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: Z6MJN

Calculation Name: 1FMD-3-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FMD

Chain ID: 3

ChEMBL ID:

UniProt ID: P15072

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2204838.140938
FMO2-HF: Nuclear repulsion 2119260.757932
FMO2-HF: Total energy -85577.383006
FMO2-MP2: Total energy -85822.566606


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(3:1:GLY)


Summations of interaction energy for fragment #1(3:1: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.
0.0371.91-0.015-1.008-0.8510.005
Interaction energy analysis for fragmet #1(3:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.020
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].
333PHE0-0.010-0.0203.783-0.1091.764-0.015-1.008-0.8510.005
434PRO0-0.0240.0045.4560.3090.3090.0000.0000.0000.000
535VAL00.0470.0148.0800.0800.0800.0000.0000.0000.000
636ALA00.0090.01311.7820.0770.0770.0000.0000.0000.000
737CYS0-0.054-0.04114.981-0.031-0.0310.0000.0000.0000.000
838SER0-0.015-0.00117.5450.0430.0430.0000.0000.0000.000
939ASP-1-0.842-0.91520.662-0.100-0.1000.0000.0000.0000.000
10310GLY0-0.076-0.04023.7360.0030.0030.0000.0000.0000.000
11311TYR0-0.009-0.00523.328-0.003-0.0030.0000.0000.0000.000
12312GLY00.0060.00124.383-0.010-0.0100.0000.0000.0000.000
13313ASN0-0.033-0.02225.663-0.009-0.0090.0000.0000.0000.000
14314MET00.005-0.00129.037-0.005-0.0050.0000.0000.0000.000
15315VAL00.0020.00331.025-0.004-0.0040.0000.0000.0000.000
16316THR0-0.015-0.01633.918-0.006-0.0060.0000.0000.0000.000
17317THR00.009-0.00236.0650.0020.0020.0000.0000.0000.000
18318ASP-1-0.856-0.90630.357-0.172-0.1720.0000.0000.0000.000
19319PRO00.0030.00231.3550.0000.0000.0000.0000.0000.000
20320LYS10.8530.93726.4290.1910.1910.0000.0000.0000.000
21321THR0-0.005-0.01429.1790.0130.0130.0000.0000.0000.000
22322ALA0-0.030-0.00728.715-0.014-0.0140.0000.0000.0000.000
23323ASP-1-0.880-0.92524.432-0.303-0.3030.0000.0000.0000.000
24324PRO0-0.043-0.02227.5840.0200.0200.0000.0000.0000.000
25325ALA00.011-0.01529.145-0.009-0.0090.0000.0000.0000.000
26326TYR0-0.027-0.00131.3310.0020.0020.0000.0000.0000.000
27327GLY00.0370.01133.6920.0000.0000.0000.0000.0000.000
28328LYS10.9030.94232.6330.1910.1910.0000.0000.0000.000
29329VAL00.0520.03936.6830.0070.0070.0000.0000.0000.000
30330TYR0-0.023-0.02038.628-0.004-0.0040.0000.0000.0000.000
31331ASN0-0.010-0.01142.4500.0050.0050.0000.0000.0000.000
32332PRO00.0460.03245.2660.0010.0010.0000.0000.0000.000
33333PRO0-0.012-0.00448.616-0.002-0.0020.0000.0000.0000.000
34334ARG10.9850.98844.6390.1020.1020.0000.0000.0000.000
35335THR0-0.012-0.02551.516-0.001-0.0010.0000.0000.0000.000
36336ALA00.0060.01052.8130.0020.0020.0000.0000.0000.000
37337LEU0-0.0140.01253.3970.0020.0020.0000.0000.0000.000
38338PRO00.006-0.01856.129-0.001-0.0010.0000.0000.0000.000
39339GLY00.0210.01157.587-0.001-0.0010.0000.0000.0000.000
40340ARG10.9450.99347.3470.0850.0850.0000.0000.0000.000
41341PHE00.0260.01652.7890.0020.0020.0000.0000.0000.000
42342THR0-0.021-0.03148.810-0.003-0.0030.0000.0000.0000.000
43343ASN00.0460.02349.5350.0000.0000.0000.0000.0000.000
44344TYR00.0290.00949.7300.0010.0010.0000.0000.0000.000
45345LEU00.0700.01953.4900.0020.0020.0000.0000.0000.000
46346ASP-1-0.868-0.90554.561-0.064-0.0640.0000.0000.0000.000
47347VAL0-0.042-0.03656.6200.0020.0020.0000.0000.0000.000
48348ALA0-0.018-0.00158.2390.0020.0020.0000.0000.0000.000
49349GLU-1-0.890-0.92559.117-0.051-0.0510.0000.0000.0000.000
50350ALA0-0.081-0.04661.3180.0020.0020.0000.0000.0000.000
51351CYS0-0.078-0.04462.4310.0010.0010.0000.0000.0000.000
52352PRO0-0.0170.01664.202-0.001-0.0010.0000.0000.0000.000
53353THR00.0060.00064.7930.0000.0000.0000.0000.0000.000
54354PHE0-0.019-0.02467.2220.0010.0010.0000.0000.0000.000
55355LEU0-0.0020.02369.141-0.001-0.0010.0000.0000.0000.000
56356MET0-0.074-0.03770.8130.0010.0010.0000.0000.0000.000
57357PHE0-0.007-0.01772.7000.0000.0000.0000.0000.0000.000
58358GLU-1-0.899-0.95875.186-0.026-0.0260.0000.0000.0000.000
59359ASN0-0.088-0.05074.8310.0000.0000.0000.0000.0000.000
60361VAL00.0140.02975.821-0.001-0.0010.0000.0000.0000.000
61362PRO00.0320.02373.9670.0000.0000.0000.0000.0000.000
62363TYR0-0.014-0.01675.1790.0000.0000.0000.0000.0000.000
63364VAL00.0400.03778.0110.0000.0000.0000.0000.0000.000
64365SER0-0.044-0.03380.4730.0000.0000.0000.0000.0000.000
65366THR00.014-0.00184.2190.0000.0000.0000.0000.0000.000
66367ARG10.9100.94486.9670.0200.0200.0000.0000.0000.000
67368THR0-0.001-0.01988.6980.0000.0000.0000.0000.0000.000
68369ASP-1-0.857-0.93290.756-0.019-0.0190.0000.0000.0000.000
69370GLY0-0.0170.00392.0470.0000.0000.0000.0000.0000.000
70371GLN00.0380.01288.515-0.001-0.0010.0000.0000.0000.000
71372ARG10.9050.97585.5430.0210.0210.0000.0000.0000.000
72373LEU00.0460.02679.7240.0000.0000.0000.0000.0000.000
73374LEU0-0.089-0.04981.2320.0000.0000.0000.0000.0000.000
74375ALA00.0220.01476.6600.0000.0000.0000.0000.0000.000
75376LYS10.9300.96974.8440.0250.0250.0000.0000.0000.000
76377PHE0-0.087-0.03669.4450.0000.0000.0000.0000.0000.000
77378ASP-1-0.758-0.91067.862-0.030-0.0300.0000.0000.0000.000
78379VAL0-0.0440.00764.900-0.001-0.0010.0000.0000.0000.000
79380SER00.0560.02362.690-0.001-0.0010.0000.0000.0000.000
80381LEU0-0.024-0.02759.2580.0000.0000.0000.0000.0000.000
81382ALA00.0150.00561.417-0.001-0.0010.0000.0000.0000.000
82383ALA0-0.0030.01362.8470.0010.0010.0000.0000.0000.000
83384LYS11.0271.00466.5740.0290.0290.0000.0000.0000.000
84385HIS00.0480.05768.861-0.001-0.0010.0000.0000.0000.000
85386MET00.0080.03464.5000.0000.0000.0000.0000.0000.000
86387SER00.006-0.03764.7350.0000.0000.0000.0000.0000.000
87388ASN0-0.067-0.03864.6020.0000.0000.0000.0000.0000.000
88389THR0-0.022-0.00463.458-0.001-0.0010.0000.0000.0000.000
89390TYR00.0580.01057.248-0.002-0.0020.0000.0000.0000.000
90391LEU00.0260.00659.453-0.002-0.0020.0000.0000.0000.000
91392ALA00.0330.01759.129-0.001-0.0010.0000.0000.0000.000
92393GLY0-0.020-0.01058.874-0.001-0.0010.0000.0000.0000.000
93394LEU0-0.061-0.02053.844-0.002-0.0020.0000.0000.0000.000
94395ALA00.030-0.01654.664-0.002-0.0020.0000.0000.0000.000
95396GLN0-0.030-0.00254.8820.0010.0010.0000.0000.0000.000
96397TYR0-0.0200.00450.4340.0000.0000.0000.0000.0000.000
97398TYR00.0150.02448.277-0.005-0.0050.0000.0000.0000.000
98399THR0-0.0110.03749.1560.0030.0030.0000.0000.0000.000
993100GLN0-0.021-0.03349.6420.0030.0030.0000.0000.0000.000
1003101TYR0-0.012-0.01253.025-0.002-0.0020.0000.0000.0000.000
1013102THR00.1010.01055.0460.0010.0010.0000.0000.0000.000
1023103GLY0-0.0160.02357.067-0.002-0.0020.0000.0000.0000.000
1033104THR0-0.0440.00759.4990.0020.0020.0000.0000.0000.000
1043105ILE0-0.016-0.01362.199-0.002-0.0020.0000.0000.0000.000
1053106ASN00.0040.01364.5420.0020.0020.0000.0000.0000.000
1063107LEU00.0280.01667.372-0.001-0.0010.0000.0000.0000.000
1073108HIS0-0.058-0.05267.7470.0010.0010.0000.0000.0000.000
1083109PHE00.0360.00772.8160.0000.0000.0000.0000.0000.000
1093110MET0-0.032-0.01675.7090.0000.0000.0000.0000.0000.000
1103111PHE0-0.008-0.00778.3360.0000.0000.0000.0000.0000.000
1113112THR0-0.034-0.03981.0010.0000.0000.0000.0000.0000.000
1123113GLY0-0.0020.02283.4300.0000.0000.0000.0000.0000.000
1133114PRO00.0100.02287.1480.0000.0000.0000.0000.0000.000
1143115THR00.005-0.01990.0990.0000.0000.0000.0000.0000.000
1153116ASP-1-0.993-0.99791.488-0.021-0.0210.0000.0000.0000.000
1163117ALA0-0.0010.02390.2380.0010.0010.0000.0000.0000.000
1173118LYS10.9090.95689.8300.0210.0210.0000.0000.0000.000
1183119ALA00.0500.00686.9410.0010.0010.0000.0000.0000.000
1193120ARG10.7870.87785.9830.0230.0230.0000.0000.0000.000
1203121TYR0-0.0080.00281.9160.0010.0010.0000.0000.0000.000
1213122MET00.0520.03880.4620.0000.0000.0000.0000.0000.000
1223123VAL0-0.0380.00274.8210.0000.0000.0000.0000.0000.000
1233124ALA00.0280.00775.8210.0000.0000.0000.0000.0000.000
1243125TYR0-0.021-0.00667.0200.0000.0000.0000.0000.0000.000
1253126VAL0-0.030-0.02872.8190.0010.0010.0000.0000.0000.000
1263127PRO00.0410.02769.872-0.001-0.0010.0000.0000.0000.000
1273128PRO00.008-0.00167.0600.0010.0010.0000.0000.0000.000
1283129GLY0-0.014-0.01070.3810.0000.0000.0000.0000.0000.000
1293130MET0-0.045-0.01972.4080.0010.0010.0000.0000.0000.000
1303131ASP-1-0.897-0.93774.613-0.022-0.0220.0000.0000.0000.000
1313132ALA0-0.078-0.05375.4870.0000.0000.0000.0000.0000.000
1323133PRO00.0350.04477.2050.0000.0000.0000.0000.0000.000
1333134ASP-1-0.890-0.95380.590-0.021-0.0210.0000.0000.0000.000
1343135ASN0-0.003-0.02083.0250.0000.0000.0000.0000.0000.000
1353136PRO00.0450.01383.4190.0000.0000.0000.0000.0000.000
1363137GLU-1-0.870-0.95783.744-0.020-0.0200.0000.0000.0000.000
1373138GLU-1-0.936-0.95782.655-0.020-0.0200.0000.0000.0000.000
1383139ALA00.007-0.00979.6270.0000.0000.0000.0000.0000.000
1393140ALA0-0.084-0.03779.663-0.001-0.0010.0000.0000.0000.000
1403141HIS0-0.047-0.02480.1680.0000.0000.0000.0000.0000.000
1413142CYS0-0.0480.00275.1200.0000.0000.0000.0000.0000.000
1423143ILE00.006-0.00171.8480.0000.0000.0000.0000.0000.000
1433144HIS0-0.051-0.02674.9870.0000.0000.0000.0000.0000.000
1443145ALA0-0.013-0.00976.8270.0000.0000.0000.0000.0000.000
1453146GLU-1-0.812-0.89778.671-0.023-0.0230.0000.0000.0000.000
1463147TRP0-0.047-0.03978.4120.0000.0000.0000.0000.0000.000
1473148ASP-1-0.890-0.91782.974-0.024-0.0240.0000.0000.0000.000
1483149THR00.0040.00984.332-0.001-0.0010.0000.0000.0000.000
1493150GLY00.0370.00185.3960.0010.0010.0000.0000.0000.000
1503151LEU0-0.060-0.02483.8110.0000.0000.0000.0000.0000.000
1513152ASN0-0.023-0.02080.2910.0000.0000.0000.0000.0000.000
1523153SER00.0760.03779.6890.0000.0000.0000.0000.0000.000
1533154LYS10.8890.95871.0020.0370.0370.0000.0000.0000.000
1543155PHE00.0540.04476.1590.0000.0000.0000.0000.0000.000
1553156THR0-0.061-0.03770.0160.0000.0000.0000.0000.0000.000
1563157PHE00.0170.00471.5820.0010.0010.0000.0000.0000.000
1573158SER0-0.011-0.00567.181-0.001-0.0010.0000.0000.0000.000
1583159ILE0-0.035-0.01966.7020.0010.0010.0000.0000.0000.000
1593160PRO00.0060.00565.570-0.002-0.0020.0000.0000.0000.000
1603161TYR0-0.0010.01658.2050.0000.0000.0000.0000.0000.000
1613162ILE0-0.043-0.02763.0980.0000.0000.0000.0000.0000.000
1623163SER00.0170.01260.1530.0010.0010.0000.0000.0000.000
1633164ALA0-0.014-0.00660.7810.0000.0000.0000.0000.0000.000
1643165ALA0-0.018-0.00155.6160.0000.0000.0000.0000.0000.000
1653166ASP-1-0.855-0.91653.810-0.045-0.0450.0000.0000.0000.000
1663167TYR0-0.057-0.01550.749-0.002-0.0020.0000.0000.0000.000
1673168THR0-0.044-0.03755.0020.0030.0030.0000.0000.0000.000
1683169TYR0-0.022-0.02152.333-0.002-0.0020.0000.0000.0000.000
1693170THR0-0.045-0.03854.5320.0020.0020.0000.0000.0000.000
1703171ALA0-0.040-0.02955.5650.0020.0020.0000.0000.0000.000
1713172SER0-0.017-0.00657.5670.0010.0010.0000.0000.0000.000
1723173HIS0-0.013-0.00657.850-0.001-0.0010.0000.0000.0000.000
1733174GLU-1-0.913-0.96060.210-0.029-0.0290.0000.0000.0000.000
1743175ALA0-0.080-0.04761.8060.0010.0010.0000.0000.0000.000
1753176GLU-1-0.907-0.94960.880-0.034-0.0340.0000.0000.0000.000
1763177THR0-0.0020.00164.8230.0000.0000.0000.0000.0000.000
1773178THR0-0.017-0.00768.4260.0000.0000.0000.0000.0000.000
1783179CYS0-0.0370.00466.304-0.001-0.0010.0000.0000.0000.000
1793180VAL00.0190.00561.5320.0000.0000.0000.0000.0000.000
1803181GLN00.0150.01261.7560.0000.0000.0000.0000.0000.000
1813182GLY00.0260.03265.4490.0000.0000.0000.0000.0000.000
1823183TRP00.013-0.05068.991-0.001-0.0010.0000.0000.0000.000
1833184VAL00.0060.02470.1820.0000.0000.0000.0000.0000.000
1843185CYS0-0.043-0.02073.0120.0000.0000.0000.0000.0000.000
1853186VAL0-0.011-0.00975.9960.0000.0000.0000.0000.0000.000
1863187TYR0-0.049-0.04578.6500.0000.0000.0000.0000.0000.000
1873188GLN00.014-0.00182.419-0.001-0.0010.0000.0000.0000.000
1883189ILE0-0.012-0.00284.7250.0000.0000.0000.0000.0000.000
1893190THR0-0.095-0.05087.8650.0010.0010.0000.0000.0000.000
1903191HIS00.017-0.00589.191-0.001-0.0010.0000.0000.0000.000
1913192GLY00.0190.01291.6480.0010.0010.0000.0000.0000.000
1923193LYS10.8810.92493.6980.0190.0190.0000.0000.0000.000
1933194ALA00.0430.02389.5530.0000.0000.0000.0000.0000.000
1943195ASP-1-0.913-0.91789.572-0.021-0.0210.0000.0000.0000.000
1953196ALA0-0.0070.01489.1940.0000.0000.0000.0000.0000.000
1963197ASP-1-0.887-0.96987.057-0.024-0.0240.0000.0000.0000.000
1973198ALA0-0.008-0.00581.7520.0000.0000.0000.0000.0000.000
1983199LEU00.0070.00379.3870.0000.0000.0000.0000.0000.000
1993200VAL0-0.003-0.00775.3070.0000.0000.0000.0000.0000.000
2003201VAL00.0170.01272.6170.0000.0000.0000.0000.0000.000
2013202SER0-0.018-0.01769.690-0.001-0.0010.0000.0000.0000.000
2023203ALA00.029-0.00266.6960.0010.0010.0000.0000.0000.000
2033204SER0-0.037-0.00464.3400.0000.0000.0000.0000.0000.000
2043205ALA00.0120.00759.7420.0010.0010.0000.0000.0000.000
2053206GLY00.0210.00361.7260.0010.0010.0000.0000.0000.000
2063207LYS10.8970.93060.2350.0490.0490.0000.0000.0000.000
2073208ASP-1-0.873-0.93257.740-0.048-0.0480.0000.0000.0000.000
2083209PHE0-0.031-0.01457.3290.0000.0000.0000.0000.0000.000
2093210GLU-1-0.891-0.95050.480-0.065-0.0650.0000.0000.0000.000
2103211LEU0-0.024-0.01852.2690.0020.0020.0000.0000.0000.000
2113212ARG10.9160.97346.9820.0570.0570.0000.0000.0000.000
2123213LEU0-0.034-0.02945.1020.0020.0020.0000.0000.0000.000
2133214PRO00.0050.00344.5860.0030.0030.0000.0000.0000.000
2143215VAL0-0.035-0.03045.956-0.002-0.0020.0000.0000.0000.000
2153216ASP-1-0.920-0.96246.914-0.065-0.0650.0000.0000.0000.000
2163217ALA0-0.0020.01748.6980.0010.0010.0000.0000.0000.000
2173218ARG10.9180.92751.4370.0480.0480.0000.0000.0000.000
2183219GLN00.0080.01953.0390.0000.0000.0000.0000.0000.000
2193220GLN00.0080.01649.3170.0010.0010.0000.0000.0000.000