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: LNG79

Calculation Name: 5I32-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I32

Chain ID: A

ChEMBL ID:

UniProt ID: Q41951

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptHSide
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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2530272.318771
FMO2-HF: Nuclear repulsion 2448353.632085
FMO2-HF: Total energy -81918.686686
FMO2-MP2: Total energy -82161.582328


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:1:GLY)


Summations of interaction energy for fragment #1(A:1: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.
-4.1860.3792.045-2.977-3.633-0.014
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.013
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].
3A3GLY00.0300.0173.818-0.4930.239-0.002-0.297-0.4330.002
4A4VAL00.008-0.0036.4030.4340.4340.0000.0000.0000.000
5A5ALA00.0430.0289.4970.1050.1050.0000.0000.0000.000
6A6PHE00.018-0.00412.1400.0540.0540.0000.0000.0000.000
7A7GLY00.0490.02015.7440.0290.0290.0000.0000.0000.000
8A8SER00.004-0.00517.3580.0220.0220.0000.0000.0000.000
9A9PHE00.0640.01521.014-0.001-0.0010.0000.0000.0000.000
10A10ASP-1-0.898-0.93724.314-0.102-0.1020.0000.0000.0000.000
11A11ASP-1-0.876-0.94419.638-0.191-0.1910.0000.0000.0000.000
12A12SER0-0.0310.00320.6720.0000.0000.0000.0000.0000.000
13A13PHE00.0110.01522.8980.0020.0020.0000.0000.0000.000
14A14SER00.0140.03123.8510.0170.0170.0000.0000.0000.000
15A15LEU00.035-0.01026.652-0.002-0.0020.0000.0000.0000.000
16A16ALA0-0.026-0.01023.8510.0020.0020.0000.0000.0000.000
17A17SER00.0390.01022.730-0.002-0.0020.0000.0000.0000.000
18A18LEU00.0020.00424.312-0.003-0.0030.0000.0000.0000.000
19A19ARG10.9090.95227.1180.0570.0570.0000.0000.0000.000
20A20ALA00.0300.03122.6120.0030.0030.0000.0000.0000.000
21A21TYR0-0.023-0.04522.230-0.008-0.0080.0000.0000.0000.000
22A22LEU00.0020.00626.0800.0020.0020.0000.0000.0000.000
23A23ALA00.0350.01225.8850.0040.0040.0000.0000.0000.000
24A24GLU-1-0.699-0.80522.282-0.146-0.1460.0000.0000.0000.000
25A25PHE0-0.0430.00425.7170.0020.0020.0000.0000.0000.000
26A26ILE0-0.001-0.00729.0450.0040.0040.0000.0000.0000.000
27A27SER00.001-0.00926.5760.0060.0060.0000.0000.0000.000
28A28THR0-0.027-0.04326.377-0.001-0.0010.0000.0000.0000.000
29A29LEU0-0.039-0.00328.3300.0030.0030.0000.0000.0000.000
30A30LEU0-0.002-0.01031.7310.0040.0040.0000.0000.0000.000
31A31PHE0-0.022-0.01326.8990.0030.0030.0000.0000.0000.000
32A32VAL0-0.009-0.00629.5860.0030.0030.0000.0000.0000.000
33A33PHE0-0.019-0.00432.0250.0040.0040.0000.0000.0000.000
34A34ALA00.0400.01733.8360.0030.0030.0000.0000.0000.000
35A35GLY00.0420.01432.8550.0030.0030.0000.0000.0000.000
36A36VAL00.003-0.00733.5780.0020.0020.0000.0000.0000.000
37A37GLY00.0520.02735.8440.0030.0030.0000.0000.0000.000
38A38SER0-0.077-0.05036.2720.0030.0030.0000.0000.0000.000
39A39ALA00.0110.00537.1530.0030.0030.0000.0000.0000.000
40A40ILE00.0150.00939.1340.0020.0020.0000.0000.0000.000
41A41ALA0-0.027-0.01841.6980.0030.0030.0000.0000.0000.000
42A42TYR0-0.040-0.02841.8300.0030.0030.0000.0000.0000.000
43A43ALA00.0350.03943.4150.0020.0020.0000.0000.0000.000
44A44LYS10.9640.98145.2800.0340.0340.0000.0000.0000.000
45A45LEU0-0.100-0.06245.5360.0020.0020.0000.0000.0000.000
46A46THR0-0.041-0.03146.4050.0020.0020.0000.0000.0000.000
47A47SER0-0.062-0.01449.1260.0010.0010.0000.0000.0000.000
48A48ASP-1-0.951-0.98246.608-0.042-0.0420.0000.0000.0000.000
49A49ALA0-0.0120.01447.091-0.001-0.0010.0000.0000.0000.000
50A50ALA00.025-0.00144.181-0.002-0.0020.0000.0000.0000.000
51A51LEU0-0.0260.00637.4160.0020.0020.0000.0000.0000.000
52A52ASP-1-0.792-0.89641.971-0.034-0.0340.0000.0000.0000.000
53A53THR00.007-0.01139.686-0.001-0.0010.0000.0000.0000.000
54A54PRO00.0120.00240.232-0.001-0.0010.0000.0000.0000.000
55A55GLY00.0640.02240.9070.0000.0000.0000.0000.0000.000
56A56LEU0-0.046-0.01134.353-0.002-0.0020.0000.0000.0000.000
57A57VAL0-0.015-0.01136.019-0.002-0.0020.0000.0000.0000.000
58A58ALA00.0060.00936.568-0.001-0.0010.0000.0000.0000.000
59A59ILE00.0150.00734.058-0.002-0.0020.0000.0000.0000.000
60A60ALA0-0.0010.01832.262-0.004-0.0040.0000.0000.0000.000
61A61VAL0-0.001-0.00331.871-0.002-0.0020.0000.0000.0000.000
62A62CYS0-0.064-0.00733.2580.0000.0000.0000.0000.0000.000
63A63HIS00.009-0.00129.567-0.007-0.0070.0000.0000.0000.000
64A64GLY00.0200.01828.397-0.004-0.0040.0000.0000.0000.000
65A65PHE0-0.021-0.03128.8560.0010.0010.0000.0000.0000.000
66A66ALA00.0160.01230.7140.0000.0000.0000.0000.0000.000
67A67LEU0-0.0150.00023.425-0.002-0.0020.0000.0000.0000.000
68A68PHE00.0210.00926.084-0.002-0.0020.0000.0000.0000.000
69A69VAL0-0.018-0.00526.8390.0010.0010.0000.0000.0000.000
70A70ALA00.0120.00927.1480.0000.0000.0000.0000.0000.000
71A71VAL00.0090.01521.617-0.004-0.0040.0000.0000.0000.000
72A72ALA0-0.012-0.01624.1650.0000.0000.0000.0000.0000.000
73A73ILE0-0.070-0.03226.0300.0030.0030.0000.0000.0000.000
74A74GLY00.0440.02824.8710.0000.0000.0000.0000.0000.000
75A75ALA0-0.0140.00821.773-0.008-0.0080.0000.0000.0000.000
76A76ASN0-0.042-0.03221.255-0.003-0.0030.0000.0000.0000.000
77A77ILE0-0.060-0.02423.4860.0050.0050.0000.0000.0000.000
78A78SER0-0.025-0.04221.8130.0000.0000.0000.0000.0000.000
79A79GLY0-0.0050.02418.764-0.025-0.0250.0000.0000.0000.000
80A80GLY0-0.055-0.01719.6390.0020.0020.0000.0000.0000.000
81A81HIS00.0260.01116.101-0.014-0.0140.0000.0000.0000.000
82A82VAL0-0.037-0.02420.1050.0030.0030.0000.0000.0000.000
83A83ASN00.028-0.00820.489-0.003-0.0030.0000.0000.0000.000
84A84PRO00.0530.03919.757-0.019-0.0190.0000.0000.0000.000
85A85ALA00.0240.00717.942-0.036-0.0360.0000.0000.0000.000
86A86VAL0-0.0060.00815.999-0.038-0.0380.0000.0000.0000.000
87A87THR00.010-0.00514.745-0.032-0.0320.0000.0000.0000.000
88A88PHE0-0.040-0.01514.372-0.064-0.0640.0000.0000.0000.000
89A89GLY00.0440.02411.924-0.089-0.0890.0000.0000.0000.000
90A90LEU00.0020.00410.119-0.127-0.1270.0000.0000.0000.000
91A91ALA0-0.0080.0059.825-0.124-0.1240.0000.0000.0000.000
92A92VAL0-0.053-0.0277.972-0.162-0.1620.0000.0000.0000.000
93A93GLY00.0180.0215.465-0.386-0.3860.0000.0000.0000.000
94A94GLY0-0.0150.0036.075-0.121-0.1210.0000.0000.0000.000
95A95GLN0-0.105-0.0676.8310.4340.4340.0000.0000.0000.000
96A96ILE0-0.025-0.00710.3350.1280.1280.0000.0000.0000.000
97A97THR0-0.0040.00412.716-0.088-0.0880.0000.0000.0000.000
98A98VAL00.0270.00314.0530.0310.0310.0000.0000.0000.000
99A99ILE0-0.0230.00216.1930.0400.0400.0000.0000.0000.000
100A100THR00.0080.00018.0020.0150.0150.0000.0000.0000.000
101A101GLY00.0350.01417.4190.0250.0250.0000.0000.0000.000
102A102VAL0-0.003-0.00218.3300.0220.0220.0000.0000.0000.000
103A103PHE00.011-0.00221.2420.0240.0240.0000.0000.0000.000
104A104TYR0-0.021-0.04019.4670.0190.0190.0000.0000.0000.000
105A105TRP0-0.031-0.00218.5940.0190.0190.0000.0000.0000.000
106A106ILE0-0.017-0.00123.1050.0170.0170.0000.0000.0000.000
107A107ALA00.0140.00825.5110.0130.0130.0000.0000.0000.000
108A108GLN0-0.011-0.03120.6110.0050.0050.0000.0000.0000.000
109A109LEU0-0.005-0.00525.8910.0100.0100.0000.0000.0000.000
110A110LEU0-0.0050.01028.4140.0110.0110.0000.0000.0000.000
111A111GLY00.0140.00729.8860.0080.0080.0000.0000.0000.000
112A112SER0-0.018-0.04729.3820.0110.0110.0000.0000.0000.000
113A113THR00.026-0.00931.3700.0060.0060.0000.0000.0000.000
114A114ALA0-0.0080.00034.0960.0060.0060.0000.0000.0000.000
115A115ALA0-0.0110.00634.1430.0060.0060.0000.0000.0000.000
116A116CYS0-0.028-0.00734.4520.0050.0050.0000.0000.0000.000
117A117PHE00.0190.00237.3820.0040.0040.0000.0000.0000.000
118A118LEU0-0.022-0.01038.0000.0040.0040.0000.0000.0000.000
119A119LEU0-0.0040.01237.3860.0040.0040.0000.0000.0000.000
120A120LYS10.8850.96041.2430.0550.0550.0000.0000.0000.000
121A121TYR0-0.019-0.00443.5460.0030.0030.0000.0000.0000.000
122A122VAL0-0.003-0.01443.1290.0020.0020.0000.0000.0000.000
123A123THR0-0.073-0.04643.4500.0020.0020.0000.0000.0000.000
124A124GLY0-0.022-0.00446.4410.0010.0010.0000.0000.0000.000
125A125GLY0-0.0040.00147.2690.0010.0010.0000.0000.0000.000
126A126LEU0-0.0050.00545.4230.0000.0000.0000.0000.0000.000
127A127ALA0-0.009-0.00843.657-0.002-0.0020.0000.0000.0000.000
128A128VAL00.0290.01037.7440.0010.0010.0000.0000.0000.000
129A129PRO0-0.0110.00637.736-0.002-0.0020.0000.0000.0000.000
130A130THR00.0180.00435.400-0.002-0.0020.0000.0000.0000.000
131A131HIS00.0020.01529.715-0.002-0.0020.0000.0000.0000.000
132A132SER00.0080.00033.478-0.002-0.0020.0000.0000.0000.000
133A133VAL0-0.020-0.00731.4070.0000.0000.0000.0000.0000.000
134A134ALA0-0.0070.00834.0400.0030.0030.0000.0000.0000.000
135A135ALA00.0380.00736.964-0.001-0.0010.0000.0000.0000.000
136A136GLY0-0.029-0.01739.8520.0020.0020.0000.0000.0000.000
137A137LEU0-0.066-0.00932.7970.0000.0000.0000.0000.0000.000
138A138GLY00.0590.03234.164-0.002-0.0020.0000.0000.0000.000
139A139SER0-0.004-0.02831.302-0.003-0.0030.0000.0000.0000.000
140A140ILE0-0.015-0.00227.424-0.009-0.0090.0000.0000.0000.000
141A141GLU-1-0.789-0.89827.743-0.096-0.0960.0000.0000.0000.000
142A142GLY00.0080.01328.396-0.002-0.0020.0000.0000.0000.000
143A143VAL0-0.001-0.01824.006-0.006-0.0060.0000.0000.0000.000
144A144VAL0-0.004-0.00523.663-0.013-0.0130.0000.0000.0000.000
145A145MET00.0120.01323.599-0.005-0.0050.0000.0000.0000.000
146A146GLU-1-0.710-0.84623.874-0.128-0.1280.0000.0000.0000.000
147A147ILE0-0.0350.01018.507-0.012-0.0120.0000.0000.0000.000
148A148ILE00.0030.00619.280-0.014-0.0140.0000.0000.0000.000
149A149ILE0-0.007-0.00620.1720.0010.0010.0000.0000.0000.000
150A150THR0-0.015-0.02618.0800.0060.0060.0000.0000.0000.000
151A151PHE0-0.0270.00512.875-0.009-0.0090.0000.0000.0000.000
152A152ALA00.0040.00816.0580.0030.0030.0000.0000.0000.000
153A153LEU00.0040.01617.8520.0120.0120.0000.0000.0000.000
154A154VAL00.011-0.00112.7050.0070.0070.0000.0000.0000.000
155A155TYR00.0230.01712.351-0.001-0.0010.0000.0000.0000.000
156A156THR0-0.035-0.02513.9100.0400.0400.0000.0000.0000.000
157A157VAL00.0030.01414.4420.0260.0260.0000.0000.0000.000
158A158TYR0-0.025-0.0407.450-0.022-0.0220.0000.0000.0000.000
159A159ALA0-0.0130.00112.0980.0520.0520.0000.0000.0000.000
160A160THR0-0.084-0.05613.7250.0320.0320.0000.0000.0000.000
161A161ALA00.017-0.00115.2650.0150.0150.0000.0000.0000.000
162A162ALA0-0.0100.01110.7570.0070.0070.0000.0000.0000.000
163A163ASP-1-0.733-0.8379.7360.3710.3710.0000.0000.0000.000
164A164PRO00.0090.0028.931-0.022-0.0220.0000.0000.0000.000
165A165LYS10.7950.8869.646-0.461-0.4610.0000.0000.0000.000
166A166LYS10.8740.94513.521-0.036-0.0360.0000.0000.0000.000
167A167GLY00.0340.01315.551-0.012-0.0120.0000.0000.0000.000
168A168SER00.003-0.01018.714-0.014-0.0140.0000.0000.0000.000
169A169LEU00.0240.01316.833-0.017-0.0170.0000.0000.0000.000
170A170GLY00.0210.00719.095-0.017-0.0170.0000.0000.0000.000
171A171THR0-0.064-0.03319.748-0.010-0.0100.0000.0000.0000.000
172A172ILE00.0060.00522.415-0.008-0.0080.0000.0000.0000.000
173A173ALA00.0220.02219.227-0.008-0.0080.0000.0000.0000.000
174A174PRO00.0300.01121.107-0.011-0.0110.0000.0000.0000.000
175A175LEU0-0.0010.00323.443-0.007-0.0070.0000.0000.0000.000
176A176ALA0-0.0040.00321.283-0.003-0.0030.0000.0000.0000.000
177A177ILE00.0170.00418.512-0.009-0.0090.0000.0000.0000.000
178A178GLY00.0120.00921.796-0.008-0.0080.0000.0000.0000.000
179A179LEU0-0.021-0.02825.442-0.002-0.0020.0000.0000.0000.000
180A180ILE0-0.0140.00920.7240.0000.0000.0000.0000.0000.000
181A181VAL00.0440.01423.326-0.005-0.0050.0000.0000.0000.000
182A182GLY00.0150.00425.5080.0010.0010.0000.0000.0000.000
183A183ALA0-0.010-0.01626.5810.0020.0020.0000.0000.0000.000
184A184ASN00.022-0.00922.6220.0070.0070.0000.0000.0000.000
185A185ILE0-0.0150.00227.105-0.002-0.0020.0000.0000.0000.000
186A186LEU0-0.034-0.01830.0190.0020.0020.0000.0000.0000.000
187A187ALA0-0.0240.00828.8640.0030.0030.0000.0000.0000.000
188A188ALA00.0490.00428.1510.0000.0000.0000.0000.0000.000
189A189GLY0-0.0180.00330.296-0.003-0.0030.0000.0000.0000.000
190A190PRO0-0.018-0.02032.986-0.001-0.0010.0000.0000.0000.000
191A191PHE0-0.054-0.00731.7240.0010.0010.0000.0000.0000.000
192A192SER00.024-0.02728.2110.0010.0010.0000.0000.0000.000
193A193GLY00.0330.03431.058-0.004-0.0040.0000.0000.0000.000
194A194GLY0-0.035-0.01827.9930.0030.0030.0000.0000.0000.000
195A195SER0-0.052-0.03826.703-0.001-0.0010.0000.0000.0000.000
196A196MET0-0.066-0.01622.1500.0030.0030.0000.0000.0000.000
197A197ASN00.014-0.00421.969-0.019-0.0190.0000.0000.0000.000
198A198PRO00.0760.04521.8910.0120.0120.0000.0000.0000.000
199A199ALA00.0300.01224.8240.0100.0100.0000.0000.0000.000
200A200ARG10.8620.94726.6140.0980.0980.0000.0000.0000.000
201A201SER00.0280.00828.0180.0060.0060.0000.0000.0000.000
202A202PHE0-0.014-0.00528.7640.0050.0050.0000.0000.0000.000
203A203GLY00.0040.00930.5750.0050.0050.0000.0000.0000.000
204A204PRO00.021-0.01332.4150.0040.0040.0000.0000.0000.000
205A205ALA00.0050.02633.3850.0040.0040.0000.0000.0000.000
206A206VAL0-0.023-0.01233.8150.0040.0040.0000.0000.0000.000
207A207ALA0-0.058-0.02736.4700.0040.0040.0000.0000.0000.000
208A208ALA0-0.056-0.02638.5170.0040.0040.0000.0000.0000.000
209A209GLY0-0.023-0.00239.4900.0030.0030.0000.0000.0000.000
210A210ASP-1-0.889-0.95038.288-0.075-0.0750.0000.0000.0000.000
211A211PHE0-0.021-0.02231.917-0.005-0.0050.0000.0000.0000.000
212A212SER0-0.0260.00234.614-0.008-0.0080.0000.0000.0000.000
213A213GLY00.0200.00833.5290.0000.0000.0000.0000.0000.000
214A214HIS00.0500.01629.442-0.012-0.0120.0000.0000.0000.000
215A215TRP00.0410.00727.586-0.010-0.0100.0000.0000.0000.000
216A216VAL00.0250.02226.745-0.015-0.0150.0000.0000.0000.000
217A217TYR0-0.061-0.05425.713-0.011-0.0110.0000.0000.0000.000
218A218TRP0-0.045-0.02722.629-0.013-0.0130.0000.0000.0000.000
219A219VAL00.001-0.00921.973-0.020-0.0200.0000.0000.0000.000
220A220GLY00.0350.01921.152-0.018-0.0180.0000.0000.0000.000
221A221PRO00.0210.00420.324-0.019-0.0190.0000.0000.0000.000
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