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: YV6L2

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2180945.486633
FMO2-HF: Nuclear repulsion 2103772.820204
FMO2-HF: Total energy -77172.666429
FMO2-MP2: Total energy -77398.004653


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.
0.0189999999999991.328-0.01-0.587-0.7120
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 : 0.016 / q_NPA : -0.003
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].
3233THR00.0020.0153.8150.4011.341-0.013-0.377-0.5500.000
4234TYR0-0.030-0.0156.5180.3480.3480.0000.0000.0000.000
5235CYS0-0.017-0.0109.9550.0370.0370.0000.0000.0000.000
6236TYR00.0610.02712.8150.0890.0890.0000.0000.0000.000
7237SER0-0.020-0.02214.8820.0580.0580.0000.0000.0000.000
8238LYS10.9430.97411.0520.1550.1550.0000.0000.0000.000
9239PRO00.0080.00613.6440.0330.0330.0000.0000.0000.000
10240ASP-1-0.863-0.91916.939-0.155-0.1550.0000.0000.0000.000
11241GLY00.0470.01920.297-0.004-0.0040.0000.0000.0000.000
12242ARG10.9090.94922.7470.1550.1550.0000.0000.0000.000
13243PRO00.0130.00825.843-0.012-0.0120.0000.0000.0000.000
14244PRO00.010-0.00428.419-0.002-0.0020.0000.0000.0000.000
15245SER00.0250.00030.0180.0060.0060.0000.0000.0000.000
16246THR0-0.039-0.01732.5130.0040.0040.0000.0000.0000.000
17247VAL0-0.0120.01032.7970.0000.0000.0000.0000.0000.000
18248SER0-0.040-0.01035.6380.0010.0010.0000.0000.0000.000
19249ASP-1-0.845-0.93337.073-0.061-0.0610.0000.0000.0000.000
20250PRO0-0.010-0.01536.158-0.003-0.0030.0000.0000.0000.000
21251VAL00.0290.02729.935-0.003-0.0030.0000.0000.0000.000
22252THR0-0.018-0.00630.3880.0090.0090.0000.0000.0000.000
23253ARG10.9020.94921.0370.0690.0690.0000.0000.0000.000
24254LEU00.0090.00924.7410.0120.0120.0000.0000.0000.000
25255GLY00.0220.01824.121-0.007-0.0070.0000.0000.0000.000
26256PRO00.0670.00919.791-0.006-0.0060.0000.0000.0000.000
27257THR0-0.017-0.01421.612-0.004-0.0040.0000.0000.0000.000
28258LEU0-0.0050.00723.9860.0030.0030.0000.0000.0000.000
29259SER0-0.029-0.00321.219-0.007-0.0070.0000.0000.0000.000
30260ARG10.9000.94920.711-0.006-0.0060.0000.0000.0000.000
31261HIS00.0500.01516.2600.0030.0030.0000.0000.0000.000
32262TYR0-0.044-0.01717.6190.0300.0300.0000.0000.0000.000
33263THR00.0250.01115.970-0.035-0.0350.0000.0000.0000.000
34264PHE0-0.020-0.00817.1330.0290.0290.0000.0000.0000.000
35265LYS10.9470.99017.3280.0780.0780.0000.0000.0000.000
36266VAL0-0.062-0.04115.9730.0090.0090.0000.0000.0000.000
37267GLY00.0350.01619.0160.0110.0110.0000.0000.0000.000
38268GLU-1-0.910-0.94919.911-0.097-0.0970.0000.0000.0000.000
39269TRP00.0480.02215.717-0.009-0.0090.0000.0000.0000.000
40270PRO0-0.009-0.01720.9890.0140.0140.0000.0000.0000.000
41271HIS0-0.003-0.01524.060-0.014-0.0140.0000.0000.0000.000
42272SER0-0.048-0.02125.797-0.005-0.0050.0000.0000.0000.000
43273GLN00.0200.02323.9230.0020.0020.0000.0000.0000.000
44274SER0-0.0050.00524.960-0.003-0.0030.0000.0000.0000.000
45275HIS10.8450.89022.5090.1680.1680.0000.0000.0000.000
46276GLY00.0130.00422.0670.0150.0150.0000.0000.0000.000
47277HIS10.8240.93122.3310.1930.1930.0000.0000.0000.000
48278ALA0-0.004-0.01020.045-0.030-0.0300.0000.0000.0000.000
49279TRP0-0.0100.00418.5380.0250.0250.0000.0000.0000.000
50280ILE0-0.016-0.00918.897-0.043-0.0430.0000.0000.0000.000
51281CYS0-0.022-0.03117.3750.0390.0390.0000.0000.0000.000
52282PRO00.0300.02318.902-0.038-0.0380.0000.0000.0000.000
53283LEU0-0.0390.02215.6920.0170.0170.0000.0000.0000.000
54284PRO0-0.032-0.04520.3210.0090.0090.0000.0000.0000.000
55285SER00.0910.00622.1550.0040.0040.0000.0000.0000.000
56286ASP-1-0.815-0.85424.612-0.146-0.1460.0000.0000.0000.000
57287LYS10.7750.87522.0370.1780.1780.0000.0000.0000.000
58288LEU00.1010.05524.3200.0050.0050.0000.0000.0000.000
59289LYS10.9980.99625.6770.1040.1040.0000.0000.0000.000
60290LYS10.8810.94224.5160.1000.1000.0000.0000.0000.000
61291MET0-0.0330.00120.1880.0050.0050.0000.0000.0000.000
62292GLY00.018-0.00124.1410.0040.0040.0000.0000.0000.000
63293SER00.0390.01825.6290.0010.0010.0000.0000.0000.000
64294PHE00.0350.02123.0760.0020.0020.0000.0000.0000.000
65295HIS0-0.018-0.01925.466-0.006-0.0060.0000.0000.0000.000
66296GLU-1-0.910-0.95627.499-0.054-0.0540.0000.0000.0000.000
67297VAL0-0.006-0.00328.4010.0020.0020.0000.0000.0000.000
68298VAL00.001-0.00426.0010.0000.0000.0000.0000.0000.000
69299LYS10.8820.95529.2710.0560.0560.0000.0000.0000.000
702100ALA0-0.0190.00432.0480.0020.0020.0000.0000.0000.000
712101HIS0-0.071-0.05231.9280.0090.0090.0000.0000.0000.000
722102HIS00.0280.03132.939-0.006-0.0060.0000.0000.0000.000
732103LEU0-0.066-0.03231.071-0.007-0.0070.0000.0000.0000.000
742104VAL0-0.015-0.02325.2400.0080.0080.0000.0000.0000.000
752105LYS10.8870.97523.2680.1540.1540.0000.0000.0000.000
762106ASN0-0.074-0.05219.9260.0270.0270.0000.0000.0000.000
772107GLY00.0450.04517.472-0.016-0.0160.0000.0000.0000.000
782108TRP0-0.007-0.01914.9270.0670.0670.0000.0000.0000.000
792109ASP-1-0.842-0.9139.760-0.648-0.6480.0000.0000.0000.000
802110VAL0-0.003-0.01310.3700.1430.1430.0000.0000.0000.000
812111VAL00.0300.0146.756-0.313-0.3130.0000.0000.0000.000
822112VAL0-0.034-0.0098.4150.2350.2350.0000.0000.0000.000
832113GLN0-0.035-0.0388.685-0.131-0.1310.0000.0000.0000.000
842114VAL0-0.0020.01310.8020.0140.0140.0000.0000.0000.000
852115ASN0-0.029-0.01113.2210.0730.0730.0000.0000.0000.000
862116ALA00.0180.00315.495-0.007-0.0070.0000.0000.0000.000
872117SER0-0.008-0.01216.5430.0320.0320.0000.0000.0000.000
882118PHE00.012-0.00917.318-0.017-0.0170.0000.0000.0000.000
892119ALA0-0.007-0.00418.409-0.001-0.0010.0000.0000.0000.000
902120HIS00.0130.02818.7350.0010.0010.0000.0000.0000.000
912121SER0-0.033-0.00518.4960.0000.0000.0000.0000.0000.000
922122GLY00.0980.03518.0500.0050.0050.0000.0000.0000.000
932123ALA0-0.072-0.04114.723-0.017-0.0170.0000.0000.0000.000
942124LEU00.0170.02913.1250.0340.0340.0000.0000.0000.000
952125CYS0-0.0060.00412.624-0.113-0.1130.0000.0000.0000.000
962126VAL0-0.019-0.00710.0220.0910.0910.0000.0000.0000.000
972127ALA00.019-0.00411.024-0.203-0.2030.0000.0000.0000.000
982128ALA0-0.0040.00012.8860.0560.0560.0000.0000.0000.000
992129VAL0-0.020-0.02014.5030.0000.0000.0000.0000.0000.000
1002130PRO0-0.020-0.00518.1480.0140.0140.0000.0000.0000.000
1012131GLU-1-0.814-0.91520.634-0.225-0.2250.0000.0000.0000.000
1022132TYR0-0.083-0.05621.2500.0140.0140.0000.0000.0000.000
1032133GLU-1-0.957-0.97723.326-0.167-0.1670.0000.0000.0000.000
1042134HIS00.0810.02926.256-0.002-0.0020.0000.0000.0000.000
1052135THR0-0.040-0.02625.8090.0140.0140.0000.0000.0000.000
1062136HIS00.0150.00928.4500.0050.0050.0000.0000.0000.000
1072137GLU-1-0.936-0.96131.726-0.107-0.1070.0000.0000.0000.000
1082138LYS10.9401.01728.4440.1660.1660.0000.0000.0000.000
1092139ALA0-0.062-0.07028.762-0.015-0.0150.0000.0000.0000.000
1102140LEU0-0.025-0.01425.9860.0060.0060.0000.0000.0000.000
1112141LYS10.9790.97726.6800.1250.1250.0000.0000.0000.000
1122142TRP0-0.051-0.02818.584-0.011-0.0110.0000.0000.0000.000
1132143SER0-0.072-0.03423.5790.0230.0230.0000.0000.0000.000
1142144GLU-1-0.896-0.95523.209-0.197-0.1970.0000.0000.0000.000
1152145LEU0-0.062-0.02824.3690.0240.0240.0000.0000.0000.000
1162146GLU-1-0.838-0.91324.854-0.191-0.1910.0000.0000.0000.000
1172147GLU-1-0.840-0.92721.862-0.270-0.2700.0000.0000.0000.000
1182148PRO0-0.004-0.00625.2270.0100.0100.0000.0000.0000.000
1192149ALA0-0.005-0.02426.0130.0040.0040.0000.0000.0000.000
1202150TYR00.0640.03325.040-0.018-0.0180.0000.0000.0000.000
1212151THR00.0200.00722.199-0.013-0.0130.0000.0000.0000.000
1222152TYR00.0200.02720.849-0.027-0.0270.0000.0000.0000.000
1232153GLN0-0.107-0.04920.123-0.021-0.0210.0000.0000.0000.000
1242154GLN00.000-0.01020.3910.0020.0020.0000.0000.0000.000
1252155LEU00.0620.04316.518-0.013-0.0130.0000.0000.0000.000
1262156SER0-0.006-0.01714.854-0.045-0.0450.0000.0000.0000.000
1272157VAL0-0.061-0.01615.146-0.035-0.0350.0000.0000.0000.000
1282158PHE0-0.0120.01016.2530.0230.0230.0000.0000.0000.000
1292159PRO0-0.030-0.01212.038-0.073-0.0730.0000.0000.0000.000
1302160HIS0-0.012-0.01210.8440.0100.0100.0000.0000.0000.000
1312161GLN00.014-0.0083.733-0.0680.1090.001-0.105-0.0720.000
1322162LEU00.0120.0178.4920.2110.2110.0000.0000.0000.000
1332163LEU0-0.039-0.0188.614-0.197-0.1970.0000.0000.0000.000
1342164ASN00.0100.00110.2030.1700.1700.0000.0000.0000.000
1352165LEU00.0460.00911.5890.0040.0040.0000.0000.0000.000
1362166ARG10.9350.98314.0400.1060.1060.0000.0000.0000.000
1372167THR0-0.077-0.0349.1980.0650.0650.0000.0000.0000.000
1382168ASN0-0.013-0.0046.7020.2500.2500.0000.0000.0000.000
1392169SER00.0540.0178.103-0.010-0.0100.0000.0000.0000.000
1402170SER0-0.027-0.0265.2810.2850.2850.0000.0000.0000.000
1412171VAL00.0090.0204.972-0.384-0.3840.0000.0000.0000.000
1422172HIS0-0.054-0.0273.4660.3910.6560.003-0.095-0.1730.000
1432173LEU0-0.004-0.0015.262-0.932-1.005-0.001-0.0100.0830.000
1442174VAL00.0140.0148.1490.3660.3660.0000.0000.0000.000
1452175MET0-0.033-0.01610.631-0.014-0.0140.0000.0000.0000.000
1462176PRO00.0040.02014.0790.0740.0740.0000.0000.0000.000
1472177TYR00.0230.00017.100-0.009-0.0090.0000.0000.0000.000
1482178ILE0-0.030-0.02119.720-0.002-0.0020.0000.0000.0000.000
1492179GLY00.0690.02722.1650.0030.0030.0000.0000.0000.000
1502180PRO0-0.0120.00425.6600.0040.0040.0000.0000.0000.000
1512181GLY00.0560.03529.0370.0120.0120.0000.0000.0000.000
1522182PRO0-0.053-0.03827.960-0.014-0.0140.0000.0000.0000.000
1532183THR00.0080.00127.485-0.005-0.0050.0000.0000.0000.000
1542184THR00.0250.02726.717-0.001-0.0010.0000.0000.0000.000
1552185ASN00.0860.05229.2400.0030.0030.0000.0000.0000.000
1562186LEU00.034-0.00624.042-0.004-0.0040.0000.0000.0000.000
1572187THR0-0.049-0.01127.910-0.005-0.0050.0000.0000.0000.000
1582188LEU0-0.044-0.03630.7940.0010.0010.0000.0000.0000.000
1592189HIS0-0.034-0.03126.2440.0070.0070.0000.0000.0000.000
1602190ASN0-0.004-0.01323.144-0.007-0.0070.0000.0000.0000.000
1612191PRO00.0310.03421.586-0.012-0.0120.0000.0000.0000.000
1622192TRP00.006-0.01516.488-0.042-0.0420.0000.0000.0000.000
1632193THR0-0.0260.00218.7210.0230.0230.0000.0000.0000.000
1642194ILE00.0090.00613.079-0.049-0.0490.0000.0000.0000.000
1652195VAL00.0400.03315.7560.0610.0610.0000.0000.0000.000
1662196ILE0-0.010-0.00313.752-0.090-0.0900.0000.0000.0000.000
1672197LEU00.0240.00215.7350.0700.0700.0000.0000.0000.000
1682198ILE00.0010.00716.682-0.044-0.0440.0000.0000.0000.000
1692199LEU0-0.028-0.00915.6860.0220.0220.0000.0000.0000.000
1702200SER0-0.042-0.01918.6570.0400.0400.0000.0000.0000.000
1712201GLU-1-0.711-0.85719.605-0.193-0.1930.0000.0000.0000.000
1722202LEU0-0.042-0.00119.4250.0030.0030.0000.0000.0000.000
1732203THR00.0010.00821.8930.0160.0160.0000.0000.0000.000
1742204GLY00.0620.02522.672-0.003-0.0030.0000.0000.0000.000
1752205PRO0-0.023-0.02623.126-0.001-0.0010.0000.0000.0000.000
1762206GLY00.0390.01625.198-0.009-0.0090.0000.0000.0000.000
1772207GLN0-0.049-0.00723.438-0.002-0.0020.0000.0000.0000.000
1782208THR00.008-0.01123.067-0.001-0.0010.0000.0000.0000.000
1792209VAL00.0000.00916.5590.0130.0130.0000.0000.0000.000
1802210PRO0-0.049-0.01918.340-0.026-0.0260.0000.0000.0000.000
1812211VAL00.0550.02114.393-0.010-0.0100.0000.0000.0000.000
1822212THR0-0.009-0.02012.9400.0320.0320.0000.0000.0000.000
1832213MET00.0270.01612.843-0.088-0.0880.0000.0000.0000.000
1842214SER0-0.0450.00511.7890.0310.0310.0000.0000.0000.000
1852215VAL00.0440.01112.825-0.091-0.0910.0000.0000.0000.000
1862216ALA00.0360.00814.5080.0710.0710.0000.0000.0000.000
1872217PRO0-0.035-0.00715.809-0.051-0.0510.0000.0000.0000.000
1882218ILE0-0.006-0.00713.8910.0320.0320.0000.0000.0000.000
1892219ASP-1-0.902-0.95918.061-0.166-0.1660.0000.0000.0000.000
1902220ALA00.009-0.00720.893-0.007-0.0070.0000.0000.0000.000
1912221MET0-0.077-0.04123.3550.0190.0190.0000.0000.0000.000
1922222VAL00.0080.00926.941-0.010-0.0100.0000.0000.0000.000
1932223ASN00.0220.01129.7940.0010.0010.0000.0000.0000.000
1942224GLY00.0500.00833.307-0.003-0.0030.0000.0000.0000.000
1952225PRO0-0.0280.00536.425-0.004-0.0040.0000.0000.0000.000
1962226LEU0-0.001-0.00135.6470.0010.0010.0000.0000.0000.000
1972227PRO0-0.024-0.01939.1800.0030.0030.0000.0000.0000.000
1982228ASN00.0320.01840.963-0.003-0.0030.0000.0000.0000.000
1992229PRO0-0.038-0.02439.9550.0000.0000.0000.0000.0000.000
2002230GLU-1-0.991-0.97842.636-0.029-0.0290.0000.0000.0000.000