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: LZ8J9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1961555.358478
FMO2-HF: Nuclear repulsion 1891289.491564
FMO2-HF: Total energy -70265.866914
FMO2-MP2: Total energy -70471.461257


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.
-4.7781.46412.605-7.618-11.227-0.027
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 : -0.001 / 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].
3A4GLU-1-0.948-0.9622.712-3.0870.4290.112-1.720-1.9080.007
4A5ALA00.0490.0122.978-1.716-0.4660.195-0.708-0.737-0.007
5A6LEU0-0.047-0.0105.6290.1280.1280.0000.0000.0000.000
6A7ILE0-0.003-0.0188.899-0.023-0.0230.0000.0000.0000.000
7A8VAL0-0.022-0.03211.6760.0190.0190.0000.0000.0000.000
8A9VAL0-0.016-0.01914.5070.0020.0020.0000.0000.0000.000
9A10ASP-1-0.701-0.84317.555-0.020-0.0200.0000.0000.0000.000
10A11MET0-0.0070.01818.7580.0060.0060.0000.0000.0000.000
11A12GLN0-0.009-0.00920.646-0.004-0.0040.0000.0000.0000.000
12A13ARG10.9030.95023.3180.0560.0560.0000.0000.0000.000
13A14ASP-1-0.751-0.87826.719-0.024-0.0240.0000.0000.0000.000
14A15PHE0-0.053-0.01624.0530.0050.0050.0000.0000.0000.000
15A16MET0-0.0280.00524.0020.0000.0000.0000.0000.0000.000
16A17PRO00.002-0.00728.2830.0020.0020.0000.0000.0000.000
17A18GLY0-0.0060.00231.609-0.002-0.0020.0000.0000.0000.000
18A19GLY0-0.0240.00431.0260.0000.0000.0000.0000.0000.000
19A20ALA0-0.045-0.02732.0190.0020.0020.0000.0000.0000.000
20A21LEU0-0.090-0.05429.8660.0030.0030.0000.0000.0000.000
21A22PRO0-0.0350.00630.084-0.001-0.0010.0000.0000.0000.000
22A23VAL00.0330.00726.6470.0030.0030.0000.0000.0000.000
23A24PRO00.0040.00029.695-0.003-0.0030.0000.0000.0000.000
24A25GLU-1-0.920-0.97030.343-0.019-0.0190.0000.0000.0000.000
25A26GLY00.0130.00526.802-0.002-0.0020.0000.0000.0000.000
26A27ASP-1-0.838-0.95225.337-0.039-0.0390.0000.0000.0000.000
27A28LYS10.8830.94226.0310.0230.0230.0000.0000.0000.000
28A29ILE0-0.027-0.00621.430-0.001-0.0010.0000.0000.0000.000
29A30ILE00.0260.03021.234-0.006-0.0060.0000.0000.0000.000
30A31PRO0-0.017-0.00820.504-0.011-0.0110.0000.0000.0000.000
31A32LYS10.8920.95218.9560.0460.0460.0000.0000.0000.000
32A33VAL00.0410.01916.326-0.009-0.0090.0000.0000.0000.000
33A34ASN00.1000.04315.800-0.026-0.0260.0000.0000.0000.000
34A35GLU-1-0.934-0.96315.753-0.092-0.0920.0000.0000.0000.000
35A36TYR0-0.039-0.04213.351-0.011-0.0110.0000.0000.0000.000
36A37ILE00.0360.02511.355-0.029-0.0290.0000.0000.0000.000
37A38ARG10.9300.97410.9250.0790.0790.0000.0000.0000.000
38A39LYS10.9360.98211.9740.0690.0690.0000.0000.0000.000
39A40PHE0-0.050-0.0456.9510.0180.0180.0000.0000.0000.000
40A41LYS11.0001.0057.2540.1960.1960.0000.0000.0000.000
41A42GLU-1-0.984-0.9898.382-0.234-0.2340.0000.0000.0000.000
42A43LYS10.8260.9217.1530.0980.0980.0000.0000.0000.000
43A44GLY00.0210.0245.1680.0720.0720.0000.0000.0000.000
44A45ALA0-0.055-0.0172.954-2.449-0.4480.461-0.961-1.501-0.007
45A46LEU00.0310.0192.591-2.303-0.5520.991-0.614-2.128-0.004
46A47ILE0-0.004-0.0073.5580.3920.4550.0180.035-0.1150.000
47A48VAL00.0050.0087.3450.0180.0180.0000.0000.0000.000
48A49ALA00.0190.0269.9410.0230.0230.0000.0000.0000.000
49A50THR0-0.030-0.02813.6370.0100.0100.0000.0000.0000.000
50A51ARG10.8910.94416.1250.0560.0560.0000.0000.0000.000
51A52ASP-1-0.805-0.91719.681-0.002-0.0020.0000.0000.0000.000
52A53TRP0-0.025-0.01922.072-0.009-0.0090.0000.0000.0000.000
53A54HIS10.8960.95724.0480.0130.0130.0000.0000.0000.000
54A55PRO00.0140.04227.565-0.004-0.0040.0000.0000.0000.000
55A56GLU-1-0.744-0.87230.401-0.016-0.0160.0000.0000.0000.000
56A57ASN00.0190.00833.8890.0020.0020.0000.0000.0000.000
57A58HIS00.0320.02128.2530.0000.0000.0000.0000.0000.000
58A59ILE00.0160.01630.585-0.001-0.0010.0000.0000.0000.000
59A60SER0-0.073-0.03030.5750.0000.0000.0000.0000.0000.000
60A61PHE00.001-0.01930.727-0.001-0.0010.0000.0000.0000.000
61A62ARG10.9720.99035.0480.0060.0060.0000.0000.0000.000
62A63GLU-1-0.958-0.96637.781-0.007-0.0070.0000.0000.0000.000
63A64ARG10.7710.88334.692-0.004-0.0040.0000.0000.0000.000
64A65GLY0-0.015-0.01039.1270.0010.0010.0000.0000.0000.000
65A66GLY00.0080.01635.7380.0010.0010.0000.0000.0000.000
66A67PRO0-0.023-0.02333.588-0.001-0.0010.0000.0000.0000.000
67A68TRP0-0.043-0.02930.366-0.003-0.0030.0000.0000.0000.000
68A69PRO00.0080.01434.2270.0010.0010.0000.0000.0000.000
69A70ARG10.8750.91633.5640.0180.0180.0000.0000.0000.000
70A71HIS10.8600.92228.0120.0100.0100.0000.0000.0000.000
71A72CYS0-0.069-0.03125.1630.0020.0020.0000.0000.0000.000
72A73VAL0-0.036-0.00427.1210.0010.0010.0000.0000.0000.000
73A74GLN0-0.028-0.03325.914-0.005-0.0050.0000.0000.0000.000
74A75ASN0-0.019-0.01826.734-0.002-0.0020.0000.0000.0000.000
75A76THR0-0.030-0.01128.3940.0010.0010.0000.0000.0000.000
76A77PRO00.0760.01128.104-0.002-0.0020.0000.0000.0000.000
77A78GLY00.0390.03227.880-0.003-0.0030.0000.0000.0000.000
78A79ALA0-0.029-0.01824.8350.0000.0000.0000.0000.0000.000
79A80GLU-1-0.911-0.93723.424-0.064-0.0640.0000.0000.0000.000
80A81PHE00.005-0.00317.1940.0030.0030.0000.0000.0000.000
81A82VAL0-0.020-0.01721.2450.0010.0010.0000.0000.0000.000
82A83VAL0-0.067-0.02416.6350.0030.0030.0000.0000.0000.000
83A84ASP-1-0.914-0.96817.691-0.115-0.1150.0000.0000.0000.000
84A85LEU0-0.081-0.04712.970-0.014-0.0140.0000.0000.0000.000
85A86PRO0-0.038-0.0169.8320.0230.0230.0000.0000.0000.000
86A87GLU-1-0.900-0.96212.535-0.204-0.2040.0000.0000.0000.000
87A88ASP-1-0.935-0.9617.768-0.627-0.6270.0000.0000.0000.000
88A89ALA0-0.038-0.0098.491-0.085-0.0850.0000.0000.0000.000
89A90VAL0-0.004-0.0077.7570.0560.0560.0000.0000.0000.000
90A91ILE0-0.009-0.00910.4980.0370.0370.0000.0000.0000.000
91A92ILE0-0.024-0.01111.8990.0230.0230.0000.0000.0000.000
92A93SER0-0.002-0.00115.167-0.004-0.0040.0000.0000.0000.000
93A94LYS10.8360.91218.8660.0110.0110.0000.0000.0000.000
94A95ALA0-0.038-0.03920.920-0.005-0.0050.0000.0000.0000.000
95A96THR00.0880.01622.457-0.001-0.0010.0000.0000.0000.000
96A97GLU-1-0.916-0.96725.3540.0140.0140.0000.0000.0000.000
97A98PRO00.0500.00128.2990.0000.0000.0000.0000.0000.000
98A99ASP-1-0.772-0.88631.3220.0090.0090.0000.0000.0000.000
99A100LYS10.7710.96423.111-0.019-0.0190.0000.0000.0000.000
100A101GLU-1-0.883-0.95927.2790.0130.0130.0000.0000.0000.000
101A102ALA0-0.050-0.03522.0730.0040.0040.0000.0000.0000.000
102A103TYR00.0410.03823.274-0.007-0.0070.0000.0000.0000.000
103A104SER0-0.013-0.02218.630-0.006-0.0060.0000.0000.0000.000
104A105GLY00.013-0.00616.125-0.003-0.0030.0000.0000.0000.000
105A106PHE0-0.044-0.03912.2830.0090.0090.0000.0000.0000.000
106A107GLU-1-0.856-0.93116.6510.0490.0490.0000.0000.0000.000
107A108GLY0-0.029-0.01020.219-0.011-0.0110.0000.0000.0000.000
108A109THR0-0.054-0.03515.944-0.002-0.0020.0000.0000.0000.000
109A110ASP-1-0.839-0.91913.5110.1010.1010.0000.0000.0000.000
110A111LEU0-0.044-0.01110.1230.0420.0420.0000.0000.0000.000
111A112ALA00.0500.00510.3610.0650.0650.0000.0000.0000.000
112A113LYS10.9360.95910.499-0.131-0.1310.0000.0000.0000.000
113A114ILE00.0680.0457.3750.1160.1160.0000.0000.0000.000
114A115LEU00.0030.0096.0650.1910.1910.0000.0000.0000.000
115A116ARG10.8660.9175.7250.1720.1720.0000.0000.0000.000
116A117GLY0-0.035-0.0017.5220.2860.2860.0000.0000.0000.000
117A118ASN0-0.080-0.0452.439-2.861-1.8161.090-0.658-1.4780.000
118A119GLY00.0200.0152.5349.9395.5629.683-2.720-2.585-0.016
119A120VAL0-0.039-0.0073.223-1.923-1.1250.056-0.253-0.6000.000
120A121LYS10.8750.9165.106-0.904-0.709-0.001-0.019-0.1750.000
121A122ARG10.8280.9106.793-0.289-0.2890.0000.0000.0000.000
122A123VAL00.0100.0137.067-0.050-0.0500.0000.0000.0000.000
123A124TYR0-0.015-0.0188.5400.0120.0120.0000.0000.0000.000
124A125ILE00.0010.01711.235-0.023-0.0230.0000.0000.0000.000
125A126CYS0-0.029-0.00214.231-0.003-0.0030.0000.0000.0000.000
126A127GLY00.0390.01516.611-0.001-0.0010.0000.0000.0000.000
127A128VAL0-0.0110.00119.3370.0060.0060.0000.0000.0000.000
128A129ALA00.0390.01522.1040.0000.0000.0000.0000.0000.000
129A130THR00.009-0.02422.9740.0030.0030.0000.0000.0000.000
130A131GLU-1-0.735-0.87923.9730.0060.0060.0000.0000.0000.000
131A132TYR0-0.035-0.01425.3640.0020.0020.0000.0000.0000.000
132A133CYS00.004-0.00120.9820.0080.0080.0000.0000.0000.000
133A134VAL0-0.0050.03218.8940.0070.0070.0000.0000.0000.000
134A135ARG10.9080.92419.510-0.026-0.0260.0000.0000.0000.000
135A136ALA0-0.031-0.00421.1540.0100.0100.0000.0000.0000.000
136A137THR00.0450.01915.3450.0130.0130.0000.0000.0000.000
137A138ALA00.003-0.00216.5060.0180.0180.0000.0000.0000.000
138A139LEU0-0.020-0.02417.5270.0180.0180.0000.0000.0000.000
139A140ASP-1-0.772-0.87317.4850.0920.0920.0000.0000.0000.000
140A141ALA0-0.044-0.02113.4670.0240.0240.0000.0000.0000.000
141A142LEU00.0120.00014.8510.0320.0320.0000.0000.0000.000
142A143LYS10.8590.93517.316-0.090-0.0900.0000.0000.0000.000
143A144HIS0-0.087-0.03114.2150.0220.0220.0000.0000.0000.000
144A145GLY00.0380.02814.6250.0470.0470.0000.0000.0000.000
145A146PHE0-0.060-0.0148.6540.0090.0090.0000.0000.0000.000
146A147GLU-1-0.837-0.86311.5140.1210.1210.0000.0000.0000.000
147A148VAL0-0.026-0.01011.668-0.005-0.0050.0000.0000.0000.000
148A149TYR0-0.104-0.11611.848-0.015-0.0150.0000.0000.0000.000
149A150LEU0-0.011-0.00914.491-0.006-0.0060.0000.0000.0000.000
150A151LEU00.0190.00013.0060.0010.0010.0000.0000.0000.000
151A152ARG10.9950.98917.220-0.001-0.0010.0000.0000.0000.000
152A153ASP-1-0.866-0.92019.730-0.038-0.0380.0000.0000.0000.000
153A154ALA0-0.012-0.01417.826-0.006-0.0060.0000.0000.0000.000
154A155VAL00.0040.01319.255-0.003-0.0030.0000.0000.0000.000
155A156LYS10.9100.96321.5140.0220.0220.0000.0000.0000.000
156A157GLY00.015-0.00725.0730.0000.0000.0000.0000.0000.000
157A158ILE0-0.058-0.02927.522-0.002-0.0020.0000.0000.0000.000
158A159LYS10.9460.95931.031-0.003-0.0030.0000.0000.0000.000
159A160PRO00.0850.04231.8140.0020.0020.0000.0000.0000.000
160A161GLU-1-0.883-0.94231.9210.0050.0050.0000.0000.0000.000
161A162ASP-1-0.967-0.98731.0740.0100.0100.0000.0000.0000.000
162A163GLU-1-0.896-0.94827.354-0.004-0.0040.0000.0000.0000.000
163A164GLU-1-0.909-0.95927.7660.0090.0090.0000.0000.0000.000
164A165ARG10.9851.00228.996-0.009-0.0090.0000.0000.0000.000
165A166ALA00.0290.03225.5920.0040.0040.0000.0000.0000.000
166A167LEU0-0.042-0.03322.8810.0050.0050.0000.0000.0000.000
167A168GLU-1-0.951-0.97724.9270.0230.0230.0000.0000.0000.000
168A169GLU-1-0.827-0.90126.2110.0410.0410.0000.0000.0000.000
169A170MET0-0.023-0.00121.3550.0070.0070.0000.0000.0000.000
170A171LYS10.9590.98622.484-0.019-0.0190.0000.0000.0000.000
171A172SER0-0.097-0.05323.6470.0050.0050.0000.0000.0000.000
172A173ARG10.9430.97223.139-0.059-0.0590.0000.0000.0000.000
173A174GLY00.0150.01220.7440.0090.0090.0000.0000.0000.000
174A175ILE0-0.061-0.02817.3630.0090.0090.0000.0000.0000.000
175A176LYS10.9180.97416.093-0.113-0.1130.0000.0000.0000.000
176A177ILE0-0.0070.00117.582-0.005-0.0050.0000.0000.0000.000
177A178VAL0-0.037-0.01915.4230.0010.0010.0000.0000.0000.000
178A179GLN00.0080.00217.968-0.002-0.0020.0000.0000.0000.000
179A180PHE0-0.0020.00612.116-0.001-0.0010.0000.0000.0000.000