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: 1N2ZZ

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 OptAll
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 -2182711.243786
FMO2-HF: Nuclear repulsion 2105536.45175
FMO2-HF: Total energy -77174.792036
FMO2-MP2: Total energy -77400.22316


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.
-0.5481.328-0.008-0.957-0.9130.003
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 : 0.057 / q_NPA : 0.028
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].
3233THR0-0.0110.0063.8710.3161.685-0.007-0.709-0.6540.003
4234TYR00.012-0.0036.6300.3690.3690.0000.0000.0000.000
5235CYS0-0.041-0.0189.6640.1250.1250.0000.0000.0000.000
6236TYR00.0610.01912.7150.1010.1010.0000.0000.0000.000
7237SER0-0.038-0.02614.6340.0850.0850.0000.0000.0000.000
8238LYS10.9170.9659.9510.4300.4300.0000.0000.0000.000
9239PRO00.0300.02213.5040.0590.0590.0000.0000.0000.000
10240ASP-1-0.784-0.87316.551-0.253-0.2530.0000.0000.0000.000
11241GLY00.0430.01919.719-0.007-0.0070.0000.0000.0000.000
12242ARG10.8420.90322.5350.2660.2660.0000.0000.0000.000
13243PRO00.0480.02125.551-0.019-0.0190.0000.0000.0000.000
14244PRO00.0390.01228.170-0.001-0.0010.0000.0000.0000.000
15245SER0-0.018-0.01029.4930.0090.0090.0000.0000.0000.000
16246THR0-0.015-0.01231.9910.0060.0060.0000.0000.0000.000
17247VAL0-0.0220.00132.5560.0000.0000.0000.0000.0000.000
18248SER00.000-0.00335.3160.0020.0020.0000.0000.0000.000
19249ASP-1-0.859-0.90436.142-0.130-0.1300.0000.0000.0000.000
20250PRO00.001-0.02035.497-0.006-0.0060.0000.0000.0000.000
21251VAL0-0.0060.00429.311-0.005-0.0050.0000.0000.0000.000
22252THR00.0030.00930.0900.0060.0060.0000.0000.0000.000
23253ARG10.8110.88920.3020.2460.2460.0000.0000.0000.000
24254LEU00.0170.01224.3060.0120.0120.0000.0000.0000.000
25255GLY00.0440.02623.392-0.014-0.0140.0000.0000.0000.000
26256PRO00.0430.00418.894-0.003-0.0030.0000.0000.0000.000
27257THR0-0.024-0.01320.933-0.013-0.0130.0000.0000.0000.000
28258LEU00.0160.02123.7960.0080.0080.0000.0000.0000.000
29259SER0-0.006-0.01020.6360.0050.0050.0000.0000.0000.000
30260ARG10.8710.94520.2300.2000.2000.0000.0000.0000.000
31261HIS00.0720.03616.1670.0070.0070.0000.0000.0000.000
32262TYR00.003-0.00517.5730.0740.0740.0000.0000.0000.000
33263THR00.013-0.00815.895-0.082-0.0820.0000.0000.0000.000
34264PHE0-0.018-0.00417.4690.0650.0650.0000.0000.0000.000
35265LYS10.8710.93417.7290.1620.1620.0000.0000.0000.000
36266VAL0-0.048-0.02716.6090.0160.0160.0000.0000.0000.000
37267GLY00.0270.01019.6460.0230.0230.0000.0000.0000.000
38268GLU-1-0.798-0.87720.793-0.189-0.1890.0000.0000.0000.000
39269TRP00.0480.02615.964-0.009-0.0090.0000.0000.0000.000
40270PRO00.008-0.00221.7460.0190.0190.0000.0000.0000.000
41271HIS00.003-0.01724.477-0.010-0.0100.0000.0000.0000.000
42272SER0-0.029-0.00825.9070.0030.0030.0000.0000.0000.000
43273GLN0-0.0330.00424.0520.0120.0120.0000.0000.0000.000
44274SER00.0460.01924.298-0.003-0.0030.0000.0000.0000.000
45275HIS10.8050.87022.2360.1270.1270.0000.0000.0000.000
46276GLY00.011-0.01322.0360.0170.0170.0000.0000.0000.000
47277HIS10.7790.86523.0230.2100.2100.0000.0000.0000.000
48278ALA00.002-0.00820.154-0.027-0.0270.0000.0000.0000.000
49279TRP0-0.043-0.02318.8380.0230.0230.0000.0000.0000.000
50280ILE00.0070.00819.191-0.057-0.0570.0000.0000.0000.000
51281CYS0-0.014-0.01918.2330.0390.0390.0000.0000.0000.000
52282PRO00.0080.01119.468-0.055-0.0550.0000.0000.0000.000
53283LEU0-0.0340.00616.1020.0070.0070.0000.0000.0000.000
54284PRO00.0340.00020.8200.0130.0130.0000.0000.0000.000
55285SER00.013-0.02122.7920.0070.0070.0000.0000.0000.000
56286ASP-1-0.820-0.88126.116-0.237-0.2370.0000.0000.0000.000
57287LYS10.8740.94322.2700.3160.3160.0000.0000.0000.000
58288LEU00.0690.04224.8160.0020.0020.0000.0000.0000.000
59289LYS10.8570.91925.9300.2220.2220.0000.0000.0000.000
60290LYS10.9200.95625.0960.2150.2150.0000.0000.0000.000
61291MET0-0.0450.00020.134-0.003-0.0030.0000.0000.0000.000
62292GLY00.011-0.00424.2320.0030.0030.0000.0000.0000.000
63293SER0-0.019-0.01025.2680.0160.0160.0000.0000.0000.000
64294PHE00.0180.00523.6340.0040.0040.0000.0000.0000.000
65295HIS0-0.017-0.02025.7470.0080.0080.0000.0000.0000.000
66296GLU-1-0.807-0.88628.127-0.149-0.1490.0000.0000.0000.000
67297VAL00.0130.01028.6800.0080.0080.0000.0000.0000.000
68298VAL00.002-0.00126.5400.0060.0060.0000.0000.0000.000
69299LYS10.7790.87829.8840.1620.1620.0000.0000.0000.000
702100ALA00.0020.01632.8350.0080.0080.0000.0000.0000.000
712101HIS0-0.052-0.04332.2390.0150.0150.0000.0000.0000.000
722102HIS00.0340.03433.683-0.010-0.0100.0000.0000.0000.000
732103LEU0-0.054-0.03231.408-0.007-0.0070.0000.0000.0000.000
742104VAL00.0220.00525.2680.0030.0030.0000.0000.0000.000
752105LYS10.8390.95422.6050.2820.2820.0000.0000.0000.000
762106ASN0-0.053-0.05219.9570.0440.0440.0000.0000.0000.000
772107GLY00.0520.03917.401-0.002-0.0020.0000.0000.0000.000
782108TRP0-0.017-0.01815.4100.0670.0670.0000.0000.0000.000
792109ASP-1-0.848-0.91010.025-1.510-1.5100.0000.0000.0000.000
802110VAL00.005-0.00710.7430.2220.2220.0000.0000.0000.000
812111VAL00.0250.0207.064-0.456-0.4560.0000.0000.0000.000
822112VAL0-0.0090.0039.0310.3580.3580.0000.0000.0000.000
832113GLN0-0.049-0.0459.182-0.134-0.1340.0000.0000.0000.000
842114VAL00.0110.00911.3600.0530.0530.0000.0000.0000.000
852115ASN0-0.049-0.01913.6770.0590.0590.0000.0000.0000.000
862116ALA00.0320.00816.0480.0040.0040.0000.0000.0000.000
872117SER00.005-0.01417.2850.0360.0360.0000.0000.0000.000
882118PHE00.011-0.00717.968-0.008-0.0080.0000.0000.0000.000
892119ALA0-0.005-0.00218.9160.0130.0130.0000.0000.0000.000
902120HIS00.0000.01819.155-0.006-0.0060.0000.0000.0000.000
912121SER0-0.042-0.02418.7880.0300.0300.0000.0000.0000.000
922122GLY00.0720.04118.162-0.012-0.0120.0000.0000.0000.000
932123ALA0-0.075-0.04714.7590.0140.0140.0000.0000.0000.000
942124LEU00.0210.02813.3180.0090.0090.0000.0000.0000.000
952125CYS0-0.032-0.00212.554-0.080-0.0800.0000.0000.0000.000
962126VAL00.0030.0029.9250.0650.0650.0000.0000.0000.000
972127ALA00.0320.00611.010-0.238-0.2380.0000.0000.0000.000
982128ALA0-0.0100.00413.1950.0650.0650.0000.0000.0000.000
992129VAL00.002-0.01314.6900.0120.0120.0000.0000.0000.000
1002130PRO0-0.012-0.01918.0820.0130.0130.0000.0000.0000.000
1012131GLU-1-0.825-0.91320.765-0.292-0.2920.0000.0000.0000.000
1022132TYR0-0.077-0.05721.7050.0260.0260.0000.0000.0000.000
1032133GLU-1-0.961-0.97523.797-0.208-0.2080.0000.0000.0000.000
1042134HIS00.004-0.02425.7730.0080.0080.0000.0000.0000.000
1052135THR00.0320.02026.3990.0230.0230.0000.0000.0000.000
1062136HIS00.0080.00228.9490.0040.0040.0000.0000.0000.000
1072137GLU-1-0.894-0.93932.588-0.148-0.1480.0000.0000.0000.000
1082138LYS10.8480.94329.7560.2000.2000.0000.0000.0000.000
1092139ALA0-0.008-0.01829.306-0.020-0.0200.0000.0000.0000.000
1102140LEU00.004-0.00426.6020.0030.0030.0000.0000.0000.000
1112141LYS10.9360.96126.7930.1790.1790.0000.0000.0000.000
1122142TRP0-0.027-0.02818.677-0.010-0.0100.0000.0000.0000.000
1132143SER0-0.059-0.02423.9820.0290.0290.0000.0000.0000.000
1142144GLU-1-0.813-0.87823.814-0.258-0.2580.0000.0000.0000.000
1152145LEU0-0.057-0.02724.6980.0240.0240.0000.0000.0000.000
1162146GLU-1-0.773-0.87125.078-0.207-0.2070.0000.0000.0000.000
1172147GLU-1-0.797-0.88421.847-0.307-0.3070.0000.0000.0000.000
1182148PRO0-0.0240.00025.2670.0160.0160.0000.0000.0000.000
1192149ALA0-0.015-0.02326.2030.0090.0090.0000.0000.0000.000
1202150TYR00.0360.01824.845-0.016-0.0160.0000.0000.0000.000
1212151THR00.0430.01521.983-0.008-0.0080.0000.0000.0000.000
1222152TYR00.0100.01420.764-0.028-0.0280.0000.0000.0000.000
1232153GLN0-0.058-0.03420.035-0.014-0.0140.0000.0000.0000.000
1242154GLN0-0.010-0.00320.4050.0160.0160.0000.0000.0000.000
1252155LEU00.0340.02416.277-0.020-0.0200.0000.0000.0000.000
1262156SER0-0.007-0.02813.970-0.037-0.0370.0000.0000.0000.000
1272157VAL0-0.046-0.00715.364-0.017-0.0170.0000.0000.0000.000
1282158PHE0-0.0100.00516.2420.0090.0090.0000.0000.0000.000
1292159PRO0-0.016-0.00912.003-0.069-0.0690.0000.0000.0000.000
1302160HIS0-0.0020.00810.7020.0270.0270.0000.0000.0000.000
1312161GLN0-0.006-0.0143.4340.0710.3720.000-0.179-0.1230.000
1322162LEU00.0340.0178.1790.2440.2440.0000.0000.0000.000
1332163LEU0-0.0100.0078.139-0.164-0.1640.0000.0000.0000.000
1342164ASN00.0110.00410.3190.0960.0960.0000.0000.0000.000
1352165LEU00.0580.02912.1120.0780.0780.0000.0000.0000.000
1362166ARG10.9130.97214.512-0.174-0.1740.0000.0000.0000.000
1372167THR0-0.066-0.0429.3450.0570.0570.0000.0000.0000.000
1382168ASN0-0.024-0.0266.4660.4220.4220.0000.0000.0000.000
1392169SER00.0690.0389.146-0.123-0.1230.0000.0000.0000.000
1402170SER0-0.025-0.0166.3500.0280.0280.0000.0000.0000.000
1412171VAL00.0210.0195.260-0.024-0.0240.0000.0000.0000.000
1422172HIS0-0.064-0.0203.873-0.614-0.408-0.001-0.069-0.1360.000
1432173LEU00.0160.0085.797-0.842-0.8420.0000.0000.0000.000
1442174VAL0-0.015-0.0048.4720.3640.3640.0000.0000.0000.000
1452175MET0-0.019-0.00310.4770.0440.0440.0000.0000.0000.000
1462176PRO00.0050.01613.8630.0550.0550.0000.0000.0000.000
1472177TYR00.005-0.00517.076-0.016-0.0160.0000.0000.0000.000
1482178ILE0-0.035-0.01919.8000.0030.0030.0000.0000.0000.000
1492179GLY00.0730.03122.1080.0020.0020.0000.0000.0000.000
1502180PRO0-0.015-0.00225.5830.0060.0060.0000.0000.0000.000
1512181GLY00.0130.00428.4970.0200.0200.0000.0000.0000.000
1522182PRO0-0.041-0.02427.497-0.019-0.0190.0000.0000.0000.000
1532183THR0-0.043-0.03427.352-0.004-0.0040.0000.0000.0000.000
1542184THR00.0060.01127.2470.0070.0070.0000.0000.0000.000
1552185ASN00.0720.05329.292-0.011-0.0110.0000.0000.0000.000
1562186LEU00.0490.01224.660-0.002-0.0020.0000.0000.0000.000
1572187THR0-0.047-0.02128.540-0.009-0.0090.0000.0000.0000.000
1582188LEU0-0.038-0.02231.2190.0070.0070.0000.0000.0000.000
1592189HIS0-0.018-0.01825.9260.0030.0030.0000.0000.0000.000
1602190ASN0-0.029-0.03123.517-0.013-0.0130.0000.0000.0000.000
1612191PRO00.0240.02821.889-0.012-0.0120.0000.0000.0000.000
1622192TRP00.000-0.00416.303-0.048-0.0480.0000.0000.0000.000
1632193THR0-0.021-0.00719.2830.0330.0330.0000.0000.0000.000
1642194ILE0-0.0020.00213.840-0.060-0.0600.0000.0000.0000.000
1652195VAL00.0380.02216.0420.0770.0770.0000.0000.0000.000
1662196ILE0-0.021-0.01513.982-0.082-0.0820.0000.0000.0000.000
1672197LEU00.0110.01816.0050.0750.0750.0000.0000.0000.000
1682198ILE0-0.0020.00316.803-0.028-0.0280.0000.0000.0000.000
1692199LEU0-0.023-0.02115.7560.0160.0160.0000.0000.0000.000
1702200SER0-0.029-0.01718.7160.0430.0430.0000.0000.0000.000
1712201GLU-1-0.750-0.85919.648-0.157-0.1570.0000.0000.0000.000
1722202LEU0-0.0400.00019.8330.0120.0120.0000.0000.0000.000
1732203THR00.0130.00521.9100.0170.0170.0000.0000.0000.000
1742204GLY00.0540.01622.5850.0030.0030.0000.0000.0000.000
1752205PRO0-0.017-0.01023.625-0.006-0.0060.0000.0000.0000.000
1762206GLY00.0450.01825.512-0.012-0.0120.0000.0000.0000.000
1772207GLN0-0.064-0.01323.9230.0020.0020.0000.0000.0000.000
1782208THR0-0.013-0.03123.5910.0080.0080.0000.0000.0000.000
1792209VAL0-0.0060.00417.3450.0130.0130.0000.0000.0000.000
1802210PRO0-0.038-0.00718.786-0.032-0.0320.0000.0000.0000.000
1812211VAL00.0400.02315.486-0.023-0.0230.0000.0000.0000.000
1822212THR0-0.017-0.02114.5090.0490.0490.0000.0000.0000.000
1832213MET00.0230.01913.029-0.125-0.1250.0000.0000.0000.000
1842214SER00.0010.01412.0310.1140.1140.0000.0000.0000.000
1852215VAL0-0.009-0.02013.128-0.137-0.1370.0000.0000.0000.000
1862216ALA00.0390.01514.8870.1030.1030.0000.0000.0000.000
1872217PRO0-0.0290.00716.185-0.069-0.0690.0000.0000.0000.000
1882218ILE0-0.012-0.01313.3970.0270.0270.0000.0000.0000.000
1892219ASP-1-0.869-0.94417.654-0.363-0.3630.0000.0000.0000.000
1902220ALA0-0.0020.00620.2620.0130.0130.0000.0000.0000.000
1912221MET0-0.064-0.01822.9610.0230.0230.0000.0000.0000.000
1922222VAL00.0110.01426.421-0.013-0.0130.0000.0000.0000.000
1932223ASN00.021-0.01129.5470.0010.0010.0000.0000.0000.000
1942224GLY00.0510.01633.081-0.004-0.0040.0000.0000.0000.000
1952225PRO0-0.011-0.00336.535-0.005-0.0050.0000.0000.0000.000
1962226LEU0-0.036-0.00936.4160.0060.0060.0000.0000.0000.000
1972227PRO0-0.022-0.02139.5670.0030.0030.0000.0000.0000.000
1982228ASN0-0.011-0.00441.474-0.008-0.0080.0000.0000.0000.000
1992229PRO0-0.039-0.01240.4050.0010.0010.0000.0000.0000.000
2002230GLU-1-0.942-0.96142.719-0.077-0.0770.0000.0000.0000.000