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: MVG3Z

Calculation Name: 1ILW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ILW

Chain ID: A

ChEMBL ID:

UniProt ID: O58727

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1968910.164834
FMO2-HF: Nuclear repulsion 1898642.317131
FMO2-HF: Total energy -70267.847703
FMO2-MP2: Total energy -70473.423691


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-15.799-8.25411.905-8.046-11.406-0.054
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.008
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].
3A4GLU-1-0.814-0.8942.595-2.4480.3550.218-1.315-1.7070.005
4A5ALA00.0420.0192.666-1.716-0.4230.754-0.866-1.181-0.011
5A6LEU0-0.0370.0025.2840.2420.273-0.001-0.002-0.0280.000
6A7ILE0-0.005-0.0158.724-0.070-0.0700.0000.0000.0000.000
7A8VAL00.018-0.01011.5130.0790.0790.0000.0000.0000.000
8A9VAL0-0.009-0.01814.663-0.001-0.0010.0000.0000.0000.000
9A10ASP-1-0.723-0.83317.466-0.237-0.2370.0000.0000.0000.000
10A11MET00.0050.03918.7740.0270.0270.0000.0000.0000.000
11A12GLN0-0.031-0.04520.727-0.004-0.0040.0000.0000.0000.000
12A13ARG10.8190.87323.3660.1240.1240.0000.0000.0000.000
13A14ASP-1-0.739-0.88426.704-0.111-0.1110.0000.0000.0000.000
14A15PHE0-0.036-0.00724.5670.0070.0070.0000.0000.0000.000
15A16MET0-0.0190.01523.8990.0030.0030.0000.0000.0000.000
16A17PRO0-0.042-0.03228.4200.0050.0050.0000.0000.0000.000
17A18GLY00.0010.00731.9840.0020.0020.0000.0000.0000.000
18A19GLY0-0.0300.00530.9120.0020.0020.0000.0000.0000.000
19A20ALA0-0.025-0.02631.9550.0040.0040.0000.0000.0000.000
20A21LEU0-0.078-0.04929.8490.0040.0040.0000.0000.0000.000
21A22PRO0-0.0380.00930.295-0.008-0.0080.0000.0000.0000.000
22A23VAL00.0310.00326.6440.0040.0040.0000.0000.0000.000
23A24PRO0-0.006-0.01129.6850.0030.0030.0000.0000.0000.000
24A25GLU-1-0.877-0.94329.881-0.088-0.0880.0000.0000.0000.000
25A26GLY00.0290.02426.292-0.003-0.0030.0000.0000.0000.000
26A27ASP-1-0.763-0.90425.322-0.100-0.1000.0000.0000.0000.000
27A28LYS10.8050.89125.8860.0820.0820.0000.0000.0000.000
28A29ILE00.0050.01921.0260.0030.0030.0000.0000.0000.000
29A30ILE00.0090.02421.236-0.010-0.0100.0000.0000.0000.000
30A31PRO0-0.010-0.00820.377-0.009-0.0090.0000.0000.0000.000
31A32LYS10.8260.91718.9750.0970.0970.0000.0000.0000.000
32A33VAL00.0390.00416.217-0.012-0.0120.0000.0000.0000.000
33A34ASN00.022-0.00415.608-0.044-0.0440.0000.0000.0000.000
34A35GLU-1-0.858-0.89815.799-0.088-0.0880.0000.0000.0000.000
35A36TYR0-0.041-0.05113.0480.0180.0180.0000.0000.0000.000
36A37ILE00.0280.00811.375-0.023-0.0230.0000.0000.0000.000
37A38ARG10.8770.96410.8230.0790.0790.0000.0000.0000.000
38A39LYS10.8560.91111.4470.1120.1120.0000.0000.0000.000
39A40PHE0-0.013-0.0246.7470.0690.0690.0000.0000.0000.000
40A41LYS10.9971.0136.9490.1340.1340.0000.0000.0000.000
41A42GLU-1-0.908-0.9698.0220.0210.0210.0000.0000.0000.000
42A43LYS10.7530.8786.6060.0800.0800.0000.0000.0000.000
43A44GLY00.0000.0145.2280.3100.3100.0000.0000.0000.000
44A45ALA0-0.064-0.0262.392-2.201-0.2291.360-1.405-1.928-0.009
45A46LEU00.0260.0122.627-2.509-0.7990.907-0.400-2.217-0.004
46A47ILE00.0170.0043.5390.4560.5410.0210.028-0.1350.000
47A48VAL0-0.0070.0007.315-0.027-0.0270.0000.0000.0000.000
48A49ALA00.0120.01310.0610.0710.0710.0000.0000.0000.000
49A50THR0-0.046-0.05013.828-0.010-0.0100.0000.0000.0000.000
50A51ARG10.8860.94416.7930.2630.2630.0000.0000.0000.000
51A52ASP-1-0.766-0.87420.285-0.195-0.1950.0000.0000.0000.000
52A53TRP00.008-0.00622.4020.0050.0050.0000.0000.0000.000
53A54HIS10.8830.96124.4580.1590.1590.0000.0000.0000.000
54A55PRO00.0110.02827.8990.0030.0030.0000.0000.0000.000
55A56GLU-1-0.729-0.85330.692-0.096-0.0960.0000.0000.0000.000
56A57ASN0-0.025-0.01834.165-0.001-0.0010.0000.0000.0000.000
57A58HIS00.0460.04728.8890.0050.0050.0000.0000.0000.000
58A59ILE00.0070.00531.3220.0040.0040.0000.0000.0000.000
59A60SER0-0.037-0.02730.8820.0030.0030.0000.0000.0000.000
60A61PHE0-0.046-0.02930.8840.0010.0010.0000.0000.0000.000
61A62ARG10.9000.94335.4200.0910.0910.0000.0000.0000.000
62A63GLU-1-0.883-0.94337.205-0.087-0.0870.0000.0000.0000.000
63A64ARG10.7420.84535.4280.1000.1000.0000.0000.0000.000
64A65GLY0-0.011-0.00139.7480.0000.0000.0000.0000.0000.000
65A66GLY00.0330.03436.091-0.001-0.0010.0000.0000.0000.000
66A67PRO00.008-0.01334.1320.0040.0040.0000.0000.0000.000
67A68TRP0-0.039-0.00330.9120.0060.0060.0000.0000.0000.000
68A69PRO00.0150.00934.2580.0040.0040.0000.0000.0000.000
69A70ARG10.8430.88333.7620.0880.0880.0000.0000.0000.000
70A71HIS10.8420.92227.8870.1430.1430.0000.0000.0000.000
71A72CYS0-0.064-0.02925.126-0.002-0.0020.0000.0000.0000.000
72A73VAL0-0.0200.01227.503-0.007-0.0070.0000.0000.0000.000
73A74GLN0-0.021-0.02026.3870.0090.0090.0000.0000.0000.000
74A75ASN0-0.026-0.02526.7700.0020.0020.0000.0000.0000.000
75A76THR0-0.035-0.01328.2390.0100.0100.0000.0000.0000.000
76A77PRO00.0540.00728.255-0.008-0.0080.0000.0000.0000.000
77A78GLY00.0200.02728.534-0.002-0.0020.0000.0000.0000.000
78A79ALA0-0.012-0.00825.255-0.008-0.0080.0000.0000.0000.000
79A80GLU-1-0.800-0.86223.589-0.134-0.1340.0000.0000.0000.000
80A81PHE00.003-0.00517.2730.0000.0000.0000.0000.0000.000
81A82VAL0-0.036-0.01921.2350.0170.0170.0000.0000.0000.000
82A83VAL0-0.007-0.00617.1410.0070.0070.0000.0000.0000.000
83A84ASP-1-0.870-0.92717.115-0.142-0.1420.0000.0000.0000.000
84A85LEU0-0.067-0.04212.676-0.016-0.0160.0000.0000.0000.000
85A86PRO0-0.032-0.0049.8560.0460.0460.0000.0000.0000.000
86A87GLU-1-0.915-0.97012.468-0.206-0.2060.0000.0000.0000.000
87A88ASP-1-0.940-0.9707.564-0.506-0.5060.0000.0000.0000.000
88A89ALA0-0.037-0.0078.451-0.165-0.1650.0000.0000.0000.000
89A90VAL00.005-0.0117.8240.0770.0770.0000.0000.0000.000
90A91ILE00.001-0.00210.7730.0090.0090.0000.0000.0000.000
91A92ILE0-0.025-0.01011.9500.0310.0310.0000.0000.0000.000
92A93SER0-0.007-0.00115.3710.0410.0410.0000.0000.0000.000
93A94LYS10.8030.89919.1380.2380.2380.0000.0000.0000.000
94A95ALA0-0.022-0.01821.2020.0160.0160.0000.0000.0000.000
95A96THR00.0380.01322.3930.0080.0080.0000.0000.0000.000
96A97GLU-1-0.909-0.95625.376-0.148-0.1480.0000.0000.0000.000
97A98PRO0-0.009-0.01828.618-0.003-0.0030.0000.0000.0000.000
98A99ASP-1-0.757-0.86231.598-0.100-0.1000.0000.0000.0000.000
99A100LYS10.8070.92123.2340.2100.2100.0000.0000.0000.000
100A101GLU-1-0.842-0.91327.798-0.143-0.1430.0000.0000.0000.000
101A102ALA0-0.024-0.02922.246-0.009-0.0090.0000.0000.0000.000
102A103TYR0-0.052-0.03023.7460.0010.0010.0000.0000.0000.000
103A104SER00.009-0.02819.435-0.029-0.0290.0000.0000.0000.000
104A105GLY00.018-0.00516.4600.0080.0080.0000.0000.0000.000
105A106PHE0-0.028-0.01612.791-0.036-0.0360.0000.0000.0000.000
106A107GLU-1-0.820-0.88917.422-0.205-0.2050.0000.0000.0000.000
107A108GLY0-0.0270.00220.5220.0200.0200.0000.0000.0000.000
108A109THR0-0.004-0.02216.220-0.005-0.0050.0000.0000.0000.000
109A110ASP-1-0.827-0.93213.739-0.386-0.3860.0000.0000.0000.000
110A111LEU00.0010.02610.307-0.085-0.0850.0000.0000.0000.000
111A112ALA00.013-0.00710.779-0.138-0.1380.0000.0000.0000.000
112A113LYS10.8910.95711.9340.3120.3120.0000.0000.0000.000
113A114ILE00.0450.0217.547-0.083-0.0830.0000.0000.0000.000
114A115LEU00.0220.0216.309-0.274-0.2740.0000.0000.0000.000
115A116ARG10.8440.9065.927-0.011-0.0110.0000.0000.0000.000
116A117GLY0-0.023-0.0027.019-0.020-0.0200.0000.0000.0000.000
117A118ASN0-0.052-0.0322.400-0.4850.6720.531-0.467-1.220-0.001
118A119GLY00.0150.0151.892-7.189-9.3978.106-3.470-2.428-0.034
119A120VAL0-0.072-0.0173.450-0.1300.4120.010-0.136-0.4160.000
120A121LYS10.8320.8915.2291.0191.179-0.001-0.013-0.1460.000
121A122ARG10.7740.8786.8170.3760.3760.0000.0000.0000.000
122A123VAL0-0.001-0.0106.917-0.274-0.2740.0000.0000.0000.000
123A124TYR00.0020.0078.2100.1650.1650.0000.0000.0000.000
124A125ILE0-0.0010.00711.080-0.040-0.0400.0000.0000.0000.000
125A126CYS0-0.050-0.01113.9110.0560.0560.0000.0000.0000.000
126A127GLY00.0490.01916.392-0.030-0.0300.0000.0000.0000.000
127A128VAL00.0030.00019.1030.0220.0220.0000.0000.0000.000
128A129ALA00.0140.00722.003-0.013-0.0130.0000.0000.0000.000
129A130THR0-0.026-0.06622.998-0.016-0.0160.0000.0000.0000.000
130A131GLU-1-0.732-0.87623.778-0.145-0.1450.0000.0000.0000.000
131A132TYR0-0.016-0.00925.4160.0040.0040.0000.0000.0000.000
132A133CYS0-0.008-0.01121.383-0.003-0.0030.0000.0000.0000.000
133A134VAL0-0.0110.03518.775-0.031-0.0310.0000.0000.0000.000
134A135ARG10.8870.91119.3940.1400.1400.0000.0000.0000.000
135A136ALA0-0.022-0.00321.151-0.011-0.0110.0000.0000.0000.000
136A137THR00.022-0.00815.248-0.023-0.0230.0000.0000.0000.000
137A138ALA00.0150.00516.445-0.047-0.0470.0000.0000.0000.000
138A139LEU0-0.006-0.00717.492-0.015-0.0150.0000.0000.0000.000
139A140ASP-1-0.774-0.86518.138-0.286-0.2860.0000.0000.0000.000
140A141ALA0-0.018-0.01113.388-0.028-0.0280.0000.0000.0000.000
141A142LEU00.002-0.00215.015-0.031-0.0310.0000.0000.0000.000
142A143LYS10.7960.90417.2500.2840.2840.0000.0000.0000.000
143A144HIS00.0060.00214.4050.0040.0040.0000.0000.0000.000
144A145GLY00.0080.01214.878-0.035-0.0350.0000.0000.0000.000
145A146PHE0-0.048-0.0139.224-0.004-0.0040.0000.0000.0000.000
146A147GLU-1-0.849-0.92411.479-0.175-0.1750.0000.0000.0000.000
147A148VAL0-0.029-0.00711.624-0.052-0.0520.0000.0000.0000.000
148A149TYR0-0.063-0.06111.9310.0980.0980.0000.0000.0000.000
149A150LEU0-0.012-0.00714.298-0.038-0.0380.0000.0000.0000.000
150A151LEU00.0130.00012.7470.0340.0340.0000.0000.0000.000
151A152ARG10.9250.94217.0260.1030.1030.0000.0000.0000.000
152A153ASP-1-0.813-0.89619.514-0.118-0.1180.0000.0000.0000.000
153A154ALA0-0.014-0.01217.6600.0060.0060.0000.0000.0000.000
154A155VAL00.0060.00719.180-0.025-0.0250.0000.0000.0000.000
155A156LYS10.8710.94421.5330.1200.1200.0000.0000.0000.000
156A157GLY00.0450.01624.910-0.014-0.0140.0000.0000.0000.000
157A158ILE0-0.048-0.03127.3740.0080.0080.0000.0000.0000.000
158A159LYS10.7950.87530.9300.1170.1170.0000.0000.0000.000
159A160PRO00.0660.03231.256-0.005-0.0050.0000.0000.0000.000
160A161GLU-1-0.821-0.89431.724-0.078-0.0780.0000.0000.0000.000
161A162ASP-1-0.819-0.89330.750-0.105-0.1050.0000.0000.0000.000
162A163GLU-1-0.904-0.94926.842-0.136-0.1360.0000.0000.0000.000
163A164GLU-1-0.898-0.95227.291-0.093-0.0930.0000.0000.0000.000
164A165ARG10.8770.92728.5300.0800.0800.0000.0000.0000.000
165A166ALA0-0.0110.00825.352-0.006-0.0060.0000.0000.0000.000
166A167LEU0-0.024-0.02222.289-0.014-0.0140.0000.0000.0000.000
167A168GLU-1-0.932-0.96724.853-0.098-0.0980.0000.0000.0000.000
168A169GLU-1-0.789-0.85026.070-0.157-0.1570.0000.0000.0000.000
169A170MET0-0.0060.00120.950-0.016-0.0160.0000.0000.0000.000
170A171LYS10.9700.98422.3380.0980.0980.0000.0000.0000.000
171A172SER0-0.100-0.05923.7560.0020.0020.0000.0000.0000.000
172A173ARG10.8800.92622.8740.1750.1750.0000.0000.0000.000
173A174GLY00.0290.02420.855-0.011-0.0110.0000.0000.0000.000
174A175ILE0-0.044-0.01517.168-0.021-0.0210.0000.0000.0000.000
175A176LYS10.8580.94015.5040.2750.2750.0000.0000.0000.000
176A177ILE0-0.014-0.00417.280-0.014-0.0140.0000.0000.0000.000
177A178VAL0-0.024-0.00815.3350.0210.0210.0000.0000.0000.000
178A179GLN00.0230.02317.912-0.013-0.0130.0000.0000.0000.000
179A180PHE00.0200.03311.6460.0100.0100.0000.0000.0000.000