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: 4JKRN

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1686063.939814
FMO2-HF: Nuclear repulsion 1620473.336039
FMO2-HF: Total energy -65590.603775
FMO2-MP2: Total energy -65783.478353


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.
0.042.1230.005-1.015-1.0720.004
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 : 0.036 / q_NPA : 0.013
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].
323GLN00.0400.0283.678-0.4891.5940.005-1.015-1.0720.004
424LYS10.9680.9866.034-0.294-0.2940.0000.0000.0000.000
525PHE00.003-0.0057.9240.0510.0510.0000.0000.0000.000
626ILE00.0130.00611.2550.0440.0440.0000.0000.0000.000
727SER0-0.039-0.04012.6320.1090.1090.0000.0000.0000.000
828LYS10.8720.93015.366-0.265-0.2650.0000.0000.0000.000
929HIS00.018-0.00718.540-0.021-0.0210.0000.0000.0000.000
10210ASN00.0060.03117.9100.0110.0110.0000.0000.0000.000
11211ALA00.0470.03220.286-0.003-0.0030.0000.0000.0000.000
12212PRO0-0.0050.00722.646-0.019-0.0190.0000.0000.0000.000
13213ILE0-0.005-0.01022.6360.0020.0020.0000.0000.0000.000
14214ASN0-0.034-0.01624.756-0.004-0.0040.0000.0000.0000.000
15215SER0-0.004-0.00727.1080.0060.0060.0000.0000.0000.000
16216THR00.0080.02129.059-0.005-0.0050.0000.0000.0000.000
17217GLN00.008-0.00332.3960.0070.0070.0000.0000.0000.000
18218LEU00.003-0.00933.8070.0000.0000.0000.0000.0000.000
19219ALA00.0200.00136.3000.0020.0020.0000.0000.0000.000
20220ALA0-0.0030.00339.094-0.002-0.0020.0000.0000.0000.000
21221THR0-0.0070.00241.0030.0030.0030.0000.0000.0000.000
22222LYS10.8530.92740.019-0.011-0.0110.0000.0000.0000.000
23223THR00.0390.00643.1580.0010.0010.0000.0000.0000.000
24224PRO0-0.0250.00440.884-0.001-0.0010.0000.0000.0000.000
25225ALA00.0650.02442.8520.0020.0020.0000.0000.0000.000
26226VAL00.0680.01943.7390.0010.0010.0000.0000.0000.000
27227ALA0-0.0270.00244.0950.0010.0010.0000.0000.0000.000
28228ALA00.0490.02240.121-0.002-0.0020.0000.0000.0000.000
29229PRO0-0.019-0.00741.936-0.002-0.0020.0000.0000.0000.000
30230VAL00.0050.01738.7350.0030.0030.0000.0000.0000.000
31231LEU0-0.021-0.01734.604-0.003-0.0030.0000.0000.0000.000
32232SER0-0.025-0.02436.493-0.004-0.0040.0000.0000.0000.000
33233VAL00.0160.01338.5690.0020.0020.0000.0000.0000.000
34234PRO00.0200.02437.178-0.002-0.0020.0000.0000.0000.000
35235ASN00.011-0.00233.877-0.004-0.0040.0000.0000.0000.000
36236LEU00.0640.03435.8580.0040.0040.0000.0000.0000.000
37237SER0-0.011-0.00831.8050.0000.0000.0000.0000.0000.000
38238ARG10.8010.88027.9390.0300.0300.0000.0000.0000.000
39239SER0-0.005-0.00129.329-0.007-0.0070.0000.0000.0000.000
40240THR00.0250.02425.5680.0130.0130.0000.0000.0000.000
41241ILE0-0.020-0.00428.173-0.008-0.0080.0000.0000.0000.000
42242LEU00.0060.00628.6220.0070.0070.0000.0000.0000.000
43243ILE00.0250.00630.793-0.005-0.0050.0000.0000.0000.000
44244ASN00.0360.03433.8880.0080.0080.0000.0000.0000.000
45245ALA00.0180.00435.679-0.002-0.0020.0000.0000.0000.000
46246THR0-0.038-0.01237.6250.0030.0030.0000.0000.0000.000
47247THR0-0.016-0.00938.8690.0000.0000.0000.0000.0000.000
48248THR00.0030.00041.8020.0010.0010.0000.0000.0000.000
49249ALA0-0.017-0.01044.1990.0020.0020.0000.0000.0000.000
50250VAL0-0.044-0.01943.815-0.002-0.0020.0000.0000.0000.000
51251THR0-0.001-0.00144.2790.0030.0030.0000.0000.0000.000
52252THR0-0.035-0.03045.019-0.002-0.0020.0000.0000.0000.000
53253HIS00.0520.04739.1660.0000.0000.0000.0000.0000.000
54254SER0-0.055-0.01341.877-0.003-0.0030.0000.0000.0000.000
55255GLY00.0440.02039.3970.0040.0040.0000.0000.0000.000
56256LEU0-0.031-0.00736.640-0.005-0.0050.0000.0000.0000.000
57257CYS00.0120.01735.9670.0050.0050.0000.0000.0000.000
58258HIS0-0.041-0.01730.635-0.004-0.0040.0000.0000.0000.000
59259VAL0-0.0110.00033.1900.0050.0050.0000.0000.0000.000
60260VAL0-0.063-0.01831.897-0.005-0.0050.0000.0000.0000.000
61261ARG10.8720.91834.9040.0080.0080.0000.0000.0000.000
62262ILE0-0.012-0.01133.701-0.001-0.0010.0000.0000.0000.000
63263ASP-1-0.889-0.94635.442-0.016-0.0160.0000.0000.0000.000
64264GLH0-0.037-0.04036.5170.0000.0000.0000.0000.0000.000
65265THR0-0.031-0.03137.9370.0000.0000.0000.0000.0000.000
66266ASN00.0190.02632.424-0.002-0.0020.0000.0000.0000.000
67267PRO00.0290.00636.7190.0040.0040.0000.0000.0000.000
68268THR0-0.059-0.02831.7910.0040.0040.0000.0000.0000.000
69269ASN00.0520.02634.8180.0010.0010.0000.0000.0000.000
70270HIS00.0150.01431.9460.0000.0000.0000.0000.0000.000
71271HIS0-0.020-0.02230.157-0.011-0.0110.0000.0000.0000.000
72272ALA00.0140.01625.2100.0080.0080.0000.0000.0000.000
73273LEU00.0140.01227.352-0.013-0.0130.0000.0000.0000.000
74274SER00.0030.01323.0210.0100.0100.0000.0000.0000.000
75275ILE00.003-0.00824.544-0.016-0.0160.0000.0000.0000.000
76276ALA0-0.016-0.02522.0560.0200.0200.0000.0000.0000.000
77277GLY00.0240.02223.806-0.017-0.0170.0000.0000.0000.000
78278SER0-0.071-0.04523.1190.0220.0220.0000.0000.0000.000
79279LEU0-0.0320.02025.502-0.013-0.0130.0000.0000.0000.000
80280SER00.0320.01028.7020.0110.0110.0000.0000.0000.000
81281ASN0-0.066-0.04830.872-0.002-0.0020.0000.0000.0000.000
82282VAL0-0.0040.00230.733-0.003-0.0030.0000.0000.0000.000
83283PRO00.0480.02133.7110.0030.0030.0000.0000.0000.000
84284ALA00.0090.00332.7500.0050.0050.0000.0000.0000.000
85285ASP-1-0.791-0.85732.8780.0700.0700.0000.0000.0000.000
86286MET0-0.073-0.01832.3720.0010.0010.0000.0000.0000.000
87287ILE00.0180.01530.8660.0100.0100.0000.0000.0000.000
88288ALA00.0010.00028.695-0.009-0.0090.0000.0000.0000.000
89289PHE00.007-0.00329.7560.0100.0100.0000.0000.0000.000
90290ALA00.0030.00429.641-0.007-0.0070.0000.0000.0000.000
91291ILE0-0.025-0.02131.6920.0010.0010.0000.0000.0000.000
92292ARG10.7860.88034.539-0.033-0.0330.0000.0000.0000.000
93293PHE00.0160.00137.0070.0010.0010.0000.0000.0000.000
94294GLU-1-0.712-0.84340.6600.0200.0200.0000.0000.0000.000
95295VAL0-0.043-0.01443.4410.0010.0010.0000.0000.0000.000
96296ALA00.0350.00946.367-0.001-0.0010.0000.0000.0000.000
97297ASP-1-0.873-0.95346.838-0.001-0.0010.0000.0000.0000.000
98298GLY00.0150.01846.266-0.001-0.0010.0000.0000.0000.000
99299VAL0-0.075-0.02547.137-0.001-0.0010.0000.0000.0000.000
1002100VAL0-0.0020.00743.0250.0010.0010.0000.0000.0000.000
1012101PRO0-0.0200.00741.6670.0000.0000.0000.0000.0000.000
1022102THR0-0.010-0.02243.313-0.001-0.0010.0000.0000.0000.000
1032103ALA0-0.013-0.01243.0270.0010.0010.0000.0000.0000.000
1042104VAL0-0.0090.01339.878-0.001-0.0010.0000.0000.0000.000
1052105PRO0-0.0060.01142.957-0.001-0.0010.0000.0000.0000.000
1062106ALA0-0.029-0.03344.8520.0020.0020.0000.0000.0000.000
1072107LEU0-0.008-0.00144.7380.0020.0020.0000.0000.0000.000
1082108TYR0-0.014-0.01338.974-0.001-0.0010.0000.0000.0000.000
1092109ASP-1-0.790-0.86537.4480.0440.0440.0000.0000.0000.000
1102110VAL0-0.004-0.01735.734-0.001-0.0010.0000.0000.0000.000
1112111TYR00.017-0.00631.1730.0010.0010.0000.0000.0000.000
1122112PRO0-0.0120.00029.9620.0000.0000.0000.0000.0000.000
1132113ILE0-0.036-0.01925.6590.0020.0020.0000.0000.0000.000
1142114GLU-1-0.894-0.95120.2340.2900.2900.0000.0000.0000.000
1152115THR0-0.084-0.04123.392-0.005-0.0050.0000.0000.0000.000
1162116PHE00.0190.00320.7930.0060.0060.0000.0000.0000.000
1172117ASN0-0.016-0.01524.874-0.008-0.0080.0000.0000.0000.000
1182118ASN00.0200.00325.384-0.001-0.0010.0000.0000.0000.000
1192119GLY00.0260.01427.471-0.003-0.0030.0000.0000.0000.000
1202120LYS10.9060.94830.096-0.070-0.0700.0000.0000.0000.000
1212121ALA00.0040.00627.192-0.008-0.0080.0000.0000.0000.000
1222122ILE00.0040.02126.9870.0090.0090.0000.0000.0000.000
1232123SER0-0.017-0.00821.905-0.007-0.0070.0000.0000.0000.000
1242124PHE00.0700.02822.6900.0080.0080.0000.0000.0000.000
1252125LYS10.8590.91716.998-0.101-0.1010.0000.0000.0000.000
1262126ASP-1-0.762-0.86520.5020.2100.2100.0000.0000.0000.000
1272127ALA0-0.050-0.03622.272-0.024-0.0240.0000.0000.0000.000
1282128VAL00.0270.03024.0160.0120.0120.0000.0000.0000.000
1292129THR0-0.013-0.00627.495-0.011-0.0110.0000.0000.0000.000
1302130ILE0-0.033-0.01229.2570.0030.0030.0000.0000.0000.000
1312131ASP-1-0.799-0.87232.7410.0340.0340.0000.0000.0000.000
1322132SER00.013-0.00134.402-0.001-0.0010.0000.0000.0000.000
1332133HIS0-0.036-0.03136.261-0.002-0.0020.0000.0000.0000.000
1342134PRO00.0190.01139.9250.0030.0030.0000.0000.0000.000
1352135ARG10.7080.81738.572-0.036-0.0360.0000.0000.0000.000
1362136THR0-0.098-0.05944.4460.0000.0000.0000.0000.0000.000
1372137VAL00.0140.00147.154-0.001-0.0010.0000.0000.0000.000
1382138GLY00.0260.03149.244-0.002-0.0020.0000.0000.0000.000
1392139ASN0-0.066-0.05045.418-0.001-0.0010.0000.0000.0000.000
1402140ASP-1-0.699-0.79042.1950.0010.0010.0000.0000.0000.000
1412141VAL0-0.031-0.01937.9540.0030.0030.0000.0000.0000.000
1422142TYR0-0.007-0.01937.814-0.004-0.0040.0000.0000.0000.000
1432143ALA00.0180.00633.8620.0040.0040.0000.0000.0000.000
1442144GLY0-0.021-0.01631.438-0.006-0.0060.0000.0000.0000.000
1452145ILE0-0.0150.00028.1370.0070.0070.0000.0000.0000.000
1462146MET0-0.0130.00232.092-0.007-0.0070.0000.0000.0000.000
1472147LEU0-0.007-0.00531.0450.0070.0070.0000.0000.0000.000
1482148TRP00.023-0.00934.542-0.007-0.0070.0000.0000.0000.000
1492149SER0-0.033-0.05635.7660.0040.0040.0000.0000.0000.000
1502150ASN0-0.009-0.00938.209-0.006-0.0060.0000.0000.0000.000
1512151ALA0-0.005-0.01540.385-0.004-0.0040.0000.0000.0000.000
1522152TRP00.0190.01136.6930.0010.0010.0000.0000.0000.000
1532153THR00.002-0.01840.429-0.003-0.0030.0000.0000.0000.000
1542154ALA00.0430.02541.999-0.001-0.0010.0000.0000.0000.000
1552155SER0-0.026-0.01639.0240.0010.0010.0000.0000.0000.000
1562156THR0-0.002-0.00236.828-0.002-0.0020.0000.0000.0000.000
1572157ILE0-0.0150.00534.3320.0010.0010.0000.0000.0000.000
1582158SER0-0.022-0.02232.8920.0000.0000.0000.0000.0000.000
1592159GLY00.0390.01129.1500.0080.0080.0000.0000.0000.000
1602160VAL0-0.041-0.02624.675-0.009-0.0090.0000.0000.0000.000
1612161LEU00.0280.01727.4210.0130.0130.0000.0000.0000.000
1622162SER0-0.046-0.04124.948-0.013-0.0130.0000.0000.0000.000
1632163VAL00.0650.04126.8570.0140.0140.0000.0000.0000.000
1642164ASN0-0.045-0.04524.004-0.013-0.0130.0000.0000.0000.000
1652165GLN00.1190.08626.8440.0120.0120.0000.0000.0000.000
1662166VAL0-0.021-0.00523.958-0.012-0.0120.0000.0000.0000.000
1672167ASN00.0410.01726.9340.0000.0000.0000.0000.0000.000
1682168ARG10.8830.93825.4480.0800.0800.0000.0000.0000.000
1692169GLU-1-0.822-0.91020.228-0.054-0.0540.0000.0000.0000.000
1702170ALA0-0.082-0.04621.160-0.005-0.0050.0000.0000.0000.000
1712171THR00.0200.01818.611-0.020-0.0200.0000.0000.0000.000
1722172VAL0-0.006-0.00115.0850.0020.0020.0000.0000.0000.000
1732173LEU00.0140.00515.392-0.007-0.0070.0000.0000.0000.000
1742174GLN00.0220.01012.107-0.005-0.0050.0000.0000.0000.000
1752175PRO0-0.001-0.00610.0600.0770.0770.0000.0000.0000.000
1762176LEU00.0040.0068.813-0.029-0.0290.0000.0000.0000.000
1772177LYS10.9150.97012.7540.4510.4510.0000.0000.0000.000