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: MMKVZ

Calculation Name: 3HVE-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HVE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H2C0

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2470591.746802
FMO2-HF: Nuclear repulsion 2379099.982278
FMO2-HF: Total energy -91491.764523
FMO2-MP2: Total energy -91755.829838


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:7:ACE )


Summations of interaction energy for fragment #1(A:7:ACE )
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.
0.9141.725-0.005-0.321-0.4850
Interaction energy analysis for fragmet #1(A:7:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.004
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].
3A9ASP -1-0.816-0.9193.8440.5051.316-0.005-0.321-0.4850.000
4A10PRO 00.0590.0376.8270.1790.1790.0000.0000.0000.000
5A11GLN 0-0.041-0.01110.1130.1670.1670.0000.0000.0000.000
6A12HIS 00.0400.0128.8530.0960.0960.0000.0000.0000.000
7A13ALA 00.0730.03610.8140.0850.0850.0000.0000.0000.000
8A14ALA 00.0560.03614.1650.0450.0450.0000.0000.0000.000
9A15ARG 10.8140.9078.5040.2070.2070.0000.0000.0000.000
10A16LEU 0-0.027-0.02614.3260.0340.0340.0000.0000.0000.000
11A17LEU 00.0030.00916.0200.0200.0200.0000.0000.0000.000
12A18ARG 10.9890.98816.2820.1140.1140.0000.0000.0000.000
13A19ALA 0-0.035-0.01518.1040.0150.0150.0000.0000.0000.000
14A20LEU 00.004-0.00119.6220.0070.0070.0000.0000.0000.000
15A21SER 0-0.0140.00422.3200.0090.0090.0000.0000.0000.000
16A22SER 0-0.037-0.02223.9270.0070.0070.0000.0000.0000.000
17A23PHE 0-0.077-0.01622.6140.0070.0070.0000.0000.0000.000
18A24ARG 10.8330.90026.9190.0480.0480.0000.0000.0000.000
19A25GLU -1-0.851-0.99329.794-0.008-0.0080.0000.0000.0000.000
20A26GLU -1-0.950-0.98632.195-0.016-0.0160.0000.0000.0000.000
21A27SER 0-0.108-0.06033.4260.0030.0030.0000.0000.0000.000
22A28ARG 10.8760.95229.7330.0000.0000.0000.0000.0000.000
23A29PHE 0-0.052-0.03925.9920.0020.0020.0000.0000.0000.000
24A30CYM -1-0.783-0.79929.677-0.035-0.0350.0000.0000.0000.000
25A31ASP -1-0.871-0.92030.529-0.036-0.0360.0000.0000.0000.000
26A32ALA 0-0.079-0.05633.3420.0000.0000.0000.0000.0000.000
27A33HIS 00.0750.02335.6830.0000.0000.0000.0000.0000.000
28A34LEU 0-0.050-0.02135.337-0.001-0.0010.0000.0000.0000.000
29A35VAL 0-0.003-0.01638.5510.0020.0020.0000.0000.0000.000
30A36LEU 00.0540.02338.995-0.002-0.0020.0000.0000.0000.000
31A37ASP -1-0.815-0.89943.066-0.028-0.0280.0000.0000.0000.000
32A38GLY 0-0.037-0.02446.3030.0010.0010.0000.0000.0000.000
33A39GLU -1-1.003-1.00943.207-0.023-0.0230.0000.0000.0000.000
34A40GLU -1-0.866-0.91841.062-0.022-0.0220.0000.0000.0000.000
35A41ILE 0-0.032-0.02035.8620.0000.0000.0000.0000.0000.000
36A42PRO 00.0040.02434.791-0.002-0.0020.0000.0000.0000.000
37A43VAL 00.013-0.00231.920-0.003-0.0030.0000.0000.0000.000
38A44GLN 00.0250.01325.7000.0000.0000.0000.0000.0000.000
39A45LYS 10.9410.94628.9850.0330.0330.0000.0000.0000.000
40A46ASN 0-0.010-0.00924.131-0.002-0.0020.0000.0000.0000.000
41A47ILE 00.0160.00623.620-0.008-0.0080.0000.0000.0000.000
42A48LEU 00.0570.02525.813-0.006-0.0060.0000.0000.0000.000
43A49ALA 00.0160.01028.531-0.002-0.0020.0000.0000.0000.000
44A50ALA 0-0.126-0.07423.927-0.003-0.0030.0000.0000.0000.000
45A51ALA 00.0210.01025.257-0.011-0.0110.0000.0000.0000.000
46A52SER 00.0310.02827.2980.0020.0020.0000.0000.0000.000
47A53PRO 0-0.033-0.02130.2490.0040.0040.0000.0000.0000.000
48A54TYR 00.0460.03532.1430.0050.0050.0000.0000.0000.000
49A55ILE 00.0240.00532.5960.0040.0040.0000.0000.0000.000
50A56ARG 10.8880.94527.7170.0950.0950.0000.0000.0000.000
51A57THR 0-0.029-0.01932.6270.0050.0050.0000.0000.0000.000
52A58LYS 10.8820.96935.5730.0440.0440.0000.0000.0000.000
53A59LEU 0-0.035-0.02131.9020.0030.0030.0000.0000.0000.000
54A60NME 0-0.0310.00234.9150.0030.0030.0000.0000.0000.000
55A70ACE 00.008-0.00437.3110.0010.0010.0000.0000.0000.000
56A71TYR 0-0.033-0.03736.956-0.001-0.0010.0000.0000.0000.000
57A72LYS 10.8720.93638.9200.0230.0230.0000.0000.0000.000
58A73ILE 0-0.044-0.00636.1840.0000.0000.0000.0000.0000.000
59A74GLU -1-0.907-0.96339.475-0.027-0.0270.0000.0000.0000.000
60A75LEU 0-0.110-0.04537.317-0.002-0.0020.0000.0000.0000.000
61A76GLU -1-0.939-0.98241.689-0.031-0.0310.0000.0000.0000.000
62A77GLY 0-0.0170.00344.492-0.001-0.0010.0000.0000.0000.000
63A78ILE 00.022-0.00139.085-0.002-0.0020.0000.0000.0000.000
64A79SER 00.0330.02642.8080.0000.0000.0000.0000.0000.000
65A80VAL 00.0260.00640.642-0.003-0.0030.0000.0000.0000.000
66A81MET 0-0.015-0.01439.655-0.001-0.0010.0000.0000.0000.000
67A82VAL 00.0540.02737.870-0.002-0.0020.0000.0000.0000.000
68A83MET 0-0.0030.01335.731-0.005-0.0050.0000.0000.0000.000
69A84ARG 10.9600.98034.6900.0290.0290.0000.0000.0000.000
70A85GLU -1-0.846-0.92133.274-0.049-0.0490.0000.0000.0000.000
71A86ILE 0-0.015-0.00732.304-0.006-0.0060.0000.0000.0000.000
72A87LEU 0-0.015-0.01830.367-0.006-0.0060.0000.0000.0000.000
73A88ASP -1-0.816-0.90129.087-0.056-0.0560.0000.0000.0000.000
74A89TYR 0-0.100-0.04527.449-0.009-0.0090.0000.0000.0000.000
75A90ILE 0-0.031-0.01725.868-0.010-0.0100.0000.0000.0000.000
76A91PHE 0-0.050-0.03623.627-0.010-0.0100.0000.0000.0000.000
77A92SER 0-0.078-0.04922.973-0.008-0.0080.0000.0000.0000.000
78A93GLY 0-0.026-0.00123.200-0.013-0.0130.0000.0000.0000.000
79A94GLN 0-0.076-0.05124.7520.0080.0080.0000.0000.0000.000
80A95ILE 00.0250.02927.8250.0050.0050.0000.0000.0000.000
81A96ARG 10.9190.95531.4040.0460.0460.0000.0000.0000.000
82A97LEU 00.0230.00934.3280.0020.0020.0000.0000.0000.000
83A98ASN 0-0.011-0.00137.041-0.001-0.0010.0000.0000.0000.000
84A99GLU -1-0.897-0.97740.273-0.042-0.0420.0000.0000.0000.000
85A100ASP -1-0.885-0.93743.635-0.032-0.0320.0000.0000.0000.000
86A101THR 0-0.049-0.01940.2190.0010.0010.0000.0000.0000.000
87A102ILE 00.0070.01039.502-0.002-0.0020.0000.0000.0000.000
88A103GLN 00.005-0.01340.516-0.002-0.0020.0000.0000.0000.000
89A104ASP -1-0.904-0.93841.913-0.038-0.0380.0000.0000.0000.000
90A105VAL 0-0.026-0.03535.807-0.001-0.0010.0000.0000.0000.000
91A106VAL 0-0.0110.00037.445-0.004-0.0040.0000.0000.0000.000
92A107GLN 00.0190.02739.324-0.001-0.0010.0000.0000.0000.000
93A108ALA 00.0200.00537.7050.0000.0000.0000.0000.0000.000
94A109ALA 0-0.014-0.00435.023-0.002-0.0020.0000.0000.0000.000
95A110ASP -1-0.971-0.99135.997-0.057-0.0570.0000.0000.0000.000
96A111LEU 00.0160.02338.104-0.002-0.0020.0000.0000.0000.000
97A112LEU 0-0.043-0.03934.2720.0000.0000.0000.0000.0000.000
98A113LEU 0-0.058-0.03234.016-0.005-0.0050.0000.0000.0000.000
99A114LEU 00.0160.02130.126-0.005-0.0050.0000.0000.0000.000
100A115THR 00.021-0.00830.2300.0030.0030.0000.0000.0000.000
101A116ASP -1-0.789-0.86227.059-0.105-0.1050.0000.0000.0000.000
102A117LEU 00.0560.01328.9860.0010.0010.0000.0000.0000.000
103A118LYS 10.9300.96131.1430.0700.0700.0000.0000.0000.000
104A119THR 0-0.041-0.02530.7470.0040.0040.0000.0000.0000.000
105A120LEU 00.0060.01928.4040.0030.0030.0000.0000.0000.000
106A121CYS 0-0.044-0.01332.4270.0060.0060.0000.0000.0000.000
107A122CYS 0-0.042-0.01935.4740.0050.0050.0000.0000.0000.000
108A123GLU -1-0.925-0.95230.707-0.096-0.0960.0000.0000.0000.000
109A124PHE 0-0.031-0.03535.5490.0040.0040.0000.0000.0000.000
110A125LEU 00.035-0.00537.3380.0030.0030.0000.0000.0000.000
111A126GLU -1-0.879-0.92137.621-0.067-0.0670.0000.0000.0000.000
112A127GLY 0-0.056-0.01839.2470.0030.0030.0000.0000.0000.000
113A128CYS 0-0.043-0.01840.4800.0020.0020.0000.0000.0000.000
114A129ILE 0-0.058-0.02043.4630.0030.0030.0000.0000.0000.000
115A130ALA 0-0.0030.01545.7230.0000.0000.0000.0000.0000.000
116A131ALA 0-0.023-0.01748.9370.0000.0000.0000.0000.0000.000
117A132GLU -1-0.826-0.93351.706-0.031-0.0310.0000.0000.0000.000
118A133ASN 00.0000.02047.5120.0020.0020.0000.0000.0000.000
119A134CYS 0-0.064-0.02848.231-0.002-0.0020.0000.0000.0000.000
120A135ILE 00.004-0.00749.878-0.001-0.0010.0000.0000.0000.000
121A136GLY 00.1110.06850.959-0.001-0.0010.0000.0000.0000.000
122A137ILE 0-0.008-0.01544.490-0.001-0.0010.0000.0000.0000.000
123A138ARG 10.8570.93846.4900.0360.0360.0000.0000.0000.000
124A139ASP -1-0.825-0.90848.656-0.034-0.0340.0000.0000.0000.000
125A140PHE 00.005-0.00642.426-0.001-0.0010.0000.0000.0000.000
126A141ALA 00.0120.00044.061-0.002-0.0020.0000.0000.0000.000
127A142LEU 0-0.0310.00744.788-0.002-0.0020.0000.0000.0000.000
128A143HIS 0-0.032-0.01646.1080.0010.0010.0000.0000.0000.000
129A144TYR 0-0.040-0.00741.9660.0000.0000.0000.0000.0000.000
130A145CYS 0-0.030-0.02242.088-0.003-0.0030.0000.0000.0000.000
131A146LEU 0-0.023-0.00339.154-0.004-0.0040.0000.0000.0000.000
132A147HIS 00.011-0.01540.1570.0010.0010.0000.0000.0000.000
133A148HIS 0-0.037-0.03438.3820.0030.0030.0000.0000.0000.000
134A149VAL 00.0700.04339.3330.0020.0020.0000.0000.0000.000
135A150HIS 0-0.023-0.02141.7300.0030.0030.0000.0000.0000.000
136A151TYR 0-0.036-0.01442.8760.0020.0020.0000.0000.0000.000
137A152LEU 00.0430.02639.9080.0030.0030.0000.0000.0000.000
138A153ALA 00.0280.01944.3080.0020.0020.0000.0000.0000.000
139A154THR 0-0.025-0.00746.9650.0030.0030.0000.0000.0000.000
140A155GLU -1-0.894-0.95045.507-0.047-0.0470.0000.0000.0000.000
141A156TYR 0-0.031-0.01147.1910.0030.0030.0000.0000.0000.000
142A157LEU 00.042-0.00249.3380.0020.0020.0000.0000.0000.000
143A158GLU -1-0.907-0.95851.582-0.037-0.0370.0000.0000.0000.000
144A159THR 0-0.046-0.02750.3110.0020.0020.0000.0000.0000.000
145A160HIS 10.8380.91049.6720.0370.0370.0000.0000.0000.000
146A161PHE 00.0340.03854.2200.0010.0010.0000.0000.0000.000
147A162ARG 10.8380.91655.9900.0310.0310.0000.0000.0000.000
148A163ASP -1-0.874-0.93755.720-0.029-0.0290.0000.0000.0000.000
149A164VAL 00.0380.04054.2590.0010.0010.0000.0000.0000.000
150A165SER 0-0.055-0.05256.9660.0010.0010.0000.0000.0000.000
151A166SER 0-0.140-0.08859.9290.0010.0010.0000.0000.0000.000
152A167THR 00.0210.01555.7040.0000.0000.0000.0000.0000.000
153A168GLU -1-0.866-0.94358.683-0.023-0.0230.0000.0000.0000.000
154A169GLU -1-0.841-0.91653.130-0.031-0.0310.0000.0000.0000.000
155A170PHE 0-0.060-0.03657.3300.0000.0000.0000.0000.0000.000
156A171LEU 0-0.010-0.00759.2110.0010.0010.0000.0000.0000.000
157A172GLU -1-1.067-1.02559.410-0.023-0.0230.0000.0000.0000.000
158A173LEU 00.0680.05158.0300.0000.0000.0000.0000.0000.000
159A174SER 00.003-0.00960.8540.0010.0010.0000.0000.0000.000
160A175PRO 00.0390.01262.582-0.001-0.0010.0000.0000.0000.000
161A176GLN 00.021-0.00662.138-0.001-0.0010.0000.0000.0000.000
162A177LYS 10.8680.93055.1120.0310.0310.0000.0000.0000.000
163A178LEU 00.0820.02459.448-0.001-0.0010.0000.0000.0000.000
164A179LYS 10.8710.93960.2630.0270.0270.0000.0000.0000.000
165A180GLU -1-0.959-1.00355.283-0.033-0.0330.0000.0000.0000.000
166A181VAL 0-0.016-0.00256.862-0.001-0.0010.0000.0000.0000.000
167A182ILE 0-0.038-0.02358.1860.0000.0000.0000.0000.0000.000
168A183SER 0-0.104-0.02958.2870.0000.0000.0000.0000.0000.000
169A184LEU 00.0480.02453.8830.0000.0000.0000.0000.0000.000
170A185GLU -1-0.933-0.93456.520-0.031-0.0310.0000.0000.0000.000
171A186NME 0-0.099-0.05656.0660.0000.0000.0000.0000.0000.000
172A192ACE 00.0520.01067.2600.0000.0000.0000.0000.0000.000
173A193ARG 10.8380.86767.1710.0210.0210.0000.0000.0000.000
174A194TYR 00.0680.03660.3580.0010.0010.0000.0000.0000.000
175A195VAL 00.0780.05262.1630.0000.0000.0000.0000.0000.000
176A196PHE 00.029-0.00764.6090.0000.0000.0000.0000.0000.000
177A197GLU -1-0.859-0.89867.173-0.020-0.0200.0000.0000.0000.000
178A198ALA 0-0.0010.00363.3340.0000.0000.0000.0000.0000.000
179A199VAL 00.007-0.00265.4590.0000.0000.0000.0000.0000.000
180A200ILE 0-0.020-0.01667.2610.0010.0010.0000.0000.0000.000
181A201ARG 10.9200.96263.3460.0230.0230.0000.0000.0000.000
182A202TRP 0-0.0130.01463.7800.0010.0010.0000.0000.0000.000
183A203ILE 0-0.062-0.01466.9930.0000.0000.0000.0000.0000.000
184A204ALA 00.0510.03667.9900.0000.0000.0000.0000.0000.000
185A205HIS 00.0250.00868.7550.0000.0000.0000.0000.0000.000
186A206ASP -1-0.724-0.83872.544-0.016-0.0160.0000.0000.0000.000
187A207THR 00.060-0.00674.7370.0000.0000.0000.0000.0000.000
188A208GLU -1-1.029-0.99375.437-0.015-0.0150.0000.0000.0000.000
189A209ILE 0-0.069-0.03471.0130.0000.0000.0000.0000.0000.000
190A210ARG 10.8230.92665.0870.0210.0210.0000.0000.0000.000
191A211LYS 10.8090.93572.0180.0160.0160.0000.0000.0000.000
192A212VAL 0-0.014-0.00874.3220.0010.0010.0000.0000.0000.000
193A213HIS 00.0900.02770.7220.0000.0000.0000.0000.0000.000
194A214MET 0-0.0330.01373.9450.0000.0000.0000.0000.0000.000
195A215LYS 10.8530.92175.2800.0150.0150.0000.0000.0000.000
196A216ASP -1-0.852-0.94273.157-0.018-0.0180.0000.0000.0000.000
197A217VAL 0-0.021-0.00571.2660.0000.0000.0000.0000.0000.000
198A218MET 0-0.031-0.01873.5640.0000.0000.0000.0000.0000.000
199A219SER 0-0.043-0.00676.4480.0000.0000.0000.0000.0000.000
200A220ALA 00.0500.01871.7690.0000.0000.0000.0000.0000.000
201A221LEU 0-0.009-0.01873.3520.0000.0000.0000.0000.0000.000
202A222TRP 0-0.065-0.02174.7660.0000.0000.0000.0000.0000.000
203A223VAL 00.0130.00074.1980.0000.0000.0000.0000.0000.000
204A224SER 00.0650.03871.3050.0000.0000.0000.0000.0000.000
205A225GLY 0-0.115-0.04573.3520.0000.0000.0000.0000.0000.000
206A226LEU 0-0.092-0.04775.9840.0010.0010.0000.0000.0000.000
207A227ASP -1-0.902-0.93572.466-0.020-0.0200.0000.0000.0000.000
208A228SER 0-0.061-0.05071.7660.0000.0000.0000.0000.0000.000
209A229SER 00.0140.00373.3320.0000.0000.0000.0000.0000.000
210A230TYR 00.0000.00773.2240.0000.0000.0000.0000.0000.000
211A231LEU 00.0130.01571.1450.0000.0000.0000.0000.0000.000
212A232ARG 10.9470.95874.2240.0160.0160.0000.0000.0000.000
213A233GLU -1-0.867-0.94476.889-0.016-0.0160.0000.0000.0000.000
214A234GLN 0-0.041-0.00870.6960.0000.0000.0000.0000.0000.000
215A235MET 0-0.0070.02270.8060.0000.0000.0000.0000.0000.000
216A236LEU 0-0.071-0.04374.2270.0000.0000.0000.0000.0000.000
217A237ASN 0-0.069-0.03775.4980.0010.0010.0000.0000.0000.000
218A238GLU -1-0.823-0.90570.835-0.018-0.0180.0000.0000.0000.000
219A239PRO 0-0.0160.00872.7620.0010.0010.0000.0000.0000.000
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