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: 5251Z

Calculation Name: 5UN0-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5UN0

Chain ID: 1

ChEMBL ID:

UniProt ID: O33260

Base Structure: X-ray

Registration Date: 2023-06-22

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2721723.533686
FMO2-HF: Nuclear repulsion 2631270.339574
FMO2-HF: Total energy -90453.194112
FMO2-MP2: Total energy -90716.640115


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(1:16:MET)


Summations of interaction energy for fragment #1(1:16:MET)
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.
-24.372-20.00132.618-15.576-21.41-0.084
Interaction energy analysis for fragmet #1(1:16:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.029
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].
3118VAL0-0.008-0.0063.6580.4602.598-0.006-1.006-1.1260.002
4119VAL00.0090.0146.096-0.355-0.3550.0000.0000.0000.000
5120ALA0-0.018-0.0139.3490.2130.2130.0000.0000.0000.000
6121ALA00.0200.00911.860-0.106-0.1060.0000.0000.0000.000
7122PHE0-0.027-0.02314.6350.0400.0400.0000.0000.0000.000
8123GLU-1-0.860-0.93718.5460.3010.3010.0000.0000.0000.000
9124GLY0-0.016-0.01521.770-0.016-0.0160.0000.0000.0000.000
10125TRP0-0.021-0.00224.827-0.009-0.0090.0000.0000.0000.000
11126ASN0-0.083-0.06421.259-0.024-0.0240.0000.0000.0000.000
12127ASP-1-0.750-0.87521.5710.2650.2650.0000.0000.0000.000
13128ALA0-0.0030.01923.307-0.006-0.0060.0000.0000.0000.000
14129GLY0-0.005-0.01825.9220.0000.0000.0000.0000.0000.000
15130ASP-1-0.883-0.94523.5690.2300.2300.0000.0000.0000.000
16131ALA00.0000.01422.5160.0150.0150.0000.0000.0000.000
17132ALA0-0.022-0.02817.8420.0220.0220.0000.0000.0000.000
18133GLY00.0280.00917.3990.0530.0530.0000.0000.0000.000
19134ASP-1-0.865-0.93718.0380.3220.3220.0000.0000.0000.000
20135ALA0-0.065-0.04716.7350.0190.0190.0000.0000.0000.000
21136VAL00.003-0.01212.2560.0430.0430.0000.0000.0000.000
22137ALA00.0040.00714.3100.0860.0860.0000.0000.0000.000
23138HIS0-0.018-0.01816.7890.0240.0240.0000.0000.0000.000
24139LEU0-0.0260.00511.042-0.012-0.0120.0000.0000.0000.000
25140ALA00.0050.00212.8080.0410.0410.0000.0000.0000.000
26141ALA0-0.028-0.00313.758-0.014-0.0140.0000.0000.0000.000
27142SER0-0.083-0.05915.463-0.041-0.0410.0000.0000.0000.000
28143TRP0-0.037-0.04910.097-0.038-0.0380.0000.0000.0000.000
29144GLN0-0.064-0.01912.7720.0410.0410.0000.0000.0000.000
30145ALA00.0250.01810.4920.0210.0210.0000.0000.0000.000
31146LEU0-0.028-0.0158.142-0.218-0.2180.0000.0000.0000.000
32147PRO0-0.030-0.0299.0770.3400.3400.0000.0000.0000.000
33148ILE0-0.057-0.0175.658-0.079-0.0790.0000.0000.0000.000
34149VAL00.0030.0029.583-0.199-0.1990.0000.0000.0000.000
35150GLU-1-0.932-0.96711.3780.5450.5450.0000.0000.0000.000
36151ILE0-0.065-0.03313.879-0.059-0.0590.0000.0000.0000.000
37152ASP-1-0.867-0.95516.9770.2650.2650.0000.0000.0000.000
38153ASP-1-0.889-0.93220.3760.1570.1570.0000.0000.0000.000
39154GLU-1-0.912-0.95422.3820.1400.1400.0000.0000.0000.000
40155ALA0-0.118-0.06323.978-0.018-0.0180.0000.0000.0000.000
41156TYR0-0.086-0.08019.504-0.032-0.0320.0000.0000.0000.000
42157TYR0-0.0050.00020.3890.0010.0010.0000.0000.0000.000
43158ASP-1-0.872-0.92526.2840.1050.1050.0000.0000.0000.000
44159TYR00.0790.01125.729-0.003-0.0030.0000.0000.0000.000
45160GLN0-0.094-0.05630.935-0.003-0.0030.0000.0000.0000.000
46161VAL0-0.071-0.01629.449-0.002-0.0020.0000.0000.0000.000
47162ASN00.0250.02225.7720.0030.0030.0000.0000.0000.000
48163ARG10.9130.95328.879-0.119-0.1190.0000.0000.0000.000
49164PRO00.0310.02028.4070.0110.0110.0000.0000.0000.000
50165VAL0-0.0210.00427.863-0.015-0.0150.0000.0000.0000.000
51166ILE0-0.0140.00429.7470.0040.0040.0000.0000.0000.000
52167ARG10.9280.96229.572-0.173-0.1730.0000.0000.0000.000
53168GLN0-0.021-0.02233.121-0.004-0.0040.0000.0000.0000.000
54169VAL0-0.040-0.02135.5740.0010.0010.0000.0000.0000.000
55170ASP-1-0.895-0.94538.3300.0890.0890.0000.0000.0000.000
56171GLY0-0.025-0.01041.806-0.003-0.0030.0000.0000.0000.000
57172VAL0-0.0180.00037.876-0.001-0.0010.0000.0000.0000.000
58173THR0-0.011-0.00634.7420.0060.0060.0000.0000.0000.000
59174ARG10.8790.91832.150-0.135-0.1350.0000.0000.0000.000
60175GLU-1-0.899-0.96225.9100.2320.2320.0000.0000.0000.000
61176LEU00.0110.01328.605-0.011-0.0110.0000.0000.0000.000
62177GLN00.0260.03022.4560.0350.0350.0000.0000.0000.000
63178TRP00.0700.02524.138-0.024-0.0240.0000.0000.0000.000
64179PRO0-0.040-0.00123.2000.0250.0250.0000.0000.0000.000
65180ALA00.0590.02019.064-0.008-0.0080.0000.0000.0000.000
66181MET0-0.0470.00314.297-0.021-0.0210.0000.0000.0000.000
67182ARG10.9050.96714.555-0.425-0.4250.0000.0000.0000.000
68183ILE00.0150.0008.1680.0940.0940.0000.0000.0000.000
69184SER0-0.005-0.0119.230-0.132-0.1320.0000.0000.0000.000
70185HIS0-0.029-0.0223.295-1.222-0.2600.367-0.288-1.0400.003
71186CYS00.0390.0356.166-1.179-1.1790.0000.0000.0000.000
72187ARG10.7840.8784.3651.2291.378-0.001-0.003-0.1450.000
73188PRO00.0000.0218.062-0.153-0.1530.0000.0000.0000.000
74189PRO0-0.018-0.01311.087-0.083-0.0830.0000.0000.0000.000
75190GLY0-0.037-0.01213.755-0.044-0.0440.0000.0000.0000.000
76191SER0-0.003-0.0068.539-0.064-0.0640.0000.0000.0000.000
77192ASP-1-0.872-0.9397.126-0.855-0.8550.0000.0000.0000.000
78193ARG10.9550.9984.282-0.538-0.348-0.001-0.016-0.1730.000
79194ASP-1-0.788-0.8912.140-7.033-4.2994.298-2.516-4.516-0.026
80195VAL0-0.034-0.0263.192-2.350-0.6680.230-1.021-0.891-0.009
81196VAL0-0.019-0.0182.7110.0480.5231.846-0.462-1.8590.002
82197LEU0-0.017-0.0045.109-1.098-1.092-0.001-0.0110.0060.000
83198MET0-0.024-0.0217.8140.0080.0080.0000.0000.0000.000
84199CYS00.023-0.00211.417-0.153-0.1530.0000.0000.0000.000
851100GLY00.0590.03015.0550.0210.0210.0000.0000.0000.000
861101VAL00.0190.01818.345-0.020-0.0200.0000.0000.0000.000
871102GLU-1-0.824-0.92320.6130.1870.1870.0000.0000.0000.000
881103PRO00.0040.02020.060-0.020-0.0200.0000.0000.0000.000
891104ASN00.0580.01422.951-0.003-0.0030.0000.0000.0000.000
901105MET0-0.072-0.03125.054-0.022-0.0220.0000.0000.0000.000
911106ARG10.9580.96123.753-0.079-0.0790.0000.0000.0000.000
921107TRP00.0490.03421.2420.0000.0000.0000.0000.0000.000
931108ARG10.9420.95919.943-0.032-0.0320.0000.0000.0000.000
941109THR00.0360.01519.527-0.010-0.0100.0000.0000.0000.000
951110PHE00.0580.04416.4690.0080.0080.0000.0000.0000.000
961111CYS0-0.045-0.02615.4990.0490.0490.0000.0000.0000.000
971112ASP-1-0.902-0.95114.4080.0330.0330.0000.0000.0000.000
981113GLU-1-0.874-0.91314.5870.2980.2980.0000.0000.0000.000
991114LEU00.002-0.00711.4080.0590.0590.0000.0000.0000.000
1001115LEU0-0.002-0.00910.0310.1070.1070.0000.0000.0000.000
1011116ALA00.0110.02410.136-0.123-0.1230.0000.0000.0000.000
1021117VAL0-0.063-0.0297.401-0.034-0.0340.0000.0000.0000.000
1031118ILE0-0.001-0.0175.8710.3930.3930.0000.0000.0000.000
1041119ASP-1-0.951-0.9695.913-1.315-1.3150.0000.0000.0000.000
1051120LYS10.9280.9477.6070.0980.0980.0000.0000.0000.000
1061121LEU0-0.070-0.0262.809-2.052-1.4312.684-0.741-2.5630.004
1071122ASN0-0.082-0.0272.437-6.019-3.1891.567-1.892-2.504-0.019
1081123VAL0-0.0090.0101.759-7.919-16.16021.558-8.040-5.278-0.040
1091124ASP-1-0.883-0.9272.7452.7933.4610.0780.438-1.184-0.001
1101125THR0-0.097-0.0634.6270.4860.643-0.001-0.018-0.1370.000
1111126VAL00.0230.0156.564-0.146-0.1460.0000.0000.0000.000
1121127VAL0-0.025-0.0168.917-0.010-0.0100.0000.0000.0000.000
1131128ILE0-0.021-0.00911.5220.1120.1120.0000.0000.0000.000
1141129LEU0-0.019-0.01614.130-0.058-0.0580.0000.0000.0000.000
1151130GLY00.0780.02716.5570.0230.0230.0000.0000.0000.000
1161131ALA0-0.040-0.02020.141-0.011-0.0110.0000.0000.0000.000
1171132LEU0-0.0050.00523.6660.0000.0000.0000.0000.0000.000
1181133LEU00.0020.00727.150-0.001-0.0010.0000.0000.0000.000
1191134ALA0-0.022-0.02530.754-0.006-0.0060.0000.0000.0000.000
1201135ASP-1-0.872-0.93332.7140.0650.0650.0000.0000.0000.000
1211136THR0-0.046-0.03431.506-0.005-0.0050.0000.0000.0000.000
1221137PRO00.0100.01234.8900.0030.0030.0000.0000.0000.000
1231138HIS00.0720.07033.8140.0040.0040.0000.0000.0000.000
1241139THR0-0.012-0.00134.5150.0030.0030.0000.0000.0000.000
1251140ARG10.8600.91134.602-0.055-0.0550.0000.0000.0000.000
1261141PRO0-0.058-0.03329.7600.0050.0050.0000.0000.0000.000
1271142VAL00.0440.03725.643-0.002-0.0020.0000.0000.0000.000
1281143PRO0-0.0020.01527.273-0.002-0.0020.0000.0000.0000.000
1291144VAL0-0.007-0.00121.6430.0090.0090.0000.0000.0000.000
1301145SER0-0.051-0.01524.051-0.012-0.0120.0000.0000.0000.000
1311146GLY00.0290.00521.3640.0150.0150.0000.0000.0000.000
1321147ALA00.0150.02020.283-0.012-0.0120.0000.0000.0000.000
1331148ALA00.0270.00417.4720.0070.0070.0000.0000.0000.000
1341149TYR00.0620.03913.6750.0000.0000.0000.0000.0000.000
1351150SER0-0.005-0.00217.165-0.003-0.0030.0000.0000.0000.000
1361151ALA00.0660.04620.0300.0100.0100.0000.0000.0000.000
1371152ALA00.0040.00920.3870.0080.0080.0000.0000.0000.000
1381153SER0-0.052-0.04717.1120.0030.0030.0000.0000.0000.000
1391154ALA00.0360.00918.9390.0110.0110.0000.0000.0000.000
1401155ARG10.9070.97217.9890.0320.0320.0000.0000.0000.000
1411156GLN0-0.052-0.02716.8260.0080.0080.0000.0000.0000.000
1421157PHE0-0.022-0.00919.5690.0080.0080.0000.0000.0000.000
1431158GLY0-0.0040.00624.347-0.008-0.0080.0000.0000.0000.000
1441159LEU0-0.025-0.01527.586-0.003-0.0030.0000.0000.0000.000
1451160GLN00.017-0.01425.3580.0020.0020.0000.0000.0000.000
1461161GLH0-0.101-0.16524.835-0.001-0.0010.0000.0000.0000.000
1471162THR00.0390.00327.023-0.004-0.0040.0000.0000.0000.000
1481163ARG00.0660.15523.769-0.005-0.0050.0000.0000.0000.000
1491164TYR0-0.0070.00028.085-0.003-0.0030.0000.0000.0000.000
1501165GLU-1-0.957-0.98029.3220.0160.0160.0000.0000.0000.000
1511166GLY0-0.009-0.00830.6290.0030.0030.0000.0000.0000.000
1521167PRO0-0.045-0.01029.340-0.001-0.0010.0000.0000.0000.000
1531168THR0-0.0120.00423.3040.0060.0060.0000.0000.0000.000
1541169GLY00.1000.05223.4950.0000.0000.0000.0000.0000.000
1551170ILE0-0.042-0.02918.032-0.016-0.0160.0000.0000.0000.000
1561171ALA00.0470.03117.4670.0000.0000.0000.0000.0000.000
1571172GLY00.0170.00517.581-0.016-0.0160.0000.0000.0000.000
1581173VAL0-0.020-0.01319.438-0.025-0.0250.0000.0000.0000.000
1591174PHE00.0760.02310.357-0.034-0.0340.0000.0000.0000.000
1601175GLN0-0.040-0.01014.823-0.042-0.0420.0000.0000.0000.000
1611176SER00.003-0.01115.645-0.041-0.0410.0000.0000.0000.000
1621177ALA0-0.035-0.02415.675-0.026-0.0260.0000.0000.0000.000
1631178CYS0-0.043-0.00311.626-0.034-0.0340.0000.0000.0000.000
1641179VAL00.0090.00213.473-0.065-0.0650.0000.0000.0000.000
1651180GLY0-0.052-0.02315.495-0.021-0.0210.0000.0000.0000.000
1661181ALA0-0.030-0.00812.888-0.007-0.0070.0000.0000.0000.000
1671182GLY0-0.045-0.01413.172-0.059-0.0590.0000.0000.0000.000
1681183ILE0-0.0030.0027.782-0.039-0.0390.0000.0000.0000.000
1691184PRO0-0.053-0.0258.9580.1300.1300.0000.0000.0000.000
1701185ALA00.0580.01810.325-0.048-0.0480.0000.0000.0000.000
1711186VAL0-0.068-0.03512.7900.0170.0170.0000.0000.0000.000
1721187THR0-0.054-0.00614.5180.0320.0320.0000.0000.0000.000
1731188PHE0-0.002-0.01415.014-0.027-0.0270.0000.0000.0000.000
1741189TRP00.0200.00719.1910.0250.0250.0000.0000.0000.000
1751190ALA00.0020.00022.251-0.015-0.0150.0000.0000.0000.000
1761191ALA0-0.015-0.01324.1190.0030.0030.0000.0000.0000.000
1771192VAL00.005-0.00726.901-0.002-0.0020.0000.0000.0000.000
1781193PRO0-0.006-0.01029.498-0.004-0.0040.0000.0000.0000.000
1791194HIS00.010-0.00533.3160.0080.0080.0000.0000.0000.000
1801195TYR00.023-0.01934.6910.0020.0020.0000.0000.0000.000
1811196VAL0-0.084-0.03132.970-0.001-0.0010.0000.0000.0000.000
1821197SER00.006-0.01031.9760.0050.0050.0000.0000.0000.000
1831198HIS0-0.061-0.03031.0040.0130.0130.0000.0000.0000.000
1841199PRO00.0240.00227.588-0.005-0.0050.0000.0000.0000.000
1851200PRO0-0.0090.03827.4520.0100.0100.0000.0000.0000.000
1861201ASN00.0470.01326.836-0.007-0.0070.0000.0000.0000.000
1871202PRO00.0580.04424.8660.0130.0130.0000.0000.0000.000
1881203LYS10.9240.96224.653-0.092-0.0920.0000.0000.0000.000
1891204ALA00.019-0.01024.198-0.002-0.0020.0000.0000.0000.000
1901205THR00.0720.05119.9780.0000.0000.0000.0000.0000.000
1911206ILE0-0.021-0.00320.0980.0120.0120.0000.0000.0000.000
1921207ALA0-0.055-0.02720.6270.0020.0020.0000.0000.0000.000
1931208LEU00.004-0.00917.868-0.010-0.0100.0000.0000.0000.000
1941209LEU00.0090.01015.4630.0050.0050.0000.0000.0000.000
1951210ARG10.9340.97116.277-0.133-0.1330.0000.0000.0000.000
1961211ARG10.9340.98417.109-0.110-0.1100.0000.0000.0000.000
1971212VAL0-0.007-0.00311.344-0.018-0.0180.0000.0000.0000.000
1981213GLU-1-0.873-0.93012.5140.1560.1560.0000.0000.0000.000
1991214ASP-1-0.950-0.97213.7350.0690.0690.0000.0000.0000.000
2001215VAL0-0.110-0.05110.642-0.029-0.0290.0000.0000.0000.000
2011216LEU0-0.046-0.0347.413-0.046-0.0460.0000.0000.0000.000
2021217ASP-1-0.968-0.9739.5510.0730.0730.0000.0000.0000.000
2031218VAL0-0.076-0.0538.8930.0040.0040.0000.0000.0000.000
2041219GLU-1-0.975-0.97312.1130.1530.1530.0000.0000.0000.000
2051220VAL0-0.013-0.01514.3980.0450.0450.0000.0000.0000.000
2061221PRO0-0.0070.01015.980-0.035-0.0350.0000.0000.0000.000
2071222LEU00.0450.00719.1450.0170.0170.0000.0000.0000.000
2081223ALA0-0.019-0.02021.3610.0020.0020.0000.0000.0000.000
2091224ASP-1-0.901-0.95223.7020.1310.1310.0000.0000.0000.000
2101225LEU00.0070.01121.195-0.012-0.0120.0000.0000.0000.000
2111226PRO0-0.014-0.01925.183-0.010-0.0100.0000.0000.0000.000
2121227ALA00.0190.01828.134-0.008-0.0080.0000.0000.0000.000
2131228GLN00.0280.00826.5580.0000.0000.0000.0000.0000.000
2141229ALA00.007-0.00128.094-0.003-0.0030.0000.0000.0000.000
2151230GLU-1-0.858-0.93730.0640.0770.0770.0000.0000.0000.000
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