-0.890-0.96148.7440.0120.0120.0000.0000.0000.000
80A87LEU00.0000.00443.4510.0000.0000.0000.0000.0000.000
81A88VAL00.0280.00644.9460.0020.0020.0000.0000.0000.000
82A89LYS10.8850.95145.371-0.011-0.0110.0000.0000.0000.000
83A90ILE00.0340.03240.8630.0000.0000.0000.0000.0000.000
84A91CYS0-0.062-0.02340.8900.0030.0030.0000.0000.0000.000
85A92SER0-0.021-0.01840.6910.0030.0030.0000.0000.0000.000
86A93GLU-1-0.954-0.96539.6290.0140.0140.0000.0000.0000.000
87A94TYR00.005-0.00831.8020.0030.0030.0000.0000.0000.000
88A95VAL00.0350.00636.4080.0030.0030.0000.0000.0000.000
89A96PHE0-0.041-0.01937.0850.0020.0020.0000.0000.0000.000
90A97SER00.017-0.00233.614-0.002-0.0020.0000.0000.0000.000
91A98LEU00.0130.02231.3430.0020.0020.0000.0000.0000.000
92A99ARG10.9140.96132.314-0.042-0.0420.0000.0000.0000.000
93A100LYS10.9420.97133.810-0.009-0.0090.0000.0000.0000.000
94A101ASP-1-0.863-0.92829.1080.0340.0340.0000.0000.0000.000
95A102ILE0-0.062-0.02627.7960.0040.0040.0000.0000.0000.000
96A103LYS10.9000.95229.527-0.028-0.0280.0000.0000.0000.000
97A104ALA00.0310.02128.924-0.001-0.0010.0000.0000.0000.000
98A105PHE0-0.020-0.01221.750-0.003-0.0030.0000.0000.0000.000
99A106LEU0-0.028-0.02325.6110.0020.0020.0000.0000.0000.000
100A107GLN00.0060.00427.320-0.001-0.0010.0000.0000.0000.000
101A108SER0-0.0010.01623.134-0.003-0.0030.0000.0000.0000.000
102A109PHE00.010-0.01920.182-0.005-0.0050.0000.0000.0000.000
103A110GLU-1-0.827-0.90423.1180.0440.0440.0000.0000.0000.000
104A111ASP-1-0.857-0.91623.256-0.029-0.0290.0000.0000.0000.000
105A112CYS0-0.053-0.02919.454-0.009-0.0090.0000.0000.0000.000
106A113VAL0-0.012-0.01220.9050.0010.0010.0000.0000.0000.000
107A114ASP-1-0.811-0.89922.5280.0300.0300.0000.0000.0000.000
108A115ARG10.8100.90618.6610.0590.0590.0000.0000.0000.000
109A116LEU0-0.068-0.01418.123-0.005-0.0050.0000.0000.0000.000
110A117VAL00.0410.03417.875-0.001-0.0010.0000.0000.0000.000
111A118GLU-1-0.927-0.97420.3730.0670.0670.0000.0000.0000.000
112A119LYS10.9280.96520.313-0.085-0.0850.0000.0000.0000.000
113A120SER0-0.061-0.05521.346-0.005-0.0050.0000.0000.0000.000
114A121PHE00.0290.01223.745-0.006-0.0060.0000.0000.0000.000
115A122PHE00.0580.02420.984-0.008-0.0080.0000.0000.0000.000
116A123SER0-0.045-0.02221.386-0.006-0.0060.0000.0000.0000.000
117A124LYS10.9981.00222.953-0.067-0.0670.0000.0000.0000.000
118A125PHE00.0030.00126.355-0.002-0.0020.0000.0000.0000.000
119A126PHE0-0.027-0.01720.1390.0010.0010.0000.0000.0000.000
120A127LYS10.8760.95223.866-0.031-0.0310.0000.0000.0000.000
121A128LEU00.0380.01925.005-0.003-0.0030.0000.0000.0000.000
122A129LYS10.8390.92725.913-0.135-0.1350.0000.0000.0000.000
123A130VAL00.013-0.00122.7430.0000.0000.0000.0000.0000.000
124A131LYS10.8610.91926.081-0.044-0.0440.0000.0000.0000.000
125A132SER00.001-0.00528.371-0.007-0.0070.0000.0000.0000.000
126A133ASP-1-0.855-0.90227.4810.1170.1170.0000.0000.0000.000
127A134ILE00.002-0.00925.106-0.002-0.0020.0000.0000.0000.000
128A135SER0-0.042-0.01329.288-0.007-0.0070.0000.0000.0000.000
129A136ARG10.9550.97832.656-0.089-0.0890.0000.0000.0000.000
130A137TYR00.0220.00927.9670.0010.0010.0000.0000.0000.000
131A138LYS10.8370.88530.898-0.041-0.0410.0000.0000.0000.000
132A139LEU0-0.0050.01134.038-0.005-0.0050.0000.0000.0000.000
133A140GLU-1-0.843-0.88735.6900.0680.0680.0000.0000.0000.000
134A141PHE0-0.076-0.05132.891-0.004-0.0040.0000.0000.0000.000
135A142GLY0-0.023-0.01336.731-0.004-0.0040.0000.0000.0000.000
136A143LEU0-0.065-0.03732.548-0.004-0.0040.0000.0000.0000.000
137A144CYS0-0.032-0.01035.757-0.001-0.0010.0000.0000.0000.000
138A145SER00.0490.04437.7790.0030.0030.0000.0000.0000.000
139A146LEU00.040-0.00139.5900.0030.0030.0000.0000.0000.000
140A147GLU-1-0.912-0.95340.8460.0350.0350.0000.0000.0000.000
141A148ASP-1-0.848-0.93537.4870.0270.0270.0000.0000.0000.000
142A149SER0-0.040-0.03735.5770.0040.0040.0000.0000.0000.000
143A150LYS10.8500.94236.632-0.039-0.0390.0000.0000.0000.000
144A151LYS10.8660.92337.648-0.032-0.0320.0000.0000.0000.000
145A152ILE00.0150.01331.7600.0010.0010.0000.0000.0000.000
146A153HIS0-0.008-0.02334.0940.0100.0100.0000.0000.0000.000
147A154GLN00.008-0.02135.5220.0040.0040.0000.0000.0000.000
148A155ASP-1-0.801-0.87334.2550.0410.0410.0000.0000.0000.000
149A156ALA0-0.0010.00131.6980.0020.0020.0000.0000.0000.000
150A157PHE0-0.005-0.02633.2150.0040.0040.0000.0000.0000.000
151A158THR00.0240.01036.1800.0000.0000.0000.0000.0000.000
152A159LEU00.0040.01929.9420.0010.0010.0000.0000.0000.000
153A160LEU0-0.039-0.03133.3680.0030.0030.0000.0000.0000.000
154A161CYS0-0.063-0.03034.4570.0010.0010.0000.0000.0000.000
155A162GLU-1-0.938-0.96336.8570.0450.0450.0000.0000.0000.000
156A163HIS0-0.055-0.01333.7420.0000.0000.0000.0000.0000.000
157A164PRO00.0320.01334.6310.0070.0070.0000.0000.0000.000
158A165ASP-1-0.912-0.95635.1160.0780.0780.0000.0000.0000.000
159A166LYS10.9110.95429.898-0.078-0.0780.0000.0000.0000.000
160A167ILE00.0200.01230.7300.0080.0080.0000.0000.0000.000
161A168GLU-1-0.778-0.87330.6020.1210.1210.0000.0000.0000.000
162A169GLN0-0.063-0.02026.4820.0120.0120.0000.0000.0000.000
163A170LEU0-0.0110.00326.1650.0090.0090.0000.0000.0000.000
164A171PRO00.0390.03925.222-0.002-0.0020.0000.0000.0000.000
165A172LEU00.0650.03527.960-0.009-0.0090.0000.0000.0000.000
166A173GLY00.0200.00930.290-0.007-0.0070.0000.0000.0000.000
167A174PHE0-0.028-0.02924.038-0.005-0.0050.0000.0000.0000.000
168A175ILE00.0300.03030.106-0.008-0.0080.0000.0000.0000.000
169A176GLN0-0.015-0.02033.293-0.001-0.0010.0000.0000.0000.000
170A177ASN0-0.033-0.01432.212-0.007-0.0070.0000.0000.0000.000
171A178LEU00.0300.02932.877-0.005-0.0050.0000.0000.0000.000
172A179ALA00.0370.02434.903-0.006-0.0060.0000.0000.0000.000
173A180TYR0-0.021-0.02137.371-0.005-0.0050.0000.0000.0000.000
174A181ILE0-0.025-0.01635.089-0.005-0.0050.0000.0000.0000.000
175A182LEU00.0320.00838.006-0.005-0.0050.0000.0000.0000.000
176A183SER0-0.057-0.02840.107-0.005-0.0050.0000.0000.0000.000
177A184GLU-1-0.877-0.92341.8430.0570.0570.0000.0000.0000.000
178A185LYS10.8680.93839.331-0.072-0.0720.0000.0000.0000.000
179A186TYR0-0.012-0.00237.674-0.001-0.0010.0000.0000.0000.000
180A187GLY00.0140.00542.994-0.003-0.0030.0000.0000.0000.000
181A188GLU-1-0.803-0.88643.2170.0400.0400.0000.0000.0000.000
182A189LYS10.8760.91445.052-0.057-0.0570.0000.0000.0000.000
183A190LYS10.9430.97846.544-0.039-0.0390.0000.0000.0000.000
184A191GLN0-0.016-0.02342.9910.0010.0010.0000.0000.0000.000
185A192VAL00.0520.02341.2820.0010.0010.0000.0000.0000.000
186A193PHE0-0.0070.00443.5600.0020.0020.0000.0000.0000.000
187A194ASN0-0.058-0.03546.0520.0000.0000.0000.0000.0000.000
188A195MET00.0430.01340.8470.0000.0000.0000.0000.0000.000
189A196LEU00.0430.01339.0150.0020.0020.0000.0000.0000.000
190A197ASN0-0.076-0.01942.7710.0000.0000.0000.0000.0000.000
191A198SER00.003-0.00744.9110.0000.0000.0000.0000.0000.000
192A199LEU00.0140.01737.4170.0000.0000.0000.0000.0000.000
193A200GLY00.0380.01041.8870.0020.0020.0000.0000.0000.000
194A201LYS10.9460.97043.459-0.050-0.0500.0000.0000.0000.000
195A202ILE00.0160.01640.7820.0000.0000.0000.0000.0000.000
196A203LEU00.0030.00037.8690.0010.0010.0000.0000.0000.000
197A204GLU-1-0.970-0.99241.3580.0610.0610.0000.0000.0000.000
198A205LEU0-0.031-0.01044.4500.0000.0000.0000.0000.0000.000
199A206GLN00.0250.00737.4400.0030.0030.0000.0000.0000.000
200A207ILE0-0.026-0.01240.7300.0010.0010.0000.0000.0000.000
201A208LYS10.8690.92342.294-0.056-0.0560.0000.0000.0000.000
202A209GLU-1-0.930-0.96143.0000.0550.0550.0000.0000.0000.000
203A210GLN0-0.0410.01137.1200.0010.0010.0000.0000.0000.000
204A211GLU-1-0.870-0.95041.2480.0650.0650.0000.0000.0000.000
205A212ASN0-0.023-0.01237.1140.0030.0030.0000.0000.0000.000
206A213MET00.0510.00339.6510.0000.0000.0000.0000.0000.000
207A214ASP-1-0.864-0.92335.3460.1150.1150.0000.0000.0000.000
208A215ARG10.7210.81433.106-0.111-0.1110.0000.0000.0000.000
209A216LYS10.8970.96236.393-0.072-0.0720.0000.0000.0000.000
210A217ALA0-0.0020.00937.835-0.001-0.0010.0000.0000.0000.000
211A218GLN00.0210.00732.0970.0010.0010.0000.0000.0000.000
212A219ILE00.0530.03235.2480.0020.0020.0000.0000.0000.000
213A220THR0-0.031-0.02936.913-0.004-0.0040.0000.0000.0000.000
214A221VAL0-0.0200.00633.913-0.003-0.0030.0000.0000.0000.000
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