FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2LK5R

Calculation Name: 1OY3-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OY3

Chain ID: D

ChEMBL ID:

UniProt ID: Q60778

Base Structure: X-ray

Registration Date: 2023-09-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2376263.264823
FMO2-HF: Nuclear repulsion 2293456.202511
FMO2-HF: Total energy -82807.062312
FMO2-MP2: Total energy -83050.258815


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(D:50:VAL)


Summations of interaction energy for fragment #1(D:50:VAL)
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.
-8.077-4.5561.37-1.953-2.938-0.015
Interaction energy analysis for fragmet #1(D:50:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.012
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].
3D52GLY00.0590.0122.485-5.538-3.0561.308-1.752-2.039-0.014
4D53TYR0-0.059-0.0085.0870.4460.576-0.001-0.011-0.1170.000
5D54VAL00.005-0.0108.336-0.130-0.1300.0000.0000.0000.000
6D55THR0-0.0670.01010.8660.0940.0940.0000.0000.0000.000
7D56GLU-1-0.963-0.99214.522-0.321-0.3210.0000.0000.0000.000
8D57ASP-1-0.880-0.93517.030-0.312-0.3120.0000.0000.0000.000
9D58GLY00.0660.02813.516-0.006-0.0060.0000.0000.0000.000
10D59ASP-1-0.865-0.93912.353-0.534-0.5340.0000.0000.0000.000
11D60THR00.007-0.0017.311-0.003-0.0030.0000.0000.0000.000
12D61ALA0-0.008-0.0227.9780.1830.1830.0000.0000.0000.000
13D62LEU00.0350.0008.0510.1870.1870.0000.0000.0000.000
14D63HIS00.0100.02210.1710.0760.0760.0000.0000.0000.000
15D64LEU00.0450.00912.5830.0850.0850.0000.0000.0000.000
16D65ALA0-0.0130.00512.5500.0680.0680.0000.0000.0000.000
17D66VAL00.003-0.00814.3780.0480.0480.0000.0000.0000.000
18D67ILE0-0.0270.00915.8550.0290.0290.0000.0000.0000.000
19D68HIS0-0.098-0.05517.1310.0400.0400.0000.0000.0000.000
20D69GLN0-0.042-0.00319.2300.0230.0230.0000.0000.0000.000
21D70HIS00.0000.00916.6200.0350.0350.0000.0000.0000.000
22D71GLU-1-0.806-0.92316.450-0.030-0.0300.0000.0000.0000.000
23D72PRO0-0.011-0.00416.3230.0170.0170.0000.0000.0000.000
24D73PHE00.0290.00510.8050.0560.0560.0000.0000.0000.000
25D74LEU00.0210.01911.9680.0220.0220.0000.0000.0000.000
26D75ASP-1-0.847-0.92811.7240.1030.1030.0000.0000.0000.000
27D76PHE0-0.077-0.0299.2430.0920.0920.0000.0000.0000.000
28D77LEU0-0.026-0.0067.7190.1170.1170.0000.0000.0000.000
29D78LEU00.012-0.0107.2340.0660.0660.0000.0000.0000.000
30D79GLY0-0.0200.0129.393-0.003-0.0030.0000.0000.0000.000
31D80PHE0-0.107-0.0565.0000.3230.3230.0000.0000.0000.000
32D81SER0-0.035-0.0324.948-0.231-0.2310.0000.0000.0000.000
33D82ALA00.0220.0295.877-0.214-0.2140.0000.0000.0000.000
34D83GLY0-0.0100.0028.6820.0780.0780.0000.0000.0000.000
35D84HIS0-0.070-0.0394.204-0.621-0.455-0.001-0.014-0.1510.000
36D85GLU-1-0.870-0.9345.837-1.063-1.0630.0000.0000.0000.000
37D86TYR0-0.049-0.0433.028-0.799-0.0750.065-0.175-0.614-0.001
38D87LEU0-0.016-0.0155.1410.1530.172-0.001-0.001-0.0170.000
39D88ASP-1-0.849-0.9048.432-0.468-0.4680.0000.0000.0000.000
40D89LEU0-0.038-0.0095.7720.0110.0110.0000.0000.0000.000
41D90GLN0-0.050-0.05110.0190.1480.1480.0000.0000.0000.000
42D91ASN0-0.0240.00313.510-0.039-0.0390.0000.0000.0000.000
43D92ASP-1-0.828-0.93514.655-0.488-0.4880.0000.0000.0000.000
44D93LEU0-0.158-0.07417.8690.0550.0550.0000.0000.0000.000
45D94GLY00.0570.00517.5360.0410.0410.0000.0000.0000.000
46D95GLN00.0020.00417.287-0.001-0.0010.0000.0000.0000.000
47D96THR00.0700.04613.242-0.043-0.0430.0000.0000.0000.000
48D97ALA00.0670.01112.0520.0520.0520.0000.0000.0000.000
49D98LEU00.0380.00914.0260.0650.0650.0000.0000.0000.000
50D99HIS0-0.0190.01516.4550.0190.0190.0000.0000.0000.000
51D100LEU0-0.0220.00415.2100.0330.0330.0000.0000.0000.000
52D101ALA00.0480.02717.8990.0290.0290.0000.0000.0000.000
53D102ALA0-0.029-0.02619.7150.0260.0260.0000.0000.0000.000
54D103ILE0-0.078-0.03321.5290.0190.0190.0000.0000.0000.000
55D104LEU0-0.016-0.00520.5140.0140.0140.0000.0000.0000.000
56D105GLY0-0.009-0.00424.1440.0160.0160.0000.0000.0000.000
57D106GLU-1-0.913-0.96220.916-0.087-0.0870.0000.0000.0000.000
58D107ALA0-0.016-0.02822.216-0.006-0.0060.0000.0000.0000.000
59D108SER00.0280.00621.3440.0040.0040.0000.0000.0000.000
60D109THR00.0320.01017.1490.0100.0100.0000.0000.0000.000
61D110VAL0-0.009-0.01617.681-0.019-0.0190.0000.0000.0000.000
62D111GLU-1-0.930-0.96018.692-0.038-0.0380.0000.0000.0000.000
63D112LYS10.8080.91215.518-0.022-0.0220.0000.0000.0000.000
64D113LEU00.0350.01912.817-0.004-0.0040.0000.0000.0000.000
65D114TYR0-0.004-0.01314.374-0.030-0.0300.0000.0000.0000.000
66D115ALA0-0.015-0.01916.649-0.007-0.0070.0000.0000.0000.000
67D116ALA0-0.058-0.03411.4480.0190.0190.0000.0000.0000.000
68D117GLY0-0.017-0.02411.941-0.020-0.0200.0000.0000.0000.000
69D118ALA0-0.039-0.00212.390-0.050-0.0500.0000.0000.0000.000
70D119GLY00.015-0.01113.3360.0580.0580.0000.0000.0000.000
71D120VAL0-0.041-0.02715.333-0.002-0.0020.0000.0000.0000.000
72D121LEU0-0.023-0.02518.6570.0160.0160.0000.0000.0000.000
73D122VAL0-0.0010.02014.6430.0070.0070.0000.0000.0000.000
74D123ALA0-0.020-0.01218.0710.0270.0270.0000.0000.0000.000
75D124GLU-1-0.814-0.89319.566-0.269-0.2690.0000.0000.0000.000
76D125ARG10.8650.92120.6480.2760.2760.0000.0000.0000.000
77D126GLY0-0.043-0.02123.1730.0120.0120.0000.0000.0000.000
78D127GLY00.0580.01024.1530.0180.0180.0000.0000.0000.000
79D128HIS0-0.077-0.03724.0870.0160.0160.0000.0000.0000.000
80D129THR00.0760.04021.472-0.019-0.0190.0000.0000.0000.000
81D130ALA00.0530.00219.5940.0100.0100.0000.0000.0000.000
82D131LEU00.0280.01421.6220.0170.0170.0000.0000.0000.000
83D132HIS0-0.006-0.01024.9650.0060.0060.0000.0000.0000.000
84D133LEU0-0.014-0.01121.7730.0130.0130.0000.0000.0000.000
85D134ALA00.0500.03525.5300.0110.0110.0000.0000.0000.000
86D135CYS0-0.113-0.05626.9510.0150.0150.0000.0000.0000.000
87D136ARG10.9040.96426.9260.1670.1670.0000.0000.0000.000
88D137VAL0-0.024-0.00827.2620.0060.0060.0000.0000.0000.000
89D138ARG10.9020.96630.4790.0770.0770.0000.0000.0000.000
90D139ALA00.0670.05827.1360.0080.0080.0000.0000.0000.000
91D140HIS0-0.073-0.08428.501-0.001-0.0010.0000.0000.0000.000
92D141THR00.0190.00028.479-0.004-0.0040.0000.0000.0000.000
93D142CYS00.0170.03524.3790.0000.0000.0000.0000.0000.000
94D143ALA00.0380.02025.055-0.006-0.0060.0000.0000.0000.000
95D144CYS0-0.039-0.02327.1710.0010.0010.0000.0000.0000.000
96D145VAL0-0.0120.01122.2970.0030.0030.0000.0000.0000.000
97D146LEU00.004-0.00720.499-0.001-0.0010.0000.0000.0000.000
98D147LEU0-0.078-0.02523.898-0.004-0.0040.0000.0000.0000.000
99D148GLN0-0.041-0.02225.5420.0200.0200.0000.0000.0000.000
100D149PRO0-0.040-0.01924.614-0.012-0.0120.0000.0000.0000.000
101D150ARG10.9180.98316.2120.1800.1800.0000.0000.0000.000
102D151PRO0-0.0060.01019.6450.0110.0110.0000.0000.0000.000
103D152SER0-0.031-0.01719.977-0.005-0.0050.0000.0000.0000.000
104D153HIS0-0.076-0.04916.889-0.016-0.0160.0000.0000.0000.000
105D154PRO00.0590.03613.560-0.011-0.0110.0000.0000.0000.000
106D155ARG10.9000.94215.330-0.123-0.1230.0000.0000.0000.000
107D156ASP-1-0.787-0.87715.5740.2640.2640.0000.0000.0000.000
108D157ALA0-0.074-0.03217.377-0.004-0.0040.0000.0000.0000.000
109D193ASP-1-0.934-0.97121.007-0.177-0.1770.0000.0000.0000.000
110D194GLU-1-0.970-0.96321.933-0.113-0.1130.0000.0000.0000.000
111D195ASP-1-0.895-0.96822.844-0.088-0.0880.0000.0000.0000.000
112D196TRP00.018-0.00223.780-0.010-0.0100.0000.0000.0000.000
113D197ARG10.9580.96824.7540.0700.0700.0000.0000.0000.000
114D198LEU0-0.0150.00524.0340.0010.0010.0000.0000.0000.000
115D199GLN0-0.023-0.02623.136-0.015-0.0150.0000.0000.0000.000
116D200LEU0-0.058-0.02625.812-0.002-0.0020.0000.0000.0000.000
117D201GLU-1-0.824-0.91329.247-0.100-0.1000.0000.0000.0000.000
118D202ALA00.0040.02725.571-0.003-0.0030.0000.0000.0000.000
119D203GLU-1-0.953-1.00127.543-0.137-0.1370.0000.0000.0000.000
120D204ASN00.0310.03927.227-0.007-0.0070.0000.0000.0000.000
121D205TYR0-0.017-0.02523.2870.0080.0080.0000.0000.0000.000
122D206ASP-1-0.999-0.98229.647-0.146-0.1460.0000.0000.0000.000
123D207GLY0-0.047-0.02831.8420.0110.0110.0000.0000.0000.000
124D208HIS0-0.057-0.03932.1200.0060.0060.0000.0000.0000.000
125D209THR00.0880.05530.630-0.009-0.0090.0000.0000.0000.000
126D210PRO00.0390.00328.1720.0060.0060.0000.0000.0000.000
127D211LEU00.0320.00830.7800.0060.0060.0000.0000.0000.000
128D212HIS0-0.005-0.00834.3740.0010.0010.0000.0000.0000.000
129D213VAL00.0240.02830.6520.0050.0050.0000.0000.0000.000
130D214ALA00.0480.02333.6610.0050.0050.0000.0000.0000.000
131D215VAL0-0.047-0.02034.9110.0070.0070.0000.0000.0000.000
132D216ILE0-0.0180.00736.2800.0050.0050.0000.0000.0000.000
133D217HIS0-0.072-0.04033.5360.0010.0010.0000.0000.0000.000
134D218LYS10.8460.92137.3630.0690.0690.0000.0000.0000.000
135D219ASP-1-0.798-0.88134.507-0.071-0.0710.0000.0000.0000.000
136D220ALA0-0.008-0.02437.6150.0000.0000.0000.0000.0000.000
137D221GLU-1-0.886-0.95436.228-0.051-0.0510.0000.0000.0000.000
138D222MET00.0570.03230.2080.0010.0010.0000.0000.0000.000
139D223VAL0-0.028-0.01234.654-0.002-0.0020.0000.0000.0000.000
140D224ARG10.8360.91437.1590.0480.0480.0000.0000.0000.000
141D225LEU00.0440.03231.7460.0010.0010.0000.0000.0000.000
142D226LEU00.0140.02230.765-0.001-0.0010.0000.0000.0000.000
143D227ARG10.8470.89933.9750.0500.0500.0000.0000.0000.000
144D228ASP-1-0.877-0.91335.960-0.049-0.0490.0000.0000.0000.000
145D229ALA0-0.034-0.00931.4020.0020.0020.0000.0000.0000.000
146D230GLY0-0.047-0.03033.062-0.003-0.0030.0000.0000.0000.000
147D231ALA0-0.034-0.00933.595-0.003-0.0030.0000.0000.0000.000
148D232ASP-1-0.817-0.91934.815-0.075-0.0750.0000.0000.0000.000
149D233LEU0-0.048-0.04737.268-0.002-0.0020.0000.0000.0000.000
150D234ASN0-0.027-0.02440.0130.0040.0040.0000.0000.0000.000
151D235LYS10.8750.94734.3060.1060.1060.0000.0000.0000.000
152D236PRO0-0.009-0.00538.952-0.001-0.0010.0000.0000.0000.000
153D237GLU-1-0.708-0.81237.310-0.100-0.1000.0000.0000.0000.000
154D238PRO00.0490.01335.6450.0060.0060.0000.0000.0000.000
155D239THR0-0.055-0.03438.3560.0030.0030.0000.0000.0000.000
156D240CYS0-0.109-0.07440.6700.0040.0040.0000.0000.0000.000
157D241GLY00.0620.03342.1510.0050.0050.0000.0000.0000.000
158D242ARG10.7850.88940.8950.0910.0910.0000.0000.0000.000
159D243THR00.0800.03541.190-0.003-0.0030.0000.0000.0000.000
160D244PRO00.0770.02338.9420.0010.0010.0000.0000.0000.000
161D245LEU00.0050.00241.1840.0010.0010.0000.0000.0000.000
162D246HIS0-0.0350.00144.3740.0010.0010.0000.0000.0000.000
163D247LEU00.0310.02438.6370.0010.0010.0000.0000.0000.000
164D248ALA00.0300.01642.7250.0010.0010.0000.0000.0000.000
165D249VAL0-0.047-0.01344.0520.0030.0030.0000.0000.0000.000
166D250GLU-1-0.931-0.96444.060-0.073-0.0730.0000.0000.0000.000
167D251ALA00.0090.00242.5270.0010.0010.0000.0000.0000.000
168D252GLN0-0.065-0.07344.4270.0050.0050.0000.0000.0000.000
169D253ALA00.0000.01543.8960.0030.0030.0000.0000.0000.000
170D254ALA00.024-0.01045.8140.0000.0000.0000.0000.0000.000
171D255SER00.0460.01444.3290.0000.0000.0000.0000.0000.000
172D256VAL00.0030.01541.1630.0010.0010.0000.0000.0000.000
173D257LEU00.0120.00743.768-0.001-0.0010.0000.0000.0000.000
174D258GLU-1-0.945-0.98146.328-0.038-0.0380.0000.0000.0000.000
175D259LEU0-0.086-0.03141.2920.0010.0010.0000.0000.0000.000
176D260LEU00.0190.00640.5620.0010.0010.0000.0000.0000.000
177D261LEU00.0050.00344.0780.0010.0010.0000.0000.0000.000
178D262LYS10.9030.95146.9580.0370.0370.0000.0000.0000.000
179D263ALA0-0.074-0.03142.8870.0020.0020.0000.0000.0000.000
180D264GLY00.0040.00544.655-0.001-0.0010.0000.0000.0000.000
181D265ALA0-0.037-0.00244.021-0.001-0.0010.0000.0000.0000.000
182D266ASP-1-0.790-0.91645.533-0.050-0.0500.0000.0000.0000.000
183D267PRO0-0.040-0.02648.069-0.002-0.0020.0000.0000.0000.000
184D268THR0-0.048-0.02550.2280.0010.0010.0000.0000.0000.000
185D269ALA0-0.0290.00746.6690.0000.0000.0000.0000.0000.000
186D270ARG10.9090.94848.7740.0530.0530.0000.0000.0000.000
187D271MET0-0.0160.00546.323-0.001-0.0010.0000.0000.0000.000
188D272TYR00.000-0.00441.2640.0040.0040.0000.0000.0000.000
189D273GLY0-0.040-0.00847.9480.0020.0020.0000.0000.0000.000
190D274GLY00.016-0.00650.7000.0020.0020.0000.0000.0000.000
191D275ARG10.9350.97451.1620.0580.0580.0000.0000.0000.000
192D276THR00.1000.06450.437-0.003-0.0030.0000.0000.0000.000
193D277PRO00.0460.01648.0390.0000.0000.0000.0000.0000.000
194D278LEU00.0480.01950.2760.0000.0000.0000.0000.0000.000
195D279GLY00.0550.00753.8690.0010.0010.0000.0000.0000.000
196D280SER0-0.068-0.04249.1630.0000.0000.0000.0000.0000.000
197D281ALA0-0.006-0.03152.0830.0000.0000.0000.0000.0000.000
198D282LEU0-0.021-0.00353.0960.0010.0010.0000.0000.0000.000
199D283LEU0-0.065-0.01554.2800.0010.0010.0000.0000.0000.000
200D284ARG10.8410.94648.0180.0590.0590.0000.0000.0000.000
201D285PRO00.0110.01452.5240.0020.0020.0000.0000.0000.000
202D286ASN00.0420.01151.1330.0040.0040.0000.0000.0000.000
203D287PRO00.0500.01754.438-0.001-0.0010.0000.0000.0000.000
204D288ILE0-0.058-0.03252.7100.0010.0010.0000.0000.0000.000
205D289LEU00.0390.03949.1000.0010.0010.0000.0000.0000.000
206D290ALA00.0810.03652.6240.0000.0000.0000.0000.0000.000
207D291ARG10.8910.96255.5520.0340.0340.0000.0000.0000.000
208D292LEU00.0120.01050.2030.0010.0010.0000.0000.0000.000
209D293LEU00.0630.03450.1550.0010.0010.0000.0000.0000.000
210D294ARG10.8690.95453.6450.0380.0380.0000.0000.0000.000
211D295ALA0-0.042-0.03455.9160.0010.0010.0000.0000.0000.000
212D296HIS0-0.045-0.02151.5160.0010.0010.0000.0000.0000.000
213D297GLY0-0.0010.01454.075-0.001-0.0010.0000.0000.0000.000
214D298ALA0-0.022-0.00553.710-0.001-0.0010.0000.0000.0000.000
215D299PRO0-0.015-0.01255.2020.0010.0010.0000.0000.0000.000
216D300GLU-1-0.898-0.96657.214-0.038-0.0380.0000.0000.0000.000
217D301PRO0-0.078-0.02756.779-0.001-0.0010.0000.0000.0000.000
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