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: KG763

Calculation Name: 2WS9-3-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WS9

Chain ID: 3

ChEMBL ID:

UniProt ID: B9VV85

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2251280.665732
FMO2-HF: Nuclear repulsion 2166346.774463
FMO2-HF: Total energy -84933.891268
FMO2-MP2: Total energy -85182.613675


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(3:1:ALA)


Summations of interaction energy for fragment #1(3:1: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.
0.7171.871-0.011-0.504-0.6390.003
Interaction energy analysis for fragmet #1(3:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015
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].
333ILE00.0520.0133.8111.5342.688-0.011-0.504-0.6390.003
434ARG10.9200.9646.090-0.783-0.7830.0000.0000.0000.000
535VAL00.0290.0209.009-0.060-0.0600.0000.0000.0000.000
636VAL0-0.006-0.00812.0230.0340.0340.0000.0000.0000.000
737SER0-0.022-0.00815.704-0.027-0.0270.0000.0000.0000.000
838VAL00.0380.02818.2660.0140.0140.0000.0000.0000.000
939PRO00.0290.00921.440-0.006-0.0060.0000.0000.0000.000
10310GLU-1-0.939-0.96024.6240.0130.0130.0000.0000.0000.000
11311SER0-0.032-0.01820.613-0.012-0.0120.0000.0000.0000.000
12312ASP-1-0.924-0.96022.819-0.045-0.0450.0000.0000.0000.000
13313SER0-0.099-0.05625.080-0.002-0.0020.0000.0000.0000.000
14314PHE00.013-0.00827.683-0.003-0.0030.0000.0000.0000.000
15315MET0-0.041-0.02528.371-0.002-0.0020.0000.0000.0000.000
16316SER00.0180.00731.117-0.003-0.0030.0000.0000.0000.000
17317SER00.0040.00933.747-0.002-0.0020.0000.0000.0000.000
18318VAL00.0450.03027.1040.0020.0020.0000.0000.0000.000
19319PRO0-0.079-0.03928.418-0.002-0.0020.0000.0000.0000.000
20320ASP-1-0.887-0.95323.835-0.075-0.0750.0000.0000.0000.000
21321ASN0-0.077-0.02325.654-0.002-0.0020.0000.0000.0000.000
22322SER00.0150.01125.404-0.003-0.0030.0000.0000.0000.000
23323THR0-0.017-0.01222.526-0.001-0.0010.0000.0000.0000.000
24324PRO0-0.0040.00523.9800.0070.0070.0000.0000.0000.000
25325LEU00.0580.00925.354-0.006-0.0060.0000.0000.0000.000
26326TYR0-0.042-0.01227.9390.0020.0020.0000.0000.0000.000
27327PRO0-0.007-0.02127.1070.0040.0040.0000.0000.0000.000
28328LYS10.9420.96228.1560.0860.0860.0000.0000.0000.000
29329VAL00.0510.05732.0380.0020.0020.0000.0000.0000.000
30330VAL00.0050.00235.4280.0000.0000.0000.0000.0000.000
31331VAL0-0.006-0.00837.7610.0020.0020.0000.0000.0000.000
32332PRO0-0.0060.00440.4600.0000.0000.0000.0000.0000.000
33333PRO00.0110.00144.1440.0000.0000.0000.0000.0000.000
34334ARG10.9600.97241.0660.0330.0330.0000.0000.0000.000
35335GLN00.0140.00847.3260.0000.0000.0000.0000.0000.000
36336VAL0-0.051-0.03149.7470.0000.0000.0000.0000.0000.000
37337PRO00.0350.01451.6460.0000.0000.0000.0000.0000.000
38338GLY00.0310.01853.6950.0000.0000.0000.0000.0000.000
39339ARG10.9801.00743.3060.0240.0240.0000.0000.0000.000
40340PHE00.0170.00949.4350.0010.0010.0000.0000.0000.000
41341THR0-0.038-0.03645.111-0.001-0.0010.0000.0000.0000.000
42342ASN00.0510.02545.6590.0000.0000.0000.0000.0000.000
43343PHE00.0590.01646.7430.0000.0000.0000.0000.0000.000
44344ILE00.0300.02550.0290.0010.0010.0000.0000.0000.000
45345ASP-1-0.901-0.95250.540-0.012-0.0120.0000.0000.0000.000
46346VAL0-0.033-0.01252.6870.0000.0000.0000.0000.0000.000
47347ALA0-0.004-0.00954.5810.0010.0010.0000.0000.0000.000
48348LYS10.8960.95753.2670.0090.0090.0000.0000.0000.000
49349GLN0-0.072-0.03155.4020.0000.0000.0000.0000.0000.000
50350THR00.0030.02059.1250.0000.0000.0000.0000.0000.000
51351TYR0-0.0200.00360.8950.0000.0000.0000.0000.0000.000
52352SER0-0.0260.00862.1340.0000.0000.0000.0000.0000.000
53353PHE0-0.008-0.01164.4430.0000.0000.0000.0000.0000.000
54354CYS00.0040.01166.6570.0000.0000.0000.0000.0000.000
55355SER0-0.048-0.02167.6920.0000.0000.0000.0000.0000.000
56356ILE00.0640.03069.5100.0000.0000.0000.0000.0000.000
57357SER0-0.015-0.01972.7650.0000.0000.0000.0000.0000.000
58358GLY0-0.0020.00671.4900.0000.0000.0000.0000.0000.000
59359LYS10.9190.96672.5560.0040.0040.0000.0000.0000.000
60360PRO00.0050.02370.8540.0000.0000.0000.0000.0000.000
61361TYR00.000-0.02972.2770.0000.0000.0000.0000.0000.000
62362PHE00.0430.03875.1470.0000.0000.0000.0000.0000.000
63363GLU-1-0.895-0.97477.737-0.004-0.0040.0000.0000.0000.000
64364VAL00.0550.04781.5360.0000.0000.0000.0000.0000.000
65365THR00.010-0.02084.2640.0000.0000.0000.0000.0000.000
66366ASN00.0210.01387.8180.0000.0000.0000.0000.0000.000
67367THR0-0.029-0.01689.9920.0000.0000.0000.0000.0000.000
68368SER0-0.047-0.05486.1070.0000.0000.0000.0000.0000.000
69369GLY0-0.0110.00087.7340.0000.0000.0000.0000.0000.000
70370ASP-1-0.901-0.95985.488-0.001-0.0010.0000.0000.0000.000
71371GLU-1-0.863-0.91883.123-0.001-0.0010.0000.0000.0000.000
72372PRO0-0.042-0.00777.9500.0000.0000.0000.0000.0000.000
73373LEU0-0.033-0.02379.5290.0000.0000.0000.0000.0000.000
74374PHE0-0.050-0.03069.9330.0000.0000.0000.0000.0000.000
75375GLN00.0620.01772.8050.0000.0000.0000.0000.0000.000
76376MET0-0.0060.02466.4230.0000.0000.0000.0000.0000.000
77377ASP-1-0.914-0.95266.608-0.001-0.0010.0000.0000.0000.000
78378VAL0-0.039-0.03162.8470.0000.0000.0000.0000.0000.000
79379SER00.0780.02460.4820.0000.0000.0000.0000.0000.000
80380LEU0-0.016-0.01256.2490.0000.0000.0000.0000.0000.000
81381SER0-0.020-0.00658.7510.0000.0000.0000.0000.0000.000
82382ALA00.0030.02160.8540.0000.0000.0000.0000.0000.000
83383ALA00.0650.03064.1350.0000.0000.0000.0000.0000.000
84384GLU-1-0.882-0.95466.530-0.004-0.0040.0000.0000.0000.000
85385LEU00.0120.00361.9590.0000.0000.0000.0000.0000.000
86386HIS0-0.0020.02262.3070.0000.0000.0000.0000.0000.000
87387GLY0-0.034-0.02062.1310.0000.0000.0000.0000.0000.000
88388THR0-0.061-0.05862.0420.0000.0000.0000.0000.0000.000
89389TYR00.0500.01153.5250.0000.0000.0000.0000.0000.000
90390VAL00.0310.00757.0920.0000.0000.0000.0000.0000.000
91391ALA00.0360.04556.6830.0000.0000.0000.0000.0000.000
92392SER00.032-0.00856.7090.0000.0000.0000.0000.0000.000
93393LEU0-0.063-0.01050.7510.0000.0000.0000.0000.0000.000
94394SER00.045-0.02252.0800.0000.0000.0000.0000.0000.000
95395SER0-0.0510.00552.2590.0000.0000.0000.0000.0000.000
96396PHE00.0130.02448.0230.0000.0000.0000.0000.0000.000
97397PHE0-0.069-0.04345.703-0.001-0.0010.0000.0000.0000.000
98398ALA00.0550.03447.6410.0010.0010.0000.0000.0000.000
99399GLN0-0.035-0.02047.8680.0010.0010.0000.0000.0000.000
1003100TYR00.0470.02750.613-0.001-0.0010.0000.0000.0000.000
1013101ARG10.8450.92451.8390.0020.0020.0000.0000.0000.000
1023102GLY00.0180.02054.350-0.001-0.0010.0000.0000.0000.000
1033103SER0-0.039-0.04057.1830.0000.0000.0000.0000.0000.000
1043104LEU00.0130.01359.859-0.001-0.0010.0000.0000.0000.000
1053105ASN00.0070.00062.2660.0010.0010.0000.0000.0000.000
1063106PHE00.0410.01064.8530.0000.0000.0000.0000.0000.000
1073107ASN0-0.081-0.03367.8500.0000.0000.0000.0000.0000.000
1083108PHE00.0430.02070.4010.0000.0000.0000.0000.0000.000
1093109ILE00.0190.00671.4810.0000.0000.0000.0000.0000.000
1103110PHE00.0060.00475.6470.0000.0000.0000.0000.0000.000
1113111THR0-0.076-0.05177.5190.0000.0000.0000.0000.0000.000
1123112GLY00.0050.01080.3610.0000.0000.0000.0000.0000.000
1133113ALA00.004-0.00783.9790.0000.0000.0000.0000.0000.000
1143114ALA00.0580.01386.4320.0000.0000.0000.0000.0000.000
1153115ALA0-0.042-0.01087.4740.0000.0000.0000.0000.0000.000
1163116THR0-0.040-0.00886.3060.0000.0000.0000.0000.0000.000
1173117LYS10.9580.97986.8880.0030.0030.0000.0000.0000.000
1183118ALA00.0230.00484.8500.0000.0000.0000.0000.0000.000
1193119LYS10.8840.95383.8450.0030.0030.0000.0000.0000.000
1203120PHE00.0250.01679.6270.0000.0000.0000.0000.0000.000
1213121LEU00.0160.03378.5920.0000.0000.0000.0000.0000.000
1223122VAL0-0.014-0.01173.3320.0000.0000.0000.0000.0000.000
1233123ALA00.0330.00874.6100.0000.0000.0000.0000.0000.000
1243124PHE00.0080.00366.3300.0000.0000.0000.0000.0000.000
1253125VAL0-0.008-0.00871.2780.0000.0000.0000.0000.0000.000
1263126PRO00.0090.00668.3860.0000.0000.0000.0000.0000.000
1273127PRO00.038-0.00465.2190.0000.0000.0000.0000.0000.000
1283128HIS0-0.0060.00568.3990.0000.0000.0000.0000.0000.000
1293129SER0-0.029-0.04971.5660.0000.0000.0000.0000.0000.000
1303130ALA0-0.053-0.06273.4080.0000.0000.0000.0000.0000.000
1313131ALA00.0540.10273.8240.0000.0000.0000.0000.0000.000
1323132PRO0-0.048-0.01875.2640.0000.0000.0000.0000.0000.000
1333133LYS10.9780.98478.4760.0000.0000.0000.0000.0000.000
1343134THR00.0420.03581.1920.0000.0000.0000.0000.0000.000
1353135ARG10.9570.96181.6140.0010.0010.0000.0000.0000.000
1363136ASP-1-0.932-0.95982.287-0.001-0.0010.0000.0000.0000.000
1373137GLU-1-0.906-0.96280.6880.0000.0000.0000.0000.0000.000
1383138ALA00.004-0.00677.5440.0000.0000.0000.0000.0000.000
1393139MET0-0.048-0.01077.9870.0000.0000.0000.0000.0000.000
1403140ALA0-0.0010.00278.9880.0000.0000.0000.0000.0000.000
1413141CYS0-0.085-0.02874.0370.0000.0000.0000.0000.0000.000
1423142ILE00.0150.01569.7590.0000.0000.0000.0000.0000.000
1433143HIS0-0.040-0.03073.8520.0000.0000.0000.0000.0000.000
1443144ALA0-0.0030.00975.0230.0000.0000.0000.0000.0000.000
1453145VAL00.011-0.00476.9870.0000.0000.0000.0000.0000.000
1463146TRP0-0.027-0.01577.5980.0000.0000.0000.0000.0000.000
1473147ASP-1-0.851-0.92780.015-0.003-0.0030.0000.0000.0000.000
1483148VAL00.0570.01981.2090.0000.0000.0000.0000.0000.000
1493149GLY0-0.084-0.04982.9740.0000.0000.0000.0000.0000.000
1503150LEU0-0.0060.02182.1290.0000.0000.0000.0000.0000.000
1513151ASN00.007-0.01678.1310.0000.0000.0000.0000.0000.000
1523152SER0-0.011-0.00379.1300.0000.0000.0000.0000.0000.000
1533153ALA00.0090.01074.0460.0000.0000.0000.0000.0000.000
1543154PHE00.0090.01074.4370.0000.0000.0000.0000.0000.000
1553155SER00.032-0.00668.3170.0000.0000.0000.0000.0000.000
1563156PHE0-0.0080.00269.7860.0000.0000.0000.0000.0000.000
1573157ASN0-0.025-0.01963.1230.0000.0000.0000.0000.0000.000
1583158VAL00.0100.02064.3270.0000.0000.0000.0000.0000.000
1593159PRO00.0250.00463.5120.0000.0000.0000.0000.0000.000
1603160TYR0-0.025-0.02855.8080.0000.0000.0000.0000.0000.000
1613161SER0-0.030-0.03361.0640.0000.0000.0000.0000.0000.000
1623162SER0-0.006-0.02558.2940.0000.0000.0000.0000.0000.000
1633163PRO00.0010.01158.2870.0000.0000.0000.0000.0000.000
1643164ALA00.0290.02954.0550.0000.0000.0000.0000.0000.000
1653165ASP-1-0.857-0.91951.1040.0010.0010.0000.0000.0000.000
1663166PHE0-0.035-0.03048.447-0.001-0.0010.0000.0000.0000.000
1673167MET0-0.0170.03152.9590.0010.0010.0000.0000.0000.000
1683168ALA00.001-0.01353.537-0.001-0.0010.0000.0000.0000.000
1693169VAL0-0.057-0.00752.4250.0000.0000.0000.0000.0000.000
1703170TYR0-0.043-0.04451.8320.0000.0000.0000.0000.0000.000
1713171SER0-0.022-0.01155.7740.0010.0010.0000.0000.0000.000
1723172ALA0-0.019-0.01458.5090.0000.0000.0000.0000.0000.000
1733173GLU-1-0.926-0.95260.4940.0010.0010.0000.0000.0000.000
1743174ALA0-0.025-0.01061.6870.0000.0000.0000.0000.0000.000
1753175THR00.0420.01757.5800.0010.0010.0000.0000.0000.000
1763176VAL0-0.016-0.02558.1970.0000.0000.0000.0000.0000.000
1773177VAL0-0.011-0.01254.8040.0000.0000.0000.0000.0000.000
1783178ASN00.0000.00257.1070.0000.0000.0000.0000.0000.000
1793179VAL00.0490.02559.434-0.001-0.0010.0000.0000.0000.000
1803180SER00.0080.00061.8490.0000.0000.0000.0000.0000.000
1813181GLY0-0.039-0.00363.6030.0000.0000.0000.0000.0000.000
1823182TRP00.0200.00167.3780.0000.0000.0000.0000.0000.000
1833183LEU0-0.0260.00568.8490.0000.0000.0000.0000.0000.000
1843184GLN00.0080.01170.7560.0000.0000.0000.0000.0000.000
1853185VAL0-0.008-0.00274.4870.0000.0000.0000.0000.0000.000
1863186TYR00.014-0.00976.9950.0000.0000.0000.0000.0000.000
1873187ALA00.0120.00480.7150.0000.0000.0000.0000.0000.000
1883188LEU0-0.052-0.03883.7330.0000.0000.0000.0000.0000.000
1893189THR0-0.022-0.01985.4820.0000.0000.0000.0000.0000.000
1903190ALA0-0.0160.00686.9400.0000.0000.0000.0000.0000.000
1913191LEU0-0.051-0.02586.4660.0000.0000.0000.0000.0000.000
1923192THR00.0120.01188.8950.0000.0000.0000.0000.0000.000
1933193SER0-0.015-0.04390.8110.0000.0000.0000.0000.0000.000
1943194THR00.0060.00792.9950.0000.0000.0000.0000.0000.000
1953195ASP-1-0.825-0.92495.128-0.003-0.0030.0000.0000.0000.000
1963196ILE0-0.053-0.02193.5540.0000.0000.0000.0000.0000.000
1973197ALA0-0.0050.00494.6240.0000.0000.0000.0000.0000.000
1983198VAL0-0.050-0.00692.4950.0000.0000.0000.0000.0000.000
1993199ASN0-0.054-0.03188.9700.0000.0000.0000.0000.0000.000
2003200SER00.0100.01890.5350.0000.0000.0000.0000.0000.000
2013201LYS10.9180.94684.9830.0040.0040.0000.0000.0000.000
2023202GLY00.0020.00984.3270.0000.0000.0000.0000.0000.000
2033203ARG10.8800.95079.1800.0050.0050.0000.0000.0000.000
2043204VAL00.0440.03475.9270.0000.0000.0000.0000.0000.000
2053205LEU0-0.025-0.00772.9930.0000.0000.0000.0000.0000.000
2063206VAL00.0210.00869.9950.0000.0000.0000.0000.0000.000
2073207ALA00.0070.00367.2590.0000.0000.0000.0000.0000.000
2083208VAL00.0100.00763.2680.0000.0000.0000.0000.0000.000
2093209SER0-0.007-0.01261.5730.0000.0000.0000.0000.0000.000
2103210ALA0-0.0200.00157.0640.0010.0010.0000.0000.0000.000
2113211GLY00.0140.01159.1120.0000.0000.0000.0000.0000.000
2123212PRO0-0.031-0.03557.8230.0000.0000.0000.0000.0000.000
2133213ASP-1-0.842-0.91255.568-0.004-0.0040.0000.0000.0000.000
2143214PHE0-0.041-0.00554.8560.0000.0000.0000.0000.0000.000
2153215SER0-0.035-0.02849.386-0.001-0.0010.0000.0000.0000.000
2163216LEU00.0220.01849.6160.0010.0010.0000.0000.0000.000
2173217ARG10.8760.94544.6070.0010.0010.0000.0000.0000.000
2183218HIS0-0.008-0.02143.2900.0000.0000.0000.0000.0000.000
2193219PRO00.0190.01442.0070.0010.0010.0000.0000.0000.000
2203220VAL0-0.025-0.02443.8230.0010.0010.0000.0000.0000.000
2213221ASP-1-0.899-0.93643.141-0.013-0.0130.0000.0000.0000.000
2223222LEU0-0.038-0.03446.3610.0010.0010.0000.0000.0000.000
2233223PRO0-0.0140.01249.5570.0000.0000.0000.0000.0000.000
2243224ASP-1-0.890-0.94251.612-0.006-0.0060.0000.0000.0000.000
2253225LYS10.8870.94154.3220.0080.0080.0000.0000.0000.000
2263226GLN00.0080.00457.2260.0000.0000.0000.0000.0000.000