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

tag_button

FMODB ID: 2JGJR

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2476857.028998
FMO2-HF: Nuclear repulsion 2393077.259339
FMO2-HF: Total energy -83779.769659
FMO2-MP2: Total energy -84022.745005


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.
-6.902-8.24912.457-3.901-7.21-0.023
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 : -0.057 / 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].
3A3HIS0-0.092-0.0573.6990.1391.523-0.005-0.557-0.8220.002
4A4ASP-1-0.836-0.8996.1420.0680.0680.0000.0000.0000.000
5A5GLY0-0.072-0.0244.2340.0170.137-0.001-0.010-0.1100.000
6A6ARG10.6780.8235.0830.9391.097-0.001-0.008-0.1490.000
7A7GLN00.0290.0154.2653.0793.3070.003-0.059-0.1720.000
8A8HIS00.0410.0064.781-0.708-0.589-0.001-0.009-0.1080.000
9A9ASP-1-0.918-0.9645.7240.4100.4100.0000.0000.0000.000
10A10GLU-1-0.879-0.9378.3261.0751.0750.0000.0000.0000.000
11A11LEU0-0.0230.00410.022-0.140-0.1400.0000.0000.0000.000
12A12ARG10.8160.90612.4610.4350.4350.0000.0000.0000.000
13A13PRO00.001-0.01413.3740.0160.0160.0000.0000.0000.000
14A14ILE00.0180.01416.434-0.044-0.0440.0000.0000.0000.000
15A15THR0-0.059-0.03219.6460.0240.0240.0000.0000.0000.000
16A16PHE0-0.010-0.02223.101-0.018-0.0180.0000.0000.0000.000
17A17ASP-1-0.835-0.92026.482-0.040-0.0400.0000.0000.0000.000
18A18LEU0-0.047-0.03028.916-0.007-0.0070.0000.0000.0000.000
19A19ASP-1-0.921-0.95331.962-0.026-0.0260.0000.0000.0000.000
20A20PHE0-0.032-0.01930.381-0.005-0.0050.0000.0000.0000.000
21A21ILE0-0.030-0.00932.958-0.005-0.0050.0000.0000.0000.000
22A22SER0-0.020-0.00836.7750.0040.0040.0000.0000.0000.000
23A23HIS0-0.0120.00239.9410.0060.0060.0000.0000.0000.000
24A24PRO0-0.020-0.02040.8950.0010.0010.0000.0000.0000.000
25A25GLU-1-0.899-0.96638.696-0.060-0.0600.0000.0000.0000.000
26A26GLY0-0.076-0.04137.7220.0030.0030.0000.0000.0000.000
27A27SER00.0150.00934.770-0.002-0.0020.0000.0000.0000.000
28A28VAL00.0180.01328.8450.0060.0060.0000.0000.0000.000
29A29LEU0-0.0180.01426.937-0.012-0.0120.0000.0000.0000.000
30A30ILE0-0.014-0.00422.5170.0120.0120.0000.0000.0000.000
31A31THR0-0.040-0.01620.054-0.023-0.0230.0000.0000.0000.000
32A32ALA00.0500.03117.5620.0330.0330.0000.0000.0000.000
33A33GLY00.0300.02115.606-0.052-0.0520.0000.0000.0000.000
34A34ASN0-0.057-0.03015.2710.0860.0860.0000.0000.0000.000
35A35THR0-0.004-0.00818.366-0.003-0.0030.0000.0000.0000.000
36A36LYS10.8680.91020.5220.1710.1710.0000.0000.0000.000
37A37VAL0-0.014-0.01223.886-0.013-0.0130.0000.0000.0000.000
38A38ILE00.0230.02226.7650.0130.0130.0000.0000.0000.000
39A39CYS0-0.056-0.04529.376-0.006-0.0060.0000.0000.0000.000
40A40ASN00.0370.01831.7770.0130.0130.0000.0000.0000.000
41A41ALA00.0080.01435.442-0.003-0.0030.0000.0000.0000.000
42A42SER0-0.038-0.01337.5850.0050.0050.0000.0000.0000.000
43A43VAL00.004-0.00341.324-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.763-0.84744.038-0.049-0.0490.0000.0000.0000.000
45A45ASP-1-0.849-0.92947.120-0.030-0.0300.0000.0000.0000.000
46A46ARG10.7730.85548.8240.0480.0480.0000.0000.0000.000
47A47VAL00.0730.03446.791-0.001-0.0010.0000.0000.0000.000
48A48PRO00.0080.01445.1650.0010.0010.0000.0000.0000.000
49A49PRO00.046-0.00848.4200.0020.0020.0000.0000.0000.000
50A50PHE0-0.039-0.01644.6800.0020.0020.0000.0000.0000.000
51A51LEU00.013-0.00145.8240.0010.0010.0000.0000.0000.000
52A52ARG10.8610.95450.5580.0430.0430.0000.0000.0000.000
53A53GLY0-0.029-0.01753.4300.0010.0010.0000.0000.0000.000
54A54GLY0-0.049-0.02751.9940.0020.0020.0000.0000.0000.000
55A55GLY0-0.008-0.00552.0810.0020.0020.0000.0000.0000.000
56A56LYS10.8230.91146.8870.0240.0240.0000.0000.0000.000
57A57GLY00.0420.02545.259-0.002-0.0020.0000.0000.0000.000
58A58TRP0-0.059-0.05040.8770.0000.0000.0000.0000.0000.000
59A59ILE00.0530.03736.6590.0010.0010.0000.0000.0000.000
60A60THR0-0.081-0.04438.168-0.004-0.0040.0000.0000.0000.000
61A61ALA0-0.001-0.01134.3900.0030.0030.0000.0000.0000.000
62A62GLU-1-0.920-0.93836.175-0.094-0.0940.0000.0000.0000.000
63A63TYR0-0.020-0.03626.039-0.006-0.0060.0000.0000.0000.000
64A64SER0-0.024-0.02832.244-0.002-0.0020.0000.0000.0000.000
65A65MET0-0.0120.00325.172-0.017-0.0170.0000.0000.0000.000
66A85GLY00.0420.01633.667-0.002-0.0020.0000.0000.0000.000
67A86ARG11.0220.99223.5400.2770.2770.0000.0000.0000.000
68A87THR00.0560.03930.117-0.006-0.0060.0000.0000.0000.000
69A88MET0-0.005-0.00231.6670.0060.0060.0000.0000.0000.000
70A89GLU-1-0.948-0.97428.015-0.179-0.1790.0000.0000.0000.000
71A90ILE00.0310.01626.3870.0050.0050.0000.0000.0000.000
72A91GLN00.0660.04929.7210.0060.0060.0000.0000.0000.000
73A92ARG10.8840.92733.0470.1270.1270.0000.0000.0000.000
74A93LEU0-0.030-0.00226.2310.0090.0090.0000.0000.0000.000
75A94ILE00.0550.02929.2260.0090.0090.0000.0000.0000.000
76A95GLY0-0.007-0.00331.3720.0090.0090.0000.0000.0000.000
77A96ARG10.7770.86130.2710.1140.1140.0000.0000.0000.000
78A97ALA00.0390.01429.5980.0080.0080.0000.0000.0000.000
79A98LEU00.0330.01231.5260.0090.0090.0000.0000.0000.000
80A99ARG10.8660.93533.6280.0710.0710.0000.0000.0000.000
81A100ALA0-0.0250.00932.9330.0050.0050.0000.0000.0000.000
82A101VAL0-0.0140.00431.6980.0050.0050.0000.0000.0000.000
83A102VAL0-0.004-0.00534.9740.0040.0040.0000.0000.0000.000
84A103ASP-1-0.833-0.92438.311-0.019-0.0190.0000.0000.0000.000
85A104LEU0-0.001-0.02940.8280.0000.0000.0000.0000.0000.000
86A105GLU-1-0.907-0.93843.464-0.018-0.0180.0000.0000.0000.000
87A106LYS10.8540.93743.9560.0080.0080.0000.0000.0000.000
88A107LEU0-0.0180.01442.1090.0010.0010.0000.0000.0000.000
89A108GLY00.0100.01345.3050.0000.0000.0000.0000.0000.000
90A109GLU-1-0.839-0.92047.522-0.032-0.0320.0000.0000.0000.000
91A110ARG10.8260.91845.8850.0270.0270.0000.0000.0000.000
92A111THR0-0.037-0.02543.523-0.002-0.0020.0000.0000.0000.000
93A112ILE0-0.015-0.01138.3800.0010.0010.0000.0000.0000.000
94A113TRP0-0.048-0.03339.795-0.003-0.0030.0000.0000.0000.000
95A114ILE0-0.002-0.01633.0740.0020.0020.0000.0000.0000.000
96A115ASP-1-0.878-0.94035.357-0.103-0.1030.0000.0000.0000.000
97A116CYS0-0.0220.01729.8280.0020.0020.0000.0000.0000.000
98A117ASP-1-0.753-0.84731.107-0.125-0.1250.0000.0000.0000.000
99A118VAL0-0.065-0.04825.052-0.003-0.0030.0000.0000.0000.000
100A119ILE0-0.017-0.00826.537-0.004-0.0040.0000.0000.0000.000
101A120GLN0-0.082-0.05421.0410.0030.0030.0000.0000.0000.000
102A121ALA0-0.028-0.02221.8590.0070.0070.0000.0000.0000.000
103A122ASP-1-0.791-0.90915.640-0.630-0.6300.0000.0000.0000.000
104A123GLY00.1180.07816.075-0.045-0.0450.0000.0000.0000.000
105A124GLY00.0870.04717.1630.0510.0510.0000.0000.0000.000
106A125THR00.0110.00618.5780.0470.0470.0000.0000.0000.000
107A126ARG10.9320.97222.1390.2650.2650.0000.0000.0000.000
108A127THR00.0320.01619.2770.0190.0190.0000.0000.0000.000
109A128ALA00.0680.03421.0120.0300.0300.0000.0000.0000.000
110A129SER00.010-0.01722.6830.0220.0220.0000.0000.0000.000
111A130ILE0-0.0200.00325.3230.0160.0160.0000.0000.0000.000
112A131THR00.0280.01423.0940.0180.0180.0000.0000.0000.000
113A132GLY00.0300.00925.7730.0130.0130.0000.0000.0000.000
114A133ALA00.015-0.01127.7280.0090.0090.0000.0000.0000.000
115A134PHE0-0.030-0.01029.0450.0080.0080.0000.0000.0000.000
116A135LEU00.0430.02827.9050.0070.0070.0000.0000.0000.000
117A136ALA00.0570.04431.3050.0060.0060.0000.0000.0000.000
118A137MET0-0.011-0.00233.7660.0030.0030.0000.0000.0000.000
119A138ALA0-0.020-0.01033.7720.0050.0050.0000.0000.0000.000
120A139ILE00.0090.00433.7660.0050.0050.0000.0000.0000.000
121A140ALA0-0.044-0.02237.0920.0030.0030.0000.0000.0000.000
122A141ILE00.023-0.00638.2120.0030.0030.0000.0000.0000.000
123A142GLY00.0170.01639.5980.0030.0030.0000.0000.0000.000
124A143LYS10.9130.94940.5270.0350.0350.0000.0000.0000.000
125A144LEU00.0310.02343.4240.0010.0010.0000.0000.0000.000
126A145ILE0-0.028-0.01342.0700.0020.0020.0000.0000.0000.000
127A146LYS10.9090.95142.1380.0070.0070.0000.0000.0000.000
128A147ALA0-0.0240.00746.8320.0010.0010.0000.0000.0000.000
129A148GLY0-0.020-0.00148.9690.0000.0000.0000.0000.0000.000
130A149THR0-0.047-0.01848.3960.0000.0000.0000.0000.0000.000
131A150ILE0-0.021-0.00544.179-0.001-0.0010.0000.0000.0000.000
132A151LYS10.9540.96648.3820.0090.0090.0000.0000.0000.000
133A152THR0-0.018-0.01345.7290.0020.0020.0000.0000.0000.000
134A153ASN00.0530.01738.325-0.005-0.0050.0000.0000.0000.000
135A154PRO0-0.001-0.00140.7440.0020.0020.0000.0000.0000.000
136A155ILE0-0.0170.01534.908-0.002-0.0020.0000.0000.0000.000
137A156THR0-0.054-0.03836.3070.0040.0040.0000.0000.0000.000
138A157ASP-1-0.791-0.89531.5880.0110.0110.0000.0000.0000.000
139A158PHE0-0.016-0.01328.711-0.004-0.0040.0000.0000.0000.000
140A159LEU00.0050.00227.6390.0000.0000.0000.0000.0000.000
141A160ALA00.0020.01322.960-0.001-0.0010.0000.0000.0000.000
142A161ALA0-0.023-0.01222.5760.0010.0010.0000.0000.0000.000
143A162ILE00.0010.00815.456-0.001-0.0010.0000.0000.0000.000
144A163SER00.0110.00415.7920.0180.0180.0000.0000.0000.000
145A164VAL0-0.011-0.01213.4500.0150.0150.0000.0000.0000.000
146A165GLY00.0590.01512.2070.0120.0120.0000.0000.0000.000
147A166ILE0-0.027-0.01710.4240.0210.0210.0000.0000.0000.000
148A167ASP-1-0.737-0.8825.908-2.846-2.8460.0000.0000.0000.000
149A168LYS10.9110.9608.6720.7320.7320.0000.0000.0000.000
150A169GLU-1-1.009-1.0044.249-1.818-1.690-0.001-0.010-0.1170.000
151A170GLN0-0.029-0.0171.927-2.397-6.07312.464-3.226-5.562-0.025
152A171GLY0-0.0060.0164.2390.1720.364-0.001-0.022-0.1700.000
153A172ILE0-0.036-0.0097.158-0.231-0.2310.0000.0000.0000.000
154A173LEU00.0210.0094.9930.0250.0250.0000.0000.0000.000
155A174LEU0-0.015-0.0168.8360.1040.1040.0000.0000.0000.000
156A175ASP-1-0.834-0.91910.592-0.249-0.2490.0000.0000.0000.000
157A176LEU00.0150.02110.082-0.026-0.0260.0000.0000.0000.000
158A177ASN0-0.0060.0039.9630.1010.1010.0000.0000.0000.000
159A178TYR0-0.053-0.03213.382-0.038-0.0380.0000.0000.0000.000
160A179GLU-1-0.892-0.9658.840-2.217-2.2170.0000.0000.0000.000
161A180GLU-1-0.730-0.8367.424-1.758-1.7580.0000.0000.0000.000
162A181ASP-1-0.996-1.00310.476-0.523-0.5230.0000.0000.0000.000
163A182SER0-0.077-0.04013.7840.0730.0730.0000.0000.0000.000
164A183SER0-0.065-0.02210.0450.0400.0400.0000.0000.0000.000
165A184ALA00.0180.03711.274-0.086-0.0860.0000.0000.0000.000
166A185GLU-1-0.935-0.98112.081-0.402-0.4020.0000.0000.0000.000
167A186VAL0-0.082-0.04213.8530.1230.1230.0000.0000.0000.000
168A187ASP-1-0.799-0.87514.307-0.591-0.5910.0000.0000.0000.000
169A188MET0-0.033-0.02516.6650.0890.0890.0000.0000.0000.000
170A189ASN0-0.056-0.00717.840-0.022-0.0220.0000.0000.0000.000
171A190VAL00.010-0.00319.6400.0210.0210.0000.0000.0000.000
172A191ILE0-0.001-0.00821.9940.0010.0010.0000.0000.0000.000
173A192MET00.0120.00522.9790.0010.0010.0000.0000.0000.000
174A193THR0-0.010-0.01125.823-0.003-0.0030.0000.0000.0000.000
175A194GLY00.0480.01226.9850.0060.0060.0000.0000.0000.000
176A195SER0-0.158-0.07628.0330.0090.0090.0000.0000.0000.000
177A196GLY00.0660.03226.1460.0060.0060.0000.0000.0000.000
178A197ARG10.8910.96127.1170.0020.0020.0000.0000.0000.000
179A198PHE00.0390.01223.149-0.004-0.0040.0000.0000.0000.000
180A199VAL0-0.074-0.02127.6700.0030.0030.0000.0000.0000.000
181A200GLU-1-0.879-0.96127.066-0.125-0.1250.0000.0000.0000.000
182A201LEU00.0010.01622.1660.0010.0010.0000.0000.0000.000
183A202GLN0-0.012-0.00723.100-0.005-0.0050.0000.0000.0000.000
184A203GLY00.0330.01820.370-0.021-0.0210.0000.0000.0000.000
185A204THR0-0.077-0.04319.8850.0410.0410.0000.0000.0000.000
186A205GLY0-0.0080.00518.764-0.039-0.0390.0000.0000.0000.000
187A206GLU-1-0.906-0.96517.474-0.362-0.3620.0000.0000.0000.000
188A207GLU-1-1.008-0.98218.876-0.270-0.2700.0000.0000.0000.000
189A208ALA0-0.012-0.00716.8530.0130.0130.0000.0000.0000.000
190A209THR0-0.088-0.05518.6650.0310.0310.0000.0000.0000.000
191A210PHE00.0260.01817.075-0.005-0.0050.0000.0000.0000.000
192A211SER0-0.023-0.01017.6400.0280.0280.0000.0000.0000.000
193A212ARG10.9690.95919.543-0.003-0.0030.0000.0000.0000.000
194A213GLU-1-0.931-0.97017.4080.0360.0360.0000.0000.0000.000
195A214ASP-1-0.779-0.87514.935-0.071-0.0710.0000.0000.0000.000
196A215LEU0-0.024-0.00916.092-0.013-0.0130.0000.0000.0000.000
197A216ASN0-0.039-0.03318.671-0.015-0.0150.0000.0000.0000.000
198A217GLY00.0070.01014.5750.0180.0180.0000.0000.0000.000
199A218LEU0-0.001-0.00113.2030.0110.0110.0000.0000.0000.000
200A219LEU0-0.027-0.02715.463-0.003-0.0030.0000.0000.0000.000
201A220GLY00.0210.02517.2370.0090.0090.0000.0000.0000.000
202A221LEU00.0130.00510.1570.0340.0340.0000.0000.0000.000
203A222ALA00.0130.00014.5800.0100.0100.0000.0000.0000.000
204A223GLU-1-0.945-0.97317.0460.0520.0520.0000.0000.0000.000
205A224LYS10.8340.91912.734-0.309-0.3090.0000.0000.0000.000
206A225GLY00.0370.01116.2480.0130.0130.0000.0000.0000.000
207A226ILE0-0.008-0.02216.790-0.006-0.0060.0000.0000.0000.000
208A227GLN0-0.026-0.01420.3110.0120.0120.0000.0000.0000.000
209A228GLU-1-0.852-0.90816.1650.2080.2080.0000.0000.0000.000
210A229LEU0-0.049-0.02419.298-0.007-0.0070.0000.0000.0000.000
211A230ILE0-0.015-0.00821.717-0.004-0.0040.0000.0000.0000.000
212A231ASP-1-0.928-0.95422.9830.0830.0830.0000.0000.0000.000
213A232LYS10.9630.96919.743-0.067-0.0670.0000.0000.0000.000
214A233GLN0-0.046-0.02724.848-0.001-0.0010.0000.0000.0000.000
215A234LYS10.8740.93927.579-0.045-0.0450.0000.0000.0000.000
216A235GLU-1-0.989-0.98525.8490.0630.0630.0000.0000.0000.000
217A236VAL0-0.0420.00027.560-0.003-0.0030.0000.0000.0000.000
218A237LEU0-0.094-0.04530.227-0.004-0.0040.0000.0000.0000.000