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: VRG61

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2109820.441091
FMO2-HF: Nuclear repulsion 2036581.547318
FMO2-HF: Total energy -73238.893773
FMO2-MP2: Total energy -73458.125074


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.
1.0863.494-0.013-0.786-1.6090.002
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 : -0.011 / q_NPA : -0.014
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].
3A7LYS10.9871.0053.7921.3012.919-0.017-0.638-0.9630.002
4A8ILE00.0000.0006.0070.3830.3830.0000.0000.0000.000
5A9ALA00.0190.0269.2120.0750.0750.0000.0000.0000.000
6A10TYR0-0.009-0.00712.1490.0730.0730.0000.0000.0000.000
7A11LEU00.0220.01615.032-0.012-0.0120.0000.0000.0000.000
8A12GLY00.0030.02718.1090.0260.0260.0000.0000.0000.000
9A13PRO00.006-0.01218.8680.0000.0000.0000.0000.0000.000
10A14SER00.011-0.02715.979-0.004-0.0040.0000.0000.0000.000
11A15GLY0-0.0130.00117.396-0.002-0.0020.0000.0000.0000.000
12A16SER0-0.032-0.00218.9860.0030.0030.0000.0000.0000.000
13A17PHE00.019-0.01319.4700.0150.0150.0000.0000.0000.000
14A18THR00.0630.01716.9910.0160.0160.0000.0000.0000.000
15A19HIS00.0520.05412.355-0.011-0.0110.0000.0000.0000.000
16A20ASN00.021-0.00614.9410.0470.0470.0000.0000.0000.000
17A21VAL0-0.0170.00916.8430.0240.0240.0000.0000.0000.000
18A22ALA00.002-0.00212.1730.0260.0260.0000.0000.0000.000
19A23LEU0-0.048-0.02911.5820.0760.0760.0000.0000.0000.000
20A24HIS0-0.026-0.00912.7180.0750.0750.0000.0000.0000.000
21A25ALA0-0.0220.00213.8670.0270.0270.0000.0000.0000.000
22A26PHE00.004-0.0248.7080.0170.0170.0000.0000.0000.000
23A27PRO00.0440.0358.8250.0930.0930.0000.0000.0000.000
24A28ALA0-0.069-0.0394.830-0.056-0.0560.0000.0000.0000.000
25A29ALA0-0.039-0.0123.9761.1341.5500.003-0.083-0.3350.000
26A30ASP-1-0.927-0.9663.775-0.966-0.5710.002-0.064-0.3340.000
27A31LEU00.0020.0035.246-0.423-0.444-0.001-0.0010.0230.000
28A32LEU0-0.014-0.0207.7170.0670.0670.0000.0000.0000.000
29A33PRO0-0.0120.00611.166-0.012-0.0120.0000.0000.0000.000
30A34PHE00.014-0.00512.713-0.024-0.0240.0000.0000.0000.000
31A35GLU-1-0.927-0.96217.503-0.045-0.0450.0000.0000.0000.000
32A36ASN00.0440.01521.1310.0050.0050.0000.0000.0000.000
33A37ILE00.0500.01621.105-0.019-0.0190.0000.0000.0000.000
34A38THR0-0.044-0.07421.254-0.020-0.0200.0000.0000.0000.000
35A39GLU-1-0.949-0.98719.468-0.178-0.1780.0000.0000.0000.000
36A40VAL0-0.066-0.01816.129-0.041-0.0410.0000.0000.0000.000
37A41ILE0-0.003-0.00516.609-0.048-0.0480.0000.0000.0000.000
38A42LYS10.9770.99318.1440.1190.1190.0000.0000.0000.000
39A43ALA00.0180.04313.827-0.038-0.0380.0000.0000.0000.000
40A44TYR0-0.025-0.00413.542-0.071-0.0710.0000.0000.0000.000
41A45GLU-1-0.861-0.90815.009-0.231-0.2310.0000.0000.0000.000
42A46SER0-0.104-0.06716.150-0.017-0.0170.0000.0000.0000.000
43A47LYS10.9100.94812.7230.4320.4320.0000.0000.0000.000
44A48GLN0-0.041-0.01711.164-0.139-0.1390.0000.0000.0000.000
45A49VAL0-0.052-0.0238.797-0.315-0.3150.0000.0000.0000.000
46A50CYS0-0.070-0.0397.603-0.027-0.0270.0000.0000.0000.000
47A51PHE00.0430.0049.3650.1880.1880.0000.0000.0000.000
48A52ALA00.0260.01812.097-0.075-0.0750.0000.0000.0000.000
49A53ILE0-0.051-0.00612.8420.0480.0480.0000.0000.0000.000
50A54VAL00.0220.00216.259-0.005-0.0050.0000.0000.0000.000
51A55PRO0-0.046-0.00519.8500.0120.0120.0000.0000.0000.000
52A56VAL00.0350.01622.938-0.011-0.0110.0000.0000.0000.000
53A57GLU-1-0.859-0.91425.676-0.003-0.0030.0000.0000.0000.000
54A58ASN0-0.0130.01727.5930.0080.0080.0000.0000.0000.000
55A59SER0-0.011-0.00529.846-0.001-0.0010.0000.0000.0000.000
56A60ILE0-0.074-0.03932.3220.0000.0000.0000.0000.0000.000
57A61GLU-1-0.891-0.95732.194-0.006-0.0060.0000.0000.0000.000
58A62GLY00.0190.03733.073-0.003-0.0030.0000.0000.0000.000
59A63SER00.007-0.00230.5240.0000.0000.0000.0000.0000.000
60A64VAL0-0.008-0.00526.502-0.001-0.0010.0000.0000.0000.000
61A65HIS00.009-0.01229.061-0.008-0.0080.0000.0000.0000.000
62A66GLU-1-0.786-0.84425.972-0.075-0.0750.0000.0000.0000.000
63A67THR00.016-0.00523.949-0.012-0.0120.0000.0000.0000.000
64A68PHE00.0180.00226.128-0.009-0.0090.0000.0000.0000.000
65A69ASP-1-0.794-0.88628.766-0.053-0.0530.0000.0000.0000.000
66A70TYR0-0.037-0.04523.0150.0040.0040.0000.0000.0000.000
67A71LEU00.0370.01022.571-0.008-0.0080.0000.0000.0000.000
68A72PHE0-0.031-0.01326.484-0.004-0.0040.0000.0000.0000.000
69A73HIS0-0.062-0.04030.119-0.005-0.0050.0000.0000.0000.000
70A74GLN0-0.069-0.02426.809-0.007-0.0070.0000.0000.0000.000
71A75ALA00.0430.04823.216-0.008-0.0080.0000.0000.0000.000
72A76LYS10.8740.93123.8680.1330.1330.0000.0000.0000.000
73A77ILE00.0110.01119.481-0.013-0.0130.0000.0000.0000.000
74A78GLU-1-0.877-0.93721.232-0.079-0.0790.0000.0000.0000.000
75A79ALA0-0.008-0.01120.127-0.016-0.0160.0000.0000.0000.000
76A80VAL0-0.0060.00615.9400.0100.0100.0000.0000.0000.000
77A81ALA0-0.016-0.02517.2420.0260.0260.0000.0000.0000.000
78A82GLU-1-0.796-0.87019.248-0.010-0.0100.0000.0000.0000.000
79A83ILE00.0010.00916.5400.0160.0160.0000.0000.0000.000
80A84ILE0-0.020-0.00921.151-0.013-0.0130.0000.0000.0000.000
81A85LEU0-0.041-0.03020.4510.0100.0100.0000.0000.0000.000
82A173GLU-1-0.891-0.95225.392-0.020-0.0200.0000.0000.0000.000
83A174ASN0-0.038-0.05124.7430.0000.0000.0000.0000.0000.000
84A175TYR0-0.016-0.03425.2880.0040.0040.0000.0000.0000.000
85A176THR00.0120.01925.9400.0060.0060.0000.0000.0000.000
86A177ARG10.7660.86824.7420.0110.0110.0000.0000.0000.000
87A178PHE00.0220.00119.715-0.007-0.0070.0000.0000.0000.000
88A179TRP0-0.013-0.00820.5390.0030.0030.0000.0000.0000.000
89A180VAL00.004-0.00614.294-0.009-0.0090.0000.0000.0000.000
90A181LEU0-0.021-0.01616.7270.0030.0030.0000.0000.0000.000
91A182GLY00.034-0.01215.046-0.042-0.0420.0000.0000.0000.000
92A183ASP-1-0.970-0.97215.065-0.230-0.2300.0000.0000.0000.000
93A184GLU-1-0.909-0.95514.733-0.129-0.1290.0000.0000.0000.000
94A185THR0-0.025-0.02814.629-0.009-0.0090.0000.0000.0000.000
95A186PRO0-0.0220.01411.0340.0280.0280.0000.0000.0000.000
96A187THR0-0.043-0.03410.456-0.003-0.0030.0000.0000.0000.000
97A188ILE00.0050.00611.3540.1020.1020.0000.0000.0000.000
98A189HIS0-0.058-0.01610.022-0.096-0.0960.0000.0000.0000.000
99A190LEU0-0.016-0.01814.846-0.020-0.0200.0000.0000.0000.000
100A191LYS10.9020.96218.413-0.077-0.0770.0000.0000.0000.000
101A192GLU-1-0.905-0.96020.7650.0660.0660.0000.0000.0000.000
102A193GLU-1-0.914-0.96522.3930.0580.0580.0000.0000.0000.000
103A194ASP-1-0.832-0.92325.1250.0130.0130.0000.0000.0000.000
104A195GLN0-0.0040.01723.041-0.004-0.0040.0000.0000.0000.000
105A196LYS10.9320.97526.149-0.008-0.0080.0000.0000.0000.000
106A197ILE00.0030.00326.664-0.005-0.0050.0000.0000.0000.000
107A198SER0-0.046-0.00627.6890.0010.0010.0000.0000.0000.000
108A199LEU00.003-0.01629.210-0.008-0.0080.0000.0000.0000.000
109A200ALA0-0.0050.00831.8570.0040.0040.0000.0000.0000.000
110A201LEU0-0.018-0.02033.319-0.003-0.0030.0000.0000.0000.000
111A202THR00.004-0.00336.9510.0000.0000.0000.0000.0000.000
112A203LEU0-0.007-0.00839.5200.0010.0010.0000.0000.0000.000
113A204PRO00.0340.00943.180-0.001-0.0010.0000.0000.0000.000
114A205ASP-1-0.926-0.96346.216-0.028-0.0280.0000.0000.0000.000
115A206ASN0-0.041-0.01542.3400.0000.0000.0000.0000.0000.000
116A207LEU00.0480.02344.8060.0010.0010.0000.0000.0000.000
117A208PRO00.011-0.01044.8360.0000.0000.0000.0000.0000.000
118A209GLY0-0.0230.00145.8350.0010.0010.0000.0000.0000.000
119A210ALA00.0070.00046.5240.0010.0010.0000.0000.0000.000
120A211LEU00.0420.02141.0330.0000.0000.0000.0000.0000.000
121A212TYR00.0300.00344.2240.0000.0000.0000.0000.0000.000
122A213LYS10.9430.99246.3070.0230.0230.0000.0000.0000.000
123A214ALA00.0560.03740.7650.0000.0000.0000.0000.0000.000
124A215LEU00.020-0.00340.7100.0000.0000.0000.0000.0000.000
125A216SER0-0.028-0.02942.7710.0020.0020.0000.0000.0000.000
126A217THR0-0.050-0.01741.1870.0010.0010.0000.0000.0000.000
127A218PHE00.001-0.00736.1550.0000.0000.0000.0000.0000.000
128A219ALA00.0160.01541.0170.0020.0020.0000.0000.0000.000
129A220TRP0-0.104-0.06143.6460.0020.0020.0000.0000.0000.000
130A221ARG10.7900.88740.9080.0210.0210.0000.0000.0000.000
131A222GLY0-0.011-0.00441.7920.0010.0010.0000.0000.0000.000
132A223ILE0-0.059-0.01636.1320.0010.0010.0000.0000.0000.000
133A224ASP-1-0.859-0.91837.068-0.001-0.0010.0000.0000.0000.000
134A225LEU0-0.043-0.04136.001-0.001-0.0010.0000.0000.0000.000
135A226THR0-0.052-0.02932.7090.0030.0030.0000.0000.0000.000
136A227LYS10.8960.94330.2700.0220.0220.0000.0000.0000.000
137A228ILE0-0.021-0.01035.197-0.003-0.0030.0000.0000.0000.000
138A229GLU-1-0.871-0.92334.132-0.016-0.0160.0000.0000.0000.000
139A230SER0-0.087-0.02936.531-0.003-0.0030.0000.0000.0000.000
140A231ARG10.8450.90133.3530.0380.0380.0000.0000.0000.000
141A232PRO0-0.001-0.00836.873-0.001-0.0010.0000.0000.0000.000
142A233LEU00.0000.00237.337-0.004-0.0040.0000.0000.0000.000
143A234LYS10.8410.92834.3670.0450.0450.0000.0000.0000.000
144A235THR0-0.002-0.03439.291-0.002-0.0020.0000.0000.0000.000
145A236ILE0-0.020-0.01242.3330.0010.0010.0000.0000.0000.000
146A237LEU0-0.013-0.02244.6040.0000.0000.0000.0000.0000.000
147A238GLY00.0020.00245.3870.0010.0010.0000.0000.0000.000
148A239GLU-1-0.830-0.85543.341-0.036-0.0360.0000.0000.0000.000
149A240TYR0-0.045-0.03640.0490.0000.0000.0000.0000.0000.000
150A241PHE0-0.0070.01332.697-0.001-0.0010.0000.0000.0000.000
151A242PHE00.027-0.01937.3530.0030.0030.0000.0000.0000.000
152A243ILE0-0.040-0.00231.022-0.003-0.0030.0000.0000.0000.000
153A244ILE0-0.013-0.00433.9230.0040.0040.0000.0000.0000.000
154A245ASP-1-0.794-0.88630.216-0.023-0.0230.0000.0000.0000.000
155A246PHE0-0.022-0.03131.7230.0020.0020.0000.0000.0000.000
156A247GLU-1-0.860-0.92731.2330.0050.0050.0000.0000.0000.000
157A248ASN0-0.070-0.04527.561-0.006-0.0060.0000.0000.0000.000
158A249HIS0-0.0080.00630.225-0.001-0.0010.0000.0000.0000.000
159A250ASN0-0.008-0.01332.434-0.002-0.0020.0000.0000.0000.000
160A251GLU-1-0.816-0.92127.671-0.030-0.0300.0000.0000.0000.000
161A252LYS10.9090.96532.5800.0260.0260.0000.0000.0000.000
162A253LEU0-0.024-0.01535.634-0.002-0.0020.0000.0000.0000.000
163A254VAL00.0490.02832.494-0.001-0.0010.0000.0000.0000.000
164A255SER0-0.008-0.00634.522-0.003-0.0030.0000.0000.0000.000
165A256PHE0-0.031-0.02135.903-0.001-0.0010.0000.0000.0000.000
166A257ALA00.0480.03637.7250.0000.0000.0000.0000.0000.000
167A258LEU0-0.013-0.00333.150-0.001-0.0010.0000.0000.0000.000
168A259GLU-1-0.928-0.95937.808-0.036-0.0360.0000.0000.0000.000
169A260GLU-1-0.785-0.87240.466-0.021-0.0210.0000.0000.0000.000
170A261LEU0-0.029-0.01337.7010.0000.0000.0000.0000.0000.000
171A262THR00.014-0.00139.540-0.001-0.0010.0000.0000.0000.000
172A263SER0-0.117-0.05241.8900.0010.0010.0000.0000.0000.000
173A264ILE0-0.062-0.02544.7050.0020.0020.0000.0000.0000.000
174A265GLY0-0.029-0.01144.5350.0010.0010.0000.0000.0000.000
175A266ILE0-0.085-0.03939.904-0.001-0.0010.0000.0000.0000.000
176A267HIS00.0220.01738.030-0.003-0.0030.0000.0000.0000.000
177A268TYR00.001-0.01232.8620.0030.0030.0000.0000.0000.000
178A269LYS10.8300.91428.0310.0930.0930.0000.0000.0000.000
179A270ILE00.010-0.00626.8460.0060.0060.0000.0000.0000.000
180A271LEU0-0.020-0.00826.693-0.010-0.0100.0000.0000.0000.000
181A272GLY00.0580.02224.163-0.009-0.0090.0000.0000.0000.000
182A273LYS10.9130.97023.7060.0790.0790.0000.0000.0000.000
183A274TYR0-0.0050.01721.678-0.006-0.0060.0000.0000.0000.000
184A275ALA00.0750.05020.6520.0010.0010.0000.0000.0000.000
185A276VAL0-0.035-0.02921.6620.0000.0000.0000.0000.0000.000
186A277TYR00.0280.00418.3000.0080.0080.0000.0000.0000.000
187A278ARG10.8410.91421.621-0.064-0.0640.0000.0000.0000.000
188A279LEU0-0.015-0.00319.4240.0120.0120.0000.0000.0000.000