Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 897MY

Calculation Name: 1TY0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TY0

Chain ID: A

ChEMBL ID:

UniProt ID: Q7BAE3

Base Structure: X-ray

Registration Date: 2023-09-23

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2663855.578646
FMO2-HF: Nuclear repulsion 2578192.097593
FMO2-HF: Total energy -85663.481053
FMO2-MP2: Total energy -85918.247815


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:LYS)


Summations of interaction energy for fragment #1(A:1:LYS)
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.
-125.432-126.78819.018-10.005-7.657-0.101
Interaction energy analysis for fragmet #1(A:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.930
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].
3A3ASP-1-0.788-0.8693.825-34.207-31.112-0.034-1.700-1.361-0.002
4A4SER0-0.090-0.0636.5902.5812.5810.0000.0000.0000.000
5A5GLU-1-0.897-0.9481.728-128.505-132.95619.052-8.305-6.296-0.099
6A6ASN00.0920.0486.0681.8331.8330.0000.0000.0000.000
7A7ILE0-0.017-0.0078.4381.9631.9630.0000.0000.0000.000
8A8LYS10.9180.9617.14534.97534.9750.0000.0000.0000.000
9A9ASP-1-0.816-0.9096.847-39.346-39.3460.0000.0000.0000.000
10A10VAL0-0.053-0.02110.0792.4212.4210.0000.0000.0000.000
11A11LYS10.7830.90113.34521.91921.9190.0000.0000.0000.000
12A12LEU00.0190.01710.2481.6571.6570.0000.0000.0000.000
13A13GLN0-0.051-0.02113.5580.4020.4020.0000.0000.0000.000
14A14LEU0-0.029-0.00315.9091.3421.3420.0000.0000.0000.000
15A15ASN00.0230.00017.6421.1921.1920.0000.0000.0000.000
16A16TYR00.0060.00518.0950.9540.9540.0000.0000.0000.000
17A17ALA0-0.027-0.01219.7290.9420.9420.0000.0000.0000.000
18A18TYR00.039-0.02421.8710.6870.6870.0000.0000.0000.000
19A19GLU-1-0.892-0.91022.098-12.369-12.3690.0000.0000.0000.000
20A20ILE0-0.078-0.04824.6600.0030.0030.0000.0000.0000.000
21A21ILE00.0130.01027.5680.1950.1950.0000.0000.0000.000
22A22PRO0-0.035-0.01431.371-0.051-0.0510.0000.0000.0000.000
23A23VAL0-0.029-0.01333.1570.2300.2300.0000.0000.0000.000
24A24ASP-1-0.917-0.96436.104-8.159-8.1590.0000.0000.0000.000
25A25TYR00.010-0.00238.8310.1830.1830.0000.0000.0000.000
26A26THR00.0370.01642.4520.0360.0360.0000.0000.0000.000
27A27ASN0-0.0190.00245.4400.1240.1240.0000.0000.0000.000
28A28CYS0-0.0110.01545.4580.0760.0760.0000.0000.0000.000
29A29ASN00.012-0.00447.6930.1020.1020.0000.0000.0000.000
30A30ILE0-0.0110.00346.549-0.126-0.1260.0000.0000.0000.000
31A31ASP-1-0.810-0.89847.936-6.301-6.3010.0000.0000.0000.000
32A32TYR0-0.089-0.05847.1740.1460.1460.0000.0000.0000.000
33A33LEU0-0.0200.00345.884-0.151-0.1510.0000.0000.0000.000
34A34THR00.0300.02442.8250.1330.1330.0000.0000.0000.000
35A35THR0-0.020-0.05942.4570.0200.0200.0000.0000.0000.000
36A36HIS0-0.0190.02138.8410.0690.0690.0000.0000.0000.000
37A37ASP-1-0.787-0.82638.748-8.508-8.5080.0000.0000.0000.000
38A38PHE0-0.016-0.00640.5970.2810.2810.0000.0000.0000.000
39A39TYR0-0.005-0.00340.762-0.109-0.1090.0000.0000.0000.000
40A40ILE0-0.022-0.01743.0570.2120.2120.0000.0000.0000.000
41A41ASP-1-0.759-0.84244.279-6.778-6.7780.0000.0000.0000.000
42A42ILE0-0.022-0.02241.3730.0000.0000.0000.0000.0000.000
43A43SER00.034-0.02545.660-0.050-0.0500.0000.0000.0000.000
44A44SER0-0.064-0.02347.795-0.010-0.0100.0000.0000.0000.000
45A45TYR0-0.010-0.05044.9810.0540.0540.0000.0000.0000.000
46A46LYS10.8480.93039.4127.8997.8990.0000.0000.0000.000
47A47LYS10.8630.94645.7756.3336.3330.0000.0000.0000.000
48A48LYS10.9660.98242.2637.4797.4790.0000.0000.0000.000
49A49ASN00.0040.00946.9910.0050.0050.0000.0000.0000.000
50A50PHE0-0.002-0.01238.929-0.139-0.1390.0000.0000.0000.000
51A51SER00.0050.02042.6820.0810.0810.0000.0000.0000.000
52A52VAL0-0.019-0.01338.209-0.224-0.2240.0000.0000.0000.000
53A53ASH0-0.063-0.08237.6470.1140.1140.0000.0000.0000.000
54A54SER0-0.076-0.04337.099-0.252-0.2520.0000.0000.0000.000
55A55GLU-1-0.779-0.87933.834-9.242-9.2420.0000.0000.0000.000
56A56VAL0-0.054-0.05235.615-0.237-0.2370.0000.0000.0000.000
57A57GLU-1-0.923-0.97333.840-9.265-9.2650.0000.0000.0000.000
58A58SER00.011-0.01237.4950.1710.1710.0000.0000.0000.000
59A59TYR0-0.021-0.00740.819-0.047-0.0470.0000.0000.0000.000
60A60ILE00.0380.03239.5170.1000.1000.0000.0000.0000.000
61A61THR00.027-0.00442.5690.1460.1460.0000.0000.0000.000
62A62THR00.0070.00144.8840.0940.0940.0000.0000.0000.000
63A63LYS10.8640.94842.6757.6007.6000.0000.0000.0000.000
64A64PHE0-0.030-0.00844.0200.0510.0510.0000.0000.0000.000
65A65THR00.0020.00148.8020.1090.1090.0000.0000.0000.000
66A66LYS10.9760.96350.8475.9365.9360.0000.0000.0000.000
67A67ASN0-0.013-0.01751.6260.0520.0520.0000.0000.0000.000
68A68GLN00.0220.04349.2900.0910.0910.0000.0000.0000.000
69A69LYS10.9000.95049.9825.9835.9830.0000.0000.0000.000
70A70VAL00.001-0.01644.9570.0080.0080.0000.0000.0000.000
71A71ASN0-0.048-0.03443.3090.0980.0980.0000.0000.0000.000
72A72ILE00.002-0.00938.460-0.067-0.0670.0000.0000.0000.000
73A73PHE00.0210.00533.425-0.022-0.0220.0000.0000.0000.000
74A74GLY0-0.017-0.00334.024-0.076-0.0760.0000.0000.0000.000
75A75LEU0-0.0180.00028.1080.0570.0570.0000.0000.0000.000
76A76PRO0-0.0260.00329.802-0.016-0.0160.0000.0000.0000.000
77A77TYR00.023-0.00227.312-0.450-0.4500.0000.0000.0000.000
78A78ILE0-0.045-0.01727.090-0.427-0.4270.0000.0000.0000.000
79A79PHE00.0100.01428.7100.3500.3500.0000.0000.0000.000
80A80THR00.0270.00431.514-0.019-0.0190.0000.0000.0000.000
81A81ARG10.9390.96234.2378.1938.1930.0000.0000.0000.000
82A82TYR00.002-0.00237.1070.1700.1700.0000.0000.0000.000
83A83ASP-1-0.884-0.92938.414-7.825-7.8250.0000.0000.0000.000
84A84VAL0-0.029-0.02938.2830.2060.2060.0000.0000.0000.000
85A85TYR0-0.0200.00935.242-0.132-0.1320.0000.0000.0000.000
86A86TYR00.0170.01033.1250.2210.2210.0000.0000.0000.000
87A87ILE00.001-0.00332.669-0.336-0.3360.0000.0000.0000.000
88A88TYR00.0190.00228.3490.1850.1850.0000.0000.0000.000
89A89GLY00.0730.04133.562-0.090-0.0900.0000.0000.0000.000
90A90GLY00.0090.00736.3680.0390.0390.0000.0000.0000.000
91A91VAL0-0.028-0.00237.1910.1530.1530.0000.0000.0000.000
92A92THR00.0090.00940.9040.0210.0210.0000.0000.0000.000
93A93PRO00.0160.00243.5610.0750.0750.0000.0000.0000.000
94A94SER0-0.0080.02447.236-0.088-0.0880.0000.0000.0000.000
95A95VAL0-0.012-0.02548.7650.1240.1240.0000.0000.0000.000
96A96ASN00.010-0.00250.4370.0350.0350.0000.0000.0000.000
97A97SER0-0.023-0.01551.440-0.030-0.0300.0000.0000.0000.000
98A98ASN0-0.039-0.00546.724-0.149-0.1490.0000.0000.0000.000
99A99SER00.0480.02547.517-0.059-0.0590.0000.0000.0000.000
100A100GLU-1-0.924-0.97046.476-6.386-6.3860.0000.0000.0000.000
101A101ASN0-0.013-0.01646.535-0.233-0.2330.0000.0000.0000.000
102A102SER00.0020.00745.3020.1260.1260.0000.0000.0000.000
103A103LYS10.9290.97443.5097.0257.0250.0000.0000.0000.000
104A104ILE00.0330.02037.955-0.001-0.0010.0000.0000.0000.000
105A105VAL0-0.031-0.03339.414-0.085-0.0850.0000.0000.0000.000
106A106GLY00.0580.01436.0720.0110.0110.0000.0000.0000.000
107A107ASN0-0.099-0.02535.0630.1840.1840.0000.0000.0000.000
108A108LEU00.0180.01927.741-0.218-0.2180.0000.0000.0000.000
109A109LEU00.0260.00730.0500.1210.1210.0000.0000.0000.000
110A110ILE00.002-0.00124.195-0.452-0.4520.0000.0000.0000.000
111A111ASP-1-0.776-0.88823.137-13.370-13.3700.0000.0000.0000.000
112A112GLY00.0040.00325.8920.2540.2540.0000.0000.0000.000
113A113VAL0-0.0080.01129.1970.4420.4420.0000.0000.0000.000
114A114GLN00.0260.00830.597-0.519-0.5190.0000.0000.0000.000
115A115GLN0-0.061-0.03828.7050.0460.0460.0000.0000.0000.000
116A116LYS10.9420.95932.1479.2229.2220.0000.0000.0000.000
117A117THR00.0190.03234.663-0.092-0.0920.0000.0000.0000.000
118A118LEU0-0.071-0.04231.7360.1050.1050.0000.0000.0000.000
119A119ILE00.012-0.01436.3070.1910.1910.0000.0000.0000.000
120A120ASN0-0.020-0.00738.9140.0000.0000.0000.0000.0000.000
121A121PRO0-0.0100.01233.6350.0030.0030.0000.0000.0000.000
122A122ILE00.0280.01633.293-0.175-0.1750.0000.0000.0000.000
123A123LYS10.9290.97236.1777.5117.5110.0000.0000.0000.000
124A124ILE0-0.035-0.01937.396-0.167-0.1670.0000.0000.0000.000
125A125ASP-1-0.807-0.90040.853-7.257-7.2570.0000.0000.0000.000
126A126LYS10.8120.92940.2608.0848.0840.0000.0000.0000.000
127A127PRO00.0170.01144.466-0.119-0.1190.0000.0000.0000.000
128A128ILE0-0.0060.00043.976-0.018-0.0180.0000.0000.0000.000
129A129PHE00.011-0.01638.213-0.016-0.0160.0000.0000.0000.000
130A130THR00.0830.04936.730-0.074-0.0740.0000.0000.0000.000
131A131ILE00.0390.00832.735-0.063-0.0630.0000.0000.0000.000
132A132GLN00.0170.01131.450-0.418-0.4180.0000.0000.0000.000
133A133GLU-1-0.777-0.87632.282-8.578-8.5780.0000.0000.0000.000
134A134PHE00.002-0.01033.437-0.131-0.1310.0000.0000.0000.000
135A135ASP-1-0.760-0.84428.367-11.703-11.7030.0000.0000.0000.000
136A136PHE00.0080.00428.409-0.276-0.2760.0000.0000.0000.000
137A137LYS10.8310.90929.4028.4288.4280.0000.0000.0000.000
138A138ILE00.0030.01329.244-0.104-0.1040.0000.0000.0000.000
139A139ARG10.8170.88423.24412.60012.6000.0000.0000.0000.000
140A140GLN00.0290.01125.758-0.207-0.2070.0000.0000.0000.000
141A141TYR00.0120.01827.324-0.103-0.1030.0000.0000.0000.000
142A142LEU00.002-0.01225.143-0.107-0.1070.0000.0000.0000.000
143A143MET0-0.046-0.03021.768-0.364-0.3640.0000.0000.0000.000
144A144GLN0-0.043-0.03523.474-0.126-0.1260.0000.0000.0000.000
145A145THR0-0.064-0.03626.1280.0790.0790.0000.0000.0000.000
146A146TYR0-0.041-0.03024.2870.2000.2000.0000.0000.0000.000
147A147LYS10.9150.97419.95712.49912.4990.0000.0000.0000.000
148A148ILE0-0.0110.02619.328-0.914-0.9140.0000.0000.0000.000
149A149TYR0-0.026-0.03617.476-0.436-0.4360.0000.0000.0000.000
150A150ASP-1-0.819-0.90216.008-19.517-19.5170.0000.0000.0000.000
151A151PRO0-0.033-0.02810.829-0.172-0.1720.0000.0000.0000.000
152A152ASN0-0.042-0.03012.446-2.134-2.1340.0000.0000.0000.000
153A153SER0-0.0200.02514.3830.9150.9150.0000.0000.0000.000
154A154PRO0-0.001-0.02215.704-0.996-0.9960.0000.0000.0000.000
155A155TYR00.0050.00117.135-0.093-0.0930.0000.0000.0000.000
156A156ILE00.0030.00213.924-0.950-0.9500.0000.0000.0000.000
157A157LYS10.9500.97716.91016.02416.0240.0000.0000.0000.000
158A158GLY00.0410.00920.1660.2280.2280.0000.0000.0000.000
159A159GLN0-0.0040.02223.5230.0230.0230.0000.0000.0000.000
160A160LEU0-0.0060.01526.7410.1630.1630.0000.0000.0000.000
161A161GLU-1-0.852-0.95029.647-9.798-9.7980.0000.0000.0000.000
162A162ILE0-0.049-0.03232.9810.1430.1430.0000.0000.0000.000
163A163ALA00.0380.02836.1900.0840.0840.0000.0000.0000.000
164A164ILE0-0.023-0.01439.4520.1360.1360.0000.0000.0000.000
165A165ASN0-0.027-0.02942.2720.1070.1070.0000.0000.0000.000
166A166GLY00.005-0.00445.8180.0360.0360.0000.0000.0000.000
167A167ASN0-0.054-0.03442.971-0.071-0.0710.0000.0000.0000.000
168A168LYS10.9620.99440.7417.2247.2240.0000.0000.0000.000
169A169HIS00.0670.02536.526-0.057-0.0570.0000.0000.0000.000
170A170GLU-1-0.881-0.92534.596-9.173-9.1730.0000.0000.0000.000
171A171SER00.0300.02330.351-0.236-0.2360.0000.0000.0000.000
172A172PHE0-0.020-0.01028.267-0.055-0.0550.0000.0000.0000.000
173A173ASN00.0270.01220.861-0.203-0.2030.0000.0000.0000.000
174A174LEU00.0230.01123.325-0.023-0.0230.0000.0000.0000.000
175A175TYR0-0.041-0.03317.382-0.181-0.1810.0000.0000.0000.000
176A176ASP-1-0.829-0.89318.925-14.363-14.3630.0000.0000.0000.000
177A177ALA00.0030.00117.5230.4700.4700.0000.0000.0000.000
178A178THR00.0230.01014.617-0.932-0.9320.0000.0000.0000.000
179A179SER00.037-0.0019.9131.7181.7180.0000.0000.0000.000
180A180SER00.010-0.00512.354-0.120-0.1200.0000.0000.0000.000
181A181SER0-0.0550.00714.8330.7290.7290.0000.0000.0000.000
182A182THR00.0380.03118.017-0.070-0.0700.0000.0000.0000.000
183A183ARG10.9070.94020.55613.11213.1120.0000.0000.0000.000
184A184SER0-0.0050.02123.3900.5090.5090.0000.0000.0000.000
185A185ASP-1-0.833-0.92920.964-14.044-14.0440.0000.0000.0000.000
186A186ILE00.0160.00519.1780.2600.2600.0000.0000.0000.000
187A187PHE0-0.011-0.01323.4330.3200.3200.0000.0000.0000.000
188A188LYS10.9580.98826.70711.52611.5260.0000.0000.0000.000
189A189LYS10.8060.89024.87012.89412.8940.0000.0000.0000.000
190A190TYR0-0.036-0.04228.2840.1800.1800.0000.0000.0000.000
191A191LYS10.8510.93231.8969.8799.8790.0000.0000.0000.000
192A192ASP-1-0.827-0.89933.837-9.122-9.1220.0000.0000.0000.000
193A193ASN0-0.046-0.04335.6170.1170.1170.0000.0000.0000.000
194A194LYS10.8530.94034.1889.5239.5230.0000.0000.0000.000
195A195THR0-0.048-0.03937.713-0.068-0.0680.0000.0000.0000.000
196A196ILE0-0.0200.00337.9820.0680.0680.0000.0000.0000.000
197A197ASN0-0.046-0.01641.8840.0410.0410.0000.0000.0000.000
198A198MET00.0470.01841.590-0.037-0.0370.0000.0000.0000.000
199A199LYS10.8910.94445.0236.4856.4850.0000.0000.0000.000
200A200ASP-1-0.847-0.92345.272-6.732-6.7320.0000.0000.0000.000
201A201PHE0-0.051-0.01638.249-0.149-0.1490.0000.0000.0000.000
202A202SER0-0.048-0.03542.2960.2220.2220.0000.0000.0000.000
203A203HIS0-0.0050.01438.3180.2210.2210.0000.0000.0000.000
204A204PHE0-0.0040.01532.789-0.069-0.0690.0000.0000.0000.000
205A205ASP-1-0.823-0.91133.198-8.887-8.8870.0000.0000.0000.000
206A206ILE0-0.013-0.01127.724-0.213-0.2130.0000.0000.0000.000
207A207TYR0-0.0030.01027.6150.0360.0360.0000.0000.0000.000
208A208LEU0-0.021-0.01023.170-0.527-0.5270.0000.0000.0000.000
209A209TRP00.006-0.01821.4940.2830.2830.0000.0000.0000.000
210A210THR0-0.044-0.04118.681-0.750-0.7500.0000.0000.0000.000
211A211LYS10.8290.92417.62313.16613.1660.0000.0000.0000.000