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: Z696N

Calculation Name: 1OYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OYS

Chain ID: A

ChEMBL ID:

UniProt ID: P28619

Base Structure: X-ray

Registration Date: 2023-06-26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2479500.247313
FMO2-HF: Nuclear repulsion 2395718.552066
FMO2-HF: Total energy -83781.695248
FMO2-MP2: Total energy -84024.459969


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.628-1.9031.197-1.288-3.633-0.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.030
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].
3A3HIS0-0.060-0.0523.874-0.9630.313-0.011-0.562-0.7030.001
4A4ASP-1-0.816-0.8716.6640.2230.2230.0000.0000.0000.000
5A5GLY0-0.057-0.0214.1020.1410.244-0.001-0.010-0.0920.000
6A6ARG10.6610.8074.3080.6490.862-0.001-0.025-0.1870.000
7A7GLN00.0230.0024.1343.0533.3410.010-0.079-0.2190.000
8A8HIS00.0390.0194.559-0.731-0.594-0.001-0.008-0.1270.000
9A9ASP-1-0.892-0.9665.6850.5070.5070.0000.0000.0000.000
10A10GLU-1-0.880-0.9178.1941.2151.2150.0000.0000.0000.000
11A11LEU0-0.0140.00610.195-0.107-0.1070.0000.0000.0000.000
12A12ARG10.7870.86512.2390.2850.2850.0000.0000.0000.000
13A13PRO0-0.009-0.02612.9590.0030.0030.0000.0000.0000.000
14A14ILE00.0490.04716.061-0.046-0.0460.0000.0000.0000.000
15A15THR0-0.121-0.06719.2150.0120.0120.0000.0000.0000.000
16A16PHE00.015-0.01522.679-0.015-0.0150.0000.0000.0000.000
17A17ASP-1-0.827-0.91526.212-0.011-0.0110.0000.0000.0000.000
18A18LEU0-0.014-0.01628.387-0.007-0.0070.0000.0000.0000.000
19A19ASP-1-0.908-0.95231.7250.0020.0020.0000.0000.0000.000
20A20PHE0-0.075-0.02529.503-0.005-0.0050.0000.0000.0000.000
21A21ILE0-0.050-0.01832.621-0.006-0.0060.0000.0000.0000.000
22A22SER0-0.007-0.00436.3990.0030.0030.0000.0000.0000.000
23A23HIS00.0110.01339.7820.0040.0040.0000.0000.0000.000
24A24PRO0-0.007-0.01540.7090.0010.0010.0000.0000.0000.000
25A25GLU-1-0.885-0.95038.192-0.032-0.0320.0000.0000.0000.000
26A26GLY0-0.045-0.04037.5020.0040.0040.0000.0000.0000.000
27A27SER0-0.0020.00834.250-0.001-0.0010.0000.0000.0000.000
28A28VAL00.0290.01028.6480.0060.0060.0000.0000.0000.000
29A29LEU0-0.0420.00526.304-0.009-0.0090.0000.0000.0000.000
30A30ILE0-0.025-0.00722.7580.0100.0100.0000.0000.0000.000
31A31THR0-0.034-0.01819.865-0.021-0.0210.0000.0000.0000.000
32A32ALA00.0450.01817.5170.0280.0280.0000.0000.0000.000
33A33GLY00.0240.01515.484-0.038-0.0380.0000.0000.0000.000
34A34ASN0-0.065-0.04214.6940.0430.0430.0000.0000.0000.000
35A35THR00.0110.01418.258-0.008-0.0080.0000.0000.0000.000
36A36LYS10.8750.91820.2500.0980.0980.0000.0000.0000.000
37A37VAL0-0.002-0.01323.645-0.012-0.0120.0000.0000.0000.000
38A38ILE00.0190.03226.8560.0130.0130.0000.0000.0000.000
39A39CYS0-0.038-0.00228.693-0.008-0.0080.0000.0000.0000.000
40A40ASN00.0540.01331.5530.0120.0120.0000.0000.0000.000
41A41ALA0-0.004-0.00435.211-0.003-0.0030.0000.0000.0000.000
42A42SER0-0.0130.00537.7350.0050.0050.0000.0000.0000.000
43A43VAL0-0.001-0.01441.542-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.754-0.84044.197-0.033-0.0330.0000.0000.0000.000
45A45ASP-1-0.820-0.88647.371-0.017-0.0170.0000.0000.0000.000
46A46ARG10.7580.84349.1400.0320.0320.0000.0000.0000.000
47A47VAL00.0740.04847.042-0.001-0.0010.0000.0000.0000.000
48A48PRO00.0540.02445.1460.0000.0000.0000.0000.0000.000
49A49PRO00.005-0.00648.3060.0020.0020.0000.0000.0000.000
50A50PHE0-0.025-0.01644.6740.0010.0010.0000.0000.0000.000
51A51LEU00.0100.00445.7610.0010.0010.0000.0000.0000.000
52A52ARG10.8100.91450.5020.0310.0310.0000.0000.0000.000
53A53GLY0-0.008-0.00653.6520.0000.0000.0000.0000.0000.000
54A54GLY0-0.0100.00252.0700.0010.0010.0000.0000.0000.000
55A55GLY0-0.031-0.02652.0170.0010.0010.0000.0000.0000.000
56A56LYS10.8000.89246.9510.0160.0160.0000.0000.0000.000
57A57GLY00.0460.02445.550-0.002-0.0020.0000.0000.0000.000
58A58TRP0-0.071-0.05541.479-0.001-0.0010.0000.0000.0000.000
59A59ILE00.0570.03336.7220.0020.0020.0000.0000.0000.000
60A60THR0-0.037-0.01538.413-0.004-0.0040.0000.0000.0000.000
61A61ALA00.0360.01934.0660.0030.0030.0000.0000.0000.000
62A62GLU-1-0.882-0.93336.184-0.072-0.0720.0000.0000.0000.000
63A63TYR0-0.025-0.03526.699-0.004-0.0040.0000.0000.0000.000
64A64SER0-0.065-0.05232.2040.0000.0000.0000.0000.0000.000
65A65MET0-0.039-0.02025.421-0.017-0.0170.0000.0000.0000.000
66A85GLY00.0430.01234.533-0.002-0.0020.0000.0000.0000.000
67A86ARG10.9460.93824.2770.2140.2140.0000.0000.0000.000
68A87THR00.0540.03530.253-0.005-0.0050.0000.0000.0000.000
69A88MET00.0740.03432.1590.0050.0050.0000.0000.0000.000
70A89GLU-1-0.862-0.89827.722-0.157-0.1570.0000.0000.0000.000
71A90ILE00.0340.02926.4070.0040.0040.0000.0000.0000.000
72A91GLN0-0.020-0.00330.1030.0030.0030.0000.0000.0000.000
73A92ARG10.8740.92233.5540.1020.1020.0000.0000.0000.000
74A93LEU0-0.0230.00426.2810.0060.0060.0000.0000.0000.000
75A94ILE00.0590.02329.4250.0080.0080.0000.0000.0000.000
76A95GLY0-0.014-0.00831.3380.0080.0080.0000.0000.0000.000
77A96ARG10.7520.85730.4590.0920.0920.0000.0000.0000.000
78A97ALA00.0260.01029.4120.0060.0060.0000.0000.0000.000
79A98LEU00.0440.01231.3120.0080.0080.0000.0000.0000.000
80A99ARG10.8260.90033.5920.0520.0520.0000.0000.0000.000
81A100ALA0-0.0200.00532.8380.0040.0040.0000.0000.0000.000
82A101VAL0-0.0080.01131.6130.0040.0040.0000.0000.0000.000
83A102VAL0-0.006-0.00334.9330.0040.0040.0000.0000.0000.000
84A103ASP-1-0.804-0.88938.268-0.008-0.0080.0000.0000.0000.000
85A104LEU00.008-0.01340.4140.0000.0000.0000.0000.0000.000
86A105GLU-1-0.880-0.92543.618-0.011-0.0110.0000.0000.0000.000
87A106LYS10.8230.89244.0280.0010.0010.0000.0000.0000.000
88A107LEU0-0.0060.01742.1790.0010.0010.0000.0000.0000.000
89A108GLY00.0400.02745.4440.0000.0000.0000.0000.0000.000
90A109GLU-1-0.849-0.92447.623-0.022-0.0220.0000.0000.0000.000
91A110ARG10.7870.89045.5680.0140.0140.0000.0000.0000.000
92A111THR0-0.009-0.01343.467-0.001-0.0010.0000.0000.0000.000
93A112ILE0-0.018-0.00538.8780.0010.0010.0000.0000.0000.000
94A113TRP0-0.073-0.04640.037-0.004-0.0040.0000.0000.0000.000
95A114ILE00.019-0.00433.2530.0030.0030.0000.0000.0000.000
96A115ASP-1-0.934-0.96235.545-0.066-0.0660.0000.0000.0000.000
97A116CYS0-0.027-0.01230.3540.0050.0050.0000.0000.0000.000
98A117ASP-1-0.757-0.83731.313-0.112-0.1120.0000.0000.0000.000
99A118VAL0-0.031-0.02825.0160.0030.0030.0000.0000.0000.000
100A119ILE00.0030.00726.609-0.010-0.0100.0000.0000.0000.000
101A120GLN0-0.073-0.04720.9910.0010.0010.0000.0000.0000.000
102A121ALA0-0.016-0.01222.2020.0080.0080.0000.0000.0000.000
103A122ASP-1-0.780-0.89415.628-0.413-0.4130.0000.0000.0000.000
104A123GLY00.1240.08616.709-0.021-0.0210.0000.0000.0000.000
105A124GLY00.0550.04417.7740.0470.0470.0000.0000.0000.000
106A125THR0-0.007-0.00118.6200.0390.0390.0000.0000.0000.000
107A126ARG10.8370.92422.1420.1980.1980.0000.0000.0000.000
108A127THR00.0310.01919.2280.0160.0160.0000.0000.0000.000
109A128ALA00.0720.04421.0970.0250.0250.0000.0000.0000.000
110A129SER00.017-0.02622.7130.0170.0170.0000.0000.0000.000
111A130ILE0-0.038-0.02025.1150.0110.0110.0000.0000.0000.000
112A131THR00.0230.01023.0440.0140.0140.0000.0000.0000.000
113A132GLY00.0410.01625.7320.0120.0120.0000.0000.0000.000
114A133ALA00.012-0.00827.7850.0060.0060.0000.0000.0000.000
115A134PHE0-0.010-0.00729.0710.0050.0050.0000.0000.0000.000
116A135LEU00.0200.02227.1640.0050.0050.0000.0000.0000.000
117A136ALA00.0510.03731.2580.0030.0030.0000.0000.0000.000
118A137MET0-0.026-0.00733.8950.0010.0010.0000.0000.0000.000
119A138ALA0-0.0050.00233.8040.0020.0020.0000.0000.0000.000
120A139ILE00.0180.02033.5030.0030.0030.0000.0000.0000.000
121A140ALA0-0.029-0.01237.1320.0010.0010.0000.0000.0000.000
122A141ILE00.013-0.01038.1390.0010.0010.0000.0000.0000.000
123A142GLY00.0170.01039.3900.0020.0020.0000.0000.0000.000
124A143LYS10.8220.90440.2910.0120.0120.0000.0000.0000.000
125A144LEU00.0020.00843.3120.0010.0010.0000.0000.0000.000
126A145ILE0-0.021-0.01141.7420.0010.0010.0000.0000.0000.000
127A146LYS10.9280.96241.363-0.011-0.0110.0000.0000.0000.000
128A147ALA0-0.0220.00346.6360.0010.0010.0000.0000.0000.000
129A148GLY0-0.025-0.01048.938-0.001-0.0010.0000.0000.0000.000
130A149THR0-0.046-0.02248.5090.0000.0000.0000.0000.0000.000
131A150ILE0-0.009-0.00143.953-0.001-0.0010.0000.0000.0000.000
132A151LYS10.9370.96348.2690.0010.0010.0000.0000.0000.000
133A152THR0-0.015-0.00745.7260.0020.0020.0000.0000.0000.000
134A153ASN00.0370.00538.778-0.004-0.0040.0000.0000.0000.000
135A154PRO0-0.0210.00640.5660.0010.0010.0000.0000.0000.000
136A155ILE00.0130.01834.911-0.002-0.0020.0000.0000.0000.000
137A156THR00.003-0.01335.5840.0030.0030.0000.0000.0000.000
138A157ASP-1-0.809-0.86031.3190.0290.0290.0000.0000.0000.000
139A158PHE0-0.002-0.00728.647-0.004-0.0040.0000.0000.0000.000
140A159LEU00.001-0.00127.704-0.001-0.0010.0000.0000.0000.000
141A160ALA00.0090.02423.268-0.001-0.0010.0000.0000.0000.000
142A161ALA0-0.024-0.01322.693-0.003-0.0030.0000.0000.0000.000
143A162ILE00.0060.00315.5690.0010.0010.0000.0000.0000.000
144A163SER00.0040.00216.5870.0090.0090.0000.0000.0000.000
145A164VAL00.0050.00113.4110.0300.0300.0000.0000.0000.000
146A165GLY00.0490.01712.4340.0080.0080.0000.0000.0000.000
147A166ILE0-0.050-0.02510.6040.0320.0320.0000.0000.0000.000
148A167ASP-1-0.709-0.8545.769-2.925-2.9250.0000.0000.0000.000
149A168LYS10.7570.8628.1200.7860.7860.0000.0000.0000.000
150A169GLU-1-0.999-1.0004.201-1.826-1.672-0.001-0.013-0.1410.000
151A170GLN0-0.066-0.0482.284-2.198-0.8531.200-0.585-1.959-0.002
152A171GLY0-0.0070.0153.9070.8411.0500.002-0.006-0.2050.000
153A172ILE0-0.053-0.0327.230-0.075-0.0750.0000.0000.0000.000
154A173LEU00.0200.0155.1530.1150.1150.0000.0000.0000.000
155A174LEU0-0.019-0.0188.9260.0270.0270.0000.0000.0000.000
156A175ASP-1-0.818-0.88210.464-0.059-0.0590.0000.0000.0000.000
157A176LEU00.0120.02510.9280.0040.0040.0000.0000.0000.000
158A177ASN00.007-0.00710.2350.0670.0670.0000.0000.0000.000
159A178TYR0-0.043-0.03113.574-0.043-0.0430.0000.0000.0000.000
160A179GLU-1-0.870-0.9229.552-1.735-1.7350.0000.0000.0000.000
161A180GLU-1-0.731-0.8177.830-1.129-1.1290.0000.0000.0000.000
162A181ASP-1-0.965-0.99411.065-0.384-0.3840.0000.0000.0000.000
163A182SER0-0.073-0.04614.5610.0500.0500.0000.0000.0000.000
164A183SER0-0.069-0.04610.975-0.039-0.0390.0000.0000.0000.000
165A184ALA0-0.0050.01311.451-0.062-0.0620.0000.0000.0000.000
166A185GLU-1-0.797-0.88111.751-0.557-0.5570.0000.0000.0000.000
167A186VAL0-0.060-0.04414.1060.1180.1180.0000.0000.0000.000
168A187ASP-1-0.803-0.88714.478-0.391-0.3910.0000.0000.0000.000
169A188MET0-0.028-0.02116.8040.0540.0540.0000.0000.0000.000
170A189ASN0-0.031-0.01218.1940.0340.0340.0000.0000.0000.000
171A190VAL0-0.013-0.00919.4530.0130.0130.0000.0000.0000.000
172A191ILE00.006-0.00821.9490.0050.0050.0000.0000.0000.000
173A192MET00.0020.00922.705-0.002-0.0020.0000.0000.0000.000
174A193THR0-0.007-0.02725.6640.0000.0000.0000.0000.0000.000
175A194GLY00.0320.01726.8880.0070.0070.0000.0000.0000.000
176A195SER0-0.154-0.09828.2060.0080.0080.0000.0000.0000.000
177A196GLY00.0730.03625.8840.0010.0010.0000.0000.0000.000
178A197ARG10.8570.94426.870-0.013-0.0130.0000.0000.0000.000
179A198PHE00.0450.00922.676-0.002-0.0020.0000.0000.0000.000
180A199VAL0-0.063-0.02527.4420.0020.0020.0000.0000.0000.000
181A200GLU-1-0.831-0.92027.083-0.095-0.0950.0000.0000.0000.000
182A201LEU0-0.038-0.01322.2910.0050.0050.0000.0000.0000.000
183A202GLN0-0.0080.00023.5800.0000.0000.0000.0000.0000.000
184A203GLY00.0010.00720.753-0.016-0.0160.0000.0000.0000.000
185A204THR0-0.045-0.03120.1620.0330.0330.0000.0000.0000.000
186A205GLY00.0090.00318.632-0.033-0.0330.0000.0000.0000.000
187A206GLU-1-0.937-0.95418.016-0.334-0.3340.0000.0000.0000.000
188A207GLU-1-0.981-0.98918.828-0.297-0.2970.0000.0000.0000.000
189A208ALA0-0.034-0.01016.4760.0060.0060.0000.0000.0000.000
190A209THR0-0.054-0.03618.4590.0230.0230.0000.0000.0000.000
191A210PHE00.0110.01917.195-0.002-0.0020.0000.0000.0000.000
192A211SER0-0.035-0.04817.2990.0440.0440.0000.0000.0000.000
193A212ARG10.8920.92119.6550.0280.0280.0000.0000.0000.000
194A213GLU-1-0.902-0.96517.822-0.025-0.0250.0000.0000.0000.000
195A214ASP-1-0.763-0.84314.225-0.202-0.2020.0000.0000.0000.000
196A215LEU0-0.0130.00516.1900.0030.0030.0000.0000.0000.000
197A216ASN0-0.015-0.01618.8880.0060.0060.0000.0000.0000.000
198A217GLY00.0140.01415.0010.0260.0260.0000.0000.0000.000
199A218LEU00.0070.00313.1560.0330.0330.0000.0000.0000.000
200A219LEU0-0.022-0.01815.6050.0150.0150.0000.0000.0000.000
201A220GLY00.0070.01817.2720.0130.0130.0000.0000.0000.000
202A221LEU00.019-0.0039.7860.0380.0380.0000.0000.0000.000
203A222ALA00.0040.00014.4530.0160.0160.0000.0000.0000.000
204A223GLU-1-0.857-0.93917.0850.0690.0690.0000.0000.0000.000
205A224LYS10.7620.87712.561-0.422-0.4220.0000.0000.0000.000
206A225GLY00.0650.02916.2490.0130.0130.0000.0000.0000.000
207A226ILE0-0.025-0.02016.814-0.006-0.0060.0000.0000.0000.000
208A227GLN0-0.045-0.03720.3850.0120.0120.0000.0000.0000.000
209A228GLU-1-0.856-0.90615.5370.2950.2950.0000.0000.0000.000
210A229LEU0-0.025-0.01519.229-0.009-0.0090.0000.0000.0000.000
211A230ILE0-0.035-0.02121.541-0.008-0.0080.0000.0000.0000.000
212A231ASP-1-0.843-0.91923.2390.0990.0990.0000.0000.0000.000
213A232LYS10.8750.92421.156-0.115-0.1150.0000.0000.0000.000
214A233GLN0-0.037-0.03924.622-0.006-0.0060.0000.0000.0000.000
215A234LYS10.7980.89727.098-0.078-0.0780.0000.0000.0000.000
216A235GLU-1-0.902-0.92624.8730.0950.0950.0000.0000.0000.000
217A236VAL0-0.0250.00227.184-0.003-0.0030.0000.0000.0000.000
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