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: VQ871

Calculation Name: 2WS9-2-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WS9

Chain ID: 2

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2180945.829269
FMO2-HF: Nuclear repulsion 2103771.710649
FMO2-HF: Total energy -77174.118619
FMO2-MP2: Total energy -77399.482557


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(2:31:GLY)


Summations of interaction energy for fragment #1(2:31:GLY)
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.
-1.0661.005-0.01-1.048-1.0140.003
Interaction energy analysis for fragmet #1(2:31:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.027
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].
3233THR0-0.0010.0143.8150.3881.908-0.014-0.782-0.7240.003
4234TYR00.007-0.0016.5270.2490.2490.0000.0000.0000.000
5235CYS0-0.020-0.0099.9550.1510.1510.0000.0000.0000.000
6236TYR00.0710.02812.8240.0700.0700.0000.0000.0000.000
7237SER0-0.030-0.02114.9060.0850.0850.0000.0000.0000.000
8238LYS10.9140.96510.7060.6430.6430.0000.0000.0000.000
9239PRO00.0120.01113.9320.0680.0680.0000.0000.0000.000
10240ASP-1-0.797-0.87416.938-0.309-0.3090.0000.0000.0000.000
11241GLY00.0490.01720.296-0.012-0.0120.0000.0000.0000.000
12242ARG10.8380.90822.9370.3120.3120.0000.0000.0000.000
13243PRO00.0470.02525.842-0.020-0.0200.0000.0000.0000.000
14244PRO00.010-0.00528.4870.0030.0030.0000.0000.0000.000
15245SER00.0140.00030.0180.0080.0080.0000.0000.0000.000
16246THR0-0.038-0.02032.5130.0080.0080.0000.0000.0000.000
17247VAL0-0.0020.01432.7380.0020.0020.0000.0000.0000.000
18248SER0-0.0160.00235.638-0.001-0.0010.0000.0000.0000.000
19249ASP-1-0.858-0.92736.781-0.151-0.1510.0000.0000.0000.000
20250PRO0-0.007-0.01636.158-0.007-0.0070.0000.0000.0000.000
21251VAL00.0130.01929.945-0.006-0.0060.0000.0000.0000.000
22252THR0-0.019-0.00130.1640.0080.0080.0000.0000.0000.000
23253ARG10.8450.90020.6990.3340.3340.0000.0000.0000.000
24254LEU00.0150.01024.4960.0130.0130.0000.0000.0000.000
25255GLY00.0330.02323.773-0.026-0.0260.0000.0000.0000.000
26256PRO00.0710.01019.133-0.001-0.0010.0000.0000.0000.000
27257THR0-0.027-0.01421.081-0.015-0.0150.0000.0000.0000.000
28258LEU00.0060.01823.4040.0160.0160.0000.0000.0000.000
29259SER0-0.0140.00820.9520.0120.0120.0000.0000.0000.000
30260ARG10.8730.93120.2960.2610.2610.0000.0000.0000.000
31261HIS00.0880.04015.972-0.009-0.0090.0000.0000.0000.000
32262TYR0-0.032-0.01817.5400.0750.0750.0000.0000.0000.000
33263THR00.0310.01115.797-0.089-0.0890.0000.0000.0000.000
34264PHE0-0.028-0.01317.3440.0710.0710.0000.0000.0000.000
35265LYS10.9020.95217.5630.1350.1350.0000.0000.0000.000
36266VAL0-0.066-0.04216.0800.0110.0110.0000.0000.0000.000
37267GLY00.0350.01619.1630.0220.0220.0000.0000.0000.000
38268GLU-1-0.833-0.89119.974-0.136-0.1360.0000.0000.0000.000
39269TRP00.0550.02615.361-0.006-0.0060.0000.0000.0000.000
40270PRO0-0.009-0.01620.9280.0230.0230.0000.0000.0000.000
41271HIS00.004-0.01123.925-0.006-0.0060.0000.0000.0000.000
42272SER0-0.041-0.01625.6370.0000.0000.0000.0000.0000.000
43273GLN0-0.0010.01823.8530.0070.0070.0000.0000.0000.000
44274SER00.0020.00324.7930.0080.0080.0000.0000.0000.000
45275HIS10.8380.88722.3330.0540.0540.0000.0000.0000.000
46276GLY00.011-0.00621.8870.0080.0080.0000.0000.0000.000
47277HIS10.7690.85922.3740.1550.1550.0000.0000.0000.000
48278ALA00.002-0.00819.922-0.017-0.0170.0000.0000.0000.000
49279TRP0-0.024-0.00518.5420.0210.0210.0000.0000.0000.000
50280ILE0-0.019-0.01118.942-0.048-0.0480.0000.0000.0000.000
51281CYS0-0.020-0.02617.8190.0340.0340.0000.0000.0000.000
52282PRO00.0190.01719.091-0.056-0.0560.0000.0000.0000.000
53283LEU0-0.0400.02115.8390.0020.0020.0000.0000.0000.000
54284PRO0-0.020-0.03020.5850.0120.0120.0000.0000.0000.000
55285SER00.1380.03922.4450.0070.0070.0000.0000.0000.000
56286ASP-1-0.774-0.82824.850-0.236-0.2360.0000.0000.0000.000
57287LYS10.7630.85922.3340.3060.3060.0000.0000.0000.000
58288LEU00.0920.05724.607-0.009-0.0090.0000.0000.0000.000
59289LYS10.9220.95725.9730.2140.2140.0000.0000.0000.000
60290LYS10.9000.94824.9390.2200.2200.0000.0000.0000.000
61291MET0-0.048-0.00219.914-0.009-0.0090.0000.0000.0000.000
62292GLY00.013-0.00324.190-0.002-0.0020.0000.0000.0000.000
63293SER0-0.002-0.01025.2040.0150.0150.0000.0000.0000.000
64294PHE00.0480.01623.2540.0050.0050.0000.0000.0000.000
65295HIS0-0.006-0.01025.3700.0120.0120.0000.0000.0000.000
66296GLU-1-0.837-0.89827.539-0.167-0.1670.0000.0000.0000.000
67297VAL00.0090.00528.3660.0100.0100.0000.0000.0000.000
68298VAL0-0.006-0.00726.0120.0070.0070.0000.0000.0000.000
69299LYS10.7860.88629.3400.1810.1810.0000.0000.0000.000
702100ALA0-0.0120.00732.1730.0100.0100.0000.0000.0000.000
712101HIS0-0.070-0.04932.0120.0160.0160.0000.0000.0000.000
722102HIS00.0560.04633.115-0.011-0.0110.0000.0000.0000.000
732103LEU0-0.064-0.03131.330-0.006-0.0060.0000.0000.0000.000
742104VAL00.002-0.01725.2880.0010.0010.0000.0000.0000.000
752105LYS10.8320.92623.1060.3260.3260.0000.0000.0000.000
762106ASN0-0.058-0.05019.8590.0450.0450.0000.0000.0000.000
772107GLY00.0380.03617.5210.0040.0040.0000.0000.0000.000
782108TRP0-0.005-0.01515.3040.0730.0730.0000.0000.0000.000
792109ASP-1-0.844-0.9089.698-1.820-1.8200.0000.0000.0000.000
802110VAL0-0.009-0.01510.5930.1860.1860.0000.0000.0000.000
812111VAL00.0340.0146.809-0.497-0.4970.0000.0000.0000.000
822112VAL0-0.027-0.0068.6260.3840.3840.0000.0000.0000.000
832113GLN0-0.045-0.0428.797-0.110-0.1100.0000.0000.0000.000
842114VAL00.0190.01710.8940.0260.0260.0000.0000.0000.000
852115ASN0-0.045-0.01713.2040.0740.0740.0000.0000.0000.000
862116ALA00.0240.00615.404-0.013-0.0130.0000.0000.0000.000
872117SER0-0.005-0.01016.5350.0450.0450.0000.0000.0000.000
882118PHE00.021-0.00417.7630.0040.0040.0000.0000.0000.000
892119ALA0-0.008-0.00518.7110.0110.0110.0000.0000.0000.000
902120HIS00.0010.01818.668-0.006-0.0060.0000.0000.0000.000
912121SER0-0.019-0.00118.5560.0420.0420.0000.0000.0000.000
922122GLY00.0810.02917.976-0.028-0.0280.0000.0000.0000.000
932123ALA0-0.059-0.03414.4480.0450.0450.0000.0000.0000.000
942124LEU00.0060.02213.016-0.018-0.0180.0000.0000.0000.000
952125CYS0-0.0170.00112.405-0.029-0.0290.0000.0000.0000.000
962126VAL00.0000.0009.7320.0360.0360.0000.0000.0000.000
972127ALA00.017-0.00210.974-0.184-0.1840.0000.0000.0000.000
982128ALA0-0.010-0.00112.9740.0200.0200.0000.0000.0000.000
992129VAL0-0.006-0.02114.6000.0170.0170.0000.0000.0000.000
1002130PRO0-0.031-0.01018.2230.0020.0020.0000.0000.0000.000
1012131GLU-1-0.818-0.91520.755-0.291-0.2910.0000.0000.0000.000
1022132TYR0-0.080-0.06721.3480.0240.0240.0000.0000.0000.000
1032133GLU-1-0.950-0.97523.407-0.194-0.1940.0000.0000.0000.000
1042134HIS00.0570.01525.8800.0060.0060.0000.0000.0000.000
1052135THR0-0.028-0.01325.8640.0170.0170.0000.0000.0000.000
1062136HIS00.0290.01928.5190.0000.0000.0000.0000.0000.000
1072137GLU-1-0.909-0.95131.820-0.143-0.1430.0000.0000.0000.000
1082138LYS10.8860.98629.6230.1750.1750.0000.0000.0000.000
1092139ALA0-0.056-0.06128.902-0.019-0.0190.0000.0000.0000.000
1102140LEU0-0.014-0.01326.1840.0030.0030.0000.0000.0000.000
1112141LYS10.9550.96526.8450.1770.1770.0000.0000.0000.000
1122142TRP0-0.036-0.03818.830-0.010-0.0100.0000.0000.0000.000
1132143SER0-0.061-0.02723.7220.0290.0290.0000.0000.0000.000
1142144GLU-1-0.826-0.89423.173-0.213-0.2130.0000.0000.0000.000
1152145LEU0-0.057-0.02224.3610.0200.0200.0000.0000.0000.000
1162146GLU-1-0.789-0.87724.804-0.154-0.1540.0000.0000.0000.000
1172147GLU-1-0.829-0.90721.720-0.263-0.2630.0000.0000.0000.000
1182148PRO0-0.009-0.01125.1280.0180.0180.0000.0000.0000.000
1192149ALA0-0.001-0.01125.7670.0050.0050.0000.0000.0000.000
1202150TYR00.0580.03424.837-0.007-0.0070.0000.0000.0000.000
1212151THR00.0150.00922.111-0.005-0.0050.0000.0000.0000.000
1222152TYR00.0250.01620.688-0.019-0.0190.0000.0000.0000.000
1232153GLN0-0.092-0.04519.913-0.009-0.0090.0000.0000.0000.000
1242154GLN00.000-0.01120.3960.0140.0140.0000.0000.0000.000
1252155LEU00.0570.04316.553-0.020-0.0200.0000.0000.0000.000
1262156SER0-0.013-0.02214.903-0.067-0.0670.0000.0000.0000.000
1272157VAL0-0.047-0.00915.153-0.017-0.0170.0000.0000.0000.000
1282158PHE0-0.0150.00716.2610.0000.0000.0000.0000.0000.000
1292159PRO0-0.022-0.01111.980-0.043-0.0430.0000.0000.0000.000
1302160HIS0-0.012-0.00810.7750.0410.0410.0000.0000.0000.000
1312161GLN00.000-0.0153.4230.2790.5960.003-0.179-0.1420.000
1322162LEU00.0220.0168.3020.1070.1070.0000.0000.0000.000
1332163LEU0-0.026-0.0088.3080.0200.0200.0000.0000.0000.000
1342164ASN00.0080.0049.9530.0050.0050.0000.0000.0000.000
1352165LEU00.0580.01411.5940.0960.0960.0000.0000.0000.000
1362166ARG10.9220.97713.994-0.372-0.3720.0000.0000.0000.000
1372167THR0-0.089-0.0469.4370.0130.0130.0000.0000.0000.000
1382168ASN0-0.019-0.0116.1070.3910.3910.0000.0000.0000.000
1392169SER00.0620.0238.097-0.163-0.1630.0000.0000.0000.000
1402170SER0-0.026-0.0165.500-0.099-0.0990.0000.0000.0000.000
1412171VAL00.0280.0244.9040.1110.1110.0000.0000.0000.000
1422172HIS0-0.051-0.0183.765-1.102-0.8680.001-0.087-0.1480.000
1432173LEU00.0020.0025.554-0.771-0.7710.0000.0000.0000.000
1442174VAL00.0050.0088.3980.3240.3240.0000.0000.0000.000
1452175MET0-0.043-0.01510.7160.1060.1060.0000.0000.0000.000
1462176PRO00.0080.02014.1070.0510.0510.0000.0000.0000.000
1472177TYR00.0150.00817.100-0.002-0.0020.0000.0000.0000.000
1482178ILE0-0.038-0.02119.7150.0070.0070.0000.0000.0000.000
1492179GLY00.0810.03122.1650.0000.0000.0000.0000.0000.000
1502180PRO0-0.0100.00425.6740.0060.0060.0000.0000.0000.000
1512181GLY00.0490.03229.0510.0170.0170.0000.0000.0000.000
1522182PRO0-0.048-0.04527.948-0.022-0.0220.0000.0000.0000.000
1532183THR0-0.023-0.01127.514-0.008-0.0080.0000.0000.0000.000
1542184THR00.0120.01127.0410.0050.0050.0000.0000.0000.000
1552185ASN00.0840.05929.523-0.007-0.0070.0000.0000.0000.000
1562186LEU00.027-0.00424.3460.0000.0000.0000.0000.0000.000
1572187THR0-0.048-0.02228.215-0.006-0.0060.0000.0000.0000.000
1582188LEU0-0.041-0.03231.0860.0060.0060.0000.0000.0000.000
1592189HIS0-0.045-0.03225.8430.0010.0010.0000.0000.0000.000
1602190ASN0-0.032-0.03123.315-0.019-0.0190.0000.0000.0000.000
1612191PRO00.0280.03021.878-0.009-0.0090.0000.0000.0000.000
1622192TRP00.001-0.00716.382-0.038-0.0380.0000.0000.0000.000
1632193THR0-0.0140.00618.8520.0300.0300.0000.0000.0000.000
1642194ILE0-0.021-0.01513.543-0.050-0.0500.0000.0000.0000.000
1652195VAL00.0490.03515.8230.0670.0670.0000.0000.0000.000
1662196ILE0-0.018-0.00613.581-0.072-0.0720.0000.0000.0000.000
1672197LEU00.0060.01115.6720.0670.0670.0000.0000.0000.000
1682198ILE00.0080.00816.524-0.007-0.0070.0000.0000.0000.000
1692199LEU0-0.019-0.00815.6710.0130.0130.0000.0000.0000.000
1702200SER0-0.010-0.00818.3870.0350.0350.0000.0000.0000.000
1712201GLU-1-0.747-0.86619.355-0.062-0.0620.0000.0000.0000.000
1722202LEU0-0.047-0.00219.3890.0220.0220.0000.0000.0000.000
1732203THR00.0180.01221.6790.0070.0070.0000.0000.0000.000
1742204GLY00.0480.02022.5430.0130.0130.0000.0000.0000.000
1752205PRO0-0.035-0.03023.113-0.014-0.0140.0000.0000.0000.000
1762206GLY00.0420.01525.031-0.009-0.0090.0000.0000.0000.000
1772207GLN0-0.047-0.00923.329-0.002-0.0020.0000.0000.0000.000
1782208THR00.008-0.01422.9310.0130.0130.0000.0000.0000.000
1792209VAL0-0.0010.00216.5680.0120.0120.0000.0000.0000.000
1802210PRO0-0.047-0.01318.477-0.033-0.0330.0000.0000.0000.000
1812211VAL00.0240.01514.503-0.011-0.0110.0000.0000.0000.000
1822212THR0-0.006-0.02213.8220.0310.0310.0000.0000.0000.000
1832213MET00.0140.00912.963-0.111-0.1110.0000.0000.0000.000
1842214SER00.0060.02411.7840.0930.0930.0000.0000.0000.000
1852215VAL0-0.007-0.01413.039-0.137-0.1370.0000.0000.0000.000
1862216ALA00.0370.01514.2600.1120.1120.0000.0000.0000.000
1872217PRO0-0.022-0.00115.805-0.070-0.0700.0000.0000.0000.000
1882218ILE0-0.016-0.01113.6380.0080.0080.0000.0000.0000.000
1892219ASP-1-0.859-0.92817.927-0.480-0.4800.0000.0000.0000.000
1902220ALA00.0100.00220.8400.0130.0130.0000.0000.0000.000
1912221MET0-0.084-0.03323.2730.0230.0230.0000.0000.0000.000
1922222VAL00.0120.00826.873-0.007-0.0070.0000.0000.0000.000
1932223ASN00.017-0.01329.780-0.001-0.0010.0000.0000.0000.000
1942224GLY00.0690.02533.347-0.002-0.0020.0000.0000.0000.000
1952225PRO0-0.0250.00636.515-0.005-0.0050.0000.0000.0000.000
1962226LEU0-0.026-0.00835.9310.0070.0070.0000.0000.0000.000
1972227PRO0-0.026-0.02439.2750.0020.0020.0000.0000.0000.000
1982228ASN0-0.0010.00641.027-0.010-0.0100.0000.0000.0000.000
1992229PRO0-0.045-0.02740.0650.0020.0020.0000.0000.0000.000
2002230GLU-1-0.937-0.95442.727-0.088-0.0880.0000.0000.0000.000