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: LJ519

Calculation Name: 2WS9-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WS9

Chain ID: 1

ChEMBL ID:

UniProt ID: B9VV85

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2668089.709436
FMO2-HF: Nuclear repulsion 2572599.768976
FMO2-HF: Total energy -95489.940461
FMO2-MP2: Total energy -95768.896573


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(1:1:VAL)


Summations of interaction energy for fragment #1(1:1:VAL)
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.
-12.856-6.6973.644-4.22-5.583-0.016
Interaction energy analysis for fragmet #1(1:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.000
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].
313ASN0-0.132-0.0783.035-3.7441.0010.082-2.740-2.087-0.001
414VAL0-0.074-0.0794.6550.4420.523-0.001-0.015-0.0650.000
515GLY0-0.014-0.0318.3680.2230.2230.0000.0000.0000.000
616GLH0-0.087-0.06710.4570.0480.0480.0000.0000.0000.000
717ASP-1-0.891-0.8808.418-1.168-1.1680.0000.0000.0000.000
818GLY0-0.128-0.0599.0210.2030.2030.0000.0000.0000.000
919GLU-1-0.883-0.9274.517-2.663-2.533-0.001-0.006-0.1230.000
10110PRO0-0.023-0.0303.837-0.522-0.3230.000-0.043-0.1560.000
11111GLY0-0.042-0.0252.021-2.786-1.7893.529-2.172-2.354-0.012
12112GLU-1-0.736-0.8493.016-4.489-4.6280.0360.765-0.661-0.003
13113THR0-0.101-0.0425.0741.3541.500-0.001-0.009-0.1370.000
14114GLU-1-0.753-0.8557.705-0.988-0.9880.0000.0000.0000.000
15115PRO00.0350.01611.0910.0260.0260.0000.0000.0000.000
16116ARG10.7960.89412.7761.0031.0030.0000.0000.0000.000
17117HIS00.0110.00714.9760.0170.0170.0000.0000.0000.000
18118ALA0-0.014-0.00817.6750.0320.0320.0000.0000.0000.000
19119LEU00.0180.00819.1140.0120.0120.0000.0000.0000.000
20120SER0-0.010-0.01222.8310.0140.0140.0000.0000.0000.000
21121PRO00.018-0.01925.5350.0020.0020.0000.0000.0000.000
22122VAL0-0.024-0.00427.5540.0040.0040.0000.0000.0000.000
23123ASP-1-0.870-0.93130.111-0.089-0.0890.0000.0000.0000.000
24124MET0-0.043-0.02030.0240.0050.0050.0000.0000.0000.000
25125HIS00.0140.01525.4840.0150.0150.0000.0000.0000.000
26126VAL00.0200.01130.6320.0100.0100.0000.0000.0000.000
27127HIS0-0.036-0.03834.1350.0050.0050.0000.0000.0000.000
28128THR00.0010.00629.8420.0010.0010.0000.0000.0000.000
29129ASP-1-0.830-0.89032.812-0.002-0.0020.0000.0000.0000.000
30130VAL00.015-0.01233.8360.0000.0000.0000.0000.0000.000
31131SER0-0.042-0.03336.3310.0000.0000.0000.0000.0000.000
32132PHE00.0350.02737.723-0.002-0.0020.0000.0000.0000.000
33133LEU0-0.065-0.03835.009-0.001-0.0010.0000.0000.0000.000
34134LEU0-0.018-0.02939.4820.0000.0000.0000.0000.0000.000
35135ASP-1-0.822-0.87742.155-0.007-0.0070.0000.0000.0000.000
36136ARG10.8350.91741.2920.0200.0200.0000.0000.0000.000
37137PHE0-0.009-0.00646.5210.0020.0020.0000.0000.0000.000
38138PHE0-0.033-0.01142.486-0.003-0.0030.0000.0000.0000.000
39139ASP-1-0.800-0.88948.331-0.007-0.0070.0000.0000.0000.000
40140VAL0-0.038-0.01248.6430.0000.0000.0000.0000.0000.000
41141GLU-1-0.796-0.88150.4350.0090.0090.0000.0000.0000.000
42142THR00.004-0.01053.644-0.002-0.0020.0000.0000.0000.000
43143LEU0-0.033-0.01157.0650.0010.0010.0000.0000.0000.000
44144GLU-1-0.862-0.93060.1270.0030.0030.0000.0000.0000.000
45145LEU0-0.0290.00463.8640.0010.0010.0000.0000.0000.000
46146SER00.0150.01366.5330.0010.0010.0000.0000.0000.000
47147ASN00.008-0.00868.898-0.001-0.0010.0000.0000.0000.000
48148LEU0-0.0040.01172.4400.0010.0010.0000.0000.0000.000
49149THR0-0.0160.00174.3390.0000.0000.0000.0000.0000.000
50150GLY0-0.0050.00174.5240.0000.0000.0000.0000.0000.000
51151SER0-0.031-0.04572.1700.0000.0000.0000.0000.0000.000
52152PRO0-0.0210.00968.0700.0010.0010.0000.0000.0000.000
53153ALA00.0100.00764.4020.0010.0010.0000.0000.0000.000
54154THR0-0.057-0.03062.403-0.001-0.0010.0000.0000.0000.000
55155HIS0-0.004-0.00755.3970.0010.0010.0000.0000.0000.000
56156VAL0-0.016-0.02654.2350.0000.0000.0000.0000.0000.000
57157LEU0-0.0200.00253.334-0.001-0.0010.0000.0000.0000.000
58158ASP-1-0.819-0.93248.8930.0260.0260.0000.0000.0000.000
59159PRO0-0.050-0.00946.8820.0000.0000.0000.0000.0000.000
60160PHE00.004-0.01543.753-0.001-0.0010.0000.0000.0000.000
61161GLY00.0470.02543.9840.0010.0010.0000.0000.0000.000
62162SER0-0.084-0.03844.9620.0000.0000.0000.0000.0000.000
63163THR00.0440.00943.6330.0020.0020.0000.0000.0000.000
64164ALA0-0.0300.00444.457-0.002-0.0020.0000.0000.0000.000
65165GLN0-0.0100.00541.0170.0020.0020.0000.0000.0000.000
66166LEU0-0.027-0.03143.728-0.004-0.0040.0000.0000.0000.000
67167ALA0-0.023-0.03140.3930.0020.0020.0000.0000.0000.000
68168TRP00.0540.04640.5420.0020.0020.0000.0000.0000.000
69169ALA00.0240.02242.0390.0030.0030.0000.0000.0000.000
70170ARG10.8580.93534.2040.0090.0090.0000.0000.0000.000
71171LEU00.0400.01236.905-0.004-0.0040.0000.0000.0000.000
72172LEU00.0390.01637.9100.0030.0030.0000.0000.0000.000
73173ASN0-0.075-0.04138.5400.0080.0080.0000.0000.0000.000
74174THR0-0.015-0.00532.7300.0040.0040.0000.0000.0000.000
75175CYS0-0.0420.00433.7560.0040.0040.0000.0000.0000.000
76176THR00.000-0.00134.9880.0020.0020.0000.0000.0000.000
77177TYR0-0.020-0.01337.134-0.001-0.0010.0000.0000.0000.000
78178PHE00.0710.02339.061-0.001-0.0010.0000.0000.0000.000
79179PHE00.0140.01041.5580.0010.0010.0000.0000.0000.000
80180SER00.0080.00542.941-0.001-0.0010.0000.0000.0000.000
81181ASP-1-0.827-0.88345.4810.0150.0150.0000.0000.0000.000
82182LEU0-0.011-0.01548.5790.0000.0000.0000.0000.0000.000
83183GLU-1-0.844-0.89950.981-0.004-0.0040.0000.0000.0000.000
84184LEU0-0.014-0.00452.5390.0000.0000.0000.0000.0000.000
85185SER0-0.026-0.00955.119-0.001-0.0010.0000.0000.0000.000
86186ILE00.013-0.00556.6540.0010.0010.0000.0000.0000.000
87187GLN0-0.021-0.02058.791-0.001-0.0010.0000.0000.0000.000
88188PHE00.0090.01560.9790.0000.0000.0000.0000.0000.000
89189LYS10.9110.96861.9370.0080.0080.0000.0000.0000.000
90190PHE00.0420.01964.0650.0010.0010.0000.0000.0000.000
91191THR0-0.030-0.01864.867-0.001-0.0010.0000.0000.0000.000
92192THR00.0330.00967.4730.0000.0000.0000.0000.0000.000
93193THR00.0150.00670.797-0.001-0.0010.0000.0000.0000.000
94194PRO00.0480.02870.3960.0010.0010.0000.0000.0000.000
95195SER0-0.017-0.00672.8650.0000.0000.0000.0000.0000.000
96196SER0-0.050-0.03375.0240.0000.0000.0000.0000.0000.000
97197VAL0-0.025-0.00372.8220.0010.0010.0000.0000.0000.000
98198GLY00.0280.02375.875-0.001-0.0010.0000.0000.0000.000
99199GLU-1-0.978-1.01376.407-0.002-0.0020.0000.0000.0000.000
1001100GLY00.0630.01673.3330.0000.0000.0000.0000.0000.000
1011101PHE0-0.0080.01171.993-0.001-0.0010.0000.0000.0000.000
1021102VAL0-0.0030.01466.4800.0010.0010.0000.0000.0000.000
1031103TRP00.001-0.00669.1130.0000.0000.0000.0000.0000.000
1041104VAL00.009-0.00262.4490.0000.0000.0000.0000.0000.000
1051105LYS10.8180.91664.752-0.009-0.0090.0000.0000.0000.000
1061106TRP00.0450.01656.5320.0000.0000.0000.0000.0000.000
1071107PHE0-0.044-0.02160.5650.0000.0000.0000.0000.0000.000
1081108PRO00.0400.02158.0590.0000.0000.0000.0000.0000.000
1091109VAL0-0.026-0.02453.4430.0000.0000.0000.0000.0000.000
1101110GLY0-0.0020.00056.9060.0010.0010.0000.0000.0000.000
1111111ALA0-0.045-0.00459.5630.0000.0000.0000.0000.0000.000
1121112PRO0-0.0020.00062.6930.0000.0000.0000.0000.0000.000
1131113THR00.056-0.00564.042-0.001-0.0010.0000.0000.0000.000
1141114LYS10.9420.99466.313-0.017-0.0170.0000.0000.0000.000
1151115THR0-0.0300.00769.0620.0000.0000.0000.0000.0000.000
1161116THR00.0540.02871.7520.0000.0000.0000.0000.0000.000
1171117ASP-1-0.825-0.88574.9850.0070.0070.0000.0000.0000.000
1181118ALA0-0.047-0.03677.0160.0000.0000.0000.0000.0000.000
1191119TRP0-0.0260.00277.7750.0000.0000.0000.0000.0000.000
1201120GLN0-0.026-0.02879.5620.0000.0000.0000.0000.0000.000
1211121LEU0-0.0150.01581.2430.0000.0000.0000.0000.0000.000
1221122GLU-1-0.786-0.90083.2450.0040.0040.0000.0000.0000.000
1231123GLY0-0.013-0.01786.7960.0000.0000.0000.0000.0000.000
1241124GLY0-0.0210.00388.4270.0000.0000.0000.0000.0000.000
1251125GLY0-0.0070.00691.5140.0000.0000.0000.0000.0000.000
1261126ASN0-0.013-0.01386.7350.0000.0000.0000.0000.0000.000
1271127SER00.0270.00385.2620.0000.0000.0000.0000.0000.000
1281128VAL0-0.056-0.01879.1200.0000.0000.0000.0000.0000.000
1291129ARG10.8550.90979.822-0.006-0.0060.0000.0000.0000.000
1301130ILE00.0270.02174.3330.0000.0000.0000.0000.0000.000
1311131GLN00.008-0.04471.4170.0010.0010.0000.0000.0000.000
1321132GLN00.0410.02173.4140.0000.0000.0000.0000.0000.000
1331133LEU0-0.031-0.02967.9400.0000.0000.0000.0000.0000.000
1341134ALA00.0230.01768.8800.0000.0000.0000.0000.0000.000
1351135VAL0-0.0080.00370.602-0.001-0.0010.0000.0000.0000.000
1361136ALA00.0180.00970.3160.0010.0010.0000.0000.0000.000
1371137GLY00.008-0.01269.5750.0000.0000.0000.0000.0000.000
1381138MET0-0.028-0.00467.361-0.001-0.0010.0000.0000.0000.000
1391139SER0-0.0110.00163.3540.0000.0000.0000.0000.0000.000
1401140PRO00.0330.00561.546-0.001-0.0010.0000.0000.0000.000
1411141THR00.0170.02064.7310.0010.0010.0000.0000.0000.000
1421142VAL0-0.046-0.01963.268-0.001-0.0010.0000.0000.0000.000
1431143VAL00.0120.00266.5980.0000.0000.0000.0000.0000.000
1441144PHE0-0.0140.00164.993-0.001-0.0010.0000.0000.0000.000
1451145LYS10.9490.99369.0080.0050.0050.0000.0000.0000.000
1461146ILE0-0.0060.01367.891-0.001-0.0010.0000.0000.0000.000
1471147ALA00.0800.01270.5080.0000.0000.0000.0000.0000.000
1481148GLY0-0.048-0.00872.7820.0000.0000.0000.0000.0000.000
1491149SER0-0.072-0.04068.139-0.001-0.0010.0000.0000.0000.000
1501150ARG10.9710.98265.8090.0090.0090.0000.0000.0000.000
1511151SER0-0.008-0.00762.695-0.001-0.0010.0000.0000.0000.000
1521152GLN0-0.104-0.05964.3160.0000.0000.0000.0000.0000.000
1531153ALA00.0260.02360.9840.0010.0010.0000.0000.0000.000
1541154CYS0-0.0370.00961.7750.0000.0000.0000.0000.0000.000
1551155GLY00.0510.00658.786-0.001-0.0010.0000.0000.0000.000
1561156PHE0-0.058-0.01357.7460.0000.0000.0000.0000.0000.000
1571157SER00.007-0.02454.0730.0000.0000.0000.0000.0000.000
1581158VAL0-0.045-0.01554.3580.0000.0000.0000.0000.0000.000
1591159PRO00.0130.00752.5480.0000.0000.0000.0000.0000.000
1601160TYR0-0.028-0.03046.9930.0010.0010.0000.0000.0000.000
1611161THR0-0.022-0.02651.2990.0010.0010.0000.0000.0000.000
1621162SER0-0.037-0.01650.2420.0020.0020.0000.0000.0000.000
1631163MET00.0160.01352.3240.0000.0000.0000.0000.0000.000
1641164TRP0-0.026-0.00747.5600.0040.0040.0000.0000.0000.000
1651165ARG10.9610.98441.787-0.062-0.0620.0000.0000.0000.000
1661166VAL0-0.051-0.02741.092-0.001-0.0010.0000.0000.0000.000
1671167VAL00.0450.03544.4750.0020.0020.0000.0000.0000.000
1681168PRO0-0.036-0.01942.3590.0010.0010.0000.0000.0000.000
1691169VAL00.0100.01040.249-0.002-0.0020.0000.0000.0000.000
1701170PHE0-0.032-0.02638.1900.0010.0010.0000.0000.0000.000
1711171TYR0-0.031-0.01841.4880.0030.0030.0000.0000.0000.000
1721172ASN00.0080.00940.404-0.005-0.0050.0000.0000.0000.000
1731173GLY00.0130.00342.8760.0040.0040.0000.0000.0000.000
1741174TRP00.0170.00146.4050.0000.0000.0000.0000.0000.000
1751175GLY0-0.044-0.01550.0320.0010.0010.0000.0000.0000.000
1761176ALA00.0100.00151.934-0.002-0.0020.0000.0000.0000.000
1771177PRO0-0.004-0.01254.5540.0020.0020.0000.0000.0000.000
1781178THR0-0.018-0.00356.3090.0020.0020.0000.0000.0000.000
1791179LYS10.9300.95450.866-0.059-0.0590.0000.0000.0000.000
1801180GLU-1-0.854-0.90254.0690.0360.0360.0000.0000.0000.000
1811181LYS10.9320.96249.283-0.045-0.0450.0000.0000.0000.000
1821182ALA00.0420.01152.561-0.002-0.0020.0000.0000.0000.000
1831183THR00.0230.01852.9330.0000.0000.0000.0000.0000.000
1841184TYR0-0.050-0.03043.7600.0010.0010.0000.0000.0000.000
1851185ASN00.0100.01844.4770.0040.0040.0000.0000.0000.000
1861186TRP0-0.024-0.04246.842-0.002-0.0020.0000.0000.0000.000
1871187LEU00.0300.02947.566-0.001-0.0010.0000.0000.0000.000
1881188PRO00.0260.03150.221-0.002-0.0020.0000.0000.0000.000
1891189GLY00.0630.00452.4710.0010.0010.0000.0000.0000.000
1901190ALA00.0130.03747.7860.0000.0000.0000.0000.0000.000
1911191HIS00.001-0.01849.346-0.002-0.0020.0000.0000.0000.000
1921192PHE00.0150.00147.0010.0010.0010.0000.0000.0000.000
1931193GLY00.0210.03252.702-0.001-0.0010.0000.0000.0000.000
1941194SER0-0.028-0.02056.1960.0000.0000.0000.0000.0000.000
1951195ILE00.0170.00658.579-0.001-0.0010.0000.0000.0000.000
1961196LEU00.0040.00261.0110.0010.0010.0000.0000.0000.000
1971197LEU0-0.0090.00361.347-0.001-0.0010.0000.0000.0000.000
1981198THR0-0.003-0.01365.5280.0000.0000.0000.0000.0000.000
1991199SER00.005-0.03469.269-0.001-0.0010.0000.0000.0000.000
2001200ASP-1-0.859-0.92171.6760.0000.0000.0000.0000.0000.000
2011201ALA0-0.035-0.01570.7090.0000.0000.0000.0000.0000.000
2021202HIS0-0.018-0.01869.2190.0010.0010.0000.0000.0000.000
2031203ASP-1-0.740-0.84369.0630.0000.0000.0000.0000.0000.000
2041204LYS10.8270.87870.5570.0000.0000.0000.0000.0000.000
2051205GLY0-0.029-0.02966.944-0.001-0.0010.0000.0000.0000.000
2061206GLY00.0230.03263.4140.0010.0010.0000.0000.0000.000
2071207CYS0-0.041-0.01760.853-0.001-0.0010.0000.0000.0000.000
2081208TYR0-0.0050.01455.829-0.001-0.0010.0000.0000.0000.000
2091209LEU00.0160.00554.8450.0000.0000.0000.0000.0000.000
2101210ARG10.8250.89351.8710.0080.0080.0000.0000.0000.000
2111211TYR0-0.042-0.05949.2790.0020.0020.0000.0000.0000.000
2121212ARG10.8640.93847.7830.0080.0080.0000.0000.0000.000
2131213PHE0-0.009-0.02044.6720.0020.0020.0000.0000.0000.000
2141214PRO00.0670.04644.7620.0000.0000.0000.0000.0000.000
2151215ARG10.8600.90243.665-0.011-0.0110.0000.0000.0000.000
2161216ALA00.0110.00941.0520.0030.0030.0000.0000.0000.000
2171217ASN0-0.019-0.00538.733-0.004-0.0040.0000.0000.0000.000
2181218MET0-0.039-0.01635.8710.0010.0010.0000.0000.0000.000
2191219TYR00.0180.00934.8960.0010.0010.0000.0000.0000.000
2201220CYS0-0.020-0.02232.0760.0000.0000.0000.0000.0000.000
2211221PRO00.0570.03528.907-0.002-0.0020.0000.0000.0000.000
2221222ARG10.8980.95830.979-0.057-0.0570.0000.0000.0000.000
2231223PRO0-0.005-0.01529.729-0.007-0.0070.0000.0000.0000.000
2241224ILE00.0350.02830.480-0.004-0.0040.0000.0000.0000.000
2251225PRO00.0220.01131.959-0.001-0.0010.0000.0000.0000.000
2261226PRO00.040-0.00432.131-0.006-0.0060.0000.0000.0000.000
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