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: V5YL1

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2723186.450409
FMO2-HF: Nuclear repulsion 2632730.683453
FMO2-HF: Total energy -90455.766956
FMO2-MP2: Total energy -90719.048285


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.
-35.551-21.81820.539-13.953-20.315-0.093
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 : -0.021 / q_NPA : 0.004
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].
3118VAL0-0.008-0.0073.819-0.0663.050-0.010-1.720-1.3850.007
4119VAL0-0.005-0.0016.258-0.377-0.3770.0000.0000.0000.000
5120ALA0-0.020-0.0109.6200.3030.3030.0000.0000.0000.000
6121ALA00.0240.02212.281-0.118-0.1180.0000.0000.0000.000
7122PHE0-0.010-0.02415.1330.0550.0550.0000.0000.0000.000
8123GLU-1-0.820-0.92019.0070.2590.2590.0000.0000.0000.000
9124GLY00.013-0.00522.149-0.010-0.0100.0000.0000.0000.000
10125TRP0-0.063-0.03225.657-0.013-0.0130.0000.0000.0000.000
11126ASN0-0.053-0.04521.529-0.044-0.0440.0000.0000.0000.000
12127ASP-1-0.768-0.87521.6100.0900.0900.0000.0000.0000.000
13128ALA0-0.0180.00323.7230.0170.0170.0000.0000.0000.000
14129GLY00.0210.00226.713-0.009-0.0090.0000.0000.0000.000
15130ASP-1-0.933-0.96923.9440.1410.1410.0000.0000.0000.000
16131ALA00.0470.02722.4540.0250.0250.0000.0000.0000.000
17132ALA0-0.032-0.02218.2420.0050.0050.0000.0000.0000.000
18133GLY00.020-0.00617.6230.0420.0420.0000.0000.0000.000
19134ASP-1-0.870-0.90918.4010.2480.2480.0000.0000.0000.000
20135ALA0-0.006-0.00617.1070.0310.0310.0000.0000.0000.000
21136VAL00.004-0.00912.7270.0430.0430.0000.0000.0000.000
22137ALA00.0090.00914.6500.1210.1210.0000.0000.0000.000
23138HIS0-0.006-0.01517.2320.0510.0510.0000.0000.0000.000
24139LEU0-0.030-0.01011.8040.0110.0110.0000.0000.0000.000
25140ALA00.005-0.00213.0410.0920.0920.0000.0000.0000.000
26141ALA0-0.019-0.00614.0030.0490.0490.0000.0000.0000.000
27142SER0-0.073-0.05015.666-0.017-0.0170.0000.0000.0000.000
28143TRP0-0.046-0.04810.155-0.036-0.0360.0000.0000.0000.000
29144GLN0-0.061-0.02613.0000.1600.1600.0000.0000.0000.000
30145ALA00.0020.00711.0170.0980.0980.0000.0000.0000.000
31146LEU0-0.0030.0009.126-0.279-0.2790.0000.0000.0000.000
32147PRO0-0.034-0.0329.7720.3790.3790.0000.0000.0000.000
33148ILE0-0.060-0.0226.2440.0310.0310.0000.0000.0000.000
34149VAL0-0.023-0.01210.165-0.144-0.1440.0000.0000.0000.000
35150GLU-1-0.846-0.90812.5640.6030.6030.0000.0000.0000.000
36151ILE0-0.043-0.01114.134-0.060-0.0600.0000.0000.0000.000
37152ASP-1-0.874-0.97117.7090.3040.3040.0000.0000.0000.000
38153ASP-1-0.914-0.93921.1030.1940.1940.0000.0000.0000.000
39154GLU-1-0.882-0.95123.1110.1500.1500.0000.0000.0000.000
40155ALA0-0.109-0.04924.535-0.026-0.0260.0000.0000.0000.000
41156TYR0-0.086-0.07919.299-0.056-0.0560.0000.0000.0000.000
42157TYR0-0.028-0.02420.788-0.010-0.0100.0000.0000.0000.000
43158ASP-1-0.841-0.91126.4950.0910.0910.0000.0000.0000.000
44159TYR00.0690.01726.225-0.008-0.0080.0000.0000.0000.000
45160GLN0-0.052-0.03431.3740.0010.0010.0000.0000.0000.000
46161VAL0-0.051-0.02729.934-0.006-0.0060.0000.0000.0000.000
47162ASN0-0.003-0.00825.7930.0050.0050.0000.0000.0000.000
48163ARG10.8300.91428.901-0.096-0.0960.0000.0000.0000.000
49164PRO00.0210.01529.0510.0090.0090.0000.0000.0000.000
50165VAL0-0.0070.01528.758-0.017-0.0170.0000.0000.0000.000
51166ILE0-0.024-0.01530.4770.0110.0110.0000.0000.0000.000
52167ARG10.8550.91428.900-0.258-0.2580.0000.0000.0000.000
53168GLN0-0.013-0.02033.8340.0010.0010.0000.0000.0000.000
54169VAL0-0.026-0.02136.2270.0000.0000.0000.0000.0000.000
55170ASP-1-0.901-0.95139.1140.1340.1340.0000.0000.0000.000
56171GLY0-0.0090.00642.287-0.004-0.0040.0000.0000.0000.000
57172VAL0-0.038-0.01838.691-0.001-0.0010.0000.0000.0000.000
58173THR00.0230.00935.2910.0020.0020.0000.0000.0000.000
59174ARG10.8720.92333.720-0.186-0.1860.0000.0000.0000.000
60175GLU-1-0.797-0.86926.7730.3130.3130.0000.0000.0000.000
61176LEU0-0.033-0.01929.576-0.022-0.0220.0000.0000.0000.000
62177GLN0-0.0180.00023.8520.0280.0280.0000.0000.0000.000
63178TRP00.0730.03424.705-0.043-0.0430.0000.0000.0000.000
64179PRO0-0.037-0.00623.7920.0310.0310.0000.0000.0000.000
65180ALA00.0680.03019.495-0.007-0.0070.0000.0000.0000.000
66181MET0-0.0450.00814.367-0.020-0.0200.0000.0000.0000.000
67182ARG10.8040.89615.223-0.397-0.3970.0000.0000.0000.000
68183ILE00.0120.0028.8500.0180.0180.0000.0000.0000.000
69184SER0-0.013-0.0139.681-0.066-0.0660.0000.0000.0000.000
70185HIS0-0.020-0.0203.469-1.567-0.7330.150-0.211-0.7720.002
71186CYS00.0260.0256.240-1.297-1.2970.0000.0000.0000.000
72187ARG10.7980.8624.193-0.805-0.617-0.001-0.011-0.1750.000
73188PRO00.0340.0388.212-0.241-0.2410.0000.0000.0000.000
74189PRO0-0.028-0.02411.091-0.049-0.0490.0000.0000.0000.000
75190GLY0-0.0270.00013.253-0.025-0.0250.0000.0000.0000.000
76191SER0-0.029-0.0199.068-0.155-0.1550.0000.0000.0000.000
77192ASP-1-0.880-0.9377.7770.6350.6350.0000.0000.0000.000
78193ARG10.8060.8984.2561.1281.295-0.001-0.007-0.1580.000
79194ASP-1-0.770-0.8492.123-1.0060.0505.906-2.371-4.591-0.014
80195VAL0-0.020-0.0173.109-3.558-1.7010.264-1.182-0.938-0.010
81196VAL0-0.014-0.0082.779-0.2060.7770.478-0.284-1.1770.001
82197LEU0-0.022-0.0015.285-1.223-1.232-0.001-0.0040.0150.000
83198MET0-0.027-0.0237.6640.0560.0560.0000.0000.0000.000
84199CYS00.0160.00011.648-0.187-0.1870.0000.0000.0000.000
851100GLY00.0640.03115.4660.0680.0680.0000.0000.0000.000
861101VAL00.0030.02218.721-0.049-0.0490.0000.0000.0000.000
871102GLU-1-0.777-0.88121.2750.0470.0470.0000.0000.0000.000
881103PRO00.0100.02620.454-0.002-0.0020.0000.0000.0000.000
891104ASN00.0190.01723.303-0.013-0.0130.0000.0000.0000.000
901105MET0-0.043-0.01725.531-0.022-0.0220.0000.0000.0000.000
911106ARG10.9370.95523.833-0.065-0.0650.0000.0000.0000.000
921107TRP00.0400.01721.477-0.010-0.0100.0000.0000.0000.000
931108ARG10.9150.97120.0450.0770.0770.0000.0000.0000.000
941109THR00.0350.01719.335-0.017-0.0170.0000.0000.0000.000
951110PHE00.0730.04417.0930.0140.0140.0000.0000.0000.000
961111CYS0-0.033-0.01315.5360.0320.0320.0000.0000.0000.000
971112ASP-1-0.900-0.96314.568-0.126-0.1260.0000.0000.0000.000
981113GLU-1-0.872-0.92114.7110.3500.3500.0000.0000.0000.000
991114LEU00.0180.00111.8210.1070.1070.0000.0000.0000.000
1001115LEU0-0.025-0.01010.1290.0160.0160.0000.0000.0000.000
1011116ALA0-0.0030.00610.250-0.122-0.1220.0000.0000.0000.000
1021117VAL0-0.025-0.0107.8050.1110.1110.0000.0000.0000.000
1031118ILE00.0190.0015.9410.5640.5640.0000.0000.0000.000
1041119ASP-1-0.842-0.9055.774-0.937-0.9370.0000.0000.0000.000
1051120LYS10.7410.8457.731-0.128-0.1280.0000.0000.0000.000
1061121LEU0-0.021-0.0043.364-1.0840.0690.692-0.377-1.4690.004
1071122ASN0-0.096-0.0422.515-3.577-1.2951.742-1.590-2.434-0.019
1081123VAL0-0.0130.0032.069-9.411-8.0905.351-3.030-3.642-0.027
1091124ASP-1-0.868-0.9181.986-15.722-15.0875.970-3.149-3.457-0.037
1101125THR0-0.096-0.0714.5912.2882.438-0.001-0.017-0.1320.000
1111126VAL00.0130.0086.608-0.238-0.2380.0000.0000.0000.000
1121127VAL0-0.006-0.0029.1660.1070.1070.0000.0000.0000.000
1131128ILE0-0.019-0.00911.7520.1730.1730.0000.0000.0000.000
1141129LEU0-0.0070.00314.442-0.040-0.0400.0000.0000.0000.000
1151130GLY00.0720.02216.9060.0390.0390.0000.0000.0000.000
1161131ALA0-0.013-0.00920.503-0.018-0.0180.0000.0000.0000.000
1171132LEU0-0.0160.00124.1090.0070.0070.0000.0000.0000.000
1181133LEU00.0120.01027.6600.0000.0000.0000.0000.0000.000
1191134ALA0-0.030-0.03131.293-0.010-0.0100.0000.0000.0000.000
1201135ASP-1-0.861-0.90733.435-0.028-0.0280.0000.0000.0000.000
1211136THR0-0.027-0.01232.029-0.012-0.0120.0000.0000.0000.000
1221137PRO0-0.014-0.00335.4790.0070.0070.0000.0000.0000.000
1231138HIS00.0610.03234.361-0.006-0.0060.0000.0000.0000.000
1241139THR0-0.0150.00834.5670.0000.0000.0000.0000.0000.000
1251140ARG10.8890.93534.9110.0410.0410.0000.0000.0000.000
1261141PRO0-0.027-0.02330.0660.0050.0050.0000.0000.0000.000
1271142VAL00.0440.03626.161-0.002-0.0020.0000.0000.0000.000
1281143PRO00.0000.01427.745-0.017-0.0170.0000.0000.0000.000
1291144VAL0-0.022-0.01022.0990.0060.0060.0000.0000.0000.000
1301145SER0-0.040-0.00424.430-0.014-0.0140.0000.0000.0000.000
1311146GLY00.0520.00621.3970.0030.0030.0000.0000.0000.000
1321147ALA0-0.025-0.00320.3450.0170.0170.0000.0000.0000.000
1331148ALA00.0210.00217.204-0.038-0.0380.0000.0000.0000.000
1341149TYR00.0410.02813.6310.0450.0450.0000.0000.0000.000
1351150SER00.0010.00917.1970.0380.0380.0000.0000.0000.000
1361151ALA00.0520.02619.7040.0040.0040.0000.0000.0000.000
1371152ALA0-0.0050.00119.4910.0190.0190.0000.0000.0000.000
1381153SER0-0.034-0.02716.486-0.007-0.0070.0000.0000.0000.000
1391154ALA00.0480.02018.2760.0070.0070.0000.0000.0000.000
1401155ARG10.9150.96617.0210.6170.6170.0000.0000.0000.000
1411156GLN0-0.047-0.02316.6280.0230.0230.0000.0000.0000.000
1421157PHE0-0.001-0.01019.3570.0320.0320.0000.0000.0000.000
1431158GLY0-0.0290.00224.614-0.016-0.0160.0000.0000.0000.000
1441159LEU0-0.042-0.01727.3180.0130.0130.0000.0000.0000.000
1451160GLN00.0310.00725.583-0.002-0.0020.0000.0000.0000.000
1461161GLH0-0.036-0.07024.8770.0090.0090.0000.0000.0000.000
1471162THR00.0310.00627.257-0.004-0.0040.0000.0000.0000.000
1481163ARG00.0090.06223.7920.0140.0140.0000.0000.0000.000
1491164TYR0-0.026-0.02228.783-0.015-0.0150.0000.0000.0000.000
1501165GLU-1-0.968-0.98030.081-0.128-0.1280.0000.0000.0000.000
1511166GLY0-0.0100.00031.2170.0110.0110.0000.0000.0000.000
1521167PRO0-0.046-0.01930.013-0.008-0.0080.0000.0000.0000.000
1531168THR00.000-0.00924.261-0.004-0.0040.0000.0000.0000.000
1541169GLY00.0790.04823.9540.0120.0120.0000.0000.0000.000
1551170ILE0-0.036-0.03018.508-0.035-0.0350.0000.0000.0000.000
1561171ALA00.0440.03017.694-0.025-0.0250.0000.0000.0000.000
1571172GLY00.0090.00617.728-0.061-0.0610.0000.0000.0000.000
1581173VAL0-0.051-0.03019.626-0.047-0.0470.0000.0000.0000.000
1591174PHE00.0790.02110.643-0.055-0.0550.0000.0000.0000.000
1601175GLN0-0.020-0.00814.992-0.042-0.0420.0000.0000.0000.000
1611176SER00.0180.00215.973-0.079-0.0790.0000.0000.0000.000
1621177ALA0-0.042-0.01615.942-0.026-0.0260.0000.0000.0000.000
1631178CYS0-0.040-0.01311.950-0.050-0.0500.0000.0000.0000.000
1641179VAL00.0010.00113.599-0.100-0.1000.0000.0000.0000.000
1651180GLY0-0.053-0.02415.967-0.013-0.0130.0000.0000.0000.000
1661181ALA0-0.035-0.01413.4280.0340.0340.0000.0000.0000.000
1671182GLY0-0.043-0.01713.470-0.071-0.0710.0000.0000.0000.000
1681183ILE00.0020.0018.507-0.145-0.1450.0000.0000.0000.000
1691184PRO0-0.051-0.0229.2080.3060.3060.0000.0000.0000.000
1701185ALA00.0630.02910.518-0.195-0.1950.0000.0000.0000.000
1711186VAL0-0.043-0.02713.0380.1190.1190.0000.0000.0000.000
1721187THR0-0.043-0.01214.7590.0350.0350.0000.0000.0000.000
1731188PHE0-0.007-0.01415.097-0.002-0.0020.0000.0000.0000.000
1741189TRP00.0390.01419.4350.0530.0530.0000.0000.0000.000
1751190ALA00.0080.00422.652-0.012-0.0120.0000.0000.0000.000
1761191ALA0-0.006-0.00524.6900.0120.0120.0000.0000.0000.000
1771192VAL00.010-0.00127.5090.0020.0020.0000.0000.0000.000
1781193PRO00.0100.00430.213-0.003-0.0030.0000.0000.0000.000
1791194HIS00.0020.00634.0630.0130.0130.0000.0000.0000.000
1801195TYR00.004-0.01135.4420.0060.0060.0000.0000.0000.000
1811196VAL0-0.058-0.03433.6380.0050.0050.0000.0000.0000.000
1821197SER0-0.003-0.01332.1540.0010.0010.0000.0000.0000.000
1831198HIS0-0.051-0.02331.5130.0080.0080.0000.0000.0000.000
1841199PRO00.0140.01027.772-0.005-0.0050.0000.0000.0000.000
1851200PRO0-0.0140.01527.3930.0080.0080.0000.0000.0000.000
1861201ASN00.0270.01227.123-0.015-0.0150.0000.0000.0000.000
1871202PRO00.0900.04525.233-0.004-0.0040.0000.0000.0000.000
1881203LYS10.7760.87025.2410.0010.0010.0000.0000.0000.000
1891204ALA00.006-0.00424.941-0.018-0.0180.0000.0000.0000.000
1901205THR0-0.008-0.01620.516-0.029-0.0290.0000.0000.0000.000
1911206ILE0-0.028-0.01620.684-0.011-0.0110.0000.0000.0000.000
1921207ALA0-0.045-0.01621.462-0.023-0.0230.0000.0000.0000.000
1931208LEU0-0.003-0.00918.557-0.044-0.0440.0000.0000.0000.000
1941209LEU0-0.018-0.00116.083-0.041-0.0410.0000.0000.0000.000
1951210ARG10.9530.97616.6200.0150.0150.0000.0000.0000.000
1961211ARG10.8040.89417.5430.2180.2180.0000.0000.0000.000
1971212VAL00.0120.01511.579-0.102-0.1020.0000.0000.0000.000
1981213GLU-1-0.839-0.91512.755-0.205-0.2050.0000.0000.0000.000
1991214ASP-1-0.874-0.92114.134-0.397-0.3970.0000.0000.0000.000
2001215VAL0-0.105-0.04810.906-0.076-0.0760.0000.0000.0000.000
2011216LEU0-0.022-0.0167.701-0.286-0.2860.0000.0000.0000.000
2021217ASP-1-0.880-0.9199.582-0.643-0.6430.0000.0000.0000.000
2031218VAL0-0.053-0.0379.3330.0630.0630.0000.0000.0000.000
2041219GLU-1-0.956-0.96012.4540.0220.0220.0000.0000.0000.000
2051220VAL00.016-0.01114.7870.0810.0810.0000.0000.0000.000
2061221PRO0-0.0070.00516.303-0.030-0.0300.0000.0000.0000.000
2071222LEU00.0220.00619.5960.0270.0270.0000.0000.0000.000
2081223ALA0-0.006-0.01421.7630.0070.0070.0000.0000.0000.000
2091224ASP-1-0.850-0.91624.1270.1010.1010.0000.0000.0000.000
2101225LEU00.0380.03721.546-0.018-0.0180.0000.0000.0000.000
2111226PRO0-0.021-0.02625.416-0.015-0.0150.0000.0000.0000.000
2121227ALA00.0010.01128.314-0.010-0.0100.0000.0000.0000.000
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2141229ALA0-0.0030.00128.355-0.004-0.0040.0000.0000.0000.000
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