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: 94JG2

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963646.617203
FMO2-HF: Nuclear repulsion 1893379.343747
FMO2-HF: Total energy -70267.273456
FMO2-MP2: Total energy -70472.872804


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.
-12.673-13.31326.563-13.726-12.199-0.069
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 : -0.006 / q_NPA : -0.013
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-1-0.849-0.8982.678-3.3210.0830.113-1.700-1.8180.007
4A5ALA00.0410.0143.030-1.894-0.6170.157-0.703-0.730-0.007
5A6LEU0-0.049-0.0045.6970.2960.2960.0000.0000.0000.000
6A7ILE00.002-0.0178.936-0.049-0.0490.0000.0000.0000.000
7A8VAL0-0.005-0.02811.6680.0750.0750.0000.0000.0000.000
8A9VAL0-0.022-0.02014.6720.0020.0020.0000.0000.0000.000
9A10ASP-1-0.720-0.83917.558-0.238-0.2380.0000.0000.0000.000
10A11MET00.0090.03218.9100.0250.0250.0000.0000.0000.000
11A12GLN0-0.016-0.02620.789-0.004-0.0040.0000.0000.0000.000
12A13ARG10.8600.90923.4580.1170.1170.0000.0000.0000.000
13A14ASP-1-0.755-0.88926.843-0.105-0.1050.0000.0000.0000.000
14A15PHE0-0.038-0.01024.1430.0060.0060.0000.0000.0000.000
15A16MET0-0.0220.00924.0080.0000.0000.0000.0000.0000.000
16A17PRO0-0.006-0.01628.4110.0060.0060.0000.0000.0000.000
17A18GLY0-0.0070.00331.7190.0000.0000.0000.0000.0000.000
18A19GLY0-0.0250.00531.1650.0030.0030.0000.0000.0000.000
19A20ALA0-0.045-0.03132.1710.0040.0040.0000.0000.0000.000
20A21LEU0-0.086-0.05029.8490.0050.0050.0000.0000.0000.000
21A22PRO0-0.0450.00130.181-0.009-0.0090.0000.0000.0000.000
22A23VAL00.0340.00926.8350.0020.0020.0000.0000.0000.000
23A24PRO00.0140.00229.8510.0020.0020.0000.0000.0000.000
24A25GLU-1-0.898-0.95330.372-0.099-0.0990.0000.0000.0000.000
25A26GLY00.0270.01426.915-0.004-0.0040.0000.0000.0000.000
26A27ASP-1-0.782-0.91925.445-0.112-0.1120.0000.0000.0000.000
27A28LYS10.8140.89726.1020.0920.0920.0000.0000.0000.000
28A29ILE0-0.0050.01221.3120.0030.0030.0000.0000.0000.000
29A30ILE00.0200.02621.283-0.015-0.0150.0000.0000.0000.000
30A31PRO0-0.004-0.00120.550-0.011-0.0110.0000.0000.0000.000
31A32LYS10.8550.92219.0270.1290.1290.0000.0000.0000.000
32A33VAL00.0350.01016.407-0.019-0.0190.0000.0000.0000.000
33A34ASN00.030-0.01015.847-0.046-0.0460.0000.0000.0000.000
34A35GLU-1-0.863-0.89115.743-0.135-0.1350.0000.0000.0000.000
35A36TYR0-0.025-0.04713.2860.0020.0020.0000.0000.0000.000
36A37ILE00.0330.01911.300-0.041-0.0410.0000.0000.0000.000
37A38ARG10.9230.97410.8930.1060.1060.0000.0000.0000.000
38A39LYS10.8820.93111.8760.1690.1690.0000.0000.0000.000
39A40PHE0-0.025-0.0366.8320.0540.0540.0000.0000.0000.000
40A41LYS10.9600.9937.1650.0820.0820.0000.0000.0000.000
41A42GLU-1-0.940-0.9788.217-0.042-0.0420.0000.0000.0000.000
42A43LYS10.7490.8807.0370.2480.2480.0000.0000.0000.000
43A44GLY00.0170.0215.1540.2490.2490.0000.0000.0000.000
44A45ALA0-0.067-0.0242.871-2.534-0.3550.587-1.081-1.685-0.009
45A46LEU00.0370.0232.472-2.344-0.5210.889-0.632-2.080-0.003
46A47ILE00.006-0.0033.7050.2960.3870.010-0.008-0.0930.000
47A48VAL00.0060.0057.4680.0430.0430.0000.0000.0000.000
48A49ALA00.0230.0309.9440.0480.0480.0000.0000.0000.000
49A50THR0-0.032-0.04013.7570.0060.0060.0000.0000.0000.000
50A51ARG10.8870.94416.1560.2300.2300.0000.0000.0000.000
51A52ASP-1-0.776-0.88919.710-0.189-0.1890.0000.0000.0000.000
52A53TRP0-0.018-0.02022.0750.0060.0060.0000.0000.0000.000
53A54HIS10.9060.96424.1000.1520.1520.0000.0000.0000.000
54A55PRO00.0180.04027.6270.0040.0040.0000.0000.0000.000
55A56GLU-1-0.727-0.85130.470-0.087-0.0870.0000.0000.0000.000
56A57ASN0-0.023-0.01433.9500.0000.0000.0000.0000.0000.000
57A58HIS00.0570.03828.4820.0040.0040.0000.0000.0000.000
58A59ILE00.0110.01230.7100.0040.0040.0000.0000.0000.000
59A60SER0-0.063-0.03830.5890.0020.0020.0000.0000.0000.000
60A61PHE0-0.038-0.02930.6790.0000.0000.0000.0000.0000.000
61A62ARG10.9250.97035.1110.0880.0880.0000.0000.0000.000
62A63GLU-1-0.904-0.94237.148-0.080-0.0800.0000.0000.0000.000
63A64ARG10.7730.87434.8790.0910.0910.0000.0000.0000.000
64A65GLY0-0.023-0.01639.2150.0000.0000.0000.0000.0000.000
65A66GLY00.0100.01835.811-0.001-0.0010.0000.0000.0000.000
66A67PRO00.004-0.01533.9830.0040.0040.0000.0000.0000.000
67A68TRP0-0.031-0.02030.4060.0050.0050.0000.0000.0000.000
68A69PRO00.0140.01934.1710.0040.0040.0000.0000.0000.000
69A70ARG10.8670.89233.6000.0800.0800.0000.0000.0000.000
70A71HIS10.8650.93327.7490.1340.1340.0000.0000.0000.000
71A72CYS0-0.074-0.01525.172-0.002-0.0020.0000.0000.0000.000
72A73VAL0-0.0280.00227.156-0.007-0.0070.0000.0000.0000.000
73A74GLN0-0.033-0.03026.0110.0070.0070.0000.0000.0000.000
74A75ASN0-0.031-0.02426.7570.0020.0020.0000.0000.0000.000
75A76THR0-0.030-0.01528.4580.0100.0100.0000.0000.0000.000
76A77PRO00.0780.01528.233-0.008-0.0080.0000.0000.0000.000
77A78GLY00.0100.02227.998-0.006-0.0060.0000.0000.0000.000
78A79ALA0-0.024-0.01724.946-0.009-0.0090.0000.0000.0000.000
79A80GLU-1-0.816-0.87823.566-0.123-0.1230.0000.0000.0000.000
80A81PHE00.000-0.00717.163-0.003-0.0030.0000.0000.0000.000
81A82VAL0-0.023-0.01821.3520.0160.0160.0000.0000.0000.000
82A83VAL0-0.048-0.01216.8240.0070.0070.0000.0000.0000.000
83A84ASP-1-0.880-0.93517.456-0.140-0.1400.0000.0000.0000.000
84A85LEU0-0.064-0.03712.788-0.028-0.0280.0000.0000.0000.000
85A86PRO0-0.027-0.0119.8280.0450.0450.0000.0000.0000.000
86A87GLU-1-0.900-0.96112.538-0.154-0.1540.0000.0000.0000.000
87A88ASP-1-0.953-0.9698.195-0.400-0.4000.0000.0000.0000.000
88A89ALA0-0.032-0.0098.540-0.142-0.1420.0000.0000.0000.000
89A90VAL0-0.003-0.0047.8060.0750.0750.0000.0000.0000.000
90A91ILE0-0.009-0.01010.513-0.006-0.0060.0000.0000.0000.000
91A92ILE0-0.029-0.01311.7790.0140.0140.0000.0000.0000.000
92A93SER0-0.005-0.00315.2320.0290.0290.0000.0000.0000.000
93A94LYS10.8040.90019.0530.2420.2420.0000.0000.0000.000
94A95ALA0-0.031-0.02621.0060.0140.0140.0000.0000.0000.000
95A96THR00.0620.01522.5960.0060.0060.0000.0000.0000.000
96A97GLU-1-0.935-0.96825.444-0.123-0.1230.0000.0000.0000.000
97A98PRO00.023-0.00628.404-0.004-0.0040.0000.0000.0000.000
98A99ASP-1-0.769-0.88331.421-0.091-0.0910.0000.0000.0000.000
99A100LYS10.8230.95622.3430.1920.1920.0000.0000.0000.000
100A101GLU-1-0.862-0.94527.383-0.135-0.1350.0000.0000.0000.000
101A102ALA0-0.060-0.04122.150-0.007-0.0070.0000.0000.0000.000
102A103TYR0-0.0050.01323.358-0.004-0.0040.0000.0000.0000.000
103A104SER0-0.014-0.04018.873-0.030-0.0300.0000.0000.0000.000
104A105GLY00.0210.00016.2140.0090.0090.0000.0000.0000.000
105A106PHE0-0.032-0.02612.450-0.035-0.0350.0000.0000.0000.000
106A107GLU-1-0.826-0.90016.775-0.203-0.2030.0000.0000.0000.000
107A108GLY0-0.029-0.01720.3720.0140.0140.0000.0000.0000.000
108A109THR0-0.037-0.03116.0460.0030.0030.0000.0000.0000.000
109A110ASP-1-0.833-0.93013.649-0.303-0.3030.0000.0000.0000.000
110A111LEU0-0.0270.00910.222-0.069-0.0690.0000.0000.0000.000
111A112ALA00.0350.00110.514-0.132-0.1320.0000.0000.0000.000
112A113LYS10.9210.96110.6010.1660.1660.0000.0000.0000.000
113A114ILE00.0560.0387.498-0.035-0.0350.0000.0000.0000.000
114A115LEU00.0090.0186.232-0.241-0.2410.0000.0000.0000.000
115A116ARG10.8630.9115.598-0.081-0.0810.0000.0000.0000.000
116A117GLY0-0.0270.0026.554-0.006-0.0060.0000.0000.0000.000
117A118ASN0-0.066-0.0422.663-0.8060.7790.500-0.745-1.340-0.001
118A119GLY00.0290.0201.672-2.353-14.44124.266-8.565-3.614-0.055
119A120VAL0-0.052-0.0143.289-0.972-0.1000.042-0.265-0.650-0.001
120A121LYS10.8040.8624.5721.3791.596-0.001-0.027-0.1890.000
121A122ARG10.7810.8706.8760.6930.6930.0000.0000.0000.000
122A123VAL00.0010.0027.142-0.243-0.2430.0000.0000.0000.000
123A124TYR0-0.014-0.0148.2930.1850.1850.0000.0000.0000.000
124A125ILE00.0050.01511.282-0.032-0.0320.0000.0000.0000.000
125A126CYS0-0.035-0.00114.2150.0520.0520.0000.0000.0000.000
126A127GLY00.0450.01416.649-0.024-0.0240.0000.0000.0000.000
127A128VAL0-0.007-0.00119.3800.0200.0200.0000.0000.0000.000
128A129ALA00.0290.01322.112-0.012-0.0120.0000.0000.0000.000
129A130THR00.015-0.01823.038-0.017-0.0170.0000.0000.0000.000
130A131GLU-1-0.766-0.89524.045-0.158-0.1580.0000.0000.0000.000
131A132TYR0-0.025-0.01825.4040.0080.0080.0000.0000.0000.000
132A133CYS00.0120.00421.077-0.003-0.0030.0000.0000.0000.000
133A134VAL0-0.0120.03119.029-0.031-0.0310.0000.0000.0000.000
134A135ARG10.9030.90619.5930.1490.1490.0000.0000.0000.000
135A136ALA0-0.029-0.00221.218-0.012-0.0120.0000.0000.0000.000
136A137THR00.027-0.00315.283-0.019-0.0190.0000.0000.0000.000
137A138ALA0-0.003-0.00216.598-0.046-0.0460.0000.0000.0000.000
138A139LEU0-0.013-0.02217.626-0.017-0.0170.0000.0000.0000.000
139A140ASP-1-0.783-0.86217.583-0.287-0.2870.0000.0000.0000.000
140A141ALA0-0.042-0.02413.521-0.023-0.0230.0000.0000.0000.000
141A142LEU00.013-0.00114.966-0.036-0.0360.0000.0000.0000.000
142A143LYS10.8280.91217.4160.2830.2830.0000.0000.0000.000
143A144HIS0-0.032-0.01113.9590.0180.0180.0000.0000.0000.000
144A145GLY00.0310.03014.199-0.041-0.0410.0000.0000.0000.000
145A146PHE0-0.067-0.0198.354-0.013-0.0130.0000.0000.0000.000
146A147GLU-1-0.866-0.91111.612-0.262-0.2620.0000.0000.0000.000
147A148VAL0-0.022-0.00811.746-0.091-0.0910.0000.0000.0000.000
148A149TYR0-0.067-0.06912.0670.1030.1030.0000.0000.0000.000
149A150LEU0-0.017-0.01314.545-0.034-0.0340.0000.0000.0000.000
150A151LEU00.0230.00413.0140.0280.0280.0000.0000.0000.000
151A152ARG10.9340.95117.2390.1360.1360.0000.0000.0000.000
152A153ASP-1-0.838-0.90119.696-0.159-0.1590.0000.0000.0000.000
153A154ALA0-0.014-0.01717.8540.0070.0070.0000.0000.0000.000
154A155VAL0-0.0010.01019.220-0.026-0.0260.0000.0000.0000.000
155A156LYS10.8830.95121.5470.1340.1340.0000.0000.0000.000
156A157GLY00.019-0.00625.109-0.012-0.0120.0000.0000.0000.000
157A158ILE0-0.057-0.03327.5730.0070.0070.0000.0000.0000.000
158A159LYS10.8590.91331.0840.1160.1160.0000.0000.0000.000
159A160PRO00.0980.04931.741-0.005-0.0050.0000.0000.0000.000
160A161GLU-1-0.818-0.88231.970-0.087-0.0870.0000.0000.0000.000
161A162ASP-1-0.851-0.93131.235-0.111-0.1110.0000.0000.0000.000
162A163GLU-1-0.908-0.95427.669-0.144-0.1440.0000.0000.0000.000
163A164GLU-1-0.918-0.97027.823-0.106-0.1060.0000.0000.0000.000
164A165ARG10.8730.93929.0530.0900.0900.0000.0000.0000.000
165A166ALA00.0160.02225.706-0.006-0.0060.0000.0000.0000.000
166A167LEU0-0.024-0.01922.857-0.016-0.0160.0000.0000.0000.000
167A168GLU-1-0.949-0.98024.987-0.116-0.1160.0000.0000.0000.000
168A169GLU-1-0.817-0.87826.813-0.171-0.1710.0000.0000.0000.000
169A170MET0-0.0040.00821.347-0.018-0.0180.0000.0000.0000.000
170A171LYS10.9720.98922.5590.1230.1230.0000.0000.0000.000
171A172SER0-0.102-0.05423.7100.0030.0030.0000.0000.0000.000
172A173ARG10.9130.95723.3810.1900.1900.0000.0000.0000.000
173A174GLY00.0250.02020.824-0.008-0.0080.0000.0000.0000.000
174A175ILE0-0.060-0.02017.444-0.025-0.0250.0000.0000.0000.000
175A176LYS10.9030.96315.8880.3200.3200.0000.0000.0000.000
176A177ILE0-0.0100.00017.625-0.021-0.0210.0000.0000.0000.000
177A178VAL0-0.030-0.01715.4030.0220.0220.0000.0000.0000.000
178A179GLN00.0220.01417.932-0.010-0.0100.0000.0000.0000.000
179A180PHE00.0080.02311.8330.0110.0110.0000.0000.0000.000