FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JLY99

Calculation Name: 3HZR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HZR

Chain ID: A

ChEMBL ID:

UniProt ID: C4LUB5

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 374
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6505028.750614
FMO2-HF: Nuclear repulsion 6356973.034979
FMO2-HF: Total energy -148055.715635
FMO2-MP2: Total energy -148492.408851


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:PRO)


Summations of interaction energy for fragment #1(A:8:PRO)
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.
-5.957-1.0921.082-2.206-3.741-0.014
Interaction energy analysis for fragmet #1(A:8:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.019
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].
3A10GLN00.0280.0122.591-5.073-1.4070.756-1.802-2.620-0.011
4A11LEU00.0340.0395.1630.4180.446-0.001-0.005-0.0220.000
5A12LEU00.0140.0107.370-0.062-0.0620.0000.0000.0000.000
6A13GLN0-0.049-0.0307.232-0.041-0.0410.0000.0000.0000.000
7A14SER00.0230.0066.377-0.130-0.1300.0000.0000.0000.000
8A15PHE00.0030.0077.5610.0750.0750.0000.0000.0000.000
9A16THR0-0.037-0.0119.530-0.003-0.0030.0000.0000.0000.000
10A17THR00.019-0.00412.4020.0030.0030.0000.0000.0000.000
11A18ARG10.8330.90015.9790.0480.0480.0000.0000.0000.000
12A19THR00.000-0.03417.9460.0060.0060.0000.0000.0000.000
13A20THR0-0.0150.00214.577-0.010-0.0100.0000.0000.0000.000
14A21ASP-1-0.781-0.87912.915-0.030-0.0300.0000.0000.0000.000
15A22TYR00.0260.01212.5270.0170.0170.0000.0000.0000.000
16A23ASN0-0.007-0.00212.1960.0370.0370.0000.0000.0000.000
17A24GLN0-0.018-0.0329.932-0.004-0.0040.0000.0000.0000.000
18A25LEU0-0.0260.0086.573-0.038-0.0380.0000.0000.0000.000
19A26ILE00.007-0.0107.7460.0810.0810.0000.0000.0000.000
20A27ASN00.004-0.0039.3260.0940.0940.0000.0000.0000.000
21A28SER0-0.053-0.0404.623-0.0450.014-0.001-0.005-0.0530.000
22A29VAL0-0.072-0.0313.930-0.426-0.0570.001-0.063-0.3070.000
23A30GLY0-0.0180.0145.7890.2720.2720.0000.0000.0000.000
24A31ILE0-0.077-0.0398.0860.0130.0130.0000.0000.0000.000
25A32ASN0-0.009-0.00211.435-0.046-0.0460.0000.0000.0000.000
26A33ALA00.0320.00514.7750.0130.0130.0000.0000.0000.000
27A34ILE0-0.067-0.03216.937-0.001-0.0010.0000.0000.0000.000
28A35THR00.0290.01120.295-0.017-0.0170.0000.0000.0000.000
29A36PRO00.041-0.00822.7310.0010.0010.0000.0000.0000.000
30A37GLN0-0.013-0.00125.9880.0010.0010.0000.0000.0000.000
31A38GLN00.0410.02020.327-0.006-0.0060.0000.0000.0000.000
32A39ILE0-0.0050.00024.638-0.001-0.0010.0000.0000.0000.000
33A40GLN00.0420.01727.486-0.003-0.0030.0000.0000.0000.000
34A41ARG10.7240.84426.870-0.087-0.0870.0000.0000.0000.000
35A42ILE00.010-0.00225.556-0.001-0.0010.0000.0000.0000.000
36A43GLU-1-0.925-0.95930.0410.0420.0420.0000.0000.0000.000
37A44LYS10.9070.94033.070-0.050-0.0500.0000.0000.0000.000
38A45LEU0-0.039-0.01430.738-0.002-0.0020.0000.0000.0000.000
39A46SER0-0.068-0.02533.471-0.001-0.0010.0000.0000.0000.000
40A47GLY0-0.025-0.00135.377-0.002-0.0020.0000.0000.0000.000
41A48LYS10.7740.87636.212-0.050-0.0500.0000.0000.0000.000
42A49ALA00.0400.02335.6100.0020.0020.0000.0000.0000.000
43A50PRO00.0130.00230.4090.0030.0030.0000.0000.0000.000
44A51HIS0-0.0090.00228.860-0.002-0.0020.0000.0000.0000.000
45A52HIS00.0220.00028.7660.0030.0030.0000.0000.0000.000
46A53TYR0-0.020-0.03025.0510.0010.0010.0000.0000.0000.000
47A54LEU00.0020.01023.7320.0060.0060.0000.0000.0000.000
48A55SER0-0.004-0.01425.487-0.002-0.0020.0000.0000.0000.000
49A56ARG10.7540.86226.316-0.038-0.0380.0000.0000.0000.000
50A57GLY00.0050.02222.202-0.003-0.0030.0000.0000.0000.000
51A58VAL0-0.058-0.01221.0520.0000.0000.0000.0000.0000.000
52A59PHE0-0.004-0.01819.8740.0070.0070.0000.0000.0000.000
53A60LEU0-0.034-0.01916.010-0.009-0.0090.0000.0000.0000.000
54A61ALA00.0090.01114.070-0.003-0.0030.0000.0000.0000.000
55A62GLU-1-0.757-0.87615.4650.1840.1840.0000.0000.0000.000
56A63LYS10.8890.94812.447-0.459-0.4590.0000.0000.0000.000
57A64SER0-0.023-0.03215.6390.0030.0030.0000.0000.0000.000
58A65LEU00.0000.01018.993-0.013-0.0130.0000.0000.0000.000
59A66ASP-1-0.768-0.88021.7590.0970.0970.0000.0000.0000.000
60A67LYS10.9340.97018.341-0.215-0.2150.0000.0000.0000.000
61A68PHE0-0.011-0.00523.761-0.007-0.0070.0000.0000.0000.000
62A69LEU0-0.0110.00125.445-0.010-0.0100.0000.0000.0000.000
63A70ASP-1-0.777-0.88626.4240.0910.0910.0000.0000.0000.000
64A71ASP-1-0.856-0.90127.5670.1030.1030.0000.0000.0000.000
65A72VAL00.0330.02129.350-0.007-0.0070.0000.0000.0000.000
66A73GLU-1-0.851-0.91531.4360.0600.0600.0000.0000.0000.000
67A74ALA0-0.036-0.02032.826-0.005-0.0050.0000.0000.0000.000
68A75LYS10.8060.89834.410-0.063-0.0630.0000.0000.0000.000
69A76LYS10.8630.93229.961-0.088-0.0880.0000.0000.0000.000
70A77PRO0-0.014-0.00332.4000.0010.0010.0000.0000.0000.000
71A78THR0-0.010-0.01828.0580.0060.0060.0000.0000.0000.000
72A79PHE0-0.052-0.03026.136-0.007-0.0070.0000.0000.0000.000
73A80ILE00.0290.02425.6730.0100.0100.0000.0000.0000.000
74A81PHE0-0.013-0.01821.808-0.008-0.0080.0000.0000.0000.000
75A82ILE00.007-0.00223.0610.0060.0060.0000.0000.0000.000
76A83GLN0-0.050-0.03219.5270.0100.0100.0000.0000.0000.000
77A84LYS10.8080.89222.792-0.081-0.0810.0000.0000.0000.000
78A85TYR00.020-0.01722.8490.0010.0010.0000.0000.0000.000
79A86PRO00.0030.01024.973-0.005-0.0050.0000.0000.0000.000
80A87GLN00.0490.00924.350-0.006-0.0060.0000.0000.0000.000
81A88LYS10.8610.90028.977-0.018-0.0180.0000.0000.0000.000
82A89GLU-1-0.862-0.91729.5240.0110.0110.0000.0000.0000.000
83A90VAL00.0170.00428.8900.0030.0030.0000.0000.0000.000
84A91ALA00.0440.02625.854-0.002-0.0020.0000.0000.0000.000
85A92LEU00.017-0.00927.3060.0050.0050.0000.0000.0000.000
86A93GLU-1-0.875-0.94820.5480.0590.0590.0000.0000.0000.000
87A94GLU-1-0.855-0.91724.0860.0790.0790.0000.0000.0000.000
88A95TYR00.0220.00625.8320.0030.0030.0000.0000.0000.000
89A96ILE0-0.0080.01822.4320.0010.0010.0000.0000.0000.000
90A97THR00.0600.01421.496-0.002-0.0020.0000.0000.0000.000
91A98LEU0-0.0380.00024.4600.0020.0020.0000.0000.0000.000
92A99GLU-1-0.729-0.82728.1800.0500.0500.0000.0000.0000.000
93A100PHE00.0040.00223.416-0.003-0.0030.0000.0000.0000.000
94A101ALA00.0410.02226.9490.0010.0010.0000.0000.0000.000
95A102ARG10.8080.88228.244-0.053-0.0530.0000.0000.0000.000
96A103TYR0-0.021-0.01729.087-0.001-0.0010.0000.0000.0000.000
97A104LEU00.0300.00325.592-0.002-0.0020.0000.0000.0000.000
98A105GLN0-0.038-0.02330.223-0.003-0.0030.0000.0000.0000.000
99A106ASP-1-0.890-0.95132.9340.0450.0450.0000.0000.0000.000
100A107ALA0-0.0370.00932.148-0.004-0.0040.0000.0000.0000.000
101A108PHE00.031-0.00428.5460.0000.0000.0000.0000.0000.000
102A109ASN0-0.0030.02134.1820.0010.0010.0000.0000.0000.000
103A110ILE00.0210.02129.926-0.002-0.0020.0000.0000.0000.000
104A111GLN00.0280.00531.997-0.003-0.0030.0000.0000.0000.000
105A112VAL0-0.0040.00729.0670.0070.0070.0000.0000.0000.000
106A113ILE0-0.031-0.00928.263-0.006-0.0060.0000.0000.0000.000
107A114ILE0-0.016-0.01727.4480.0070.0070.0000.0000.0000.000
108A115GLN00.0390.01924.1140.0050.0050.0000.0000.0000.000
109A116ILE0-0.033-0.02326.7420.0010.0010.0000.0000.0000.000
110A117LEU00.0310.02822.109-0.005-0.0050.0000.0000.0000.000
111A118ASP-1-0.801-0.91426.4990.0500.0500.0000.0000.0000.000
112A119ASP-1-0.822-0.92227.5380.0660.0660.0000.0000.0000.000
113A120ILE00.027-0.00222.106-0.005-0.0050.0000.0000.0000.000
114A121LYS10.7710.88925.141-0.043-0.0430.0000.0000.0000.000
115A122VAL0-0.059-0.02226.867-0.006-0.0060.0000.0000.0000.000
116A123LEU0-0.0010.01125.327-0.006-0.0060.0000.0000.0000.000
117A124ASN0-0.005-0.01321.480-0.007-0.0070.0000.0000.0000.000
118A125ARG10.8140.90023.899-0.013-0.0130.0000.0000.0000.000
119A126GLU-1-0.777-0.83623.5490.0300.0300.0000.0000.0000.000
120A127ALA0-0.049-0.02728.1680.0000.0000.0000.0000.0000.000
121A128THR00.019-0.01631.5110.0010.0010.0000.0000.0000.000
122A129ILE00.0780.02633.9050.0020.0020.0000.0000.0000.000
123A130ASN0-0.015-0.01135.0390.0020.0020.0000.0000.0000.000
124A131GLU-1-0.820-0.86034.4410.0180.0180.0000.0000.0000.000
125A132ALA00.0730.04031.2180.0010.0010.0000.0000.0000.000
126A133SER00.0390.04032.7770.0030.0030.0000.0000.0000.000
127A134LYS10.9460.97435.489-0.020-0.0200.0000.0000.0000.000
128A135MET0-0.040-0.01030.327-0.001-0.0010.0000.0000.0000.000
129A136SER00.0530.00632.0400.0040.0040.0000.0000.0000.000
130A137ASN0-0.074-0.04233.3100.0010.0010.0000.0000.0000.000
131A138ASP-1-0.817-0.91736.0680.0280.0280.0000.0000.0000.000
132A139LEU00.0170.02828.7150.0000.0000.0000.0000.0000.000
133A140MET00.0190.00232.9590.0020.0020.0000.0000.0000.000
134A141LYS10.8300.91934.732-0.028-0.0280.0000.0000.0000.000
135A142TYR00.018-0.00632.795-0.002-0.0020.0000.0000.0000.000
136A143ILE00.0170.01529.8990.0010.0010.0000.0000.0000.000
137A144LEU00.007-0.00832.9910.0000.0000.0000.0000.0000.000
138A145ALA00.0070.02035.927-0.001-0.0010.0000.0000.0000.000
139A146PHE00.0010.00130.807-0.002-0.0020.0000.0000.0000.000
140A147GLY0-0.038-0.00635.184-0.001-0.0010.0000.0000.0000.000
141A148PHE0-0.006-0.00730.2810.0000.0000.0000.0000.0000.000
142A149ASN00.0390.01936.138-0.005-0.0050.0000.0000.0000.000
143A150GLU-1-0.794-0.87437.4070.0420.0420.0000.0000.0000.000
144A151ASP-1-0.846-0.89938.5960.0430.0430.0000.0000.0000.000
145A152LYS10.7650.87536.078-0.055-0.0550.0000.0000.0000.000
146A153THR00.0470.00632.7340.0060.0060.0000.0000.0000.000
147A154PHE0-0.0100.02332.214-0.005-0.0050.0000.0000.0000.000
148A155ILE00.0220.00631.7520.0060.0060.0000.0000.0000.000
149A156TYR0-0.064-0.03627.591-0.005-0.0050.0000.0000.0000.000
150A157THR0-0.015-0.03330.9580.0020.0020.0000.0000.0000.000
151A158ASP-1-0.727-0.86827.3100.0890.0890.0000.0000.0000.000
152A159TYR0-0.024-0.01530.515-0.002-0.0020.0000.0000.0000.000
153A160GLN0-0.068-0.02533.504-0.005-0.0050.0000.0000.0000.000
154A161TYR0-0.035-0.05430.850-0.005-0.0050.0000.0000.0000.000
155A162PHE00.0710.04128.0030.0010.0010.0000.0000.0000.000
156A163GLY00.003-0.00132.2410.0020.0020.0000.0000.0000.000
157A164LYS10.8140.90533.974-0.052-0.0520.0000.0000.0000.000
158A165MET00.0130.02727.1170.0030.0030.0000.0000.0000.000
159A166TYR0-0.049-0.03327.9270.0020.0020.0000.0000.0000.000
160A167ARG10.9550.98129.298-0.056-0.0560.0000.0000.0000.000
161A168THR00.021-0.01226.400-0.001-0.0010.0000.0000.0000.000
162A169ILE00.0170.01424.7070.0110.0110.0000.0000.0000.000
163A170SER0-0.021-0.00624.5220.0060.0060.0000.0000.0000.000
164A171LEU0-0.035-0.02824.8820.0000.0000.0000.0000.0000.000
165A172VAL00.0190.01119.5430.0070.0070.0000.0000.0000.000
166A173GLU-1-0.862-0.92920.4730.0960.0960.0000.0000.0000.000
167A174LYS10.8850.95121.473-0.085-0.0850.0000.0000.0000.000
168A175ALA0-0.0070.00019.240-0.005-0.0050.0000.0000.0000.000
169A176THR0-0.018-0.00615.8860.0450.0450.0000.0000.0000.000
170A177ALA00.0120.02015.303-0.026-0.0260.0000.0000.0000.000
171A178TYR00.046-0.00114.8280.0310.0310.0000.0000.0000.000
172A179ASN00.006-0.01112.9610.0280.0280.0000.0000.0000.000
173A180VAL0-0.0020.0059.798-0.038-0.0380.0000.0000.0000.000
174A181VAL00.003-0.00310.0210.1070.1070.0000.0000.0000.000
175A182GLN0-0.013-0.01212.116-0.009-0.0090.0000.0000.0000.000
176A183PRO00.0020.0247.676-0.050-0.0500.0000.0000.0000.000
177A184PHE0-0.017-0.0048.180-0.055-0.0550.0000.0000.0000.000
178A185PHE00.001-0.0129.672-0.025-0.0250.0000.0000.0000.000
179A186ASN0-0.023-0.01110.216-0.029-0.0290.0000.0000.0000.000
180A187PHE00.0000.00413.6570.0050.0050.0000.0000.0000.000
181A188GLU-1-0.902-0.95616.696-0.072-0.0720.0000.0000.0000.000
182A189TYR0-0.044-0.01318.954-0.003-0.0030.0000.0000.0000.000
183A190SER0-0.009-0.00621.3760.0070.0070.0000.0000.0000.000
184A191ASP-1-0.782-0.88520.7850.0140.0140.0000.0000.0000.000
185A192ASN0-0.069-0.04023.1680.0070.0070.0000.0000.0000.000
186A193ILE00.0740.01523.9180.0050.0050.0000.0000.0000.000
187A194GLY00.0140.01524.1710.0070.0070.0000.0000.0000.000
188A195LYS10.8940.93719.791-0.019-0.0190.0000.0000.0000.000
189A196LEU0-0.0140.00719.4800.0110.0110.0000.0000.0000.000
190A197ALA00.0200.01719.6250.0160.0160.0000.0000.0000.000
191A198SER0-0.037-0.03620.1050.0100.0100.0000.0000.0000.000
192A199PRO00.0220.00816.5710.0090.0090.0000.0000.0000.000
193A200SER00.0570.03818.6970.0250.0250.0000.0000.0000.000
194A201ILE0-0.033-0.00321.1290.0030.0030.0000.0000.0000.000
195A202MET0-0.060-0.01418.6520.0040.0040.0000.0000.0000.000
196A203THR00.0470.01116.8810.0120.0120.0000.0000.0000.000
197A204ALA00.0380.02320.1870.0020.0020.0000.0000.0000.000
198A205SER0-0.029-0.01523.405-0.003-0.0030.0000.0000.0000.000
199A206MET0-0.0090.01917.7020.0050.0050.0000.0000.0000.000
200A207PHE00.0220.00819.3270.0020.0020.0000.0000.0000.000
201A208SER0-0.017-0.00725.094-0.007-0.0070.0000.0000.0000.000
202A209GLN00.0500.01526.630-0.006-0.0060.0000.0000.0000.000
203A210SER0-0.038-0.01526.329-0.009-0.0090.0000.0000.0000.000
204A211TYR0-0.0110.00827.192-0.005-0.0050.0000.0000.0000.000
205A212SER00.0550.03232.188-0.003-0.0030.0000.0000.0000.000
206A213HIS10.8350.93534.786-0.058-0.0580.0000.0000.0000.000
207A214PHE0-0.009-0.01634.205-0.004-0.0040.0000.0000.0000.000
208A215PHE00.0130.00830.9750.0010.0010.0000.0000.0000.000
209A216SER00.0110.01534.7770.0000.0000.0000.0000.0000.000
210A217SER0-0.023-0.02033.330-0.003-0.0030.0000.0000.0000.000
211A218PRO00.0150.01028.2280.0020.0020.0000.0000.0000.000
212A219ALA00.0060.00928.702-0.005-0.0050.0000.0000.0000.000
213A220ARG10.9000.93722.931-0.130-0.1300.0000.0000.0000.000
214A221CYS00.0000.01722.758-0.007-0.0070.0000.0000.0000.000
215A222LEU0-0.0070.02321.5330.0130.0130.0000.0000.0000.000
216A223VAL00.0390.00919.069-0.017-0.0170.0000.0000.0000.000
217A224LEU0-0.038-0.01020.2110.0050.0050.0000.0000.0000.000
218A225ASP-1-0.768-0.86315.5930.2340.2340.0000.0000.0000.000
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