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: 5JK9Z

Calculation Name: 5H5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H5T

Chain ID: A

ChEMBL ID:

UniProt ID: P16328

Base Structure: X-ray

Registration Date: 2023-09-24

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1818305.023104
FMO2-HF: Nuclear repulsion 1745700.717741
FMO2-HF: Total energy -72604.305363
FMO2-MP2: Total energy -72817.088853


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:72:SER)


Summations of interaction energy for fragment #1(A:72: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.
-3.2120.4550.384-2.03-2.0210.004
Interaction energy analysis for fragmet #1(A:72:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.007
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].
3A74VAL00.0390.0403.810-2.3950.555-0.025-1.598-1.3260.003
4A75ALA00.011-0.0026.3400.1050.1050.0000.0000.0000.000
5A76SER0-0.0170.00810.0010.0200.0200.0000.0000.0000.000
6A77SER00.043-0.00613.2720.0280.0280.0000.0000.0000.000
7A78THR00.0100.01416.780-0.005-0.0050.0000.0000.0000.000
8A79THR00.0010.00319.9850.0140.0140.0000.0000.0000.000
9A80GLU-1-0.880-0.92720.008-0.191-0.1910.0000.0000.0000.000
10A81ASP-1-0.912-0.95721.092-0.124-0.1240.0000.0000.0000.000
11A82LEU0-0.069-0.01218.7760.0160.0160.0000.0000.0000.000
12A83LYS10.9270.96516.7080.1540.1540.0000.0000.0000.000
13A84VAL00.0350.01712.7200.0290.0290.0000.0000.0000.000
14A85SER0-0.025-0.00410.327-0.080-0.0800.0000.0000.0000.000
15A86THR00.0360.0046.237-0.012-0.0120.0000.0000.0000.000
16A87THR0-0.0030.0076.338-0.074-0.0740.0000.0000.0000.000
17A88ALA00.0370.0012.681-1.137-0.4930.409-0.474-0.5800.001
18A89GLY0-0.003-0.0143.510-1.272-1.3850.0010.0930.0190.000
19A90ALA00.0100.0296.577-0.147-0.1470.0000.0000.0000.000
20A91ALA00.0280.0267.557-0.245-0.2450.0000.0000.0000.000
21A92ALA00.014-0.0028.570-0.053-0.0530.0000.0000.0000.000
22A93GLY00.0130.00610.0280.0990.0990.0000.0000.0000.000
23A94THR0-0.0190.00213.664-0.039-0.0390.0000.0000.0000.000
24A95TYR0-0.030-0.02712.6170.0550.0550.0000.0000.0000.000
25A96LYS10.9610.98418.0780.1090.1090.0000.0000.0000.000
26A97ILE00.019-0.00318.0430.0130.0130.0000.0000.0000.000
27A98ASN00.0090.02722.425-0.005-0.0050.0000.0000.0000.000
28A99VAL0-0.0020.00024.0020.0060.0060.0000.0000.0000.000
29A100THR0-0.011-0.02226.6350.0000.0000.0000.0000.0000.000
30A101GLN0-0.062-0.03429.2280.0030.0030.0000.0000.0000.000
31A102LEU0-0.0170.01426.930-0.002-0.0020.0000.0000.0000.000
32A103ALA0-0.009-0.01027.8600.0040.0040.0000.0000.0000.000
33A104ALA0-0.002-0.00529.531-0.005-0.0050.0000.0000.0000.000
34A105ALA00.0210.00832.3080.0040.0040.0000.0000.0000.000
35A106GLN0-0.003-0.00433.8890.0000.0000.0000.0000.0000.000
36A107SER0-0.040-0.01237.4970.0010.0010.0000.0000.0000.000
37A108LEU00.0200.00639.392-0.001-0.0010.0000.0000.0000.000
38A109ALA00.0280.00242.975-0.001-0.0010.0000.0000.0000.000
39A110THR00.0250.00745.6350.0010.0010.0000.0000.0000.000
40A111LYS10.9440.98349.1440.0070.0070.0000.0000.0000.000
41A112THR0-0.0410.00251.9180.0000.0000.0000.0000.0000.000
42A113THR0-0.015-0.00550.9320.0000.0000.0000.0000.0000.000
43A114PHE00.0470.00552.2410.0010.0010.0000.0000.0000.000
44A115ALA00.0520.04053.615-0.001-0.0010.0000.0000.0000.000
45A116THR0-0.044-0.03453.405-0.001-0.0010.0000.0000.0000.000
46A117THR0-0.002-0.01748.1540.0000.0000.0000.0000.0000.000
47A118LYS10.9520.96850.9980.0090.0090.0000.0000.0000.000
48A119GLU-1-0.936-0.96253.460-0.007-0.0070.0000.0000.0000.000
49A120GLN00.0000.00354.5320.0010.0010.0000.0000.0000.000
50A121LEU00.0120.00351.2170.0000.0000.0000.0000.0000.000
51A122GLY00.0160.00855.1780.0000.0000.0000.0000.0000.000
52A123ASP-1-0.898-0.96056.0490.0010.0010.0000.0000.0000.000
53A124THR0-0.016-0.02159.0740.0000.0000.0000.0000.0000.000
54A125SER0-0.059-0.01960.7360.0000.0000.0000.0000.0000.000
55A126VAL0-0.037-0.00457.2290.0010.0010.0000.0000.0000.000
56A127THR0-0.013-0.00958.2040.0000.0000.0000.0000.0000.000
57A128SER0-0.053-0.02853.3950.0000.0000.0000.0000.0000.000
58A129ARG10.7780.88951.848-0.005-0.0050.0000.0000.0000.000
59A130THR00.0250.01047.6920.0010.0010.0000.0000.0000.000
60A131ILE0-0.0110.00145.420-0.001-0.0010.0000.0000.0000.000
61A132LYS10.9550.99645.530-0.014-0.0140.0000.0000.0000.000
62A133ILE00.003-0.01540.544-0.002-0.0020.0000.0000.0000.000
63A134GLU-1-0.943-0.98541.3100.0170.0170.0000.0000.0000.000
64A135GLN00.027-0.00435.5570.0000.0000.0000.0000.0000.000
65A136PRO0-0.0220.00936.6060.0030.0030.0000.0000.0000.000
66A137GLY00.0160.01133.7770.0030.0030.0000.0000.0000.000
67A138ARG10.7500.87433.895-0.015-0.0150.0000.0000.0000.000
68A139LYS10.8270.89535.941-0.042-0.0420.0000.0000.0000.000
69A140GLU-1-0.895-0.93637.8210.0360.0360.0000.0000.0000.000
70A141PRO00.0230.00639.498-0.001-0.0010.0000.0000.0000.000
71A142LEU00.0110.02538.3820.0020.0020.0000.0000.0000.000
72A143GLU-1-0.942-0.98141.2230.0160.0160.0000.0000.0000.000
73A144ILE00.0110.01241.1940.0010.0010.0000.0000.0000.000
74A145LYS10.9270.96744.850-0.017-0.0170.0000.0000.0000.000
75A146LEU0-0.008-0.00347.8460.0000.0000.0000.0000.0000.000
76A147ASP-1-0.875-0.96050.2360.0120.0120.0000.0000.0000.000
77A148LYS10.8980.93749.201-0.011-0.0110.0000.0000.0000.000
78A149GLY0-0.0020.01153.205-0.001-0.0010.0000.0000.0000.000
79A150ASP-1-0.800-0.91052.103-0.003-0.0030.0000.0000.0000.000
80A151THR0-0.044-0.02551.8440.0010.0010.0000.0000.0000.000
81A152SER00.0070.01251.214-0.001-0.0010.0000.0000.0000.000
82A153MET0-0.0090.00246.6620.0010.0010.0000.0000.0000.000
83A154GLU-1-0.883-0.94846.442-0.010-0.0100.0000.0000.0000.000
84A155ALA00.0230.03646.0570.0010.0010.0000.0000.0000.000
85A156ILE0-0.007-0.00945.8760.0020.0020.0000.0000.0000.000
86A157ARG10.8300.91041.4340.0110.0110.0000.0000.0000.000
87A158ASP-1-0.853-0.93041.960-0.005-0.0050.0000.0000.0000.000
88A159ALA00.0110.01841.9520.0020.0020.0000.0000.0000.000
89A160ILE0-0.049-0.03939.5860.0020.0020.0000.0000.0000.000
90A161ASN0-0.015-0.02037.7270.0020.0020.0000.0000.0000.000
91A162ASP-1-0.916-0.94737.2400.0070.0070.0000.0000.0000.000
92A163ALA0-0.090-0.04438.1710.0030.0030.0000.0000.0000.000
93A164ASP-1-0.956-0.96632.2940.0210.0210.0000.0000.0000.000
94A165SER00.0150.01933.6150.0040.0040.0000.0000.0000.000
95A166GLY0-0.019-0.00432.2580.0000.0000.0000.0000.0000.000
96A167ILE0-0.043-0.03033.071-0.003-0.0030.0000.0000.0000.000
97A168ALA00.0260.03134.7670.0010.0010.0000.0000.0000.000
98A169ALA0-0.0040.00236.763-0.001-0.0010.0000.0000.0000.000
99A170SER0-0.048-0.02838.775-0.002-0.0020.0000.0000.0000.000
100A171ILE00.019-0.00440.8340.0010.0010.0000.0000.0000.000
101A172VAL00.0160.01742.049-0.002-0.0020.0000.0000.0000.000
102A173LYS10.8640.93844.5310.0240.0240.0000.0000.0000.000
103A174VAL0-0.003-0.00146.755-0.002-0.0020.0000.0000.0000.000
104A175LYS10.8130.88748.5350.0180.0180.0000.0000.0000.000
105A176GLU-1-0.894-0.95651.109-0.020-0.0200.0000.0000.0000.000
106A177ASN0-0.043-0.01953.5520.0010.0010.0000.0000.0000.000
107A178GLU-1-0.790-0.86852.212-0.017-0.0170.0000.0000.0000.000
108A179PHE0-0.048-0.02948.011-0.002-0.0020.0000.0000.0000.000
109A180GLN00.0250.00346.9550.0000.0000.0000.0000.0000.000
110A181LEU0-0.004-0.00244.511-0.001-0.0010.0000.0000.0000.000
111A182VAL0-0.011-0.00740.3530.0000.0000.0000.0000.0000.000
112A183LEU00.0210.00840.5550.0010.0010.0000.0000.0000.000
113A184THR0-0.004-0.00134.785-0.002-0.0020.0000.0000.0000.000
114A185ALA00.0140.03335.1920.0020.0020.0000.0000.0000.000
115A186ASN00.0520.01229.746-0.008-0.0080.0000.0000.0000.000
116A187SER0-0.066-0.07328.549-0.001-0.0010.0000.0000.0000.000
117A188GLY00.0440.03330.4420.0040.0040.0000.0000.0000.000
118A189THR0-0.015-0.03031.7120.0010.0010.0000.0000.0000.000
119A190ASP-1-0.907-0.95431.7110.0160.0160.0000.0000.0000.000
120A191ASN0-0.072-0.04130.8280.0070.0070.0000.0000.0000.000
121A192THR0-0.0060.00035.128-0.001-0.0010.0000.0000.0000.000
122A193MET0-0.019-0.00938.4990.0030.0030.0000.0000.0000.000
123A194LYS10.9200.98241.055-0.010-0.0100.0000.0000.0000.000
124A195ILE00.0150.01543.1890.0020.0020.0000.0000.0000.000
125A196THR0-0.032-0.01546.116-0.001-0.0010.0000.0000.0000.000
126A197VAL00.0200.00348.7750.0010.0010.0000.0000.0000.000
127A198GLU-1-0.941-0.97250.2440.0130.0130.0000.0000.0000.000
128A199GLY00.019-0.01253.1750.0000.0000.0000.0000.0000.000
129A200ASP-1-0.742-0.86054.8350.0020.0020.0000.0000.0000.000
130A201THR00.0360.00855.6030.0000.0000.0000.0000.0000.000
131A202LYS10.9441.00057.3130.0020.0020.0000.0000.0000.000
132A203LEU00.0260.01150.821-0.001-0.0010.0000.0000.0000.000
133A204ASN00.0090.00352.5080.0000.0000.0000.0000.0000.000
134A205ASP-1-0.907-0.95353.067-0.001-0.0010.0000.0000.0000.000
135A206LEU0-0.102-0.03951.425-0.001-0.0010.0000.0000.0000.000
136A207LEU0-0.018-0.05147.260-0.001-0.0010.0000.0000.0000.000
137A208ALA0-0.0100.02048.1250.0000.0000.0000.0000.0000.000
138A209TYR0-0.028-0.02544.193-0.002-0.0020.0000.0000.0000.000
139A210ASP-1-0.792-0.91046.9180.0050.0050.0000.0000.0000.000
140A211SER00.048-0.00442.499-0.002-0.0020.0000.0000.0000.000
141A212THR0-0.075-0.01744.538-0.001-0.0010.0000.0000.0000.000
142A213THR0-0.056-0.03045.950-0.001-0.0010.0000.0000.0000.000
143A214ASN0-0.040-0.00844.781-0.001-0.0010.0000.0000.0000.000
144A215THR0-0.045-0.01247.493-0.001-0.0010.0000.0000.0000.000
145A216GLY00.0340.00849.4080.0010.0010.0000.0000.0000.000
146A217ASN0-0.053-0.03251.0860.0000.0000.0000.0000.0000.000
147A218MET0-0.0110.02845.306-0.001-0.0010.0000.0000.0000.000
148A219GLN0-0.055-0.03847.1310.0010.0010.0000.0000.0000.000
149A220GLU-1-0.847-0.92541.935-0.013-0.0130.0000.0000.0000.000
150A221LEU0-0.059-0.03342.477-0.001-0.0010.0000.0000.0000.000
151A222VAL0-0.031-0.01136.384-0.003-0.0030.0000.0000.0000.000
152A223LYS11.0021.01138.8880.0200.0200.0000.0000.0000.000
153A224ALA0-0.009-0.00135.403-0.002-0.0020.0000.0000.0000.000
154A225GLU-1-0.922-0.97133.006-0.025-0.0250.0000.0000.0000.000
155A226ASN0-0.0030.00929.8450.0000.0000.0000.0000.0000.000
156A227ALA00.0010.00325.795-0.004-0.0040.0000.0000.0000.000
157A228LYS10.9430.96627.8130.0300.0300.0000.0000.0000.000
158A229LEU0-0.009-0.00721.504-0.008-0.0080.0000.0000.0000.000
159A230ASN0-0.034-0.02025.2330.0000.0000.0000.0000.0000.000
160A231VAL00.0370.01218.608-0.015-0.0150.0000.0000.0000.000
161A232ASN0-0.060-0.03918.5660.0030.0030.0000.0000.0000.000
162A233GLY00.0320.01322.6690.0070.0070.0000.0000.0000.000
163A234ILE0-0.035-0.00422.0760.0100.0100.0000.0000.0000.000
164A235ASP-1-0.858-0.91024.715-0.046-0.0460.0000.0000.0000.000
165A236ILE0-0.067-0.03222.0650.0080.0080.0000.0000.0000.000
166A237GLU-1-0.881-0.95025.358-0.017-0.0170.0000.0000.0000.000
167A238ARG10.8320.89420.2890.0060.0060.0000.0000.0000.000
168A239GLN00.1090.06726.041-0.007-0.0070.0000.0000.0000.000
169A240SER00.0510.04223.427-0.005-0.0050.0000.0000.0000.000
170A241ASN00.0410.01724.082-0.002-0.0020.0000.0000.0000.000
171A242THR0-0.0060.01818.530-0.020-0.0200.0000.0000.0000.000
172A243VAL0-0.006-0.00219.1010.0170.0170.0000.0000.0000.000
173A244THR00.0300.01216.100-0.022-0.0220.0000.0000.0000.000
174A245ASP-1-0.876-0.94315.9000.0940.0940.0000.0000.0000.000
175A246ALA0-0.0410.00716.7550.0050.0050.0000.0000.0000.000
176A247PRO00.0210.00613.838-0.019-0.0190.0000.0000.0000.000
177A248GLN00.043-0.00413.8280.0080.0080.0000.0000.0000.000
178A249GLY0-0.038-0.01210.263-0.006-0.0060.0000.0000.0000.000
179A250ILE0-0.0020.0069.655-0.084-0.0840.0000.0000.0000.000
180A251THR0-0.028-0.00812.1160.0610.0610.0000.0000.0000.000
181A252LEU0-0.003-0.00814.329-0.052-0.0520.0000.0000.0000.000
182A253THR0-0.012-0.01117.0820.0280.0280.0000.0000.0000.000
183A254LEU0-0.049-0.02719.712-0.015-0.0150.0000.0000.0000.000
184A255THR0-0.017-0.03822.6620.0070.0070.0000.0000.0000.000
185A256LYS10.9710.98025.0790.1020.1020.0000.0000.0000.000
186A257LYS10.9490.98126.4160.0600.0600.0000.0000.0000.000
187A258VAL0-0.0120.00323.574-0.003-0.0030.0000.0000.0000.000
188A259THR00.020-0.00426.9600.0070.0070.0000.0000.0000.000
189A260ASP-1-0.928-0.97525.661-0.101-0.1010.0000.0000.0000.000
190A261ALA0-0.0050.01521.389-0.009-0.0090.0000.0000.0000.000
191A262THR0-0.024-0.02718.0720.0120.0120.0000.0000.0000.000
192A263VAL0-0.0040.00813.912-0.017-0.0170.0000.0000.0000.000
193A264THR00.001-0.00912.7200.0380.0380.0000.0000.0000.000
194A265VAL0-0.0130.0088.413-0.064-0.0640.0000.0000.0000.000
195A266THR0-0.009-0.0117.4180.0900.0900.0000.0000.0000.000
196A267LYS10.8610.9294.3381.8111.997-0.001-0.051-0.1340.000