Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 98JK2

Calculation Name: 4HYN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYN

Chain ID: A

ChEMBL ID:

UniProt ID: G4FDE4

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2206027.637939
FMO2-HF: Nuclear repulsion 2126926.423841
FMO2-HF: Total energy -79101.214098
FMO2-MP2: Total energy -79325.425672


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-6.012-4.672-0.003-0.604-0.7340
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.073 / q_NPA : -0.060
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].
3A24VAL0-0.051-0.0473.677-0.0411.243-0.002-0.597-0.6850.000
4A25LEU0-0.0220.0065.6300.7220.7220.0000.0000.0000.000
5A26THR0-0.042-0.0248.9520.2330.2330.0000.0000.0000.000
6A27PRO0-0.028-0.04210.653-0.028-0.0280.0000.0000.0000.000
7A28GLU-1-0.866-0.92013.707-0.126-0.1260.0000.0000.0000.000
8A29GLU-1-0.856-0.93011.215-0.730-0.7300.0000.0000.0000.000
9A30LYS10.8700.9379.2960.5090.5090.0000.0000.0000.000
10A31ASP-1-0.877-0.94015.316-0.072-0.0720.0000.0000.0000.000
11A32MET0-0.0200.01817.0650.0140.0140.0000.0000.0000.000
12A33ILE0-0.053-0.02516.0940.0100.0100.0000.0000.0000.000
13A34GLY00.0500.01819.2580.0160.0160.0000.0000.0000.000
14A35GLU-1-0.968-0.97921.421-0.099-0.0990.0000.0000.0000.000
15A36ILE0-0.031-0.02421.7810.0110.0110.0000.0000.0000.000
16A37GLY00.0100.01123.2530.0050.0050.0000.0000.0000.000
17A38ASN0-0.010-0.02924.3770.0190.0190.0000.0000.0000.000
18A39ILE0-0.038-0.00227.2810.0100.0100.0000.0000.0000.000
19A40ALA0-0.007-0.00526.6100.0070.0070.0000.0000.0000.000
20A41MET00.008-0.00126.5760.0040.0040.0000.0000.0000.000
21A42GLY00.0670.03828.6620.0090.0090.0000.0000.0000.000
22A43SER0-0.032-0.02531.3210.0110.0110.0000.0000.0000.000
23A44ALA0-0.030-0.02031.0080.0060.0060.0000.0000.0000.000
24A45ALA00.0270.01632.5020.0050.0050.0000.0000.0000.000
25A46THR00.0190.01034.1740.0080.0080.0000.0000.0000.000
26A47THR0-0.039-0.01736.1770.0060.0060.0000.0000.0000.000
27A48LEU00.0000.00035.1590.0040.0040.0000.0000.0000.000
28A49SER0-0.033-0.06137.8250.0050.0050.0000.0000.0000.000
29A50MET0-0.055-0.02339.8250.0040.0040.0000.0000.0000.000
30A51ILE0-0.055-0.01539.6030.0020.0020.0000.0000.0000.000
31A52LEU0-0.041-0.01539.1710.0030.0030.0000.0000.0000.000
32A53GLY0-0.025-0.01243.1320.0000.0000.0000.0000.0000.000
33A54ARG10.8660.92941.3780.0460.0460.0000.0000.0000.000
34A55ASP-1-0.868-0.88440.090-0.048-0.0480.0000.0000.0000.000
35A56ILE0-0.060-0.04934.3540.0000.0000.0000.0000.0000.000
36A57HIS00.0040.01532.334-0.005-0.0050.0000.0000.0000.000
37A58ILE0-0.018-0.02627.948-0.002-0.0020.0000.0000.0000.000
38A59THR00.0170.02626.1580.0040.0040.0000.0000.0000.000
39A60VAL0-0.023-0.01221.103-0.008-0.0080.0000.0000.0000.000
40A61PRO0-0.045-0.00822.4100.0010.0010.0000.0000.0000.000
41A62THR00.0020.00116.6150.0170.0170.0000.0000.0000.000
42A63VAL00.0160.01214.479-0.029-0.0290.0000.0000.0000.000
43A64ARG10.8360.90111.5360.2180.2180.0000.0000.0000.000
44A65GLU-1-0.781-0.8836.567-2.512-2.5120.0000.0000.0000.000
45A66GLU-1-0.878-0.9258.259-0.268-0.2680.0000.0000.0000.000
46A67LYS10.9550.9794.3400.3160.372-0.001-0.007-0.0490.000
47A68MET00.0330.0208.0350.2170.2170.0000.0000.0000.000
48A69LYS10.7670.8778.5750.3750.3750.0000.0000.0000.000
49A70ASN0-0.035-0.0278.8830.1200.1200.0000.0000.0000.000
50A71VAL00.0710.05912.2820.0460.0460.0000.0000.0000.000
51A72LYS10.7970.89114.4390.1810.1810.0000.0000.0000.000
52A73SER0-0.051-0.02814.9670.0260.0260.0000.0000.0000.000
53A74ASP-1-0.897-0.93414.320-0.217-0.2170.0000.0000.0000.000
54A75PHE0-0.076-0.03717.1970.0180.0180.0000.0000.0000.000
55A76SER0-0.015-0.00820.8110.0030.0030.0000.0000.0000.000
56A77GLY00.0490.02923.862-0.002-0.0020.0000.0000.0000.000
57A78GLU-1-0.922-0.97726.582-0.087-0.0870.0000.0000.0000.000
58A79GLN0-0.049-0.03424.418-0.003-0.0030.0000.0000.0000.000
59A80VAL0-0.0040.00228.048-0.001-0.0010.0000.0000.0000.000
60A81VAL0-0.021-0.00623.801-0.008-0.0080.0000.0000.0000.000
61A82VAL00.0170.00026.3430.0080.0080.0000.0000.0000.000
62A83SER0-0.027-0.01424.755-0.016-0.0160.0000.0000.0000.000
63A84VAL0-0.007-0.00425.4150.0170.0170.0000.0000.0000.000
64A85GLU-1-0.926-0.97723.867-0.288-0.2880.0000.0000.0000.000
65A86TYR0-0.038-0.02422.4350.0260.0260.0000.0000.0000.000
66A87THR0-0.020-0.02425.528-0.012-0.0120.0000.0000.0000.000
67A88GLU-1-0.899-0.95427.791-0.147-0.1470.0000.0000.0000.000
68A89GLY00.0520.03726.5440.0080.0080.0000.0000.0000.000
69A90LEU0-0.067-0.05721.084-0.023-0.0230.0000.0000.0000.000
70A91GLU-1-0.942-0.96721.931-0.252-0.2520.0000.0000.0000.000
71A92GLY00.0090.00120.153-0.047-0.0470.0000.0000.0000.000
72A93LEU0-0.0070.01620.0760.0310.0310.0000.0000.0000.000
73A94ASN0-0.019-0.00720.012-0.052-0.0520.0000.0000.0000.000
74A95VAL0-0.004-0.00620.5520.0310.0310.0000.0000.0000.000
75A96LEU00.0210.01321.754-0.012-0.0120.0000.0000.0000.000
76A97VAL0-0.035-0.01821.1200.0060.0060.0000.0000.0000.000
77A98LEU00.0390.00424.1610.0060.0060.0000.0000.0000.000
78A99ASP-1-0.821-0.91627.351-0.078-0.0780.0000.0000.0000.000
79A100LYS10.9270.95328.7870.0790.0790.0000.0000.0000.000
80A101LYS10.9300.97532.1500.0500.0500.0000.0000.0000.000
81A102LEU00.0350.04029.2190.0030.0030.0000.0000.0000.000
82A103VAL0-0.017-0.01431.2790.0010.0010.0000.0000.0000.000
83A104ALA0-0.025-0.01733.7870.0020.0020.0000.0000.0000.000
84A105VAL0-0.0040.01335.7640.0030.0030.0000.0000.0000.000
85A106ILE00.0320.00332.9820.0020.0020.0000.0000.0000.000
86A107ALA0-0.018-0.00737.1060.0010.0010.0000.0000.0000.000
87A108ASP-1-0.874-0.95639.260-0.044-0.0440.0000.0000.0000.000
88A109LEU0-0.036-0.00538.5960.0020.0020.0000.0000.0000.000
89A110MET0-0.058-0.01939.1100.0010.0010.0000.0000.0000.000
90A111MET0-0.089-0.04042.1410.0000.0000.0000.0000.0000.000
91A112GLY0-0.046-0.01445.0160.0030.0030.0000.0000.0000.000
92A113GLY0-0.0090.01245.5480.0030.0030.0000.0000.0000.000
93A114SER0-0.048-0.04045.103-0.001-0.0010.0000.0000.0000.000
94A115GLY00.0620.02341.0430.0000.0000.0000.0000.0000.000
95A116GLU-1-0.988-0.99740.161-0.034-0.0340.0000.0000.0000.000
96A117VAL0-0.0120.01339.8810.0020.0020.0000.0000.0000.000
97A118GLU-1-0.967-0.99740.184-0.030-0.0300.0000.0000.0000.000
98A119THR0-0.047-0.03439.4340.0010.0010.0000.0000.0000.000
99A120GLU-1-0.932-0.97533.028-0.059-0.0590.0000.0000.0000.000
100A121GLU-1-0.932-0.96636.508-0.051-0.0510.0000.0000.0000.000
101A122LEU0-0.021-0.01333.838-0.001-0.0010.0000.0000.0000.000
102A123ASP-1-0.824-0.91738.609-0.057-0.0570.0000.0000.0000.000
103A124GLU-1-0.894-0.96738.745-0.083-0.0830.0000.0000.0000.000
104A125ILE0-0.046-0.01640.758-0.002-0.0020.0000.0000.0000.000
105A126LYS10.8920.94639.1250.0540.0540.0000.0000.0000.000
106A127LEU00.008-0.01134.949-0.003-0.0030.0000.0000.0000.000
107A128SER0-0.046-0.00836.928-0.006-0.0060.0000.0000.0000.000
108A129ALA00.0210.01339.487-0.002-0.0020.0000.0000.0000.000
109A130VAL0-0.008-0.00433.428-0.001-0.0010.0000.0000.0000.000
110A131GLY00.0140.00834.672-0.006-0.0060.0000.0000.0000.000
111A132GLU-1-0.929-0.95935.756-0.088-0.0880.0000.0000.0000.000
112A133ALA00.0240.00935.782-0.002-0.0020.0000.0000.0000.000
113A134MET0-0.050-0.03430.856-0.007-0.0070.0000.0000.0000.000
114A135ASN0-0.039-0.01532.796-0.011-0.0110.0000.0000.0000.000
115A136GLN00.0380.01834.914-0.005-0.0050.0000.0000.0000.000
116A137MET0-0.042-0.00631.691-0.003-0.0030.0000.0000.0000.000
117A138MET00.015-0.00626.490-0.002-0.0020.0000.0000.0000.000
118A139GLY00.0400.03230.655-0.008-0.0080.0000.0000.0000.000
119A140SER00.0100.01133.3310.0020.0020.0000.0000.0000.000
120A141ALA0-0.0040.00928.015-0.001-0.0010.0000.0000.0000.000
121A142ALA00.0350.01728.568-0.007-0.0070.0000.0000.0000.000
122A143THR0-0.016-0.01029.605-0.002-0.0020.0000.0000.0000.000
123A144SER0-0.006-0.00230.4650.0000.0000.0000.0000.0000.000
124A145LEU00.0130.00023.7160.0000.0000.0000.0000.0000.000
125A146SER0-0.022-0.02427.817-0.006-0.0060.0000.0000.0000.000
126A147GLU-1-0.968-0.98129.742-0.101-0.1010.0000.0000.0000.000
127A148LEU0-0.065-0.02325.8090.0030.0030.0000.0000.0000.000
128A149LEU0-0.003-0.02822.9610.0010.0010.0000.0000.0000.000
129A150GLY0-0.093-0.02226.9160.0000.0000.0000.0000.0000.000
130A151ILE0-0.059-0.03426.1070.0020.0020.0000.0000.0000.000
131A152THR0-0.014-0.00929.5410.0040.0040.0000.0000.0000.000
132A153ILE00.0160.02425.676-0.010-0.0100.0000.0000.0000.000
133A154ASN0-0.038-0.00629.2170.0120.0120.0000.0000.0000.000
134A155ILE00.014-0.00528.014-0.016-0.0160.0000.0000.0000.000
135A156SER0-0.0200.00929.1060.0120.0120.0000.0000.0000.000
136A157PRO0-0.004-0.01731.363-0.001-0.0010.0000.0000.0000.000
137A158PRO00.0320.01930.432-0.005-0.0050.0000.0000.0000.000
138A159LYS10.9270.98027.6770.1830.1830.0000.0000.0000.000
139A160VAL0-0.012-0.01229.629-0.010-0.0100.0000.0000.0000.000
140A161GLU-1-0.927-0.96327.402-0.155-0.1550.0000.0000.0000.000
141A162ILE0-0.025-0.00329.407-0.004-0.0040.0000.0000.0000.000
142A163LEU00.001-0.00223.1830.0000.0000.0000.0000.0000.000
143A164ASN00.0570.00827.2280.0030.0030.0000.0000.0000.000
144A165PHE0-0.0020.00220.541-0.008-0.0080.0000.0000.0000.000
145A166ASP-1-0.841-0.91823.646-0.069-0.0690.0000.0000.0000.000
146A167ASP-1-0.935-0.95226.216-0.081-0.0810.0000.0000.0000.000
147A168PRO0-0.038-0.02523.862-0.013-0.0130.0000.0000.0000.000
148A169ASN0-0.057-0.03523.637-0.010-0.0100.0000.0000.0000.000
149A170THR0-0.0310.00024.676-0.014-0.0140.0000.0000.0000.000
150A171GLN0-0.017-0.01620.681-0.023-0.0230.0000.0000.0000.000
151A172PHE00.0360.02118.0710.0110.0110.0000.0000.0000.000
152A173PRO00.0420.02019.987-0.015-0.0150.0000.0000.0000.000
153A174PRO00.004-0.00318.328-0.030-0.0300.0000.0000.0000.000
154A175VAL0-0.0070.00615.761-0.010-0.0100.0000.0000.0000.000
155A176THR00.0040.00611.838-0.023-0.0230.0000.0000.0000.000
156A177ASP-1-0.861-0.92914.872-0.503-0.5030.0000.0000.0000.000
157A178ASN0-0.042-0.03511.110-0.032-0.0320.0000.0000.0000.000
158A179PRO00.0370.00411.671-0.098-0.0980.0000.0000.0000.000
159A180GLU-1-0.851-0.9407.048-0.556-0.5560.0000.0000.0000.000
160A181LYS10.8510.9436.5840.3670.3670.0000.0000.0000.000
161A182ASP-1-0.818-0.9255.569-3.340-3.3400.0000.0000.0000.000
162A183VAL0-0.046-0.0198.4120.2210.2210.0000.0000.0000.000
163A184ALA00.0050.00710.722-0.100-0.1000.0000.0000.0000.000
164A185VAL00.003-0.00613.2970.0600.0600.0000.0000.0000.000
165A186VAL0-0.025-0.02615.4400.0210.0210.0000.0000.0000.000
166A187GLU-1-0.924-0.97018.372-0.084-0.0840.0000.0000.0000.000
167A188PHE0-0.006-0.00720.9610.0020.0020.0000.0000.0000.000
168A189GLU-1-0.941-0.98524.597-0.046-0.0460.0000.0000.0000.000
169A190MET0-0.018-0.01827.398-0.003-0.0030.0000.0000.0000.000
170A191GLU-1-0.946-0.97630.818-0.039-0.0390.0000.0000.0000.000
171A192ILE00.0380.01834.182-0.002-0.0020.0000.0000.0000.000
172A193GLU-1-0.861-0.93937.241-0.034-0.0340.0000.0000.0000.000
173A194GLY0-0.042-0.02540.6450.0000.0000.0000.0000.0000.000
174A195LEU0-0.0200.00738.2110.0010.0010.0000.0000.0000.000
175A196PRO0-0.053-0.02535.5710.0010.0010.0000.0000.0000.000
176A197LYS10.9400.97530.9960.0280.0280.0000.0000.0000.000
177A198SER0-0.0300.00230.5610.0000.0000.0000.0000.0000.000
178A199LYS10.9480.96823.7150.0840.0840.0000.0000.0000.000
179A200PHE0-0.0110.00625.1640.0030.0030.0000.0000.0000.000
180A201TYR00.0170.00819.4700.0070.0070.0000.0000.0000.000
181A202GLN00.0420.03419.8340.0170.0170.0000.0000.0000.000
182A203VAL0-0.052-0.01215.967-0.021-0.0210.0000.0000.0000.000
183A204ILE00.0510.02516.4470.0260.0260.0000.0000.0000.000
184A205SER00.0490.02213.688-0.077-0.0770.0000.0000.0000.000
185A206ALA00.0430.01010.0430.0660.0660.0000.0000.0000.000
186A207ASP-1-0.964-0.98411.953-0.843-0.8430.0000.0000.0000.000
187A208LEU0-0.002-0.00313.7610.0740.0740.0000.0000.0000.000
188A209VAL00.0090.01213.6370.0610.0610.0000.0000.0000.000
189A210LYS11.0171.01411.6580.8150.8150.0000.0000.0000.000
190A211LYS10.8760.95914.3810.3890.3890.0000.0000.0000.000
191A212MET0-0.011-0.01817.8260.0470.0470.0000.0000.0000.000
192A213TYR00.0750.02215.7210.0480.0480.0000.0000.0000.000
193A214GLU-1-0.950-0.97017.057-0.344-0.3440.0000.0000.0000.000
194A215TYR0-0.088-0.04819.5780.0380.0380.0000.0000.0000.000
195A216PHE00.0210.00720.5930.0230.0230.0000.0000.0000.000
196A217THR00.000-0.01618.8600.0270.0270.0000.0000.0000.000
197A218LYS10.9110.96821.9070.1660.1660.0000.0000.0000.000
198A219LYS10.9330.95924.6920.1420.1420.0000.0000.0000.000
199A220GLN0-0.0050.01722.3820.0050.0050.0000.0000.0000.000
200A221SER0-0.062-0.02924.4950.0160.0160.0000.0000.0000.000
201A222GLU-1-1.022-0.99426.987-0.098-0.0980.0000.0000.0000.000
202A223ALA0-0.026-0.01130.3370.0020.0020.0000.0000.0000.000