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: LZM79

Calculation Name: 3OSY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OSY

Chain ID: A

ChEMBL ID:

UniProt ID: B8YLV9

Base Structure: X-ray

Registration Date: 2023-06-21

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 187
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2002224.756632
FMO2-HF: Nuclear repulsion 1929624.280537
FMO2-HF: Total energy -72600.476096
FMO2-MP2: Total energy -72810.613254


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:-5:PRO)


Summations of interaction energy for fragment #1(A:-5:PRO)
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.
-7.734-2.7092.892-2.601-5.313-0.003
Interaction energy analysis for fragmet #1(A:-5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.038
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].
3A-3GLY00.0240.0212.920-3.140-0.3420.045-1.348-1.4950.006
4A-2SER00.0580.0134.915-0.637-0.593-0.001-0.006-0.0370.000
5A-1HIS00.0520.0383.4790.1730.5380.018-0.123-0.2600.000
6A0MET0-0.021-0.0082.052-1.085-0.4392.157-0.784-2.018-0.006
7A1GLY0-0.0190.0015.3910.3190.329-0.001-0.001-0.0080.000
8A2PRO00.0380.0028.7880.0910.0910.0000.0000.0000.000
9A3SER00.0410.0107.4160.2180.2180.0000.0000.0000.000
10A4LEU00.0360.0214.7610.0160.095-0.001-0.012-0.0660.000
11A5ASP-1-0.968-0.9588.5190.0460.0460.0000.0000.0000.000
12A6PHE00.007-0.00912.2030.0910.0910.0000.0000.0000.000
13A7ALA00.0310.0259.9510.0690.0690.0000.0000.0000.000
14A8LEU00.0480.01011.1930.0840.0840.0000.0000.0000.000
15A9SER0-0.099-0.04613.3210.0470.0470.0000.0000.0000.000
16A10LEU0-0.043-0.03515.0320.0320.0320.0000.0000.0000.000
17A11LEU00.0440.01414.2950.0100.0100.0000.0000.0000.000
18A12ARG10.9811.00016.533-0.035-0.0350.0000.0000.0000.000
19A13ARG10.8560.92619.3010.0590.0590.0000.0000.0000.000
20A14ASN0-0.026-0.04119.923-0.002-0.0020.0000.0000.0000.000
21A15VAL0-0.0170.03216.422-0.006-0.0060.0000.0000.0000.000
22A16ARG10.8910.94219.6670.0150.0150.0000.0000.0000.000
23A17GLN0-0.0090.01520.476-0.018-0.0180.0000.0000.0000.000
24A18VAL0-0.010-0.02323.232-0.006-0.0060.0000.0000.0000.000
25A19GLN0-0.0100.00225.6990.0120.0120.0000.0000.0000.000
26A20THR0-0.024-0.02428.373-0.002-0.0020.0000.0000.0000.000
27A21ASP-1-0.916-0.95831.0210.0110.0110.0000.0000.0000.000
28A22GLN0-0.036-0.01429.3320.0050.0050.0000.0000.0000.000
29A23GLY0-0.020-0.00327.5510.0030.0030.0000.0000.0000.000
30A24HIS0-0.022-0.01823.672-0.004-0.0040.0000.0000.0000.000
31A25PHE00.0250.01722.504-0.007-0.0070.0000.0000.0000.000
32A26THR0-0.023-0.00817.4850.0230.0230.0000.0000.0000.000
33A27MET0-0.0030.02420.756-0.024-0.0240.0000.0000.0000.000
34A28LEU0-0.0140.00319.0990.0030.0030.0000.0000.0000.000
35A29GLY00.0210.02221.790-0.001-0.0010.0000.0000.0000.000
36A30VAL0-0.050-0.07123.282-0.015-0.0150.0000.0000.0000.000
37A31ARG10.9650.96825.2710.0910.0910.0000.0000.0000.000
38A32ASP-1-0.922-0.94828.223-0.064-0.0640.0000.0000.0000.000
39A33ARG10.9520.97730.4680.0320.0320.0000.0000.0000.000
40A34LEU00.0260.03029.0750.0020.0020.0000.0000.0000.000
41A35ALA00.0100.00926.056-0.004-0.0040.0000.0000.0000.000
42A36VAL0-0.0030.00123.018-0.002-0.0020.0000.0000.0000.000
43A37LEU00.009-0.00224.1090.0050.0050.0000.0000.0000.000
44A38PRO00.0200.02022.337-0.013-0.0130.0000.0000.0000.000
45A39ARG00.0380.05324.9370.0090.0090.0000.0000.0000.000
46A40HIS0-0.067-0.04723.5560.0040.0040.0000.0000.0000.000
47A41SER0-0.031-0.02926.7300.0120.0120.0000.0000.0000.000
48A42GLN0-0.061-0.03128.6730.0040.0040.0000.0000.0000.000
49A43PRO00.0150.02030.3530.0070.0070.0000.0000.0000.000
50A44GLY00.0760.04132.627-0.002-0.0020.0000.0000.0000.000
51A45LYS10.9620.96436.0270.0010.0010.0000.0000.0000.000
52A46THR0-0.035-0.01436.0510.0000.0000.0000.0000.0000.000
53A47ILE0-0.0090.02030.0640.0000.0000.0000.0000.0000.000
54A48TRP00.0020.00430.2490.0020.0020.0000.0000.0000.000
55A49ILE00.014-0.01427.028-0.003-0.0030.0000.0000.0000.000
56A50GLU-1-0.846-0.92523.5720.0770.0770.0000.0000.0000.000
57A51HIS00.0040.00626.8870.0010.0010.0000.0000.0000.000
58A52LYS10.9330.97630.791-0.038-0.0380.0000.0000.0000.000
59A53LEU0-0.019-0.00532.279-0.004-0.0040.0000.0000.0000.000
60A54VAL0-0.026-0.00832.153-0.002-0.0020.0000.0000.0000.000
61A55ASN0-0.008-0.01034.9300.0010.0010.0000.0000.0000.000
62A56VAL0-0.034-0.03333.388-0.002-0.0020.0000.0000.0000.000
63A57LEU0-0.065-0.03735.9730.0010.0010.0000.0000.0000.000
64A58ASP-1-0.908-0.95536.322-0.053-0.0530.0000.0000.0000.000
65A59ALA0-0.016-0.00634.116-0.002-0.0020.0000.0000.0000.000
66A60VAL00.0250.01733.4290.0010.0010.0000.0000.0000.000
67A61GLU-1-0.892-0.94531.543-0.080-0.0800.0000.0000.0000.000
68A62LEU0-0.002-0.00228.187-0.002-0.0020.0000.0000.0000.000
69A63VAL00.010-0.01130.612-0.002-0.0020.0000.0000.0000.000
70A64ASP-1-0.850-0.92328.679-0.158-0.1580.0000.0000.0000.000
71A65GLU-1-0.904-0.97230.594-0.158-0.1580.0000.0000.0000.000
72A66GLN0-0.096-0.04330.5140.0030.0030.0000.0000.0000.000
73A67GLY0-0.0040.00633.9290.0060.0060.0000.0000.0000.000
74A68VAL0-0.047-0.01830.0490.0060.0060.0000.0000.0000.000
75A69ASN00.0130.00430.508-0.004-0.0040.0000.0000.0000.000
76A70LEU0-0.029-0.02325.469-0.009-0.0090.0000.0000.0000.000
77A71GLH00.001-0.01725.557-0.007-0.0070.0000.0000.0000.000
78A72LEU0-0.027-0.01122.824-0.001-0.0010.0000.0000.0000.000
79A73THR00.0580.02226.7720.0010.0010.0000.0000.0000.000
80A74LEU0-0.044-0.02028.105-0.004-0.0040.0000.0000.0000.000
81A75ILE0-0.0010.00729.5290.0060.0060.0000.0000.0000.000
82A76THR00.0410.00231.190-0.007-0.0070.0000.0000.0000.000
83A77LEU0-0.028-0.02029.1860.0060.0060.0000.0000.0000.000
84A78ASP-1-0.893-0.96133.610-0.015-0.0150.0000.0000.0000.000
85A79THR00.0290.01532.3090.0030.0030.0000.0000.0000.000
86A80ASN0-0.070-0.05035.456-0.002-0.0020.0000.0000.0000.000
87A81GLU-1-0.933-0.96530.7030.0060.0060.0000.0000.0000.000
88A82LYS10.9060.97631.0830.0350.0350.0000.0000.0000.000
89A83PHE00.0060.01625.1350.0030.0030.0000.0000.0000.000
90A84ARG10.8700.93418.5890.1290.1290.0000.0000.0000.000
91A85ASP-1-0.783-0.91024.942-0.139-0.1390.0000.0000.0000.000
92A86ILE0-0.080-0.00720.746-0.010-0.0100.0000.0000.0000.000
93A87THR00.0370.00722.127-0.031-0.0310.0000.0000.0000.000
94A88LYS10.9430.97922.9010.1370.1370.0000.0000.0000.000
95A89PHE0-0.043-0.02518.317-0.002-0.0020.0000.0000.0000.000
96A90ILE0-0.0270.01819.058-0.049-0.0490.0000.0000.0000.000
97A91PRO0-0.0020.00818.8020.0160.0160.0000.0000.0000.000
98A92GLU-1-0.864-0.92621.584-0.204-0.2040.0000.0000.0000.000
99A93ASN0-0.026-0.04023.8100.0060.0060.0000.0000.0000.000
100A94ILE00.0060.01720.505-0.026-0.0260.0000.0000.0000.000
101A95SER0-0.051-0.02917.684-0.002-0.0020.0000.0000.0000.000
102A96THR0-0.0130.00715.4490.0060.0060.0000.0000.0000.000
103A97ALA0-0.043-0.03710.7600.0190.0190.0000.0000.0000.000
104A98SER00.0120.0059.8390.1020.1020.0000.0000.0000.000
105A99ASP-1-0.845-0.9115.105-4.073-3.902-0.001-0.004-0.1650.000
106A100ALA0-0.087-0.0316.5520.0560.0560.0000.0000.0000.000
107A101THR0-0.056-0.0365.640-0.270-0.2700.0000.0000.0000.000
108A102LEU00.0120.0067.4550.1120.1120.0000.0000.0000.000
109A103VAL0-0.023-0.02010.3660.1290.1290.0000.0000.0000.000
110A104ILE00.0250.00012.473-0.029-0.0290.0000.0000.0000.000
111A105ASN00.001-0.02215.0490.0960.0960.0000.0000.0000.000
112A106THR00.0600.03317.933-0.014-0.0140.0000.0000.0000.000
113A107GLU-1-0.874-0.93420.3840.1370.1370.0000.0000.0000.000
114A108HIS0-0.016-0.02121.6390.0260.0260.0000.0000.0000.000
115A109MET0-0.091-0.03315.0080.0350.0350.0000.0000.0000.000
116A110PRO00.0440.03017.352-0.030-0.0300.0000.0000.0000.000
117A111SER0-0.042-0.02914.9900.0410.0410.0000.0000.0000.000
118A112MET00.0100.0319.1450.1090.1090.0000.0000.0000.000
119A113PHE0-0.033-0.0257.579-0.165-0.1650.0000.0000.0000.000
120A114VAL00.0240.0086.8380.3830.3830.0000.0000.0000.000
121A115PRO0-0.036-0.0042.414-1.314-0.4620.677-0.321-1.207-0.003
122A116VAL0-0.010-0.0245.0760.0990.159-0.001-0.002-0.0570.000
123A117GLY0-0.0130.0135.5140.1330.1330.0000.0000.0000.000
124A118ASP-1-0.874-0.9436.446-1.201-1.2010.0000.0000.0000.000
125A119VAL0-0.064-0.0209.9880.1640.1640.0000.0000.0000.000
126A120VAL00.0360.00212.5480.0260.0260.0000.0000.0000.000
127A121GLN00.0020.01415.9760.0600.0600.0000.0000.0000.000
128A122TYR0-0.018-0.00619.6430.0000.0000.0000.0000.0000.000
129A123GLY00.0430.00621.9070.0120.0120.0000.0000.0000.000
130A124PHE0-0.0080.01625.524-0.001-0.0010.0000.0000.0000.000
131A125LEU0-0.023-0.02027.520-0.013-0.0130.0000.0000.0000.000
132A126ASN0-0.037-0.00930.7400.0190.0190.0000.0000.0000.000
133A127LEU00.1340.04833.737-0.005-0.0050.0000.0000.0000.000
134A128SER0-0.059-0.01435.139-0.004-0.0040.0000.0000.0000.000
135A129GLY0-0.012-0.01231.655-0.008-0.0080.0000.0000.0000.000
136A130LYS10.9340.98227.4230.2160.2160.0000.0000.0000.000
137A131PRO00.014-0.00925.1220.0090.0090.0000.0000.0000.000
138A132THR0-0.035-0.00427.963-0.003-0.0030.0000.0000.0000.000
139A133HIS00.0460.01628.630-0.011-0.0110.0000.0000.0000.000
140A134ARG10.9090.92722.5940.2650.2650.0000.0000.0000.000
141A135THR00.0360.04421.2360.0130.0130.0000.0000.0000.000
142A136MET0-0.048-0.03816.6350.0020.0020.0000.0000.0000.000
143A137MET0-0.008-0.00316.1990.0530.0530.0000.0000.0000.000
144A138TYR00.037-0.00210.979-0.074-0.0740.0000.0000.0000.000
145A139ASN00.003-0.0049.8320.2060.2060.0000.0000.0000.000
146A140PHE0-0.001-0.01610.856-0.069-0.0690.0000.0000.0000.000
147A141PRO0-0.0110.00211.7090.0480.0480.0000.0000.0000.000
148A142THR0-0.023-0.00213.5770.0620.0620.0000.0000.0000.000
149A143LYS10.9840.95616.031-0.058-0.0580.0000.0000.0000.000
150A144ALA0-0.049-0.00118.7310.0050.0050.0000.0000.0000.000
151A145GLY00.0620.06319.3560.0230.0230.0000.0000.0000.000
152A146GLN0-0.040-0.03916.407-0.017-0.0170.0000.0000.0000.000
153A147CYM-1-0.814-0.88917.925-0.067-0.0670.0000.0000.0000.000
154A148GLY00.028-0.01819.9310.0230.0230.0000.0000.0000.000
155A149GLY0-0.048-0.01715.728-0.013-0.0130.0000.0000.0000.000
156A150VAL00.0240.01414.823-0.025-0.0250.0000.0000.0000.000
157A151VAL00.0080.02111.539-0.037-0.0370.0000.0000.0000.000
158A152THR0-0.033-0.01510.3490.0270.0270.0000.0000.0000.000
159A153SER00.0660.0179.726-0.180-0.1800.0000.0000.0000.000
160A154VAL00.0210.0069.6200.0670.0670.0000.0000.0000.000
161A155GLY0-0.0110.00611.7250.0860.0860.0000.0000.0000.000
162A156LYS10.9180.96414.1730.6000.6000.0000.0000.0000.000
163A157ILE00.004-0.00814.403-0.060-0.0600.0000.0000.0000.000
164A158ILE0-0.006-0.02412.9990.0230.0230.0000.0000.0000.000
165A159GLY00.031-0.00316.2080.0220.0220.0000.0000.0000.000
166A160ILE00.0030.02616.824-0.016-0.0160.0000.0000.0000.000
167A161HIS00.0020.02215.758-0.043-0.0430.0000.0000.0000.000
168A162ILE0-0.005-0.01317.7420.0330.0330.0000.0000.0000.000
169A163GLY00.0570.02819.4880.0230.0230.0000.0000.0000.000
170A164GLY0-0.011-0.00418.723-0.037-0.0370.0000.0000.0000.000
171A165ASN00.0190.03219.4610.0200.0200.0000.0000.0000.000
172A166GLY00.0440.02618.8390.0160.0160.0000.0000.0000.000
173A167ARG10.8730.92916.6630.1640.1640.0000.0000.0000.000
174A168GLN00.0080.00115.444-0.018-0.0180.0000.0000.0000.000
175A169GLY00.0180.00915.3000.0620.0620.0000.0000.0000.000
176A170PHE00.009-0.02116.099-0.059-0.0590.0000.0000.0000.000
177A171CYS0-0.0350.01015.7110.0170.0170.0000.0000.0000.000
178A172ALA00.0720.04318.484-0.015-0.0150.0000.0000.0000.000
179A173GLY0-0.005-0.01119.437-0.015-0.0150.0000.0000.0000.000
180A174LEU0-0.0020.00319.9370.0330.0330.0000.0000.0000.000
181A175LYS10.8540.92421.4940.1810.1810.0000.0000.0000.000
182A176ARG10.9030.95123.6910.2440.2440.0000.0000.0000.000
183A177SER0-0.003-0.01026.0240.0150.0150.0000.0000.0000.000
184A178TYR00.0290.00724.8660.0100.0100.0000.0000.0000.000
185A179PHE00.0320.01924.1770.0070.0070.0000.0000.0000.000
186A180ALA0-0.0120.00229.4550.0050.0050.0000.0000.0000.000
187A181SER0-0.0140.00232.2850.0090.0090.0000.0000.0000.000