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: 94G72

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1741030.889025
FMO2-HF: Nuclear repulsion 1668414.520993
FMO2-HF: Total energy -72616.368032
FMO2-MP2: Total energy -72823.392125


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.
-28.046-17.4913.655-6.762-7.448-0.011
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 : 0.048 / 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].
3H7LYS10.9050.9233.359-4.992-1.2680.017-2.068-1.6740.008
4H8ALA0-0.030-0.0282.657-5.250-4.0092.350-1.336-2.2560.013
5H9ILE00.0520.0384.113-2.513-2.1600.011-0.081-0.2830.001
6H10GLU-1-0.926-0.9625.5740.3390.3390.0000.0000.0000.000
7H11ILE0-0.084-0.0476.007-0.190-0.1900.0000.0000.0000.000
8H12TRP00.0280.0167.957-0.204-0.2040.0000.0000.0000.000
9H13LYS11.0331.0019.382-0.239-0.2390.0000.0000.0000.000
10H14ILE00.0090.01311.870-0.068-0.0680.0000.0000.0000.000
11H15ARG10.8990.95310.006-0.903-0.9030.0000.0000.0000.000
12H16ARG10.8640.92913.836-0.122-0.1220.0000.0000.0000.000
13H17LEU00.0000.02515.693-0.043-0.0430.0000.0000.0000.000
14H18VAL0-0.052-0.00117.538-0.030-0.0300.0000.0000.0000.000
15H19LYS10.9680.97918.298-0.163-0.1630.0000.0000.0000.000
16H33THR00.004-0.00326.1330.0050.0050.0000.0000.0000.000
17H34LEU0-0.016-0.00627.402-0.006-0.0060.0000.0000.0000.000
18H35ILE00.0230.00223.0080.0130.0130.0000.0000.0000.000
19H36ILE0-0.0200.00325.137-0.013-0.0130.0000.0000.0000.000
20H37PRO0-0.0120.00323.8010.0270.0270.0000.0000.0000.000
21H45TYR00.039-0.00130.2250.0000.0000.0000.0000.0000.000
22H46SER0-0.0130.00034.025-0.004-0.0040.0000.0000.0000.000
23H47ASN0-0.027-0.02636.5820.0000.0000.0000.0000.0000.000
24H48MET00.0060.01835.191-0.002-0.0020.0000.0000.0000.000
25H49LEU00.0160.00635.961-0.002-0.0020.0000.0000.0000.000
26H50ALA0-0.074-0.03939.977-0.005-0.0050.0000.0000.0000.000
27H51GLU-1-0.966-0.98743.5390.0560.0560.0000.0000.0000.000
28H52GLU-1-0.940-0.96239.7580.0900.0900.0000.0000.0000.000
29H74SER00.009-0.00336.632-0.002-0.0020.0000.0000.0000.000
30H75THR00.003-0.01030.881-0.004-0.0040.0000.0000.0000.000
31H76ARG10.9780.98033.530-0.065-0.0650.0000.0000.0000.000
32H77GLU-1-0.941-0.95534.7950.0610.0610.0000.0000.0000.000
33H78ARG10.8840.94926.640-0.109-0.1090.0000.0000.0000.000
34H79LEU0-0.0190.00729.3790.0050.0050.0000.0000.0000.000
35H89GLY00.022-0.00320.9860.0180.0180.0000.0000.0000.000
36H90LEU0-0.034-0.01321.729-0.007-0.0070.0000.0000.0000.000
37H91VAL0-0.0040.00820.065-0.013-0.0130.0000.0000.0000.000
38H92ILE00.0250.01222.818-0.013-0.0130.0000.0000.0000.000
39H110ASP-1-0.855-0.94622.5280.1470.1470.0000.0000.0000.000
40H111PHE0-0.087-0.03216.0760.0110.0110.0000.0000.0000.000
41H130THR0-0.006-0.02022.167-0.006-0.0060.0000.0000.0000.000
42H131GLU-1-0.852-0.95421.4080.2760.2760.0000.0000.0000.000
43H132ALA0-0.0280.01120.6820.0410.0410.0000.0000.0000.000
44H133LEU00.0290.00717.3590.0310.0310.0000.0000.0000.000
45H134ALA0-0.026-0.01616.5760.0860.0860.0000.0000.0000.000
46H135GLU-1-0.975-0.98316.8010.4380.4380.0000.0000.0000.000
47H136LEU0-0.0230.00314.2700.0450.0450.0000.0000.0000.000
48H137LEU0-0.111-0.05211.8290.1660.1660.0000.0000.0000.000
49H274ASN00.0450.00812.635-0.052-0.0520.0000.0000.0000.000
50H275VAL00.003-0.0047.662-0.063-0.0630.0000.0000.0000.000
51H276LYS10.9990.9846.556-0.948-0.9480.0000.0000.0000.000
52H277TYR00.0560.0437.352-0.166-0.1660.0000.0000.0000.000
53H278VAL0-0.036-0.0228.684-0.121-0.1210.0000.0000.0000.000
54H279GLN00.005-0.0042.7530.4590.9310.085-0.189-0.3670.001
55H280GLU-1-0.747-0.8217.171-0.405-0.4050.0000.0000.0000.000
56H281LYS10.9060.9518.5170.1330.1330.0000.0000.0000.000
57H282LYS10.9440.9718.4130.4200.4200.0000.0000.0000.000
58H283LEU0-0.004-0.0045.5610.0860.0860.0000.0000.0000.000
59H284ILE00.0480.0228.6360.0440.0440.0000.0000.0000.000
60H285GLN0-0.015-0.01211.7830.0920.0920.0000.0000.0000.000
61H286ARG10.8830.9537.9601.1951.1950.0000.0000.0000.000
62H287PHE0-0.012-0.02212.5750.0320.0320.0000.0000.0000.000
63H288PHE0-0.001-0.01114.1730.0520.0520.0000.0000.0000.000
64H289ASP-1-0.875-0.93916.273-0.338-0.3380.0000.0000.0000.000
65H290GLU-1-0.857-0.86516.320-0.374-0.3740.0000.0000.0000.000
66H291ILE0-0.064-0.02818.9020.0190.0190.0000.0000.0000.000
67H292SER0-0.102-0.05020.7280.0360.0360.0000.0000.0000.000
68H293LEU0-0.078-0.04721.5580.0250.0250.0000.0000.0000.000
69H294ASP-1-0.972-0.96422.972-0.198-0.1980.0000.0000.0000.000
70H295SER0-0.109-0.10519.9640.0080.0080.0000.0000.0000.000
71H296GLY00.0450.01422.2370.0190.0190.0000.0000.0000.000
72H297LYS10.8900.94017.7520.3520.3520.0000.0000.0000.000
73H298TYR00.014-0.00317.525-0.033-0.0330.0000.0000.0000.000
74H299CYS00.0250.04317.5430.0230.0230.0000.0000.0000.000
75H300PHE00.0250.01517.195-0.073-0.0730.0000.0000.0000.000
76H301GLY00.1800.09119.5710.0270.0270.0000.0000.0000.000
77H302VAL00.0450.08119.878-0.038-0.0380.0000.0000.0000.000
78H303VAL00.0150.00721.018-0.018-0.0180.0000.0000.0000.000
79H304ASP-1-0.815-0.90822.408-0.247-0.2470.0000.0000.0000.000
80H305THR0-0.129-0.13115.977-0.016-0.0160.0000.0000.0000.000
81H306MET0-0.077-0.03716.786-0.029-0.0290.0000.0000.0000.000
82H307ASN00.0520.03120.0750.0010.0010.0000.0000.0000.000
83H308ALA0-0.014-0.00118.3180.0000.0000.0000.0000.0000.000
84H309LEU0-0.100-0.05514.281-0.032-0.0320.0000.0000.0000.000
85H310GLN0-0.053-0.01117.800-0.007-0.0070.0000.0000.0000.000
86H311GLU-1-0.951-0.98421.211-0.207-0.2070.0000.0000.0000.000
87H312GLY0-0.030-0.00920.335-0.026-0.0260.0000.0000.0000.000
88H313ALA00.003-0.00515.818-0.015-0.0150.0000.0000.0000.000
89H314VAL00.0070.02312.4300.0030.0030.0000.0000.0000.000
90H315GLU-1-1.003-0.99510.408-0.992-0.9920.0000.0000.0000.000
91H316THR00.010-0.0066.800-0.268-0.2680.0000.0000.0000.000
92H317LEU0-0.016-0.0058.9140.1670.1670.0000.0000.0000.000
93H318LEU0-0.024-0.0188.895-0.302-0.3020.0000.0000.0000.000
94H319CYS00.0270.0089.8250.1950.1950.0000.0000.0000.000
95H320PHE00.0300.02710.563-0.032-0.0320.0000.0000.0000.000
96H321ALA0-0.014-0.01811.2250.0310.0310.0000.0000.0000.000
97H322ASP-1-0.992-0.99512.5050.0520.0520.0000.0000.0000.000
98H323LEU0-0.023-0.02715.2560.0030.0030.0000.0000.0000.000
99H324ASP-1-0.921-0.94517.112-0.077-0.0770.0000.0000.0000.000
100H325MET00.0220.00819.221-0.009-0.0090.0000.0000.0000.000
101H326ILE0-0.0490.00320.298-0.003-0.0030.0000.0000.0000.000
102H327ARG10.9430.96720.4400.1800.1800.0000.0000.0000.000
103H328TYR00.0150.01723.3370.0100.0100.0000.0000.0000.000
104H339ILE0-0.062-0.05224.0300.0040.0040.0000.0000.0000.000
105H340THR00.0170.02127.446-0.005-0.0050.0000.0000.0000.000
106H341TYR0-0.012-0.02721.508-0.001-0.0010.0000.0000.0000.000
107H342MET00.0250.02625.1670.0100.0100.0000.0000.0000.000
108H343THR00.0060.00323.929-0.001-0.0010.0000.0000.0000.000
109H344LYS10.9300.95825.6530.0400.0400.0000.0000.0000.000
110H345GLU-1-0.844-0.90728.169-0.100-0.1000.0000.0000.0000.000
111H346GLN0-0.039-0.04027.901-0.002-0.0020.0000.0000.0000.000
112H347GLU-1-0.970-0.98732.009-0.042-0.0420.0000.0000.0000.000
113H348GLU-1-0.958-0.96234.562-0.055-0.0550.0000.0000.0000.000
114H349LYS10.8830.95234.7460.0640.0640.0000.0000.0000.000
115H350ASP-1-0.861-0.92236.182-0.040-0.0400.0000.0000.0000.000
116H351SER0-0.080-0.05633.837-0.003-0.0030.0000.0000.0000.000
117H369SER0-0.022-0.02525.2900.0010.0010.0000.0000.0000.000
118H370SER00.0180.00126.141-0.003-0.0030.0000.0000.0000.000
119H371MET0-0.0160.01719.7730.0050.0050.0000.0000.0000.000
120H372LEU00.0710.03518.454-0.006-0.0060.0000.0000.0000.000
121H373LEU00.0290.01116.595-0.011-0.0110.0000.0000.0000.000
122H374SER00.005-0.00714.084-0.047-0.0470.0000.0000.0000.000
123H375GLU-1-0.910-0.95113.470-0.050-0.0500.0000.0000.0000.000
124H376TRP00.015-0.01615.120-0.009-0.0090.0000.0000.0000.000
125H377LEU00.0260.00712.601-0.018-0.0180.0000.0000.0000.000
126H378ALA0-0.005-0.00910.764-0.093-0.0930.0000.0000.0000.000
127H379GLU-1-0.965-0.99411.723-0.074-0.0740.0000.0000.0000.000
128H380HIS10.8750.95014.4460.2620.2620.0000.0000.0000.000
129H381TYR00.0020.0027.854-0.173-0.1730.0000.0000.0000.000
130H382LYS10.9290.9719.5330.5760.5760.0000.0000.0000.000
131H383ASP-1-0.953-0.96312.525-0.317-0.3170.0000.0000.0000.000
132H384TYR00.0280.00314.4570.0540.0540.0000.0000.0000.000
133H385GLY0-0.054-0.01213.5100.0120.0120.0000.0000.0000.000
134H386ALA0-0.0240.00310.106-0.101-0.1010.0000.0000.0000.000
135H387ASN0-0.043-0.0086.497-0.052-0.0520.0000.0000.0000.000
136H388LEU00.002-0.0096.4000.2670.2670.0000.0000.0000.000
137H389GLU-1-0.924-0.9672.758-13.854-9.0891.192-3.088-2.868-0.034
138H390PHE0-0.035-0.0165.4270.5870.5870.0000.0000.0000.000
139H391VAL0-0.030-0.0196.879-0.019-0.0190.0000.0000.0000.000
140H392SER0-0.011-0.0419.5580.1290.1290.0000.0000.0000.000
141H393ASP-1-0.869-0.91812.595-0.122-0.1220.0000.0000.0000.000
142H394ARG10.8460.92313.985-0.056-0.0560.0000.0000.0000.000
143H395SER0-0.057-0.05012.898-0.005-0.0050.0000.0000.0000.000
144H396GLN00.011-0.00315.321-0.030-0.0300.0000.0000.0000.000
145H397GLU-1-0.764-0.90114.189-0.254-0.2540.0000.0000.0000.000
146H398GLY00.0540.03914.390-0.019-0.0190.0000.0000.0000.000
147H399MET0-0.007-0.01315.086-0.002-0.0020.0000.0000.0000.000
148H400GLN0-0.053-0.01718.4510.0050.0050.0000.0000.0000.000
149H401PHE0-0.011-0.00713.312-0.004-0.0040.0000.0000.0000.000
150H402VAL00.0190.00316.240-0.008-0.0080.0000.0000.0000.000
151H403LYS10.8760.92918.3740.1050.1050.0000.0000.0000.000
152H404GLY0-0.018-0.00320.8520.0180.0180.0000.0000.0000.000
153H405PHE00.0130.00418.659-0.006-0.0060.0000.0000.0000.000
154H406GLY00.0010.00619.670-0.023-0.0230.0000.0000.0000.000
155H407GLY0-0.0060.00916.6230.0120.0120.0000.0000.0000.000
156H408ILE0-0.035-0.03414.940-0.032-0.0320.0000.0000.0000.000
157H409GLY0-0.023-0.01114.4670.0590.0590.0000.0000.0000.000
158H410ALA0-0.042-0.04512.922-0.115-0.1150.0000.0000.0000.000
159H411VAL00.0440.04911.5880.0710.0710.0000.0000.0000.000
160H412MET00.0260.01313.592-0.068-0.0680.0000.0000.0000.000
161H413ARG10.9670.97212.1620.6500.6500.0000.0000.0000.000
162H414TYR0-0.094-0.09417.0360.0290.0290.0000.0000.0000.000
163H415GLN0-0.0100.02120.651-0.004-0.0040.0000.0000.0000.000
164H416LEU00.011-0.00920.9000.0020.0020.0000.0000.0000.000
165H417ASP-1-0.892-0.91124.711-0.187-0.1870.0000.0000.0000.000
166H418LEU0-0.031-0.00722.946-0.012-0.0120.0000.0000.0000.000
167H419SER00.0430.01726.7490.0170.0170.0000.0000.0000.000
168H420MET0-0.047-0.03627.2850.0000.0000.0000.0000.0000.000
169H421LEU0-0.038-0.04328.402-0.015-0.0150.0000.0000.0000.000
170H422ASP-1-0.942-0.97931.726-0.117-0.1170.0000.0000.0000.000
171H423PRO0-0.086-0.10433.143-0.004-0.0040.0000.0000.0000.000
172H424GLU-1-0.860-0.94633.879-0.142-0.1420.0000.0000.0000.000
173H425SER0-0.1700.25036.086-0.001-0.0010.0000.0000.0000.000
174H426ASP-1-0.903-1.09738.780-0.097-0.0970.0000.0000.0000.000
175H427GLU-1-0.986-1.05739.798-0.088-0.0880.0000.0000.0000.000