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: JL3Y9

Calculation Name: 3E20-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E20

Chain ID: K

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 -1742259.317737
FMO2-HF: Nuclear repulsion 1669642.703626
FMO2-HF: Total energy -72616.614111
FMO2-MP2: Total energy -72823.564384


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(K:5:ALA)


Summations of interaction energy for fragment #1(K: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.
-31.075-21.2177.227-8.359-8.726-0.018
Interaction energy analysis for fragmet #1(K:5:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.027
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].
3K7LYS10.9020.9233.218-5.571-1.9520.007-1.949-1.6770.009
4K8ALA0-0.050-0.0361.906-5.610-5.3114.437-2.278-2.4580.019
5K9ILE00.0500.0393.531-2.260-2.0040.0000.105-0.3620.001
6K10GLU-1-0.916-0.9615.2310.3300.445-0.001-0.003-0.1100.000
7K11ILE0-0.065-0.0416.435-0.141-0.1410.0000.0000.0000.000
8K12TRP00.0200.0117.221-0.106-0.1060.0000.0000.0000.000
9K13LYS11.0150.9968.6570.1540.1540.0000.0000.0000.000
10K14ILE00.0190.02011.108-0.002-0.0020.0000.0000.0000.000
11K15ARG10.9140.9599.506-0.427-0.4270.0000.0000.0000.000
12K16ARG10.8610.92113.1680.1740.1740.0000.0000.0000.000
13K17LEU00.0150.03615.028-0.016-0.0160.0000.0000.0000.000
14K18VAL0-0.043-0.00116.9960.0020.0020.0000.0000.0000.000
15K19LYS10.9590.97716.4310.0120.0120.0000.0000.0000.000
16K33THR00.0200.00625.2310.0010.0010.0000.0000.0000.000
17K34LEU0-0.019-0.01526.9930.0010.0010.0000.0000.0000.000
18K35ILE00.0230.00722.8130.0060.0060.0000.0000.0000.000
19K36ILE0-0.032-0.00524.943-0.009-0.0090.0000.0000.0000.000
20K37PRO0-0.0060.00624.2590.0260.0260.0000.0000.0000.000
21K45TYR00.015-0.00530.302-0.001-0.0010.0000.0000.0000.000
22K46SER00.009-0.00533.881-0.003-0.0030.0000.0000.0000.000
23K47ASN0-0.021-0.01136.602-0.003-0.0030.0000.0000.0000.000
24K48MET0-0.0110.00834.537-0.001-0.0010.0000.0000.0000.000
25K49LEU00.0070.00235.378-0.002-0.0020.0000.0000.0000.000
26K50ALA0-0.038-0.02039.305-0.004-0.0040.0000.0000.0000.000
27K51GLU-1-0.955-0.98743.0790.0340.0340.0000.0000.0000.000
28K52GLU-1-0.961-0.97039.0960.0590.0590.0000.0000.0000.000
29K74SER00.007-0.00131.1270.0020.0020.0000.0000.0000.000
30K75THR00.058-0.00630.596-0.002-0.0020.0000.0000.0000.000
31K76ARG10.8960.94432.454-0.040-0.0400.0000.0000.0000.000
32K77GLU-1-0.928-0.94934.3270.0260.0260.0000.0000.0000.000
33K78ARG10.8830.96726.211-0.059-0.0590.0000.0000.0000.000
34K79LEU0-0.0060.00527.881-0.001-0.0010.0000.0000.0000.000
35K89GLY00.0160.00021.4880.0140.0140.0000.0000.0000.000
36K90LEU0-0.023-0.00922.119-0.009-0.0090.0000.0000.0000.000
37K91VAL0-0.010-0.00119.593-0.006-0.0060.0000.0000.0000.000
38K92ILE00.0160.01022.182-0.014-0.0140.0000.0000.0000.000
39K110ASP-1-0.881-0.95021.6000.0750.0750.0000.0000.0000.000
40K111PHE0-0.057-0.02116.3690.0050.0050.0000.0000.0000.000
41K130THR00.0450.01622.333-0.003-0.0030.0000.0000.0000.000
42K131GLU-1-0.906-0.99321.5090.1800.1800.0000.0000.0000.000
43K132ALA0-0.0430.00321.0690.0320.0320.0000.0000.0000.000
44K133LEU00.0350.00416.0880.0320.0320.0000.0000.0000.000
45K134ALA0-0.054-0.02016.3190.0450.0450.0000.0000.0000.000
46K135GLU-1-0.940-0.97216.8990.3950.3950.0000.0000.0000.000
47K136LEU0-0.0090.01114.2480.0630.0630.0000.0000.0000.000
48K137LEU0-0.118-0.05111.2110.1410.1410.0000.0000.0000.000
49K274ASN00.0430.00813.082-0.066-0.0660.0000.0000.0000.000
50K275VAL00.005-0.0058.555-0.079-0.0790.0000.0000.0000.000
51K276LYS10.9970.9857.178-0.699-0.6990.0000.0000.0000.000
52K277TYR00.0540.0417.651-0.228-0.2280.0000.0000.0000.000
53K278VAL0-0.034-0.0218.995-0.134-0.1340.0000.0000.0000.000
54K279GLN00.006-0.0053.1320.9451.2980.013-0.114-0.2520.000
55K280GLU-1-0.749-0.8247.265-0.804-0.8040.0000.0000.0000.000
56K281LYS10.9020.9518.2800.1490.1490.0000.0000.0000.000
57K282LYS10.9440.9718.6730.1390.1390.0000.0000.0000.000
58K283LEU00.002-0.0035.4450.1280.1280.0000.0000.0000.000
59K284ILE00.0440.0218.6700.0430.0430.0000.0000.0000.000
60K285GLN0-0.015-0.01311.8250.0960.0960.0000.0000.0000.000
61K286ARG10.8710.9447.5761.1961.1960.0000.0000.0000.000
62K287PHE0-0.012-0.01912.4890.0330.0330.0000.0000.0000.000
63K288PHE0-0.002-0.01214.0190.0540.0540.0000.0000.0000.000
64K289ASP-1-0.868-0.93416.179-0.324-0.3240.0000.0000.0000.000
65K290GLU-1-0.869-0.88216.064-0.377-0.3770.0000.0000.0000.000
66K291ILE0-0.061-0.02718.6650.0140.0140.0000.0000.0000.000
67K292SER0-0.107-0.05120.6060.0410.0410.0000.0000.0000.000
68K293LEU0-0.077-0.04921.3350.0290.0290.0000.0000.0000.000
69K294ASP-1-0.970-0.96322.761-0.216-0.2160.0000.0000.0000.000
70K295SER0-0.092-0.08919.7910.0120.0120.0000.0000.0000.000
71K296GLY00.0510.01922.1380.0210.0210.0000.0000.0000.000
72K297LYS10.8660.93017.6070.3550.3550.0000.0000.0000.000
73K298TYR00.001-0.02717.513-0.038-0.0380.0000.0000.0000.000
74K299CYS00.1260.07717.2490.0440.0440.0000.0000.0000.000
75K300PHE0-0.0440.00716.729-0.092-0.0920.0000.0000.0000.000
76K301GLY00.1920.08018.8550.0280.0280.0000.0000.0000.000
77K302VAL0-0.0030.06719.155-0.032-0.0320.0000.0000.0000.000
78K303VAL00.0310.01620.232-0.025-0.0250.0000.0000.0000.000
79K304ASP-1-0.811-0.90521.670-0.321-0.3210.0000.0000.0000.000
80K305THR0-0.116-0.13515.043-0.017-0.0170.0000.0000.0000.000
81K306MET0-0.083-0.04115.855-0.038-0.0380.0000.0000.0000.000
82K307ASN00.0600.03419.1330.0030.0030.0000.0000.0000.000
83K308ALA0-0.022-0.00617.8130.0070.0070.0000.0000.0000.000
84K309LEU0-0.106-0.06013.716-0.034-0.0340.0000.0000.0000.000
85K310GLN0-0.050-0.00817.259-0.009-0.0090.0000.0000.0000.000
86K311GLU-1-0.948-0.98020.622-0.247-0.2470.0000.0000.0000.000
87K312GLY0-0.035-0.01119.992-0.029-0.0290.0000.0000.0000.000
88K313ALA00.011-0.00415.434-0.020-0.0200.0000.0000.0000.000
89K314VAL0-0.0010.01812.1670.0100.0100.0000.0000.0000.000
90K315GLU-1-0.937-0.95710.055-0.961-0.9610.0000.0000.0000.000
91K316THR0-0.004-0.0216.654-0.275-0.2750.0000.0000.0000.000
92K317LEU0-0.027-0.0108.5350.1840.1840.0000.0000.0000.000
93K318LEU0-0.025-0.0198.028-0.412-0.4120.0000.0000.0000.000
94K319CYS00.0200.0049.2840.2740.2740.0000.0000.0000.000
95K320PHE00.0300.02710.299-0.125-0.1250.0000.0000.0000.000
96K321ALA0-0.014-0.01810.5800.0360.0360.0000.0000.0000.000
97K322ASP-1-1.002-0.99911.991-0.200-0.2000.0000.0000.0000.000
98K323LEU0-0.022-0.02614.7860.0350.0350.0000.0000.0000.000
99K324ASP-1-0.919-0.94416.777-0.206-0.2060.0000.0000.0000.000
100K325MET00.0210.00918.7240.0060.0060.0000.0000.0000.000
101K326ILE0-0.0470.00519.855-0.021-0.0210.0000.0000.0000.000
102K327ARG10.9400.96419.6960.3090.3090.0000.0000.0000.000
103K328TYR00.0180.01922.7020.0120.0120.0000.0000.0000.000
104K339ILE0-0.060-0.05223.1680.0040.0040.0000.0000.0000.000
105K340THR00.0180.02226.598-0.002-0.0020.0000.0000.0000.000
106K341TYR0-0.015-0.02920.4690.0010.0010.0000.0000.0000.000
107K342MET00.0270.02524.5760.0170.0170.0000.0000.0000.000
108K343THR00.0050.00123.482-0.010-0.0100.0000.0000.0000.000
109K344LYS10.9320.96025.2530.1450.1450.0000.0000.0000.000
110K345GLU-1-0.844-0.90727.820-0.183-0.1830.0000.0000.0000.000
111K346GLN0-0.038-0.04027.561-0.006-0.0060.0000.0000.0000.000
112K347GLU-1-0.969-0.98731.623-0.112-0.1120.0000.0000.0000.000
113K348GLU-1-0.958-0.96234.174-0.112-0.1120.0000.0000.0000.000
114K349LYS10.8840.95234.2480.1210.1210.0000.0000.0000.000
115K350ASP-1-0.862-0.92235.739-0.092-0.0920.0000.0000.0000.000
116K351SER0-0.081-0.05733.2330.0000.0000.0000.0000.0000.000
117K369SER0-0.023-0.02524.6520.0010.0010.0000.0000.0000.000
118K370SER00.0210.00325.6270.0010.0010.0000.0000.0000.000
119K371MET0-0.0150.01619.287-0.003-0.0030.0000.0000.0000.000
120K372LEU00.0710.03518.131-0.002-0.0020.0000.0000.0000.000
121K373LEU00.0230.00615.876-0.027-0.0270.0000.0000.0000.000
122K374SER00.004-0.00813.706-0.077-0.0770.0000.0000.0000.000
123K375GLU-1-0.909-0.95113.008-0.314-0.3140.0000.0000.0000.000
124K376TRP00.021-0.01414.577-0.020-0.0200.0000.0000.0000.000
125K377LEU00.0250.00711.761-0.009-0.0090.0000.0000.0000.000
126K378ALA0-0.005-0.00910.113-0.111-0.1110.0000.0000.0000.000
127K379GLU-1-0.970-0.99611.119-0.255-0.2550.0000.0000.0000.000
128K380HIS10.8750.95013.6260.4420.4420.0000.0000.0000.000
129K381TYR0-0.0020.0007.245-0.171-0.1710.0000.0000.0000.000
130K382LYS10.9280.9709.1200.6270.6270.0000.0000.0000.000
131K383ASP-1-0.954-0.96312.084-0.382-0.3820.0000.0000.0000.000
132K384TYR00.0310.00614.0220.0550.0550.0000.0000.0000.000
133K385GLY0-0.059-0.01812.9970.0200.0200.0000.0000.0000.000
134K386ALA0-0.0170.0079.663-0.080-0.0800.0000.0000.0000.000
135K387ASN0-0.040-0.0066.067-0.012-0.0120.0000.0000.0000.000
136K388LEU00.000-0.0095.7930.3180.3180.0000.0000.0000.000
137K389GLU-1-0.907-0.9652.555-16.930-11.7452.772-4.114-3.843-0.047
138K390PHE0-0.038-0.0144.8120.8510.882-0.001-0.006-0.0240.000
139K391VAL0-0.025-0.0176.463-0.122-0.1220.0000.0000.0000.000
140K392SER0-0.020-0.0439.1700.2010.2010.0000.0000.0000.000
141K393ASP-1-0.865-0.91911.992-0.294-0.2940.0000.0000.0000.000
142K394ARG10.8410.92013.9590.1760.1760.0000.0000.0000.000
143K395SER0-0.056-0.04512.7920.0300.0300.0000.0000.0000.000
144K396GLN00.011-0.00515.287-0.040-0.0400.0000.0000.0000.000
145K397GLU-1-0.759-0.89914.169-0.305-0.3050.0000.0000.0000.000
146K398GLY00.0560.03914.176-0.030-0.0300.0000.0000.0000.000
147K399MET0-0.004-0.00814.832-0.004-0.0040.0000.0000.0000.000
148K400GLN0-0.051-0.01618.4040.0080.0080.0000.0000.0000.000
149K401PHE0-0.005-0.00112.854-0.007-0.0070.0000.0000.0000.000
150K402VAL00.012-0.00615.962-0.011-0.0110.0000.0000.0000.000
151K403LYS10.8760.92918.1600.1970.1970.0000.0000.0000.000
152K404GLY0-0.017-0.00220.5940.0280.0280.0000.0000.0000.000
153K405PHE00.0130.00518.2240.0000.0000.0000.0000.0000.000
154K406GLY00.0000.00619.075-0.034-0.0340.0000.0000.0000.000
155K407GLY0-0.0100.00716.2670.0030.0030.0000.0000.0000.000
156K408ILE0-0.044-0.03514.302-0.071-0.0710.0000.0000.0000.000
157K409GLY00.000-0.00213.7050.0960.0960.0000.0000.0000.000
158K410ALA0-0.032-0.02412.463-0.169-0.1690.0000.0000.0000.000
159K411VAL00.0300.04411.5270.0970.0970.0000.0000.0000.000
160K412MET00.0250.01813.337-0.064-0.0640.0000.0000.0000.000
161K413ARG10.9460.97212.1750.6490.6490.0000.0000.0000.000
162K414TYR0-0.061-0.04816.5270.0360.0360.0000.0000.0000.000
163K415GLN0-0.020-0.00220.251-0.015-0.0150.0000.0000.0000.000
164K416LEU0-0.027-0.03520.7290.0110.0110.0000.0000.0000.000
165K417ASP-1-0.898-0.92924.385-0.226-0.2260.0000.0000.0000.000
166K418LEU0-0.0170.00922.542-0.007-0.0070.0000.0000.0000.000
167K419SER00.0440.01826.2850.0220.0220.0000.0000.0000.000
168K420MET0-0.050-0.03726.392-0.002-0.0020.0000.0000.0000.000
169K421LEU0-0.034-0.04127.610-0.021-0.0210.0000.0000.0000.000
170K422ASP-1-0.944-0.98130.947-0.168-0.1680.0000.0000.0000.000
171K423PRO0-0.088-0.10432.431-0.004-0.0040.0000.0000.0000.000
172K424GLU-1-0.859-0.94633.199-0.177-0.1770.0000.0000.0000.000
173K425SER0-0.1710.24435.431-0.002-0.0020.0000.0000.0000.000
174K426ASP-1-0.901-1.09338.097-0.123-0.1230.0000.0000.0000.000
175K427GLU-1-0.986-1.05639.048-0.119-0.1190.0000.0000.0000.000