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: MV38Z

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1741422.129051
FMO2-HF: Nuclear repulsion 1668802.979502
FMO2-HF: Total energy -72619.14955
FMO2-MP2: Total energy -72825.948153


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.
-28.294-17.6674.936-7.399-8.164-0.023
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 : 0.033 / 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].
3H7LYS10.8890.9153.355-4.499-0.8980.017-1.963-1.6560.007
4H8ALA0-0.031-0.0282.649-4.819-3.7372.701-1.452-2.3310.014
5H9ILE00.0510.0364.113-2.470-2.1030.012-0.086-0.2920.001
6H10GLU-1-0.871-0.9445.5340.1970.1970.0000.0000.0000.000
7H11ILE0-0.095-0.0536.038-0.165-0.1650.0000.0000.0000.000
8H12TRP00.0130.0107.871-0.175-0.1750.0000.0000.0000.000
9H13LYS10.9520.9659.330-0.171-0.1710.0000.0000.0000.000
10H14ILE00.0090.01011.809-0.056-0.0560.0000.0000.0000.000
11H15ARG10.9050.95410.309-0.868-0.8680.0000.0000.0000.000
12H16ARG10.8310.90313.751-0.108-0.1080.0000.0000.0000.000
13H17LEU0-0.0190.01515.645-0.042-0.0420.0000.0000.0000.000
14H18VAL0-0.051-0.00917.602-0.027-0.0270.0000.0000.0000.000
15H19LYS10.9760.98918.632-0.155-0.1550.0000.0000.0000.000
16H33THR00.0160.01026.0690.0040.0040.0000.0000.0000.000
17H34LEU0-0.025-0.01627.415-0.004-0.0040.0000.0000.0000.000
18H35ILE00.0210.00022.7710.0120.0120.0000.0000.0000.000
19H36ILE0-0.0200.00325.136-0.012-0.0120.0000.0000.0000.000
20H37PRO0-0.0080.00523.7980.0260.0260.0000.0000.0000.000
21H45TYR00.038-0.00430.3610.0000.0000.0000.0000.0000.000
22H46SER0-0.023-0.00334.025-0.005-0.0050.0000.0000.0000.000
23H47ASN0-0.017-0.02036.582-0.001-0.0010.0000.0000.0000.000
24H48MET0-0.0010.00934.986-0.001-0.0010.0000.0000.0000.000
25H49LEU00.0230.01935.714-0.003-0.0030.0000.0000.0000.000
26H50ALA0-0.022-0.01139.977-0.005-0.0050.0000.0000.0000.000
27H51GLU-1-0.962-0.98043.4860.0520.0520.0000.0000.0000.000
28H52GLU-1-0.919-0.95739.6870.0830.0830.0000.0000.0000.000
29H74SER00.009-0.00336.653-0.002-0.0020.0000.0000.0000.000
30H75THR00.004-0.01230.903-0.001-0.0010.0000.0000.0000.000
31H76ARG10.8920.93633.530-0.063-0.0630.0000.0000.0000.000
32H77GLU-1-0.944-0.95634.7950.0550.0550.0000.0000.0000.000
33H78ARG10.8410.90026.617-0.101-0.1010.0000.0000.0000.000
34H79LEU0-0.0310.00329.2180.0050.0050.0000.0000.0000.000
35H89GLY00.0540.02820.0740.0080.0080.0000.0000.0000.000
36H90LEU0-0.074-0.04421.729-0.008-0.0080.0000.0000.0000.000
37H91VAL00.0060.00920.279-0.012-0.0120.0000.0000.0000.000
38H92ILE00.0010.00722.818-0.016-0.0160.0000.0000.0000.000
39H110ASP-1-0.822-0.92422.7220.1310.1310.0000.0000.0000.000
40H111PHE0-0.0330.00216.3570.0080.0080.0000.0000.0000.000
41H130THR00.0180.00722.385-0.007-0.0070.0000.0000.0000.000
42H131GLU-1-0.873-0.97321.4570.2660.2660.0000.0000.0000.000
43H132ALA0-0.0230.00820.7010.0410.0410.0000.0000.0000.000
44H133LEU00.0270.01017.1010.0310.0310.0000.0000.0000.000
45H134ALA0-0.026-0.01816.5760.0850.0850.0000.0000.0000.000
46H135GLU-1-0.978-0.98416.8800.4140.4140.0000.0000.0000.000
47H136LEU0-0.032-0.00314.2940.0440.0440.0000.0000.0000.000
48H137LEU0-0.113-0.04711.7390.1730.1730.0000.0000.0000.000
49H274ASN00.0560.02112.570-0.038-0.0380.0000.0000.0000.000
50H275VAL0-0.008-0.0127.717-0.057-0.0570.0000.0000.0000.000
51H276LYS10.9940.9836.559-1.040-1.0400.0000.0000.0000.000
52H277TYR00.0590.0387.371-0.161-0.1610.0000.0000.0000.000
53H278VAL0-0.027-0.0188.829-0.125-0.1250.0000.0000.0000.000
54H279GLN00.0340.0113.1250.4830.8150.016-0.091-0.2570.000
55H280GLU-1-0.740-0.8277.026-0.374-0.3740.0000.0000.0000.000
56H281LYS10.8900.9498.3650.1340.1340.0000.0000.0000.000
57H282LYS10.8940.9477.4920.5140.5140.0000.0000.0000.000
58H283LEU0-0.039-0.0155.4310.0740.0740.0000.0000.0000.000
59H284ILE00.0490.0238.5740.0490.0490.0000.0000.0000.000
60H285GLN0-0.014-0.00711.7070.0970.0970.0000.0000.0000.000
61H286ARG10.8690.9397.7651.1821.1820.0000.0000.0000.000
62H287PHE00.000-0.02112.5340.0350.0350.0000.0000.0000.000
63H288PHE00.002-0.00714.1540.0490.0490.0000.0000.0000.000
64H289ASP-1-0.860-0.93016.362-0.310-0.3100.0000.0000.0000.000
65H290GLU-1-0.808-0.84516.154-0.361-0.3610.0000.0000.0000.000
66H291ILE0-0.071-0.03118.8720.0180.0180.0000.0000.0000.000
67H292SER0-0.079-0.04720.4250.0300.0300.0000.0000.0000.000
68H293LEU0-0.090-0.04621.7260.0230.0230.0000.0000.0000.000
69H294ASP-1-0.941-0.95222.978-0.201-0.2010.0000.0000.0000.000
70H295SER0-0.062-0.06020.1490.0090.0090.0000.0000.0000.000
71H296GLY00.0780.04022.1690.0170.0170.0000.0000.0000.000
72H297LYS10.7680.85017.2590.3680.3680.0000.0000.0000.000
73H298TYR00.0170.00317.379-0.035-0.0350.0000.0000.0000.000
74H299CYS00.0030.02917.4780.0240.0240.0000.0000.0000.000
75H300PHE00.0280.02217.065-0.072-0.0720.0000.0000.0000.000
76H301GLY00.1570.08119.4230.0270.0270.0000.0000.0000.000
77H302VAL0-0.0150.00019.911-0.036-0.0360.0000.0000.0000.000
78H303VAL00.0340.01321.044-0.018-0.0180.0000.0000.0000.000
79H304ASP-1-0.804-0.90222.143-0.243-0.2430.0000.0000.0000.000
80H305THR0-0.030-0.03615.736-0.033-0.0330.0000.0000.0000.000
81H306MET0-0.079-0.03616.270-0.029-0.0290.0000.0000.0000.000
82H307ASN00.0470.02420.0170.0010.0010.0000.0000.0000.000
83H308ALA0-0.019-0.00418.3190.0010.0010.0000.0000.0000.000
84H309LEU0-0.110-0.05014.383-0.029-0.0290.0000.0000.0000.000
85H310GLN0-0.104-0.04617.7790.0040.0040.0000.0000.0000.000
86H311GLU-1-0.891-0.94921.206-0.205-0.2050.0000.0000.0000.000
87H312GLY0-0.034-0.01020.330-0.025-0.0250.0000.0000.0000.000
88H313ALA00.007-0.00215.881-0.016-0.0160.0000.0000.0000.000
89H314VAL00.0020.01212.6330.0020.0020.0000.0000.0000.000
90H315GLU-1-0.905-0.92510.402-0.967-0.9670.0000.0000.0000.000
91H316THR0-0.028-0.0466.701-0.289-0.2890.0000.0000.0000.000
92H317LEU0-0.021-0.0068.8470.1600.1600.0000.0000.0000.000
93H318LEU0-0.018-0.0188.775-0.307-0.3070.0000.0000.0000.000
94H319CYS00.0310.0079.8490.1980.1980.0000.0000.0000.000
95H320PHE00.0480.02910.566-0.035-0.0350.0000.0000.0000.000
96H321ALA0-0.018-0.01611.1960.0290.0290.0000.0000.0000.000
97H322ASP-1-0.979-0.98812.4860.0430.0430.0000.0000.0000.000
98H323LEU0-0.020-0.01615.2900.0050.0050.0000.0000.0000.000
99H324ASP-1-0.841-0.89517.105-0.066-0.0660.0000.0000.0000.000
100H325MET00.0260.01119.168-0.006-0.0060.0000.0000.0000.000
101H326ILE0-0.0400.00420.293-0.006-0.0060.0000.0000.0000.000
102H327ARG10.9260.96220.2870.1960.1960.0000.0000.0000.000
103H328TYR00.0440.03023.3380.0080.0080.0000.0000.0000.000
104H339ILE0-0.030-0.01824.0250.0010.0010.0000.0000.0000.000
105H340THR0-0.031-0.02127.463-0.004-0.0040.0000.0000.0000.000
106H341TYR00.017-0.01921.362-0.002-0.0020.0000.0000.0000.000
107H342MET00.0060.01925.1790.0100.0100.0000.0000.0000.000
108H343THR0-0.036-0.05323.837-0.003-0.0030.0000.0000.0000.000
109H344LYS10.7860.87723.9210.0680.0680.0000.0000.0000.000
110H345GLU-1-0.796-0.86027.986-0.104-0.1040.0000.0000.0000.000
111H346GLN0-0.008-0.02428.2930.0000.0000.0000.0000.0000.000
112H347GLU-1-0.957-0.97832.002-0.045-0.0450.0000.0000.0000.000
113H348GLU-1-0.986-0.97734.622-0.056-0.0560.0000.0000.0000.000
114H349LYS10.8380.91334.8170.0610.0610.0000.0000.0000.000
115H350ASP-1-0.838-0.91736.178-0.046-0.0460.0000.0000.0000.000
116H351SER0-0.049-0.01633.7190.0020.0020.0000.0000.0000.000
117H369SER0-0.007-0.01625.2810.0030.0030.0000.0000.0000.000
118H370SER0-0.010-0.00726.128-0.003-0.0030.0000.0000.0000.000
119H371MET0-0.0230.01019.6230.0030.0030.0000.0000.0000.000
120H372LEU00.0850.04518.380-0.007-0.0070.0000.0000.0000.000
121H373LEU00.007-0.00616.769-0.012-0.0120.0000.0000.0000.000
122H374SER00.009-0.00613.982-0.059-0.0590.0000.0000.0000.000
123H375GLU-1-0.865-0.91813.460-0.045-0.0450.0000.0000.0000.000
124H376TRP00.020-0.01715.108-0.012-0.0120.0000.0000.0000.000
125H377LEU00.0260.01612.601-0.016-0.0160.0000.0000.0000.000
126H378ALA0-0.005-0.00710.760-0.094-0.0940.0000.0000.0000.000
127H379GLU-1-0.890-0.94611.717-0.083-0.0830.0000.0000.0000.000
128H380HIS10.8240.90814.4480.2760.2760.0000.0000.0000.000
129H381TYR00.0230.0187.753-0.163-0.1630.0000.0000.0000.000
130H382LYS10.9150.9589.6320.6070.6070.0000.0000.0000.000
131H383ASP-1-0.912-0.93812.627-0.296-0.2960.0000.0000.0000.000
132H384TYR00.0460.01114.5400.0470.0470.0000.0000.0000.000
133H385GLY0-0.060-0.01713.5800.0130.0130.0000.0000.0000.000
134H386ALA0-0.0090.0279.933-0.075-0.0750.0000.0000.0000.000
135H387ASN0-0.094-0.0646.4360.1290.1290.0000.0000.0000.000
136H388LEU00.0310.0146.4510.2360.2360.0000.0000.0000.000
137H389GLU-1-0.905-0.9592.616-15.477-10.2322.190-3.807-3.628-0.045
138H390PHE0-0.023-0.0085.4350.5950.5950.0000.0000.0000.000
139H391VAL0-0.046-0.0266.873-0.020-0.0200.0000.0000.0000.000
140H392SER0-0.013-0.0149.5560.1240.1240.0000.0000.0000.000
141H393ASP-1-0.842-0.91912.580-0.113-0.1130.0000.0000.0000.000
142H394ARG10.8250.90614.136-0.023-0.0230.0000.0000.0000.000
143H395SER0-0.046-0.04812.929-0.005-0.0050.0000.0000.0000.000
144H396GLN00.0020.00215.342-0.027-0.0270.0000.0000.0000.000
145H397GLU-1-0.747-0.89714.034-0.243-0.2430.0000.0000.0000.000
146H398GLY00.0630.04114.377-0.020-0.0200.0000.0000.0000.000
147H399MET0-0.022-0.02015.046-0.002-0.0020.0000.0000.0000.000
148H400GLN0-0.039-0.01818.4420.0060.0060.0000.0000.0000.000
149H401PHE0-0.027-0.01013.495-0.003-0.0030.0000.0000.0000.000
150H402VAL00.013-0.00115.998-0.008-0.0080.0000.0000.0000.000
151H403LYS10.8730.93318.3850.1080.1080.0000.0000.0000.000
152H404GLY0-0.0100.00020.8610.0180.0180.0000.0000.0000.000
153H405PHE00.010-0.00118.817-0.002-0.0020.0000.0000.0000.000
154H406GLY00.0020.00719.696-0.024-0.0240.0000.0000.0000.000
155H407GLY0-0.0060.01016.6390.0120.0120.0000.0000.0000.000
156H408ILE0-0.034-0.03814.846-0.033-0.0330.0000.0000.0000.000
157H409GLY0-0.040-0.01814.4970.0620.0620.0000.0000.0000.000
158H410ALA0-0.048-0.04412.796-0.115-0.1150.0000.0000.0000.000
159H411VAL00.0320.04711.3430.0740.0740.0000.0000.0000.000
160H412MET00.0290.01513.514-0.062-0.0620.0000.0000.0000.000
161H413ARG10.9070.95911.8320.6250.6250.0000.0000.0000.000
162H414TYR0-0.030-0.04217.0010.0240.0240.0000.0000.0000.000
163H415GLN0-0.039-0.00520.606-0.002-0.0020.0000.0000.0000.000
164H416LEU0-0.010-0.02721.3530.0010.0010.0000.0000.0000.000
165H417ASP-1-0.892-0.91924.651-0.183-0.1830.0000.0000.0000.000
166H418LEU0-0.046-0.01222.616-0.011-0.0110.0000.0000.0000.000
167H419SER00.0430.01426.6680.0190.0190.0000.0000.0000.000
168H420MET0-0.123-0.05227.181-0.004-0.0040.0000.0000.0000.000
169H421LEU00.043-0.00428.332-0.013-0.0130.0000.0000.0000.000
170H422ASP-1-0.938-0.98731.648-0.118-0.1180.0000.0000.0000.000
171H423PRO0-0.100-0.09733.037-0.004-0.0040.0000.0000.0000.000
172H424GLU-1-0.855-0.95533.762-0.136-0.1360.0000.0000.0000.000
173H425SER0-0.1410.08635.988-0.001-0.0010.0000.0000.0000.000
174H426ASP-1-0.869-0.94238.683-0.095-0.0950.0000.0000.0000.000
175H427GLU-1-1.055-1.05339.961-0.084-0.0840.0000.0000.0000.000