FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 85R3Y

Calculation Name: 4F8T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F8T

Chain ID: A

ChEMBL ID:

UniProt ID: O00478

Base Structure: X-ray

Registration Date: 2023-09-19

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075994.543252
FMO2-HF: Nuclear repulsion 1995270.088082
FMO2-HF: Total energy -80724.45517
FMO2-MP2: Total energy -80957.785753


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:1:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-6.96-1.5410.829-3.015-3.234-0.01
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.004
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].
3A3SER00.0370.0093.583-0.2202.793-0.038-1.500-1.4760.008
4A4VAL0-0.022-0.0076.129-0.535-0.5350.0000.0000.0000.000
5A5LEU0-0.026-0.0079.8690.3990.3990.0000.0000.0000.000
6A6GLY00.0650.03712.616-0.159-0.1590.0000.0000.0000.000
7A7PRO0-0.047-0.02916.3130.0140.0140.0000.0000.0000.000
8A8SER0-0.007-0.01319.1850.0450.0450.0000.0000.0000.000
9A9GLY00.0290.01220.7330.0470.0470.0000.0000.0000.000
10A10PRO0-0.092-0.03323.126-0.021-0.0210.0000.0000.0000.000
11A11ILE00.0170.01023.584-0.006-0.0060.0000.0000.0000.000
12A12LEU0-0.026-0.01526.8660.0060.0060.0000.0000.0000.000
13A13ALA00.0240.01730.579-0.011-0.0110.0000.0000.0000.000
14A14MET0-0.008-0.00432.4140.0140.0140.0000.0000.0000.000
15A15VAL0-0.028-0.03835.485-0.008-0.0080.0000.0000.0000.000
16A16GLY0-0.026-0.00336.6130.0010.0010.0000.0000.0000.000
17A17GLU-1-0.893-0.93034.013-0.037-0.0370.0000.0000.0000.000
18A18ASP-1-0.865-0.94730.820-0.104-0.1040.0000.0000.0000.000
19A19ALA0-0.027-0.01828.2470.0100.0100.0000.0000.0000.000
20A20ASP-1-0.784-0.86524.484-0.181-0.1810.0000.0000.0000.000
21A21LEU0-0.033-0.03221.9160.0290.0290.0000.0000.0000.000
22A22PRO0-0.040-0.02519.293-0.044-0.0440.0000.0000.0000.000
23A23CYS0-0.063-0.02114.2860.0590.0590.0000.0000.0000.000
24A24HIS0-0.007-0.01013.540-0.159-0.1590.0000.0000.0000.000
25A25LEU00.0130.0277.3110.2010.2010.0000.0000.0000.000
26A26PHE0-0.0220.0256.8860.1620.1620.0000.0000.0000.000
27A27PRO00.018-0.0145.627-0.298-0.2980.0000.0000.0000.000
28A28THR00.011-0.0198.588-0.421-0.4210.0000.0000.0000.000
29A29MET0-0.0210.0024.403-0.434-0.345-0.001-0.025-0.0630.000
30A30SER00.0050.0009.3690.2240.2240.0000.0000.0000.000
31A31ALA00.0510.0068.932-0.398-0.3980.0000.0000.0000.000
32A32GLU-1-1.010-1.00510.648-0.667-0.6670.0000.0000.0000.000
33A33THR0-0.013-0.0159.8990.0930.0930.0000.0000.0000.000
34A34MET0-0.0440.0135.9480.1780.1780.0000.0000.0000.000
35A35GLU-1-0.870-0.92211.011-0.348-0.3480.0000.0000.0000.000
36A36LEU0-0.051-0.02612.491-0.074-0.0740.0000.0000.0000.000
37A37ARG10.8080.89513.1900.5380.5380.0000.0000.0000.000
38A38TRP00.0860.04616.478-0.007-0.0070.0000.0000.0000.000
39A39VAL0-0.034-0.01718.6040.0110.0110.0000.0000.0000.000
40A40SER00.0770.04421.0110.0330.0330.0000.0000.0000.000
41A41SER0-0.016-0.01921.3550.0230.0230.0000.0000.0000.000
42A42SER0-0.009-0.02823.7090.0160.0160.0000.0000.0000.000
43A43LEU00.0330.02227.3290.0050.0050.0000.0000.0000.000
44A44ARG10.8490.93925.030-0.109-0.1090.0000.0000.0000.000
45A45GLN00.0490.06625.556-0.023-0.0230.0000.0000.0000.000
46A46VAL00.0000.00121.1000.0010.0010.0000.0000.0000.000
47A47VAL00.0070.00522.6810.0040.0040.0000.0000.0000.000
48A48ASN00.004-0.00922.134-0.012-0.0120.0000.0000.0000.000
49A49VAL0-0.015-0.01217.943-0.009-0.0090.0000.0000.0000.000
50A50TYR00.0310.02616.0860.0520.0520.0000.0000.0000.000
51A51ALA00.0540.01416.618-0.077-0.0770.0000.0000.0000.000
52A52ASP-1-0.904-0.94316.797-0.521-0.5210.0000.0000.0000.000
53A53GLY0-0.026-0.01518.4250.0410.0410.0000.0000.0000.000
54A54LYS10.8840.94220.3490.3610.3610.0000.0000.0000.000
55A55GLU-1-0.797-0.90721.011-0.328-0.3280.0000.0000.0000.000
56A56VAL0-0.076-0.03921.9830.0250.0250.0000.0000.0000.000
57A57GLU-1-0.800-0.91424.457-0.135-0.1350.0000.0000.0000.000
58A58ASP-1-0.846-0.92526.500-0.165-0.1650.0000.0000.0000.000
59A59ARG10.8210.91618.7570.2980.2980.0000.0000.0000.000
60A60GLN0-0.0110.00024.4120.0260.0260.0000.0000.0000.000
61A61SER0-0.028-0.05426.5920.0130.0130.0000.0000.0000.000
62A62ALA00.0510.02228.596-0.003-0.0030.0000.0000.0000.000
63A63PRO0-0.035-0.01530.062-0.002-0.0020.0000.0000.0000.000
64A64TYR00.015-0.01227.7050.0040.0040.0000.0000.0000.000
65A65ARG10.8360.92829.4930.1110.1110.0000.0000.0000.000
66A66GLY0-0.0070.00830.0120.0100.0100.0000.0000.0000.000
67A67ARG10.8070.89730.5950.0700.0700.0000.0000.0000.000
68A68THR0-0.029-0.02125.929-0.003-0.0030.0000.0000.0000.000
69A69SER00.0100.01925.361-0.007-0.0070.0000.0000.0000.000
70A70ILE0-0.034-0.01518.5480.0000.0000.0000.0000.0000.000
71A71LEU0-0.028-0.00621.424-0.016-0.0160.0000.0000.0000.000
72A72ARG10.9500.95515.6560.6430.6430.0000.0000.0000.000
73A73ASP-1-0.848-0.91719.118-0.396-0.3960.0000.0000.0000.000
74A74GLY0-0.073-0.03518.6500.0000.0000.0000.0000.0000.000
75A75ILE00.0340.01813.870-0.058-0.0580.0000.0000.0000.000
76A76THR00.0060.00513.569-0.164-0.1640.0000.0000.0000.000
77A77ALA0-0.027-0.01413.676-0.090-0.0900.0000.0000.0000.000
78A78GLY00.0550.03011.705-0.034-0.0340.0000.0000.0000.000
79A79LYS10.8790.94112.3890.4850.4850.0000.0000.0000.000
80A80ALA00.0290.01715.580-0.014-0.0140.0000.0000.0000.000
81A81ALA0-0.032-0.01717.1220.0540.0540.0000.0000.0000.000
82A82LEU0-0.0100.02820.206-0.020-0.0200.0000.0000.0000.000
83A83ARG10.8880.92622.3030.2030.2030.0000.0000.0000.000
84A84ILE0-0.042-0.02625.945-0.007-0.0070.0000.0000.0000.000
85A85HIS00.006-0.00528.441-0.006-0.0060.0000.0000.0000.000
86A86ASN0-0.056-0.02631.8970.0110.0110.0000.0000.0000.000
87A87VAL00.0080.01730.9210.0050.0050.0000.0000.0000.000
88A88THR00.0250.01333.4500.0090.0090.0000.0000.0000.000
89A89ALA00.0690.01933.7690.0020.0020.0000.0000.0000.000
90A90SER0-0.017-0.01633.4840.0080.0080.0000.0000.0000.000
91A91ASP-1-0.795-0.87029.849-0.044-0.0440.0000.0000.0000.000
92A92SER0-0.0320.01728.8810.0060.0060.0000.0000.0000.000
93A93GLY00.0070.00427.6620.0040.0040.0000.0000.0000.000
94A94LYS10.9330.96422.398-0.254-0.2540.0000.0000.0000.000
95A95TYR00.006-0.03521.106-0.020-0.0200.0000.0000.0000.000
96A96LEU0-0.072-0.03016.1650.0450.0450.0000.0000.0000.000
97A98TYR00.001-0.01612.1530.0970.0970.0000.0000.0000.000
98A99PHE00.0400.0169.0210.0160.0160.0000.0000.0000.000
99A100GLN00.002-0.0068.595-0.060-0.0600.0000.0000.0000.000
100A101ASP-1-0.928-0.9705.454-2.747-2.7470.0000.0000.0000.000
101A102GLY00.0360.0276.938-0.009-0.0090.0000.0000.0000.000
102A103ASP-1-0.898-0.9549.002-0.435-0.4350.0000.0000.0000.000
103A104PHE0-0.048-0.0143.059-2.683-0.3660.868-1.490-1.695-0.018
104A105TYR0-0.020-0.0306.693-0.132-0.1320.0000.0000.0000.000
105A106GLU-1-0.892-0.9135.7561.3041.3040.0000.0000.0000.000
106A107LYS10.9160.9418.129-0.592-0.5920.0000.0000.0000.000
107A108ALA00.0050.00711.5810.2340.2340.0000.0000.0000.000
108A109LEU0-0.034-0.02413.878-0.076-0.0760.0000.0000.0000.000
109A110VAL00.0250.00817.5250.0120.0120.0000.0000.0000.000
110A111GLU-1-0.968-0.99420.3540.1690.1690.0000.0000.0000.000
111A112LEU00.0230.02823.948-0.009-0.0090.0000.0000.0000.000
112A113LYS10.8760.93527.052-0.122-0.1220.0000.0000.0000.000
113A114VAL00.0470.02430.311-0.007-0.0070.0000.0000.0000.000
114A115ALA0-0.020-0.01033.4420.0110.0110.0000.0000.0000.000
115A116ALA00.008-0.00536.803-0.009-0.0090.0000.0000.0000.000
116A117LEU0-0.003-0.00940.1830.0070.0070.0000.0000.0000.000
117A118GLY00.0640.00043.196-0.004-0.0040.0000.0000.0000.000
118A119SER00.0390.01746.332-0.002-0.0020.0000.0000.0000.000
119A120ASP-1-0.864-0.92949.7780.0120.0120.0000.0000.0000.000
120A121LEU0-0.057-0.03051.3690.0000.0000.0000.0000.0000.000
121A122HIS00.0110.02054.595-0.002-0.0020.0000.0000.0000.000
122A123ILE0-0.005-0.01557.4310.0030.0030.0000.0000.0000.000
123A124GLU-1-0.937-0.96259.9300.0200.0200.0000.0000.0000.000
124A125VAL00.007-0.00962.4510.0020.0020.0000.0000.0000.000
125A126LYS10.9120.95861.493-0.028-0.0280.0000.0000.0000.000
126A127GLY00.0230.00365.997-0.001-0.0010.0000.0000.0000.000
127A128TYR0-0.086-0.04068.1560.0010.0010.0000.0000.0000.000
128A129GLU-1-0.921-0.97864.7650.0350.0350.0000.0000.0000.000
129A130ASP-1-0.887-0.94467.2120.0390.0390.0000.0000.0000.000
130A131GLY0-0.035-0.00869.5560.0010.0010.0000.0000.0000.000
131A132GLY0-0.048-0.02168.5760.0000.0000.0000.0000.0000.000
132A133ILE00.0010.00666.7240.0000.0000.0000.0000.0000.000
133A134HIS00.0170.01761.7690.0020.0020.0000.0000.0000.000
134A135LEU0-0.026-0.02061.481-0.002-0.0020.0000.0000.0000.000
135A136GLU-1-0.820-0.88657.2970.0310.0310.0000.0000.0000.000
136A137CYS0-0.093-0.00754.0320.0010.0010.0000.0000.0000.000
137A138ARG10.8900.92653.734-0.022-0.0220.0000.0000.0000.000
138A139SER0-0.0030.01349.875-0.002-0.0020.0000.0000.0000.000
139A140THR0-0.024-0.01948.7090.0010.0010.0000.0000.0000.000
140A141GLY00.0690.01445.118-0.001-0.0010.0000.0000.0000.000
141A142TRP0-0.0110.03243.369-0.001-0.0010.0000.0000.0000.000
142A143TYR0-0.0230.02834.1150.0040.0040.0000.0000.0000.000
143A144PRO00.0180.00436.148-0.003-0.0030.0000.0000.0000.000
144A145GLN00.037-0.01338.530-0.003-0.0030.0000.0000.0000.000
145A146PRO0-0.0440.00140.7490.0060.0060.0000.0000.0000.000
146A147GLN0-0.003-0.00543.239-0.002-0.0020.0000.0000.0000.000
147A148ILE00.0240.00345.220-0.005-0.0050.0000.0000.0000.000
148A149LYS10.9300.98249.019-0.057-0.0570.0000.0000.0000.000
149A150TRP00.0370.00051.682-0.004-0.0040.0000.0000.0000.000
150A151SER0-0.028-0.01454.2690.0040.0040.0000.0000.0000.000
151A152ASP-1-0.754-0.86556.3060.0450.0450.0000.0000.0000.000
152A153THR00.010-0.01358.3740.0020.0020.0000.0000.0000.000
153A154LYS10.8910.95059.671-0.046-0.0460.0000.0000.0000.000
154A155GLY0-0.060-0.02456.0830.0020.0020.0000.0000.0000.000
155A156GLU-1-0.969-0.97654.7910.0680.0680.0000.0000.0000.000
156A157ASN0-0.033-0.02150.816-0.004-0.0040.0000.0000.0000.000
157A158ILE00.0050.00355.1510.0000.0000.0000.0000.0000.000
158A159PRO0-0.078-0.05255.4420.0000.0000.0000.0000.0000.000
159A160ALA0-0.001-0.00254.224-0.003-0.0030.0000.0000.0000.000
160A161VAL0-0.0130.00854.8480.0030.0030.0000.0000.0000.000
161A162GLU-1-0.931-0.96347.9160.0580.0580.0000.0000.0000.000
162A163ALA0-0.027-0.01152.5190.0010.0010.0000.0000.0000.000
163A164PRO0-0.022-0.02349.4380.0020.0020.0000.0000.0000.000
164A165VAL00.0120.01744.043-0.004-0.0040.0000.0000.0000.000
165A166VAL0-0.005-0.00546.9910.0000.0000.0000.0000.0000.000
166A167ALA0-0.019-0.00742.621-0.001-0.0010.0000.0000.0000.000
167A168ASP-1-0.805-0.90643.5720.0050.0050.0000.0000.0000.000
168A169GLY0-0.019-0.01643.6010.0010.0010.0000.0000.0000.000
169A170VAL0-0.050-0.02640.510-0.002-0.0020.0000.0000.0000.000
170A171GLY0-0.0070.00139.5180.0000.0000.0000.0000.0000.000
171A172LEU0-0.095-0.03740.0770.0070.0070.0000.0000.0000.000
172A173TYR00.0070.00038.7330.0020.0020.0000.0000.0000.000
173A174ALA0-0.052-0.01444.530-0.002-0.0020.0000.0000.0000.000
174A175VAL0-0.014-0.01246.6920.0030.0030.0000.0000.0000.000
175A176ALA00.0370.00249.475-0.003-0.0030.0000.0000.0000.000
176A177ALA00.0280.02352.5550.0030.0030.0000.0000.0000.000
177A178SER00.0200.01754.419-0.003-0.0030.0000.0000.0000.000
178A179VAL00.0010.00657.3860.0030.0030.0000.0000.0000.000
179A180ILE0-0.0010.00159.875-0.002-0.0020.0000.0000.0000.000
180A181MET0-0.051-0.00963.5130.0010.0010.0000.0000.0000.000
181A182ARG10.9410.95163.572-0.042-0.0420.0000.0000.0000.000
182A183GLY00.0130.02267.8060.0010.0010.0000.0000.0000.000
183A184SER00.019-0.00568.6010.0000.0000.0000.0000.0000.000
184A185SER0-0.041-0.02466.1110.0010.0010.0000.0000.0000.000
185A186GLY00.0370.02467.6680.0000.0000.0000.0000.0000.000
186A187GLY00.0190.02164.289-0.001-0.0010.0000.0000.0000.000
187A188GLY0-0.0010.01163.9660.0010.0010.0000.0000.0000.000
188A189VAL00.0040.00759.8190.0020.0020.0000.0000.0000.000
189A190SER0-0.005-0.01056.131-0.003-0.0030.0000.0000.0000.000
190A192ILE00.014-0.01749.094-0.002-0.0020.0000.0000.0000.000
191A193ILE00.0400.01346.8350.0030.0030.0000.0000.0000.000
192A194ARG10.9290.97141.526-0.066-0.0660.0000.0000.0000.000
193A195ASN00.0310.01738.9890.0100.0100.0000.0000.0000.000
194A196SER0-0.033-0.03938.433-0.003-0.0030.0000.0000.0000.000
195A197LEU0-0.0120.00132.4700.0060.0060.0000.0000.0000.000
196A198LEU00.0280.00235.8740.0000.0000.0000.0000.0000.000
197A199GLY0-0.0290.00138.244-0.002-0.0020.0000.0000.0000.000
198A200LEU0-0.055-0.02340.508-0.004-0.0040.0000.0000.0000.000
199A201GLU-1-0.903-0.97043.3440.0520.0520.0000.0000.0000.000
200A202LYS10.7970.89546.594-0.016-0.0160.0000.0000.0000.000
201A203THR0-0.031-0.02249.6810.0020.0020.0000.0000.0000.000
202A204ALA00.0400.03652.989-0.003-0.0030.0000.0000.0000.000
203A205SER0-0.011-0.01156.6420.0020.0020.0000.0000.0000.000
204A206ILE0-0.0060.00859.602-0.002-0.0020.0000.0000.0000.000
205A207SER0-0.024-0.04562.9930.0020.0020.0000.0000.0000.000
206A208ILE0-0.013-0.00666.156-0.002-0.0020.0000.0000.0000.000
207A209ALA0-0.0050.00269.2060.0010.0010.0000.0000.0000.000
208A210ASP-1-0.837-0.94572.8910.0250.0250.0000.0000.0000.000
209A211PRO0-0.060-0.03674.9350.0000.0000.0000.0000.0000.000
210A212PHE0-0.0200.00572.7340.0000.0000.0000.0000.0000.000
211A213PHE00.0230.02768.3920.0000.0000.0000.0000.0000.000