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

tag_button

FMODB ID: 6G3RZ

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2375292.494813
FMO2-HF: Nuclear repulsion 2292484.11213
FMO2-HF: Total energy -82808.382683
FMO2-MP2: Total energy -83051.448523


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.
-8.251-4.1250.569-1.858-2.835-0.01
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 : -0.019 / 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].
3D52GLY00.0600.0132.754-5.065-2.3280.482-1.575-1.644-0.009
4D53TYR0-0.061-0.0095.1920.3470.473-0.001-0.008-0.1170.000
5D54VAL00.012-0.0078.545-0.135-0.1350.0000.0000.0000.000
6D55THR0-0.064-0.00711.0980.0870.0870.0000.0000.0000.000
7D56GLU-1-0.964-0.98814.733-0.246-0.2460.0000.0000.0000.000
8D57ASP-1-0.876-0.93117.260-0.262-0.2620.0000.0000.0000.000
9D58GLY00.0570.03213.727-0.009-0.0090.0000.0000.0000.000
10D59ASP-1-0.871-0.94212.510-0.457-0.4570.0000.0000.0000.000
11D60THR00.010-0.0127.4330.0050.0050.0000.0000.0000.000
12D61ALA0-0.007-0.0257.9320.1540.1540.0000.0000.0000.000
13D62LEU00.0110.0077.5740.1620.1620.0000.0000.0000.000
14D63HIS00.0100.03910.1040.0730.0730.0000.0000.0000.000
15D64LEU00.0410.01312.5990.0730.0730.0000.0000.0000.000
16D65ALA0-0.0050.01212.5760.0600.0600.0000.0000.0000.000
17D66VAL0-0.004-0.00614.4080.0380.0380.0000.0000.0000.000
18D67ILE0-0.0110.01216.2370.0260.0260.0000.0000.0000.000
19D68HIS0-0.107-0.06416.9010.0350.0350.0000.0000.0000.000
20D69GLN0-0.076-0.03819.1370.0290.0290.0000.0000.0000.000
21D70HIS0-0.0040.00216.7410.0280.0280.0000.0000.0000.000
22D71GLU-1-0.771-0.88116.470-0.030-0.0300.0000.0000.0000.000
23D72PRO0-0.008-0.00516.2810.0130.0130.0000.0000.0000.000
24D73PHE00.0130.00011.2810.0520.0520.0000.0000.0000.000
25D74LEU00.0320.02212.0270.0180.0180.0000.0000.0000.000
26D75ASP-1-0.849-0.92211.6710.0580.0580.0000.0000.0000.000
27D76PHE0-0.063-0.0249.6070.0710.0710.0000.0000.0000.000
28D77LEU00.0020.0037.6620.0970.0970.0000.0000.0000.000
29D78LEU00.0090.0037.1170.0380.0380.0000.0000.0000.000
30D79GLY0-0.0230.0099.207-0.020-0.0200.0000.0000.0000.000
31D80PHE0-0.113-0.0584.7830.1760.264-0.001-0.003-0.0830.000
32D81SER0-0.040-0.0484.813-0.215-0.2150.0000.0000.0000.000
33D82ALA00.0260.0315.735-0.222-0.2220.0000.0000.0000.000
34D83GLY0-0.0050.0048.3990.0440.0440.0000.0000.0000.000
35D84HIS0-0.070-0.0363.966-0.847-0.5830.000-0.026-0.2380.000
36D85GLU-1-0.884-0.9435.744-1.075-1.0750.0000.0000.0000.000
37D86TYR0-0.043-0.0463.077-0.8920.0020.090-0.245-0.738-0.001
38D87LEU0-0.024-0.0125.2220.1810.198-0.001-0.001-0.0150.000
39D88ASP-1-0.818-0.9008.429-0.444-0.4440.0000.0000.0000.000
40D89LEU0-0.042-0.0085.9290.0260.0260.0000.0000.0000.000
41D90GLN0-0.064-0.05110.1530.1310.1310.0000.0000.0000.000
42D91ASN0-0.016-0.00313.586-0.029-0.0290.0000.0000.0000.000
43D92ASP-1-0.827-0.93114.781-0.410-0.4100.0000.0000.0000.000
44D93LEU0-0.147-0.06518.0320.0440.0440.0000.0000.0000.000
45D94GLY00.0680.00617.6400.0340.0340.0000.0000.0000.000
46D95GLN0-0.018-0.00317.3170.0010.0010.0000.0000.0000.000
47D96THR00.0640.03313.367-0.037-0.0370.0000.0000.0000.000
48D97ALA00.0600.00911.9560.0500.0500.0000.0000.0000.000
49D98LEU00.0380.01113.9470.0610.0610.0000.0000.0000.000
50D99HIS0-0.0240.01216.4760.0170.0170.0000.0000.0000.000
51D100LEU0-0.018-0.00115.2880.0310.0310.0000.0000.0000.000
52D101ALA00.0530.03117.8250.0270.0270.0000.0000.0000.000
53D102ALA0-0.037-0.02719.5990.0240.0240.0000.0000.0000.000
54D103ILE0-0.074-0.03021.4280.0170.0170.0000.0000.0000.000
55D104LEU0-0.018-0.00620.3000.0140.0140.0000.0000.0000.000
56D105GLY0-0.008-0.00224.0570.0140.0140.0000.0000.0000.000
57D106GLU-1-0.876-0.93120.844-0.084-0.0840.0000.0000.0000.000
58D107ALA0-0.006-0.03022.231-0.008-0.0080.0000.0000.0000.000
59D108SER00.0080.00221.2750.0010.0010.0000.0000.0000.000
60D109THR00.017-0.01017.3880.0040.0040.0000.0000.0000.000
61D110VAL0-0.013-0.01417.670-0.020-0.0200.0000.0000.0000.000
62D111GLU-1-0.933-0.96318.600-0.061-0.0610.0000.0000.0000.000
63D112LYS10.7980.89315.428-0.016-0.0160.0000.0000.0000.000
64D113LEU00.0360.01512.464-0.012-0.0120.0000.0000.0000.000
65D114TYR0-0.001-0.01114.252-0.036-0.0360.0000.0000.0000.000
66D115ALA0-0.009-0.01616.491-0.011-0.0110.0000.0000.0000.000
67D116ALA0-0.055-0.03711.3300.0110.0110.0000.0000.0000.000
68D117GLY0-0.011-0.01711.741-0.034-0.0340.0000.0000.0000.000
69D118ALA0-0.0390.00012.322-0.049-0.0490.0000.0000.0000.000
70D119GLY00.019-0.00313.2880.0590.0590.0000.0000.0000.000
71D120VAL0-0.039-0.03015.2970.0030.0030.0000.0000.0000.000
72D121LEU0-0.023-0.02218.6450.0190.0190.0000.0000.0000.000
73D122VAL00.0010.02114.6900.0100.0100.0000.0000.0000.000
74D123ALA0-0.025-0.01618.1370.0260.0260.0000.0000.0000.000
75D124GLU-1-0.784-0.87519.709-0.243-0.2430.0000.0000.0000.000
76D125ARG10.8330.89820.7830.2420.2420.0000.0000.0000.000
77D126GLY0-0.039-0.02323.2520.0110.0110.0000.0000.0000.000
78D127GLY00.042-0.00124.2750.0160.0160.0000.0000.0000.000
79D128HIS0-0.075-0.02124.3310.0140.0140.0000.0000.0000.000
80D129THR00.0830.03121.537-0.018-0.0180.0000.0000.0000.000
81D130ALA00.0560.00519.5810.0120.0120.0000.0000.0000.000
82D131LEU00.0390.01921.6550.0180.0180.0000.0000.0000.000
83D132HIS0-0.0080.01224.9730.0050.0050.0000.0000.0000.000
84D133LEU0-0.010-0.00621.9020.0120.0120.0000.0000.0000.000
85D134ALA00.0560.03525.4650.0120.0120.0000.0000.0000.000
86D135CYS0-0.120-0.05626.9780.0140.0140.0000.0000.0000.000
87D136ARG10.8900.95927.2200.1550.1550.0000.0000.0000.000
88D137VAL0-0.034-0.01627.1430.0070.0070.0000.0000.0000.000
89D138ARG10.8420.93830.4030.0750.0750.0000.0000.0000.000
90D139ALA00.0740.06327.1470.0070.0070.0000.0000.0000.000
91D140HIS0-0.048-0.07828.482-0.002-0.0020.0000.0000.0000.000
92D141THR00.0230.00128.401-0.004-0.0040.0000.0000.0000.000
93D142CYS00.0150.03824.282-0.001-0.0010.0000.0000.0000.000
94D143ALA00.0360.01424.995-0.007-0.0070.0000.0000.0000.000
95D144CYS0-0.045-0.02127.1020.0000.0000.0000.0000.0000.000
96D145VAL00.0000.01922.2000.0010.0010.0000.0000.0000.000
97D146LEU00.0110.00020.347-0.003-0.0030.0000.0000.0000.000
98D147LEU0-0.068-0.01523.812-0.005-0.0050.0000.0000.0000.000
99D148GLN0-0.040-0.02925.3440.0180.0180.0000.0000.0000.000
100D149PRO0-0.036-0.01824.446-0.012-0.0120.0000.0000.0000.000
101D150ARG10.8940.96616.1870.2240.2240.0000.0000.0000.000
102D151PRO00.0010.00919.5890.0100.0100.0000.0000.0000.000
103D152SER0-0.003-0.00619.754-0.010-0.0100.0000.0000.0000.000
104D153HIS0-0.114-0.06616.420-0.012-0.0120.0000.0000.0000.000
105D154PRO00.0620.03813.246-0.003-0.0030.0000.0000.0000.000
106D155ARG10.9140.95615.094-0.063-0.0630.0000.0000.0000.000
107D156ASP-1-0.767-0.86215.3510.1670.1670.0000.0000.0000.000
108D157ALA0-0.106-0.05817.127-0.011-0.0110.0000.0000.0000.000
109D193ASP-1-0.952-0.98621.019-0.201-0.2010.0000.0000.0000.000
110D194GLU-1-0.949-0.94821.605-0.139-0.1390.0000.0000.0000.000
111D195ASP-1-0.886-0.96222.704-0.100-0.1000.0000.0000.0000.000
112D196TRP00.0240.00523.679-0.008-0.0080.0000.0000.0000.000
113D197ARG10.9200.94624.6490.0810.0810.0000.0000.0000.000
114D198LEU0-0.023-0.00124.2360.0030.0030.0000.0000.0000.000
115D199GLN0-0.036-0.04223.176-0.010-0.0100.0000.0000.0000.000
116D200LEU0-0.069-0.03525.7840.0000.0000.0000.0000.0000.000
117D201GLU-1-0.820-0.91529.224-0.099-0.0990.0000.0000.0000.000
118D202ALA00.0110.03025.578-0.003-0.0030.0000.0000.0000.000
119D203GLU-1-0.965-1.00527.571-0.130-0.1300.0000.0000.0000.000
120D204ASN0-0.016-0.00727.342-0.006-0.0060.0000.0000.0000.000
121D205TYR00.003-0.01023.2280.0070.0070.0000.0000.0000.000
122D206ASP-1-0.949-0.95229.786-0.135-0.1350.0000.0000.0000.000
123D207GLY0-0.037-0.02731.9650.0100.0100.0000.0000.0000.000
124D208HIS0-0.059-0.03832.2340.0080.0080.0000.0000.0000.000
125D209THR00.0800.05030.659-0.008-0.0080.0000.0000.0000.000
126D210PRO00.0380.00428.0970.0060.0060.0000.0000.0000.000
127D211LEU00.0200.01130.8080.0060.0060.0000.0000.0000.000
128D212HIS00.0100.00634.4490.0020.0020.0000.0000.0000.000
129D213VAL00.0250.03030.6520.0050.0050.0000.0000.0000.000
130D214ALA00.0490.03033.6340.0050.0050.0000.0000.0000.000
131D215VAL0-0.044-0.02334.9430.0070.0070.0000.0000.0000.000
132D216ILE0-0.0210.00636.4090.0050.0050.0000.0000.0000.000
133D217HIS0-0.072-0.04733.5210.0020.0020.0000.0000.0000.000
134D218LYS10.8470.92337.4280.0630.0630.0000.0000.0000.000
135D219ASP-1-0.783-0.88934.729-0.067-0.0670.0000.0000.0000.000
136D220ALA0-0.008-0.01637.618-0.001-0.0010.0000.0000.0000.000
137D221GLU-1-0.811-0.88136.186-0.051-0.0510.0000.0000.0000.000
138D222MET00.0140.01730.0830.0000.0000.0000.0000.0000.000
139D223VAL0-0.014-0.00734.628-0.002-0.0020.0000.0000.0000.000
140D224ARG10.7830.86837.1410.0490.0490.0000.0000.0000.000
141D225LEU00.0370.02531.3360.0010.0010.0000.0000.0000.000
142D226LEU00.0240.01230.538-0.002-0.0020.0000.0000.0000.000
143D227ARG10.8230.87533.9310.0530.0530.0000.0000.0000.000
144D228ASP-1-0.852-0.88736.037-0.054-0.0540.0000.0000.0000.000
145D229ALA0-0.0190.00131.2930.0010.0010.0000.0000.0000.000
146D230GLY0-0.036-0.02332.974-0.003-0.0030.0000.0000.0000.000
147D231ALA0-0.026-0.00433.592-0.003-0.0030.0000.0000.0000.000
148D232ASP-1-0.798-0.90334.774-0.077-0.0770.0000.0000.0000.000
149D233LEU0-0.028-0.03637.244-0.001-0.0010.0000.0000.0000.000
150D234ASN0-0.039-0.02740.0000.0050.0050.0000.0000.0000.000
151D235LYS10.8300.92135.0130.1020.1020.0000.0000.0000.000
152D236PRO00.001-0.00638.9750.0000.0000.0000.0000.0000.000
153D237GLU-1-0.676-0.78537.382-0.094-0.0940.0000.0000.0000.000
154D238PRO00.0560.02035.7140.0060.0060.0000.0000.0000.000
155D239THR0-0.085-0.06038.4980.0040.0040.0000.0000.0000.000
156D240CYS0-0.097-0.06940.7930.0040.0040.0000.0000.0000.000
157D241GLY00.0620.03442.2560.0050.0050.0000.0000.0000.000
158D242ARG10.7570.87241.1220.0850.0850.0000.0000.0000.000
159D243THR00.0870.03141.254-0.003-0.0030.0000.0000.0000.000
160D244PRO00.0850.02838.9460.0010.0010.0000.0000.0000.000
161D245LEU00.0020.00541.2160.0020.0020.0000.0000.0000.000
162D246HIS0-0.048-0.00144.4340.0010.0010.0000.0000.0000.000
163D247LEU00.0300.02238.7750.0020.0020.0000.0000.0000.000
164D248ALA00.0310.01842.7900.0010.0010.0000.0000.0000.000
165D249VAL0-0.048-0.01744.0990.0030.0030.0000.0000.0000.000
166D250GLU-1-0.836-0.88744.287-0.065-0.0650.0000.0000.0000.000
167D251ALA00.0020.00142.5640.0010.0010.0000.0000.0000.000
168D252GLN0-0.056-0.05644.5010.0050.0050.0000.0000.0000.000
169D253ALA00.0050.01143.9470.0030.0030.0000.0000.0000.000
170D254ALA00.026-0.00445.855-0.001-0.0010.0000.0000.0000.000
171D255SER00.0160.00645.2400.0000.0000.0000.0000.0000.000
172D256VAL00.0360.02341.0850.0000.0000.0000.0000.0000.000
173D257LEU00.0140.00743.774-0.001-0.0010.0000.0000.0000.000
174D258GLU-1-0.837-0.91946.339-0.038-0.0380.0000.0000.0000.000
175D259LEU0-0.077-0.02041.4740.0010.0010.0000.0000.0000.000
176D260LEU00.0200.00740.4460.0000.0000.0000.0000.0000.000
177D261LEU00.0090.00044.0610.0000.0000.0000.0000.0000.000
178D262LYS10.7970.88947.2120.0400.0400.0000.0000.0000.000
179D263ALA0-0.067-0.02942.7980.0010.0010.0000.0000.0000.000
180D264GLY00.0010.00444.602-0.001-0.0010.0000.0000.0000.000
181D265ALA0-0.043-0.00843.962-0.001-0.0010.0000.0000.0000.000
182D266ASP-1-0.780-0.90845.516-0.050-0.0500.0000.0000.0000.000
183D267PRO0-0.046-0.02748.062-0.002-0.0020.0000.0000.0000.000
184D268THR0-0.047-0.03250.2370.0020.0020.0000.0000.0000.000
185D269ALA0-0.0230.00946.6970.0000.0000.0000.0000.0000.000
186D270ARG10.8040.86348.8050.0500.0500.0000.0000.0000.000
187D271MET0-0.0290.00046.405-0.001-0.0010.0000.0000.0000.000
188D272TYR0-0.010-0.01841.2730.0040.0040.0000.0000.0000.000
189D273GLY0-0.041-0.00748.0400.0020.0020.0000.0000.0000.000
190D274GLY00.0250.00450.7880.0020.0020.0000.0000.0000.000
191D275ARG10.9250.96851.2620.0540.0540.0000.0000.0000.000
192D276THR00.1090.06750.505-0.003-0.0030.0000.0000.0000.000
193D277PRO00.0510.01948.0280.0010.0010.0000.0000.0000.000
194D278LEU00.0530.02450.3250.0010.0010.0000.0000.0000.000
195D279GLY00.0580.01453.9140.0010.0010.0000.0000.0000.000
196D280SER0-0.057-0.03149.2120.0000.0000.0000.0000.0000.000
197D281ALA00.001-0.02152.0950.0000.0000.0000.0000.0000.000
198D282LEU0-0.034-0.00653.1600.0010.0010.0000.0000.0000.000
199D283LEU0-0.066-0.01454.3950.0010.0010.0000.0000.0000.000
200D284ARG10.7460.86747.9910.0560.0560.0000.0000.0000.000
201D285PRO00.0160.00952.6740.0020.0020.0000.0000.0000.000
202D286ASN00.0070.00150.9180.0040.0040.0000.0000.0000.000
203D287PRO00.0600.01754.500-0.001-0.0010.0000.0000.0000.000
204D288ILE0-0.050-0.02552.8350.0000.0000.0000.0000.0000.000
205D289LEU00.0280.02649.2110.0000.0000.0000.0000.0000.000
206D290ALA00.0680.03752.6590.0000.0000.0000.0000.0000.000
207D291ARG10.9060.95855.5880.0330.0330.0000.0000.0000.000
208D292LEU00.0070.00750.2530.0010.0010.0000.0000.0000.000
209D293LEU00.0630.03050.1270.0000.0000.0000.0000.0000.000
210D294ARG10.7730.85053.6570.0370.0370.0000.0000.0000.000
211D295ALA0-0.051-0.03855.9430.0010.0010.0000.0000.0000.000
212D296HIS0-0.047-0.02252.0500.0010.0010.0000.0000.0000.000
213D297GLY00.0030.01554.056-0.001-0.0010.0000.0000.0000.000
214D298ALA0-0.019-0.00153.683-0.001-0.0010.0000.0000.0000.000
215D299PRO0-0.013-0.01055.1630.0020.0020.0000.0000.0000.000
216D300GLU-1-0.795-0.86057.243-0.037-0.0370.0000.0000.0000.000
217D301PRO0-0.050-0.02356.886-0.001-0.0010.0000.0000.0000.000
218D302GLU-1-0.822-0.88557.737-0.043-0.0430.0000.0000.0000.000
219D303ASP-1-0.949-0.95960.343-0.037-0.0370.0000.0000.0000.000
220D304GLY0-0.053-0.02559.435-0.001-0.0010.0000.0000.0000.000