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: VRLG1

Calculation Name: 2WVN-A-Xray372

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: 2023-06-20

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2522121.647514
FMO2-HF: Nuclear repulsion 2438288.467191
FMO2-HF: Total energy -83833.180323
FMO2-MP2: Total energy -84078.825407


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:11:ALA)


Summations of interaction energy for fragment #1(A:11: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.
-10.131-5.7970.581-2.611-2.304-0.017
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.014
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].
3A13ASN0-0.0170.0073.583-2.075-0.4360.001-0.998-0.6410.003
4A14VAL00.0620.0166.1930.2080.2080.0000.0000.0000.000
5A15ALA00.0460.0287.9950.2560.2560.0000.0000.0000.000
6A16GLY00.0440.0287.8440.1950.1950.0000.0000.0000.000
7A17LEU0-0.0370.0064.1400.2180.358-0.001-0.016-0.1240.000
8A18PHE00.0340.0157.4910.2780.2780.0000.0000.0000.000
9A19ASN00.000-0.01011.2630.1910.1910.0000.0000.0000.000
10A20ASN0-0.017-0.0268.2410.2430.2430.0000.0000.0000.000
11A21CYS00.0210.02010.6060.1160.1160.0000.0000.0000.000
12A22VAL0-0.048-0.00912.3460.0490.0490.0000.0000.0000.000
13A23ASP-1-0.750-0.87913.413-0.028-0.0280.0000.0000.0000.000
14A24CYS0-0.065-0.02712.3090.0590.0590.0000.0000.0000.000
15A25PHE0-0.018-0.02415.2150.0250.0250.0000.0000.0000.000
16A26GLU-1-0.877-0.92318.106-0.047-0.0470.0000.0000.0000.000
17A27TYR0-0.074-0.02616.3400.0170.0170.0000.0000.0000.000
18A28VAL0-0.047-0.01119.0680.0190.0190.0000.0000.0000.000
19A29GLN00.0430.02021.565-0.005-0.0050.0000.0000.0000.000
20A30LEU0-0.008-0.00525.1970.0110.0110.0000.0000.0000.000
21A31GLY00.0650.03028.050-0.006-0.0060.0000.0000.0000.000
22A32ARG11.0131.00930.243-0.054-0.0540.0000.0000.0000.000
23A33PRO0-0.011-0.01332.109-0.006-0.0060.0000.0000.0000.000
24A34PHE0-0.022-0.00428.146-0.003-0.0030.0000.0000.0000.000
25A35GLY00.0060.00733.749-0.005-0.0050.0000.0000.0000.000
26A36ARG10.9170.94236.388-0.029-0.0290.0000.0000.0000.000
27A37ASP-1-0.939-0.96234.3870.0320.0320.0000.0000.0000.000
28A38TYR00.0370.02329.673-0.002-0.0020.0000.0000.0000.000
29A39GLU-1-0.783-0.89931.9710.0020.0020.0000.0000.0000.000
30A40ARG10.9710.97732.474-0.024-0.0240.0000.0000.0000.000
31A41CYS0-0.038-0.02229.405-0.001-0.0010.0000.0000.0000.000
32A42GLN00.0000.00325.3190.0090.0090.0000.0000.0000.000
33A43LEU00.0300.01827.546-0.004-0.0040.0000.0000.0000.000
34A44ARG10.8460.93328.081-0.027-0.0270.0000.0000.0000.000
35A45LEU00.0040.00922.522-0.001-0.0010.0000.0000.0000.000
36A46ASP-1-0.773-0.86523.598-0.018-0.0180.0000.0000.0000.000
37A47ILE00.004-0.00324.768-0.013-0.0130.0000.0000.0000.000
38A48ALA0-0.0060.00222.294-0.011-0.0110.0000.0000.0000.000
39A49LYS10.8490.92519.7790.0400.0400.0000.0000.0000.000
40A50ALA00.009-0.01020.870-0.024-0.0240.0000.0000.0000.000
41A51ARG10.7910.88423.1780.0350.0350.0000.0000.0000.000
42A52LEU00.0200.01215.420-0.017-0.0170.0000.0000.0000.000
43A53SER0-0.044-0.02518.818-0.037-0.0370.0000.0000.0000.000
44A54ARG10.8020.86619.8100.0630.0630.0000.0000.0000.000
45A55TRP00.0070.02114.516-0.033-0.0330.0000.0000.0000.000
46A56GLY00.006-0.01217.549-0.024-0.0240.0000.0000.0000.000
47A57GLU-1-0.912-0.95318.228-0.240-0.2400.0000.0000.0000.000
48A58ALA0-0.026-0.02121.384-0.008-0.0080.0000.0000.0000.000
49A59VAL0-0.087-0.03216.894-0.001-0.0010.0000.0000.0000.000
50A60LYS10.9390.96319.0380.2000.2000.0000.0000.0000.000
51A61ILE00.0010.00412.294-0.048-0.0480.0000.0000.0000.000
52A62ASN00.005-0.01714.911-0.162-0.1620.0000.0000.0000.000
53A63ASP-1-0.974-0.98016.608-0.381-0.3810.0000.0000.0000.000
54A64ASP-1-0.815-0.88417.286-0.467-0.4670.0000.0000.0000.000
55A65PRO00.019-0.01115.649-0.078-0.0780.0000.0000.0000.000
56A66ARG10.8620.92113.9800.2790.2790.0000.0000.0000.000
57A67PHE0-0.0180.00511.424-0.110-0.1100.0000.0000.0000.000
58A68HIS0-0.062-0.03710.464-0.204-0.2040.0000.0000.0000.000
59A69SER0-0.028-0.0198.990-0.028-0.0280.0000.0000.0000.000
60A70ASP-1-0.903-0.9572.613-11.837-9.4420.582-1.580-1.397-0.020
61A71ALA00.006-0.0035.2570.0470.0470.0000.0000.0000.000
62A72PRO00.0080.0247.5170.2210.2210.0000.0000.0000.000
63A73THR00.026-0.01310.7280.0950.0950.0000.0000.0000.000
64A74ASP-1-0.903-0.96013.985-0.266-0.2660.0000.0000.0000.000
65A75LYS10.9940.98114.4560.0930.0930.0000.0000.0000.000
66A76SER00.0290.01815.2260.0130.0130.0000.0000.0000.000
67A77VAL0-0.028-0.00610.9690.0080.0080.0000.0000.0000.000
68A78GLN0-0.038-0.01710.7800.0120.0120.0000.0000.0000.000
69A79LEU0-0.0120.01611.3230.0540.0540.0000.0000.0000.000
70A80ALA00.0090.01512.8500.0560.0560.0000.0000.0000.000
71A81LYS10.9130.9533.5631.9992.1100.000-0.017-0.0940.000
72A82SER00.0200.0108.7890.1340.1340.0000.0000.0000.000
73A83ILE00.014-0.00510.5680.0860.0860.0000.0000.0000.000
74A84VAL0-0.005-0.0058.9410.0550.0550.0000.0000.0000.000
75A85GLU-1-0.922-0.9795.1750.7270.776-0.0010.000-0.0480.000
76A86GLU-1-0.933-0.9719.0370.3940.3940.0000.0000.0000.000
77A87ILE0-0.0050.00112.6690.0090.0090.0000.0000.0000.000
78A88LEU0-0.018-0.0207.4880.0060.0060.0000.0000.0000.000
79A89LEU00.0160.02310.3730.0310.0310.0000.0000.0000.000
80A90LEU0-0.0140.01112.764-0.021-0.0210.0000.0000.0000.000
81A91PHE00.000-0.01013.735-0.009-0.0090.0000.0000.0000.000
82A92GLU-1-0.904-0.95510.9140.8190.8190.0000.0000.0000.000
83A93SER0-0.100-0.04614.516-0.016-0.0160.0000.0000.0000.000
84A94ALA0-0.018-0.00317.696-0.024-0.0240.0000.0000.0000.000
85A95GLN00.0580.02315.1570.0160.0160.0000.0000.0000.000
86A96LYS10.9000.94615.771-0.490-0.4900.0000.0000.0000.000
87A97THR0-0.061-0.03820.118-0.013-0.0130.0000.0000.0000.000
88A98SER0-0.0060.00322.377-0.011-0.0110.0000.0000.0000.000
89A99LYS10.9620.96417.582-0.340-0.3400.0000.0000.0000.000
90A100ARG10.8920.94522.512-0.228-0.2280.0000.0000.0000.000
91A101TYR0-0.0030.01326.206-0.009-0.0090.0000.0000.0000.000
92A102GLU-1-0.853-0.92125.7710.1350.1350.0000.0000.0000.000
93A103LEU0-0.071-0.03526.800-0.004-0.0040.0000.0000.0000.000
94A104VAL0-0.072-0.03129.796-0.004-0.0040.0000.0000.0000.000
95A105ALA0-0.0200.02132.032-0.007-0.0070.0000.0000.0000.000
96A106ASP-1-0.819-0.87833.6740.0660.0660.0000.0000.0000.000
97A107GLN0-0.003-0.03534.598-0.003-0.0030.0000.0000.0000.000
98A108GLN0-0.064-0.03935.103-0.005-0.0050.0000.0000.0000.000
99A109ASP-1-0.974-0.99434.0220.0670.0670.0000.0000.0000.000
100A110LEU0-0.021-0.02629.3200.0030.0030.0000.0000.0000.000
101A111VAL0-0.045-0.00431.0100.0000.0000.0000.0000.0000.000
102A112VAL0-0.036-0.01927.5270.0010.0010.0000.0000.0000.000
103A113PHE0-0.095-0.03730.730-0.005-0.0050.0000.0000.0000.000
104A114GLU-1-0.910-0.96029.6110.0310.0310.0000.0000.0000.000
105A115ASP-1-0.694-0.82930.992-0.009-0.0090.0000.0000.0000.000
106A116LYS10.8740.92132.786-0.025-0.0250.0000.0000.0000.000
107A117ASP-1-0.866-0.92234.9750.0230.0230.0000.0000.0000.000
108A118MET0-0.0610.00231.0990.0000.0000.0000.0000.0000.000
109A119LYS10.9280.95336.827-0.005-0.0050.0000.0000.0000.000
110A120PRO0-0.021-0.04238.291-0.001-0.0010.0000.0000.0000.000
111A121ILE00.0000.01038.452-0.002-0.0020.0000.0000.0000.000
112A122GLY00.0750.05135.804-0.003-0.0030.0000.0000.0000.000
113A123ARG10.8710.93233.8320.0020.0020.0000.0000.0000.000
114A124ALA0-0.056-0.02933.419-0.004-0.0040.0000.0000.0000.000
115A125LEU00.0320.01433.364-0.006-0.0060.0000.0000.0000.000
116A126HIS0-0.061-0.04626.709-0.004-0.0040.0000.0000.0000.000
117A127ARG10.8050.87228.7940.0140.0140.0000.0000.0000.000
118A128ARG10.9911.01029.4950.0440.0440.0000.0000.0000.000
119A129LEU00.002-0.00427.279-0.009-0.0090.0000.0000.0000.000
120A130ASN00.020-0.00524.941-0.012-0.0120.0000.0000.0000.000
121A131ASP-1-0.941-0.95124.864-0.079-0.0790.0000.0000.0000.000
122A132LEU0-0.032-0.02326.220-0.016-0.0160.0000.0000.0000.000
123A133VAL0-0.017-0.00120.525-0.016-0.0160.0000.0000.0000.000
124A134SER00.001-0.01321.753-0.023-0.0230.0000.0000.0000.000
125A135ARG10.8980.95522.4570.1100.1100.0000.0000.0000.000
126A136ARG10.8250.89620.8700.1350.1350.0000.0000.0000.000
127A137GLN0-0.051-0.01115.806-0.047-0.0470.0000.0000.0000.000
128A138LYS10.9640.98116.9580.4190.4190.0000.0000.0000.000
129A139GLN0-0.020-0.02610.532-0.077-0.0770.0000.0000.0000.000
130A140THR00.0560.04615.7490.0250.0250.0000.0000.0000.000
131A141SER0-0.0150.00011.3740.0520.0520.0000.0000.0000.000
132A142LEU0-0.024-0.00810.692-0.120-0.1200.0000.0000.0000.000
133A143ALA0-0.004-0.0068.1060.0370.0370.0000.0000.0000.000
134A144LYS10.9510.96710.064-0.108-0.1080.0000.0000.0000.000
135A145LYS10.7900.88411.1360.0560.0560.0000.0000.0000.000
136A146THR0-0.053-0.03514.671-0.019-0.0190.0000.0000.0000.000
137A147ALA00.0190.01418.1030.0120.0120.0000.0000.0000.000
138A148TRP0-0.032-0.00817.4780.0220.0220.0000.0000.0000.000
139A149ALA00.0940.05921.808-0.012-0.0120.0000.0000.0000.000
140A150LEU00.0150.00422.5490.0180.0180.0000.0000.0000.000
141A151TYR0-0.019-0.04525.555-0.015-0.0150.0000.0000.0000.000
142A152ASP-1-0.822-0.92528.3430.1020.1020.0000.0000.0000.000
143A153GLY00.0530.02128.6650.0020.0020.0000.0000.0000.000
144A154LYS10.9020.95829.313-0.075-0.0750.0000.0000.0000.000
145A155SER0-0.015-0.01224.3800.0080.0080.0000.0000.0000.000
146A156LEU0-0.0330.00424.0800.0080.0080.0000.0000.0000.000
147A157GLU-1-0.847-0.94025.0490.0430.0430.0000.0000.0000.000
148A158LYS10.9260.99022.436-0.168-0.1680.0000.0000.0000.000
149A159ILE00.005-0.00219.5800.0010.0010.0000.0000.0000.000
150A160VAL00.0260.02021.670-0.010-0.0100.0000.0000.0000.000
151A161ASP-1-0.883-0.95823.8000.0400.0400.0000.0000.0000.000
152A162GLN0-0.071-0.05220.1140.0000.0000.0000.0000.0000.000
153A163VAL00.0010.00718.058-0.006-0.0060.0000.0000.0000.000
154A164ALA00.0090.00920.233-0.021-0.0210.0000.0000.0000.000
155A165ARG10.8290.91122.553-0.027-0.0270.0000.0000.0000.000
156A166PHE00.0430.02017.237-0.012-0.0120.0000.0000.0000.000
157A167VAL0-0.028-0.01618.841-0.028-0.0280.0000.0000.0000.000
158A168ASP-1-0.803-0.88220.193-0.041-0.0410.0000.0000.0000.000
159A169GLU-1-1.036-1.02218.3640.0090.0090.0000.0000.0000.000
160A170LEU00.0100.00014.685-0.018-0.0180.0000.0000.0000.000
161A171GLU-1-0.879-0.94418.598-0.120-0.1200.0000.0000.0000.000
162A172LYS10.9911.00222.0360.0420.0420.0000.0000.0000.000
163A173ALA0-0.088-0.02418.418-0.003-0.0030.0000.0000.0000.000
164A174PHE0-0.055-0.04815.818-0.047-0.0470.0000.0000.0000.000
165A175PRO00.0470.04521.8630.0160.0160.0000.0000.0000.000
166A176ILE0-0.015-0.02221.534-0.007-0.0070.0000.0000.0000.000
167A177GLU-1-0.845-0.92425.769-0.097-0.0970.0000.0000.0000.000
168A178ALA0-0.028-0.00827.8280.0060.0060.0000.0000.0000.000
169A179VAL0-0.019-0.01726.1890.0040.0040.0000.0000.0000.000
170A180CYS00.007-0.00324.788-0.003-0.0030.0000.0000.0000.000
171A181HIS00.0400.02527.3210.0030.0030.0000.0000.0000.000
172A182LYS10.9600.98530.9680.0940.0940.0000.0000.0000.000
173A183LEU0-0.030-0.03225.1520.0030.0030.0000.0000.0000.000
174A184ALA0-0.0040.01229.1770.0020.0020.0000.0000.0000.000
175A185GLU-1-0.916-0.96330.483-0.065-0.0650.0000.0000.0000.000
176A186ILE0-0.035-0.01831.1890.0020.0020.0000.0000.0000.000
177A187GLU-1-0.813-0.85226.648-0.095-0.0950.0000.0000.0000.000
178A188ILE00.016-0.00831.0930.0060.0060.0000.0000.0000.000
179A189GLU-1-0.945-0.96634.501-0.078-0.0780.0000.0000.0000.000
180A190GLU-1-0.940-0.97135.705-0.066-0.0660.0000.0000.0000.000
181A191VAL0-0.119-0.04835.1580.0040.0040.0000.0000.0000.000
182A192GLU-1-0.856-0.94738.300-0.045-0.0450.0000.0000.0000.000
183A193ASP-1-0.880-0.93441.177-0.024-0.0240.0000.0000.0000.000
184A194GLU-1-0.806-0.92341.783-0.018-0.0180.0000.0000.0000.000
185A195ALA0-0.059-0.01042.2890.0010.0010.0000.0000.0000.000
186A196SER0-0.005-0.02238.1400.0020.0020.0000.0000.0000.000
187A197LEU00.0240.01737.7730.0000.0000.0000.0000.0000.000
188A198THR0-0.004-0.01138.1830.0000.0000.0000.0000.0000.000
189A199ILE0-0.056-0.02035.4180.0030.0030.0000.0000.0000.000
190A200LEU0-0.007-0.00632.1440.0030.0030.0000.0000.0000.000
191A201LYS10.9820.99934.1350.0140.0140.0000.0000.0000.000
192A202ASP-1-0.958-0.97935.703-0.004-0.0040.0000.0000.0000.000
193A203ALA0-0.066-0.03932.0380.0040.0040.0000.0000.0000.000
194A204ALA00.0570.03330.4760.0040.0040.0000.0000.0000.000
195A205GLY00.0370.03230.959-0.001-0.0010.0000.0000.0000.000
196A206GLY0-0.041-0.04031.5790.0060.0060.0000.0000.0000.000
197A207ILE0-0.085-0.05526.5250.0070.0070.0000.0000.0000.000
198A208ASP-1-0.739-0.88226.768-0.065-0.0650.0000.0000.0000.000
199A209ALA00.0130.01428.8770.0000.0000.0000.0000.0000.000
200A210ALA00.0500.02729.0100.0010.0010.0000.0000.0000.000
201A211MET00.0090.01228.5510.0030.0030.0000.0000.0000.000
202A212SER0-0.067-0.02631.7420.0030.0030.0000.0000.0000.000
203A213ASP-1-0.855-0.92634.531-0.036-0.0360.0000.0000.0000.000
204A214ALA0-0.0220.00634.3930.0010.0010.0000.0000.0000.000
205A215ALA0-0.007-0.00535.8470.0010.0010.0000.0000.0000.000
206A216ALA0-0.042-0.03437.5350.0020.0020.0000.0000.0000.000
207A217GLN0-0.017-0.02138.0520.0020.0020.0000.0000.0000.000
208A218LYS10.8120.91538.9140.0490.0490.0000.0000.0000.000
209A219ILE0-0.023-0.01941.3830.0010.0010.0000.0000.0000.000
210A220ASP-1-0.923-0.96743.708-0.023-0.0230.0000.0000.0000.000
211A221ALA0-0.087-0.03644.6930.0010.0010.0000.0000.0000.000
212A222ILE0-0.067-0.01745.1010.0000.0000.0000.0000.0000.000
213A223VAL0-0.068-0.01547.8320.0020.0020.0000.0000.0000.000