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: ZN2GN

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 OptAll
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 -2377787.398328
FMO2-HF: Nuclear repulsion 2294978.412865
FMO2-HF: Total energy -82808.985462
FMO2-MP2: Total energy -83051.897001


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.
-8.498-3.8460.849-2.053-3.446-0.012
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 : -0.009 / 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].
3D52GLY00.0580.0132.673-4.829-2.0170.626-1.660-1.778-0.010
4D53TYR0-0.067-0.0155.2140.3450.455-0.001-0.006-0.1020.000
5D54VAL00.0150.0018.485-0.122-0.1220.0000.0000.0000.000
6D55THR0-0.066-0.03111.0870.0860.0860.0000.0000.0000.000
7D56GLU-1-0.959-0.99014.813-0.254-0.2540.0000.0000.0000.000
8D57ASP-1-0.888-0.92017.117-0.269-0.2690.0000.0000.0000.000
9D58GLY00.0630.03213.884-0.003-0.0030.0000.0000.0000.000
10D59ASP-1-0.883-0.95312.266-0.483-0.4830.0000.0000.0000.000
11D60THR00.025-0.0107.390-0.003-0.0030.0000.0000.0000.000
12D61ALA00.008-0.0117.7030.1570.1570.0000.0000.0000.000
13D62LEU00.0050.0096.9850.1770.1770.0000.0000.0000.000
14D63HIS00.0010.0329.8830.0660.0660.0000.0000.0000.000
15D64LEU00.0250.00812.3330.0780.0780.0000.0000.0000.000
16D65ALA0-0.0050.00612.3920.0610.0610.0000.0000.0000.000
17D66VAL0-0.017-0.00414.1960.0420.0420.0000.0000.0000.000
18D67ILE0-0.0070.00715.9880.0280.0280.0000.0000.0000.000
19D68HIS0-0.109-0.05816.8550.0370.0370.0000.0000.0000.000
20D69GLN0-0.064-0.04319.1420.0320.0320.0000.0000.0000.000
21D70HIS00.0010.00616.5020.0250.0250.0000.0000.0000.000
22D71GLU-1-0.737-0.84616.188-0.048-0.0480.0000.0000.0000.000
23D72PRO0-0.009-0.00916.0580.0120.0120.0000.0000.0000.000
24D73PHE0-0.016-0.00711.1270.0530.0530.0000.0000.0000.000
25D74LEU00.0500.02511.5160.0120.0120.0000.0000.0000.000
26D75ASP-1-0.855-0.92011.3520.0310.0310.0000.0000.0000.000
27D76PHE0-0.071-0.03310.0640.0680.0680.0000.0000.0000.000
28D77LEU00.0080.0027.2730.1230.1230.0000.0000.0000.000
29D78LEU00.0100.0116.9330.0050.0050.0000.0000.0000.000
30D79GLY0-0.034-0.0028.918-0.021-0.0210.0000.0000.0000.000
31D80PHE0-0.087-0.0444.6740.1970.287-0.001-0.004-0.0860.000
32D81SER0-0.036-0.0474.580-0.309-0.184-0.001-0.006-0.1180.000
33D82ALA0-0.0050.0065.549-0.214-0.2140.0000.0000.0000.000
34D83GLY0-0.023-0.0088.2780.0370.0370.0000.0000.0000.000
35D84HIS0-0.047-0.0123.968-0.824-0.5420.000-0.022-0.2600.000
36D85GLU-1-0.889-0.9596.075-1.134-1.1340.0000.0000.0000.000
37D86TYR0-0.039-0.0322.830-1.262-0.0550.227-0.352-1.081-0.002
38D87LEU0-0.038-0.0134.9690.1780.204-0.001-0.003-0.0210.000
39D88ASP-1-0.825-0.9008.231-0.430-0.4300.0000.0000.0000.000
40D89LEU0-0.024-0.0055.9230.0360.0360.0000.0000.0000.000
41D90GLN0-0.103-0.0689.9050.1380.1380.0000.0000.0000.000
42D91ASN00.0000.00413.271-0.037-0.0370.0000.0000.0000.000
43D92ASP-1-0.840-0.92714.871-0.394-0.3940.0000.0000.0000.000
44D93LEU0-0.110-0.04718.1170.0430.0430.0000.0000.0000.000
45D94GLY00.0420.00017.6250.0350.0350.0000.0000.0000.000
46D95GLN0-0.020-0.00217.113-0.004-0.0040.0000.0000.0000.000
47D96THR00.0840.02513.135-0.039-0.0390.0000.0000.0000.000
48D97ALA00.0500.01011.8480.0560.0560.0000.0000.0000.000
49D98LEU00.0480.01513.7890.0610.0610.0000.0000.0000.000
50D99HIS0-0.0290.00916.0750.0170.0170.0000.0000.0000.000
51D100LEU0-0.027-0.00315.1040.0320.0320.0000.0000.0000.000
52D101ALA00.0550.03117.6080.0270.0270.0000.0000.0000.000
53D102ALA0-0.034-0.02019.3990.0250.0250.0000.0000.0000.000
54D103ILE0-0.072-0.03621.3020.0170.0170.0000.0000.0000.000
55D104LEU0-0.020-0.00220.1700.0150.0150.0000.0000.0000.000
56D105GLY0-0.0020.00223.8960.0140.0140.0000.0000.0000.000
57D106GLU-1-0.840-0.92720.320-0.107-0.1070.0000.0000.0000.000
58D107ALA0-0.013-0.02521.516-0.007-0.0070.0000.0000.0000.000
59D108SER0-0.032-0.01920.5590.0000.0000.0000.0000.0000.000
60D109THR00.033-0.00816.8910.0010.0010.0000.0000.0000.000
61D110VAL0-0.014-0.01716.952-0.023-0.0230.0000.0000.0000.000
62D111GLU-1-0.936-0.97018.054-0.069-0.0690.0000.0000.0000.000
63D112LYS10.7850.88015.1970.0010.0010.0000.0000.0000.000
64D113LEU00.0190.00611.887-0.010-0.0100.0000.0000.0000.000
65D114TYR0-0.010-0.01413.679-0.036-0.0360.0000.0000.0000.000
66D115ALA0-0.002-0.01315.775-0.013-0.0130.0000.0000.0000.000
67D116ALA0-0.029-0.01710.7800.0150.0150.0000.0000.0000.000
68D117GLY00.025-0.00211.241-0.032-0.0320.0000.0000.0000.000
69D118ALA0-0.0250.01011.988-0.023-0.0230.0000.0000.0000.000
70D119GLY00.0450.00812.9030.0650.0650.0000.0000.0000.000
71D120VAL0-0.053-0.02915.063-0.002-0.0020.0000.0000.0000.000
72D121LEU0-0.029-0.01918.3780.0180.0180.0000.0000.0000.000
73D122VAL00.0030.01514.2270.0080.0080.0000.0000.0000.000
74D123ALA0-0.039-0.02917.6460.0250.0250.0000.0000.0000.000
75D124GLU-1-0.800-0.87819.525-0.241-0.2410.0000.0000.0000.000
76D125ARG10.8170.89020.5930.2440.2440.0000.0000.0000.000
77D126GLY0-0.005-0.00523.1170.0130.0130.0000.0000.0000.000
78D127GLY00.019-0.00623.7820.0170.0170.0000.0000.0000.000
79D128HIS0-0.082-0.03324.0840.0090.0090.0000.0000.0000.000
80D129THR00.1020.02621.187-0.019-0.0190.0000.0000.0000.000
81D130ALA00.0400.00819.1440.0120.0120.0000.0000.0000.000
82D131LEU00.0430.02921.2330.0180.0180.0000.0000.0000.000
83D132HIS00.0000.02424.6380.0050.0050.0000.0000.0000.000
84D133LEU00.003-0.00521.5240.0120.0120.0000.0000.0000.000
85D134ALA00.0380.02724.8280.0120.0120.0000.0000.0000.000
86D135CYS0-0.100-0.04826.4270.0150.0150.0000.0000.0000.000
87D136ARG10.8560.94127.2470.1590.1590.0000.0000.0000.000
88D137VAL0-0.036-0.01826.5470.0090.0090.0000.0000.0000.000
89D138ARG10.8220.92729.7260.0800.0800.0000.0000.0000.000
90D139ALA00.0730.05526.8340.0070.0070.0000.0000.0000.000
91D140HIS0-0.027-0.05927.991-0.003-0.0030.0000.0000.0000.000
92D141THR00.0050.00327.757-0.003-0.0030.0000.0000.0000.000
93D142CYS00.0130.03323.770-0.001-0.0010.0000.0000.0000.000
94D143ALA00.0380.01424.546-0.007-0.0070.0000.0000.0000.000
95D144CYS0-0.053-0.03326.6770.0000.0000.0000.0000.0000.000
96D145VAL00.0070.01721.8750.0020.0020.0000.0000.0000.000
97D146LEU00.0230.01819.854-0.005-0.0050.0000.0000.0000.000
98D147LEU0-0.086-0.02423.456-0.005-0.0050.0000.0000.0000.000
99D148GLN0-0.038-0.02824.7590.0180.0180.0000.0000.0000.000
100D149PRO0-0.007-0.00523.907-0.013-0.0130.0000.0000.0000.000
101D150ARG10.8780.95915.6470.2310.2310.0000.0000.0000.000
102D151PRO00.0150.00619.4460.0110.0110.0000.0000.0000.000
103D152SER0-0.021-0.01119.515-0.008-0.0080.0000.0000.0000.000
104D153HIS0-0.077-0.03916.045-0.011-0.0110.0000.0000.0000.000
105D154PRO00.0370.02112.9900.0010.0010.0000.0000.0000.000
106D155ARG10.9040.93515.153-0.057-0.0570.0000.0000.0000.000
107D156ASP-1-0.789-0.85915.4880.1710.1710.0000.0000.0000.000
108D157ALA0-0.099-0.05416.809-0.022-0.0220.0000.0000.0000.000
109D193ASP-1-0.940-0.97620.247-0.204-0.2040.0000.0000.0000.000
110D194GLU-1-0.977-0.99221.291-0.135-0.1350.0000.0000.0000.000
111D195ASP-1-0.903-0.95222.273-0.102-0.1020.0000.0000.0000.000
112D196TRP00.0620.02423.225-0.008-0.0080.0000.0000.0000.000
113D197ARG10.8600.92124.1880.0780.0780.0000.0000.0000.000
114D198LEU0-0.0080.00523.7550.0030.0030.0000.0000.0000.000
115D199GLN0-0.036-0.04522.964-0.008-0.0080.0000.0000.0000.000
116D200LEU0-0.073-0.03425.5320.0010.0010.0000.0000.0000.000
117D201GLU-1-0.815-0.92229.127-0.098-0.0980.0000.0000.0000.000
118D202ALA00.0200.03225.339-0.002-0.0020.0000.0000.0000.000
119D203GLU-1-0.967-0.99427.364-0.133-0.1330.0000.0000.0000.000
120D204ASN0-0.013-0.00426.885-0.007-0.0070.0000.0000.0000.000
121D205TYR0-0.016-0.01722.5510.0100.0100.0000.0000.0000.000
122D206ASP-1-0.888-0.92529.221-0.138-0.1380.0000.0000.0000.000
123D207GLY0-0.030-0.01731.3980.0100.0100.0000.0000.0000.000
124D208HIS0-0.063-0.04531.6500.0080.0080.0000.0000.0000.000
125D209THR00.0510.03630.111-0.009-0.0090.0000.0000.0000.000
126D210PRO00.031-0.00127.5220.0070.0070.0000.0000.0000.000
127D211LEU00.0320.01830.2540.0070.0070.0000.0000.0000.000
128D212HIS0-0.015-0.01233.9420.0010.0010.0000.0000.0000.000
129D213VAL00.0260.02630.0270.0050.0050.0000.0000.0000.000
130D214ALA00.0440.02933.0130.0050.0050.0000.0000.0000.000
131D215VAL0-0.047-0.02334.3870.0070.0070.0000.0000.0000.000
132D216ILE0-0.0150.00136.0380.0050.0050.0000.0000.0000.000
133D217HIS0-0.048-0.02732.9930.0020.0020.0000.0000.0000.000
134D218LYS10.8890.94636.6310.0650.0650.0000.0000.0000.000
135D219ASP-1-0.806-0.90134.571-0.069-0.0690.0000.0000.0000.000
136D220ALA0-0.002-0.01237.223-0.001-0.0010.0000.0000.0000.000
137D221GLU-1-0.835-0.87835.605-0.051-0.0510.0000.0000.0000.000
138D222MET0-0.0070.00629.655-0.001-0.0010.0000.0000.0000.000
139D223VAL0-0.005-0.01233.958-0.002-0.0020.0000.0000.0000.000
140D224ARG10.7950.88236.5220.0520.0520.0000.0000.0000.000
141D225LEU00.0390.01830.6780.0000.0000.0000.0000.0000.000
142D226LEU00.0160.01029.950-0.001-0.0010.0000.0000.0000.000
143D227ARG10.8120.86933.3030.0530.0530.0000.0000.0000.000
144D228ASP-1-0.858-0.89535.576-0.054-0.0540.0000.0000.0000.000
145D229ALA00.0030.01530.7210.0010.0010.0000.0000.0000.000
146D230GLY0-0.007-0.00232.654-0.002-0.0020.0000.0000.0000.000
147D231ALA0-0.0050.00533.278-0.002-0.0020.0000.0000.0000.000
148D232ASP-1-0.795-0.89734.541-0.074-0.0740.0000.0000.0000.000
149D233LEU0-0.022-0.03037.167-0.002-0.0020.0000.0000.0000.000
150D234ASN0-0.043-0.02939.6470.0060.0060.0000.0000.0000.000
151D235LYS10.8200.90535.0850.0990.0990.0000.0000.0000.000
152D236PRO00.0000.00438.600-0.001-0.0010.0000.0000.0000.000
153D237GLU-1-0.675-0.78037.052-0.094-0.0940.0000.0000.0000.000
154D238PRO00.0530.02935.1580.0060.0060.0000.0000.0000.000
155D239THR0-0.067-0.05637.6630.0040.0040.0000.0000.0000.000
156D240CYS0-0.088-0.05940.0680.0050.0050.0000.0000.0000.000
157D241GLY00.0780.04241.7430.0050.0050.0000.0000.0000.000
158D242ARG10.7180.84740.9790.0830.0830.0000.0000.0000.000
159D243THR00.0970.03340.955-0.003-0.0030.0000.0000.0000.000
160D244PRO00.0750.02338.5930.0010.0010.0000.0000.0000.000
161D245LEU0-0.0010.00840.9300.0020.0020.0000.0000.0000.000
162D246HIS0-0.052-0.00944.1290.0000.0000.0000.0000.0000.000
163D247LEU00.0370.02438.3470.0020.0020.0000.0000.0000.000
164D248ALA00.0160.01342.3630.0010.0010.0000.0000.0000.000
165D249VAL0-0.059-0.02643.6770.0030.0030.0000.0000.0000.000
166D250GLU-1-0.834-0.89443.696-0.065-0.0650.0000.0000.0000.000
167D251ALA00.0080.00841.9340.0010.0010.0000.0000.0000.000
168D252GLN0-0.043-0.04943.9310.0040.0040.0000.0000.0000.000
169D253ALA00.0290.02143.1870.0030.0030.0000.0000.0000.000
170D254ALA00.001-0.01045.1720.0000.0000.0000.0000.0000.000
171D255SER00.014-0.00144.7980.0000.0000.0000.0000.0000.000
172D256VAL00.0370.02240.5220.0010.0010.0000.0000.0000.000
173D257LEU00.0150.00843.250-0.001-0.0010.0000.0000.0000.000
174D258GLU-1-0.819-0.90745.843-0.040-0.0400.0000.0000.0000.000
175D259LEU0-0.051-0.02141.5280.0010.0010.0000.0000.0000.000
176D260LEU00.0110.00639.9720.0000.0000.0000.0000.0000.000
177D261LEU0-0.002-0.00143.6850.0000.0000.0000.0000.0000.000
178D262LYS10.7980.88947.0620.0400.0400.0000.0000.0000.000
179D263ALA0-0.057-0.01842.1900.0010.0010.0000.0000.0000.000
180D264GLY00.0000.00943.733-0.001-0.0010.0000.0000.0000.000
181D265ALA0-0.025-0.00143.401-0.001-0.0010.0000.0000.0000.000
182D266ASP-1-0.790-0.90644.936-0.050-0.0500.0000.0000.0000.000
183D267PRO0-0.039-0.02347.616-0.002-0.0020.0000.0000.0000.000
184D268THR0-0.045-0.04649.9920.0010.0010.0000.0000.0000.000
185D269ALA00.0350.03546.2960.0000.0000.0000.0000.0000.000
186D270ARG10.7290.81848.0510.0490.0490.0000.0000.0000.000
187D271MET0-0.0230.01746.022-0.001-0.0010.0000.0000.0000.000
188D272TYR0-0.016-0.03740.9730.0040.0040.0000.0000.0000.000
189D273GLY0-0.032-0.00347.8250.0020.0020.0000.0000.0000.000
190D274GLY00.0100.01050.6970.0020.0020.0000.0000.0000.000
191D275ARG10.9190.97150.6300.0540.0540.0000.0000.0000.000
192D276THR00.1260.07550.060-0.003-0.0030.0000.0000.0000.000
193D277PRO00.0220.00547.5420.0000.0000.0000.0000.0000.000
194D278LEU00.0390.01449.9110.0000.0000.0000.0000.0000.000
195D279GLY00.0470.01753.6130.0010.0010.0000.0000.0000.000
196D280SER0-0.025-0.00748.4000.0000.0000.0000.0000.0000.000
197D281ALA00.002-0.00551.6030.0000.0000.0000.0000.0000.000
198D282LEU0-0.041-0.02452.7740.0010.0010.0000.0000.0000.000
199D283LEU0-0.044-0.00353.7610.0010.0010.0000.0000.0000.000
200D284ARG10.7640.86747.7080.0550.0550.0000.0000.0000.000
201D285PRO00.0080.01652.3280.0020.0020.0000.0000.0000.000
202D286ASN00.0180.00650.1390.0040.0040.0000.0000.0000.000
203D287PRO00.0510.01553.780-0.001-0.0010.0000.0000.0000.000
204D288ILE0-0.038-0.02652.4440.0010.0010.0000.0000.0000.000
205D289LEU00.0210.02448.7440.0000.0000.0000.0000.0000.000
206D290ALA00.0690.03452.0900.0000.0000.0000.0000.0000.000
207D291ARG10.8850.94755.1720.0330.0330.0000.0000.0000.000
208D292LEU00.0050.00049.8100.0010.0010.0000.0000.0000.000
209D293LEU00.0370.01949.8120.0000.0000.0000.0000.0000.000
210D294ARG10.8120.87653.2470.0370.0370.0000.0000.0000.000
211D295ALA0-0.056-0.02455.3400.0010.0010.0000.0000.0000.000
212D296HIS0-0.043-0.02451.3120.0010.0010.0000.0000.0000.000
213D297GLY00.0100.01553.434-0.001-0.0010.0000.0000.0000.000
214D298ALA0-0.021-0.01853.126-0.001-0.0010.0000.0000.0000.000
215D299PRO0-0.029-0.01654.4230.0020.0020.0000.0000.0000.000
216D300GLU-1-0.806-0.87456.660-0.038-0.0380.0000.0000.0000.000
217D301PRO0-0.052-0.02756.455-0.001-0.0010.0000.0000.0000.000
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