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: 5N2GZ

Calculation Name: 5A9B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5A9B

Chain ID: A

ChEMBL ID:

UniProt ID: P11041

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2368954.072176
FMO2-HF: Nuclear repulsion 2286143.580321
FMO2-HF: Total energy -82810.491855
FMO2-MP2: Total energy -83055.054396


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:SER)


Summations of interaction energy for fragment #1(A:8: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.
-16.34-8.8053.132-4.801-5.8650.032
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.098 / q_NPA : 0.052
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].
3A10ARG10.9790.9752.254-14.631-7.9163.123-4.642-5.1960.032
4A11ASP-1-0.822-0.9023.792-3.972-3.2190.010-0.154-0.6090.000
5A12PHE00.028-0.0095.151-0.068-0.001-0.001-0.005-0.0600.000
6A13ARG10.9670.9937.4730.7390.7390.0000.0000.0000.000
7A14GLY00.0580.0327.7490.0680.0680.0000.0000.0000.000
8A15ARG10.8100.8936.874-0.526-0.5260.0000.0000.0000.000
9A16GLU-1-0.834-0.9149.8940.0010.0010.0000.0000.0000.000
10A17GLN0-0.0070.00912.0500.0610.0610.0000.0000.0000.000
11A18ARG10.9350.9616.0251.8041.8040.0000.0000.0000.000
12A19LEU00.0040.01313.4790.0390.0390.0000.0000.0000.000
13A20PHE00.0350.03015.9490.0380.0380.0000.0000.0000.000
14A21ASN0-0.043-0.02816.1630.0490.0490.0000.0000.0000.000
15A22SER00.019-0.00916.4370.0300.0300.0000.0000.0000.000
16A23GLU-1-0.916-0.95519.179-0.080-0.0800.0000.0000.0000.000
17A24GLN0-0.0010.01321.6080.0070.0070.0000.0000.0000.000
18A25TYR0-0.038-0.00822.3040.0200.0200.0000.0000.0000.000
19A26ASN0-0.078-0.07021.6770.0250.0250.0000.0000.0000.000
20A27TYR00.0320.02524.9940.0130.0130.0000.0000.0000.000
21A28ASN00.0150.02527.3670.0160.0160.0000.0000.0000.000
22A29SER00.032-0.00328.1890.0090.0090.0000.0000.0000.000
23A30SER0-0.021-0.00529.2740.0090.0090.0000.0000.0000.000
24A31LEU0-0.031-0.03431.032-0.001-0.0010.0000.0000.0000.000
25A32ASN00.0020.01531.3840.0070.0070.0000.0000.0000.000
26A33GLY0-0.0070.01432.0580.0000.0000.0000.0000.0000.000
27A34GLU-1-0.880-0.94232.908-0.052-0.0520.0000.0000.0000.000
28A35VAL0-0.118-0.05434.163-0.005-0.0050.0000.0000.0000.000
29A36SER00.003-0.01435.7530.0030.0030.0000.0000.0000.000
30A37VAL0-0.044-0.02337.563-0.002-0.0020.0000.0000.0000.000
31A38TRP0-0.009-0.00934.2660.0010.0010.0000.0000.0000.000
32A39VAL0-0.029-0.02040.9420.0000.0000.0000.0000.0000.000
33A40TYR00.0410.01637.8030.0010.0010.0000.0000.0000.000
34A41ALA00.0210.00644.3810.0010.0010.0000.0000.0000.000
35A42TYR00.017-0.01741.7490.0010.0010.0000.0000.0000.000
36A43TYR0-0.010-0.03448.4520.0020.0020.0000.0000.0000.000
37A44SER00.007-0.00651.344-0.001-0.0010.0000.0000.0000.000
38A45ASP-1-0.830-0.87552.464-0.040-0.0400.0000.0000.0000.000
39A46GLY00.0100.01449.2650.0000.0000.0000.0000.0000.000
40A47SER0-0.072-0.05147.648-0.002-0.0020.0000.0000.0000.000
41A48VAL0-0.002-0.01443.8100.0000.0000.0000.0000.0000.000
42A49LEU0-0.031-0.00846.3400.0000.0000.0000.0000.0000.000
43A50VAL00.0130.00541.125-0.001-0.0010.0000.0000.0000.000
44A51ILE0-0.044-0.02144.5960.0020.0020.0000.0000.0000.000
45A52ASN0-0.001-0.00138.481-0.002-0.0020.0000.0000.0000.000
46A53LYS10.8840.94541.5870.0430.0430.0000.0000.0000.000
47A54ASN0-0.0070.01637.479-0.007-0.0070.0000.0000.0000.000
48A55SER00.0830.03839.0110.0040.0040.0000.0000.0000.000
49A56GLN00.0850.04837.206-0.002-0.0020.0000.0000.0000.000
50A57TYR00.0370.02538.4160.0010.0010.0000.0000.0000.000
51A58LYS10.8510.90040.1460.0330.0330.0000.0000.0000.000
52A59VAL00.0190.02440.0020.0010.0010.0000.0000.0000.000
53A60GLY00.0540.01442.8490.0000.0000.0000.0000.0000.000
54A61ILE0-0.041-0.00744.8200.0010.0010.0000.0000.0000.000
55A62SER00.0440.00947.5020.0000.0000.0000.0000.0000.000
56A63GLU-1-0.797-0.84849.012-0.037-0.0370.0000.0000.0000.000
57A64THR0-0.017-0.01452.2670.0010.0010.0000.0000.0000.000
58A65PHE0-0.0010.01248.4560.0000.0000.0000.0000.0000.000
59A66LYS10.9960.98354.1860.0290.0290.0000.0000.0000.000
60A67VAL00.0330.02956.533-0.001-0.0010.0000.0000.0000.000
61A68LEU0-0.026-0.00654.2190.0010.0010.0000.0000.0000.000
62A69LYS10.9460.98458.4340.0290.0290.0000.0000.0000.000
63A70GLU-1-0.880-0.92861.366-0.023-0.0230.0000.0000.0000.000
64A101GLY0-0.0060.00262.2150.0010.0010.0000.0000.0000.000
65A102SER0-0.037-0.02863.2300.0000.0000.0000.0000.0000.000
66A103GLY0-0.057-0.05559.5490.0000.0000.0000.0000.0000.000
67A104ALA00.0070.02155.1870.0000.0000.0000.0000.0000.000
68A105LYS10.9050.94556.5910.0330.0330.0000.0000.0000.000
69A106PRO00.0020.02152.885-0.001-0.0010.0000.0000.0000.000
70A107ARG10.8300.89451.7640.0390.0390.0000.0000.0000.000
71A108ALA00.0230.02848.1970.0000.0000.0000.0000.0000.000
72A109ILE00.0180.01246.4420.0000.0000.0000.0000.0000.000
73A110GLN00.0140.02439.449-0.003-0.0030.0000.0000.0000.000
74A111ILE0-0.047-0.01742.0040.0000.0000.0000.0000.0000.000
75A112ILE00.0040.00135.977-0.002-0.0020.0000.0000.0000.000
76A113PHE00.0040.00537.2730.0030.0030.0000.0000.0000.000
77A114SER00.0710.03432.850-0.004-0.0040.0000.0000.0000.000
78A115PRO00.0430.00829.0440.0060.0060.0000.0000.0000.000
79A116SER00.0080.00831.7660.0010.0010.0000.0000.0000.000
80A117VAL00.0050.02232.8880.0060.0060.0000.0000.0000.000
81A118ASN00.0170.00135.521-0.005-0.0050.0000.0000.0000.000
82A119VAL00.0660.02936.3110.0040.0040.0000.0000.0000.000
83A120ARG10.9410.96939.0130.0520.0520.0000.0000.0000.000
84A121THR0-0.077-0.04440.9780.0030.0030.0000.0000.0000.000
85A122ILE0-0.0150.00639.4600.0020.0020.0000.0000.0000.000
86A123LYS10.8480.94643.7410.0400.0400.0000.0000.0000.000
87A124MET0-0.026-0.01747.276-0.002-0.0020.0000.0000.0000.000
88A125ALA00.0610.04249.3840.0010.0010.0000.0000.0000.000
89A126LYS10.9280.95952.4690.0360.0360.0000.0000.0000.000
90A127GLY00.102-0.04354.4880.0010.0010.0000.0000.0000.000
91A128ASN00.002-0.02056.858-0.002-0.0020.0000.0000.0000.000
92A129ALA00.0830.02758.6310.0000.0000.0000.0000.0000.000
93A130VAL0-0.035-0.01360.121-0.001-0.0010.0000.0000.0000.000
94A131SER00.015-0.01461.9890.0010.0010.0000.0000.0000.000
95A132VAL0-0.049-0.01161.7620.0000.0000.0000.0000.0000.000
96A133PRO0-0.0980.06359.8710.0000.0000.0000.0000.0000.000
97A134ASP-1-0.886-0.91758.423-0.030-0.0300.0000.0000.0000.000
98A135GLU-1-0.867-0.91661.182-0.024-0.0240.0000.0000.0000.000
99A136TYR0-0.001-0.00164.5320.0010.0010.0000.0000.0000.000
100A137LEU00.0590.01563.2850.0000.0000.0000.0000.0000.000
101A138GLN0-0.023-0.01764.620-0.001-0.0010.0000.0000.0000.000
102A139ARG10.8420.91264.3700.0220.0220.0000.0000.0000.000
103A140SER00.0040.02360.3240.0000.0000.0000.0000.0000.000
104A141HIS00.0300.02254.0810.0020.0020.0000.0000.0000.000
105A142PRO0-0.028-0.02155.818-0.001-0.0010.0000.0000.0000.000
106A143TRP0-0.021-0.03150.675-0.002-0.0020.0000.0000.0000.000
107A144GLU-1-0.867-0.92451.071-0.033-0.0330.0000.0000.0000.000
108A145ALA0-0.017-0.01246.978-0.002-0.0020.0000.0000.0000.000
109A146THR00.007-0.00746.127-0.001-0.0010.0000.0000.0000.000
110A147GLY00.0430.01842.204-0.002-0.0020.0000.0000.0000.000
111A148ILE0-0.029-0.02341.320-0.003-0.0030.0000.0000.0000.000
112A149LYS10.9510.97442.4870.0420.0420.0000.0000.0000.000
113A150TYR0-0.028-0.00138.7290.0000.0000.0000.0000.0000.000
114A151ARG10.9150.95837.0280.0710.0710.0000.0000.0000.000
115A152LYS10.9230.95531.9450.0890.0890.0000.0000.0000.000
116A153ILE00.0440.03931.139-0.001-0.0010.0000.0000.0000.000
117A154LYS10.9200.94927.5430.1270.1270.0000.0000.0000.000
118A155ARG10.8760.93823.6760.1910.1910.0000.0000.0000.000
119A156ASP-1-0.806-0.89820.948-0.234-0.2340.0000.0000.0000.000
120A157GLY0-0.029-0.00822.024-0.011-0.0110.0000.0000.0000.000
121A158GLU-1-0.734-0.83222.147-0.196-0.1960.0000.0000.0000.000
122A159ILE0-0.092-0.06024.7750.0090.0090.0000.0000.0000.000
123A160VAL00.0600.02426.3610.0000.0000.0000.0000.0000.000
124A161GLY00.0280.00428.8550.0060.0060.0000.0000.0000.000
125A162TYR0-0.080-0.02632.584-0.003-0.0030.0000.0000.0000.000
126A163SER00.004-0.01635.8320.0040.0040.0000.0000.0000.000
127A164HIS00.0040.00538.612-0.001-0.0010.0000.0000.0000.000
128A165TYR0-0.045-0.03642.3050.0000.0000.0000.0000.0000.000
129A166PHE0-0.029-0.02344.3110.0020.0020.0000.0000.0000.000
130A167GLU-1-0.822-0.89548.076-0.047-0.0470.0000.0000.0000.000
131A168LEU0-0.057-0.03450.7210.0010.0010.0000.0000.0000.000
132A169PRO00.0510.04053.9710.0000.0000.0000.0000.0000.000
133A170HIS00.0340.01055.9330.0000.0000.0000.0000.0000.000
134A171GLU-1-0.905-0.96558.989-0.030-0.0300.0000.0000.0000.000
135A172TYR00.0060.01158.8050.0010.0010.0000.0000.0000.000
136A173ASN0-0.010-0.00759.183-0.001-0.0010.0000.0000.0000.000
137A174SER0-0.026-0.03457.1770.0000.0000.0000.0000.0000.000
138A175ILE00.0190.01652.1680.0000.0000.0000.0000.0000.000
139A176SER0-0.028-0.00954.758-0.001-0.0010.0000.0000.0000.000
140A177LEU0-0.005-0.00648.3220.0000.0000.0000.0000.0000.000
141A178ALA00.0240.00950.2600.0000.0000.0000.0000.0000.000
142A179VAL0-0.016-0.00244.8120.0000.0000.0000.0000.0000.000
143A180SER00.0210.00245.2710.0010.0010.0000.0000.0000.000
144A181GLY00.0020.00841.588-0.001-0.0010.0000.0000.0000.000
145A182VAL0-0.011-0.01240.7830.0010.0010.0000.0000.0000.000
146A183HIS10.8200.90433.0610.0590.0590.0000.0000.0000.000
147A184LYS10.8210.90230.1610.0940.0940.0000.0000.0000.000
148A185ASN0-0.004-0.01335.400-0.001-0.0010.0000.0000.0000.000
149A186PRO00.0060.01931.6350.0010.0010.0000.0000.0000.000
150A187SER00.003-0.00433.5920.0010.0010.0000.0000.0000.000
151A188SER00.0220.01635.734-0.001-0.0010.0000.0000.0000.000
152A189TYR0-0.017-0.02238.1090.0030.0030.0000.0000.0000.000
153A190ASN00.0110.00640.008-0.003-0.0030.0000.0000.0000.000
154A191VAL00.0570.03040.0950.0020.0020.0000.0000.0000.000
155A192GLY00.0170.01943.0100.0010.0010.0000.0000.0000.000
156A193SER0-0.032-0.02645.2040.0020.0020.0000.0000.0000.000
157A194ALA0-0.007-0.01447.8970.0000.0000.0000.0000.0000.000
158A195HIS00.0490.01744.8870.0000.0000.0000.0000.0000.000
159A196ASN00.0030.02142.755-0.001-0.0010.0000.0000.0000.000
160A197VAL00.0250.01845.618-0.002-0.0020.0000.0000.0000.000
161A198MET00.0320.01048.125-0.002-0.0020.0000.0000.0000.000
162A199ASP-1-0.843-0.91543.246-0.021-0.0210.0000.0000.0000.000
163A200VAL0-0.040-0.01543.702-0.003-0.0030.0000.0000.0000.000
164A201PHE0-0.0020.01345.509-0.002-0.0020.0000.0000.0000.000
165A202GLN00.0420.03145.9430.0000.0000.0000.0000.0000.000
166A203SER0-0.083-0.06042.541-0.002-0.0020.0000.0000.0000.000
167A204CYS0-0.109-0.06044.318-0.002-0.0020.0000.0000.0000.000
168A205ASP-1-0.892-0.94247.152-0.024-0.0240.0000.0000.0000.000
169A206LEU0-0.052-0.02642.598-0.001-0.0010.0000.0000.0000.000
170A207ALA0-0.0390.00342.649-0.003-0.0030.0000.0000.0000.000
171A208LEU00.0260.02639.8910.0010.0010.0000.0000.0000.000
172A209ARG10.7940.83942.5080.0350.0350.0000.0000.0000.000
173A210PHE0-0.007-0.00140.0730.0010.0010.0000.0000.0000.000
174A211CYS0-0.080-0.03644.1820.0000.0000.0000.0000.0000.000
175A212ASN00.0330.02342.5560.0020.0020.0000.0000.0000.000
176A213ARG10.8440.92245.5980.0410.0410.0000.0000.0000.000
177A214TYR00.0210.00541.3350.0000.0000.0000.0000.0000.000
178A215TRP00.013-0.01645.5690.0020.0020.0000.0000.0000.000
179A216ALA00.0240.01444.9460.0010.0010.0000.0000.0000.000
180A217GLU-1-0.732-0.84540.329-0.070-0.0700.0000.0000.0000.000
181A218LEU00.0150.01638.646-0.003-0.0030.0000.0000.0000.000
182A219GLU-1-0.821-0.90739.248-0.056-0.0560.0000.0000.0000.000
183A220LEU00.0000.00939.525-0.002-0.0020.0000.0000.0000.000
184A221VAL00.0410.00734.704-0.003-0.0030.0000.0000.0000.000
185A222ASN0-0.012-0.00635.173-0.010-0.0100.0000.0000.0000.000
186A223HIS0-0.001-0.00935.431-0.003-0.0030.0000.0000.0000.000
187A224TYR0-0.0030.00337.2930.0010.0010.0000.0000.0000.000
188A225ILE0-0.018-0.00533.133-0.003-0.0030.0000.0000.0000.000
189A226SER0-0.013-0.02330.926-0.007-0.0070.0000.0000.0000.000
190A227PRO0-0.049-0.00930.311-0.009-0.0090.0000.0000.0000.000
191A228ASN0-0.064-0.03530.788-0.001-0.0010.0000.0000.0000.000
192A229ALA0-0.027-0.00127.527-0.002-0.0020.0000.0000.0000.000
193A230TYR0-0.0010.00229.534-0.001-0.0010.0000.0000.0000.000
194A231PRO0-0.042-0.01831.184-0.004-0.0040.0000.0000.0000.000
195A232TYR0-0.045-0.06232.3710.0090.0090.0000.0000.0000.000
196A233LEU0-0.018-0.00934.020-0.007-0.0070.0000.0000.0000.000
197A234ASP-1-0.773-0.85536.567-0.081-0.0810.0000.0000.0000.000
198A235ILE00.006-0.00638.6430.0000.0000.0000.0000.0000.000
199A236ASN0-0.077-0.02938.4740.0050.0050.0000.0000.0000.000
200A237ASN0-0.036-0.01436.8490.0000.0000.0000.0000.0000.000
201A238HIS00.0170.01332.959-0.009-0.0090.0000.0000.0000.000
202A239SER0-0.028-0.01830.6720.0030.0030.0000.0000.0000.000
203A240TYR0-0.055-0.04630.243-0.009-0.0090.0000.0000.0000.000
204A241GLY00.0590.01828.7670.0050.0050.0000.0000.0000.000
205A242VAL0-0.037-0.03022.985-0.008-0.0080.0000.0000.0000.000
206A243ALA0-0.0160.01321.4530.0100.0100.0000.0000.0000.000
207A244LEU0-0.028-0.02020.370-0.018-0.0180.0000.0000.0000.000
208A245SER0-0.154-0.10119.220-0.019-0.0190.0000.0000.0000.000
209A246ASN00.0100.00915.269-0.016-0.0160.0000.0000.0000.000