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: 4JR4N

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2250360.286988
FMO2-HF: Nuclear repulsion 2165424.634725
FMO2-HF: Total energy -84935.652263
FMO2-MP2: Total energy -85184.332944


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.
-0.0640.923-0.008-0.441-0.5380.002
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 : 0.013 / 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].
333ILE00.031-0.0013.811-0.8090.178-0.008-0.441-0.5380.002
434ARG10.9230.9666.1370.9200.9200.0000.0000.0000.000
535VAL00.0370.0198.307-0.017-0.0170.0000.0000.0000.000
636VAL0-0.016-0.01411.6890.0760.0760.0000.0000.0000.000
737SER00.0010.01115.175-0.011-0.0110.0000.0000.0000.000
838VAL00.0140.01517.9950.0170.0170.0000.0000.0000.000
939PRO00.0290.01221.1550.0090.0090.0000.0000.0000.000
10310GLU-1-0.940-0.96624.272-0.095-0.0950.0000.0000.0000.000
11311SER0-0.038-0.04420.540-0.005-0.0050.0000.0000.0000.000
12312ASP-1-0.919-0.95023.047-0.064-0.0640.0000.0000.0000.000
13313SER0-0.103-0.04225.0800.0080.0080.0000.0000.0000.000
14314PHE00.026-0.00227.683-0.004-0.0040.0000.0000.0000.000
15315MET0-0.052-0.03027.995-0.008-0.0080.0000.0000.0000.000
16316SER00.0490.02331.145-0.005-0.0050.0000.0000.0000.000
17317SER0-0.026-0.00533.839-0.001-0.0010.0000.0000.0000.000
18318VAL00.0330.02727.743-0.003-0.0030.0000.0000.0000.000
19319PRO0-0.048-0.02728.5720.0020.0020.0000.0000.0000.000
20320ASP-1-0.853-0.92023.775-0.154-0.1540.0000.0000.0000.000
21321ASN0-0.137-0.06725.0380.0150.0150.0000.0000.0000.000
22322SER00.0310.01625.488-0.004-0.0040.0000.0000.0000.000
23323THR00.0220.00522.762-0.006-0.0060.0000.0000.0000.000
24324PRO0-0.026-0.00724.0260.0110.0110.0000.0000.0000.000
25325LEU00.023-0.00425.2990.0000.0000.0000.0000.0000.000
26326TYR0-0.033-0.00827.9460.0050.0050.0000.0000.0000.000
27327PRO0-0.003-0.02027.069-0.001-0.0010.0000.0000.0000.000
28328LYS10.9450.96428.1390.0580.0580.0000.0000.0000.000
29329VAL00.0540.05332.0670.0030.0030.0000.0000.0000.000
30330VAL0-0.0040.00335.460-0.003-0.0030.0000.0000.0000.000
31331VAL00.002-0.00637.8060.0030.0030.0000.0000.0000.000
32332PRO00.0010.00440.511-0.001-0.0010.0000.0000.0000.000
33333PRO00.0010.00244.197-0.001-0.0010.0000.0000.0000.000
34334ARG10.9480.96840.9320.0430.0430.0000.0000.0000.000
35335GLN00.0250.00947.400-0.002-0.0020.0000.0000.0000.000
36336VAL0-0.041-0.02749.782-0.001-0.0010.0000.0000.0000.000
37337PRO00.0260.00851.739-0.001-0.0010.0000.0000.0000.000
38338GLY00.0270.02053.7900.0000.0000.0000.0000.0000.000
39339ARG10.9761.00443.3090.0440.0440.0000.0000.0000.000
40340PHE00.0170.01049.4660.0000.0000.0000.0000.0000.000
41341THR0-0.017-0.02445.134-0.001-0.0010.0000.0000.0000.000
42342ASN00.0230.01245.786-0.001-0.0010.0000.0000.0000.000
43343PHE00.0600.02546.5070.0010.0010.0000.0000.0000.000
44344ILE00.0280.01650.0620.0020.0020.0000.0000.0000.000
45345ASP-1-0.891-0.95050.580-0.037-0.0370.0000.0000.0000.000
46346VAL0-0.038-0.01552.8680.0010.0010.0000.0000.0000.000
47347ALA00.0040.01054.6840.0010.0010.0000.0000.0000.000
48348LYS10.8670.94953.1030.0360.0360.0000.0000.0000.000
49349GLN0-0.072-0.02455.0780.0010.0010.0000.0000.0000.000
50350THR0-0.002-0.00758.3920.0010.0010.0000.0000.0000.000
51351TYR0-0.0180.02061.0210.0000.0000.0000.0000.0000.000
52352SER0-0.047-0.01362.2400.0000.0000.0000.0000.0000.000
53353PHE00.002-0.00664.5620.0000.0000.0000.0000.0000.000
54354CYS0-0.016-0.00966.7720.0000.0000.0000.0000.0000.000
55355SER0-0.036-0.01967.8420.0010.0010.0000.0000.0000.000
56356ILE00.0540.02669.5740.0000.0000.0000.0000.0000.000
57357SER0-0.017-0.01372.7990.0010.0010.0000.0000.0000.000
58358GLY00.0100.00471.5910.0010.0010.0000.0000.0000.000
59359LYS10.8910.95972.6590.0130.0130.0000.0000.0000.000
60360PRO00.0120.02170.8780.0000.0000.0000.0000.0000.000
61361TYR0-0.006-0.02472.3890.0000.0000.0000.0000.0000.000
62362PHE00.0420.03475.2220.0000.0000.0000.0000.0000.000
63363GLU-1-0.793-0.89277.769-0.012-0.0120.0000.0000.0000.000
64364VAL00.0650.04981.5690.0000.0000.0000.0000.0000.000
65365THR00.007-0.01384.2970.0000.0000.0000.0000.0000.000
66366ASN00.0260.02487.8510.0000.0000.0000.0000.0000.000
67367THR0-0.051-0.03490.0200.0000.0000.0000.0000.0000.000
68368SER0-0.044-0.04786.0810.0000.0000.0000.0000.0000.000
69369GLY00.0040.01087.7700.0000.0000.0000.0000.0000.000
70370ASP-1-0.846-0.92185.524-0.013-0.0130.0000.0000.0000.000
71371GLU-1-0.834-0.90183.104-0.013-0.0130.0000.0000.0000.000
72372PRO0-0.033-0.00577.9360.0000.0000.0000.0000.0000.000
73373LEU0-0.044-0.03179.6710.0000.0000.0000.0000.0000.000
74374PHE0-0.053-0.03370.0210.0000.0000.0000.0000.0000.000
75375GLN00.0680.03072.9750.0000.0000.0000.0000.0000.000
76376MET0-0.0110.01566.7710.0000.0000.0000.0000.0000.000
77377ASP-1-0.844-0.93066.270-0.019-0.0190.0000.0000.0000.000
78378VAL0-0.058-0.03162.8540.0000.0000.0000.0000.0000.000
79379SER00.0520.00660.548-0.001-0.0010.0000.0000.0000.000
80380LEU0-0.010-0.00457.0480.0010.0010.0000.0000.0000.000
81381SER0-0.015-0.00558.6950.0000.0000.0000.0000.0000.000
82382ALA00.0000.02060.8910.0010.0010.0000.0000.0000.000
83383ALA00.0650.03064.1710.0000.0000.0000.0000.0000.000
84384GLU-1-0.862-0.94266.566-0.018-0.0180.0000.0000.0000.000
85385LEU0-0.022-0.00562.0880.0000.0000.0000.0000.0000.000
86386HIS00.0200.01262.491-0.001-0.0010.0000.0000.0000.000
87387GLY0-0.032-0.01762.2140.0000.0000.0000.0000.0000.000
88388THR0-0.060-0.03061.816-0.001-0.0010.0000.0000.0000.000
89389TYR00.0740.02453.970-0.001-0.0010.0000.0000.0000.000
90390VAL00.0320.01057.060-0.001-0.0010.0000.0000.0000.000
91391ALA00.0270.04056.716-0.001-0.0010.0000.0000.0000.000
92392SER00.021-0.00856.7430.0000.0000.0000.0000.0000.000
93393LEU0-0.078-0.01950.776-0.001-0.0010.0000.0000.0000.000
94394SER00.040-0.02852.113-0.002-0.0020.0000.0000.0000.000
95395SER0-0.0460.01252.295-0.001-0.0010.0000.0000.0000.000
96396PHE00.0170.02048.1130.0000.0000.0000.0000.0000.000
97397PHE0-0.055-0.03345.545-0.003-0.0030.0000.0000.0000.000
98398ALA00.0540.03747.6540.0020.0020.0000.0000.0000.000
99399GLN0-0.035-0.02148.2620.0000.0000.0000.0000.0000.000
1003100TYR00.0430.02450.650-0.001-0.0010.0000.0000.0000.000
1013101ARG10.8090.87851.8900.0380.0380.0000.0000.0000.000
1023102GLY00.0110.02254.3860.0000.0000.0000.0000.0000.000
1033103SER0-0.041-0.04257.2180.0010.0010.0000.0000.0000.000
1043104LEU00.0100.01159.625-0.001-0.0010.0000.0000.0000.000
1053105ASN00.0110.01562.2990.0010.0010.0000.0000.0000.000
1063106PHE00.0400.00764.8840.0000.0000.0000.0000.0000.000
1073107ASN0-0.075-0.03367.5720.0010.0010.0000.0000.0000.000
1083108PHE00.0420.02370.4310.0000.0000.0000.0000.0000.000
1093109ILE00.0260.00571.6380.0000.0000.0000.0000.0000.000
1103110PHE00.0020.00975.7090.0000.0000.0000.0000.0000.000
1113111THR0-0.077-0.04877.5440.0000.0000.0000.0000.0000.000
1123112GLY00.0050.00580.4830.0000.0000.0000.0000.0000.000
1133113ALA00.001-0.00884.1010.0000.0000.0000.0000.0000.000
1143114ALA00.0520.01186.5530.0000.0000.0000.0000.0000.000
1153115ALA0-0.0320.00087.6000.0000.0000.0000.0000.0000.000
1163116THR0-0.075-0.04286.5530.0000.0000.0000.0000.0000.000
1173117LYS10.8380.92086.7580.0130.0130.0000.0000.0000.000
1183118ALA00.0290.01284.8190.0000.0000.0000.0000.0000.000
1193119LYS10.8650.93183.9160.0130.0130.0000.0000.0000.000
1203120PHE00.0190.01079.6740.0000.0000.0000.0000.0000.000
1213121LEU00.0070.02678.5200.0000.0000.0000.0000.0000.000
1223122VAL0-0.013-0.00773.3950.0000.0000.0000.0000.0000.000
1233123ALA00.0320.00674.6300.0000.0000.0000.0000.0000.000
1243124PHE00.0140.00566.2100.0000.0000.0000.0000.0000.000
1253125VAL0-0.012-0.00971.3140.0000.0000.0000.0000.0000.000
1263126PRO00.0250.01968.4110.0000.0000.0000.0000.0000.000
1273127PRO00.026-0.00165.3090.0010.0010.0000.0000.0000.000
1283128HIS00.0010.00668.4400.0000.0000.0000.0000.0000.000
1293129SER0-0.057-0.05971.6080.0000.0000.0000.0000.0000.000
1303130ALA0-0.017-0.03973.4500.0000.0000.0000.0000.0000.000
1313131ALA00.0490.08873.6140.0000.0000.0000.0000.0000.000
1323132PRO0-0.056-0.02275.3040.0000.0000.0000.0000.0000.000
1333133LYS10.8830.92678.5150.0140.0140.0000.0000.0000.000
1343134THR00.0090.00881.2320.0000.0000.0000.0000.0000.000
1353135ARG10.8100.87081.6390.0130.0130.0000.0000.0000.000
1363136ASP-1-0.863-0.92482.324-0.013-0.0130.0000.0000.0000.000
1373137GLU-1-0.795-0.88080.768-0.014-0.0140.0000.0000.0000.000
1383138ALA00.008-0.00377.6220.0000.0000.0000.0000.0000.000
1393139MET0-0.056-0.01478.0240.0000.0000.0000.0000.0000.000
1403140ALA0-0.0050.00079.0980.0000.0000.0000.0000.0000.000
1413141CYS0-0.077-0.02774.0780.0000.0000.0000.0000.0000.000
1423142ILE00.0230.02069.8620.0000.0000.0000.0000.0000.000
1433143HIS0-0.020-0.02573.8880.0000.0000.0000.0000.0000.000
1443144ALA0-0.0110.00775.0340.0000.0000.0000.0000.0000.000
1453145VAL00.0180.00477.0200.0000.0000.0000.0000.0000.000
1463146TRP0-0.013-0.01077.5510.0000.0000.0000.0000.0000.000
1473147ASP-1-0.773-0.87280.046-0.013-0.0130.0000.0000.0000.000
1483148VAL00.0720.03381.2790.0000.0000.0000.0000.0000.000
1493149GLY0-0.045-0.03883.0030.0000.0000.0000.0000.0000.000
1503150LEU0-0.0090.02082.1260.0000.0000.0000.0000.0000.000
1513151ASN00.007-0.01578.1450.0000.0000.0000.0000.0000.000
1523152SER00.0070.00379.2710.0000.0000.0000.0000.0000.000
1533153ALA00.0070.01074.0490.0000.0000.0000.0000.0000.000
1543154PHE00.0010.00474.1990.0000.0000.0000.0000.0000.000
1553155SER00.0200.00268.2210.0000.0000.0000.0000.0000.000
1563156PHE00.0050.00069.5640.0000.0000.0000.0000.0000.000
1573157ASN0-0.030-0.03463.0310.0000.0000.0000.0000.0000.000
1583158VAL00.0050.01264.5150.0000.0000.0000.0000.0000.000
1593159PRO00.0180.00463.544-0.001-0.0010.0000.0000.0000.000
1603160TYR0-0.010-0.01855.9120.0000.0000.0000.0000.0000.000
1613161SER0-0.063-0.04661.1000.0000.0000.0000.0000.0000.000
1623162SER00.001-0.04258.3190.0010.0010.0000.0000.0000.000
1633163PRO00.0020.01158.316-0.001-0.0010.0000.0000.0000.000
1643164ALA00.0200.02554.139-0.001-0.0010.0000.0000.0000.000
1653165ASP-1-0.822-0.88451.208-0.038-0.0380.0000.0000.0000.000
1663166PHE0-0.037-0.02548.533-0.001-0.0010.0000.0000.0000.000
1673167MET00.0040.07052.9970.0000.0000.0000.0000.0000.000
1683168ALA00.002-0.01253.575-0.001-0.0010.0000.0000.0000.000
1693169VAL0-0.049-0.01052.5460.0010.0010.0000.0000.0000.000
1703170TYR0-0.040-0.04151.6940.0020.0020.0000.0000.0000.000
1713171SER0-0.044-0.03055.8140.0000.0000.0000.0000.0000.000
1723172ALA0-0.010-0.00858.5210.0000.0000.0000.0000.0000.000
1733173GLU-1-0.927-0.95260.535-0.018-0.0180.0000.0000.0000.000
1743174ALA0-0.032-0.01361.730-0.001-0.0010.0000.0000.0000.000
1753175THR00.0710.02257.6130.0000.0000.0000.0000.0000.000
1763176VAL0-0.025-0.02358.2540.0000.0000.0000.0000.0000.000
1773177VAL0-0.003-0.01454.6810.0000.0000.0000.0000.0000.000
1783178ASN0-0.0090.00357.1480.0000.0000.0000.0000.0000.000
1793179VAL00.0360.02359.4750.0000.0000.0000.0000.0000.000
1803180SER00.012-0.00361.761-0.001-0.0010.0000.0000.0000.000
1813181GLY0-0.0080.01063.6420.0000.0000.0000.0000.0000.000
1823182TRP0-0.028-0.01967.4170.0000.0000.0000.0000.0000.000
1833183LEU0-0.0380.00368.8220.0000.0000.0000.0000.0000.000
1843184GLN00.016-0.00270.7920.0000.0000.0000.0000.0000.000
1853185VAL0-0.013-0.01074.5120.0000.0000.0000.0000.0000.000
1863186TYR00.016-0.00277.0300.0000.0000.0000.0000.0000.000
1873187ALA00.0080.00580.7500.0000.0000.0000.0000.0000.000
1883188LEU0-0.048-0.03483.5690.0000.0000.0000.0000.0000.000
1893189THR0-0.003-0.01485.5160.0000.0000.0000.0000.0000.000
1903190ALA0-0.0250.00286.9730.0000.0000.0000.0000.0000.000
1913191LEU0-0.054-0.02586.5790.0000.0000.0000.0000.0000.000
1923192THR00.0150.00988.9270.0000.0000.0000.0000.0000.000
1933193SER00.015-0.01790.8410.0000.0000.0000.0000.0000.000
1943194THR00.0010.00393.0530.0000.0000.0000.0000.0000.000
1953195ASP-1-0.818-0.91995.252-0.009-0.0090.0000.0000.0000.000
1963196ILE0-0.056-0.02493.4600.0000.0000.0000.0000.0000.000
1973197ALA0-0.0090.00294.7410.0000.0000.0000.0000.0000.000
1983198VAL0-0.054-0.00992.5930.0000.0000.0000.0000.0000.000
1993199ASN0-0.070-0.03789.2070.0000.0000.0000.0000.0000.000
2003200SER00.0340.02590.6330.0000.0000.0000.0000.0000.000
2013201LYS10.8580.89285.0540.0110.0110.0000.0000.0000.000
2023202GLY00.0150.01384.4160.0000.0000.0000.0000.0000.000
2033203ARG10.8160.91079.1720.0130.0130.0000.0000.0000.000
2043204VAL00.0360.03075.8500.0000.0000.0000.0000.0000.000
2053205LEU0-0.014-0.00773.1570.0000.0000.0000.0000.0000.000
2063206VAL00.0170.00769.8800.0000.0000.0000.0000.0000.000
2073207ALA00.0020.00567.3890.0000.0000.0000.0000.0000.000
2083208VAL0-0.002-0.00263.1650.0000.0000.0000.0000.0000.000
2093209SER0-0.001-0.01461.5880.0000.0000.0000.0000.0000.000
2103210ALA0-0.0130.00457.0290.0000.0000.0000.0000.0000.000
2113211GLY00.0220.01259.1420.0000.0000.0000.0000.0000.000
2123212PRO0-0.023-0.03457.853-0.001-0.0010.0000.0000.0000.000
2133213ASP-1-0.826-0.90055.629-0.032-0.0320.0000.0000.0000.000
2143214PHE0-0.029-0.00254.888-0.001-0.0010.0000.0000.0000.000
2153215SER0-0.034-0.03249.376-0.001-0.0010.0000.0000.0000.000
2163216LEU00.0370.02549.6160.0010.0010.0000.0000.0000.000
2173217ARG10.8500.93345.3160.0430.0430.0000.0000.0000.000
2183218HIS00.010-0.01843.4730.0010.0010.0000.0000.0000.000
2193219PRO00.0270.02141.9420.0020.0020.0000.0000.0000.000
2203220VAL0-0.018-0.02343.860-0.001-0.0010.0000.0000.0000.000
2213221ASP-1-0.914-0.94143.143-0.038-0.0380.0000.0000.0000.000
2223222LEU0-0.041-0.03446.3980.0010.0010.0000.0000.0000.000
2233223PRO0-0.0010.01849.5590.0000.0000.0000.0000.0000.000
2243224ASP-1-0.908-0.95451.624-0.020-0.0200.0000.0000.0000.000
2253225LYS10.9020.94554.3220.0180.0180.0000.0000.0000.000
2263226GLN00.0020.00557.2420.0010.0010.0000.0000.0000.000