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: QY9RY

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2205135.373884
FMO2-HF: Nuclear repulsion 2119554.974155
FMO2-HF: Total energy -85580.399729
FMO2-MP2: Total energy -85825.161845


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.
0.171.845-0.011-0.926-0.7390.003
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 : 0.036 / q_NPA : 0.018
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].
333PHE00.0110.0033.8700.1911.866-0.011-0.926-0.7390.003
434PRO0-0.0100.0096.2350.1760.1760.0000.0000.0000.000
535VAL00.015-0.0108.4530.0410.0410.0000.0000.0000.000
636ALA00.0120.01112.1810.0680.0680.0000.0000.0000.000
737CYS0-0.050-0.02815.342-0.029-0.0290.0000.0000.0000.000
838SER0-0.003-0.00417.5470.0320.0320.0000.0000.0000.000
939ASP-1-0.867-0.92920.707-0.100-0.1000.0000.0000.0000.000
10310GLY0-0.037-0.02123.9000.0020.0020.0000.0000.0000.000
11311TYR0-0.037-0.01123.441-0.004-0.0040.0000.0000.0000.000
12312GLY00.0120.00424.764-0.007-0.0070.0000.0000.0000.000
13313ASN0-0.035-0.02525.659-0.004-0.0040.0000.0000.0000.000
14314MET00.0040.00229.125-0.005-0.0050.0000.0000.0000.000
15315VAL00.0230.00531.237-0.003-0.0030.0000.0000.0000.000
16316THR00.0090.00334.009-0.006-0.0060.0000.0000.0000.000
17317THR0-0.017-0.01236.1240.0050.0050.0000.0000.0000.000
18318ASP-1-0.804-0.87430.279-0.176-0.1760.0000.0000.0000.000
19319PRO0-0.0170.00231.2520.0010.0010.0000.0000.0000.000
20320LYS10.8070.89226.2750.1900.1900.0000.0000.0000.000
21321THR0-0.003-0.00329.1710.0120.0120.0000.0000.0000.000
22322ALA0-0.017-0.01028.729-0.014-0.0140.0000.0000.0000.000
23323ASP-1-0.897-0.94325.090-0.293-0.2930.0000.0000.0000.000
24324PRO0-0.051-0.02127.6510.0190.0190.0000.0000.0000.000
25325ALA00.0300.00329.115-0.011-0.0110.0000.0000.0000.000
26326TYR0-0.035-0.02031.3230.0070.0070.0000.0000.0000.000
27327GLY00.0240.00334.166-0.003-0.0030.0000.0000.0000.000
28328LYS10.9170.95532.1150.1910.1910.0000.0000.0000.000
29329VAL00.0430.04437.1120.0070.0070.0000.0000.0000.000
30330TYR0-0.006-0.01538.450-0.005-0.0050.0000.0000.0000.000
31331ASN0-0.021-0.01041.6850.0080.0080.0000.0000.0000.000
32332PRO00.0610.02745.0770.0000.0000.0000.0000.0000.000
33333PRO0-0.0110.00648.725-0.002-0.0020.0000.0000.0000.000
34334ARG10.9640.96444.7100.1000.1000.0000.0000.0000.000
35335THR0-0.002-0.00851.924-0.001-0.0010.0000.0000.0000.000
36336ALA0-0.004-0.00252.9100.0020.0020.0000.0000.0000.000
37337LEU00.0160.02253.2360.0020.0020.0000.0000.0000.000
38338PRO00.001-0.00956.301-0.001-0.0010.0000.0000.0000.000
39339GLY00.0200.01357.949-0.001-0.0010.0000.0000.0000.000
40340ARG10.8990.96147.9500.0820.0820.0000.0000.0000.000
41341PHE00.0200.02952.6320.0010.0010.0000.0000.0000.000
42342THR0-0.109-0.08349.796-0.004-0.0040.0000.0000.0000.000
43343ASN00.0140.00649.828-0.002-0.0020.0000.0000.0000.000
44344TYR00.0440.01849.7180.0010.0010.0000.0000.0000.000
45345LEU00.0520.01253.5760.0030.0030.0000.0000.0000.000
46346ASP-1-0.797-0.87654.158-0.065-0.0650.0000.0000.0000.000
47347VAL0-0.021-0.02457.0670.0020.0020.0000.0000.0000.000
48348ALA00.0150.01558.4040.0020.0020.0000.0000.0000.000
49349GLU-1-0.790-0.87059.535-0.047-0.0470.0000.0000.0000.000
50350ALA0-0.040-0.02361.5230.0020.0020.0000.0000.0000.000
51351CYS0-0.074-0.03262.9990.0010.0010.0000.0000.0000.000
52352PRO0-0.0130.01064.5380.0000.0000.0000.0000.0000.000
53353THR00.002-0.00764.9240.0000.0000.0000.0000.0000.000
54354PHE0-0.015-0.02067.6110.0000.0000.0000.0000.0000.000
55355LEU00.0150.04769.048-0.001-0.0010.0000.0000.0000.000
56356MET0-0.077-0.01370.9400.0010.0010.0000.0000.0000.000
57357PHE00.025-0.00272.8960.0000.0000.0000.0000.0000.000
58358GLU-1-0.837-0.90275.870-0.027-0.0270.0000.0000.0000.000
59359ASN0-0.030-0.03775.1070.0000.0000.0000.0000.0000.000
60361VAL00.0060.03075.728-0.001-0.0010.0000.0000.0000.000
61362PRO00.0130.00573.9140.0000.0000.0000.0000.0000.000
62363TYR0-0.024-0.02675.305-0.001-0.0010.0000.0000.0000.000
63364VAL00.0190.02478.1530.0000.0000.0000.0000.0000.000
64365SER0-0.061-0.03780.6590.0000.0000.0000.0000.0000.000
65366THR00.007-0.02284.4730.0000.0000.0000.0000.0000.000
66367ARG10.8740.93387.1920.0200.0200.0000.0000.0000.000
67368THR0-0.019-0.01189.0420.0010.0010.0000.0000.0000.000
68369ASP-1-0.761-0.85390.738-0.019-0.0190.0000.0000.0000.000
69370GLY0-0.025-0.01492.1030.0000.0000.0000.0000.0000.000
70371GLN00.0380.01088.786-0.001-0.0010.0000.0000.0000.000
71372ARG10.8530.91784.5250.0210.0210.0000.0000.0000.000
72373LEU00.0480.04379.819-0.001-0.0010.0000.0000.0000.000
73374LEU0-0.079-0.05081.4330.0000.0000.0000.0000.0000.000
74375ALA0-0.011-0.00976.6350.0000.0000.0000.0000.0000.000
75376LYS10.9270.97275.0490.0240.0240.0000.0000.0000.000
76377PHE0-0.049-0.01969.8530.0000.0000.0000.0000.0000.000
77378ASP-1-0.778-0.88668.212-0.029-0.0290.0000.0000.0000.000
78379VAL0-0.016-0.00664.800-0.001-0.0010.0000.0000.0000.000
79380SER00.0120.00362.329-0.001-0.0010.0000.0000.0000.000
80381LEU0-0.020-0.01659.1200.0000.0000.0000.0000.0000.000
81382ALA00.0030.00661.087-0.001-0.0010.0000.0000.0000.000
82383ALA00.0080.03062.7600.0010.0010.0000.0000.0000.000
83384LYS10.9070.92266.5140.0280.0280.0000.0000.0000.000
84385HIS00.0200.02268.993-0.001-0.0010.0000.0000.0000.000
85386MET00.0190.00964.6390.0000.0000.0000.0000.0000.000
86387SER0-0.015-0.02465.017-0.002-0.0020.0000.0000.0000.000
87388ASN0-0.073-0.03765.0070.0000.0000.0000.0000.0000.000
88389THR00.0030.00364.302-0.001-0.0010.0000.0000.0000.000
89390TYR00.015-0.01056.643-0.001-0.0010.0000.0000.0000.000
90391LEU00.0100.00359.562-0.002-0.0020.0000.0000.0000.000
91392ALA00.0500.03359.379-0.001-0.0010.0000.0000.0000.000
92393GLY0-0.020-0.01159.079-0.001-0.0010.0000.0000.0000.000
93394LEU0-0.046-0.00753.733-0.002-0.0020.0000.0000.0000.000
94395ALA00.0520.00354.775-0.002-0.0020.0000.0000.0000.000
95396GLN0-0.0080.00655.1230.0010.0010.0000.0000.0000.000
96397TYR0-0.047-0.00450.6240.0010.0010.0000.0000.0000.000
97398TYR0-0.008-0.00149.093-0.005-0.0050.0000.0000.0000.000
98399THR0-0.0300.00149.3860.0030.0030.0000.0000.0000.000
993100GLN00.0130.00049.6550.0020.0020.0000.0000.0000.000
1003101TYR0-0.003-0.01153.353-0.002-0.0020.0000.0000.0000.000
1013102THR00.0240.00155.5240.0010.0010.0000.0000.0000.000
1023103GLY00.0310.02157.303-0.002-0.0020.0000.0000.0000.000
1033104THR0-0.079-0.06159.9490.0020.0020.0000.0000.0000.000
1043105ILE0-0.023-0.00762.382-0.002-0.0020.0000.0000.0000.000
1053106ASN0-0.048-0.01064.6930.0030.0030.0000.0000.0000.000
1063107LEU00.0320.01567.424-0.001-0.0010.0000.0000.0000.000
1073108HIS0-0.017-0.01167.7010.0010.0010.0000.0000.0000.000
1083109PHE00.0330.00972.8270.0000.0000.0000.0000.0000.000
1093110MET0-0.016-0.01976.5180.0000.0000.0000.0000.0000.000
1103111PHE00.0010.01078.7060.0000.0000.0000.0000.0000.000
1113112THR0-0.061-0.04781.725-0.001-0.0010.0000.0000.0000.000
1123113GLY00.0450.04083.7250.0000.0000.0000.0000.0000.000
1133114PRO0-0.050-0.01787.5290.0000.0000.0000.0000.0000.000
1143115THR0-0.015-0.02990.4680.0000.0000.0000.0000.0000.000
1153116ASP-1-0.917-0.95791.734-0.020-0.0200.0000.0000.0000.000
1163117ALA0-0.0010.04090.4700.0000.0000.0000.0000.0000.000
1173118LYS10.8980.94290.2640.0210.0210.0000.0000.0000.000
1183119ALA00.0460.01687.4340.0010.0010.0000.0000.0000.000
1193120ARG10.7680.85285.7110.0220.0220.0000.0000.0000.000
1203121TYR00.007-0.00282.2420.0000.0000.0000.0000.0000.000
1213122MET00.0250.02280.6490.0000.0000.0000.0000.0000.000
1223123VAL0-0.046-0.01574.9250.0000.0000.0000.0000.0000.000
1233124ALA00.0460.01276.1710.0000.0000.0000.0000.0000.000
1243125TYR0-0.028-0.02367.5660.0000.0000.0000.0000.0000.000
1253126VAL0-0.007-0.01772.7360.0010.0010.0000.0000.0000.000
1263127PRO00.0430.02569.6100.0000.0000.0000.0000.0000.000
1273128PRO0-0.0080.00066.9780.0010.0010.0000.0000.0000.000
1283129GLY0-0.015-0.01770.2790.0000.0000.0000.0000.0000.000
1293130MET0-0.054-0.01772.3830.0010.0010.0000.0000.0000.000
1303131ASP-1-0.884-0.94774.683-0.022-0.0220.0000.0000.0000.000
1313132ALA0-0.053-0.02975.3110.0000.0000.0000.0000.0000.000
1323133PRO00.0410.03477.2230.0000.0000.0000.0000.0000.000
1333134ASP-1-0.921-0.96980.676-0.020-0.0200.0000.0000.0000.000
1343135ASN0-0.030-0.03183.1460.0000.0000.0000.0000.0000.000
1353136PRO00.0460.00883.7770.0000.0000.0000.0000.0000.000
1363137GLU-1-0.830-0.90684.126-0.019-0.0190.0000.0000.0000.000
1373138GLU-1-0.957-0.96983.042-0.019-0.0190.0000.0000.0000.000
1383139ALA00.005-0.00980.0120.0000.0000.0000.0000.0000.000
1393140ALA0-0.017-0.01379.732-0.001-0.0010.0000.0000.0000.000
1403141HIS0-0.070-0.02080.4810.0000.0000.0000.0000.0000.000
1413142CYS0-0.050-0.00375.5600.0000.0000.0000.0000.0000.000
1423143ILE00.0160.00771.8130.0000.0000.0000.0000.0000.000
1433144HIS0-0.047-0.02674.9280.0000.0000.0000.0000.0000.000
1443145ALA0-0.019-0.00377.0130.0000.0000.0000.0000.0000.000
1453146GLU-1-0.842-0.91478.764-0.022-0.0220.0000.0000.0000.000
1463147TRP0-0.040-0.01678.9990.0000.0000.0000.0000.0000.000
1473148ASP-1-0.780-0.87883.309-0.023-0.0230.0000.0000.0000.000
1483149THR0-0.039-0.00484.744-0.001-0.0010.0000.0000.0000.000
1493150GLY00.014-0.00885.5480.0010.0010.0000.0000.0000.000
1503151LEU0-0.050-0.01683.7580.0000.0000.0000.0000.0000.000
1513152ASN0-0.007-0.01279.5760.0000.0000.0000.0000.0000.000
1523153SER00.0460.02880.5370.0000.0000.0000.0000.0000.000
1533154LYS10.8430.93271.2800.0360.0360.0000.0000.0000.000
1543155PHE00.0210.01977.0260.0000.0000.0000.0000.0000.000
1553156THR0-0.036-0.03870.5050.0000.0000.0000.0000.0000.000
1563157PHE0-0.018-0.00772.2390.0000.0000.0000.0000.0000.000
1573158SER0-0.003-0.00867.6510.0000.0000.0000.0000.0000.000
1583159ILE0-0.0020.00567.1900.0010.0010.0000.0000.0000.000
1593160PRO00.0080.00665.902-0.002-0.0020.0000.0000.0000.000
1603161TYR00.0260.00558.7060.0000.0000.0000.0000.0000.000
1613162ILE0-0.023-0.02063.3810.0000.0000.0000.0000.0000.000
1623163SER00.0170.02560.3950.0010.0010.0000.0000.0000.000
1633164ALA0-0.036-0.01861.3090.0000.0000.0000.0000.0000.000
1643165ALA0-0.024-0.01355.9900.0000.0000.0000.0000.0000.000
1653166ASP-1-0.893-0.94753.933-0.043-0.0430.0000.0000.0000.000
1663167TYR0-0.049-0.04751.290-0.002-0.0020.0000.0000.0000.000
1673168THR0-0.036-0.01455.3510.0030.0030.0000.0000.0000.000
1683169TYR0-0.0040.00452.837-0.003-0.0030.0000.0000.0000.000
1693170THR0-0.026-0.02654.9730.0020.0020.0000.0000.0000.000
1703171ALA0-0.025-0.02156.6390.0010.0010.0000.0000.0000.000
1713172SER00.001-0.02558.4080.0000.0000.0000.0000.0000.000
1723173HIS0-0.052-0.03458.700-0.001-0.0010.0000.0000.0000.000
1733174GLU-1-0.900-0.95660.177-0.028-0.0280.0000.0000.0000.000
1743175ALA0-0.081-0.03962.0850.0010.0010.0000.0000.0000.000
1753176GLU-1-0.833-0.89260.989-0.033-0.0330.0000.0000.0000.000
1763177THR0-0.048-0.02565.1600.0000.0000.0000.0000.0000.000
1773178THR0-0.0040.00068.2040.0010.0010.0000.0000.0000.000
1783179CYS0-0.061-0.02066.1960.0000.0000.0000.0000.0000.000
1793180VAL00.0630.01661.2370.0010.0010.0000.0000.0000.000
1803181GLN0-0.046-0.02562.095-0.001-0.0010.0000.0000.0000.000
1813182GLY00.0110.03465.5650.0000.0000.0000.0000.0000.000
1823183TRP00.025-0.01968.870-0.001-0.0010.0000.0000.0000.000
1833184VAL0-0.0070.00570.6030.0000.0000.0000.0000.0000.000
1843185CYS0-0.048-0.00972.9430.0000.0000.0000.0000.0000.000
1853186VAL00.011-0.00276.1240.0000.0000.0000.0000.0000.000
1863187TYR0-0.003-0.02378.8150.0000.0000.0000.0000.0000.000
1873188GLN0-0.053-0.04582.618-0.001-0.0010.0000.0000.0000.000
1883189ILE0-0.0030.01385.2890.0000.0000.0000.0000.0000.000
1893190THR0-0.040-0.03688.3240.0010.0010.0000.0000.0000.000
1903191HIS0-0.035-0.02689.558-0.001-0.0010.0000.0000.0000.000
1913192GLY00.0010.00592.0600.0010.0010.0000.0000.0000.000
1923193LYS10.8430.90194.0150.0190.0190.0000.0000.0000.000
1933194ALA00.0560.03289.7220.0000.0000.0000.0000.0000.000
1943195ASP-1-0.865-0.90589.762-0.020-0.0200.0000.0000.0000.000
1953196ALA0-0.047-0.02289.0030.0000.0000.0000.0000.0000.000
1963197ASP-1-0.814-0.91486.737-0.024-0.0240.0000.0000.0000.000
1973198ALA0-0.010-0.00481.8770.0000.0000.0000.0000.0000.000
1983199LEU00.0060.01279.6500.0000.0000.0000.0000.0000.000
1993200VAL0-0.001-0.00975.6850.0000.0000.0000.0000.0000.000
2003201VAL00.0090.00373.7240.0000.0000.0000.0000.0000.000
2013202SER0-0.023-0.01969.915-0.001-0.0010.0000.0000.0000.000
2023203ALA00.0170.00566.6360.0010.0010.0000.0000.0000.000
2033204SER0-0.0120.00864.1030.0000.0000.0000.0000.0000.000
2043205ALA00.0440.02059.9540.0010.0010.0000.0000.0000.000
2053206GLY00.0370.01261.6690.0010.0010.0000.0000.0000.000
2063207LYS10.7820.86359.8710.0480.0480.0000.0000.0000.000
2073208ASP-1-0.847-0.89557.868-0.046-0.0460.0000.0000.0000.000
2083209PHE0-0.039-0.01157.2960.0000.0000.0000.0000.0000.000
2093210GLU-1-0.801-0.86550.611-0.062-0.0620.0000.0000.0000.000
2103211LEU0-0.022-0.02152.7980.0020.0020.0000.0000.0000.000
2113212ARG10.8180.91548.5500.0550.0550.0000.0000.0000.000
2123213LEU00.007-0.00645.6190.0020.0020.0000.0000.0000.000
2133214PRO00.0300.02344.9380.0030.0030.0000.0000.0000.000
2143215VAL0-0.033-0.01846.197-0.002-0.0020.0000.0000.0000.000
2153216ASP-1-0.852-0.92647.264-0.061-0.0610.0000.0000.0000.000
2163217ALA00.004-0.00248.8690.0010.0010.0000.0000.0000.000
2173218ARG10.8630.91951.8190.0500.0500.0000.0000.0000.000
2183219GLN0-0.038-0.01452.6250.0010.0010.0000.0000.0000.000
2193220GLN0-0.023-0.00549.1030.0020.0020.0000.0000.0000.000