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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: 987Y2

Calculation Name: 3F5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5T

Chain ID: A

ChEMBL ID:

UniProt ID: A5A5U1

Base Structure: X-ray

Registration Date: 2023-09-22

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1817373.074177
FMO2-HF: Nuclear repulsion 1740869.333044
FMO2-HF: Total energy -76503.741133
FMO2-MP2: Total energy -76724.252088


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:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
-7.326-1.6931.701-2.824-4.508-0.009
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.000
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].
3A7SER00.0400.0172.587-5.522-2.4570.680-1.578-2.166-0.006
4A8SER00.017-0.0072.372-1.882-0.0391.011-1.026-1.827-0.003
5A9PHE00.0110.0204.1120.5870.9320.001-0.096-0.2500.000
6A10GLN00.020-0.0026.0400.0020.0020.0000.0000.0000.000
7A11VAL00.0230.0227.0100.0790.0790.0000.0000.0000.000
8A12ASP-1-0.816-0.8888.0580.1260.1260.0000.0000.0000.000
9A13CYS0-0.089-0.0439.8590.0370.0370.0000.0000.0000.000
10A14PHE0-0.0410.00411.8430.0140.0140.0000.0000.0000.000
11A15LEU00.0330.01111.7050.0070.0070.0000.0000.0000.000
12A16TRP0-0.040-0.03514.1910.0050.0050.0000.0000.0000.000
13A17HIS0-0.014-0.01216.0370.0040.0040.0000.0000.0000.000
14A18VAL0-0.026-0.00717.3720.0000.0000.0000.0000.0000.000
15A19ARG10.7840.88315.155-0.008-0.0080.0000.0000.0000.000
16A20LYS10.7670.87120.268-0.051-0.0510.0000.0000.0000.000
17A21ARG10.9960.98422.342-0.029-0.0290.0000.0000.0000.000
18A22PHE00.0380.02324.8320.0000.0000.0000.0000.0000.000
19A23ALA0-0.005-0.00825.438-0.001-0.0010.0000.0000.0000.000
20A24ASP-1-0.881-0.91025.9060.0420.0420.0000.0000.0000.000
21A25GLN0-0.109-0.05927.6400.0060.0060.0000.0000.0000.000
22A26GLU-1-0.844-0.91929.8620.0050.0050.0000.0000.0000.000
23A27LEU0-0.049-0.00231.6460.0010.0010.0000.0000.0000.000
24A28GLY00.0380.01428.0300.0020.0020.0000.0000.0000.000
25A29ASP-1-0.780-0.91926.982-0.013-0.0130.0000.0000.0000.000
26A30ALA0-0.0240.00327.3630.0040.0040.0000.0000.0000.000
27A31PRO00.0820.02524.9570.0040.0040.0000.0000.0000.000
28A32PHE0-0.046-0.03022.5770.0020.0020.0000.0000.0000.000
29A33LEU00.012-0.00122.3140.0060.0060.0000.0000.0000.000
30A34ASP-1-0.890-0.94123.2150.0320.0320.0000.0000.0000.000
31A35ARG10.9000.96218.8480.0280.0280.0000.0000.0000.000
32A36LEU00.0130.02918.2020.0130.0130.0000.0000.0000.000
33A37ARG10.9860.99519.014-0.038-0.0380.0000.0000.0000.000
34A38ALA0-0.0040.00217.9440.0190.0190.0000.0000.0000.000
35A39ASP-1-0.777-0.87914.7000.0810.0810.0000.0000.0000.000
36A40GLN0-0.0190.00814.4550.0430.0430.0000.0000.0000.000
37A41ALA0-0.012-0.01615.9920.0330.0330.0000.0000.0000.000
38A42SER0-0.008-0.01212.5330.0540.0540.0000.0000.0000.000
39A43LEU0-0.001-0.00710.1530.1120.1120.0000.0000.0000.000
40A44ARG10.8950.94911.877-0.100-0.1000.0000.0000.0000.000
41A45GLY00.0150.01012.9900.0350.0350.0000.0000.0000.000
42A46ARG10.8330.8956.411-0.674-0.6740.0000.0000.0000.000
43A47GLY00.0440.0268.2650.1940.1940.0000.0000.0000.000
44A48ASN0-0.054-0.03810.378-0.025-0.0250.0000.0000.0000.000
45A49THR0-0.009-0.0047.589-0.050-0.0500.0000.0000.0000.000
46A50LEU0-0.071-0.0313.636-0.3610.0190.009-0.124-0.2650.000
47A51GLY0-0.0070.0307.702-0.009-0.0090.0000.0000.0000.000
48A52LEU0-0.060-0.0357.7370.0130.0130.0000.0000.0000.000
49A53ASP-1-0.845-0.93110.8460.2880.2880.0000.0000.0000.000
50A54ILE00.0470.01513.329-0.013-0.0130.0000.0000.0000.000
51A55GLU-1-0.834-0.85514.4880.1240.1240.0000.0000.0000.000
52A56THR0-0.027-0.04713.2430.0060.0060.0000.0000.0000.000
53A57ALA0-0.0040.00110.268-0.003-0.0030.0000.0000.0000.000
54A58THR00.024-0.00711.477-0.062-0.0620.0000.0000.0000.000
55A59ARG10.7620.85314.028-0.186-0.1860.0000.0000.0000.000
56A60ALA00.0230.00810.650-0.022-0.0220.0000.0000.0000.000
57A61GLY00.0500.00610.847-0.034-0.0340.0000.0000.0000.000
58A62LYS10.9290.97011.819-0.099-0.0990.0000.0000.0000.000
59A63GLN00.0260.01913.700-0.037-0.0370.0000.0000.0000.000
60A64ILE0-0.046-0.0186.909-0.024-0.0240.0000.0000.0000.000
61A65VAL0-0.022-0.01111.207-0.064-0.0640.0000.0000.0000.000
62A66GLU-1-0.893-0.98313.1760.0240.0240.0000.0000.0000.000
63A67ARG10.7890.89614.632-0.010-0.0100.0000.0000.0000.000
64A68ILE00.0230.01011.788-0.006-0.0060.0000.0000.0000.000
65A69LEU0-0.090-0.02715.248-0.008-0.0080.0000.0000.0000.000
66A70GLU-1-0.847-0.94318.2450.0110.0110.0000.0000.0000.000
67A71GLY0-0.071-0.03219.092-0.009-0.0090.0000.0000.0000.000
68A72GLU-1-0.872-0.90822.436-0.022-0.0220.0000.0000.0000.000
69A73SER0-0.049-0.02120.029-0.006-0.0060.0000.0000.0000.000
70A74ASP-1-0.759-0.84322.309-0.027-0.0270.0000.0000.0000.000
71A75LYS10.9040.95318.2230.1120.1120.0000.0000.0000.000
72A76ALA0-0.031-0.03623.994-0.001-0.0010.0000.0000.0000.000
73A77LEU0-0.0070.01627.2030.0020.0020.0000.0000.0000.000
74A78LYS10.8270.88728.5520.0270.0270.0000.0000.0000.000
75A79MET00.0340.00033.3920.0020.0020.0000.0000.0000.000
76A80PRO00.0580.04431.5100.0000.0000.0000.0000.0000.000
77A81ALA0-0.055-0.01932.349-0.003-0.0030.0000.0000.0000.000
78A82SER00.0050.00830.9770.0010.0010.0000.0000.0000.000
79A83ARG10.9670.97433.2110.0290.0290.0000.0000.0000.000
80A84TYR0-0.037-0.03633.386-0.004-0.0040.0000.0000.0000.000
81A85LEU0-0.0150.01135.4470.0030.0030.0000.0000.0000.000
82A86THR0-0.026-0.02336.649-0.003-0.0030.0000.0000.0000.000
83A87ASP-1-0.700-0.78839.447-0.030-0.0300.0000.0000.0000.000
84A88MET0-0.073-0.02638.4320.0010.0010.0000.0000.0000.000
85A89THR00.018-0.00538.912-0.001-0.0010.0000.0000.0000.000
86A90LEU00.034-0.01433.000-0.001-0.0010.0000.0000.0000.000
87A91GLU-1-0.792-0.83936.258-0.039-0.0390.0000.0000.0000.000
88A92GLU-1-0.717-0.82938.799-0.034-0.0340.0000.0000.0000.000
89A93MET0-0.066-0.03234.216-0.002-0.0020.0000.0000.0000.000
90A94SER0-0.069-0.04134.087-0.002-0.0020.0000.0000.0000.000
91A95ARG10.7880.88235.7990.0350.0350.0000.0000.0000.000
92A96ASP-1-0.878-0.93737.885-0.054-0.0540.0000.0000.0000.000
93A97TRP0-0.099-0.06239.3060.0040.0040.0000.0000.0000.000
94A98PHE0-0.021-0.01041.449-0.002-0.0020.0000.0000.0000.000
95A99MET0-0.0390.01241.4190.0010.0010.0000.0000.0000.000
96A100LEU0-0.012-0.01045.825-0.001-0.0010.0000.0000.0000.000
97A101MET0-0.037-0.02348.9230.0000.0000.0000.0000.0000.000
98A102PRO00.000-0.00643.5830.0000.0000.0000.0000.0000.000
99A103LYS10.9550.99944.7080.0350.0350.0000.0000.0000.000
100A104GLN0-0.005-0.01539.000-0.001-0.0010.0000.0000.0000.000
101A105LYS10.9350.97439.9790.0440.0440.0000.0000.0000.000
102A106VAL00.0420.01733.891-0.002-0.0020.0000.0000.0000.000
103A107ALA0-0.067-0.04237.1000.0020.0020.0000.0000.0000.000
104A108GLY00.0610.03835.3060.0000.0000.0000.0000.0000.000
105A109SER0-0.026-0.02230.754-0.002-0.0020.0000.0000.0000.000
106A110LEU0-0.0070.01832.457-0.003-0.0030.0000.0000.0000.000
107A111CYS0-0.047-0.01534.2510.0020.0020.0000.0000.0000.000
108A112ILE00.0110.00736.1570.0010.0010.0000.0000.0000.000
109A113LYS10.8550.90836.6060.0570.0570.0000.0000.0000.000
110A114MET00.0250.01141.7010.0010.0010.0000.0000.0000.000
111A115ASP-1-0.732-0.86545.341-0.036-0.0360.0000.0000.0000.000
112A116GLN0-0.018-0.03047.8400.0000.0000.0000.0000.0000.000
113A117ALA00.0000.00450.8070.0010.0010.0000.0000.0000.000
114A118ILE0-0.053-0.01450.2560.0010.0010.0000.0000.0000.000
115A119MET00.0410.02753.2930.0000.0000.0000.0000.0000.000
116A120ASP-1-0.840-0.88956.648-0.022-0.0220.0000.0000.0000.000
117A121LYS10.7620.87554.7710.0240.0240.0000.0000.0000.000
118A122THR0-0.006-0.01055.4450.0000.0000.0000.0000.0000.000
119A123ILE00.002-0.00849.681-0.001-0.0010.0000.0000.0000.000
120A124ILE0-0.026-0.00548.6620.0010.0010.0000.0000.0000.000
121A125LEU0-0.027-0.00245.279-0.002-0.0020.0000.0000.0000.000
122A126LYS10.8460.89543.0840.0330.0330.0000.0000.0000.000
123A127ALA0-0.027-0.03439.877-0.002-0.0020.0000.0000.0000.000
124A128ASN00.0280.03236.0550.0040.0040.0000.0000.0000.000
125A129PHE00.015-0.00335.085-0.004-0.0040.0000.0000.0000.000
126A130SER00.0470.03032.2500.0030.0030.0000.0000.0000.000
127A131VAL0-0.015-0.01634.8520.0010.0010.0000.0000.0000.000
128A132ILE0-0.003-0.00534.2190.0000.0000.0000.0000.0000.000
129A133PHE0-0.027-0.01737.4910.0010.0010.0000.0000.0000.000
130A134ASP-1-0.935-0.96340.997-0.023-0.0230.0000.0000.0000.000
131A135ARG10.8230.88336.1420.0380.0380.0000.0000.0000.000
132A136LEU00.0130.01636.737-0.001-0.0010.0000.0000.0000.000
133A137GLU-1-0.857-0.90032.757-0.044-0.0440.0000.0000.0000.000
134A138THR0-0.020-0.01729.761-0.004-0.0040.0000.0000.0000.000
135A139LEU0-0.019-0.00133.1720.0020.0020.0000.0000.0000.000
136A140ILE0-0.050-0.03430.348-0.005-0.0050.0000.0000.0000.000
137A141LEU0-0.009-0.01533.144-0.004-0.0040.0000.0000.0000.000
138A142LEU0-0.0010.00836.0480.0030.0030.0000.0000.0000.000
139A143ARG10.7700.86337.7100.0470.0470.0000.0000.0000.000
140A144ALA00.0140.01042.1460.0020.0020.0000.0000.0000.000
141A145PHE0-0.034-0.02242.305-0.001-0.0010.0000.0000.0000.000
142A146THR0-0.010-0.02647.7810.0010.0010.0000.0000.0000.000
143A147GLU-1-0.788-0.87150.964-0.024-0.0240.0000.0000.0000.000
144A148GLU-1-0.914-0.93653.045-0.025-0.0250.0000.0000.0000.000
145A149GLY0-0.015-0.00549.1320.0000.0000.0000.0000.0000.000
146A150ALA0-0.018-0.01047.355-0.002-0.0020.0000.0000.0000.000
147A151ILE0-0.014-0.00841.4090.0010.0010.0000.0000.0000.000
148A152VAL00.0330.00645.3670.0000.0000.0000.0000.0000.000
149A153GLY00.016-0.00644.2160.0000.0000.0000.0000.0000.000
150A154GLU-1-0.792-0.86737.720-0.055-0.0550.0000.0000.0000.000
151A155ILE0-0.006-0.00237.7070.0000.0000.0000.0000.0000.000
152A156SER00.0410.01433.513-0.001-0.0010.0000.0000.0000.000
153A157PRO0-0.0190.00530.7290.0000.0000.0000.0000.0000.000
154A158LEU00.006-0.00329.473-0.004-0.0040.0000.0000.0000.000
155A159PRO0-0.002-0.01524.3470.0000.0000.0000.0000.0000.000
156A160SER0-0.036-0.01825.432-0.002-0.0020.0000.0000.0000.000
157A161LEU00.014-0.00721.001-0.001-0.0010.0000.0000.0000.000
158A162PRO0-0.045-0.00824.7840.0020.0020.0000.0000.0000.000
159A163GLY00.0620.05528.3630.0020.0020.0000.0000.0000.000
160A164HIS0-0.013-0.00529.1320.0060.0060.0000.0000.0000.000
161A165THR00.041-0.01032.8770.0010.0010.0000.0000.0000.000
162A166GLY00.0470.00835.5350.0000.0000.0000.0000.0000.000
163A167GLU-1-0.801-0.88738.497-0.031-0.0310.0000.0000.0000.000
164A168ASP-1-0.866-0.90336.210-0.049-0.0490.0000.0000.0000.000
165A169VAL00.007-0.01136.8330.0000.0000.0000.0000.0000.000
166A170LYS10.8300.91039.4900.0330.0330.0000.0000.0000.000
167A171ASN0-0.023-0.02242.1580.0030.0030.0000.0000.0000.000
168A172ALA0-0.006-0.00240.1780.0010.0010.0000.0000.0000.000
169A173ILE00.0330.01342.1520.0010.0010.0000.0000.0000.000
170A174GLY00.0300.03044.6370.0010.0010.0000.0000.0000.000
171A175VAL0-0.041-0.02644.7650.0010.0010.0000.0000.0000.000
172A176LEU0-0.048-0.01443.4720.0000.0000.0000.0000.0000.000
173A177ILE0-0.008-0.01346.4770.0000.0000.0000.0000.0000.000
174A178GLY00.0540.03149.6730.0010.0010.0000.0000.0000.000
175A179GLY0-0.075-0.05049.4100.0010.0010.0000.0000.0000.000
176A180LEU0-0.001-0.01447.8850.0000.0000.0000.0000.0000.000
177A181GLU-1-0.894-0.94751.506-0.024-0.0240.0000.0000.0000.000
178A182TRP0-0.057-0.01554.0750.0010.0010.0000.0000.0000.000
179A183ASN0-0.123-0.05653.8440.0010.0010.0000.0000.0000.000
180A184ASP-1-0.861-0.93356.712-0.022-0.0220.0000.0000.0000.000
181A185ASN0-0.084-0.05454.0770.0010.0010.0000.0000.0000.000
182A186THR0-0.0020.00256.2700.0000.0000.0000.0000.0000.000
183A187VAL00.002-0.00250.275-0.001-0.0010.0000.0000.0000.000
184A188ARG10.8320.90252.1200.0240.0240.0000.0000.0000.000
185A189VAL00.005-0.00647.583-0.002-0.0020.0000.0000.0000.000
186A190THR0-0.022-0.03045.3040.0020.0020.0000.0000.0000.000
187A191GLU-1-0.878-0.95848.340-0.022-0.0220.0000.0000.0000.000
188A192THR0-0.052-0.05942.4450.0010.0010.0000.0000.0000.000
189A193ILE0-0.004-0.00443.220-0.001-0.0010.0000.0000.0000.000
190A194GLN0-0.007-0.00345.135-0.001-0.0010.0000.0000.0000.000
191A195ARG10.9080.97546.6590.0220.0220.0000.0000.0000.000
192A196PHE0-0.055-0.03542.1520.0010.0010.0000.0000.0000.000
193A197ALA0-0.0160.00842.493-0.001-0.0010.0000.0000.0000.000