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: QV47Y

Calculation Name: 1GFF-2-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GFF

Chain ID: 2

ChEMBL ID:

UniProt ID: P03642

Base Structure: X-ray

Registration Date: 2023-09-23

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1692197.207317
FMO2-HF: Nuclear repulsion 1626620.341851
FMO2-HF: Total energy -65576.865466
FMO2-MP2: Total energy -65771.280226


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(2:1:MET)


Summations of interaction energy for fragment #1(2:1: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.
-2.2471.1060.165-1.774-1.7440.004
Interaction energy analysis for fragmet #1(2:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.010
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].
323GLN00.0230.0133.000-2.5040.8490.165-1.774-1.7440.004
424LYS10.9520.9835.689-0.348-0.3480.0000.0000.0000.000
525PHE00.035-0.0027.645-0.087-0.0870.0000.0000.0000.000
626ILE00.0300.01911.0950.0230.0230.0000.0000.0000.000
727SER0-0.037-0.02512.5730.1020.1020.0000.0000.0000.000
828LYS10.9460.97815.240-0.232-0.2320.0000.0000.0000.000
929HIS00.007-0.00818.231-0.020-0.0200.0000.0000.0000.000
10210ASN0-0.0090.00217.887-0.009-0.0090.0000.0000.0000.000
11211ALA00.0230.01420.454-0.004-0.0040.0000.0000.0000.000
12212PRO00.002-0.00223.111-0.017-0.0170.0000.0000.0000.000
13213ILE00.001-0.00723.2660.0010.0010.0000.0000.0000.000
14214ASN0-0.028-0.01125.166-0.001-0.0010.0000.0000.0000.000
15215SER0-0.0240.00527.6660.0060.0060.0000.0000.0000.000
16216THR0-0.009-0.00629.536-0.005-0.0050.0000.0000.0000.000
17217GLN00.003-0.01733.0720.0080.0080.0000.0000.0000.000
18218LEU0-0.0080.00134.4120.0010.0010.0000.0000.0000.000
19219ALA0-0.017-0.02636.4860.0010.0010.0000.0000.0000.000
20220ALA00.009-0.00139.170-0.002-0.0020.0000.0000.0000.000
21221THR00.138-0.17440.7820.0040.0040.0000.0000.0000.000
22222LYS10.8300.91041.052-0.019-0.0190.0000.0000.0000.000
23223THR00.005-0.07943.4730.0010.0010.0000.0000.0000.000
24224PRO0-0.0420.03341.022-0.002-0.0020.0000.0000.0000.000
25225ALA00.1020.00942.8870.0020.0020.0000.0000.0000.000
26226VAL01.0320.18843.6160.0010.0010.0000.0000.0000.000
27227ALA0-0.921-0.44543.6180.0020.0020.0000.0000.0000.000
28228ALA0-0.146-0.22740.310-0.002-0.0020.0000.0000.0000.000
29229PRO0-0.027-0.04342.363-0.002-0.0020.0000.0000.0000.000
30230VAL0-0.0160.02439.0920.0030.0030.0000.0000.0000.000
31231LEU0-0.049-0.01934.900-0.003-0.0030.0000.0000.0000.000
32232SER0-0.0200.00336.164-0.003-0.0030.0000.0000.0000.000
33233VAL0-0.015-0.00838.2790.0020.0020.0000.0000.0000.000
34234PRO00.0320.01537.256-0.002-0.0020.0000.0000.0000.000
35235ASN00.0110.00633.594-0.004-0.0040.0000.0000.0000.000
36236LEU00.0290.03335.1720.0020.0020.0000.0000.0000.000
37237SER00.0800.01730.8130.0030.0030.0000.0000.0000.000
38238ARG10.8440.93527.7570.0260.0260.0000.0000.0000.000
39239SER0-0.063-0.01529.444-0.005-0.0050.0000.0000.0000.000
40240THR00.047-0.00425.7790.0090.0090.0000.0000.0000.000
41241ILE00.0290.01928.924-0.008-0.0080.0000.0000.0000.000
42242LEU0-0.015-0.01829.5300.0070.0070.0000.0000.0000.000
43243ILE00.1670.09331.459-0.006-0.0060.0000.0000.0000.000
44244ASN00.0990.06034.5630.0090.0090.0000.0000.0000.000
45245ALA0-0.0290.03935.551-0.004-0.0040.0000.0000.0000.000
46246THR0-0.1200.18437.5070.0020.0020.0000.0000.0000.000
47247THR0-0.007-0.02638.6190.0000.0000.0000.0000.0000.000
48248THR0-0.0340.03041.8560.0010.0010.0000.0000.0000.000
49249ALA0-0.010-0.19144.0370.0020.0020.0000.0000.0000.000
50250VAL00.041-0.04643.049-0.002-0.0020.0000.0000.0000.000
51251THR00.0330.01043.8480.0030.0030.0000.0000.0000.000
52252THR0-0.031-0.05144.735-0.002-0.0020.0000.0000.0000.000
53253HIS00.0140.04539.143-0.001-0.0010.0000.0000.0000.000
54254SER00.1130.49742.773-0.002-0.0020.0000.0000.0000.000
55255GLY0-0.023-0.02139.8090.0030.0030.0000.0000.0000.000
56256LEU0-0.0160.09637.000-0.004-0.0040.0000.0000.0000.000
57257CYS0-0.043-0.02535.8190.0040.0040.0000.0000.0000.000
58258HIS00.016-0.00230.790-0.004-0.0040.0000.0000.0000.000
59259VAL00.0850.06533.2210.0060.0060.0000.0000.0000.000
60260VAL0-0.146-0.03631.532-0.005-0.0050.0000.0000.0000.000
61261ARG10.9900.96434.6720.0060.0060.0000.0000.0000.000
62262ILE00.003-0.00433.529-0.003-0.0030.0000.0000.0000.000
63263ASP-1-0.944-0.97934.771-0.015-0.0150.0000.0000.0000.000
64264GLH0-0.188-0.21236.2720.0020.0020.0000.0000.0000.000
65265THR0-0.074-0.09137.652-0.001-0.0010.0000.0000.0000.000
66266ASN00.1150.10033.277-0.007-0.0070.0000.0000.0000.000
67267PRO0-0.0310.00436.7370.0040.0040.0000.0000.0000.000
68268THR0-0.076-0.02531.8620.0020.0020.0000.0000.0000.000
69269ASN00.1020.02035.0500.0010.0010.0000.0000.0000.000
70270HIS00.0530.04132.1680.0020.0020.0000.0000.0000.000
71271HIS0-0.045-0.02230.109-0.007-0.0070.0000.0000.0000.000
72272ALA00.0150.00825.3280.0080.0080.0000.0000.0000.000
73273LEU00.003-0.00327.395-0.010-0.0100.0000.0000.0000.000
74274SER00.0190.01822.8910.0080.0080.0000.0000.0000.000
75275ILE00.0230.00924.963-0.016-0.0160.0000.0000.0000.000
76276ALA0-0.017-0.05222.1940.0150.0150.0000.0000.0000.000
77277GLY0-0.0020.01324.115-0.017-0.0170.0000.0000.0000.000
78278SER0-0.064-0.02223.6900.0220.0220.0000.0000.0000.000
79279LEU0-0.0830.01526.060-0.014-0.0140.0000.0000.0000.000
80280SER00.0600.04728.9530.0110.0110.0000.0000.0000.000
81281ASN0-0.088-0.04931.085-0.001-0.0010.0000.0000.0000.000
82282VAL0-0.166-0.16630.737-0.005-0.0050.0000.0000.0000.000
83283PRO00.0690.04033.2170.0040.0040.0000.0000.0000.000
84284ALA00.0270.01631.9030.0030.0030.0000.0000.0000.000
85285ASP-1-1.538-0.84332.9680.0670.0670.0000.0000.0000.000
86286MET00.0960.15931.1160.0030.0030.0000.0000.0000.000
87287ILE0-0.0010.01630.7750.0100.0100.0000.0000.0000.000
88288ALA00.0100.00028.910-0.008-0.0080.0000.0000.0000.000
89289PHE0-0.0190.00029.7380.0090.0090.0000.0000.0000.000
90290ALA0-0.020-0.01429.924-0.004-0.0040.0000.0000.0000.000
91291ILE00.018-0.03331.963-0.001-0.0010.0000.0000.0000.000
92292ARG10.8240.89334.505-0.029-0.0290.0000.0000.0000.000
93293PHE00.0160.01737.0690.0010.0010.0000.0000.0000.000
94294GLU-1-0.723-0.84840.5730.0180.0180.0000.0000.0000.000
95295VAL0-0.0530.00243.1260.0010.0010.0000.0000.0000.000
96296ALA00.058-0.00145.672-0.001-0.0010.0000.0000.0000.000
97297ASP-1-0.775-0.86546.2990.0010.0010.0000.0000.0000.000
98298GLY0-0.0400.01346.313-0.001-0.0010.0000.0000.0000.000
99299VAL0-0.089-0.03547.406-0.001-0.0010.0000.0000.0000.000
1002100VAL00.0270.05543.3400.0010.0010.0000.0000.0000.000
1012101PRO0-0.027-0.00341.4220.0010.0010.0000.0000.0000.000
1022102THR0-0.040-0.02843.784-0.001-0.0010.0000.0000.0000.000
1032103ALA0-0.014-0.04042.6440.0010.0010.0000.0000.0000.000
1042104VAL0-0.0210.02439.694-0.002-0.0020.0000.0000.0000.000
1052105PRO00.0240.00842.8390.0000.0000.0000.0000.0000.000
1062106ALA0-0.034-0.01644.5140.0020.0020.0000.0000.0000.000
1072107LEU0-0.031-0.01844.7160.0020.0020.0000.0000.0000.000
1082108TYR00.024-0.00439.296-0.003-0.0030.0000.0000.0000.000
1092109ASP-1-0.866-0.90037.6700.0400.0400.0000.0000.0000.000
1102110VAL0-0.004-0.02435.4550.0000.0000.0000.0000.0000.000
1112111TYR00.007-0.00631.078-0.001-0.0010.0000.0000.0000.000
1122112PRO00.004-0.00429.6700.0010.0010.0000.0000.0000.000
1132113ILE0-0.060-0.03325.5300.0010.0010.0000.0000.0000.000
1142114GLU-1-0.971-0.97220.5490.2510.2510.0000.0000.0000.000
1152115THR0-0.089-0.02223.4400.0040.0040.0000.0000.0000.000
1162116PHE00.0390.01020.2710.0030.0030.0000.0000.0000.000
1172117ASN00.038-0.00824.649-0.002-0.0020.0000.0000.0000.000
1182118ASN00.0190.01325.448-0.001-0.0010.0000.0000.0000.000
1192119GLY00.0040.00827.087-0.004-0.0040.0000.0000.0000.000
1202120LYS10.9410.96429.514-0.077-0.0770.0000.0000.0000.000
1212121ALA00.0510.00226.449-0.008-0.0080.0000.0000.0000.000
1222122ILE0-0.040-0.00926.2330.0100.0100.0000.0000.0000.000
1232123SER00.006-0.01221.210-0.011-0.0110.0000.0000.0000.000
1242124PHE00.0690.02422.7070.0030.0030.0000.0000.0000.000
1252125LYS10.9200.96617.492-0.135-0.1350.0000.0000.0000.000
1262126ASP-1-0.725-0.86220.5020.2040.2040.0000.0000.0000.000
1272127ALA0-0.094-0.05122.279-0.019-0.0190.0000.0000.0000.000
1282128VAL00.0390.04024.0200.0100.0100.0000.0000.0000.000
1292129THR0-0.050-0.05227.098-0.009-0.0090.0000.0000.0000.000
1302130ILE0-0.0110.04329.3730.0030.0030.0000.0000.0000.000
1312131ASP-1-0.764-0.88432.8680.0300.0300.0000.0000.0000.000
1322132SER0-0.026-0.01334.398-0.001-0.0010.0000.0000.0000.000
1332133HIS0-0.0170.00736.199-0.001-0.0010.0000.0000.0000.000
1342134PRO0-0.028-0.03939.9700.0030.0030.0000.0000.0000.000
1352135ARG10.7630.86638.388-0.032-0.0320.0000.0000.0000.000
1362136THR0-0.091-0.03944.0040.0000.0000.0000.0000.0000.000
1372137VAL00.002-0.02646.806-0.001-0.0010.0000.0000.0000.000
1382138GLY00.0150.00648.083-0.001-0.0010.0000.0000.0000.000
1392139ASN0-0.002-0.01145.7800.0000.0000.0000.0000.0000.000
1402140ASP-1-0.685-0.72142.2630.0010.0010.0000.0000.0000.000
1412141VAL0-0.051-0.01537.9130.0030.0030.0000.0000.0000.000
1422142TYR0-0.063-0.09637.694-0.003-0.0030.0000.0000.0000.000
1432143ALA00.0430.00133.5310.0030.0030.0000.0000.0000.000
1442144GLY0-0.051-0.04131.776-0.005-0.0050.0000.0000.0000.000
1452145ILE0-0.031-0.01528.2900.0050.0050.0000.0000.0000.000
1462146MET00.0140.01831.916-0.007-0.0070.0000.0000.0000.000
1472147LEU0-0.0210.00731.7470.0070.0070.0000.0000.0000.000
1482148TRP00.0080.00334.851-0.006-0.0060.0000.0000.0000.000
1492149SER00.580-0.11435.5590.0120.0120.0000.0000.0000.000
1502150ASN00.027-0.02637.793-0.008-0.0080.0000.0000.0000.000
1512151ALA00.0350.00540.301-0.004-0.0040.0000.0000.0000.000
1522152TRP0-0.037-0.01736.6840.0020.0020.0000.0000.0000.000
1532153THR00.0170.23040.869-0.004-0.0040.0000.0000.0000.000
1542154ALA0-0.0080.02042.1180.0000.0000.0000.0000.0000.000
1552155SER00.007-0.02638.8900.0010.0010.0000.0000.0000.000
1562156THR0-0.0140.00237.137-0.002-0.0020.0000.0000.0000.000
1572157ILE0-0.034-0.00634.5130.0020.0020.0000.0000.0000.000
1582158SER0-0.003-0.01332.578-0.002-0.0020.0000.0000.0000.000
1592159GLY00.058-0.02529.1960.0090.0090.0000.0000.0000.000
1602160VAL0-0.023-0.03025.513-0.009-0.0090.0000.0000.0000.000
1612161LEU0-0.0140.00627.7690.0120.0120.0000.0000.0000.000
1622162SER00.0090.00724.944-0.017-0.0170.0000.0000.0000.000
1632163VAL0-0.008-0.01226.6950.0130.0130.0000.0000.0000.000
1642164ASN00.012-0.00424.772-0.008-0.0080.0000.0000.0000.000
1652165GLN00.0250.04527.3510.0090.0090.0000.0000.0000.000
1662166VAL00.019-0.02624.092-0.010-0.0100.0000.0000.0000.000
1672167ASN0-0.076-0.01226.6130.0000.0000.0000.0000.0000.000
1682168ARG10.9390.96326.3470.0630.0630.0000.0000.0000.000
1692169GLU-1-0.920-0.95420.477-0.043-0.0430.0000.0000.0000.000
1702170ALA0-0.056-0.03521.214-0.005-0.0050.0000.0000.0000.000
1712171THR0-0.004-0.00318.731-0.009-0.0090.0000.0000.0000.000
1722172VAL00.0200.00814.8180.0070.0070.0000.0000.0000.000
1732173LEU00.0200.01614.9330.0020.0020.0000.0000.0000.000
1742174GLN00.0410.03112.1860.0000.0000.0000.0000.0000.000
1752175PRO00.0230.0009.8260.0660.0660.0000.0000.0000.000
1762176LEU0-0.017-0.0028.435-0.001-0.0010.0000.0000.0000.000
1772177LYS10.9030.95812.6930.4360.4360.0000.0000.0000.000