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: KGZ73

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1690789.437699
FMO2-HF: Nuclear repulsion 1625202.621662
FMO2-HF: Total energy -65586.816037
FMO2-MP2: Total energy -65780.223524


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.
-1.4221.4310.043-1.483-1.4130.007
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 : 0.018 / q_NPA : 0.007
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].
323GLN00.0310.0213.360-1.9570.8960.043-1.483-1.4130.007
424LYS10.9480.9826.104-0.139-0.1390.0000.0000.0000.000
525PHE00.040-0.0027.950-0.099-0.0990.0000.0000.0000.000
626ILE00.0200.01511.4100.0340.0340.0000.0000.0000.000
727SER0-0.039-0.03912.8510.0900.0900.0000.0000.0000.000
828LYS10.8920.95115.548-0.232-0.2320.0000.0000.0000.000
929HIS0-0.030-0.02618.570-0.019-0.0190.0000.0000.0000.000
10210ASN00.0330.02718.2630.0010.0010.0000.0000.0000.000
11211ALA00.0610.04120.768-0.002-0.0020.0000.0000.0000.000
12212PRO0-0.0160.00523.254-0.018-0.0180.0000.0000.0000.000
13213ILE0-0.006-0.01723.253-0.001-0.0010.0000.0000.0000.000
14214ASN0-0.020-0.00625.153-0.003-0.0030.0000.0000.0000.000
15215SER0-0.024-0.00127.4560.0060.0060.0000.0000.0000.000
16216THR0-0.002-0.00429.361-0.005-0.0050.0000.0000.0000.000
17217GLN0-0.005-0.01032.9680.0080.0080.0000.0000.0000.000
18218LEU00.0240.00734.1480.0010.0010.0000.0000.0000.000
19219ALA00.037-0.01136.2390.0000.0000.0000.0000.0000.000
20220ALA0-0.014-0.00638.920-0.002-0.0020.0000.0000.0000.000
21221THR00.0080.01440.5570.0030.0030.0000.0000.0000.000
22222LYS10.8640.91740.738-0.008-0.0080.0000.0000.0000.000
23223THR00.0220.00443.3240.0010.0010.0000.0000.0000.000
24224PRO0-0.017-0.00240.983-0.001-0.0010.0000.0000.0000.000
25225ALA00.0820.01742.8590.0030.0030.0000.0000.0000.000
26226VAL00.1500.09543.7170.0010.0010.0000.0000.0000.000
27227ALA0-0.072-0.00243.8180.0010.0010.0000.0000.0000.000
28228ALA0-0.005-0.09140.563-0.002-0.0020.0000.0000.0000.000
29229PRO0-0.019-0.04342.496-0.002-0.0020.0000.0000.0000.000
30230VAL00.0040.02239.3240.0030.0030.0000.0000.0000.000
31231LEU0-0.056-0.02034.687-0.003-0.0030.0000.0000.0000.000
32232SER00.0250.00036.348-0.004-0.0040.0000.0000.0000.000
33233VAL0-0.033-0.00738.2610.0020.0020.0000.0000.0000.000
34234PRO00.0100.01437.415-0.003-0.0030.0000.0000.0000.000
35235ASN00.0210.00834.445-0.004-0.0040.0000.0000.0000.000
36236LEU00.0320.02635.3620.0030.0030.0000.0000.0000.000
37237SER00.027-0.00331.5500.0010.0010.0000.0000.0000.000
38238ARG10.8020.88827.8670.0390.0390.0000.0000.0000.000
39239SER0-0.049-0.00729.658-0.005-0.0050.0000.0000.0000.000
40240THR00.0700.01225.7410.0080.0080.0000.0000.0000.000
41241ILE00.0070.02728.893-0.008-0.0080.0000.0000.0000.000
42242LEU00.0070.00028.5470.0060.0060.0000.0000.0000.000
43243ILE0-0.0160.00131.195-0.005-0.0050.0000.0000.0000.000
44244ASN00.1280.05934.5930.0080.0080.0000.0000.0000.000
45245ALA0-0.0440.03635.312-0.003-0.0030.0000.0000.0000.000
46246THR0-0.043-0.02537.2580.0030.0030.0000.0000.0000.000
47247THR0-0.011-0.02238.5070.0000.0000.0000.0000.0000.000
48248THR0-0.0100.01741.6140.0010.0010.0000.0000.0000.000
49249ALA0-0.022-0.20544.2530.0020.0020.0000.0000.0000.000
50250VAL00.048-0.04743.733-0.002-0.0020.0000.0000.0000.000
51251THR00.0150.00344.2150.0030.0030.0000.0000.0000.000
52252THR0-0.050-0.05045.112-0.002-0.0020.0000.0000.0000.000
53253HIS00.0130.03439.243-0.001-0.0010.0000.0000.0000.000
54254SER00.0030.01843.024-0.002-0.0020.0000.0000.0000.000
55255GLY00.008-0.01739.8920.0030.0030.0000.0000.0000.000
56256LEU0-0.0180.10336.899-0.004-0.0040.0000.0000.0000.000
57257CYS0-0.044-0.02935.9930.0050.0050.0000.0000.0000.000
58258HIS00.007-0.00731.212-0.004-0.0040.0000.0000.0000.000
59259VAL00.0580.04533.4010.0060.0060.0000.0000.0000.000
60260VAL0-0.085-0.03732.016-0.005-0.0050.0000.0000.0000.000
61261ARG10.8840.92934.9650.0130.0130.0000.0000.0000.000
62262ILE00.003-0.00533.622-0.004-0.0040.0000.0000.0000.000
63263ASP-1-0.911-0.94535.179-0.022-0.0220.0000.0000.0000.000
64264GLH0-0.042-0.06036.5530.0020.0020.0000.0000.0000.000
65265THR0-0.057-0.04337.872-0.001-0.0010.0000.0000.0000.000
66266ASN00.0580.01532.738-0.004-0.0040.0000.0000.0000.000
67267PRO0-0.0240.00437.1420.0040.0040.0000.0000.0000.000
68268THR0-0.050-0.00732.0320.0030.0030.0000.0000.0000.000
69269ASN00.0650.01935.223-0.001-0.0010.0000.0000.0000.000
70270HIS00.0370.03632.3580.0000.0000.0000.0000.0000.000
71271HIS0-0.032-0.01330.288-0.009-0.0090.0000.0000.0000.000
72272ALA00.0120.00625.5770.0080.0080.0000.0000.0000.000
73273LEU00.009-0.00527.650-0.012-0.0120.0000.0000.0000.000
74274SER00.0300.02523.0740.0070.0070.0000.0000.0000.000
75275ILE00.0130.01025.256-0.016-0.0160.0000.0000.0000.000
76276ALA0-0.005-0.04222.2820.0130.0130.0000.0000.0000.000
77277GLY0-0.0100.01024.232-0.018-0.0180.0000.0000.0000.000
78278SER0-0.061-0.02023.4720.0210.0210.0000.0000.0000.000
79279LEU0-0.082-0.01625.822-0.014-0.0140.0000.0000.0000.000
80280SER00.0540.05029.0550.0110.0110.0000.0000.0000.000
81281ASN0-0.072-0.04331.119-0.001-0.0010.0000.0000.0000.000
82282VAL00.0130.00731.017-0.005-0.0050.0000.0000.0000.000
83283PRO00.0650.03533.7580.0040.0040.0000.0000.0000.000
84284ALA00.0410.02532.5540.0030.0030.0000.0000.0000.000
85285ASP-1-0.904-0.93633.5140.0640.0640.0000.0000.0000.000
86286MET0-0.083-0.01632.0210.0000.0000.0000.0000.0000.000
87287ILE00.0290.02031.1820.0100.0100.0000.0000.0000.000
88288ALA00.006-0.00229.106-0.008-0.0080.0000.0000.0000.000
89289PHE0-0.0040.01129.9020.0090.0090.0000.0000.0000.000
90290ALA0-0.023-0.02130.130-0.006-0.0060.0000.0000.0000.000
91291ILE0-0.032-0.03232.2170.0000.0000.0000.0000.0000.000
92292ARG10.8060.88834.775-0.027-0.0270.0000.0000.0000.000
93293PHE00.0380.02037.3230.0020.0020.0000.0000.0000.000
94294GLU-1-0.742-0.86840.8540.0160.0160.0000.0000.0000.000
95295VAL0-0.057-0.00343.3950.0010.0010.0000.0000.0000.000
96296ALA00.0490.00245.9720.0000.0000.0000.0000.0000.000
97297ASP-1-0.845-0.91146.729-0.005-0.0050.0000.0000.0000.000
98298GLY0-0.0360.00546.556-0.001-0.0010.0000.0000.0000.000
99299VAL0-0.098-0.04247.734-0.001-0.0010.0000.0000.0000.000
1002100VAL00.0100.01043.4080.0000.0000.0000.0000.0000.000
1012101PRO0-0.029-0.00141.8590.0010.0010.0000.0000.0000.000
1022102THR0-0.019-0.02643.973-0.001-0.0010.0000.0000.0000.000
1032103ALA0-0.001-0.01642.8680.0010.0010.0000.0000.0000.000
1042104VAL0-0.0290.01139.873-0.002-0.0020.0000.0000.0000.000
1052105PRO0-0.0020.00943.1350.0000.0000.0000.0000.0000.000
1062106ALA0-0.029-0.02444.7920.0020.0020.0000.0000.0000.000
1072107LEU0-0.033-0.02444.9190.0020.0020.0000.0000.0000.000
1082108TYR00.0220.00139.195-0.001-0.0010.0000.0000.0000.000
1092109ASP-1-0.805-0.86237.6770.0380.0380.0000.0000.0000.000
1102110VAL00.002-0.01235.606-0.001-0.0010.0000.0000.0000.000
1112111TYR00.0290.00031.2290.0000.0000.0000.0000.0000.000
1122112PRO0-0.016-0.00530.0630.0000.0000.0000.0000.0000.000
1132113ILE0-0.035-0.01925.7840.0010.0010.0000.0000.0000.000
1142114GLU-1-0.936-0.96320.8240.2580.2580.0000.0000.0000.000
1152115THR0-0.081-0.02523.5940.0010.0010.0000.0000.0000.000
1162116PHE00.0430.01420.9150.0060.0060.0000.0000.0000.000
1172117ASN0-0.010-0.01025.157-0.007-0.0070.0000.0000.0000.000
1182118ASN00.0250.02825.586-0.003-0.0030.0000.0000.0000.000
1192119GLY0-0.022-0.02127.627-0.004-0.0040.0000.0000.0000.000
1202120LYS10.9760.97430.160-0.064-0.0640.0000.0000.0000.000
1212121ALA00.0550.00827.113-0.009-0.0090.0000.0000.0000.000
1222122ILE0-0.0220.01526.6340.0100.0100.0000.0000.0000.000
1232123SER00.009-0.00921.788-0.010-0.0100.0000.0000.0000.000
1242124PHE00.0400.00022.8540.0080.0080.0000.0000.0000.000
1252125LYS10.8860.94817.400-0.083-0.0830.0000.0000.0000.000
1262126ASP-1-0.738-0.85820.7470.1940.1940.0000.0000.0000.000
1272127ALA0-0.069-0.04622.464-0.023-0.0230.0000.0000.0000.000
1282128VAL00.0430.04524.2230.0110.0110.0000.0000.0000.000
1292129THR0-0.035-0.02227.760-0.011-0.0110.0000.0000.0000.000
1302130ILE0-0.0150.01429.5240.0030.0030.0000.0000.0000.000
1312131ASP-1-0.784-0.87533.0460.0280.0280.0000.0000.0000.000
1322132SER00.001-0.01934.602-0.001-0.0010.0000.0000.0000.000
1332133HIS0-0.045-0.01936.414-0.002-0.0020.0000.0000.0000.000
1342134PRO00.022-0.00440.1810.0030.0030.0000.0000.0000.000
1352135ARG10.6910.81238.556-0.031-0.0310.0000.0000.0000.000
1362136THR0-0.117-0.05344.1980.0010.0010.0000.0000.0000.000
1372137VAL00.0350.00247.039-0.001-0.0010.0000.0000.0000.000
1382138GLY00.0150.00948.335-0.001-0.0010.0000.0000.0000.000
1392139ASN0-0.001-0.01645.538-0.002-0.0020.0000.0000.0000.000
1402140ASP-1-0.733-0.79842.661-0.004-0.0040.0000.0000.0000.000
1412141VAL0-0.035-0.02637.8000.0030.0030.0000.0000.0000.000
1422142TYR0-0.013-0.03637.999-0.004-0.0040.0000.0000.0000.000
1432143ALA00.0390.01133.8990.0040.0040.0000.0000.0000.000
1442144GLY0-0.051-0.03532.120-0.006-0.0060.0000.0000.0000.000
1452145ILE0-0.029-0.00128.2460.0060.0060.0000.0000.0000.000
1462146MET0-0.003-0.00132.142-0.007-0.0070.0000.0000.0000.000
1472147LEU0-0.0110.00631.6580.0070.0070.0000.0000.0000.000
1482148TRP00.0440.00534.912-0.006-0.0060.0000.0000.0000.000
1492149SER0-0.041-0.05735.8430.0050.0050.0000.0000.0000.000
1502150ASN0-0.021-0.02238.174-0.006-0.0060.0000.0000.0000.000
1512151ALA00.0140.00040.871-0.004-0.0040.0000.0000.0000.000
1522152TRP0-0.008-0.00636.9150.0020.0020.0000.0000.0000.000
1532153THR00.0080.24940.810-0.004-0.0040.0000.0000.0000.000
1542154ALA00.0040.01842.306-0.001-0.0010.0000.0000.0000.000
1552155SER0-0.009-0.02638.9650.0010.0010.0000.0000.0000.000
1562156THR00.0130.00537.161-0.001-0.0010.0000.0000.0000.000
1572157ILE0-0.036-0.00234.4260.0010.0010.0000.0000.0000.000
1582158SER00.004-0.00332.630-0.003-0.0030.0000.0000.0000.000
1592159GLY00.056-0.00128.9450.0090.0090.0000.0000.0000.000
1602160VAL0-0.045-0.03225.197-0.009-0.0090.0000.0000.0000.000
1612161LEU00.0200.01027.6530.0130.0130.0000.0000.0000.000
1622162SER0-0.039-0.02724.991-0.013-0.0130.0000.0000.0000.000
1632163VAL00.0240.01426.8620.0140.0140.0000.0000.0000.000
1642164ASN0-0.031-0.03124.539-0.011-0.0110.0000.0000.0000.000
1652165GLN00.1030.07827.7150.0120.0120.0000.0000.0000.000
1662166VAL00.0250.00224.086-0.011-0.0110.0000.0000.0000.000
1672167ASN00.0000.01226.8960.0010.0010.0000.0000.0000.000
1682168ARG10.9390.96226.1120.0860.0860.0000.0000.0000.000
1692169GLU-1-0.872-0.93620.626-0.062-0.0620.0000.0000.0000.000
1702170ALA0-0.087-0.04321.710-0.006-0.0060.0000.0000.0000.000
1712171THR0-0.006-0.00219.077-0.012-0.0120.0000.0000.0000.000
1722172VAL00.0040.00215.3330.0040.0040.0000.0000.0000.000
1732173LEU00.0210.01215.2640.0070.0070.0000.0000.0000.000
1742174GLN00.0160.01112.221-0.002-0.0020.0000.0000.0000.000
1752175PRO00.0210.0059.8520.0760.0760.0000.0000.0000.000
1762176LEU0-0.015-0.0068.6940.0010.0010.0000.0000.0000.000
1772177LYS10.9240.97412.6460.4540.4540.0000.0000.0000.000