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: 4L91N

Calculation Name: 5LSB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSB

Chain ID: A

ChEMBL ID:

UniProt ID: Q02554

Base Structure: X-ray

Registration Date: 2023-09-26

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 DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1877863.136129
FMO2-HF: Nuclear repulsion 1806331.642518
FMO2-HF: Total energy -71531.493611
FMO2-MP2: Total energy -71745.150478


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:8:GLY)


Summations of interaction energy for fragment #1(A:8:GLY)
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.
-3.0761.2890.453-2.232-2.587-0.003
Interaction energy analysis for fragmet #1(A:8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.022
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].
3A10THR0-0.0010.0252.734-3.1610.4000.037-1.788-1.810-0.002
4A11VAL0-0.0120.0003.908-1.522-1.3760.000-0.102-0.0450.000
5A12TYR0-0.022-0.0126.6630.3140.3140.0000.0000.0000.000
6A13VAL00.0040.0019.338-0.049-0.0490.0000.0000.0000.000
7A14GLY00.022-0.00112.7810.0500.0500.0000.0000.0000.000
8A15ASN0-0.054-0.04815.7650.0080.0080.0000.0000.0000.000
9A16ILE0-0.0140.00315.925-0.001-0.0010.0000.0000.0000.000
10A17ASP-1-0.762-0.85620.286-0.042-0.0420.0000.0000.0000.000
11A18PRO00.0660.02123.3760.0020.0020.0000.0000.0000.000
12A19ARG10.8080.86924.5450.0510.0510.0000.0000.0000.000
13A20ILE0-0.0380.01120.7660.0030.0030.0000.0000.0000.000
14A21THR00.0750.04622.7890.0050.0050.0000.0000.0000.000
15A22LYS10.9580.96116.880-0.103-0.1030.0000.0000.0000.000
16A23GLU-1-0.936-0.95719.703-0.007-0.0070.0000.0000.0000.000
17A24GLN00.0890.03621.630-0.009-0.0090.0000.0000.0000.000
18A25LEU0-0.028-0.00516.291-0.013-0.0130.0000.0000.0000.000
19A26TYR0-0.011-0.01216.819-0.026-0.0260.0000.0000.0000.000
20A27GLU-1-0.914-0.96118.291-0.061-0.0610.0000.0000.0000.000
21A28LEU0-0.026-0.00618.032-0.009-0.0090.0000.0000.0000.000
22A29PHE00.004-0.03613.373-0.023-0.0230.0000.0000.0000.000
23A30ILE0-0.018-0.00315.727-0.028-0.0280.0000.0000.0000.000
24A31GLN0-0.062-0.01717.7760.0010.0010.0000.0000.0000.000
25A32ILE0-0.102-0.03114.014-0.013-0.0130.0000.0000.0000.000
26A33ASN00.0300.00311.8180.0130.0130.0000.0000.0000.000
27A34PRO00.0280.04213.8150.0230.0230.0000.0000.0000.000
28A35VAL00.000-0.01712.381-0.024-0.0240.0000.0000.0000.000
29A36LEU0-0.055-0.00210.0200.0170.0170.0000.0000.0000.000
30A37ARG10.9380.96111.320-0.454-0.4540.0000.0000.0000.000
31A38ILE00.0350.02311.684-0.015-0.0150.0000.0000.0000.000
32A39LYS10.9150.96312.020-0.141-0.1410.0000.0000.0000.000
33A40TYR0-0.012-0.04413.589-0.036-0.0360.0000.0000.0000.000
34A41PRO0-0.057-0.02715.0850.0140.0140.0000.0000.0000.000
35A42LYS10.9220.97118.171-0.031-0.0310.0000.0000.0000.000
36A43ASP-1-0.736-0.87121.9660.0180.0180.0000.0000.0000.000
37A44LYS10.8900.92222.842-0.054-0.0540.0000.0000.0000.000
38A45VAL00.0020.01526.6540.0000.0000.0000.0000.0000.000
39A46LEU00.0150.00827.265-0.001-0.0010.0000.0000.0000.000
40A47GLN0-0.072-0.02827.3880.0000.0000.0000.0000.0000.000
41A48ALA00.0240.02826.240-0.002-0.0020.0000.0000.0000.000
42A49TYR0-0.070-0.04820.4530.0070.0070.0000.0000.0000.000
43A50GLN00.0190.00519.4120.0080.0080.0000.0000.0000.000
44A51GLY00.1040.07519.997-0.005-0.0050.0000.0000.0000.000
45A52TYR0-0.099-0.04813.395-0.016-0.0160.0000.0000.0000.000
46A53ALA0-0.009-0.01613.7670.0370.0370.0000.0000.0000.000
47A54PHE0-0.017-0.0038.155-0.039-0.0390.0000.0000.0000.000
48A55ILE00.0100.0049.1940.1140.1140.0000.0000.0000.000
49A56GLU-1-0.883-0.9406.8781.0161.0160.0000.0000.0000.000
50A57PHE00.0430.0037.353-0.053-0.0530.0000.0000.0000.000
51A58TYR00.0670.0148.0720.2840.2840.0000.0000.0000.000
52A59ASN0-0.012-0.0016.3710.0580.0580.0000.0000.0000.000
53A60GLN00.007-0.0052.773-0.953-0.6540.421-0.302-0.419-0.001
54A61GLY00.0390.0214.750-0.140-0.092-0.001-0.006-0.0400.000
55A62ASP-1-0.831-0.9248.440-0.364-0.3640.0000.0000.0000.000
56A63ALA0-0.0080.0035.2120.0590.093-0.001-0.010-0.0230.000
57A64GLN0-0.047-0.0354.0670.3920.505-0.001-0.010-0.1020.000
58A65TYR0-0.036-0.0117.8530.1810.1810.0000.0000.0000.000
59A66ALA00.0520.01410.0710.0930.0930.0000.0000.0000.000
60A67ILE0-0.065-0.0306.7450.0930.0930.0000.0000.0000.000
61A68LYS10.9100.95010.9920.5600.5600.0000.0000.0000.000
62A69ILE00.0120.02913.5580.0500.0500.0000.0000.0000.000
63A70MET00.0380.02614.1910.0550.0550.0000.0000.0000.000
64A71ASN0-0.042-0.00214.0430.0370.0370.0000.0000.0000.000
65A72ASN0-0.057-0.04515.9910.0280.0280.0000.0000.0000.000
66A73THR00.0470.02118.8900.0160.0160.0000.0000.0000.000
67A74VAL00.0370.02019.9000.0180.0180.0000.0000.0000.000
68A75ARG10.8200.89321.4900.0950.0950.0000.0000.0000.000
69A76LEU00.0370.02120.1850.0070.0070.0000.0000.0000.000
70A77TYR00.002-0.01924.3180.0020.0020.0000.0000.0000.000
71A78ASP-1-0.875-0.94027.591-0.072-0.0720.0000.0000.0000.000
72A79ARG10.8590.95123.5640.0790.0790.0000.0000.0000.000
73A80LEU0-0.033-0.00121.040-0.005-0.0050.0000.0000.0000.000
74A81ILE00.0350.03016.565-0.002-0.0020.0000.0000.0000.000
75A82LYS10.8190.91615.3390.1780.1780.0000.0000.0000.000
76A83VAL00.0420.01610.4230.0120.0120.0000.0000.0000.000
77A84ARG10.9430.96710.0000.3450.3450.0000.0000.0000.000
78A85GLN00.0730.0454.797-0.275-0.212-0.001-0.004-0.0580.000
79A86VAL00.0060.0104.2570.2850.386-0.001-0.010-0.0900.000
80A106PRO0-0.040-0.02319.899-0.004-0.0040.0000.0000.0000.000
81A107ILE0-0.013-0.00522.9110.0030.0030.0000.0000.0000.000
82A108ALA00.0730.05025.464-0.001-0.0010.0000.0000.0000.000
83A109LYS10.8360.93627.7490.0870.0870.0000.0000.0000.000
84A110LEU00.0300.01630.1410.0010.0010.0000.0000.0000.000
85A111PHE0-0.023-0.02433.772-0.003-0.0030.0000.0000.0000.000
86A112ILE00.0060.00935.9540.0030.0030.0000.0000.0000.000
87A113LYS10.9520.97338.8600.0380.0380.0000.0000.0000.000
88A114ASN0-0.041-0.05541.7790.0020.0020.0000.0000.0000.000
89A115LEU0-0.013-0.00839.2920.0020.0020.0000.0000.0000.000
90A116ALA00.0420.02543.9310.0000.0000.0000.0000.0000.000
91A117ASP-1-0.857-0.94644.853-0.034-0.0340.0000.0000.0000.000
92A118SER0-0.059-0.04345.0210.0000.0000.0000.0000.0000.000
93A119ILE0-0.081-0.02240.9660.0000.0000.0000.0000.0000.000
94A120ASP-1-0.868-0.93839.973-0.040-0.0400.0000.0000.0000.000
95A121SER00.012-0.00234.170-0.001-0.0010.0000.0000.0000.000
96A122ASP-1-0.802-0.91236.363-0.040-0.0400.0000.0000.0000.000
97A123GLN0-0.036-0.03737.8690.0020.0020.0000.0000.0000.000
98A124LEU00.0140.01936.3920.0010.0010.0000.0000.0000.000
99A125VAL00.0360.02633.3990.0010.0010.0000.0000.0000.000
100A126LYS10.9290.95836.0010.0290.0290.0000.0000.0000.000
101A127ILE0-0.072-0.03039.2010.0020.0020.0000.0000.0000.000
102A128PHE00.044-0.00635.6510.0010.0010.0000.0000.0000.000
103A129ASN00.0260.01034.469-0.001-0.0010.0000.0000.0000.000
104A130LYS10.8670.95036.2850.0260.0260.0000.0000.0000.000
105A131PHE0-0.0080.00237.3350.0020.0020.0000.0000.0000.000
106A132GLY00.0170.00233.9940.0010.0010.0000.0000.0000.000
107A133LYS10.9570.99728.4320.0390.0390.0000.0000.0000.000
108A134LEU00.0110.00529.686-0.002-0.0020.0000.0000.0000.000
109A135ILE0-0.016-0.00322.522-0.002-0.0020.0000.0000.0000.000
110A136ARG10.8700.92618.9690.1120.1120.0000.0000.0000.000
111A137GLU-1-0.868-0.92226.496-0.074-0.0740.0000.0000.0000.000
112A138PRO0-0.052-0.03629.319-0.004-0.0040.0000.0000.0000.000
113A139GLU-1-0.926-0.95029.599-0.087-0.0870.0000.0000.0000.000
114A140ILE00.000-0.00432.0060.0020.0020.0000.0000.0000.000
115A141PHE0-0.012-0.01234.141-0.002-0.0020.0000.0000.0000.000
116A142TYR00.0380.01736.7820.0030.0030.0000.0000.0000.000
117A143LEU00.0050.00937.890-0.002-0.0020.0000.0000.0000.000
118A144SER0-0.003-0.01241.4100.0020.0020.0000.0000.0000.000
119A145ASN0-0.019-0.01943.9200.0040.0040.0000.0000.0000.000
120A146GLY00.0690.02843.135-0.002-0.0020.0000.0000.0000.000
121A147LYS10.9190.97144.2180.0350.0350.0000.0000.0000.000
122A148LEU00.0310.02743.3250.0010.0010.0000.0000.0000.000
123A149LYS10.9330.99240.8800.0370.0370.0000.0000.0000.000
124A150CYS0-0.067-0.02338.3960.0020.0020.0000.0000.0000.000
125A151ALA00.0460.01335.627-0.001-0.0010.0000.0000.0000.000
126A152TYR0-0.031-0.01130.8440.0010.0010.0000.0000.0000.000
127A153VAL00.0300.01332.028-0.001-0.0010.0000.0000.0000.000
128A154TYR0-0.032-0.02026.636-0.004-0.0040.0000.0000.0000.000
129A155PHE00.0370.00529.2120.0010.0010.0000.0000.0000.000
130A156GLU-1-0.963-1.00425.666-0.055-0.0550.0000.0000.0000.000
131A157ASP-1-0.818-0.90827.042-0.033-0.0330.0000.0000.0000.000
132A158PHE0-0.001-0.02627.495-0.002-0.0020.0000.0000.0000.000
133A159GLU-1-0.871-0.91031.847-0.023-0.0230.0000.0000.0000.000
134A160LYS10.8270.91333.0900.0260.0260.0000.0000.0000.000
135A161ALA0-0.004-0.00432.7640.0000.0000.0000.0000.0000.000
136A162ASP-1-0.814-0.89134.754-0.034-0.0340.0000.0000.0000.000
137A163LEU0-0.072-0.03037.6410.0020.0020.0000.0000.0000.000
138A164ALA00.008-0.00137.3890.0010.0010.0000.0000.0000.000
139A165ILE00.0100.01236.7610.0000.0000.0000.0000.0000.000
140A166LYS10.9210.96540.4310.0210.0210.0000.0000.0000.000
141A167SER0-0.045-0.02842.8440.0020.0020.0000.0000.0000.000
142A168LEU0-0.031-0.01340.5220.0010.0010.0000.0000.0000.000
143A169ASN00.0320.02342.968-0.002-0.0020.0000.0000.0000.000
144A170ASN0-0.029-0.02044.4050.0010.0010.0000.0000.0000.000
145A171GLN0-0.0030.00746.7830.0020.0020.0000.0000.0000.000
146A172LEU0-0.037-0.00948.011-0.001-0.0010.0000.0000.0000.000
147A173VAL00.0260.00844.6430.0010.0010.0000.0000.0000.000
148A174ALA00.0350.00847.757-0.001-0.0010.0000.0000.0000.000
149A175ASN0-0.018-0.03149.4790.0000.0000.0000.0000.0000.000
150A176ASN0-0.0050.02748.186-0.001-0.0010.0000.0000.0000.000
151A177ARG10.9080.95848.8540.0230.0230.0000.0000.0000.000
152A178ILE00.0260.03742.528-0.001-0.0010.0000.0000.0000.000
153A179THR0-0.007-0.00742.2590.0010.0010.0000.0000.0000.000
154A180VAL0-0.036-0.02738.463-0.002-0.0020.0000.0000.0000.000
155A181ASP-1-0.853-0.92038.531-0.040-0.0400.0000.0000.0000.000
156A182TYR0-0.025-0.03032.690-0.005-0.0050.0000.0000.0000.000
157A183ALA0-0.017-0.00531.4760.0000.0000.0000.0000.0000.000
158A184PHE00.0810.04832.7570.0000.0000.0000.0000.0000.000
159A185LYS10.9081.05826.7490.0710.0710.0000.0000.0000.000
160A186DGL0-1.250-0.45027.512-0.011-0.0110.0000.0000.0000.000
161A187ASN-1-0.123-0.76532.924-0.069-0.0690.0000.0000.0000.000
162A188GLY00.4810.17832.601-0.003-0.0030.0000.0000.0000.000
163A189LYS10.8630.90525.9160.0900.0900.0000.0000.0000.000
164A190GLY00.1330.06430.5670.0030.0030.0000.0000.0000.000
165A191ASN0-0.097-0.04128.9490.0040.0040.0000.0000.0000.000
166A192ALA00.1040.04131.253-0.001-0.0010.0000.0000.0000.000
167A193LYS10.9050.95227.3070.0510.0510.0000.0000.0000.000
168A194TYR0-0.066-0.02725.437-0.007-0.0070.0000.0000.0000.000
169A195GLY00.0970.06428.0180.0030.0030.0000.0000.0000.000
170A196ASP-1-0.896-0.96022.774-0.064-0.0640.0000.0000.0000.000
171A197ASP-1-0.926-0.97123.437-0.055-0.0550.0000.0000.0000.000
172A198VAL00.0460.02325.4440.0020.0020.0000.0000.0000.000
173A199ASP-1-0.847-0.92622.506-0.015-0.0150.0000.0000.0000.000
174A200ARG10.8820.93220.3630.0730.0730.0000.0000.0000.000
175A201LEU0-0.0060.01021.9680.0010.0010.0000.0000.0000.000
176A202LEU0-0.029-0.00324.7740.0040.0040.0000.0000.0000.000
177A203ASN0-0.113-0.07420.0020.0160.0160.0000.0000.0000.000
178A204LYS10.8820.95920.086-0.001-0.0010.0000.0000.0000.000
179A205GLU-1-0.905-0.94816.460-0.063-0.0630.0000.0000.0000.000