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: R93Z8

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2204736.380417
FMO2-HF: Nuclear repulsion 2119157.253854
FMO2-HF: Total energy -85579.126563
FMO2-MP2: Total energy -85824.071123


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.
0.0481.914-0.015-1-0.8510.005
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 : 0.033 / 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].
333PHE00.010-0.0123.783-0.0971.769-0.015-1.000-0.8510.005
434PRO0-0.0180.0105.6030.3020.3020.0000.0000.0000.000
535VAL00.0170.0008.0790.0830.0830.0000.0000.0000.000
636ALA00.0190.01411.7810.0790.0790.0000.0000.0000.000
737CYS0-0.059-0.03714.980-0.033-0.0330.0000.0000.0000.000
838SER00.0030.00317.5440.0430.0430.0000.0000.0000.000
939ASP-1-0.856-0.92220.662-0.099-0.0990.0000.0000.0000.000
10310GLY0-0.059-0.03123.7350.0030.0030.0000.0000.0000.000
11311TYR0-0.019-0.00923.327-0.005-0.0050.0000.0000.0000.000
12312GLY00.0110.00424.382-0.009-0.0090.0000.0000.0000.000
13313ASN0-0.048-0.02625.661-0.006-0.0060.0000.0000.0000.000
14314MET00.004-0.00329.035-0.005-0.0050.0000.0000.0000.000
15315VAL00.0210.00931.023-0.004-0.0040.0000.0000.0000.000
16316THR0-0.016-0.01833.916-0.007-0.0070.0000.0000.0000.000
17317THR00.009-0.00136.0930.0030.0030.0000.0000.0000.000
18318ASP-1-0.809-0.87330.107-0.182-0.1820.0000.0000.0000.000
19319PRO0-0.0080.00631.2700.0010.0010.0000.0000.0000.000
20320LYS10.8180.90226.1630.1910.1910.0000.0000.0000.000
21321THR0-0.008-0.01829.1900.0130.0130.0000.0000.0000.000
22322ALA0-0.040-0.01028.715-0.015-0.0150.0000.0000.0000.000
23323ASP-1-0.877-0.92224.758-0.301-0.3010.0000.0000.0000.000
24324PRO0-0.048-0.02527.5720.0200.0200.0000.0000.0000.000
25325ALA00.009-0.01629.143-0.009-0.0090.0000.0000.0000.000
26326TYR0-0.0200.00031.3290.0020.0020.0000.0000.0000.000
27327GLY00.0330.00933.6930.0000.0000.0000.0000.0000.000
28328LYS10.9040.94432.1180.1950.1950.0000.0000.0000.000
29329VAL00.0560.03736.6850.0070.0070.0000.0000.0000.000
30330TYR0-0.027-0.02138.376-0.004-0.0040.0000.0000.0000.000
31331ASN0-0.025-0.01342.0310.0070.0070.0000.0000.0000.000
32332PRO00.0800.04745.2660.0000.0000.0000.0000.0000.000
33333PRO0-0.016-0.01148.616-0.002-0.0020.0000.0000.0000.000
34334ARG10.9690.98144.5530.1020.1020.0000.0000.0000.000
35335THR0-0.024-0.02451.528-0.001-0.0010.0000.0000.0000.000
36336ALA00.0120.01052.8130.0020.0020.0000.0000.0000.000
37337LEU00.0050.02053.1680.0020.0020.0000.0000.0000.000
38338PRO0-0.003-0.02456.129-0.001-0.0010.0000.0000.0000.000
39339GLY00.0170.01157.587-0.001-0.0010.0000.0000.0000.000
40340ARG10.9390.99147.6370.0840.0840.0000.0000.0000.000
41341PHE00.0270.01652.5310.0020.0020.0000.0000.0000.000
42342THR0-0.050-0.03949.277-0.003-0.0030.0000.0000.0000.000
43343ASN00.0140.01249.535-0.002-0.0020.0000.0000.0000.000
44344TYR00.0460.02149.5600.0010.0010.0000.0000.0000.000
45345LEU00.0590.01553.7260.0020.0020.0000.0000.0000.000
46346ASP-1-0.844-0.91054.222-0.065-0.0650.0000.0000.0000.000
47347VAL0-0.017-0.02456.6490.0020.0020.0000.0000.0000.000
48348ALA0-0.0170.00458.2490.0020.0020.0000.0000.0000.000
49349GLU-1-0.785-0.85859.181-0.050-0.0500.0000.0000.0000.000
50350ALA0-0.070-0.04261.3210.0020.0020.0000.0000.0000.000
51351CYS0-0.076-0.03562.8950.0020.0020.0000.0000.0000.000
52352PRO0-0.0050.02064.202-0.001-0.0010.0000.0000.0000.000
53353THR00.0240.01264.5300.0000.0000.0000.0000.0000.000
54354PHE0-0.030-0.03167.2220.0010.0010.0000.0000.0000.000
55355LEU00.0110.02868.776-0.001-0.0010.0000.0000.0000.000
56356MET0-0.076-0.02170.8130.0010.0010.0000.0000.0000.000
57357PHE00.011-0.01672.7000.0000.0000.0000.0000.0000.000
58358GLU-1-0.820-0.91175.114-0.027-0.0270.0000.0000.0000.000
59359ASN0-0.082-0.06174.7930.0000.0000.0000.0000.0000.000
60361VAL00.0040.02675.8210.0000.0000.0000.0000.0000.000
61362PRO00.0410.02473.7190.0000.0000.0000.0000.0000.000
62363TYR0-0.031-0.01875.1780.0000.0000.0000.0000.0000.000
63364VAL00.0340.03177.8950.0000.0000.0000.0000.0000.000
64365SER0-0.048-0.03280.4720.0000.0000.0000.0000.0000.000
65366THR00.012-0.01084.2180.0000.0000.0000.0000.0000.000
66367ARG10.8980.94986.9770.0200.0200.0000.0000.0000.000
67368THR00.0160.00388.6970.0000.0000.0000.0000.0000.000
68369ASP-1-0.804-0.90290.755-0.020-0.0200.0000.0000.0000.000
69370GLY0-0.030-0.00692.0470.0000.0000.0000.0000.0000.000
70371GLN00.0320.00788.388-0.001-0.0010.0000.0000.0000.000
71372ARG10.8790.94584.4330.0220.0220.0000.0000.0000.000
72373LEU00.0370.02379.6610.0000.0000.0000.0000.0000.000
73374LEU0-0.069-0.04081.1630.0000.0000.0000.0000.0000.000
74375ALA00.0230.01776.6980.0000.0000.0000.0000.0000.000
75376LYS10.9400.96974.7480.0250.0250.0000.0000.0000.000
76377PHE0-0.086-0.03469.5150.0000.0000.0000.0000.0000.000
77378ASP-1-0.779-0.88967.906-0.030-0.0300.0000.0000.0000.000
78379VAL0-0.0130.00964.868-0.001-0.0010.0000.0000.0000.000
79380SER00.0490.01562.634-0.001-0.0010.0000.0000.0000.000
80381LEU0-0.036-0.02659.2830.0000.0000.0000.0000.0000.000
81382ALA00.0150.00661.344-0.001-0.0010.0000.0000.0000.000
82383ALA00.0000.01562.8460.0010.0010.0000.0000.0000.000
83384LYS10.9370.95566.5730.0280.0280.0000.0000.0000.000
84385HIS00.0350.02868.860-0.001-0.0010.0000.0000.0000.000
85386MET00.0150.02864.2570.0000.0000.0000.0000.0000.000
86387SER00.0240.00264.7270.0000.0000.0000.0000.0000.000
87388ASN0-0.047-0.02764.6020.0000.0000.0000.0000.0000.000
88389THR0-0.053-0.03163.802-0.001-0.0010.0000.0000.0000.000
89390TYR00.0360.00157.010-0.001-0.0010.0000.0000.0000.000
90391LEU00.0220.00659.367-0.002-0.0020.0000.0000.0000.000
91392ALA00.0400.02659.128-0.001-0.0010.0000.0000.0000.000
92393GLY0-0.017-0.00558.873-0.001-0.0010.0000.0000.0000.000
93394LEU0-0.038-0.00853.770-0.002-0.0020.0000.0000.0000.000
94395ALA00.047-0.00554.664-0.002-0.0020.0000.0000.0000.000
95396GLN0-0.0180.00454.8820.0010.0010.0000.0000.0000.000
96397TYR0-0.0320.00150.4600.0010.0010.0000.0000.0000.000
97398TYR0-0.0010.01648.601-0.005-0.0050.0000.0000.0000.000
98399THR0-0.0030.01849.2430.0030.0030.0000.0000.0000.000
993100GLN00.006-0.00149.1170.0020.0020.0000.0000.0000.000
1003101TYR0-0.015-0.00653.024-0.002-0.0020.0000.0000.0000.000
1013102THR00.0610.01655.0450.0010.0010.0000.0000.0000.000
1023103GLY0-0.0050.01857.066-0.002-0.0020.0000.0000.0000.000
1033104THR0-0.051-0.01559.4980.0020.0020.0000.0000.0000.000
1043105ILE0-0.023-0.01462.215-0.002-0.0020.0000.0000.0000.000
1053106ASN0-0.0140.01064.5410.0020.0020.0000.0000.0000.000
1063107LEU00.0220.01267.371-0.001-0.0010.0000.0000.0000.000
1073108HIS0-0.030-0.03167.6660.0010.0010.0000.0000.0000.000
1083109PHE00.0360.00872.8150.0000.0000.0000.0000.0000.000
1093110MET0-0.023-0.01476.1390.0000.0000.0000.0000.0000.000
1103111PHE00.0000.00078.3350.0000.0000.0000.0000.0000.000
1113112THR0-0.068-0.05181.1710.0000.0000.0000.0000.0000.000
1123113GLY00.0130.03383.4300.0000.0000.0000.0000.0000.000
1133114PRO0-0.0110.01387.1470.0000.0000.0000.0000.0000.000
1143115THR00.000-0.01890.0990.0000.0000.0000.0000.0000.000
1153116ASP-1-0.946-0.96591.488-0.021-0.0210.0000.0000.0000.000
1163117ALA0-0.0060.02690.2120.0010.0010.0000.0000.0000.000
1173118LYS10.9160.95489.8260.0210.0210.0000.0000.0000.000
1183119ALA00.0500.00986.9610.0010.0010.0000.0000.0000.000
1193120ARG10.7760.85986.0970.0230.0230.0000.0000.0000.000
1203121TYR0-0.0020.00681.9130.0000.0000.0000.0000.0000.000
1213122MET00.0610.03780.6440.0000.0000.0000.0000.0000.000
1223123VAL0-0.050-0.00274.9440.0000.0000.0000.0000.0000.000
1233124ALA00.0330.01175.8370.0000.0000.0000.0000.0000.000
1243125TYR0-0.039-0.03267.2770.0000.0000.0000.0000.0000.000
1253126VAL0-0.021-0.02472.8180.0010.0010.0000.0000.0000.000
1263127PRO00.0500.03569.860-0.001-0.0010.0000.0000.0000.000
1273128PRO00.004-0.00667.0520.0010.0010.0000.0000.0000.000
1283129GLY0-0.016-0.01470.3800.0000.0000.0000.0000.0000.000
1293130MET0-0.051-0.01972.4070.0010.0010.0000.0000.0000.000
1303131ASP-1-0.895-0.94474.612-0.023-0.0230.0000.0000.0000.000
1313132ALA0-0.075-0.04875.4520.0000.0000.0000.0000.0000.000
1323133PRO00.0410.04077.2040.0000.0000.0000.0000.0000.000
1333134ASP-1-0.913-0.96380.589-0.021-0.0210.0000.0000.0000.000
1343135ASN0-0.039-0.03483.0240.0000.0000.0000.0000.0000.000
1353136PRO00.0580.01783.4140.0000.0000.0000.0000.0000.000
1363137GLU-1-0.837-0.92083.743-0.020-0.0200.0000.0000.0000.000
1373138GLU-1-0.925-0.95782.766-0.020-0.0200.0000.0000.0000.000
1383139ALA00.008-0.00979.6430.0000.0000.0000.0000.0000.000
1393140ALA0-0.083-0.03979.662-0.001-0.0010.0000.0000.0000.000
1403141HIS0-0.056-0.02280.2430.0000.0000.0000.0000.0000.000
1413142CYS0-0.0530.00075.2500.0000.0000.0000.0000.0000.000
1423143ILE00.0160.00171.8280.0000.0000.0000.0000.0000.000
1433144HIS0-0.058-0.03574.9860.0000.0000.0000.0000.0000.000
1443145ALA0-0.005-0.00476.8100.0000.0000.0000.0000.0000.000
1453146GLU-1-0.834-0.90178.670-0.023-0.0230.0000.0000.0000.000
1463147TRP0-0.033-0.02678.658-0.001-0.0010.0000.0000.0000.000
1473148ASP-1-0.830-0.89182.974-0.024-0.0240.0000.0000.0000.000
1483149THR0-0.0120.00384.332-0.001-0.0010.0000.0000.0000.000
1493150GLY00.015-0.00885.3990.0010.0010.0000.0000.0000.000
1503151LEU0-0.061-0.02183.7080.0000.0000.0000.0000.0000.000
1513152ASN0-0.024-0.02279.8280.0000.0000.0000.0000.0000.000
1523153SER00.0690.03379.7220.0000.0000.0000.0000.0000.000
1533154LYS10.8780.95170.7480.0380.0380.0000.0000.0000.000
1543155PHE00.0470.04276.6190.0000.0000.0000.0000.0000.000
1553156THR0-0.046-0.03869.9600.0000.0000.0000.0000.0000.000
1563157PHE00.0110.00171.7460.0010.0010.0000.0000.0000.000
1573158SER0-0.006-0.00667.383-0.001-0.0010.0000.0000.0000.000
1583159ILE0-0.024-0.01266.8410.0010.0010.0000.0000.0000.000
1593160PRO00.005-0.00265.552-0.002-0.0020.0000.0000.0000.000
1603161TYR00.0130.01258.1810.0000.0000.0000.0000.0000.000
1613162ILE0-0.039-0.03063.0980.0000.0000.0000.0000.0000.000
1623163SER00.0210.02260.3280.0020.0020.0000.0000.0000.000
1633164ALA0-0.023-0.01160.8250.0000.0000.0000.0000.0000.000
1643165ALA0-0.0080.00455.6760.0000.0000.0000.0000.0000.000
1653166ASP-1-0.858-0.92453.719-0.045-0.0450.0000.0000.0000.000
1663167TYR0-0.095-0.05850.957-0.002-0.0020.0000.0000.0000.000
1673168THR0-0.046-0.03655.0020.0030.0030.0000.0000.0000.000
1683169TYR0-0.016-0.01352.335-0.002-0.0020.0000.0000.0000.000
1693170THR0-0.048-0.03654.7140.0020.0020.0000.0000.0000.000
1703171ALA0-0.038-0.02355.5590.0020.0020.0000.0000.0000.000
1713172SER00.002-0.01757.5660.0010.0010.0000.0000.0000.000
1723173HIS0-0.045-0.01158.3690.0000.0000.0000.0000.0000.000
1733174GLU-1-0.907-0.95760.209-0.029-0.0290.0000.0000.0000.000
1743175ALA0-0.082-0.04861.8050.0010.0010.0000.0000.0000.000
1753176GLU-1-0.904-0.93460.704-0.034-0.0340.0000.0000.0000.000
1763177THR0-0.018-0.00864.8220.0000.0000.0000.0000.0000.000
1773178THR00.005-0.00168.5490.0000.0000.0000.0000.0000.000
1783179CYS0-0.053-0.01366.281-0.001-0.0010.0000.0000.0000.000
1793180VAL00.032-0.00161.4040.0000.0000.0000.0000.0000.000
1803181GLN00.0040.00561.6750.0000.0000.0000.0000.0000.000
1813182GLY00.0340.04365.4480.0000.0000.0000.0000.0000.000
1823183TRP00.012-0.03368.990-0.001-0.0010.0000.0000.0000.000
1833184VAL00.0110.02170.4170.0000.0000.0000.0000.0000.000
1843185CYS0-0.047-0.01373.0110.0000.0000.0000.0000.0000.000
1853186VAL0-0.010-0.01175.9520.0000.0000.0000.0000.0000.000
1863187TYR0-0.047-0.05078.6490.0000.0000.0000.0000.0000.000
1873188GLN0-0.019-0.02982.418-0.001-0.0010.0000.0000.0000.000
1883189ILE0-0.0140.00484.9830.0000.0000.0000.0000.0000.000
1893190THR0-0.074-0.05187.8650.0010.0010.0000.0000.0000.000
1903191HIS0-0.010-0.00789.306-0.001-0.0010.0000.0000.0000.000
1913192GLY00.0120.01191.6470.0010.0010.0000.0000.0000.000
1923193LYS10.8330.88993.6970.0200.0200.0000.0000.0000.000
1933194ALA00.0430.02589.4890.0000.0000.0000.0000.0000.000
1943195ASP-1-0.871-0.90289.571-0.021-0.0210.0000.0000.0000.000
1953196ALA0-0.050-0.01289.1110.0000.0000.0000.0000.0000.000
1963197ASP-1-0.829-0.93886.826-0.024-0.0240.0000.0000.0000.000
1973198ALA0-0.029-0.01581.8240.0000.0000.0000.0000.0000.000
1983199LEU00.004-0.00479.4490.0000.0000.0000.0000.0000.000
1993200VAL0-0.005-0.01175.3190.0000.0000.0000.0000.0000.000
2003201VAL00.0250.01772.8000.0000.0000.0000.0000.0000.000
2013202SER0-0.026-0.01369.727-0.001-0.0010.0000.0000.0000.000
2023203ALA00.020-0.00166.7370.0010.0010.0000.0000.0000.000
2033204SER0-0.0240.00264.1970.0000.0000.0000.0000.0000.000
2043205ALA0-0.008-0.00259.7270.0010.0010.0000.0000.0000.000
2053206GLY00.0360.00761.7450.0010.0010.0000.0000.0000.000
2063207LYS10.7750.85060.1340.0500.0500.0000.0000.0000.000
2073208ASP-1-0.860-0.91357.753-0.048-0.0480.0000.0000.0000.000
2083209PHE0-0.009-0.00657.4570.0000.0000.0000.0000.0000.000
2093210GLU-1-0.849-0.91850.652-0.064-0.0640.0000.0000.0000.000
2103211LEU0-0.010-0.01252.2920.0020.0020.0000.0000.0000.000
2113212ARG10.8770.95548.2400.0570.0570.0000.0000.0000.000
2123213LEU0-0.016-0.02445.5120.0020.0020.0000.0000.0000.000
2133214PRO00.0100.00844.5270.0030.0030.0000.0000.0000.000
2143215VAL0-0.045-0.03445.956-0.002-0.0020.0000.0000.0000.000
2153216ASP-1-0.908-0.96246.928-0.065-0.0650.0000.0000.0000.000
2163217ALA0-0.0120.01448.6980.0010.0010.0000.0000.0000.000
2173218ARG10.8890.90651.4370.0490.0490.0000.0000.0000.000
2183219GLN0-0.041-0.00853.0370.0010.0010.0000.0000.0000.000
2193220GLN00.0410.03249.3170.0010.0010.0000.0000.0000.000