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: LL529

Calculation Name: 2WVN-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WVN

Chain ID: A

ChEMBL ID:

UniProt ID: Q03689

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2530740.231123
FMO2-HF: Nuclear repulsion 2446736.170155
FMO2-HF: Total energy -84004.060968
FMO2-MP2: Total energy -84250.227661


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:10:ACE )


Summations of interaction energy for fragment #1(A:10: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.
-3.288-0.2670.444-1.705-1.76-0.01
Interaction energy analysis for fragmet #1(A:10:ACE )
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 : -0.009
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].
3A12LEU 0-0.0100.0063.8720.9851.787-0.004-0.363-0.436-0.001
4A13ASN 0-0.0250.0045.4170.1990.1990.0000.0000.0000.000
5A14VAL 00.0660.0187.640-0.050-0.0500.0000.0000.0000.000
6A15ALA 00.0460.0288.907-0.045-0.0450.0000.0000.0000.000
7A16GLY 00.0420.02710.371-0.012-0.0120.0000.0000.0000.000
8A17LEU 0-0.0350.0064.884-0.052-0.0520.0000.0000.0000.000
9A18PHE 00.0310.0139.1980.0120.0120.0000.0000.0000.000
10A19ASN 00.001-0.01012.4630.0130.0130.0000.0000.0000.000
11A20ASN 0-0.015-0.02511.348-0.008-0.0080.0000.0000.0000.000
12A21CYS 00.0210.01911.8680.0190.0190.0000.0000.0000.000
13A22VAL 0-0.047-0.00814.2170.0060.0060.0000.0000.0000.000
14A23ASP -1-0.750-0.87816.623-0.149-0.1490.0000.0000.0000.000
15A24CYS 0-0.064-0.02714.907-0.008-0.0080.0000.0000.0000.000
16A25PHE 0-0.017-0.02417.8830.0060.0060.0000.0000.0000.000
17A26GLU -1-0.882-0.92320.909-0.058-0.0580.0000.0000.0000.000
18A27TYR 0-0.075-0.02719.941-0.003-0.0030.0000.0000.0000.000
19A28VAL 0-0.044-0.01021.4820.0010.0010.0000.0000.0000.000
20A29GLN 00.0430.01924.1640.0050.0050.0000.0000.0000.000
21A30LEU 0-0.010-0.00627.7310.0030.0030.0000.0000.0000.000
22A31GLY 00.0670.03030.336-0.001-0.0010.0000.0000.0000.000
23A32ARG 11.0131.01032.5810.0220.0220.0000.0000.0000.000
24A33PRO 0-0.008-0.01234.1220.0030.0030.0000.0000.0000.000
25A34PHE 0-0.031-0.00829.6110.0030.0030.0000.0000.0000.000
26A35GLY 00.0140.01035.4940.0020.0020.0000.0000.0000.000
27A36ARG 10.9170.94238.3370.0010.0010.0000.0000.0000.000
28A37ASP -1-0.942-0.96335.7260.0000.0000.0000.0000.0000.000
29A38TYR 00.0380.02332.0510.0020.0020.0000.0000.0000.000
30A39GLU -1-0.786-0.89933.858-0.009-0.0090.0000.0000.0000.000
31A40ARG 10.9710.97634.214-0.009-0.0090.0000.0000.0000.000
32A41CYS 0-0.037-0.02130.8860.0030.0030.0000.0000.0000.000
33A42GLN 0-0.0010.00327.6540.0000.0000.0000.0000.0000.000
34A43LEU 00.0290.01729.3070.0010.0010.0000.0000.0000.000
35A44ARG 10.8440.93228.985-0.016-0.0160.0000.0000.0000.000
36A45LEU 00.0120.01123.9140.0040.0040.0000.0000.0000.000
37A46ASP -1-0.773-0.86525.067-0.020-0.0200.0000.0000.0000.000
38A47ILE 00.002-0.00426.2710.0020.0020.0000.0000.0000.000
39A48ALA 0-0.0130.00022.9690.0050.0050.0000.0000.0000.000
40A49LYS 10.8570.92821.6770.0490.0490.0000.0000.0000.000
41A50ALA 00.009-0.01022.1860.0010.0010.0000.0000.0000.000
42A51ARG 10.7890.88423.307-0.057-0.0570.0000.0000.0000.000
43A52LEU 00.0210.01216.0540.0090.0090.0000.0000.0000.000
44A53SER 0-0.042-0.02519.6970.0050.0050.0000.0000.0000.000
45A54ARG 10.8010.86620.939-0.026-0.0260.0000.0000.0000.000
46A55TRP 00.0050.02014.7100.0050.0050.0000.0000.0000.000
47A56GLY 00.007-0.01218.2580.0080.0080.0000.0000.0000.000
48A57GLU -1-0.911-0.95319.0060.0020.0020.0000.0000.0000.000
49A58ALA 0-0.027-0.02122.3330.0020.0020.0000.0000.0000.000
50A59VAL 0-0.086-0.03017.3380.0020.0020.0000.0000.0000.000
51A60LYS 10.9370.96219.737-0.033-0.0330.0000.0000.0000.000
52A61ILE 0-0.0010.00413.1890.0010.0010.0000.0000.0000.000
53A62ASN 00.007-0.01616.187-0.017-0.0170.0000.0000.0000.000
54A63ASP -1-0.975-0.98118.133-0.018-0.0180.0000.0000.0000.000
55A64ASP -1-0.814-0.88418.0850.1120.1120.0000.0000.0000.000
56A65PRO 00.022-0.01016.3410.0070.0070.0000.0000.0000.000
57A66ARG 10.8610.92114.397-0.151-0.1510.0000.0000.0000.000
58A67PHE 0-0.0180.00511.9740.0710.0710.0000.0000.0000.000
59A68HIS 0-0.063-0.03811.529-0.058-0.0580.0000.0000.0000.000
60A69SER 0-0.026-0.0189.533-0.032-0.0320.0000.0000.0000.000
61A70ASP -1-0.907-0.9603.172-1.777-0.3900.119-0.905-0.600-0.008
62A71ALA 00.011-0.0014.6990.5970.7450.000-0.009-0.1390.000
63A72PRO 00.0070.0236.615-0.220-0.2200.0000.0000.0000.000
64A73THR 00.028-0.0139.9580.0790.0790.0000.0000.0000.000
65A74ASP -1-0.905-0.96012.8720.2520.2520.0000.0000.0000.000
66A75LYS 10.9940.98113.372-0.260-0.2600.0000.0000.0000.000
67A76SER 00.0320.01914.0910.0500.0500.0000.0000.0000.000
68A77VAL 0-0.030-0.00710.7590.0140.0140.0000.0000.0000.000
69A78GLN 0-0.041-0.0189.4280.1200.1200.0000.0000.0000.000
70A79LEU 0-0.0060.01710.0410.0820.0820.0000.0000.0000.000
71A80ALA 00.0090.01511.8050.0090.0090.0000.0000.0000.000
72A81LYS 10.9090.9512.828-4.890-4.6610.325-0.246-0.3080.000
73A82SER 00.0150.0087.9760.0160.0160.0000.0000.0000.000
74A83ILE 00.017-0.0049.179-0.072-0.0720.0000.0000.0000.000
75A84VAL 0-0.007-0.0059.157-0.070-0.0700.0000.0000.0000.000
76A85GLU -1-0.926-0.9803.7741.2941.7490.004-0.182-0.277-0.001
77A86GLU -1-0.926-0.9688.3570.1640.1640.0000.0000.0000.000
78A87ILE 0-0.0060.00111.698-0.055-0.0550.0000.0000.0000.000
79A88LEU 0-0.018-0.0208.426-0.042-0.0420.0000.0000.0000.000
80A89LEU 00.0180.02410.031-0.036-0.0360.0000.0000.0000.000
81A90LEU 0-0.0120.01212.979-0.016-0.0160.0000.0000.0000.000
82A91PHE 0-0.005-0.01115.325-0.013-0.0130.0000.0000.0000.000
83A92GLU -1-0.898-0.95312.077-0.178-0.1780.0000.0000.0000.000
84A93SER 0-0.101-0.04715.9210.0030.0030.0000.0000.0000.000
85A94ALA 0-0.019-0.00418.429-0.002-0.0020.0000.0000.0000.000
86A95GLN 00.0580.02317.541-0.002-0.0020.0000.0000.0000.000
87A96LYS 10.8980.94517.2630.1010.1010.0000.0000.0000.000
88A97THR 0-0.056-0.03621.6480.0050.0050.0000.0000.0000.000
89A98SER 0-0.0120.00024.0190.0000.0000.0000.0000.0000.000
90A99LYS 10.9650.96519.8410.1070.1070.0000.0000.0000.000
91A100ARG 10.8900.94623.3170.0230.0230.0000.0000.0000.000
92A101TYR 0-0.0010.01227.8700.0040.0040.0000.0000.0000.000
93A102GLU -1-0.858-0.92228.415-0.057-0.0570.0000.0000.0000.000
94A103LEU 0-0.069-0.03428.7400.0000.0000.0000.0000.0000.000
95A104VAL 0-0.071-0.03131.8530.0020.0020.0000.0000.0000.000
96A105ALA 0-0.0220.01934.0420.0030.0030.0000.0000.0000.000
97A106ASP -1-0.818-0.87835.705-0.023-0.0230.0000.0000.0000.000
98A107GLN 0-0.003-0.03537.227-0.001-0.0010.0000.0000.0000.000
99A108GLN 0-0.064-0.03937.837-0.001-0.0010.0000.0000.0000.000
100A109ASP -1-0.975-0.99536.147-0.020-0.0200.0000.0000.0000.000
101A110LEU 0-0.018-0.02532.055-0.001-0.0010.0000.0000.0000.000
102A111VAL 0-0.047-0.00533.897-0.003-0.0030.0000.0000.0000.000
103A112VAL 0-0.037-0.02030.4230.0030.0030.0000.0000.0000.000
104A113PHE 0-0.095-0.03633.4350.0010.0010.0000.0000.0000.000
105A114GLU -1-0.908-0.96132.838-0.047-0.0470.0000.0000.0000.000
106A115ASP -1-0.696-0.82933.765-0.027-0.0270.0000.0000.0000.000
107A116LYS 10.8760.92335.5920.0310.0310.0000.0000.0000.000
108A117ASP -1-0.866-0.92137.784-0.024-0.0240.0000.0000.0000.000
109A118MET 0-0.0630.00133.3580.0020.0020.0000.0000.0000.000
110A119LYS 10.9310.95439.2560.0050.0050.0000.0000.0000.000
111A120PRO 0-0.022-0.04240.648-0.001-0.0010.0000.0000.0000.000
112A121ILE 00.0010.01140.854-0.001-0.0010.0000.0000.0000.000
113A122GLY 00.0740.05037.7810.0010.0010.0000.0000.0000.000
114A123ARG 10.8710.93136.1710.0190.0190.0000.0000.0000.000
115A124ALA 0-0.054-0.02835.941-0.002-0.0020.0000.0000.0000.000
116A125LEU 00.0300.01335.249-0.001-0.0010.0000.0000.0000.000
117A126HIS 0-0.062-0.04729.241-0.003-0.0030.0000.0000.0000.000
118A127ARG 10.8100.87431.1630.0270.0270.0000.0000.0000.000
119A128ARG 10.9901.00932.0510.0070.0070.0000.0000.0000.000
120A129LEU 00.001-0.00429.1740.0010.0010.0000.0000.0000.000
121A130ASN 00.018-0.00627.3350.0000.0000.0000.0000.0000.000
122A131ASP -1-0.938-0.95027.406-0.033-0.0330.0000.0000.0000.000
123A132LEU 0-0.031-0.02227.907-0.002-0.0020.0000.0000.0000.000
124A133VAL 0-0.019-0.00122.827-0.001-0.0010.0000.0000.0000.000
125A134SER 00.000-0.01424.052-0.007-0.0070.0000.0000.0000.000
126A135ARG 10.8990.95625.1770.0150.0150.0000.0000.0000.000
127A136ARG 10.8240.89522.608-0.002-0.0020.0000.0000.0000.000
128A137GLN 0-0.050-0.01118.382-0.015-0.0150.0000.0000.0000.000
129A138LYS 10.9640.98119.5170.0550.0550.0000.0000.0000.000
130A139GLN 0-0.023-0.02714.0710.0150.0150.0000.0000.0000.000
131A140THR 00.0590.04718.998-0.002-0.0020.0000.0000.0000.000
132A141SER 0-0.0160.00015.8630.0020.0020.0000.0000.0000.000
133A142LEU 0-0.024-0.00814.958-0.052-0.0520.0000.0000.0000.000
134A143ALA 0-0.003-0.00612.555-0.010-0.0100.0000.0000.0000.000
135A144LYS 10.9510.96814.6890.2240.2240.0000.0000.0000.000
136A145LYS 10.7880.88314.6810.1990.1990.0000.0000.0000.000
137A146THR 0-0.053-0.03518.5780.0080.0080.0000.0000.0000.000
138A147ALA 00.0220.01521.5370.0010.0010.0000.0000.0000.000
139A148TRP 0-0.034-0.00820.0820.0020.0020.0000.0000.0000.000
140A149ALA 00.0970.06024.6710.0040.0040.0000.0000.0000.000
141A150LEU 00.0090.00124.0030.0020.0020.0000.0000.0000.000
142A151TYR 0-0.019-0.04527.4450.0020.0020.0000.0000.0000.000
143A152ASP -1-0.820-0.92429.453-0.001-0.0010.0000.0000.0000.000
144A153GLY 00.0550.02129.7960.0000.0000.0000.0000.0000.000
145A154LYS 10.9010.95829.557-0.010-0.0100.0000.0000.0000.000
146A155SER 0-0.014-0.01225.3670.0050.0050.0000.0000.0000.000
147A156LEU 0-0.0320.00424.8360.0000.0000.0000.0000.0000.000
148A157GLU -1-0.846-0.93925.7540.0190.0190.0000.0000.0000.000
149A158LYS 10.9270.99022.327-0.026-0.0260.0000.0000.0000.000
150A159ILE 00.005-0.00220.3700.0070.0070.0000.0000.0000.000
151A160VAL 00.0280.02121.9420.0070.0070.0000.0000.0000.000
152A161ASP -1-0.884-0.95923.8760.0410.0410.0000.0000.0000.000
153A162GLN 0-0.071-0.05218.9950.0010.0010.0000.0000.0000.000
154A163VAL 00.0000.00618.4180.0140.0140.0000.0000.0000.000
155A164ALA 00.0090.01020.1300.0090.0090.0000.0000.0000.000
156A165ARG 10.8300.91121.655-0.059-0.0590.0000.0000.0000.000
157A166PHE 00.0460.02116.2310.0070.0070.0000.0000.0000.000
158A167VAL 0-0.031-0.01718.2080.0170.0170.0000.0000.0000.000
159A168ASP -1-0.801-0.88219.8540.0790.0790.0000.0000.0000.000
160A169GLU -1-1.037-1.02117.3330.2060.2060.0000.0000.0000.000
161A170LEU 00.009-0.00214.3150.0200.0200.0000.0000.0000.000
162A171GLU -1-0.885-0.94518.1010.0730.0730.0000.0000.0000.000
163A172LYS 10.9991.00621.606-0.140-0.1400.0000.0000.0000.000
164A173ALA 0-0.090-0.02417.6370.0010.0010.0000.0000.0000.000
165A174PHE 0-0.059-0.05015.6000.0120.0120.0000.0000.0000.000
166A175PRO 00.0470.04521.487-0.007-0.0070.0000.0000.0000.000
167A176ILE 0-0.013-0.02221.573-0.008-0.0080.0000.0000.0000.000
168A177GLU -1-0.845-0.92325.6690.0840.0840.0000.0000.0000.000
169A178ALA 0-0.028-0.00827.707-0.006-0.0060.0000.0000.0000.000
170A179VAL 0-0.019-0.01826.710-0.005-0.0050.0000.0000.0000.000
171A180CYS 00.005-0.00424.985-0.005-0.0050.0000.0000.0000.000
172A181HIS 00.0440.02727.606-0.007-0.0070.0000.0000.0000.000
173A182LYS 10.9610.98531.208-0.024-0.0240.0000.0000.0000.000
174A183LEU 0-0.033-0.03325.794-0.004-0.0040.0000.0000.0000.000
175A184ALA 00.0010.01429.842-0.004-0.0040.0000.0000.0000.000
176A185GLU -1-0.917-0.96431.0120.0190.0190.0000.0000.0000.000
177A186ILE 0-0.037-0.01832.061-0.002-0.0020.0000.0000.0000.000
178A187GLU -1-0.817-0.85327.5800.0110.0110.0000.0000.0000.000
179A188ILE 00.021-0.00732.288-0.003-0.0030.0000.0000.0000.000
180A189GLU -1-0.944-0.96535.6590.0040.0040.0000.0000.0000.000
181A190GLU -1-0.941-0.97137.369-0.008-0.0080.0000.0000.0000.000
182A191VAL 0-0.119-0.04936.695-0.002-0.0020.0000.0000.0000.000
183A192GLU -1-0.854-0.94639.8710.0040.0040.0000.0000.0000.000
184A193ASP -1-0.884-0.93642.888-0.001-0.0010.0000.0000.0000.000
185A194GLU -1-0.806-0.92343.1680.0060.0060.0000.0000.0000.000
186A195ALA 0-0.057-0.00943.4560.0010.0010.0000.0000.0000.000
187A196SER 0-0.002-0.02139.7240.0000.0000.0000.0000.0000.000
188A197LEU 00.0180.01538.9030.0010.0010.0000.0000.0000.000
189A198THR 0-0.003-0.01139.0850.0020.0020.0000.0000.0000.000
190A199ILE 0-0.054-0.01936.7780.0010.0010.0000.0000.0000.000
191A200LEU 0-0.008-0.00733.3480.0010.0010.0000.0000.0000.000
192A201LYS 10.9831.00034.863-0.014-0.0140.0000.0000.0000.000
193A202ASP -1-0.954-0.97736.0810.0140.0140.0000.0000.0000.000
194A203ALA 0-0.070-0.04133.0610.0020.0020.0000.0000.0000.000
195A204ALA 00.0600.03330.9940.0010.0010.0000.0000.0000.000
196A205GLY 00.0390.03431.0920.0050.0050.0000.0000.0000.000
197A206GLY 0-0.042-0.04031.233-0.001-0.0010.0000.0000.0000.000
198A207ILE 0-0.090-0.05526.6170.0040.0040.0000.0000.0000.000
199A208ASP -1-0.743-0.88526.6800.0350.0350.0000.0000.0000.000
200A209ALA 00.0180.01528.845-0.004-0.0040.0000.0000.0000.000
201A210ALA 00.0510.02829.134-0.003-0.0030.0000.0000.0000.000
202A211MET 00.0050.01029.369-0.004-0.0040.0000.0000.0000.000
203A212SER 0-0.063-0.02432.085-0.003-0.0030.0000.0000.0000.000
204A213ASP -1-0.853-0.92634.6280.0310.0310.0000.0000.0000.000
205A214ALA 0-0.0240.00534.752-0.002-0.0020.0000.0000.0000.000
206A215ALA 0-0.010-0.00536.260-0.002-0.0020.0000.0000.0000.000
207A216ALA 0-0.042-0.03438.095-0.001-0.0010.0000.0000.0000.000
208A217GLN 0-0.013-0.01938.351-0.001-0.0010.0000.0000.0000.000
209A218LYS 10.8100.91440.062-0.006-0.0060.0000.0000.0000.000
210A219ILE 0-0.025-0.02041.965-0.001-0.0010.0000.0000.0000.000
211A220ASP -1-0.916-0.96444.3490.0140.0140.0000.0000.0000.000
212A221ALA 0-0.075-0.02945.230-0.001-0.0010.0000.0000.0000.000
213A222ILE 0-0.043-0.01746.018-0.001-0.0010.0000.0000.0000.000
214A223VAL 0-0.074-0.02448.634-0.001-0.0010.0000.0000.0000.000
215A224NME 0-0.042-0.00550.6950.0000.0000.0000.0000.0000.000