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: YNZR2

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2369798.328467
FMO2-HF: Nuclear repulsion 2286987.030909
FMO2-HF: Total energy -82811.297558
FMO2-MP2: Total energy -83055.829216


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.
-16.237-10.7273.702-3.948-5.2640.03
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 : 0.101 / q_NPA : 0.054
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].
3A10ARG10.9970.9922.171-14.750-10.1013.685-3.728-4.6060.029
4A11ASP-1-0.796-0.8703.534-3.443-2.6480.018-0.215-0.5980.001
5A12PHE00.0410.0015.301-0.123-0.057-0.001-0.005-0.0600.000
6A13ARG10.9130.9557.2990.6860.6860.0000.0000.0000.000
7A14GLY00.0820.0378.2390.0900.0900.0000.0000.0000.000
8A15ARG10.7660.8976.819-0.553-0.5530.0000.0000.0000.000
9A16GLU-1-0.823-0.91710.186-0.006-0.0060.0000.0000.0000.000
10A17GLN0-0.0070.00512.1990.0500.0500.0000.0000.0000.000
11A18ARG10.9130.9406.0421.6561.6560.0000.0000.0000.000
12A19LEU0-0.0150.02213.5760.0410.0410.0000.0000.0000.000
13A20PHE00.0670.03216.0220.0270.0270.0000.0000.0000.000
14A21ASN0-0.023-0.01916.5000.0440.0440.0000.0000.0000.000
15A22SER00.008-0.02016.5080.0230.0230.0000.0000.0000.000
16A23GLU-1-0.926-0.96219.263-0.075-0.0750.0000.0000.0000.000
17A24GLN00.0130.01521.7380.0060.0060.0000.0000.0000.000
18A25TYR0-0.0270.00022.4800.0180.0180.0000.0000.0000.000
19A26ASN0-0.059-0.05721.8160.0240.0240.0000.0000.0000.000
20A27TYR00.0150.00725.0830.0120.0120.0000.0000.0000.000
21A28ASN00.0060.01327.3600.0100.0100.0000.0000.0000.000
22A29SER00.017-0.00627.6970.0080.0080.0000.0000.0000.000
23A30SER0-0.059-0.02329.1110.0090.0090.0000.0000.0000.000
24A31LEU0-0.013-0.02630.870-0.001-0.0010.0000.0000.0000.000
25A32ASN00.0030.01731.0490.0060.0060.0000.0000.0000.000
26A33GLY00.0250.03431.8190.0000.0000.0000.0000.0000.000
27A34GLU-1-0.855-0.93732.775-0.047-0.0470.0000.0000.0000.000
28A35VAL0-0.128-0.03833.977-0.005-0.0050.0000.0000.0000.000
29A36SER0-0.001-0.02435.4670.0030.0030.0000.0000.0000.000
30A37VAL0-0.037-0.01737.333-0.002-0.0020.0000.0000.0000.000
31A38TRP0-0.001-0.00134.2520.0000.0000.0000.0000.0000.000
32A39VAL0-0.024-0.01840.9020.0000.0000.0000.0000.0000.000
33A40TYR00.0580.03037.4040.0010.0010.0000.0000.0000.000
34A41ALA00.006-0.00343.9610.0010.0010.0000.0000.0000.000
35A42TYR00.0150.00341.5400.0010.0010.0000.0000.0000.000
36A43TYR0-0.028-0.04748.1140.0020.0020.0000.0000.0000.000
37A44SER00.014-0.00351.167-0.001-0.0010.0000.0000.0000.000
38A45ASP-1-0.823-0.86351.996-0.036-0.0360.0000.0000.0000.000
39A46GLY00.0170.01849.1860.0000.0000.0000.0000.0000.000
40A47SER0-0.090-0.05947.337-0.002-0.0020.0000.0000.0000.000
41A48VAL0-0.001-0.01543.4030.0000.0000.0000.0000.0000.000
42A49LEU0-0.030-0.00245.9960.0000.0000.0000.0000.0000.000
43A50VAL00.014-0.00241.134-0.001-0.0010.0000.0000.0000.000
44A51ILE0-0.029-0.00644.6030.0020.0020.0000.0000.0000.000
45A52ASN00.010-0.00638.410-0.002-0.0020.0000.0000.0000.000
46A53LYS10.8520.93241.2560.0390.0390.0000.0000.0000.000
47A54ASN0-0.0020.01837.457-0.007-0.0070.0000.0000.0000.000
48A55SER00.0760.02538.7900.0040.0040.0000.0000.0000.000
49A56GLN00.0760.04837.005-0.001-0.0010.0000.0000.0000.000
50A57TYR00.0470.02338.3030.0010.0010.0000.0000.0000.000
51A58LYS10.8290.90239.9170.0320.0320.0000.0000.0000.000
52A59VAL00.0070.02539.6970.0020.0020.0000.0000.0000.000
53A60GLY00.0670.01842.5710.0000.0000.0000.0000.0000.000
54A61ILE0-0.040-0.00944.2040.0010.0010.0000.0000.0000.000
55A62SER00.0430.00147.2870.0010.0010.0000.0000.0000.000
56A63GLU-1-0.796-0.84249.015-0.033-0.0330.0000.0000.0000.000
57A64THR0-0.042-0.03852.3520.0010.0010.0000.0000.0000.000
58A65PHE00.0350.03748.1460.0000.0000.0000.0000.0000.000
59A66LYS10.9610.96653.8880.0270.0270.0000.0000.0000.000
60A67VAL00.0150.02456.287-0.001-0.0010.0000.0000.0000.000
61A68LEU0-0.0070.01453.9570.0010.0010.0000.0000.0000.000
62A69LYS10.8820.91258.1080.0260.0260.0000.0000.0000.000
63A70GLU-1-0.879-0.92961.244-0.021-0.0210.0000.0000.0000.000
64A101GLY00.0020.01062.1760.0010.0010.0000.0000.0000.000
65A102SER0-0.026-0.01163.4150.0000.0000.0000.0000.0000.000
66A103GLY00.002-0.00859.4780.0000.0000.0000.0000.0000.000
67A104ALA00.0110.02354.8540.0000.0000.0000.0000.0000.000
68A105LYS10.8950.93456.6400.0290.0290.0000.0000.0000.000
69A106PRO00.0130.01952.813-0.001-0.0010.0000.0000.0000.000
70A107ARG10.8070.88451.4630.0350.0350.0000.0000.0000.000
71A108ALA00.0310.03547.8680.0000.0000.0000.0000.0000.000
72A109ILE0-0.006-0.00246.2230.0000.0000.0000.0000.0000.000
73A110GLN00.0180.01539.312-0.003-0.0030.0000.0000.0000.000
74A111ILE0-0.051-0.01341.9200.0000.0000.0000.0000.0000.000
75A112ILE0-0.0070.00035.943-0.002-0.0020.0000.0000.0000.000
76A113PHE0-0.001-0.00836.9770.0030.0030.0000.0000.0000.000
77A114SER00.0580.02232.723-0.004-0.0040.0000.0000.0000.000
78A115PRO00.0320.01228.6770.0050.0050.0000.0000.0000.000
79A116SER00.0110.00931.2520.0000.0000.0000.0000.0000.000
80A117VAL00.0060.02032.5540.0060.0060.0000.0000.0000.000
81A118ASN00.007-0.00435.092-0.005-0.0050.0000.0000.0000.000
82A119VAL00.0670.03136.1110.0040.0040.0000.0000.0000.000
83A120ARG10.9300.96638.7620.0450.0450.0000.0000.0000.000
84A121THR0-0.059-0.03740.7590.0030.0030.0000.0000.0000.000
85A122ILE0-0.0210.00639.1810.0020.0020.0000.0000.0000.000
86A123LYS10.8490.94043.5300.0350.0350.0000.0000.0000.000
87A124MET0-0.017-0.00347.232-0.002-0.0020.0000.0000.0000.000
88A125ALA00.0520.03049.0570.0010.0010.0000.0000.0000.000
89A126LYS10.8310.90152.5190.0290.0290.0000.0000.0000.000
90A127GLY00.0840.03354.4360.0010.0010.0000.0000.0000.000
91A128ASN0-0.0290.00956.787-0.002-0.0020.0000.0000.0000.000
92A129ALA00.0580.02458.2630.0000.0000.0000.0000.0000.000
93A130VAL0-0.018-0.00159.8810.0000.0000.0000.0000.0000.000
94A131SER00.007-0.00561.3550.0010.0010.0000.0000.0000.000
95A132VAL0-0.025-0.00961.3270.0000.0000.0000.0000.0000.000
96A133PRO00.0250.03460.2140.0000.0000.0000.0000.0000.000
97A134ASP-1-0.821-0.91057.373-0.027-0.0270.0000.0000.0000.000
98A135GLU-1-0.886-0.93660.715-0.021-0.0210.0000.0000.0000.000
99A136TYR00.0270.01464.0930.0000.0000.0000.0000.0000.000
100A137LEU00.0450.01862.8930.0000.0000.0000.0000.0000.000
101A138GLN0-0.011-0.00764.578-0.001-0.0010.0000.0000.0000.000
102A139ARG10.8240.89864.1260.0190.0190.0000.0000.0000.000
103A140SER0-0.030-0.00960.1230.0000.0000.0000.0000.0000.000
104A141HIS00.0370.02953.7590.0010.0010.0000.0000.0000.000
105A142PRO0-0.025-0.01555.975-0.001-0.0010.0000.0000.0000.000
106A143TRP0-0.018-0.02750.747-0.001-0.0010.0000.0000.0000.000
107A144GLU-1-0.844-0.92750.886-0.030-0.0300.0000.0000.0000.000
108A145ALA0-0.018-0.00147.294-0.002-0.0020.0000.0000.0000.000
109A146THR0-0.013-0.02645.602-0.001-0.0010.0000.0000.0000.000
110A147GLY00.0440.02942.015-0.002-0.0020.0000.0000.0000.000
111A148ILE0-0.031-0.02841.190-0.003-0.0030.0000.0000.0000.000
112A149LYS10.9570.97842.2820.0370.0370.0000.0000.0000.000
113A150TYR0-0.030-0.00738.3650.0000.0000.0000.0000.0000.000
114A151ARG10.8960.95036.9320.0620.0620.0000.0000.0000.000
115A152LYS10.9310.95531.7410.0750.0750.0000.0000.0000.000
116A153ILE00.0470.04030.809-0.001-0.0010.0000.0000.0000.000
117A154LYS10.8500.90426.5060.1190.1190.0000.0000.0000.000
118A155ARG10.8640.91523.2120.1750.1750.0000.0000.0000.000
119A156ASP-1-0.834-0.89720.819-0.206-0.2060.0000.0000.0000.000
120A157GLY00.0380.02921.400-0.013-0.0130.0000.0000.0000.000
121A158GLU-1-0.723-0.82422.202-0.165-0.1650.0000.0000.0000.000
122A159ILE0-0.054-0.03724.3380.0090.0090.0000.0000.0000.000
123A160VAL00.0600.02525.8770.0000.0000.0000.0000.0000.000
124A161GLY00.0200.00428.3690.0040.0040.0000.0000.0000.000
125A162TYR0-0.083-0.02832.179-0.002-0.0020.0000.0000.0000.000
126A163SER00.037-0.00635.4650.0030.0030.0000.0000.0000.000
127A164HIS00.0030.01038.2700.0000.0000.0000.0000.0000.000
128A165TYR0-0.041-0.05041.979-0.001-0.0010.0000.0000.0000.000
129A166PHE0-0.035-0.02544.2070.0010.0010.0000.0000.0000.000
130A167GLU-1-0.812-0.88147.997-0.041-0.0410.0000.0000.0000.000
131A168LEU0-0.046-0.02050.7270.0010.0010.0000.0000.0000.000
132A169PRO00.0440.02653.9930.0000.0000.0000.0000.0000.000
133A170HIS00.0350.01055.4300.0000.0000.0000.0000.0000.000
134A171GLU-1-0.860-0.94358.865-0.026-0.0260.0000.0000.0000.000
135A172TYR0-0.0120.01558.6640.0010.0010.0000.0000.0000.000
136A173ASN00.0030.00359.225-0.001-0.0010.0000.0000.0000.000
137A174SER0-0.029-0.04357.0840.0000.0000.0000.0000.0000.000
138A175ILE0-0.022-0.00452.1870.0000.0000.0000.0000.0000.000
139A176SER0-0.015-0.00754.496-0.001-0.0010.0000.0000.0000.000
140A177LEU0-0.021-0.02048.2770.0000.0000.0000.0000.0000.000
141A178ALA00.0230.01650.0340.0000.0000.0000.0000.0000.000
142A179VAL0-0.016-0.01144.6470.0000.0000.0000.0000.0000.000
143A180SER00.0320.01445.0120.0000.0000.0000.0000.0000.000
144A181GLY0-0.0100.00041.6660.0000.0000.0000.0000.0000.000
145A182VAL0-0.008-0.00440.4320.0010.0010.0000.0000.0000.000
146A183HIS10.8330.91732.6910.0540.0540.0000.0000.0000.000
147A184LYS10.8000.88629.4320.0860.0860.0000.0000.0000.000
148A185ASN00.0490.01935.060-0.001-0.0010.0000.0000.0000.000
149A186PRO0-0.0040.00831.4330.0000.0000.0000.0000.0000.000
150A187SER0-0.012-0.01433.2190.0030.0030.0000.0000.0000.000
151A188SER00.0040.00735.909-0.001-0.0010.0000.0000.0000.000
152A189TYR00.001-0.01137.9960.0020.0020.0000.0000.0000.000
153A190ASN00.0080.00139.919-0.002-0.0020.0000.0000.0000.000
154A191VAL00.0430.02340.0400.0020.0020.0000.0000.0000.000
155A192GLY00.0240.01843.0210.0000.0000.0000.0000.0000.000
156A193SER0-0.041-0.03145.1850.0020.0020.0000.0000.0000.000
157A194ALA00.003-0.01147.8310.0000.0000.0000.0000.0000.000
158A195HIS00.0440.03644.8700.0000.0000.0000.0000.0000.000
159A196ASN00.0240.01842.553-0.001-0.0010.0000.0000.0000.000
160A197VAL00.0160.01545.380-0.002-0.0020.0000.0000.0000.000
161A198MET00.0190.01247.806-0.001-0.0010.0000.0000.0000.000
162A199ASP-1-0.845-0.92142.843-0.020-0.0200.0000.0000.0000.000
163A200VAL0-0.053-0.02343.597-0.002-0.0020.0000.0000.0000.000
164A201PHE00.0040.01145.351-0.002-0.0020.0000.0000.0000.000
165A202GLN00.0060.00445.7080.0000.0000.0000.0000.0000.000
166A203SER0-0.081-0.05942.396-0.002-0.0020.0000.0000.0000.000
167A204CYS0-0.118-0.06944.069-0.002-0.0020.0000.0000.0000.000
168A205ASP-1-0.843-0.91447.031-0.022-0.0220.0000.0000.0000.000
169A206LEU0-0.030-0.01042.5440.0000.0000.0000.0000.0000.000
170A207ALA0-0.033-0.00342.768-0.003-0.0030.0000.0000.0000.000
171A208LEU00.0190.01439.5020.0000.0000.0000.0000.0000.000
172A209ARG10.8040.85742.0730.0320.0320.0000.0000.0000.000
173A210PHE00.0060.00239.9680.0010.0010.0000.0000.0000.000
174A211CYS0-0.088-0.04844.0070.0000.0000.0000.0000.0000.000
175A212ASN00.0200.02342.3890.0020.0020.0000.0000.0000.000
176A213ARG10.8190.89345.6330.0370.0370.0000.0000.0000.000
177A214TYR00.0360.01941.359-0.001-0.0010.0000.0000.0000.000
178A215TRP00.027-0.00745.3550.0020.0020.0000.0000.0000.000
179A216ALA00.0250.01644.5140.0010.0010.0000.0000.0000.000
180A217GLU-1-0.717-0.83340.042-0.063-0.0630.0000.0000.0000.000
181A218LEU00.0290.01638.479-0.003-0.0030.0000.0000.0000.000
182A219GLU-1-0.827-0.90439.139-0.051-0.0510.0000.0000.0000.000
183A220LEU00.0060.00939.223-0.002-0.0020.0000.0000.0000.000
184A221VAL00.0360.01034.404-0.003-0.0030.0000.0000.0000.000
185A222ASN0-0.038-0.01234.898-0.010-0.0100.0000.0000.0000.000
186A223HIS00.010-0.00635.337-0.003-0.0030.0000.0000.0000.000
187A224TYR0-0.008-0.00137.2940.0020.0020.0000.0000.0000.000
188A225ILE0-0.036-0.01232.691-0.002-0.0020.0000.0000.0000.000
189A226SER0-0.012-0.02130.735-0.006-0.0060.0000.0000.0000.000
190A227PRO0-0.045-0.01730.227-0.008-0.0080.0000.0000.0000.000
191A228ASN0-0.055-0.02531.066-0.001-0.0010.0000.0000.0000.000
192A229ALA0-0.020-0.00727.277-0.002-0.0020.0000.0000.0000.000
193A230TYR00.0150.01029.293-0.002-0.0020.0000.0000.0000.000
194A231PRO0-0.042-0.01330.952-0.003-0.0030.0000.0000.0000.000
195A232TYR0-0.051-0.06632.0800.0080.0080.0000.0000.0000.000
196A233LEU0-0.026-0.01433.691-0.006-0.0060.0000.0000.0000.000
197A234ASP-1-0.772-0.84836.255-0.071-0.0710.0000.0000.0000.000
198A235ILE00.003-0.00438.4770.0000.0000.0000.0000.0000.000
199A236ASN0-0.080-0.03237.8110.0050.0050.0000.0000.0000.000
200A237ASN0-0.040-0.01835.9190.0010.0010.0000.0000.0000.000
201A238HIS00.0160.00933.028-0.008-0.0080.0000.0000.0000.000
202A239SER0-0.035-0.02630.3940.0040.0040.0000.0000.0000.000
203A240TYR0-0.054-0.04130.042-0.009-0.0090.0000.0000.0000.000
204A241GLY00.0690.03228.6430.0050.0050.0000.0000.0000.000
205A242VAL0-0.052-0.03722.760-0.007-0.0070.0000.0000.0000.000
206A243ALA0-0.0180.00821.4050.0090.0090.0000.0000.0000.000
207A244LEU0-0.039-0.02419.863-0.014-0.0140.0000.0000.0000.000
208A245SER0-0.106-0.08018.687-0.021-0.0210.0000.0000.0000.000
209A246ASN0-0.039-0.01314.597-0.026-0.0260.0000.0000.0000.000