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

tag_button

FMODB ID: 4L9GN

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2369587.406325
FMO2-HF: Nuclear repulsion 2286778.197181
FMO2-HF: Total energy -82809.209144
FMO2-MP2: Total energy -83053.855099


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.
-17.918-13.0887.727-5.621-6.9350.043
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 : 0.055
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].
3A10ARG10.9450.9532.009-15.187-11.2177.705-5.522-6.1530.042
4A11ASP-1-0.858-0.9143.665-4.507-3.7140.023-0.093-0.7230.001
5A12PHE00.047-0.0115.230-0.190-0.123-0.001-0.006-0.0590.000
6A13ARG11.0261.0338.6510.3840.3840.0000.0000.0000.000
7A14GLY00.0230.0087.7000.0290.0290.0000.0000.0000.000
8A15ARG10.8290.9137.178-0.352-0.3520.0000.0000.0000.000
9A16GLU-1-0.845-0.9249.8470.0320.0320.0000.0000.0000.000
10A17GLN0-0.0210.00512.0070.0470.0470.0000.0000.0000.000
11A18ARG10.9260.9516.3651.6381.6380.0000.0000.0000.000
12A19LEU0-0.013-0.00213.4300.0290.0290.0000.0000.0000.000
13A20PHE00.0490.04415.8980.0360.0360.0000.0000.0000.000
14A21ASN00.0210.01116.4280.0500.0500.0000.0000.0000.000
15A22SER00.005-0.01516.5440.0250.0250.0000.0000.0000.000
16A23GLU-1-0.910-0.95419.210-0.088-0.0880.0000.0000.0000.000
17A24GLN0-0.0010.01221.6070.0070.0070.0000.0000.0000.000
18A25TYR0-0.036-0.00722.2940.0180.0180.0000.0000.0000.000
19A26ASN0-0.078-0.07221.5970.0230.0230.0000.0000.0000.000
20A27TYR00.0400.02925.0280.0130.0130.0000.0000.0000.000
21A28ASN00.0440.03627.4060.0170.0170.0000.0000.0000.000
22A29SER0-0.017-0.01928.2700.0090.0090.0000.0000.0000.000
23A30SER0-0.030-0.01529.3240.0080.0080.0000.0000.0000.000
24A31LEU0-0.034-0.04131.066-0.001-0.0010.0000.0000.0000.000
25A32ASN0-0.0030.01131.7650.0070.0070.0000.0000.0000.000
26A33GLY0-0.0130.01732.0990.0010.0010.0000.0000.0000.000
27A34GLU-1-0.887-0.94832.942-0.052-0.0520.0000.0000.0000.000
28A35VAL0-0.089-0.03234.199-0.006-0.0060.0000.0000.0000.000
29A36SER0-0.005-0.04035.7860.0030.0030.0000.0000.0000.000
30A37VAL0-0.044-0.01837.599-0.003-0.0030.0000.0000.0000.000
31A38TRP0-0.002-0.00434.3150.0010.0010.0000.0000.0000.000
32A39VAL0-0.025-0.02040.9770.0000.0000.0000.0000.0000.000
33A40TYR00.0220.00738.2070.0010.0010.0000.0000.0000.000
34A41ALA00.0250.00944.4140.0000.0000.0000.0000.0000.000
35A42TYR00.019-0.00941.8030.0010.0010.0000.0000.0000.000
36A43TYR0-0.003-0.02048.4830.0020.0020.0000.0000.0000.000
37A44SER00.003-0.00951.374-0.001-0.0010.0000.0000.0000.000
38A45ASP-1-0.849-0.91152.395-0.038-0.0380.0000.0000.0000.000
39A46GLY00.0110.01549.2950.0000.0000.0000.0000.0000.000
40A47SER0-0.072-0.02947.679-0.002-0.0020.0000.0000.0000.000
41A48VAL00.005-0.01143.7280.0000.0000.0000.0000.0000.000
42A49LEU0-0.027-0.00846.3030.0000.0000.0000.0000.0000.000
43A50VAL00.0110.00241.173-0.001-0.0010.0000.0000.0000.000
44A51ILE0-0.052-0.02444.6040.0020.0020.0000.0000.0000.000
45A52ASN0-0.012-0.00538.496-0.002-0.0020.0000.0000.0000.000
46A53LYS10.8900.96141.5960.0430.0430.0000.0000.0000.000
47A54ASN00.0090.03237.451-0.007-0.0070.0000.0000.0000.000
48A55SER00.0740.02939.0350.0040.0040.0000.0000.0000.000
49A56GLN00.1030.06336.976-0.002-0.0020.0000.0000.0000.000
50A57TYR00.0310.02438.4550.0010.0010.0000.0000.0000.000
51A58LYS10.8840.92640.1810.0350.0350.0000.0000.0000.000
52A59VAL00.0300.02440.1070.0020.0020.0000.0000.0000.000
53A60GLY00.025-0.00142.884-0.001-0.0010.0000.0000.0000.000
54A61ILE0-0.035-0.01344.8990.0010.0010.0000.0000.0000.000
55A62SER00.006-0.00647.5370.0000.0000.0000.0000.0000.000
56A63GLU-1-0.763-0.85949.004-0.037-0.0370.0000.0000.0000.000
57A64THR0-0.004-0.00852.3030.0010.0010.0000.0000.0000.000
58A65PHE0-0.0120.00448.4090.0000.0000.0000.0000.0000.000
59A66LYS10.9930.97954.2200.0280.0280.0000.0000.0000.000
60A67VAL00.0160.02956.567-0.001-0.0010.0000.0000.0000.000
61A68LEU0-0.040-0.01154.3290.0010.0010.0000.0000.0000.000
62A69LYS10.9770.99658.4140.0280.0280.0000.0000.0000.000
63A70GLU-1-0.892-0.90361.324-0.021-0.0210.0000.0000.0000.000
64A101GLY00.003-0.00362.2140.0010.0010.0000.0000.0000.000
65A102SER0-0.032-0.05863.2190.0000.0000.0000.0000.0000.000
66A103GLY0-0.081-0.06259.5260.0000.0000.0000.0000.0000.000
67A104ALA00.0200.02455.2550.0000.0000.0000.0000.0000.000
68A105LYS10.9490.97256.6180.0330.0330.0000.0000.0000.000
69A106PRO0-0.0050.01952.889-0.001-0.0010.0000.0000.0000.000
70A107ARG10.8380.90751.7800.0400.0400.0000.0000.0000.000
71A108ALA00.0180.02448.1950.0000.0000.0000.0000.0000.000
72A109ILE00.0220.01646.4870.0000.0000.0000.0000.0000.000
73A110GLN00.0220.02439.181-0.005-0.0050.0000.0000.0000.000
74A111ILE0-0.048-0.01242.0230.0000.0000.0000.0000.0000.000
75A112ILE00.0020.00236.043-0.002-0.0020.0000.0000.0000.000
76A113PHE00.0110.00537.2880.0030.0030.0000.0000.0000.000
77A114SER00.0690.03132.797-0.004-0.0040.0000.0000.0000.000
78A115PRO00.012-0.00929.0810.0060.0060.0000.0000.0000.000
79A116SER0-0.035-0.02131.7970.0000.0000.0000.0000.0000.000
80A117VAL00.0040.02032.9200.0060.0060.0000.0000.0000.000
81A118ASN00.0150.00235.550-0.006-0.0060.0000.0000.0000.000
82A119VAL00.0660.03636.4070.0050.0050.0000.0000.0000.000
83A120ARG10.9450.96739.0390.0610.0610.0000.0000.0000.000
84A121THR0-0.085-0.05041.0010.0030.0030.0000.0000.0000.000
85A122ILE0-0.0120.00639.5920.0020.0020.0000.0000.0000.000
86A123LYS10.8600.94743.7690.0430.0430.0000.0000.0000.000
87A124MET0-0.030-0.01847.306-0.002-0.0020.0000.0000.0000.000
88A125ALA00.0610.04349.4140.0010.0010.0000.0000.0000.000
89A126LYS10.9350.96151.9050.0390.0390.0000.0000.0000.000
90A127GLY00.154-0.28254.5190.0010.0010.0000.0000.0000.000
91A128ASN00.069-0.00156.923-0.002-0.0020.0000.0000.0000.000
92A129ALA00.0470.02958.6610.0000.0000.0000.0000.0000.000
93A130VAL0-0.044-0.01960.154-0.001-0.0010.0000.0000.0000.000
94A131SER00.030-0.02062.0220.0010.0010.0000.0000.0000.000
95A132VAL0-0.054-0.00961.8580.0000.0000.0000.0000.0000.000
96A133PRO0-0.1820.30559.7130.0000.0000.0000.0000.0000.000
97A134ASP-1-0.921-0.95258.266-0.031-0.0310.0000.0000.0000.000
98A135GLU-1-0.891-0.93761.210-0.026-0.0260.0000.0000.0000.000
99A136TYR0-0.002-0.00464.5600.0010.0010.0000.0000.0000.000
100A137LEU00.0360.01263.1860.0000.0000.0000.0000.0000.000
101A138GLN0-0.008-0.01064.649-0.001-0.0010.0000.0000.0000.000
102A139ARG10.8970.95464.2830.0240.0240.0000.0000.0000.000
103A140SER00.0060.01260.423-0.001-0.0010.0000.0000.0000.000
104A141HIS00.0410.02754.0920.0020.0020.0000.0000.0000.000
105A142PRO0-0.031-0.02055.663-0.001-0.0010.0000.0000.0000.000
106A143TRP0-0.040-0.04050.398-0.002-0.0020.0000.0000.0000.000
107A144GLU-1-0.857-0.91851.197-0.036-0.0360.0000.0000.0000.000
108A145ALA0-0.010-0.01146.958-0.002-0.0020.0000.0000.0000.000
109A146THR0-0.013-0.01346.002-0.001-0.0010.0000.0000.0000.000
110A147GLY00.0540.02342.234-0.002-0.0020.0000.0000.0000.000
111A148ILE0-0.021-0.01841.344-0.004-0.0040.0000.0000.0000.000
112A149LYS10.9420.96942.5070.0460.0460.0000.0000.0000.000
113A150TYR0-0.041-0.00638.7870.0000.0000.0000.0000.0000.000
114A151ARG10.9350.96936.9230.0730.0730.0000.0000.0000.000
115A152LYS10.9180.95131.7400.1010.1010.0000.0000.0000.000
116A153ILE00.0420.03331.161-0.001-0.0010.0000.0000.0000.000
117A154LYS10.9300.95327.5950.1260.1260.0000.0000.0000.000
118A155ARG10.9180.96325.1040.1690.1690.0000.0000.0000.000
119A156ASP-1-0.850-0.91720.861-0.250-0.2500.0000.0000.0000.000
120A157GLY0-0.051-0.02222.044-0.012-0.0120.0000.0000.0000.000
121A158GLU-1-0.753-0.85222.112-0.205-0.2050.0000.0000.0000.000
122A159ILE0-0.104-0.06424.7990.0110.0110.0000.0000.0000.000
123A160VAL00.0560.02226.4320.0000.0000.0000.0000.0000.000
124A161GLY00.0270.00328.8850.0070.0070.0000.0000.0000.000
125A162TYR0-0.075-0.02532.613-0.004-0.0040.0000.0000.0000.000
126A163SER00.010-0.01235.8590.0040.0040.0000.0000.0000.000
127A164HIS00.0140.01238.639-0.001-0.0010.0000.0000.0000.000
128A165TYR00.0050.00442.3320.0010.0010.0000.0000.0000.000
129A166PHE0-0.030-0.02444.3380.0010.0010.0000.0000.0000.000
130A167GLU-1-0.879-0.94348.102-0.047-0.0470.0000.0000.0000.000
131A168LEU0-0.067-0.03850.7470.0010.0010.0000.0000.0000.000
132A169PRO00.0500.02953.9980.0000.0000.0000.0000.0000.000
133A170HIS00.0120.00356.2730.0010.0010.0000.0000.0000.000
134A171GLU-1-0.901-0.95159.015-0.031-0.0310.0000.0000.0000.000
135A172TYR00.0090.01058.8050.0010.0010.0000.0000.0000.000
136A173ASN0-0.022-0.02459.213-0.001-0.0010.0000.0000.0000.000
137A174SER0-0.050-0.05057.2050.0000.0000.0000.0000.0000.000
138A175ILE00.0260.01852.4030.0000.0000.0000.0000.0000.000
139A176SER0-0.0170.00454.7910.0000.0000.0000.0000.0000.000
140A177LEU0-0.009-0.00948.5140.0000.0000.0000.0000.0000.000
141A178ALA00.0350.01750.3100.0000.0000.0000.0000.0000.000
142A179VAL0-0.012-0.00144.686-0.001-0.0010.0000.0000.0000.000
143A180SER0-0.027-0.01845.2990.0000.0000.0000.0000.0000.000
144A181GLY00.0480.02641.621-0.001-0.0010.0000.0000.0000.000
145A182VAL0-0.003-0.00740.6980.0010.0010.0000.0000.0000.000
146A183HIS10.8110.90533.0610.0630.0630.0000.0000.0000.000
147A184LYS10.9160.95330.1880.1000.1000.0000.0000.0000.000
148A185ASN0-0.010-0.01235.430-0.001-0.0010.0000.0000.0000.000
149A186PRO00.0010.02031.6920.0000.0000.0000.0000.0000.000
150A187SER00.011-0.00133.6190.0010.0010.0000.0000.0000.000
151A188SER00.0140.01135.760-0.001-0.0010.0000.0000.0000.000
152A189TYR0-0.031-0.04938.1420.0030.0030.0000.0000.0000.000
153A190ASN00.004-0.00440.023-0.002-0.0020.0000.0000.0000.000
154A191VAL00.0440.00740.1810.0020.0020.0000.0000.0000.000
155A192GLY00.0210.01843.0410.0010.0010.0000.0000.0000.000
156A193SER0-0.027-0.00845.3400.0020.0020.0000.0000.0000.000
157A194ALA00.010-0.00447.9100.0000.0000.0000.0000.0000.000
158A195HIS00.0560.02145.1220.0010.0010.0000.0000.0000.000
159A196ASN0-0.0010.04143.1210.0000.0000.0000.0000.0000.000
160A197VAL00.0390.02645.652-0.002-0.0020.0000.0000.0000.000
161A198MET00.0190.00448.159-0.001-0.0010.0000.0000.0000.000
162A199ASP-1-0.841-0.91343.252-0.023-0.0230.0000.0000.0000.000
163A200VAL0-0.038-0.01143.806-0.002-0.0020.0000.0000.0000.000
164A201PHE0-0.0090.01145.545-0.001-0.0010.0000.0000.0000.000
165A202GLN00.0470.02845.8730.0000.0000.0000.0000.0000.000
166A203SER0-0.081-0.06342.583-0.002-0.0020.0000.0000.0000.000
167A204CYS0-0.112-0.07244.279-0.002-0.0020.0000.0000.0000.000
168A205ASP-1-0.903-0.94147.137-0.024-0.0240.0000.0000.0000.000
169A206LEU0-0.051-0.02742.4930.0000.0000.0000.0000.0000.000
170A207ALA0-0.060-0.01042.597-0.002-0.0020.0000.0000.0000.000
171A208LEU00.0340.03440.0860.0020.0020.0000.0000.0000.000
172A209ARG10.8110.86842.4600.0340.0340.0000.0000.0000.000
173A210PHE0-0.009-0.00140.2110.0010.0010.0000.0000.0000.000
174A211CYS0-0.070-0.03444.137-0.001-0.0010.0000.0000.0000.000
175A212ASN00.0280.02642.2620.0030.0030.0000.0000.0000.000
176A213ARG10.8780.94145.5560.0380.0380.0000.0000.0000.000
177A214TYR00.0170.00741.1610.0000.0000.0000.0000.0000.000
178A215TRP00.011-0.01345.5300.0010.0010.0000.0000.0000.000
179A216ALA00.0210.01244.9280.0010.0010.0000.0000.0000.000
180A217GLU-1-0.733-0.83040.326-0.069-0.0690.0000.0000.0000.000
181A218LEU00.0180.01938.555-0.003-0.0030.0000.0000.0000.000
182A219GLU-1-0.829-0.90739.212-0.052-0.0520.0000.0000.0000.000
183A220LEU0-0.0120.00139.511-0.002-0.0020.0000.0000.0000.000
184A221VAL00.0330.00434.713-0.003-0.0030.0000.0000.0000.000
185A222ASN0-0.003-0.01835.135-0.009-0.0090.0000.0000.0000.000
186A223HIS00.000-0.00735.397-0.001-0.0010.0000.0000.0000.000
187A224TYR00.0000.00537.2730.0010.0010.0000.0000.0000.000
188A225ILE0-0.024-0.00733.183-0.002-0.0020.0000.0000.0000.000
189A226SER0-0.013-0.01130.991-0.008-0.0080.0000.0000.0000.000
190A227PRO0-0.046-0.00730.271-0.008-0.0080.0000.0000.0000.000
191A228ASN0-0.052-0.02730.749-0.001-0.0010.0000.0000.0000.000
192A229ALA0-0.0230.00227.532-0.003-0.0030.0000.0000.0000.000
193A230TYR00.0000.00229.490-0.002-0.0020.0000.0000.0000.000
194A231PRO0-0.049-0.02131.287-0.004-0.0040.0000.0000.0000.000
195A232TYR0-0.048-0.07832.4030.0090.0090.0000.0000.0000.000
196A233LEU0-0.019-0.00934.048-0.007-0.0070.0000.0000.0000.000
197A234ASP-1-0.774-0.85036.594-0.080-0.0800.0000.0000.0000.000
198A235ILE00.004-0.01338.6700.0000.0000.0000.0000.0000.000
199A236ASN0-0.063-0.02538.6670.0040.0040.0000.0000.0000.000
200A237ASN0-0.044-0.02436.993-0.002-0.0020.0000.0000.0000.000
201A238HIS00.0050.00532.454-0.009-0.0090.0000.0000.0000.000
202A239SER0-0.044-0.02430.6440.0030.0030.0000.0000.0000.000
203A240TYR0-0.059-0.04630.288-0.008-0.0080.0000.0000.0000.000
204A241GLY00.0530.01328.7990.0040.0040.0000.0000.0000.000
205A242VAL0-0.018-0.01823.007-0.007-0.0070.0000.0000.0000.000
206A243ALA0-0.0090.01821.5100.0110.0110.0000.0000.0000.000
207A244LEU0-0.029-0.02120.403-0.016-0.0160.0000.0000.0000.000
208A245SER0-0.139-0.08519.254-0.016-0.0160.0000.0000.0000.000
209A246ASN00.0180.01214.5210.0140.0140.0000.0000.0000.000