FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G5481

Calculation Name: 1SVA-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SVA

Chain ID: 1

ChEMBL ID:

UniProt ID: P03087

Base Structure: X-ray

Registration Date: 2023-09-23

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 348
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4549266.573771
FMO2-HF: Nuclear repulsion 4412855.041617
FMO2-HF: Total energy -136411.532154
FMO2-MP2: Total energy -136806.617394


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(1:14:PRO)


Summations of interaction energy for fragment #1(1:14:PRO)
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.
-0.3092.312-0.003-1.197-1.420.003
Interaction energy analysis for fragmet #1(1:14:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.030
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].
3116LYS10.9991.0193.661-0.3452.213-0.002-1.188-1.3680.003
4117PRO0-0.019-0.0064.9220.1700.233-0.001-0.009-0.0520.000
5118LYS10.9940.9658.2230.3080.3080.0000.0000.0000.000
6119GLU-1-0.930-0.96111.116-0.537-0.5370.0000.0000.0000.000
7120PRO0-0.056-0.02514.0120.0410.0410.0000.0000.0000.000
8121VAL00.0620.02716.8930.0030.0030.0000.0000.0000.000
9122GLN0-0.0130.00119.7250.0180.0180.0000.0000.0000.000
10123VAL00.010-0.00422.7440.0120.0120.0000.0000.0000.000
11124PRO0-0.0220.00625.757-0.005-0.0050.0000.0000.0000.000
12125LYS11.0030.99127.8120.1540.1540.0000.0000.0000.000
13126LEU00.0170.01129.2240.0080.0080.0000.0000.0000.000
14127VAL0-0.049-0.02531.386-0.006-0.0060.0000.0000.0000.000
15128ILE00.0380.00934.1390.0000.0000.0000.0000.0000.000
16129LYS10.9600.99134.4470.0890.0890.0000.0000.0000.000
17130GLY0-0.012-0.03437.204-0.002-0.0020.0000.0000.0000.000
18131GLY00.0420.03240.3110.0010.0010.0000.0000.0000.000
19132ILE00.0170.00843.774-0.002-0.0020.0000.0000.0000.000
20133GLU-1-0.824-0.93345.132-0.059-0.0590.0000.0000.0000.000
21134VAL0-0.047-0.00239.911-0.001-0.0010.0000.0000.0000.000
22135LEU00.0220.01242.860-0.002-0.0020.0000.0000.0000.000
23136GLY0-0.048-0.01744.8100.0000.0000.0000.0000.0000.000
24137VAL0-0.054-0.02340.130-0.001-0.0010.0000.0000.0000.000
25138LYS10.8770.92343.3960.0570.0570.0000.0000.0000.000
26139THR00.0060.00739.278-0.003-0.0030.0000.0000.0000.000
27140GLY00.011-0.00439.1900.0020.0020.0000.0000.0000.000
28141VAL00.0270.01440.3160.0030.0030.0000.0000.0000.000
29142ASP-1-0.865-0.94236.825-0.079-0.0790.0000.0000.0000.000
30143SER0-0.102-0.01936.945-0.003-0.0030.0000.0000.0000.000
31144PHE0-0.022-0.01733.0740.0030.0030.0000.0000.0000.000
32145THR0-0.040-0.02737.823-0.003-0.0030.0000.0000.0000.000
33146GLU-1-0.889-0.95135.394-0.077-0.0770.0000.0000.0000.000
34147VAL00.0060.01039.803-0.001-0.0010.0000.0000.0000.000
35148GLU-1-0.879-0.93237.705-0.065-0.0650.0000.0000.0000.000
36149CYS0-0.023-0.00842.6790.0000.0000.0000.0000.0000.000
37150PHE0-0.071-0.04846.0900.0000.0000.0000.0000.0000.000
38151LEU00.0050.02748.7370.0000.0000.0000.0000.0000.000
39152ASN0-0.002-0.01152.0490.0000.0000.0000.0000.0000.000
40153PRO0-0.0050.01354.3290.0000.0000.0000.0000.0000.000
41154GLN0-0.033-0.03356.9660.0010.0010.0000.0000.0000.000
42155MET0-0.070-0.02559.4050.0000.0000.0000.0000.0000.000
43156GLY00.0600.04762.5450.0010.0010.0000.0000.0000.000
44157ASN0-0.068-0.03961.372-0.001-0.0010.0000.0000.0000.000
45158PRO0-0.0200.00464.9440.0000.0000.0000.0000.0000.000
46159ASP-1-0.807-0.90866.399-0.018-0.0180.0000.0000.0000.000
47160GLU-1-0.959-0.98764.103-0.021-0.0210.0000.0000.0000.000
48161HIS0-0.085-0.04262.958-0.001-0.0010.0000.0000.0000.000
49162GLN0-0.004-0.00862.4880.0000.0000.0000.0000.0000.000
50163LYS11.0141.00158.6240.0270.0270.0000.0000.0000.000
51164GLY0-0.071-0.03258.2590.0000.0000.0000.0000.0000.000
52165LEU0-0.016-0.02759.2740.0010.0010.0000.0000.0000.000
53166SER00.0700.06362.3120.0000.0000.0000.0000.0000.000
54167LYS10.8780.93265.5050.0150.0150.0000.0000.0000.000
55168SER00.009-0.01268.7130.0000.0000.0000.0000.0000.000
56169LEU0-0.016-0.01466.7100.0000.0000.0000.0000.0000.000
57170ALA0-0.055-0.01370.8220.0010.0010.0000.0000.0000.000
58171ALA00.0390.00573.4690.0000.0000.0000.0000.0000.000
59172GLU-1-0.960-0.97575.499-0.009-0.0090.0000.0000.0000.000
60173LYS10.8770.97677.2650.0130.0130.0000.0000.0000.000
61174GLN00.0220.02679.8910.0000.0000.0000.0000.0000.000
62175PHE0-0.032-0.03978.3600.0000.0000.0000.0000.0000.000
63176THR00.0250.00181.5460.0000.0000.0000.0000.0000.000
64177ASP-1-0.949-0.97083.449-0.011-0.0110.0000.0000.0000.000
65178ASP-1-0.828-0.92576.828-0.013-0.0130.0000.0000.0000.000
66179SER0-0.039-0.04677.6860.0000.0000.0000.0000.0000.000
67180PRO0-0.049-0.01073.5240.0000.0000.0000.0000.0000.000
68181ASP-1-0.774-0.89873.173-0.015-0.0150.0000.0000.0000.000
69182LYS10.9400.98067.3910.0210.0210.0000.0000.0000.000
70183GLU-1-0.907-0.95368.593-0.018-0.0180.0000.0000.0000.000
71184GLN0-0.068-0.05868.3160.0000.0000.0000.0000.0000.000
72185LEU0-0.021-0.00267.9110.0000.0000.0000.0000.0000.000
73186PRO00.0410.03462.479-0.001-0.0010.0000.0000.0000.000
74187CYS0-0.0490.01262.8340.0010.0010.0000.0000.0000.000
75188TYR0-0.0590.01359.769-0.001-0.0010.0000.0000.0000.000
76189SER0-0.031-0.00156.4210.0000.0000.0000.0000.0000.000
77190VAL0-0.022-0.02356.3110.0000.0000.0000.0000.0000.000
78191ALA0-0.007-0.00353.7670.0000.0000.0000.0000.0000.000
79192ARG10.9400.96754.2280.0350.0350.0000.0000.0000.000
80193ILE0-0.0180.01447.9690.0000.0000.0000.0000.0000.000
81194PRO0-0.003-0.00651.2710.0000.0000.0000.0000.0000.000
82195LEU0-0.006-0.00947.326-0.002-0.0020.0000.0000.0000.000
83196PRO0-0.015-0.01146.6170.0020.0020.0000.0000.0000.000
84197ASN00.1110.06949.566-0.001-0.0010.0000.0000.0000.000
85198ILE0-0.042-0.01446.144-0.002-0.0020.0000.0000.0000.000
86199ASN00.008-0.01549.3950.0000.0000.0000.0000.0000.000
871100GLU-1-0.844-0.91651.220-0.050-0.0500.0000.0000.0000.000
881101ASP-1-0.813-0.88952.098-0.047-0.0470.0000.0000.0000.000
891102LEU0-0.088-0.04653.429-0.001-0.0010.0000.0000.0000.000
901103THR0-0.015-0.02354.3680.0020.0020.0000.0000.0000.000
911104CYS0-0.024-0.01748.7700.0000.0000.0000.0000.0000.000
921105GLY00.0150.03052.019-0.001-0.0010.0000.0000.0000.000
931106ASN0-0.144-0.08148.3850.0020.0020.0000.0000.0000.000
941107ILE00.0410.03251.117-0.002-0.0020.0000.0000.0000.000
951108LEU0-0.044-0.01846.104-0.002-0.0020.0000.0000.0000.000
961109MET00.0300.03549.0550.0020.0020.0000.0000.0000.000
971110TRP00.013-0.00243.030-0.004-0.0040.0000.0000.0000.000
981111GLU-1-0.673-0.79745.500-0.046-0.0460.0000.0000.0000.000
991112ALA0-0.005-0.00644.912-0.003-0.0030.0000.0000.0000.000
1001113VAL00.015-0.00340.6590.0020.0020.0000.0000.0000.000
1011114THR0-0.003-0.01938.8940.0010.0010.0000.0000.0000.000
1021115VAL00.002-0.00242.188-0.001-0.0010.0000.0000.0000.000
1031116LYS10.9601.00334.3340.0630.0630.0000.0000.0000.000
1041117THR00.035-0.00341.6700.0000.0000.0000.0000.0000.000
1051118GLU-1-0.855-0.92041.383-0.039-0.0390.0000.0000.0000.000
1061119VAL00.0600.03145.2330.0000.0000.0000.0000.0000.000
1071120ILE0-0.0270.00245.4000.0000.0000.0000.0000.0000.000
1081121GLY00.0370.00046.5010.0010.0010.0000.0000.0000.000
1091122VAL00.0680.02446.5680.0020.0020.0000.0000.0000.000
1101123THR00.000-0.00245.5310.0010.0010.0000.0000.0000.000
1111124ALA00.0350.02948.4400.0010.0010.0000.0000.0000.000
1121125MET0-0.065-0.03051.3500.0010.0010.0000.0000.0000.000
1131126LEU00.0080.00348.1500.0010.0010.0000.0000.0000.000
1141127ASN0-0.047-0.01652.5730.0020.0020.0000.0000.0000.000
1151128LEU0-0.019-0.00655.2310.0000.0000.0000.0000.0000.000
1161129HIS0-0.026-0.02755.0720.0010.0010.0000.0000.0000.000
1171130SER00.0530.05559.3940.0000.0000.0000.0000.0000.000
1181131GLY00.0230.00661.1680.0010.0010.0000.0000.0000.000
1191132THR0-0.0230.00160.8240.0000.0000.0000.0000.0000.000
1201133GLN00.0840.07163.6400.0000.0000.0000.0000.0000.000
1211134LYS10.9050.94964.5750.0080.0080.0000.0000.0000.000
1221135THR0-0.091-0.05462.1390.0000.0000.0000.0000.0000.000
1231136HIS00.052-0.01163.0730.0000.0000.0000.0000.0000.000
1241137GLU-1-0.867-0.91266.728-0.006-0.0060.0000.0000.0000.000
1251138ASN0-0.057-0.03765.0600.0000.0000.0000.0000.0000.000
1261139GLY0-0.036-0.01562.7220.0000.0000.0000.0000.0000.000
1271140ALA00.0270.02059.0170.0000.0000.0000.0000.0000.000
1281141GLY00.0560.01660.1280.0000.0000.0000.0000.0000.000
1291142LYS10.9420.98560.8380.0110.0110.0000.0000.0000.000
1301143PRO0-0.019-0.01457.141-0.001-0.0010.0000.0000.0000.000
1311144ILE00.004-0.00756.6720.0000.0000.0000.0000.0000.000
1321145GLN0-0.059-0.02757.8260.0010.0010.0000.0000.0000.000
1331146GLY00.0540.03559.8180.0000.0000.0000.0000.0000.000
1341147SER0-0.048-0.03760.367-0.001-0.0010.0000.0000.0000.000
1351148ASN00.0020.01656.321-0.001-0.0010.0000.0000.0000.000
1361149PHE00.036-0.00257.6130.0000.0000.0000.0000.0000.000
1371150HIS0-0.016-0.01052.7360.0000.0000.0000.0000.0000.000
1381151PHE00.021-0.00954.0570.0000.0000.0000.0000.0000.000
1391152PHE0-0.017-0.03147.687-0.001-0.0010.0000.0000.0000.000
1401153ALA00.0280.00652.0880.0010.0010.0000.0000.0000.000
1411154VAL0-0.036-0.02147.743-0.001-0.0010.0000.0000.0000.000
1421155GLY00.011-0.01051.0410.0010.0010.0000.0000.0000.000
1431156GLY0-0.0010.00052.732-0.001-0.0010.0000.0000.0000.000
1441157GLU-1-0.838-0.93153.767-0.030-0.0300.0000.0000.0000.000
1451158PRO0-0.023-0.01656.686-0.001-0.0010.0000.0000.0000.000
1461159LEU0-0.0210.00557.2450.0000.0000.0000.0000.0000.000
1471160GLU-1-0.837-0.92459.370-0.024-0.0240.0000.0000.0000.000
1481161LEU0-0.060-0.02461.6750.0000.0000.0000.0000.0000.000
1491162GLN00.0610.00264.5200.0000.0000.0000.0000.0000.000
1501163GLY0-0.033-0.02566.9340.0000.0000.0000.0000.0000.000
1511164VAL0-0.038-0.03068.8290.0000.0000.0000.0000.0000.000
1521165LEU0-0.049-0.01270.1030.0000.0000.0000.0000.0000.000
1531166ALA00.0780.05972.1910.0010.0010.0000.0000.0000.000
1541167ASN00.009-0.02374.1310.0000.0000.0000.0000.0000.000
1551168TYR0-0.0010.00377.0600.0000.0000.0000.0000.0000.000
1561169ARG10.8600.93878.0130.0100.0100.0000.0000.0000.000
1571170THR00.0520.03175.3690.0000.0000.0000.0000.0000.000
1581171LYS10.8260.91078.4080.0110.0110.0000.0000.0000.000
1591172TYR00.0620.02372.2280.0000.0000.0000.0000.0000.000
1601173PRO0-0.0240.00573.5920.0000.0000.0000.0000.0000.000
1611174ALA00.0090.01074.356-0.001-0.0010.0000.0000.0000.000
1621175GLN00.0230.01370.8550.0000.0000.0000.0000.0000.000
1631176THR0-0.088-0.03869.847-0.001-0.0010.0000.0000.0000.000
1641177VAL00.0270.03468.7450.0000.0000.0000.0000.0000.000
1651178THR00.0350.01169.7550.0000.0000.0000.0000.0000.000
1661179PRO0-0.016-0.00271.3140.0000.0000.0000.0000.0000.000
1671180LYS10.9700.96973.3750.0160.0160.0000.0000.0000.000
1681181ASN0-0.023-0.01276.8450.0000.0000.0000.0000.0000.000
1691182ALA00.0530.02778.3240.0000.0000.0000.0000.0000.000
1701183THR00.0270.02579.2900.0000.0000.0000.0000.0000.000
1711184VAL00.064-0.00579.3850.0000.0000.0000.0000.0000.000
1721185ASP-1-0.815-0.90977.698-0.012-0.0120.0000.0000.0000.000
1731186SER0-0.0640.00575.050-0.001-0.0010.0000.0000.0000.000
1741187GLN00.0350.01073.9470.0000.0000.0000.0000.0000.000
1751188GLN0-0.123-0.04373.0880.0000.0000.0000.0000.0000.000
1761189MET0-0.0130.00268.841-0.001-0.0010.0000.0000.0000.000
1771190ASN00.043-0.00672.8060.0000.0000.0000.0000.0000.000
1781191THR00.048-0.00372.2470.0000.0000.0000.0000.0000.000
1791192ASP-1-0.871-0.90273.303-0.015-0.0150.0000.0000.0000.000
1801193HIS10.6570.82071.5070.0150.0150.0000.0000.0000.000
1811194LYS10.8900.97467.1290.0180.0180.0000.0000.0000.000
1821195ALA0-0.009-0.01767.3840.0000.0000.0000.0000.0000.000
1831196VAL0-0.0050.00262.8580.0000.0000.0000.0000.0000.000
1841197LEU0-0.0060.03059.7130.0000.0000.0000.0000.0000.000
1851198ASP-1-0.852-0.91061.289-0.026-0.0260.0000.0000.0000.000
1861199LYS10.9050.94963.0270.0240.0240.0000.0000.0000.000
1871200ASP-1-0.764-0.89158.778-0.027-0.0270.0000.0000.0000.000
1881201ASN0-0.010-0.02061.7840.0010.0010.0000.0000.0000.000
1891202ALA0-0.032-0.00863.7100.0010.0010.0000.0000.0000.000
1901203TYR0-0.005-0.04664.6220.0010.0010.0000.0000.0000.000
1911204PRO00.0520.00064.696-0.001-0.0010.0000.0000.0000.000
1921205VAL0-0.004-0.07761.5090.0000.0000.0000.0000.0000.000
1931206GLU-1-0.911-0.95264.328-0.016-0.0160.0000.0000.0000.000
1941207CYS0-0.071-0.01267.1840.0010.0010.0000.0000.0000.000
1951208TRP0-0.015-0.02564.7660.0000.0000.0000.0000.0000.000
1961209VAL00.0320.05162.3570.0000.0000.0000.0000.0000.000
1971210PRO00.000-0.00358.6230.0000.0000.0000.0000.0000.000
1981211ASP-1-0.754-0.86561.478-0.019-0.0190.0000.0000.0000.000
1991212PRO0-0.018-0.01860.626-0.001-0.0010.0000.0000.0000.000
2001213SER0-0.150-0.12361.4380.0000.0000.0000.0000.0000.000
2011214LYS10.9740.97862.5150.0210.0210.0000.0000.0000.000
2021215ASN00.0040.05857.656-0.002-0.0020.0000.0000.0000.000
2031216GLU-1-0.863-0.95257.029-0.025-0.0250.0000.0000.0000.000
2041217ASN0-0.031-0.01653.974-0.002-0.0020.0000.0000.0000.000
2051218THR00.003-0.02053.271-0.002-0.0020.0000.0000.0000.000
2061219ARG10.8970.95449.5170.0340.0340.0000.0000.0000.000
2071220TYR00.0330.02052.427-0.001-0.0010.0000.0000.0000.000
2081221PHE0-0.017-0.00448.8610.0000.0000.0000.0000.0000.000
2091222GLY00.0190.00452.907-0.001-0.0010.0000.0000.0000.000
2101223THR0-0.058-0.03753.0400.0010.0010.0000.0000.0000.000
2111224TYR0-0.0140.04456.1500.0000.0000.0000.0000.0000.000
2121225THR00.0220.01057.0210.0010.0010.0000.0000.0000.000
2131226GLY00.019-0.00359.6110.0000.0000.0000.0000.0000.000
2141227GLY00.020-0.05162.8390.0010.0010.0000.0000.0000.000
2151228GLU-1-0.946-0.96963.998-0.010-0.0100.0000.0000.0000.000
2161229ASN0-0.018-0.02462.8140.0000.0000.0000.0000.0000.000
2171230VAL0-0.0120.06958.5100.0010.0010.0000.0000.0000.000
2181231PRO00.0000.00955.317-0.001-0.0010.0000.0000.0000.000
2191232PRO00.0380.01553.9200.0000.0000.0000.0000.0000.000
2201233VAL0-0.010-0.01948.8630.0000.0000.0000.0000.0000.000
2211234LEU0-0.018-0.01148.094-0.001-0.0010.0000.0000.0000.000
2221235HIS00.0020.00643.0360.0000.0000.0000.0000.0000.000
2231236ILE0-0.0300.01541.465-0.001-0.0010.0000.0000.0000.000
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2251238ASN00.0500.04033.0770.0030.0030.0000.0000.0000.000
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