FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MV6VZ

Calculation Name: 3LH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LH9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8C0E2

Base Structure: X-ray

Registration Date: 2023-06-21

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 289
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4017127.661591
FMO2-HF: Nuclear repulsion 3899387.452
FMO2-HF: Total energy -117740.209591
FMO2-MP2: Total energy -118088.296993


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:9:SER)


Summations of interaction energy for fragment #1(A:9:SER)
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.
-7.853-5.6837.2-3.793-5.5780.013
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.034
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].
3A11GLU-1-0.934-0.9573.841-2.519-0.431-0.024-0.992-1.072-0.003
4A12VAL0-0.018-0.0065.9950.1210.1210.0000.0000.0000.000
5A13GLU-1-0.926-0.9639.497-0.252-0.2520.0000.0000.0000.000
6A14ILE0-0.053-0.02812.6020.0180.0180.0000.0000.0000.000
7A15LEU0-0.014-0.00315.5440.0060.0060.0000.0000.0000.000
8A16LEU0-0.029-0.01218.6800.0090.0090.0000.0000.0000.000
9A17ASN00.010-0.00722.397-0.006-0.0060.0000.0000.0000.000
10A18ASP-1-0.884-0.94825.068-0.053-0.0530.0000.0000.0000.000
11A19ALA0-0.015-0.00322.6560.0000.0000.0000.0000.0000.000
12A20GLU-1-0.973-0.99524.698-0.072-0.0720.0000.0000.0000.000
13A21SER00.0120.01526.7080.0060.0060.0000.0000.0000.000
14A22ARG10.8440.94827.0030.0660.0660.0000.0000.0000.000
15A23LYS10.8150.90829.3110.0440.0440.0000.0000.0000.000
16A24ARG10.9510.97122.6940.0880.0880.0000.0000.0000.000
17A25ALA0-0.032-0.02428.9620.0050.0050.0000.0000.0000.000
18A26GLU-1-0.932-0.96829.168-0.060-0.0600.0000.0000.0000.000
19A27HIS0-0.034-0.01728.4740.0040.0040.0000.0000.0000.000
20A28LYS10.9540.99128.7250.0510.0510.0000.0000.0000.000
21A29THR00.006-0.02024.730-0.001-0.0010.0000.0000.0000.000
22A30GLU-1-0.784-0.88626.052-0.069-0.0690.0000.0000.0000.000
23A31ASP-1-0.828-0.88726.232-0.069-0.0690.0000.0000.0000.000
24A32GLY0-0.048-0.02429.0770.0040.0040.0000.0000.0000.000
25A33LYS10.9120.96027.1740.0660.0660.0000.0000.0000.000
26A34LYS10.9110.95828.8050.0490.0490.0000.0000.0000.000
27A35GLU-1-0.876-0.92922.733-0.097-0.0970.0000.0000.0000.000
28A36LYS10.9040.95225.8020.0650.0650.0000.0000.0000.000
29A37TYR00.0320.01922.653-0.008-0.0080.0000.0000.0000.000
30A38PHE00.003-0.00921.5670.0050.0050.0000.0000.0000.000
31A39LEU0-0.0100.00926.4680.0000.0000.0000.0000.0000.000
32A40PHE0-0.004-0.02426.1250.0000.0000.0000.0000.0000.000
33A41TYR0-0.010-0.01331.2430.0010.0010.0000.0000.0000.000
34A42ASP-1-0.764-0.89233.556-0.039-0.0390.0000.0000.0000.000
35A43GLY00.0000.01434.4420.0010.0010.0000.0000.0000.000
36A44GLU-1-0.824-0.90932.047-0.049-0.0490.0000.0000.0000.000
37A45THR00.0790.02028.889-0.001-0.0010.0000.0000.0000.000
38A46VAL0-0.045-0.01424.246-0.003-0.0030.0000.0000.0000.000
39A47SER00.0260.01124.469-0.001-0.0010.0000.0000.0000.000
40A48GLY00.0420.01721.800-0.003-0.0030.0000.0000.0000.000
41A49LYS10.8750.94818.1350.0900.0900.0000.0000.0000.000
42A50VAL0-0.0080.00312.745-0.018-0.0180.0000.0000.0000.000
43A51SER00.025-0.00112.7320.0400.0400.0000.0000.0000.000
44A52LEU0-0.012-0.0098.192-0.075-0.0750.0000.0000.0000.000
45A53SER00.0350.0207.5320.1930.1930.0000.0000.0000.000
46A54LEU0-0.022-0.0125.373-0.903-0.9030.0000.0000.0000.000
47A55LYS10.9120.9651.9722.7260.6966.510-1.648-2.8320.009
48A56ASN0-0.021-0.0354.302-0.0200.2120.000-0.056-0.1760.000
49A57PRO00.0310.0286.3540.3720.3720.0000.0000.0000.000
50A58ASN0-0.0060.0129.1350.0100.0100.0000.0000.0000.000
51A59LYS10.9070.9372.231-8.449-7.0640.712-0.974-1.1230.007
52A60ARG10.9090.9977.513-0.597-0.5970.0000.0000.0000.000
53A61LEU0-0.026-0.0213.8780.5510.8450.003-0.090-0.2080.000
54A62GLU-1-0.901-0.9496.638-0.065-0.0650.0000.0000.0000.000
55A63HIS0-0.024-0.0037.982-0.177-0.1770.0000.0000.0000.000
56A64GLN0-0.019-0.04010.3190.0400.0400.0000.0000.0000.000
57A65GLY00.0460.02213.105-0.006-0.0060.0000.0000.0000.000
58A66ILE0-0.026-0.01211.123-0.033-0.0330.0000.0000.0000.000
59A67LYS10.9691.00413.7070.1200.1200.0000.0000.0000.000
60A68ILE00.0080.00615.352-0.024-0.0240.0000.0000.0000.000
61A69GLU-1-0.874-0.95217.873-0.086-0.0860.0000.0000.0000.000
62A70PHE0-0.009-0.01220.438-0.008-0.0080.0000.0000.0000.000
63A71ILE00.0520.03020.8830.0050.0050.0000.0000.0000.000
64A72GLY00.0060.00424.421-0.002-0.0020.0000.0000.0000.000
65A73GLN0-0.010-0.01823.5250.0030.0030.0000.0000.0000.000
66A74ILE0-0.025-0.02828.1190.0000.0000.0000.0000.0000.000
67A75GLU-1-0.784-0.89824.908-0.078-0.0780.0000.0000.0000.000
68A76LEU00.020-0.00229.2530.0020.0020.0000.0000.0000.000
69A77TYR00.016-0.01129.557-0.003-0.0030.0000.0000.0000.000
70A78TYR0-0.030-0.00931.8130.0000.0000.0000.0000.0000.000
71A79ASP-1-0.919-0.96231.866-0.048-0.0480.0000.0000.0000.000
72A80ARG10.7690.89325.4850.0680.0680.0000.0000.0000.000
73A81GLY0-0.024-0.02425.251-0.002-0.0020.0000.0000.0000.000
74A82ASN0-0.070-0.02525.423-0.005-0.0050.0000.0000.0000.000
75A83HIS00.0050.00322.4830.0070.0070.0000.0000.0000.000
76A84HIS00.0260.01427.3170.0030.0030.0000.0000.0000.000
77A85GLU-1-0.890-0.95024.182-0.071-0.0710.0000.0000.0000.000
78A86PHE0-0.086-0.04528.6340.0040.0040.0000.0000.0000.000
79A87VAL0-0.0180.01328.0940.0030.0030.0000.0000.0000.000
80A88SER00.0560.01425.605-0.005-0.0050.0000.0000.0000.000
81A89LEU0-0.069-0.01925.0950.0050.0050.0000.0000.0000.000
82A90VAL00.0460.02220.720-0.007-0.0070.0000.0000.0000.000
83A91LYS10.9310.96321.2420.0480.0480.0000.0000.0000.000
84A92ASP-1-0.901-0.95718.858-0.059-0.0590.0000.0000.0000.000
85A93LEU0-0.053-0.03615.9210.0060.0060.0000.0000.0000.000
86A94ALA0-0.020-0.00814.8070.0160.0160.0000.0000.0000.000
87A95ARG10.9560.97816.653-0.032-0.0320.0000.0000.0000.000
88A96PRO00.0080.00014.8520.0120.0120.0000.0000.0000.000
89A97GLY00.0020.00613.618-0.002-0.0020.0000.0000.0000.000
90A98GLU-1-0.885-0.96510.3180.5590.5590.0000.0000.0000.000
91A99ILE0-0.0480.0058.654-0.046-0.0460.0000.0000.0000.000
92A100THR00.009-0.0169.1130.2810.2810.0000.0000.0000.000
93A101GLN00.013-0.01710.502-0.021-0.0210.0000.0000.0000.000
94A102SER00.0110.02210.009-0.045-0.0450.0000.0000.0000.000
95A103GLN00.0050.00511.2870.0870.0870.0000.0000.0000.000
96A104ALA00.0270.01713.113-0.057-0.0570.0000.0000.0000.000
97A105PHE0-0.030-0.01212.6960.0320.0320.0000.0000.0000.000
98A106ASP-1-0.803-0.89817.623-0.073-0.0730.0000.0000.0000.000
99A107PHE0-0.064-0.03518.7600.0040.0040.0000.0000.0000.000
100A108GLU-1-0.895-0.97022.229-0.043-0.0430.0000.0000.0000.000
101A109PHE0-0.069-0.02121.9170.0040.0040.0000.0000.0000.000
102A110THR00.0440.02727.130-0.002-0.0020.0000.0000.0000.000
103A111HIS0-0.036-0.02030.8770.0000.0000.0000.0000.0000.000
104A112VAL0-0.0080.00628.060-0.001-0.0010.0000.0000.0000.000
105A113GLU-1-0.913-0.95031.116-0.037-0.0370.0000.0000.0000.000
106A114LYS10.7020.83329.3380.0470.0470.0000.0000.0000.000
107A115PRO00.0500.03933.0200.0010.0010.0000.0000.0000.000
108A116TYR0-0.018-0.00133.7780.0030.0030.0000.0000.0000.000
109A117GLU-1-0.757-0.82433.764-0.045-0.0450.0000.0000.0000.000
110A118SER00.0300.01329.3170.0000.0000.0000.0000.0000.000
111A119TYR0-0.070-0.05931.5550.0030.0030.0000.0000.0000.000
112A120THR0-0.019-0.00629.614-0.003-0.0030.0000.0000.0000.000
113A121GLY0-0.019-0.01431.9780.0020.0020.0000.0000.0000.000
114A122GLN0-0.049-0.01333.643-0.003-0.0030.0000.0000.0000.000
115A123ASN0-0.004-0.01734.713-0.002-0.0020.0000.0000.0000.000
116A124VAL0-0.022-0.00532.6870.0000.0000.0000.0000.0000.000
117A125LYS10.8670.93125.1880.0740.0740.0000.0000.0000.000
118A126LEU0-0.059-0.01330.2260.0000.0000.0000.0000.0000.000
119A127ARG10.7920.87220.2020.0950.0950.0000.0000.0000.000
120A128TYR00.004-0.04325.9990.0020.0020.0000.0000.0000.000
121A129PHE0-0.032-0.01319.496-0.003-0.0030.0000.0000.0000.000
122A130LEU0-0.0150.00619.1490.0040.0040.0000.0000.0000.000
123A131ARG10.8900.94215.4430.1030.1030.0000.0000.0000.000
124A132ALA0-0.007-0.00413.0590.0090.0090.0000.0000.0000.000
125A133THR0-0.012-0.01111.766-0.023-0.0230.0000.0000.0000.000
126A134ILE0-0.038-0.0156.7740.0300.0300.0000.0000.0000.000
127A135SER00.0480.0199.447-0.066-0.0660.0000.0000.0000.000
128A136ARG10.9000.9453.4790.6750.8130.000-0.029-0.1090.000
129A137ARG10.8890.9628.1010.0410.0410.0000.0000.0000.000
130A138LEU0-0.032-0.0078.9060.0270.0270.0000.0000.0000.000
131A139ASN00.0690.0148.0780.1410.1410.0000.0000.0000.000
132A140ASP-1-0.852-0.9098.162-0.423-0.4230.0000.0000.0000.000
133A141VAL0-0.051-0.0174.666-0.124-0.061-0.001-0.004-0.0580.000
134A142VAL00.0260.0137.6890.0440.0440.0000.0000.0000.000
135A143LYS10.9360.97610.8060.2480.2480.0000.0000.0000.000
136A144GLU-1-0.813-0.90912.389-0.115-0.1150.0000.0000.0000.000
137A145MET0-0.058-0.02416.156-0.009-0.0090.0000.0000.0000.000
138A146ASP-1-0.787-0.87718.730-0.089-0.0890.0000.0000.0000.000
139A147ILE0-0.073-0.03022.298-0.002-0.0020.0000.0000.0000.000
140A148VAL0-0.015-0.01025.2600.0020.0020.0000.0000.0000.000
141A149VAL00.0230.01428.7800.0010.0010.0000.0000.0000.000
142A150HIS00.0030.00231.8350.0010.0010.0000.0000.0000.000
143A151THR00.0340.00435.4600.0010.0010.0000.0000.0000.000
144A152LEU0-0.035-0.01238.5220.0010.0010.0000.0000.0000.000
145A153SER0-0.044-0.01841.6600.0010.0010.0000.0000.0000.000
146A154THR0-0.010-0.01345.1960.0000.0000.0000.0000.0000.000
147A155TYR00.032-0.00747.6160.0010.0010.0000.0000.0000.000
148A156PRO0-0.0020.00852.0140.0000.0000.0000.0000.0000.000
149A157GLU-1-0.885-0.94452.334-0.023-0.0230.0000.0000.0000.000
150A158LEU0-0.0100.00855.6920.0010.0010.0000.0000.0000.000
151A159ASN0-0.064-0.04658.8100.0000.0000.0000.0000.0000.000
152A160SER00.0080.00061.1880.0000.0000.0000.0000.0000.000
153A161SER0-0.069-0.02161.8260.0000.0000.0000.0000.0000.000
154A162ILE0-0.0070.00358.4060.0000.0000.0000.0000.0000.000
155A163LYS10.9440.98361.6560.0150.0150.0000.0000.0000.000
156A164MET0-0.086-0.02058.0290.0000.0000.0000.0000.0000.000
157A165GLU-1-0.824-0.90562.734-0.015-0.0150.0000.0000.0000.000
158A166VAL0-0.091-0.04562.2350.0000.0000.0000.0000.0000.000
159A167GLY00.0220.00664.9080.0000.0000.0000.0000.0000.000
160A168ILE0-0.041-0.02467.8830.0000.0000.0000.0000.0000.000
161A169GLU-1-0.918-0.95571.385-0.012-0.0120.0000.0000.0000.000
162A170ASP-1-0.905-0.95574.030-0.012-0.0120.0000.0000.0000.000
163A171CYS0-0.029-0.01274.0360.0000.0000.0000.0000.0000.000
164A172LEU0-0.049-0.00168.5660.0000.0000.0000.0000.0000.000
165A173HIS0-0.052-0.03969.5080.0000.0000.0000.0000.0000.000
166A174ILE00.003-0.00565.1080.0000.0000.0000.0000.0000.000
167A175GLU-1-0.831-0.92465.795-0.015-0.0150.0000.0000.0000.000
168A176PHE0-0.042-0.02257.3520.0000.0000.0000.0000.0000.000
169A177GLU-1-0.816-0.91262.726-0.016-0.0160.0000.0000.0000.000
170A178TYR0-0.045-0.03256.514-0.001-0.0010.0000.0000.0000.000
171A179ASN00.0870.03956.5250.0000.0000.0000.0000.0000.000
172A180LYS10.8580.94052.8990.0230.0230.0000.0000.0000.000
173A181SER00.0650.03555.3740.0000.0000.0000.0000.0000.000
174A182LYS10.9040.95450.9380.0220.0220.0000.0000.0000.000
175A183TYR0-0.0070.00249.7440.0010.0010.0000.0000.0000.000
176A184HIS00.0380.03346.192-0.002-0.0020.0000.0000.0000.000
177A185LEU00.039-0.00840.6420.0000.0000.0000.0000.0000.000
178A186LYS10.9230.95541.5710.0340.0340.0000.0000.0000.000
179A187ASP-1-0.830-0.90046.227-0.023-0.0230.0000.0000.0000.000
180A188VAL0-0.032-0.02349.7770.0000.0000.0000.0000.0000.000
181A189ILE0-0.014-0.01151.3060.0010.0010.0000.0000.0000.000
182A190VAL0-0.027-0.01554.4570.0000.0000.0000.0000.0000.000
183A191GLY00.031-0.00258.0940.0000.0000.0000.0000.0000.000
184A192LYS10.8580.93660.7910.0160.0160.0000.0000.0000.000
185A193ILE00.0320.02061.4760.0000.0000.0000.0000.0000.000
186A194TYR0-0.016-0.03164.8560.0000.0000.0000.0000.0000.000
187A195PHE00.023-0.00267.0460.0000.0000.0000.0000.0000.000
188A196LEU00.0130.01469.9690.0000.0000.0000.0000.0000.000
189A197SER0-0.032-0.04872.4120.0010.0010.0000.0000.0000.000
190A198VAL0-0.041-0.01672.1250.0000.0000.0000.0000.0000.000
191A199GLU-1-0.918-0.93474.050-0.012-0.0120.0000.0000.0000.000
192A200ILE0-0.058-0.01972.2150.0000.0000.0000.0000.0000.000
193A201LYS10.9840.98671.8980.0130.0130.0000.0000.0000.000
194A202ILE00.019-0.00466.2810.0000.0000.0000.0000.0000.000
195A203LYS10.8880.96363.5580.0170.0170.0000.0000.0000.000
196A204HIS0-0.046-0.05557.7460.0000.0000.0000.0000.0000.000
197A205MET00.0300.02061.7280.0000.0000.0000.0000.0000.000
198A206GLU-1-0.788-0.83454.698-0.023-0.0230.0000.0000.0000.000
199A207ILE0-0.0060.01255.2690.0000.0000.0000.0000.0000.000
200A208ASH0-0.091-0.09151.561-0.001-0.0010.0000.0000.0000.000
201A209ILE0-0.009-0.00347.6810.0000.0000.0000.0000.0000.000
202A210ILE0-0.047-0.03347.754-0.001-0.0010.0000.0000.0000.000
203A211LYS10.9781.00038.3720.0400.0400.0000.0000.0000.000
204A212ARG10.8280.89444.7480.0260.0260.0000.0000.0000.000
205A213GLU-1-0.747-0.85237.468-0.043-0.0430.0000.0000.0000.000
206A214THR0-0.019-0.00741.7660.0010.0010.0000.0000.0000.000
207A215THR00.004-0.00136.314-0.001-0.0010.0000.0000.0000.000
208A216GLY00.0120.01539.2340.0010.0010.0000.0000.0000.000
209A217THR00.013-0.01735.252-0.002-0.0020.0000.0000.0000.000
210A218GLY00.0250.02037.8590.0010.0010.0000.0000.0000.000
211A219PRO0-0.039-0.02439.2470.0010.0010.0000.0000.0000.000
212A220ASN0-0.0080.00840.6500.0030.0030.0000.0000.0000.000
213A221VAL00.005-0.00541.436-0.001-0.0010.0000.0000.0000.000
214A222TYR0-0.027-0.00339.1650.0000.0000.0000.0000.0000.000
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216A224GLU-1-0.884-0.93039.932-0.036-0.0360.0000.0000.0000.000
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