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: 3Q68L

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2390655.349659
FMO2-HF: Nuclear repulsion 2303800.024827
FMO2-HF: Total energy -86855.324833
FMO2-MP2: Total energy -87111.704459


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.
-5.219-4.7880.0540.45-0.9350
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 : -0.052 / q_NPA : -0.041
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].
3A6LEU00.0210.0043.3600.9690.8860.0520.543-0.5120.000
4A7ARG10.9180.9564.2473.9844.128-0.001-0.009-0.1340.000
5A8PHE00.010-0.0079.2410.2950.2950.0000.0000.0000.000
6A9PHE00.0020.00410.950-0.067-0.0670.0000.0000.0000.000
7A10VAL0-0.001-0.00415.5370.0780.0780.0000.0000.0000.000
8A11LEU00.0310.02318.9000.0140.0140.0000.0000.0000.000
9A12THR00.017-0.02121.9650.0340.0340.0000.0000.0000.000
10A13ILE00.0560.03424.709-0.010-0.0100.0000.0000.0000.000
11A14PHE0-0.068-0.04426.3600.0210.0210.0000.0000.0000.000
12A15PRO00.0610.02922.358-0.024-0.0240.0000.0000.0000.000
13A16HIS00.039-0.00322.407-0.053-0.0530.0000.0000.0000.000
14A17ILE0-0.0050.02723.873-0.006-0.0060.0000.0000.0000.000
15A18ILE00.019-0.00118.268-0.013-0.0130.0000.0000.0000.000
16A19SER0-0.007-0.00618.969-0.033-0.0330.0000.0000.0000.000
17A20CYS00.016-0.01319.956-0.007-0.0070.0000.0000.0000.000
18A21TYR0-0.086-0.05618.8420.0300.0300.0000.0000.0000.000
19A22SER0-0.004-0.02015.686-0.039-0.0390.0000.0000.0000.000
20A23GLU-1-0.933-0.95316.491-0.666-0.6660.0000.0000.0000.000
21A24TYR0-0.065-0.03418.9820.0520.0520.0000.0000.0000.000
22A25GLY00.0120.00318.482-0.033-0.0330.0000.0000.0000.000
23A26ILE00.015-0.01214.887-0.038-0.0380.0000.0000.0000.000
24A27VAL00.0980.06913.910-0.063-0.0630.0000.0000.0000.000
25A28LYS10.9921.01413.1050.4240.4240.0000.0000.0000.000
26A29GLN0-0.109-0.04613.322-0.118-0.1180.0000.0000.0000.000
27A30ALA00.019-0.0039.859-0.057-0.0570.0000.0000.0000.000
28A31ILE00.0330.0288.583-0.289-0.2890.0000.0000.0000.000
29A32LYS10.8790.9329.1390.7300.7300.0000.0000.0000.000
30A33LYS10.7920.8988.8030.1370.1370.0000.0000.0000.000
31A34GLY00.0220.0285.1180.1280.1280.0000.0000.0000.000
32A35LYS10.8420.9193.828-3.133-2.7630.003-0.084-0.2890.000
33A36VAL00.017-0.0045.645-0.222-0.2220.0000.0000.0000.000
34A37GLU-1-0.833-0.8776.163-4.095-4.0950.0000.0000.0000.000
35A38VAL0-0.0030.0029.3900.1070.1070.0000.0000.0000.000
36A39TYR0-0.045-0.0538.5000.1610.1610.0000.0000.0000.000
37A40PRO0-0.019-0.00814.6300.0710.0710.0000.0000.0000.000
38A41ILE0-0.014-0.00616.336-0.009-0.0090.0000.0000.0000.000
39A42ASP-1-0.755-0.88520.107-0.373-0.3730.0000.0000.0000.000
40A43LEU00.029-0.00523.7010.0140.0140.0000.0000.0000.000
41A44ARG10.8390.89825.9950.3730.3730.0000.0000.0000.000
42A45GLU-1-0.968-0.96124.208-0.371-0.3710.0000.0000.0000.000
43A46PHE0-0.018-0.01920.717-0.005-0.0050.0000.0000.0000.000
44A47ALA0-0.0030.00326.5580.0140.0140.0000.0000.0000.000
45A48PRO00.0400.01229.7010.0130.0130.0000.0000.0000.000
46A49LYS10.9120.95931.9800.1730.1730.0000.0000.0000.000
47A50GLY00.012-0.00233.0700.0090.0090.0000.0000.0000.000
48A51GLN0-0.037-0.00334.110-0.004-0.0040.0000.0000.0000.000
49A52VAL00.0210.00130.066-0.005-0.0050.0000.0000.0000.000
50A53ASP-1-0.916-0.95532.565-0.223-0.2230.0000.0000.0000.000
51A54ASP-1-0.865-0.92235.219-0.159-0.1590.0000.0000.0000.000
52A55VAL0-0.017-0.02538.700-0.003-0.0030.0000.0000.0000.000
53A56PRO0-0.0310.01240.1040.0000.0000.0000.0000.0000.000
54A57TYR00.007-0.00941.0990.0060.0060.0000.0000.0000.000
55A58GLY0-0.022-0.02444.153-0.001-0.0010.0000.0000.0000.000
56A59GLY0-0.027-0.01046.7140.0030.0030.0000.0000.0000.000
57A60LEU00.0200.01143.3140.0020.0020.0000.0000.0000.000
58A61PRO0-0.039-0.02244.3330.0000.0000.0000.0000.0000.000
59A62GLY00.0370.02041.636-0.003-0.0030.0000.0000.0000.000
60A63MET0-0.074-0.02637.1030.0040.0040.0000.0000.0000.000
61A64VAL00.0220.01335.068-0.005-0.0050.0000.0000.0000.000
62A65LEU0-0.017-0.01729.282-0.002-0.0020.0000.0000.0000.000
63A66LYS10.8470.91732.9270.2160.2160.0000.0000.0000.000
64A67PRO0-0.010-0.01730.681-0.017-0.0170.0000.0000.0000.000
65A68GLU-1-0.828-0.91529.330-0.226-0.2260.0000.0000.0000.000
66A69PRO00.0390.02828.063-0.011-0.0110.0000.0000.0000.000
67A70ILE00.0120.00624.795-0.033-0.0330.0000.0000.0000.000
68A71TYR0-0.060-0.05024.398-0.027-0.0270.0000.0000.0000.000
69A72GLU-1-0.859-0.92324.494-0.295-0.2950.0000.0000.0000.000
70A73ALA0-0.027-0.01221.628-0.029-0.0290.0000.0000.0000.000
71A74TYR0-0.042-0.04220.204-0.073-0.0730.0000.0000.0000.000
72A75ASP-1-0.870-0.93519.680-0.361-0.3610.0000.0000.0000.000
73A76TYR00.0410.01716.956-0.059-0.0590.0000.0000.0000.000
74A77VAL0-0.053-0.02914.714-0.051-0.0510.0000.0000.0000.000
75A78VAL0-0.043-0.03415.197-0.078-0.0780.0000.0000.0000.000
76A79GLU-1-0.989-0.98716.208-0.333-0.3330.0000.0000.0000.000
77A80ASN0-0.080-0.04414.5830.0310.0310.0000.0000.0000.000
78A81TYR0-0.053-0.0239.886-0.170-0.1700.0000.0000.0000.000
79A82GLY00.0070.01810.940-0.127-0.1270.0000.0000.0000.000
80A83LYS10.9470.96613.1830.3150.3150.0000.0000.0000.000
81A84PRO0-0.0040.00614.391-0.085-0.0850.0000.0000.0000.000
82A85PHE0-0.004-0.01015.3470.1060.1060.0000.0000.0000.000
83A86VAL00.011-0.01617.234-0.073-0.0730.0000.0000.0000.000
84A87LEU0-0.027-0.01419.1610.0500.0500.0000.0000.0000.000
85A88ILE00.0120.02721.399-0.029-0.0290.0000.0000.0000.000
86A89THR0-0.033-0.03623.4310.0090.0090.0000.0000.0000.000
87A90GLU-1-0.779-0.87226.134-0.238-0.2380.0000.0000.0000.000
88A91PRO0-0.062-0.00929.827-0.001-0.0010.0000.0000.0000.000
89A92TRP0-0.032-0.01631.9980.0050.0050.0000.0000.0000.000
90A93GLY00.0780.04929.9670.0160.0160.0000.0000.0000.000
91A94GLU-1-0.897-0.97827.853-0.263-0.2630.0000.0000.0000.000
92A95LYS10.9360.97928.4460.1710.1710.0000.0000.0000.000
93A96LEU00.0400.03322.0460.0050.0050.0000.0000.0000.000
94A97ASN00.008-0.03724.1240.0290.0290.0000.0000.0000.000
95A98GLN00.0390.00219.812-0.042-0.0420.0000.0000.0000.000
96A99LYS10.9110.98820.9050.1400.1400.0000.0000.0000.000
97A100LEU00.0920.04320.167-0.006-0.0060.0000.0000.0000.000
98A101VAL0-0.0020.02617.345-0.043-0.0430.0000.0000.0000.000
99A102ASN0-0.006-0.01416.231-0.045-0.0450.0000.0000.0000.000
100A103GLU-1-0.902-0.91115.108-0.263-0.2630.0000.0000.0000.000
101A104LEU0-0.041-0.03514.879-0.051-0.0510.0000.0000.0000.000
102A105SER0-0.048-0.06312.158-0.124-0.1240.0000.0000.0000.000
103A106LYS10.8900.94310.355-0.008-0.0080.0000.0000.0000.000
104A107LYS10.8670.96010.5740.5460.5460.0000.0000.0000.000
105A108GLU-1-0.870-0.9376.669-1.611-1.6110.0000.0000.0000.000
106A109ARG10.8580.9238.7920.8880.8880.0000.0000.0000.000
107A110ILE0-0.0360.00211.5650.2480.2480.0000.0000.0000.000
108A111MET00.0290.04814.524-0.074-0.0740.0000.0000.0000.000
109A112ILE0-0.028-0.02717.3190.0600.0600.0000.0000.0000.000
110A113ILE00.0150.00220.112-0.011-0.0110.0000.0000.0000.000
111A114CYS0-0.055-0.02122.8660.0170.0170.0000.0000.0000.000
112A115GLY00.0590.01425.4650.0160.0160.0000.0000.0000.000
113A116ARG10.8710.91529.1190.2860.2860.0000.0000.0000.000
114A117TYR0-0.022-0.00332.1400.0030.0030.0000.0000.0000.000
115A118GLU-1-0.861-0.93335.906-0.177-0.1770.0000.0000.0000.000
116A119GLY00.0010.00733.5160.0050.0050.0000.0000.0000.000
117A120VAL0-0.055-0.02329.155-0.006-0.0060.0000.0000.0000.000
118A121ASP-1-0.707-0.80132.355-0.176-0.1760.0000.0000.0000.000
119A122GLU-1-0.791-0.91332.330-0.203-0.2030.0000.0000.0000.000
120A123ARG10.7640.83632.4430.1710.1710.0000.0000.0000.000
121A124VAL00.0370.03526.979-0.004-0.0040.0000.0000.0000.000
122A125LYS10.8440.90727.6930.2110.2110.0000.0000.0000.000
123A126LYS10.8430.93628.3120.1890.1890.0000.0000.0000.000
124A127ILE00.0080.01423.5220.0070.0070.0000.0000.0000.000
125A128VAL0-0.034-0.00623.237-0.039-0.0390.0000.0000.0000.000
126A129ASP-1-0.895-0.92020.497-0.373-0.3730.0000.0000.0000.000
127A130MET0-0.084-0.05220.5710.0210.0210.0000.0000.0000.000
128A131GLU-1-0.849-0.94224.036-0.265-0.2650.0000.0000.0000.000
129A132ILE0-0.100-0.04422.9540.0130.0130.0000.0000.0000.000
130A133SER0-0.018-0.00626.7180.0100.0100.0000.0000.0000.000
131A134LEU00.0730.01430.297-0.006-0.0060.0000.0000.0000.000
132A135GLY0-0.050-0.02832.3160.0020.0020.0000.0000.0000.000
133A136ASP-1-0.934-0.94833.129-0.139-0.1390.0000.0000.0000.000
134A137PHE0-0.083-0.04430.8130.0070.0070.0000.0000.0000.000
135A138ILE00.0290.02534.907-0.006-0.0060.0000.0000.0000.000
136A139LEU0-0.025-0.00129.6340.0000.0000.0000.0000.0000.000
137A140SER0-0.011-0.01733.368-0.001-0.0010.0000.0000.0000.000
138A141GLY0-0.012-0.03030.2280.0000.0000.0000.0000.0000.000
139A142GLY00.0240.02626.7780.0050.0050.0000.0000.0000.000
140A143GLU-1-0.755-0.86524.316-0.399-0.3990.0000.0000.0000.000
141A144ILE00.0170.00123.656-0.034-0.0340.0000.0000.0000.000
142A145VAL00.0210.01923.811-0.011-0.0110.0000.0000.0000.000
143A146ALA00.0250.01320.468-0.025-0.0250.0000.0000.0000.000
144A147LEU0-0.013-0.00519.484-0.059-0.0590.0000.0000.0000.000
145A148ALA00.0050.02019.479-0.027-0.0270.0000.0000.0000.000
146A149VAL0-0.004-0.00117.366-0.005-0.0050.0000.0000.0000.000
147A150ILE0-0.004-0.00214.319-0.038-0.0380.0000.0000.0000.000
148A151ASP-1-0.916-0.92515.132-0.498-0.4980.0000.0000.0000.000
149A152ALA0-0.001-0.01716.8350.0180.0180.0000.0000.0000.000
150A153VAL0-0.005-0.01312.4250.0490.0490.0000.0000.0000.000
151A154SER0-0.007-0.01211.926-0.049-0.0490.0000.0000.0000.000
152A155ARG10.9400.96412.6480.3010.3010.0000.0000.0000.000
153A156VAL0-0.058-0.02114.2450.0930.0930.0000.0000.0000.000
154A157LEU00.0040.0248.2110.0780.0780.0000.0000.0000.000
155A158PRO00.0130.0098.6870.0520.0520.0000.0000.0000.000
156A159GLY00.000-0.0109.0290.1480.1480.0000.0000.0000.000
157A160VAL0-0.022-0.00210.090-0.132-0.1320.0000.0000.0000.000
158A161LEU00.0520.02512.213-0.026-0.0260.0000.0000.0000.000
159A162SER0-0.039-0.02715.8850.0620.0620.0000.0000.0000.000
160A163GLH0-0.025-0.00317.131-0.016-0.0160.0000.0000.0000.000
161A164PRO00.0300.02318.4980.0190.0190.0000.0000.0000.000
162A179TYR0-0.022-0.02233.621-0.003-0.0030.0000.0000.0000.000
163A180PRO0-0.052-0.01735.603-0.004-0.0040.0000.0000.0000.000
164A181VAL00.0350.02932.8560.0060.0060.0000.0000.0000.000
165A182TYR00.0430.01036.037-0.004-0.0040.0000.0000.0000.000
166A183THR0-0.001-0.01933.9430.0050.0050.0000.0000.0000.000
167A184ARG10.9410.96535.9520.0360.0360.0000.0000.0000.000
168A185PRO00.0330.01338.0220.0050.0050.0000.0000.0000.000
169A186ARG10.9851.01941.0770.0310.0310.0000.0000.0000.000
170A187GLU-1-0.899-0.97143.392-0.039-0.0390.0000.0000.0000.000
171A188TYR0-0.001-0.00943.494-0.002-0.0020.0000.0000.0000.000
172A189ARG10.9530.98545.7500.0780.0780.0000.0000.0000.000
173A190GLY00.0570.03248.4170.0000.0000.0000.0000.0000.000
174A191MET0-0.036-0.01445.5460.0020.0020.0000.0000.0000.000
175A192LYS10.9360.97446.2780.0330.0330.0000.0000.0000.000
176A193VAL0-0.020-0.00541.374-0.001-0.0010.0000.0000.0000.000
177A194PRO00.0200.00542.9280.0030.0030.0000.0000.0000.000
178A195GLU-1-0.840-0.92244.193-0.022-0.0220.0000.0000.0000.000
179A196GLU-1-0.883-0.91845.546-0.020-0.0200.0000.0000.0000.000
180A197LEU0-0.111-0.10239.4130.0040.0040.0000.0000.0000.000
181A198LEU00.000-0.04941.0390.0000.0000.0000.0000.0000.000
182A199SER0-0.0470.00742.5220.0010.0010.0000.0000.0000.000
183A200GLY0-0.016-0.11542.818-0.002-0.0020.0000.0000.0000.000
184A201HIS00.0770.01541.2390.0030.0030.0000.0000.0000.000
185A202HIS0-0.006-0.02843.8580.0000.0000.0000.0000.0000.000
186A203LYS10.9201.06843.1430.0030.0030.0000.0000.0000.000
187A204LEU0-0.0050.03439.284-0.003-0.0030.0000.0000.0000.000
188A205ILE00.0260.02640.7340.0010.0010.0000.0000.0000.000
189A206GLU-1-0.874-0.95343.125-0.007-0.0070.0000.0000.0000.000
190A207LEU0-0.0180.04139.083-0.005-0.0050.0000.0000.0000.000
191A208TRP00.031-0.01134.735-0.006-0.0060.0000.0000.0000.000
192A209LYN0-0.0160.00440.478-0.002-0.0020.0000.0000.0000.000
193A210LEU00.0490.03540.259-0.003-0.0030.0000.0000.0000.000
194A211TRP00.0140.01032.613-0.003-0.0030.0000.0000.0000.000
195A212HIS10.8900.93937.6130.0050.0050.0000.0000.0000.000
196A213ARG10.8790.93641.0020.0070.0070.0000.0000.0000.000
197A214ILE00.0250.00841.114-0.003-0.0030.0000.0000.0000.000
198A215GLU-1-0.896-0.93434.971-0.036-0.0360.0000.0000.0000.000
199A216ASN00.004-0.01938.665-0.005-0.0050.0000.0000.0000.000
200A217THR0-0.052-0.03841.251-0.005-0.0050.0000.0000.0000.000
201A218VAL00.0380.00237.889-0.002-0.0020.0000.0000.0000.000
202A219LYS10.9250.98333.9610.0540.0540.0000.0000.0000.000
203A220LYS10.9240.96139.0610.0480.0480.0000.0000.0000.000
204A221ARG10.9270.98841.5460.0580.0580.0000.0000.0000.000
205A222PRO0-0.0090.00038.678-0.001-0.0010.0000.0000.0000.000
206A223ASP-1-0.833-0.91240.000-0.108-0.1080.0000.0000.0000.000
207A224LEU0-0.072-0.06842.6420.0040.0040.0000.0000.0000.000
208A225ILE00.0100.02246.3810.0020.0020.0000.0000.0000.000
209A226PRO0-0.042-0.03646.5170.0010.0010.0000.0000.0000.000
210A227LYS10.9871.01640.8210.0990.0990.0000.0000.0000.000
211A228ASP-1-0.841-0.93746.259-0.072-0.0720.0000.0000.0000.000
212A229LEU00.0470.02448.0320.0020.0020.0000.0000.0000.000
213A230THR0-0.081-0.04549.3500.0030.0030.0000.0000.0000.000
214A231GLU-1-0.940-1.01444.679-0.080-0.0800.0000.0000.0000.000
215A232LEU0-0.0350.00945.4830.0020.0020.0000.0000.0000.000
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