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

tag_button

FMODB ID: 72GNK

Calculation Name: 3E20-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E20

Chain ID: H

ChEMBL ID:

UniProt ID: P79063

Base Structure: X-ray

Registration Date: 2023-06-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1742537.595784
FMO2-HF: Nuclear repulsion 1669916.875323
FMO2-HF: Total energy -72620.720461
FMO2-MP2: Total energy -72827.373725


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(H:5:ALA)


Summations of interaction energy for fragment #1(H:5:ALA)
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.
-29.442-20.7879.185-8.394-9.444-0.022
Interaction energy analysis for fragmet #1(H:5:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.017
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].
3H7LYS10.8930.9313.003-4.501-1.4280.210-1.549-1.7340.008
4H8ALA0-0.009-0.0142.372-7.657-6.9204.388-2.175-2.9500.021
5H9ILE00.0420.0333.797-2.498-2.0410.027-0.182-0.3020.002
6H10GLU-1-0.800-0.9015.5530.2060.2060.0000.0000.0000.000
7H11ILE0-0.072-0.0366.065-0.219-0.2190.0000.0000.0000.000
8H12TRP00.002-0.0017.700-0.250-0.2500.0000.0000.0000.000
9H13LYS10.8790.9369.301-0.262-0.2620.0000.0000.0000.000
10H14ILE00.0050.00111.766-0.077-0.0770.0000.0000.0000.000
11H15ARG10.8870.94010.629-0.836-0.8360.0000.0000.0000.000
12H16ARG10.8190.89113.651-0.151-0.1510.0000.0000.0000.000
13H17LEU0-0.0360.00215.579-0.044-0.0440.0000.0000.0000.000
14H18VAL0-0.035-0.00817.505-0.023-0.0230.0000.0000.0000.000
15H19LYS10.9440.97417.985-0.162-0.1620.0000.0000.0000.000
16H33THR00.0430.02525.950-0.001-0.0010.0000.0000.0000.000
17H34LEU0-0.063-0.03927.353-0.005-0.0050.0000.0000.0000.000
18H35ILE00.0170.00422.7460.0120.0120.0000.0000.0000.000
19H36ILE0-0.030-0.00324.905-0.016-0.0160.0000.0000.0000.000
20H37PRO0-0.0050.00123.4610.0270.0270.0000.0000.0000.000
21H45TYR00.035-0.00630.0310.0000.0000.0000.0000.0000.000
22H46SER00.0000.01133.747-0.004-0.0040.0000.0000.0000.000
23H47ASN0-0.024-0.02736.368-0.001-0.0010.0000.0000.0000.000
24H48MET0-0.0260.00134.990-0.002-0.0020.0000.0000.0000.000
25H49LEU00.0320.01635.266-0.003-0.0030.0000.0000.0000.000
26H50ALA0-0.029-0.01039.586-0.004-0.0040.0000.0000.0000.000
27H51GLU-1-0.938-0.96743.1950.0560.0560.0000.0000.0000.000
28H52GLU-1-0.926-0.95539.2860.0830.0830.0000.0000.0000.000
29H74SER00.0220.00036.700-0.002-0.0020.0000.0000.0000.000
30H75THR0-0.001-0.01431.1040.0010.0010.0000.0000.0000.000
31H76ARG10.8630.92033.456-0.070-0.0700.0000.0000.0000.000
32H77GLU-1-0.917-0.95634.8780.0650.0650.0000.0000.0000.000
33H78ARG10.8000.87026.533-0.116-0.1160.0000.0000.0000.000
34H79LEU0-0.0380.00228.8940.0080.0080.0000.0000.0000.000
35H89GLY00.0700.03619.6310.0050.0050.0000.0000.0000.000
36H90LEU0-0.076-0.03421.1020.0040.0040.0000.0000.0000.000
37H91VAL00.0300.01819.923-0.013-0.0130.0000.0000.0000.000
38H92ILE0-0.011-0.00822.680-0.016-0.0160.0000.0000.0000.000
39H110ASP-1-0.795-0.87822.6840.1460.1460.0000.0000.0000.000
40H111PHE0-0.029-0.00716.6200.0090.0090.0000.0000.0000.000
41H130THR00.0410.01922.175-0.008-0.0080.0000.0000.0000.000
42H131GLU-1-0.884-0.97021.2270.2730.2730.0000.0000.0000.000
43H132ALA00.0120.01720.5790.0410.0410.0000.0000.0000.000
44H133LEU0-0.022-0.00817.2480.0280.0280.0000.0000.0000.000
45H134ALA0-0.010-0.01316.4880.0840.0840.0000.0000.0000.000
46H135GLU-1-0.959-0.98716.5320.4240.4240.0000.0000.0000.000
47H136LEU0-0.035-0.00314.2660.0400.0400.0000.0000.0000.000
48H137LEU0-0.105-0.03811.8270.2040.2040.0000.0000.0000.000
49H274ASN00.0740.02313.254-0.034-0.0340.0000.0000.0000.000
50H275VAL0-0.031-0.0298.292-0.052-0.0520.0000.0000.0000.000
51H276LYS10.9620.9837.028-1.012-1.0120.0000.0000.0000.000
52H277TYR00.0960.0447.492-0.179-0.1790.0000.0000.0000.000
53H278VAL0-0.029-0.0129.018-0.100-0.1000.0000.0000.0000.000
54H279GLN00.0180.0173.0950.5740.9490.019-0.108-0.2850.000
55H280GLU-1-0.769-0.8506.885-0.394-0.3940.0000.0000.0000.000
56H281LYS10.9000.9588.5060.1500.1500.0000.0000.0000.000
57H282LYS10.8990.9547.1130.7350.7350.0000.0000.0000.000
58H283LEU0-0.040-0.0135.1680.0550.0550.0000.0000.0000.000
59H284ILE00.0270.0198.5880.0410.0410.0000.0000.0000.000
60H285GLN0-0.048-0.02611.7360.0780.0780.0000.0000.0000.000
61H286ARG10.8000.8967.5071.1651.1650.0000.0000.0000.000
62H287PHE0-0.001-0.01012.5060.0150.0150.0000.0000.0000.000
63H288PHE00.019-0.00613.9930.0500.0500.0000.0000.0000.000
64H289ASP-1-0.819-0.90516.363-0.299-0.2990.0000.0000.0000.000
65H290GLU-1-0.832-0.87516.281-0.356-0.3560.0000.0000.0000.000
66H291ILE0-0.024-0.00318.8340.0260.0260.0000.0000.0000.000
67H292SER0-0.082-0.06120.1070.0290.0290.0000.0000.0000.000
68H293LEU0-0.090-0.04121.7510.0240.0240.0000.0000.0000.000
69H294ASP-1-0.884-0.93023.287-0.213-0.2130.0000.0000.0000.000
70H295SER0-0.055-0.03020.3660.0120.0120.0000.0000.0000.000
71H296GLY00.0680.04522.7500.0060.0060.0000.0000.0000.000
72H297LYS10.7780.84917.3830.3680.3680.0000.0000.0000.000
73H298TYR0-0.022-0.02117.207-0.065-0.0650.0000.0000.0000.000
74H299CYS00.0250.03316.9300.0270.0270.0000.0000.0000.000
75H300PHE0-0.020-0.00416.921-0.064-0.0640.0000.0000.0000.000
76H301GLY00.1290.07719.1200.0240.0240.0000.0000.0000.000
77H302VAL0-0.027-0.01619.849-0.030-0.0300.0000.0000.0000.000
78H303VAL00.0430.03221.090-0.011-0.0110.0000.0000.0000.000
79H304ASP-1-0.806-0.90621.512-0.244-0.2440.0000.0000.0000.000
80H305THR0-0.040-0.04815.327-0.032-0.0320.0000.0000.0000.000
81H306MET0-0.069-0.02815.957-0.030-0.0300.0000.0000.0000.000
82H307ASN00.0210.00619.633-0.001-0.0010.0000.0000.0000.000
83H308ALA00.0190.00318.1750.0030.0030.0000.0000.0000.000
84H309LEU0-0.106-0.04414.155-0.038-0.0380.0000.0000.0000.000
85H310GLN0-0.104-0.05517.430-0.001-0.0010.0000.0000.0000.000
86H311GLU-1-0.879-0.92720.871-0.185-0.1850.0000.0000.0000.000
87H312GLY0-0.034-0.01120.813-0.016-0.0160.0000.0000.0000.000
88H313ALA00.007-0.01315.554-0.008-0.0080.0000.0000.0000.000
89H314VAL0-0.0050.00812.2080.0000.0000.0000.0000.0000.000
90H315GLU-1-0.891-0.9219.872-1.003-1.0030.0000.0000.0000.000
91H316THR0-0.014-0.0646.577-0.281-0.2810.0000.0000.0000.000
92H317LEU0-0.0250.0028.9630.1230.1230.0000.0000.0000.000
93H318LEU0-0.012-0.0148.114-0.375-0.3750.0000.0000.0000.000
94H319CYS00.0040.0019.4910.2080.2080.0000.0000.0000.000
95H320PHE00.0300.01210.201-0.046-0.0460.0000.0000.0000.000
96H321ALA0-0.003-0.00310.6940.0110.0110.0000.0000.0000.000
97H322ASP-1-0.942-0.97112.0800.0460.0460.0000.0000.0000.000
98H323LEU0-0.040-0.03114.9950.0040.0040.0000.0000.0000.000
99H324ASP-1-0.836-0.88716.794-0.059-0.0590.0000.0000.0000.000
100H325MET00.0240.01519.014-0.002-0.0020.0000.0000.0000.000
101H326ILE0-0.055-0.01019.990-0.002-0.0020.0000.0000.0000.000
102H327ARG10.9250.97220.2320.1850.1850.0000.0000.0000.000
103H328TYR00.010-0.02023.3780.0080.0080.0000.0000.0000.000
104H339ILE0-0.0080.00024.0750.0000.0000.0000.0000.0000.000
105H340THR0-0.029-0.02027.524-0.002-0.0020.0000.0000.0000.000
106H341TYR00.026-0.01120.760-0.009-0.0090.0000.0000.0000.000
107H342MET0-0.0100.01824.7080.0090.0090.0000.0000.0000.000
108H343THR0-0.013-0.04523.518-0.006-0.0060.0000.0000.0000.000
109H344LYS10.7550.86223.9130.0600.0600.0000.0000.0000.000
110H345GLU-1-0.781-0.86227.722-0.102-0.1020.0000.0000.0000.000
111H346GLN0-0.032-0.01928.2280.0010.0010.0000.0000.0000.000
112H347GLU-1-0.922-0.96331.520-0.043-0.0430.0000.0000.0000.000
113H348GLU-1-0.969-0.99034.659-0.051-0.0510.0000.0000.0000.000
114H349LYS10.7950.89034.8150.0540.0540.0000.0000.0000.000
115H350ASP-1-0.870-0.91435.312-0.046-0.0460.0000.0000.0000.000
116H351SER00.0050.00333.4020.0000.0000.0000.0000.0000.000
117H369SER0-0.007-0.01025.3840.0010.0010.0000.0000.0000.000
118H370SER00.0240.02225.723-0.006-0.0060.0000.0000.0000.000
119H371MET0-0.041-0.00619.3610.0060.0060.0000.0000.0000.000
120H372LEU00.0660.03417.939-0.011-0.0110.0000.0000.0000.000
121H373LEU0-0.002-0.01116.722-0.008-0.0080.0000.0000.0000.000
122H374SER00.0310.00613.377-0.054-0.0540.0000.0000.0000.000
123H375GLU-1-0.838-0.89913.070-0.018-0.0180.0000.0000.0000.000
124H376TRP00.017-0.01614.735-0.011-0.0110.0000.0000.0000.000
125H377LEU00.0160.01112.448-0.014-0.0140.0000.0000.0000.000
126H378ALA0-0.020-0.01410.346-0.086-0.0860.0000.0000.0000.000
127H379GLU-1-0.874-0.93211.332-0.032-0.0320.0000.0000.0000.000
128H380HIS10.8190.89013.8460.2440.2440.0000.0000.0000.000
129H381TYR00.0360.0177.468-0.161-0.1610.0000.0000.0000.000
130H382LYS10.9060.9579.3930.5980.5980.0000.0000.0000.000
131H383ASP-1-0.882-0.91612.548-0.247-0.2470.0000.0000.0000.000
132H384TYR00.0190.01514.6710.0410.0410.0000.0000.0000.000
133H385GLY0-0.017-0.00613.361-0.014-0.0140.0000.0000.0000.000
134H386ALA00.0300.0399.828-0.060-0.0600.0000.0000.0000.000
135H387ASN0-0.095-0.0546.2150.0930.0930.0000.0000.0000.000
136H388LEU00.0250.0156.2420.2880.2880.0000.0000.0000.000
137H389GLU-1-0.901-0.9592.394-14.090-10.0774.541-4.380-4.173-0.053
138H390PHE0-0.013-0.0104.8410.7230.7230.0000.0000.0000.000
139H391VAL0-0.031-0.0096.5340.0500.0500.0000.0000.0000.000
140H392SER0-0.010-0.0309.2400.1420.1420.0000.0000.0000.000
141H393ASP-1-0.811-0.88712.566-0.103-0.1030.0000.0000.0000.000
142H394ARG10.8180.89514.369-0.011-0.0110.0000.0000.0000.000
143H395SER0-0.051-0.04213.2460.0080.0080.0000.0000.0000.000
144H396GLN0-0.0010.00815.801-0.026-0.0260.0000.0000.0000.000
145H397GLU-1-0.735-0.89714.428-0.244-0.2440.0000.0000.0000.000
146H398GLY00.0700.03814.299-0.035-0.0350.0000.0000.0000.000
147H399MET0-0.052-0.03415.0160.0020.0020.0000.0000.0000.000
148H400GLN0-0.053-0.03418.5510.0090.0090.0000.0000.0000.000
149H401PHE0-0.0160.00313.0540.0010.0010.0000.0000.0000.000
150H402VAL00.008-0.00615.8610.0000.0000.0000.0000.0000.000
151H403LYS10.8820.93418.1220.1100.1100.0000.0000.0000.000
152H404GLY0-0.012-0.00120.9120.0200.0200.0000.0000.0000.000
153H405PHE0-0.006-0.00418.530-0.003-0.0030.0000.0000.0000.000
154H406GLY00.0430.02919.766-0.016-0.0160.0000.0000.0000.000
155H407GLY0-0.050-0.01616.0540.0120.0120.0000.0000.0000.000
156H408ILE0-0.011-0.02314.407-0.043-0.0430.0000.0000.0000.000
157H409GLY00.0180.01614.1290.0620.0620.0000.0000.0000.000
158H410ALA0-0.027-0.03012.392-0.122-0.1220.0000.0000.0000.000
159H411VAL00.0310.04911.1490.0750.0750.0000.0000.0000.000
160H412MET00.0250.01513.484-0.056-0.0560.0000.0000.0000.000
161H413ARG10.8280.91511.2440.6510.6510.0000.0000.0000.000
162H414TYR0-0.052-0.02516.7370.0190.0190.0000.0000.0000.000
163H415GLN0-0.031-0.01720.405-0.005-0.0050.0000.0000.0000.000
164H416LEU0-0.010-0.01820.5230.0110.0110.0000.0000.0000.000
165H417ASP-1-0.821-0.89824.023-0.175-0.1750.0000.0000.0000.000
166H418LEU0-0.048-0.01422.523-0.012-0.0120.0000.0000.0000.000
167H419SER0-0.023-0.01926.4080.0120.0120.0000.0000.0000.000
168H420MET0-0.083-0.04626.523-0.005-0.0050.0000.0000.0000.000
169H421LEU0-0.047-0.04828.184-0.008-0.0080.0000.0000.0000.000
170H422ASP-1-0.881-0.94231.243-0.114-0.1140.0000.0000.0000.000
171H423PRO0-0.090-0.03633.029-0.004-0.0040.0000.0000.0000.000
172H424GLU-1-0.923-0.95333.726-0.129-0.1290.0000.0000.0000.000
173H425SER0-0.049-0.02335.440-0.003-0.0030.0000.0000.0000.000
174H426ASP-1-0.888-0.92038.120-0.091-0.0910.0000.0000.0000.000
175H427GLU-1-1.075-1.04339.664-0.078-0.0780.0000.0000.0000.000