Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: GN241

Calculation Name: 4LUB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LUB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DUV6

Base Structure: X-ray

Registration Date: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115000.223553
FMO2-HF: Nuclear repulsion 2041760.150445
FMO2-HF: Total energy -73240.073108
FMO2-MP2: Total energy -73459.382502


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:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
1.9484.0420-0.634-1.4610.002
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.020
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].
3A7LYS10.9050.9543.8611.6162.973-0.006-0.504-0.8480.002
4A8ILE0-0.010-0.0065.7460.4810.4810.0000.0000.0000.000
5A9ALA00.0330.0339.1780.1060.1060.0000.0000.0000.000
6A10TYR0-0.023-0.02112.1360.0700.0700.0000.0000.0000.000
7A11LEU00.0320.02615.201-0.005-0.0050.0000.0000.0000.000
8A12GLY00.0240.03318.1330.0250.0250.0000.0000.0000.000
9A13PRO00.014-0.00418.9410.0010.0010.0000.0000.0000.000
10A14SER00.019-0.01715.1400.0020.0020.0000.0000.0000.000
11A15GLY0-0.009-0.00717.2220.0030.0030.0000.0000.0000.000
12A16SER0-0.047-0.02119.0640.0050.0050.0000.0000.0000.000
13A17PHE00.0380.00619.4430.0140.0140.0000.0000.0000.000
14A18THR00.0650.02717.4760.0140.0140.0000.0000.0000.000
15A19HIS00.0370.05412.147-0.021-0.0210.0000.0000.0000.000
16A20ASN0-0.053-0.04415.0250.0450.0450.0000.0000.0000.000
17A21VAL0-0.0100.00316.9070.0240.0240.0000.0000.0000.000
18A22ALA00.0210.00512.1870.0210.0210.0000.0000.0000.000
19A23LEU0-0.035-0.02011.4200.0670.0670.0000.0000.0000.000
20A24HIS0-0.008-0.00912.8200.0760.0760.0000.0000.0000.000
21A25ALA0-0.0130.01213.9530.0160.0160.0000.0000.0000.000
22A26PHE00.026-0.0018.905-0.005-0.0050.0000.0000.0000.000
23A27PRO00.0160.0188.8930.1220.1220.0000.0000.0000.000
24A28ALA0-0.062-0.0365.693-0.094-0.0940.0000.0000.0000.000
25A29ALA0-0.0190.0004.1062.1162.4140.001-0.042-0.2570.000
26A30ASP-1-0.876-0.9243.605-1.269-0.8240.006-0.086-0.3650.000
27A31LEU0-0.003-0.0025.118-0.404-0.410-0.001-0.0020.0090.000
28A32LEU0-0.006-0.0117.8300.0990.0990.0000.0000.0000.000
29A33PRO0-0.0120.00111.059-0.011-0.0110.0000.0000.0000.000
30A34PHE0-0.005-0.01412.312-0.017-0.0170.0000.0000.0000.000
31A35GLU-1-0.920-0.95017.209-0.048-0.0480.0000.0000.0000.000
32A36ASN00.0210.00220.9800.0030.0030.0000.0000.0000.000
33A37ILE00.030-0.00121.087-0.021-0.0210.0000.0000.0000.000
34A38THR0-0.039-0.05021.312-0.022-0.0220.0000.0000.0000.000
35A39GLU-1-0.914-0.98119.374-0.187-0.1870.0000.0000.0000.000
36A40VAL0-0.077-0.01816.352-0.041-0.0410.0000.0000.0000.000
37A41ILE0-0.020-0.00616.626-0.048-0.0480.0000.0000.0000.000
38A42LYS10.9310.96417.8590.1240.1240.0000.0000.0000.000
39A43ALA00.0030.04013.419-0.034-0.0340.0000.0000.0000.000
40A44TYR0-0.060-0.03213.244-0.098-0.0980.0000.0000.0000.000
41A45GLU-1-0.835-0.90014.862-0.236-0.2360.0000.0000.0000.000
42A46SER0-0.093-0.06616.081-0.003-0.0030.0000.0000.0000.000
43A47LYS10.9130.94712.6480.4410.4410.0000.0000.0000.000
44A48GLN0-0.032-0.01110.716-0.132-0.1320.0000.0000.0000.000
45A49VAL0-0.068-0.0358.489-0.297-0.2970.0000.0000.0000.000
46A50CYS0-0.045-0.0267.316-0.114-0.1140.0000.0000.0000.000
47A51PHE00.0470.0239.7960.1930.1930.0000.0000.0000.000
48A52ALA00.0150.00812.034-0.084-0.0840.0000.0000.0000.000
49A53ILE0-0.035-0.00112.6560.0480.0480.0000.0000.0000.000
50A54VAL00.0270.00116.264-0.004-0.0040.0000.0000.0000.000
51A55PRO0-0.029-0.00319.8720.0140.0140.0000.0000.0000.000
52A56VAL00.0230.02323.011-0.011-0.0110.0000.0000.0000.000
53A57GLU-1-0.809-0.89625.887-0.022-0.0220.0000.0000.0000.000
54A58ASN00.0180.00327.7960.0100.0100.0000.0000.0000.000
55A59SER0-0.015-0.01130.190-0.002-0.0020.0000.0000.0000.000
56A60ILE0-0.061-0.01732.6670.0020.0020.0000.0000.0000.000
57A61GLU-1-0.916-0.96832.233-0.013-0.0130.0000.0000.0000.000
58A62GLY00.0100.02633.730-0.003-0.0030.0000.0000.0000.000
59A63SER0-0.016-0.05330.7220.0000.0000.0000.0000.0000.000
60A64VAL0-0.036-0.01226.5590.0000.0000.0000.0000.0000.000
61A65HIS00.0510.02129.239-0.009-0.0090.0000.0000.0000.000
62A66GLU-1-0.779-0.85725.683-0.090-0.0900.0000.0000.0000.000
63A67THR00.024-0.01423.530-0.009-0.0090.0000.0000.0000.000
64A68PHE00.0450.01826.203-0.009-0.0090.0000.0000.0000.000
65A69ASP-1-0.793-0.84629.007-0.061-0.0610.0000.0000.0000.000
66A70TYR0-0.010-0.03522.9030.0060.0060.0000.0000.0000.000
67A71LEU00.0330.00822.550-0.009-0.0090.0000.0000.0000.000
68A72PHE0-0.0060.02426.419-0.003-0.0030.0000.0000.0000.000
69A73HIS0-0.031-0.01830.017-0.006-0.0060.0000.0000.0000.000
70A74GLN0-0.105-0.04326.630-0.002-0.0020.0000.0000.0000.000
71A75ALA00.0600.04823.105-0.007-0.0070.0000.0000.0000.000
72A76LYS10.8580.92223.6100.1460.1460.0000.0000.0000.000
73A77ILE00.0170.01719.169-0.010-0.0100.0000.0000.0000.000
74A78GLU-1-0.770-0.86221.318-0.096-0.0960.0000.0000.0000.000
75A79ALA0-0.023-0.01320.372-0.024-0.0240.0000.0000.0000.000
76A80VAL00.0100.00516.5710.0150.0150.0000.0000.0000.000
77A81ALA00.000-0.00517.6600.0230.0230.0000.0000.0000.000
78A82GLU-1-0.759-0.82719.556-0.042-0.0420.0000.0000.0000.000
79A83ILE0-0.021-0.01316.8630.0160.0160.0000.0000.0000.000
80A84ILE0-0.028-0.00621.512-0.009-0.0090.0000.0000.0000.000
81A85LEU0-0.014-0.01220.5890.0100.0100.0000.0000.0000.000
82A173GLU-1-0.893-0.95225.343-0.035-0.0350.0000.0000.0000.000
83A174ASN0-0.037-0.03724.460-0.002-0.0020.0000.0000.0000.000
84A175TYR0-0.025-0.02225.0350.0030.0030.0000.0000.0000.000
85A176THR00.0020.01626.3150.0060.0060.0000.0000.0000.000
86A177ARG10.7390.84425.0740.0320.0320.0000.0000.0000.000
87A178PHE00.026-0.00220.071-0.004-0.0040.0000.0000.0000.000
88A179TRP0-0.016-0.02220.7340.0020.0020.0000.0000.0000.000
89A180VAL0-0.020-0.01114.349-0.009-0.0090.0000.0000.0000.000
90A181LEU00.0000.00017.1510.0080.0080.0000.0000.0000.000
91A182GLY00.041-0.00815.495-0.054-0.0540.0000.0000.0000.000
92A183ASP-1-0.890-0.92215.466-0.311-0.3110.0000.0000.0000.000
93A184GLU-1-0.962-0.98315.092-0.178-0.1780.0000.0000.0000.000
94A185THR0-0.028-0.03515.130-0.019-0.0190.0000.0000.0000.000
95A186PRO0-0.0290.01011.4270.0240.0240.0000.0000.0000.000
96A187THR0-0.016-0.03110.9360.0120.0120.0000.0000.0000.000
97A188ILE0-0.0130.01011.6990.1080.1080.0000.0000.0000.000
98A189HIS0-0.063-0.03010.045-0.069-0.0690.0000.0000.0000.000
99A190LEU0-0.021-0.01214.917-0.016-0.0160.0000.0000.0000.000
100A191LYS10.8660.93218.589-0.051-0.0510.0000.0000.0000.000
101A192GLU-1-0.814-0.88721.0120.0200.0200.0000.0000.0000.000
102A193GLU-1-0.901-0.92522.7540.0370.0370.0000.0000.0000.000
103A194ASP-1-0.805-0.90225.674-0.010-0.0100.0000.0000.0000.000
104A195GLN0-0.044-0.03422.803-0.008-0.0080.0000.0000.0000.000
105A196LYS10.8900.96126.3210.0200.0200.0000.0000.0000.000
106A197ILE00.0010.00026.883-0.008-0.0080.0000.0000.0000.000
107A198SER0-0.022-0.01227.9260.0040.0040.0000.0000.0000.000
108A199LEU00.015-0.00229.434-0.009-0.0090.0000.0000.0000.000
109A200ALA0-0.0010.02131.9750.0050.0050.0000.0000.0000.000
110A201LEU0-0.026-0.01533.582-0.002-0.0020.0000.0000.0000.000
111A202THR00.010-0.00937.2000.0000.0000.0000.0000.0000.000
112A203LEU0-0.015-0.00239.7100.0000.0000.0000.0000.0000.000
113A204PRO00.028-0.00443.334-0.001-0.0010.0000.0000.0000.000
114A205ASP-1-0.919-0.95846.423-0.034-0.0340.0000.0000.0000.000
115A206ASN0-0.055-0.03442.6120.0000.0000.0000.0000.0000.000
116A207LEU00.0160.01444.5380.0010.0010.0000.0000.0000.000
117A208PRO00.027-0.00545.0060.0000.0000.0000.0000.0000.000
118A209GLY0-0.0190.00146.0510.0010.0010.0000.0000.0000.000
119A210ALA0-0.005-0.01046.2680.0010.0010.0000.0000.0000.000
120A211LEU00.0290.02341.0710.0000.0000.0000.0000.0000.000
121A212TYR00.0410.00744.3770.0000.0000.0000.0000.0000.000
122A213LYS10.9461.00146.3850.0300.0300.0000.0000.0000.000
123A214ALA00.0520.04040.9380.0000.0000.0000.0000.0000.000
124A215LEU00.0230.00641.1350.0000.0000.0000.0000.0000.000
125A216SER0-0.032-0.03743.0170.0020.0020.0000.0000.0000.000
126A217THR0-0.047-0.02541.4670.0010.0010.0000.0000.0000.000
127A218PHE00.0190.01236.590-0.001-0.0010.0000.0000.0000.000
128A219ALA00.0250.01941.0820.0010.0010.0000.0000.0000.000
129A220TRP0-0.115-0.07043.6750.0020.0020.0000.0000.0000.000
130A221ARG10.7300.83740.8140.0310.0310.0000.0000.0000.000
131A222GLY0-0.0140.00241.8280.0000.0000.0000.0000.0000.000
132A223ILE0-0.053-0.01936.2360.0000.0000.0000.0000.0000.000
133A224ASP-1-0.862-0.93137.908-0.014-0.0140.0000.0000.0000.000
134A225LEU0-0.057-0.04336.288-0.002-0.0020.0000.0000.0000.000
135A226THR0-0.052-0.04132.9520.0010.0010.0000.0000.0000.000
136A227LYS10.8230.90830.9310.0370.0370.0000.0000.0000.000
137A228ILE0-0.005-0.00835.522-0.003-0.0030.0000.0000.0000.000
138A229GLU-1-0.814-0.85533.840-0.029-0.0290.0000.0000.0000.000
139A230SER0-0.093-0.04536.895-0.002-0.0020.0000.0000.0000.000
140A231ARG10.8520.88933.5240.0490.0490.0000.0000.0000.000
141A232PRO00.0000.00037.023-0.001-0.0010.0000.0000.0000.000
142A233LEU0-0.033-0.01437.319-0.004-0.0040.0000.0000.0000.000
143A234LYS10.8130.88834.4140.0540.0540.0000.0000.0000.000
144A235THR0-0.005-0.01239.0600.0000.0000.0000.0000.0000.000
145A236ILE0-0.002-0.00942.1870.0020.0020.0000.0000.0000.000
146A237LEU0-0.027-0.01544.275-0.001-0.0010.0000.0000.0000.000
147A238GLY00.0200.00345.1230.0020.0020.0000.0000.0000.000
148A239GLU-1-0.822-0.86243.058-0.042-0.0420.0000.0000.0000.000
149A240TYR0-0.045-0.03040.2640.0000.0000.0000.0000.0000.000
150A241PHE0-0.0130.00532.422-0.001-0.0010.0000.0000.0000.000
151A242PHE00.015-0.02337.6080.0030.0030.0000.0000.0000.000
152A243ILE0-0.0180.00731.616-0.003-0.0030.0000.0000.0000.000
153A244ILE0-0.019-0.01134.0130.0050.0050.0000.0000.0000.000
154A245ASP-1-0.755-0.84930.654-0.046-0.0460.0000.0000.0000.000
155A246PHE0-0.031-0.01831.8400.0040.0040.0000.0000.0000.000
156A247GLU-1-0.838-0.91431.263-0.014-0.0140.0000.0000.0000.000
157A248ASN0-0.077-0.07027.663-0.003-0.0030.0000.0000.0000.000
158A249HIS0-0.047-0.02730.671-0.002-0.0020.0000.0000.0000.000
159A250ASN0-0.020-0.01732.459-0.001-0.0010.0000.0000.0000.000
160A251GLU-1-0.782-0.87128.334-0.057-0.0570.0000.0000.0000.000
161A252LYS10.7890.90032.6700.0400.0400.0000.0000.0000.000
162A253LEU0-0.022-0.01135.848-0.001-0.0010.0000.0000.0000.000
163A254VAL00.0750.03332.6700.0000.0000.0000.0000.0000.000
164A255SER0-0.058-0.04534.728-0.003-0.0030.0000.0000.0000.000
165A256PHE0-0.010-0.02336.1050.0000.0000.0000.0000.0000.000
166A257ALA00.0400.03038.0180.0010.0010.0000.0000.0000.000
167A258LEU00.0040.01033.1970.0000.0000.0000.0000.0000.000
168A259GLU-1-0.805-0.87437.913-0.046-0.0460.0000.0000.0000.000
169A260GLU-1-0.728-0.82840.544-0.029-0.0290.0000.0000.0000.000
170A261LEU00.0000.01138.0120.0010.0010.0000.0000.0000.000
171A262THR0-0.025-0.02939.678-0.001-0.0010.0000.0000.0000.000
172A263SER0-0.111-0.06241.9220.0010.0010.0000.0000.0000.000
173A264ILE0-0.049-0.02344.9940.0020.0020.0000.0000.0000.000
174A265GLY0-0.0160.00144.6150.0010.0010.0000.0000.0000.000
175A266ILE0-0.084-0.04540.3520.0000.0000.0000.0000.0000.000
176A267HIS00.0310.02038.379-0.004-0.0040.0000.0000.0000.000
177A268TYR0-0.006-0.01233.5320.0010.0010.0000.0000.0000.000
178A269LYS10.7710.86527.8530.1100.1100.0000.0000.0000.000
179A270ILE00.0020.00027.2950.0050.0050.0000.0000.0000.000
180A271LEU0-0.029-0.01926.921-0.009-0.0090.0000.0000.0000.000
181A272GLY00.0490.01524.532-0.012-0.0120.0000.0000.0000.000
182A273LYS10.8160.89423.9700.1140.1140.0000.0000.0000.000
183A274TYR0-0.061-0.02721.888-0.010-0.0100.0000.0000.0000.000
184A275ALA00.0720.06720.4210.0060.0060.0000.0000.0000.000
185A276VAL0-0.024-0.01621.922-0.005-0.0050.0000.0000.0000.000
186A277TYR00.001-0.03818.7720.0110.0110.0000.0000.0000.000
187A278ARG10.8300.89821.953-0.040-0.0400.0000.0000.0000.000
188A279LEU0-0.007-0.00219.6460.0110.0110.0000.0000.0000.000