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

tag_button

FMODB ID: YZR82

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 OptHSide
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 -2720287.963712
FMO2-HF: Nuclear repulsion 2629833.083375
FMO2-HF: Total energy -90454.880337
FMO2-MP2: Total energy -90718.232375


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.
-31.964-25.25334.494-19.065-22.14-0.086
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 : -0.022 / q_NPA : -0.012
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].
3118VAL0-0.005-0.0093.748-0.2243.202-0.014-1.811-1.6010.008
4119VAL00.0050.0116.196-0.485-0.4850.0000.0000.0000.000
5120ALA0-0.012-0.0069.4380.3130.3130.0000.0000.0000.000
6121ALA00.0230.01111.951-0.145-0.1450.0000.0000.0000.000
7122PHE0-0.016-0.01914.8290.0650.0650.0000.0000.0000.000
8123GLU-1-0.853-0.93918.6330.3220.3220.0000.0000.0000.000
9124GLY0-0.012-0.01521.851-0.023-0.0230.0000.0000.0000.000
10125TRP0-0.034-0.00824.996-0.015-0.0150.0000.0000.0000.000
11126ASN0-0.075-0.06521.347-0.043-0.0430.0000.0000.0000.000
12127ASP-1-0.741-0.86821.4420.1830.1830.0000.0000.0000.000
13128ALA00.0000.03123.3960.0050.0050.0000.0000.0000.000
14129GLY00.006-0.01126.005-0.006-0.0060.0000.0000.0000.000
15130ASP-1-0.910-0.96023.6380.2040.2040.0000.0000.0000.000
16131ALA00.0250.02322.5920.0180.0180.0000.0000.0000.000
17132ALA0-0.033-0.03118.0100.0190.0190.0000.0000.0000.000
18133GLY00.014-0.00517.4740.0540.0540.0000.0000.0000.000
19134ASP-1-0.871-0.94218.0990.3380.3380.0000.0000.0000.000
20135ALA0-0.078-0.04116.8370.0280.0280.0000.0000.0000.000
21136VAL00.018-0.01012.3610.0510.0510.0000.0000.0000.000
22137ALA00.0050.00914.3550.1270.1270.0000.0000.0000.000
23138HIS0-0.016-0.02216.8200.0560.0560.0000.0000.0000.000
24139LEU0-0.030-0.00611.158-0.003-0.0030.0000.0000.0000.000
25140ALA00.0100.00412.8200.0840.0840.0000.0000.0000.000
26141ALA0-0.028-0.00413.7750.0250.0250.0000.0000.0000.000
27142SER0-0.074-0.04115.521-0.027-0.0270.0000.0000.0000.000
28143TRP0-0.040-0.0579.879-0.026-0.0260.0000.0000.0000.000
29144GLN0-0.059-0.01512.9130.1220.1220.0000.0000.0000.000
30145ALA0-0.002-0.00410.5920.0890.0890.0000.0000.0000.000
31146LEU00.003-0.0058.784-0.296-0.2960.0000.0000.0000.000
32147PRO0-0.021-0.0229.4620.4290.4290.0000.0000.0000.000
33148ILE0-0.065-0.0195.810-0.024-0.0240.0000.0000.0000.000
34149VAL0-0.007-0.0069.751-0.232-0.2320.0000.0000.0000.000
35150GLU-1-0.851-0.91311.9200.6960.6960.0000.0000.0000.000
36151ILE0-0.056-0.02513.744-0.066-0.0660.0000.0000.0000.000
37152ASP-1-0.879-0.96117.1910.3620.3620.0000.0000.0000.000
38153ASP-1-0.895-0.93320.5920.2330.2330.0000.0000.0000.000
39154GLU-1-0.898-0.95222.6000.1910.1910.0000.0000.0000.000
40155ALA0-0.122-0.06223.986-0.031-0.0310.0000.0000.0000.000
41156TYR0-0.085-0.07919.222-0.056-0.0560.0000.0000.0000.000
42157TYR0-0.0070.00220.504-0.009-0.0090.0000.0000.0000.000
43158ASP-1-0.861-0.92026.3040.1190.1190.0000.0000.0000.000
44159TYR00.0900.01525.906-0.007-0.0070.0000.0000.0000.000
45160GLN0-0.062-0.03731.027-0.001-0.0010.0000.0000.0000.000
46161VAL0-0.066-0.02429.526-0.004-0.0040.0000.0000.0000.000
47162ASN0-0.0010.00026.0000.0050.0050.0000.0000.0000.000
48163ARG10.8760.94028.915-0.131-0.1310.0000.0000.0000.000
49164PRO00.0320.02028.6030.0130.0130.0000.0000.0000.000
50165VAL0-0.0220.00128.507-0.020-0.0200.0000.0000.0000.000
51166ILE0-0.020-0.00530.0950.0100.0100.0000.0000.0000.000
52167ARG10.8660.91629.010-0.271-0.2710.0000.0000.0000.000
53168GLN0-0.012-0.01633.6060.0000.0000.0000.0000.0000.000
54169VAL0-0.054-0.02435.958-0.001-0.0010.0000.0000.0000.000
55170ASP-1-0.884-0.94338.7750.1400.1400.0000.0000.0000.000
56171GLY0-0.027-0.01042.254-0.003-0.0030.0000.0000.0000.000
57172VAL0-0.016-0.00238.477-0.001-0.0010.0000.0000.0000.000
58173THR00.0100.00335.0070.0030.0030.0000.0000.0000.000
59174ARG10.8800.91833.356-0.203-0.2030.0000.0000.0000.000
60175GLU-1-0.819-0.89426.5940.3360.3360.0000.0000.0000.000
61176LEU0-0.012-0.00129.107-0.020-0.0200.0000.0000.0000.000
62177GLN0-0.021-0.00223.1890.0410.0410.0000.0000.0000.000
63178TRP00.0760.03024.566-0.042-0.0420.0000.0000.0000.000
64179PRO0-0.032-0.00123.3920.0360.0360.0000.0000.0000.000
65180ALA00.0450.01519.350-0.005-0.0050.0000.0000.0000.000
66181MET0-0.0510.00414.421-0.030-0.0300.0000.0000.0000.000
67182ARG10.8590.93714.731-0.501-0.5010.0000.0000.0000.000
68183ILE0-0.004-0.0108.3170.0590.0590.0000.0000.0000.000
69184SER0-0.002-0.0109.635-0.062-0.0620.0000.0000.0000.000
70185HIS0-0.052-0.0533.388-1.823-0.8480.382-0.295-1.0620.003
71186CYS00.0250.0386.152-1.392-1.3920.0000.0000.0000.000
72187ARG10.7830.8554.238-0.225-0.027-0.001-0.011-0.1860.000
73188PRO00.0010.0238.029-0.244-0.2440.0000.0000.0000.000
74189PRO0-0.014-0.01211.110-0.067-0.0670.0000.0000.0000.000
75190GLY0-0.041-0.01613.766-0.028-0.0280.0000.0000.0000.000
76191SER0-0.020-0.0118.926-0.106-0.1060.0000.0000.0000.000
77192ASP-1-0.856-0.9137.7700.1680.1680.0000.0000.0000.000
78193ARG10.8430.9204.2620.9001.064-0.001-0.010-0.1530.000
79194ASP-1-0.764-0.8482.134-1.859-0.4905.532-2.289-4.612-0.015
80195VAL0-0.047-0.0343.187-2.934-1.2650.211-1.003-0.878-0.008
81196VAL0-0.029-0.0192.707-0.0290.7891.290-0.418-1.6900.002
82197LEU0-0.013-0.0015.156-1.240-1.245-0.001-0.0080.0140.000
83198MET0-0.019-0.0197.5000.0390.0390.0000.0000.0000.000
84199CYS00.007-0.00611.486-0.208-0.2080.0000.0000.0000.000
851100GLY00.0820.04015.1220.0550.0550.0000.0000.0000.000
861101VAL00.0200.01918.412-0.046-0.0460.0000.0000.0000.000
871102GLU-1-0.806-0.89820.6420.1260.1260.0000.0000.0000.000
881103PRO00.0050.01720.080-0.017-0.0170.0000.0000.0000.000
891104ASN00.0470.02722.984-0.012-0.0120.0000.0000.0000.000
901105MET0-0.063-0.02825.069-0.028-0.0280.0000.0000.0000.000
911106ARG10.9600.96523.845-0.095-0.0950.0000.0000.0000.000
921107TRP00.0480.02821.281-0.006-0.0060.0000.0000.0000.000
931108ARG10.9430.96519.9890.0310.0310.0000.0000.0000.000
941109THR00.0280.01719.572-0.020-0.0200.0000.0000.0000.000
951110PHE00.0520.03716.8930.0170.0170.0000.0000.0000.000
961111CYS0-0.057-0.03215.5520.0500.0500.0000.0000.0000.000
971112ASP-1-0.900-0.95714.452-0.027-0.0270.0000.0000.0000.000
981113GLU-1-0.861-0.91214.6170.4520.4520.0000.0000.0000.000
991114LEU00.007-0.00111.5140.0970.0970.0000.0000.0000.000
1001115LEU0-0.005-0.01310.0610.1120.1120.0000.0000.0000.000
1011116ALA00.0050.02010.168-0.112-0.1120.0000.0000.0000.000
1021117VAL0-0.046-0.0227.6490.0820.0820.0000.0000.0000.000
1031118ILE00.007-0.0135.8980.5370.5370.0000.0000.0000.000
1041119ASP-1-0.892-0.9245.936-0.948-0.9480.0000.0000.0000.000
1051120LYS10.8050.8767.538-0.262-0.2620.0000.0000.0000.000
1061121LEU0-0.023-0.0073.130-1.750-0.6811.476-0.551-1.9950.004
1071122ASN0-0.086-0.0272.428-5.500-2.2661.513-2.138-2.609-0.019
1081123VAL00.0040.0261.699-7.477-16.62423.531-9.343-5.040-0.041
1091124ASP-1-0.892-0.9372.600-11.064-8.2830.577-1.169-2.188-0.020
1101125THR0-0.083-0.0604.5721.9682.128-0.001-0.019-0.1400.000
1111126VAL00.0170.0176.6140.0080.0080.0000.0000.0000.000
1121127VAL0-0.018-0.0148.9960.0150.0150.0000.0000.0000.000
1131128ILE0-0.023-0.01011.6220.1890.1890.0000.0000.0000.000
1141129LEU0-0.020-0.01314.231-0.066-0.0660.0000.0000.0000.000
1151130GLY00.0810.02716.6510.0470.0470.0000.0000.0000.000
1161131ALA0-0.043-0.02220.236-0.021-0.0210.0000.0000.0000.000
1171132LEU0-0.0020.00623.7580.0070.0070.0000.0000.0000.000
1181133LEU00.0040.00927.245-0.002-0.0020.0000.0000.0000.000
1191134ALA0-0.015-0.02030.847-0.009-0.0090.0000.0000.0000.000
1201135ASP-1-0.865-0.90132.8080.0040.0040.0000.0000.0000.000
1211136THR0-0.028-0.02331.512-0.012-0.0120.0000.0000.0000.000
1221137PRO00.0030.00334.9780.0070.0070.0000.0000.0000.000
1231138HIS00.0710.04833.889-0.003-0.0030.0000.0000.0000.000
1241139THR0-0.0070.00534.5860.0020.0020.0000.0000.0000.000
1251140ARG10.8470.90734.6760.0150.0150.0000.0000.0000.000
1261141PRO0-0.044-0.02929.7460.0050.0050.0000.0000.0000.000
1271142VAL00.0520.04325.5610.0010.0010.0000.0000.0000.000
1281143PRO0-0.0060.01227.355-0.015-0.0150.0000.0000.0000.000
1291144VAL0-0.015-0.00921.7060.0080.0080.0000.0000.0000.000
1301145SER0-0.057-0.01624.155-0.015-0.0150.0000.0000.0000.000
1311146GLY00.0440.01121.3700.0110.0110.0000.0000.0000.000
1321147ALA00.0080.01520.3390.0020.0020.0000.0000.0000.000
1331148ALA00.0360.01017.311-0.024-0.0240.0000.0000.0000.000
1341149TYR00.0690.03713.6430.0330.0330.0000.0000.0000.000
1351150SER0-0.018-0.00717.1530.0370.0370.0000.0000.0000.000
1361151ALA00.0610.02819.8440.0050.0050.0000.0000.0000.000
1371152ALA00.0000.00519.9040.0180.0180.0000.0000.0000.000
1381153SER0-0.051-0.03016.557-0.007-0.0070.0000.0000.0000.000
1391154ALA00.0410.01718.441-0.003-0.0030.0000.0000.0000.000
1401155ARG10.9180.97317.3070.5460.5460.0000.0000.0000.000
1411156GLN0-0.044-0.02516.6040.0160.0160.0000.0000.0000.000
1421157PHE0-0.016-0.00919.6040.0300.0300.0000.0000.0000.000
1431158GLY0-0.0080.00824.279-0.013-0.0130.0000.0000.0000.000
1441159LEU0-0.026-0.00927.3700.0000.0000.0000.0000.0000.000
1451160GLN00.009-0.02425.249-0.009-0.0090.0000.0000.0000.000
1461161GLH0-0.048-0.07824.6840.0070.0070.0000.0000.0000.000
1471162THR00.0540.01927.097-0.001-0.0010.0000.0000.0000.000
1481163ARG0-0.0380.04723.7300.0080.0080.0000.0000.0000.000
1491164TYR0-0.011-0.00128.161-0.015-0.0150.0000.0000.0000.000
1501165GLU-1-0.952-0.97929.401-0.089-0.0890.0000.0000.0000.000
1511166GLY0-0.005-0.00230.7140.0090.0090.0000.0000.0000.000
1521167PRO0-0.048-0.01729.412-0.007-0.0070.0000.0000.0000.000
1531168THR00.008-0.00423.6810.0020.0020.0000.0000.0000.000
1541169GLY00.0940.05623.5500.0130.0130.0000.0000.0000.000
1551170ILE0-0.036-0.03518.141-0.031-0.0310.0000.0000.0000.000
1561171ALA00.0390.02717.528-0.019-0.0190.0000.0000.0000.000
1571172GLY00.0160.00517.649-0.047-0.0470.0000.0000.0000.000
1581173VAL0-0.026-0.01519.633-0.043-0.0430.0000.0000.0000.000
1591174PHE00.0780.02810.495-0.058-0.0580.0000.0000.0000.000
1601175GLN0-0.031-0.01914.881-0.039-0.0390.0000.0000.0000.000
1611176SER00.004-0.00715.722-0.083-0.0830.0000.0000.0000.000
1621177ALA0-0.056-0.03015.775-0.029-0.0290.0000.0000.0000.000
1631178CYS0-0.049-0.01111.918-0.032-0.0320.0000.0000.0000.000
1641179VAL00.0130.00113.547-0.105-0.1050.0000.0000.0000.000
1651180GLY0-0.050-0.01915.677-0.026-0.0260.0000.0000.0000.000
1661181ALA0-0.036-0.01113.0590.0160.0160.0000.0000.0000.000
1671182GLY0-0.045-0.01513.299-0.058-0.0580.0000.0000.0000.000
1681183ILE0-0.010-0.0048.221-0.147-0.1470.0000.0000.0000.000
1691184PRO0-0.054-0.0219.0940.2970.2970.0000.0000.0000.000
1701185ALA00.0630.02310.471-0.136-0.1360.0000.0000.0000.000
1711186VAL0-0.052-0.02312.9220.0940.0940.0000.0000.0000.000
1721187THR0-0.0440.00014.5930.0480.0480.0000.0000.0000.000
1731188PHE00.001-0.01315.022-0.017-0.0170.0000.0000.0000.000
1741189TRP00.0210.00219.2880.0500.0500.0000.0000.0000.000
1751190ALA00.0000.00222.348-0.018-0.0180.0000.0000.0000.000
1761191ALA0-0.009-0.01024.2090.0120.0120.0000.0000.0000.000
1771192VAL00.009-0.00326.8800.0000.0000.0000.0000.0000.000
1781193PRO00.003-0.00429.584-0.003-0.0030.0000.0000.0000.000
1791194HIS00.011-0.00233.4010.0140.0140.0000.0000.0000.000
1801195TYR00.027-0.00234.7790.0050.0050.0000.0000.0000.000
1811196VAL0-0.075-0.02733.3440.0040.0040.0000.0000.0000.000
1821197SER00.016-0.00532.0560.0010.0010.0000.0000.0000.000
1831198HIS0-0.064-0.03531.0810.0120.0120.0000.0000.0000.000
1841199PRO00.0250.00427.595-0.008-0.0080.0000.0000.0000.000
1851200PRO0-0.0240.03127.5160.0140.0140.0000.0000.0000.000
1861201ASN00.0380.00926.799-0.014-0.0140.0000.0000.0000.000
1871202PRO00.0540.03924.9170.0090.0090.0000.0000.0000.000
1881203LYS10.8130.89024.714-0.031-0.0310.0000.0000.0000.000
1891204ALA00.0320.00124.359-0.014-0.0140.0000.0000.0000.000
1901205THR00.0630.04420.104-0.021-0.0210.0000.0000.0000.000
1911206ILE0-0.023-0.00720.163-0.004-0.0040.0000.0000.0000.000
1921207ALA0-0.042-0.01920.689-0.017-0.0170.0000.0000.0000.000
1931208LEU00.004-0.01418.030-0.040-0.0400.0000.0000.0000.000
1941209LEU0-0.0040.00615.488-0.033-0.0330.0000.0000.0000.000
1951210ARG10.9400.97516.336-0.028-0.0280.0000.0000.0000.000
1961211ARG10.8150.90817.3080.1410.1410.0000.0000.0000.000
1971212VAL00.0070.00211.340-0.093-0.0930.0000.0000.0000.000
1981213GLU-1-0.843-0.91312.521-0.133-0.1330.0000.0000.0000.000
1991214ASP-1-0.882-0.92113.734-0.335-0.3350.0000.0000.0000.000
2001215VAL0-0.102-0.04710.712-0.088-0.0880.0000.0000.0000.000
2011216LEU0-0.032-0.0207.522-0.244-0.2440.0000.0000.0000.000
2021217ASP-1-0.898-0.9409.543-0.654-0.6540.0000.0000.0000.000
2031218VAL0-0.053-0.0268.9300.0090.0090.0000.0000.0000.000
2041219GLU-1-0.975-0.97512.1170.0500.0500.0000.0000.0000.000
2051220VAL00.000-0.01714.4960.0870.0870.0000.0000.0000.000
2061221PRO0-0.0240.00616.037-0.037-0.0370.0000.0000.0000.000
2071222LEU00.0480.01219.1590.0260.0260.0000.0000.0000.000
2081223ALA0-0.014-0.02121.3890.0120.0120.0000.0000.0000.000
2091224ASP-1-0.870-0.92323.7180.1270.1270.0000.0000.0000.000
2101225LEU00.0300.02521.113-0.017-0.0170.0000.0000.0000.000
2111226PRO0-0.006-0.01725.269-0.013-0.0130.0000.0000.0000.000
2121227ALA00.0070.01328.175-0.009-0.0090.0000.0000.0000.000
2131228GLN0-0.023-0.02726.650-0.002-0.0020.0000.0000.0000.000
2141229ALA00.009-0.00228.097-0.004-0.0040.0000.0000.0000.000
2151230GLU-1-0.860-0.91730.1170.0400.0400.0000.0000.0000.000
2161231ALA0-0.031-0.01833.303-0.005-0.0050.0000.0000.0000.000
2171232TRP00.0350.01431.451-0.010-0.0100.0000.0000.0000.000
2181233GLU-1-0.816-0.90533.4550.0220.0220.0000.0000.0000.000
2191234ARG10.7450.84635.242-0.069-0.0690.0000.0000.0000.000
2201235GLU-1-0.884-0.94137.5020.0740.0740.0000.0000.0000.000
2211236ILE00.0010.02234.2800.0010.0010.0000.0000.0000.000
2221237THR0-0.099-0.05738.730-0.006-0.0060.0000.0000.0000.000
2231238GLU-1-0.925-0.95241.1350.0590.0590.0000.0000.0000.000
2241239THR0-0.063-0.01842.174-0.001-0.0010.0000.0000.0000.000
2251240ILE0-0.029-0.01343.030-0.002-0.0020.0000.0000.0000.000
2261241ALA0-0.044-0.02746.051-0.003-0.0030.0000.0000.0000.000
2271242GLU-1-1.004-0.99949.7290.0200.0200.0000.0000.0000.000
2281243ASP-1-0.909-0.93445.6690.0280.0280.0000.0000.0000.000
2291244HIS0-0.039-0.05545.152-0.001-0.0010.0000.0000.0000.000
2301245GLU-1-0.882-0.92041.8110.0110.0110.0000.0000.0000.000
2311246LEU00.012-0.00840.511-0.004-0.0040.0000.0000.0000.000
2321247ALA0-0.041-0.01042.708-0.004-0.0040.0000.0000.0000.000
2331248GLU-1-0.945-0.97444.100-0.009-0.0090.0000.0000.0000.000
2341249TYR0-0.004-0.03237.868-0.003-0.0030.0000.0000.0000.000
2351250VAL0-0.102-0.04539.653-0.005-0.0050.0000.0000.0000.000
2361251GLN0-0.0240.00540.353-0.007-0.0070.0000.0000.0000.000