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: LJ199

Calculation Name: 1OY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OY5

Chain ID: A

ChEMBL ID:

UniProt ID: O67463

Base Structure: X-ray

Registration Date: 2023-06-20

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2389983.138287
FMO2-HF: Nuclear repulsion 2303124.802234
FMO2-HF: Total energy -86858.336053
FMO2-MP2: Total energy -87114.490723


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:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
-5.957-5.6520.0610.494-0.8610
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.055
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].
3A6LEU00.0280.0043.3241.1170.9030.0590.594-0.4400.000
4A7ARG10.8610.8994.2144.2984.442-0.001-0.011-0.1310.000
5A8PHE00.005-0.0149.0950.3300.3300.0000.0000.0000.000
6A9PHE00.0100.00910.830-0.070-0.0700.0000.0000.0000.000
7A10VAL0-0.002-0.00815.4300.0850.0850.0000.0000.0000.000
8A11LEU00.0300.02418.7560.0150.0150.0000.0000.0000.000
9A12THR00.023-0.02721.8600.0380.0380.0000.0000.0000.000
10A13ILE00.0540.04124.571-0.013-0.0130.0000.0000.0000.000
11A14PHE0-0.046-0.02726.1950.0200.0200.0000.0000.0000.000
12A15PRO00.0470.02421.995-0.021-0.0210.0000.0000.0000.000
13A16HIS00.038-0.00222.197-0.039-0.0390.0000.0000.0000.000
14A17ILE00.0000.02523.739-0.003-0.0030.0000.0000.0000.000
15A18ILE00.0300.00818.200-0.009-0.0090.0000.0000.0000.000
16A19SER00.0130.00918.810-0.034-0.0340.0000.0000.0000.000
17A20CYS0-0.016-0.01919.863-0.003-0.0030.0000.0000.0000.000
18A21TYR0-0.057-0.04418.7950.0330.0330.0000.0000.0000.000
19A22SER0-0.019-0.02815.634-0.030-0.0300.0000.0000.0000.000
20A23GLU-1-0.894-0.91816.485-0.573-0.5730.0000.0000.0000.000
21A24TYR0-0.081-0.05318.8130.0620.0620.0000.0000.0000.000
22A25GLY00.0350.01618.461-0.031-0.0310.0000.0000.0000.000
23A26ILE00.010-0.01514.761-0.027-0.0270.0000.0000.0000.000
24A27VAL00.0960.06413.969-0.052-0.0520.0000.0000.0000.000
25A28LYS10.9350.98013.0850.3690.3690.0000.0000.0000.000
26A29GLN0-0.068-0.03213.275-0.107-0.1070.0000.0000.0000.000
27A30ALA00.020-0.0019.898-0.027-0.0270.0000.0000.0000.000
28A31ILE00.0270.0298.567-0.258-0.2580.0000.0000.0000.000
29A32LYS10.8750.9368.8220.6200.6200.0000.0000.0000.000
30A33LYS10.7690.8748.746-0.045-0.0450.0000.0000.0000.000
31A34GLY00.0140.0224.8260.2680.2680.0000.0000.0000.000
32A35LYS10.8510.9243.822-3.787-3.4120.003-0.089-0.2900.000
33A36VAL00.017-0.0015.608-0.206-0.2060.0000.0000.0000.000
34A37GLU-1-0.795-0.8415.421-4.689-4.6890.0000.0000.0000.000
35A38VAL00.003-0.0019.2740.1100.1100.0000.0000.0000.000
36A39TYR0-0.027-0.0278.5560.1880.1880.0000.0000.0000.000
37A40PRO0-0.029-0.00914.4810.0690.0690.0000.0000.0000.000
38A41ILE0-0.002-0.00716.344-0.014-0.0140.0000.0000.0000.000
39A42ASP-1-0.750-0.86320.016-0.364-0.3640.0000.0000.0000.000
40A43LEU00.018-0.01123.6070.0100.0100.0000.0000.0000.000
41A44ARG10.8500.88625.9280.3690.3690.0000.0000.0000.000
42A45GLU-1-0.981-0.96624.397-0.366-0.3660.0000.0000.0000.000
43A46PHE0-0.016-0.02120.864-0.009-0.0090.0000.0000.0000.000
44A47ALA0-0.0030.00626.5650.0130.0130.0000.0000.0000.000
45A48PRO00.0400.01329.9490.0140.0140.0000.0000.0000.000
46A49LYS10.8230.91532.0220.2000.2000.0000.0000.0000.000
47A50GLY00.015-0.00233.0570.0100.0100.0000.0000.0000.000
48A51GLN0-0.0390.00334.098-0.004-0.0040.0000.0000.0000.000
49A52VAL00.0180.00329.861-0.006-0.0060.0000.0000.0000.000
50A53ASP-1-0.875-0.93132.510-0.236-0.2360.0000.0000.0000.000
51A54ASP-1-0.828-0.92335.146-0.167-0.1670.0000.0000.0000.000
52A55VAL0-0.029-0.01438.641-0.002-0.0020.0000.0000.0000.000
53A56PRO0-0.0160.01940.024-0.001-0.0010.0000.0000.0000.000
54A57TYR00.000-0.01340.7880.0060.0060.0000.0000.0000.000
55A58GLY0-0.017-0.02244.112-0.001-0.0010.0000.0000.0000.000
56A59GLY0-0.028-0.00946.6600.0030.0030.0000.0000.0000.000
57A60LEU00.0220.01043.1280.0030.0030.0000.0000.0000.000
58A61PRO0-0.041-0.02644.650-0.001-0.0010.0000.0000.0000.000
59A62GLY00.0060.00941.523-0.002-0.0020.0000.0000.0000.000
60A63MET0-0.075-0.03236.9630.0020.0020.0000.0000.0000.000
61A64VAL00.0130.01635.101-0.004-0.0040.0000.0000.0000.000
62A65LEU0-0.010-0.01429.124-0.003-0.0030.0000.0000.0000.000
63A66LYS10.8020.88632.9080.2210.2210.0000.0000.0000.000
64A67PRO00.005-0.01030.635-0.018-0.0180.0000.0000.0000.000
65A68GLU-1-0.785-0.88729.348-0.238-0.2380.0000.0000.0000.000
66A69PRO00.0620.04028.068-0.014-0.0140.0000.0000.0000.000
67A70ILE0-0.0070.00024.822-0.035-0.0350.0000.0000.0000.000
68A71TYR0-0.055-0.04524.414-0.030-0.0300.0000.0000.0000.000
69A72GLU-1-0.880-0.93524.565-0.327-0.3270.0000.0000.0000.000
70A73ALA0-0.014-0.00721.681-0.034-0.0340.0000.0000.0000.000
71A74TYR0-0.032-0.03620.244-0.084-0.0840.0000.0000.0000.000
72A75ASP-1-0.875-0.94019.764-0.417-0.4170.0000.0000.0000.000
73A76TYR00.0480.02816.804-0.055-0.0550.0000.0000.0000.000
74A77VAL0-0.029-0.01914.550-0.060-0.0600.0000.0000.0000.000
75A78VAL0-0.036-0.03115.319-0.099-0.0990.0000.0000.0000.000
76A79GLU-1-0.989-0.98216.288-0.424-0.4240.0000.0000.0000.000
77A80ASN0-0.098-0.05814.8510.0100.0100.0000.0000.0000.000
78A81TYR0-0.066-0.03010.136-0.190-0.1900.0000.0000.0000.000
79A82GLY00.0050.01911.021-0.168-0.1680.0000.0000.0000.000
80A83LYS10.8600.93513.2950.4470.4470.0000.0000.0000.000
81A84PRO00.0230.02014.559-0.086-0.0860.0000.0000.0000.000
82A85PHE0-0.011-0.01815.3780.1270.1270.0000.0000.0000.000
83A86VAL0-0.004-0.01417.283-0.067-0.0670.0000.0000.0000.000
84A87LEU0-0.025-0.01219.4450.0560.0560.0000.0000.0000.000
85A88ILE00.0200.02721.399-0.033-0.0330.0000.0000.0000.000
86A89THR0-0.029-0.01223.4400.0100.0100.0000.0000.0000.000
87A90GLU-1-0.794-0.91626.091-0.229-0.2290.0000.0000.0000.000
88A91PRO0-0.049-0.01029.7860.0000.0000.0000.0000.0000.000
89A92TRP0-0.015-0.00431.9590.0080.0080.0000.0000.0000.000
90A93GLY00.0770.04629.9170.0150.0150.0000.0000.0000.000
91A94GLU-1-0.920-0.98127.807-0.237-0.2370.0000.0000.0000.000
92A95LYS10.8090.90728.3860.1520.1520.0000.0000.0000.000
93A96LEU00.0290.03221.7410.0030.0030.0000.0000.0000.000
94A97ASN00.034-0.02024.0980.0200.0200.0000.0000.0000.000
95A98GLN00.017-0.00320.179-0.044-0.0440.0000.0000.0000.000
96A99LYS10.8700.94421.1760.1400.1400.0000.0000.0000.000
97A100LEU00.0810.03720.4230.0010.0010.0000.0000.0000.000
98A101VAL00.0100.02517.478-0.035-0.0350.0000.0000.0000.000
99A102ASN0-0.007-0.02416.432-0.013-0.0130.0000.0000.0000.000
100A103GLU-1-0.837-0.89115.365-0.196-0.1960.0000.0000.0000.000
101A104LEU0-0.050-0.03815.098-0.043-0.0430.0000.0000.0000.000
102A105SER0-0.018-0.01612.220-0.117-0.1170.0000.0000.0000.000
103A106LYS10.8800.94010.612-0.064-0.0640.0000.0000.0000.000
104A107LYS10.8660.95510.7600.4830.4830.0000.0000.0000.000
105A108GLU-1-0.825-0.8956.922-1.655-1.6550.0000.0000.0000.000
106A109ARG10.8340.8938.7920.9340.9340.0000.0000.0000.000
107A110ILE0-0.0320.00311.5650.2620.2620.0000.0000.0000.000
108A111MET00.0320.03814.524-0.075-0.0750.0000.0000.0000.000
109A112ILE0-0.036-0.03317.2450.0640.0640.0000.0000.0000.000
110A113ILE00.0210.00420.062-0.013-0.0130.0000.0000.0000.000
111A114CYS0-0.061-0.02222.7440.0200.0200.0000.0000.0000.000
112A115GLY00.0480.01825.3470.0130.0130.0000.0000.0000.000
113A116ARG10.8640.90329.0160.2750.2750.0000.0000.0000.000
114A117TYR0-0.054-0.03631.9900.0020.0020.0000.0000.0000.000
115A118GLU-1-0.806-0.90335.760-0.174-0.1740.0000.0000.0000.000
116A119GLY00.0030.00733.4070.0050.0050.0000.0000.0000.000
117A120VAL0-0.044-0.01829.007-0.007-0.0070.0000.0000.0000.000
118A121ASP-1-0.734-0.82032.280-0.185-0.1850.0000.0000.0000.000
119A122GLU-1-0.731-0.90632.300-0.211-0.2110.0000.0000.0000.000
120A123ARG10.8010.87132.4390.1790.1790.0000.0000.0000.000
121A124VAL00.0280.02726.951-0.006-0.0060.0000.0000.0000.000
122A125LYS10.7920.89227.7100.2040.2040.0000.0000.0000.000
123A126LYS10.7660.90028.4110.2070.2070.0000.0000.0000.000
124A127ILE00.0130.02223.6330.0030.0030.0000.0000.0000.000
125A128VAL0-0.049-0.01523.392-0.042-0.0420.0000.0000.0000.000
126A129ASP-1-0.871-0.93020.399-0.399-0.3990.0000.0000.0000.000
127A130MET0-0.071-0.03921.5250.0240.0240.0000.0000.0000.000
128A131GLU-1-0.793-0.91324.139-0.263-0.2630.0000.0000.0000.000
129A132ILE0-0.090-0.03922.8180.0150.0150.0000.0000.0000.000
130A133SER0-0.008-0.00126.6980.0080.0080.0000.0000.0000.000
131A134LEU00.0530.01430.279-0.004-0.0040.0000.0000.0000.000
132A135GLY0-0.009-0.01732.2590.0050.0050.0000.0000.0000.000
133A136ASP-1-0.877-0.90633.073-0.123-0.1230.0000.0000.0000.000
134A137PHE0-0.044-0.02730.9000.0060.0060.0000.0000.0000.000
135A138ILE00.0170.01534.858-0.006-0.0060.0000.0000.0000.000
136A139LEU0-0.0170.00629.5320.0010.0010.0000.0000.0000.000
137A140SER0-0.012-0.01933.306-0.002-0.0020.0000.0000.0000.000
138A141GLY0-0.005-0.02130.221-0.001-0.0010.0000.0000.0000.000
139A142GLY00.0130.02426.7370.0070.0070.0000.0000.0000.000
140A143GLU-1-0.751-0.86024.290-0.379-0.3790.0000.0000.0000.000
141A144ILE00.014-0.00323.622-0.031-0.0310.0000.0000.0000.000
142A145VAL00.0160.01924.133-0.005-0.0050.0000.0000.0000.000
143A146ALA00.0310.01720.456-0.021-0.0210.0000.0000.0000.000
144A147LEU0-0.0110.00119.443-0.054-0.0540.0000.0000.0000.000
145A148ALA0-0.0040.01419.436-0.019-0.0190.0000.0000.0000.000
146A149VAL0-0.002-0.00117.2890.0030.0030.0000.0000.0000.000
147A150ILE00.0060.00114.254-0.025-0.0250.0000.0000.0000.000
148A151ASP-1-0.904-0.91815.084-0.423-0.4230.0000.0000.0000.000
149A152ALA0-0.008-0.02016.7820.0320.0320.0000.0000.0000.000
150A153VAL0-0.011-0.01312.3840.0630.0630.0000.0000.0000.000
151A154SER0-0.011-0.02211.875-0.020-0.0200.0000.0000.0000.000
152A155ARG10.9180.95112.5920.2460.2460.0000.0000.0000.000
153A156VAL0-0.064-0.02414.3760.0920.0920.0000.0000.0000.000
154A157LEU00.0230.0348.1400.1020.1020.0000.0000.0000.000
155A158PRO00.0120.0088.7700.0230.0230.0000.0000.0000.000
156A159GLY00.008-0.0078.9720.2100.2100.0000.0000.0000.000
157A160VAL0-0.0120.00610.003-0.146-0.1460.0000.0000.0000.000
158A161LEU00.0410.02712.170-0.044-0.0440.0000.0000.0000.000
159A162SER0-0.029-0.02015.8380.0770.0770.0000.0000.0000.000
160A163GLH0-0.042-0.03417.080-0.012-0.0120.0000.0000.0000.000
161A164PRO00.0400.04718.2360.0160.0160.0000.0000.0000.000
162A179TYR0-0.020-0.02233.528-0.004-0.0040.0000.0000.0000.000
163A180PRO0-0.012-0.00335.546-0.002-0.0020.0000.0000.0000.000
164A181VAL00.0190.02232.7060.0060.0060.0000.0000.0000.000
165A182TYR00.0420.01035.986-0.005-0.0050.0000.0000.0000.000
166A183THR00.002-0.01733.7050.0060.0060.0000.0000.0000.000
167A184ARG10.9470.97035.744-0.002-0.0020.0000.0000.0000.000
168A185PRO00.0320.01238.0220.0040.0040.0000.0000.0000.000
169A186ARG10.9120.97041.0440.0090.0090.0000.0000.0000.000
170A187GLU-1-0.853-0.93043.355-0.017-0.0170.0000.0000.0000.000
171A188TYR00.015-0.00443.233-0.003-0.0030.0000.0000.0000.000
172A189ARG10.9440.98045.0390.0560.0560.0000.0000.0000.000
173A190GLY00.0540.02848.3820.0000.0000.0000.0000.0000.000
174A191MET0-0.036-0.01244.8530.0020.0020.0000.0000.0000.000
175A192LYS10.8860.94246.2380.0120.0120.0000.0000.0000.000
176A193VAL0-0.042-0.02041.126-0.001-0.0010.0000.0000.0000.000
177A194PRO00.0400.01642.7400.0020.0020.0000.0000.0000.000
178A195GLU-1-0.788-0.88944.145-0.003-0.0030.0000.0000.0000.000
179A196GLU-1-0.907-0.92845.3660.0030.0030.0000.0000.0000.000
180A197LEU0-0.103-0.07239.3280.0050.0050.0000.0000.0000.000
181A198LEU0-0.051-0.05440.9920.0010.0010.0000.0000.0000.000
182A199SER0-0.0070.01042.4790.0020.0020.0000.0000.0000.000
183A200GLY00.012-0.05642.830-0.002-0.0020.0000.0000.0000.000
184A201HIS00.0410.03440.7640.0040.0040.0000.0000.0000.000
185A202HIS0-0.024-0.02343.810-0.001-0.0010.0000.0000.0000.000
186A203LYS10.9661.00143.527-0.022-0.0220.0000.0000.0000.000
187A204LEU0-0.0090.03339.233-0.002-0.0020.0000.0000.0000.000
188A205ILE00.0240.02340.6780.0020.0020.0000.0000.0000.000
189A206GLU-1-0.864-0.95143.0680.0160.0160.0000.0000.0000.000
190A207LEU00.0030.02338.467-0.005-0.0050.0000.0000.0000.000
191A208TRP00.042-0.00534.556-0.005-0.0050.0000.0000.0000.000
192A209LYN0-0.0140.02640.419-0.003-0.0030.0000.0000.0000.000
193A210LEU00.0680.04340.493-0.003-0.0030.0000.0000.0000.000
194A211TRP00.0130.00432.601-0.002-0.0020.0000.0000.0000.000
195A212HIS10.8190.89636.849-0.023-0.0230.0000.0000.0000.000
196A213ARG10.8750.91540.938-0.014-0.0140.0000.0000.0000.000
197A214ILE00.0280.00841.463-0.003-0.0030.0000.0000.0000.000
198A215GLU-1-0.809-0.87435.148-0.002-0.0020.0000.0000.0000.000
199A216ASN00.009-0.01638.600-0.004-0.0040.0000.0000.0000.000
200A217THR0-0.042-0.01441.186-0.005-0.0050.0000.0000.0000.000
201A218VAL00.0210.00137.939-0.002-0.0020.0000.0000.0000.000
202A219LYS10.8390.92834.3610.0150.0150.0000.0000.0000.000
203A220LYS10.9160.95938.9960.0270.0270.0000.0000.0000.000
204A221ARG10.9330.96741.4860.0370.0370.0000.0000.0000.000
205A222PRO00.0020.01238.4230.0000.0000.0000.0000.0000.000
206A223ASP-1-0.826-0.91239.939-0.085-0.0850.0000.0000.0000.000
207A224LEU0-0.073-0.06642.5830.0040.0040.0000.0000.0000.000
208A225ILE0-0.0110.00046.3220.0020.0020.0000.0000.0000.000
209A226PRO0-0.039-0.03646.5790.0010.0010.0000.0000.0000.000
210A227LYS10.8600.94142.0390.0670.0670.0000.0000.0000.000
211A228ASP-1-0.802-0.90945.660-0.059-0.0590.0000.0000.0000.000
212A229LEU00.0510.03547.9690.0020.0020.0000.0000.0000.000
213A230THR0-0.058-0.03549.3360.0020.0020.0000.0000.0000.000
214A231GLU-1-0.887-0.94444.049-0.068-0.0680.0000.0000.0000.000
215A232LEU0-0.0090.00445.1850.0010.0010.0000.0000.0000.000
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