FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 494VN

Calculation Name: 3IOY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IOY

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GA85

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 277
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3528715.94958
FMO2-HF: Nuclear repulsion 3422654.806853
FMO2-HF: Total energy -106061.142727
FMO2-MP2: Total energy -106370.267158


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-19.871-4.70311.229-7.94-18.453-0.046
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.005
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].
3A3ASP-1-0.852-0.9152.993-2.2800.1690.295-1.128-1.616-0.002
4A4PHE00.0850.0312.469-3.090-1.1233.771-1.327-4.410-0.008
5A5ALA00.0450.0274.7820.0360.116-0.001-0.006-0.0730.000
6A6GLY0-0.0180.0048.3540.0610.0610.0000.0000.0000.000
7A7ARG10.8000.9083.091-1.1050.0550.536-0.356-1.340-0.003
8A8THR00.0160.0007.308-0.018-0.0180.0000.0000.0000.000
9A9ALA0-0.002-0.0107.548-0.061-0.0610.0000.0000.0000.000
10A10PHE00.0100.0049.0580.0650.0650.0000.0000.0000.000
11A11VAL00.0180.00210.804-0.048-0.0480.0000.0000.0000.000
12A12THR00.0470.03213.0120.0310.0310.0000.0000.0000.000
13A13GLY00.0300.01416.182-0.017-0.0170.0000.0000.0000.000
14A14GLY0-0.028-0.02016.268-0.008-0.0080.0000.0000.0000.000
15A15ALA00.0340.01716.874-0.002-0.0020.0000.0000.0000.000
16A16ASN0-0.062-0.04520.1400.0130.0130.0000.0000.0000.000
17A17GLY00.0740.04619.505-0.015-0.0150.0000.0000.0000.000
18A18VAL00.034-0.00614.888-0.006-0.0060.0000.0000.0000.000
19A19GLY00.0260.02415.185-0.035-0.0350.0000.0000.0000.000
20A20ILE00.0160.01614.964-0.026-0.0260.0000.0000.0000.000
21A21GLY00.0200.02215.375-0.006-0.0060.0000.0000.0000.000
22A22LEU0-0.038-0.03210.176-0.045-0.0450.0000.0000.0000.000
23A23VAL00.0180.00810.898-0.053-0.0530.0000.0000.0000.000
24A24ARG10.8020.85912.6190.2360.2360.0000.0000.0000.000
25A25GLN0-0.065-0.05411.071-0.022-0.0220.0000.0000.0000.000
26A26LEU0-0.005-0.0206.759-0.085-0.0850.0000.0000.0000.000
27A27LEU00.0010.0129.203-0.017-0.0170.0000.0000.0000.000
28A28ASN0-0.030-0.00111.981-0.033-0.0330.0000.0000.0000.000
29A29GLN0-0.042-0.0167.053-0.192-0.1920.0000.0000.0000.000
30A30GLY00.0120.0048.198-0.042-0.0420.0000.0000.0000.000
31A31CYS0-0.064-0.0167.133-0.028-0.0280.0000.0000.0000.000
32A32LYS10.9110.9549.3620.2340.2340.0000.0000.0000.000
33A33VAL0-0.044-0.03210.558-0.052-0.0520.0000.0000.0000.000
34A34ALA00.0000.00112.7240.0410.0410.0000.0000.0000.000
35A35ILE0-0.025-0.02014.525-0.026-0.0260.0000.0000.0000.000
36A36ALA00.0390.03416.6280.0240.0240.0000.0000.0000.000
37A37ASP-1-0.850-0.96118.345-0.198-0.1980.0000.0000.0000.000
38A38ILE00.0570.04621.3600.0120.0120.0000.0000.0000.000
39A39ARG10.8010.87924.7060.1240.1240.0000.0000.0000.000
40A40GLN00.0570.01225.652-0.010-0.0100.0000.0000.0000.000
41A41ASP-1-0.772-0.87726.496-0.109-0.1090.0000.0000.0000.000
42A42SER0-0.089-0.03924.2150.0020.0020.0000.0000.0000.000
43A43ILE00.0100.02021.397-0.010-0.0100.0000.0000.0000.000
44A44ASP-1-0.820-0.89523.377-0.125-0.1250.0000.0000.0000.000
45A45LYS10.9260.96726.0560.1380.1380.0000.0000.0000.000
46A46ALA00.0050.01520.669-0.002-0.0020.0000.0000.0000.000
47A47LEU0-0.0010.00220.025-0.008-0.0080.0000.0000.0000.000
48A48ALA00.0040.00122.7070.0010.0010.0000.0000.0000.000
49A49THR0-0.071-0.05023.5260.0000.0000.0000.0000.0000.000
50A50LEU00.0360.01117.628-0.003-0.0030.0000.0000.0000.000
51A51GLU-1-0.882-0.93921.151-0.138-0.1380.0000.0000.0000.000
52A52ALA0-0.079-0.02923.7870.0070.0070.0000.0000.0000.000
53A53GLU-1-0.870-0.90119.689-0.216-0.2160.0000.0000.0000.000
54A54GLY0-0.026-0.00421.500-0.006-0.0060.0000.0000.0000.000
55A55SER0-0.028-0.02917.569-0.008-0.0080.0000.0000.0000.000
56A56GLY00.0560.03318.847-0.011-0.0110.0000.0000.0000.000
57A57PRO0-0.083-0.05119.346-0.002-0.0020.0000.0000.0000.000
58A58GLU-1-0.851-0.91014.108-0.185-0.1850.0000.0000.0000.000
59A59VAL00.0000.01215.272-0.033-0.0330.0000.0000.0000.000
60A60MET0-0.0360.00016.9570.0260.0260.0000.0000.0000.000
61A61GLY00.012-0.00518.062-0.023-0.0230.0000.0000.0000.000
62A62VAL0-0.0020.02118.8260.0130.0130.0000.0000.0000.000
63A63GLN0-0.035-0.03221.297-0.008-0.0080.0000.0000.0000.000
64A64LEU0-0.019-0.01618.8190.0020.0020.0000.0000.0000.000
65A65ASP-1-0.822-0.90922.779-0.130-0.1300.0000.0000.0000.000
66A66VAL0-0.043-0.01319.1670.0000.0000.0000.0000.0000.000
67A67ALA00.0340.02321.624-0.002-0.0020.0000.0000.0000.000
68A68SER00.0250.01324.4770.0080.0080.0000.0000.0000.000
69A69ARG10.8910.93322.7470.0950.0950.0000.0000.0000.000
70A70GLU-1-0.947-0.95922.979-0.075-0.0750.0000.0000.0000.000
71A71GLY00.0500.02124.227-0.001-0.0010.0000.0000.0000.000
72A72PHE0-0.001-0.00215.564-0.010-0.0100.0000.0000.0000.000
73A73LYS10.8200.89519.3730.0700.0700.0000.0000.0000.000
74A74MET00.0070.00020.6420.0010.0010.0000.0000.0000.000
75A75ALA00.0640.03019.5590.0000.0000.0000.0000.0000.000
76A76ALA0-0.025-0.01516.401-0.011-0.0110.0000.0000.0000.000
77A77ASP-1-0.777-0.87117.228-0.091-0.0910.0000.0000.0000.000
78A78GLU-1-0.936-0.96219.818-0.121-0.1210.0000.0000.0000.000
79A79VAL00.015-0.00914.259-0.001-0.0010.0000.0000.0000.000
80A80GLU-1-0.756-0.84413.646-0.143-0.1430.0000.0000.0000.000
81A81ALA0-0.047-0.00916.5740.0130.0130.0000.0000.0000.000
82A82ARG10.8590.92818.9700.1510.1510.0000.0000.0000.000
83A83PHE0-0.020-0.03314.1960.0050.0050.0000.0000.0000.000
84A84GLY00.0270.04613.839-0.014-0.0140.0000.0000.0000.000
85A85PRO0-0.028-0.02111.288-0.023-0.0230.0000.0000.0000.000
86A86VAL0-0.007-0.0029.296-0.038-0.0380.0000.0000.0000.000
87A87SER0-0.033-0.0335.664-0.005-0.0050.0000.0000.0000.000
88A88ILE0-0.010-0.0062.666-1.135-0.2780.325-0.176-1.0060.000
89A89LEU0-0.0160.0085.3810.1140.116-0.001-0.0010.0010.000
90A90CYS0-0.031-0.0118.071-0.109-0.1090.0000.0000.0000.000
91A91ASN0-0.010-0.01110.3820.0860.0860.0000.0000.0000.000
92A92ASN00.011-0.01213.675-0.023-0.0230.0000.0000.0000.000
93A93ALA0-0.0150.00815.4530.0170.0170.0000.0000.0000.000
94A94GLY00.011-0.00619.051-0.007-0.0070.0000.0000.0000.000
95A95VAL0-0.041-0.01221.8840.0040.0040.0000.0000.0000.000
96A96ASN00.022-0.01325.6120.0030.0030.0000.0000.0000.000
97A97LEU00.0490.03027.7940.0020.0020.0000.0000.0000.000
98A98PHE0-0.061-0.03031.502-0.001-0.0010.0000.0000.0000.000
99A99GLN00.0280.01133.3900.0030.0030.0000.0000.0000.000
100A100PRO00.0620.04634.147-0.007-0.0070.0000.0000.0000.000
101A101ILE0-0.029-0.01832.3620.0000.0000.0000.0000.0000.000
102A102GLU-1-0.909-0.96536.119-0.064-0.0640.0000.0000.0000.000
103A103GLU-1-0.963-0.97538.844-0.061-0.0610.0000.0000.0000.000
104A104SER0-0.064-0.02935.369-0.004-0.0040.0000.0000.0000.000
105A105SER0-0.045-0.04237.4350.0030.0030.0000.0000.0000.000
106A106TYR00.002-0.02736.038-0.002-0.0020.0000.0000.0000.000
107A107ASP-1-0.867-0.92334.690-0.070-0.0700.0000.0000.0000.000
108A108ASP-1-0.805-0.88133.412-0.085-0.0850.0000.0000.0000.000
109A109TRP0-0.011-0.01929.661-0.011-0.0110.0000.0000.0000.000
110A110ASP-1-0.899-0.95230.006-0.087-0.0870.0000.0000.0000.000
111A111TRP0-0.023-0.01028.829-0.008-0.0080.0000.0000.0000.000
112A112LEU0-0.014-0.01327.078-0.010-0.0100.0000.0000.0000.000
113A113LEU0-0.010-0.00525.479-0.014-0.0140.0000.0000.0000.000
114A114GLY00.0020.00624.770-0.008-0.0080.0000.0000.0000.000
115A115VAL0-0.020-0.01322.119-0.009-0.0090.0000.0000.0000.000
116A116ASN0-0.023-0.01621.250-0.025-0.0250.0000.0000.0000.000
117A117LEU0-0.014-0.00520.342-0.017-0.0170.0000.0000.0000.000
118A118HIS00.009-0.00520.626-0.011-0.0110.0000.0000.0000.000
119A119GLY00.0470.03120.280-0.003-0.0030.0000.0000.0000.000
120A120VAL0-0.014-0.00715.033-0.018-0.0180.0000.0000.0000.000
121A121VAL00.003-0.00516.487-0.011-0.0110.0000.0000.0000.000
122A122ASN0-0.0180.00418.4300.0150.0150.0000.0000.0000.000
123A123GLY00.0680.04715.2760.0100.0100.0000.0000.0000.000
124A124VAL0-0.023-0.02913.090-0.008-0.0080.0000.0000.0000.000
125A125THR0-0.047-0.04514.6180.0200.0200.0000.0000.0000.000
126A126THR0-0.051-0.02916.3720.0250.0250.0000.0000.0000.000
127A127PHE00.0070.00511.5120.0090.0090.0000.0000.0000.000
128A128VAL00.0010.01010.9910.0070.0070.0000.0000.0000.000
129A129PRO0-0.020-0.00612.7950.0360.0360.0000.0000.0000.000
130A130ARG10.8610.91313.6380.1430.1430.0000.0000.0000.000
131A131MET0-0.0320.0107.4800.0150.0150.0000.0000.0000.000
132A132VAL0-0.015-0.01211.5090.0790.0790.0000.0000.0000.000
133A133GLU-1-0.974-0.98813.1470.0420.0420.0000.0000.0000.000
134A134ARG10.8590.90212.0380.1130.1130.0000.0000.0000.000
135A135VAL0-0.065-0.0349.2310.0570.0570.0000.0000.0000.000
136A136LYS10.8290.91512.134-0.056-0.0560.0000.0000.0000.000
137A137ALA00.0010.01015.7830.0110.0110.0000.0000.0000.000
138A138GLY0-0.031-0.00714.1440.0030.0030.0000.0000.0000.000
139A139GLU-1-0.966-0.98013.3460.0940.0940.0000.0000.0000.000
140A140GLN0-0.014-0.0166.856-0.060-0.0600.0000.0000.0000.000
141A141LYS10.8510.9217.550-0.613-0.6130.0000.0000.0000.000
142A142GLY00.0570.0414.101-0.0520.1120.000-0.032-0.1320.000
143A143GLY00.0380.0093.059-0.964-0.2750.057-0.224-0.523-0.001
144A144HIS0-0.025-0.0212.293-4.672-2.2922.517-1.532-3.366-0.012
145A145VAL00.0020.0134.1950.1860.2610.002-0.021-0.0550.000
146A146VAL0-0.010-0.0076.289-0.072-0.0720.0000.0000.0000.000
147A147ASN00.0180.0018.7080.0720.0720.0000.0000.0000.000
148A148THR0-0.004-0.02412.497-0.029-0.0290.0000.0000.0000.000
149A149ALA00.0360.02514.9040.0420.0420.0000.0000.0000.000
150A150SER00.008-0.01717.5120.0190.0190.0000.0000.0000.000
151A151MET00.0110.01519.658-0.006-0.0060.0000.0000.0000.000
152A152ALA00.0340.02321.7760.0140.0140.0000.0000.0000.000
153A153ALA0-0.065-0.02720.0580.0120.0120.0000.0000.0000.000
154A154PHE0-0.017-0.03618.719-0.004-0.0040.0000.0000.0000.000
155A155LEU00.0090.01424.1580.0110.0110.0000.0000.0000.000
156A156ALA0-0.008-0.00226.998-0.001-0.0010.0000.0000.0000.000
157A157ALA00.0310.03128.8330.0090.0090.0000.0000.0000.000
158A158GLY00.019-0.00231.871-0.002-0.0020.0000.0000.0000.000
159A159SER0-0.025-0.01233.0530.0040.0040.0000.0000.0000.000
160A160PRO0-0.0220.00728.316-0.002-0.0020.0000.0000.0000.000
161A161GLY00.0750.03029.554-0.006-0.0060.0000.0000.0000.000
162A162ILE00.0420.03528.822-0.005-0.0050.0000.0000.0000.000
163A163TYR0-0.0050.00422.676-0.013-0.0130.0000.0000.0000.000
164A164ASN00.0380.00625.187-0.020-0.0200.0000.0000.0000.000
165A165THR00.0090.00525.290-0.005-0.0050.0000.0000.0000.000
166A166THR0-0.071-0.04023.658-0.007-0.0070.0000.0000.0000.000
167A167LYS10.8730.94519.1410.2210.2210.0000.0000.0000.000
168A168PHE00.0430.02420.412-0.020-0.0200.0000.0000.0000.000
169A169ALA0-0.0240.00521.431-0.005-0.0050.0000.0000.0000.000
170A170VAL0-0.0020.00216.444-0.006-0.0060.0000.0000.0000.000
171A171ARG10.8450.91616.8320.1480.1480.0000.0000.0000.000
172A172GLY00.0280.02117.226-0.011-0.0110.0000.0000.0000.000
173A173LEU0-0.0240.00015.6040.0080.0080.0000.0000.0000.000
174A174SER00.022-0.01912.930-0.015-0.0150.0000.0000.0000.000
175A175GLU-1-0.825-0.87313.498-0.223-0.2230.0000.0000.0000.000
176A176SER0-0.035-0.02915.5860.0260.0260.0000.0000.0000.000
177A177LEU0-0.030-0.00711.8420.0280.0280.0000.0000.0000.000
178A178HIS00.0550.0368.6950.1930.1930.0000.0000.0000.000
179A179TYR0-0.007-0.01211.8150.0600.0600.0000.0000.0000.000
180A180SER0-0.121-0.06114.1980.0670.0670.0000.0000.0000.000
181A181LEU00.0300.00510.0260.0710.0710.0000.0000.0000.000
182A182LEU00.0510.0338.3620.0900.0900.0000.0000.0000.000
183A183LYS10.8270.9139.7910.0640.0640.0000.0000.0000.000
184A184TYR0-0.005-0.01010.5110.0150.0150.0000.0000.0000.000
185A185GLU-1-0.894-0.9585.8821.6121.6120.0000.0000.0000.000
186A186ILE0-0.056-0.0115.075-0.0150.143-0.001-0.004-0.1520.000
187A187GLY00.0540.0224.447-0.0130.084-0.001-0.011-0.0850.000
188A188VAL0-0.039-0.0215.5880.1870.1870.0000.0000.0000.000
189A189SER0-0.011-0.0047.384-0.114-0.1140.0000.0000.0000.000
190A190VAL0-0.0020.0009.0950.0620.0620.0000.0000.0000.000
191A191LEU0-0.0220.00211.7280.0020.0020.0000.0000.0000.000
192A192CYS0-0.052-0.03513.3060.0570.0570.0000.0000.0000.000
193A193PRO00.0150.01616.2380.0160.0160.0000.0000.0000.000
194A194GLY00.0850.03818.7250.0190.0190.0000.0000.0000.000
195A195LEU00.0020.00022.275-0.006-0.0060.0000.0000.0000.000
196A196VAL0-0.021-0.00320.127-0.015-0.0150.0000.0000.0000.000
197A197LYS10.7590.86022.9190.1670.1670.0000.0000.0000.000
198A227ALA00.022-0.00936.7060.0000.0000.0000.0000.0000.000
199A228GLY00.0190.00734.833-0.001-0.0010.0000.0000.0000.000
200A229VAL00.0110.00330.119-0.004-0.0040.0000.0000.0000.000
201A230HIS0-0.016-0.00629.216-0.009-0.0090.0000.0000.0000.000
202A231GLU-1-0.854-0.91028.525-0.122-0.1220.0000.0000.0000.000
203A232PHE0-0.038-0.01528.451-0.006-0.0060.0000.0000.0000.000
204A233GLY00.0100.02225.652-0.005-0.0050.0000.0000.0000.000
205A234MET0-0.050-0.02819.396-0.012-0.0120.0000.0000.0000.000
206A235GLU-1-0.784-0.88720.527-0.189-0.1890.0000.0000.0000.000
207A236PRO00.0280.00817.938-0.027-0.0270.0000.0000.0000.000
208A237ASP-1-0.753-0.86315.473-0.345-0.3450.0000.0000.0000.000
209A238VAL0-0.048-0.01314.904-0.039-0.0390.0000.0000.0000.000
210A239ILE0-0.012-0.00914.109-0.034-0.0340.0000.0000.0000.000
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212A241ALA00.0160.00210.269-0.106-0.1060.0000.0000.0000.000
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