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: NN8QQ

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2663846.156864
FMO2-HF: Nuclear repulsion 2578181.871272
FMO2-HF: Total energy -85664.285592
FMO2-MP2: Total energy -85919.005971


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.
-150.515-156.6433.211-16.371-10.713-0.173
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 : 0.827 / q_NPA : 0.871
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-1-0.830-0.8943.825-35.397-32.356-0.034-1.673-1.333-0.002
4A4SER0-0.075-0.0426.5973.4713.4710.0000.0000.0000.000
5A5GLU-1-0.781-0.8671.739-153.535-162.70133.245-14.698-9.380-0.171
6A6ASN00.0640.0265.9992.4192.4190.0000.0000.0000.000
7A7ILE0-0.004-0.0018.4581.9951.9950.0000.0000.0000.000
8A8LYS10.9060.9547.57033.34233.3420.0000.0000.0000.000
9A9ASP-1-0.833-0.9146.830-38.771-38.7710.0000.0000.0000.000
10A10VAL0-0.060-0.0249.9992.4932.4930.0000.0000.0000.000
11A11LYS10.7620.88513.20021.79921.7990.0000.0000.0000.000
12A12LEU00.0230.01710.2851.6611.6610.0000.0000.0000.000
13A13GLN0-0.034-0.01313.5670.7740.7740.0000.0000.0000.000
14A14LEU0-0.035-0.00815.9011.3631.3630.0000.0000.0000.000
15A15ASN00.018-0.00317.6431.2411.2410.0000.0000.0000.000
16A16TYR00.0100.00918.0501.0111.0110.0000.0000.0000.000
17A17ALA0-0.028-0.01119.7730.9500.9500.0000.0000.0000.000
18A18TYR00.035-0.02121.8860.6800.6800.0000.0000.0000.000
19A19GLU-1-0.881-0.89122.163-12.362-12.3620.0000.0000.0000.000
20A20ILE0-0.092-0.05124.6890.0160.0160.0000.0000.0000.000
21A21ILE00.0140.00327.6150.2060.2060.0000.0000.0000.000
22A22PRO0-0.025-0.00331.421-0.053-0.0530.0000.0000.0000.000
23A23VAL0-0.038-0.02033.1800.2440.2440.0000.0000.0000.000
24A24ASP-1-0.875-0.95836.137-8.202-8.2020.0000.0000.0000.000
25A25TYR00.0130.00638.8450.1680.1680.0000.0000.0000.000
26A26THR00.0630.03442.468-0.040-0.0400.0000.0000.0000.000
27A27ASN0-0.038-0.01645.4360.1180.1180.0000.0000.0000.000
28A28CYS0-0.0240.00845.6360.0640.0640.0000.0000.0000.000
29A29ASN00.0200.00547.7050.0950.0950.0000.0000.0000.000
30A30ILE0-0.0100.00646.568-0.126-0.1260.0000.0000.0000.000
31A31ASP-1-0.804-0.88847.968-6.284-6.2840.0000.0000.0000.000
32A32TYR0-0.057-0.05047.4100.2200.2200.0000.0000.0000.000
33A33LEU0-0.0250.00745.830-0.152-0.1520.0000.0000.0000.000
34A34THR00.0120.01142.7840.1430.1430.0000.0000.0000.000
35A35THR0-0.005-0.02742.5550.0360.0360.0000.0000.0000.000
36A36HIS0-0.031-0.00838.8370.0320.0320.0000.0000.0000.000
37A37ASP-1-0.779-0.83639.290-8.361-8.3610.0000.0000.0000.000
38A38PHE0-0.016-0.01640.6340.2780.2780.0000.0000.0000.000
39A39TYR0-0.047-0.02940.481-0.103-0.1030.0000.0000.0000.000
40A40ILE0-0.029-0.02342.8760.2110.2110.0000.0000.0000.000
41A41ASP-1-0.759-0.84244.328-6.785-6.7850.0000.0000.0000.000
42A42ILE0-0.026-0.02441.328-0.007-0.0070.0000.0000.0000.000
43A43SER00.051-0.01845.721-0.057-0.0570.0000.0000.0000.000
44A44SER0-0.042-0.01047.882-0.013-0.0130.0000.0000.0000.000
45A45TYR0-0.022-0.03945.0720.0610.0610.0000.0000.0000.000
46A46LYS10.8390.92439.4907.8897.8890.0000.0000.0000.000
47A47LYS10.8420.93045.8816.3906.3900.0000.0000.0000.000
48A48LYS10.8430.90742.3507.4917.4910.0000.0000.0000.000
49A49ASN0-0.0070.00546.2720.0380.0380.0000.0000.0000.000
50A50PHE0-0.001-0.01738.768-0.134-0.1340.0000.0000.0000.000
51A51SER00.0000.01742.7680.0880.0880.0000.0000.0000.000
52A52VAL0-0.015-0.01638.167-0.222-0.2220.0000.0000.0000.000
53A53ASH0-0.045-0.04237.9990.1360.1360.0000.0000.0000.000
54A54SER0-0.057-0.04237.095-0.252-0.2520.0000.0000.0000.000
55A55GLU-1-0.745-0.85533.651-9.384-9.3840.0000.0000.0000.000
56A56VAL0-0.026-0.04135.585-0.235-0.2350.0000.0000.0000.000
57A57GLU-1-0.898-0.96533.583-9.346-9.3460.0000.0000.0000.000
58A58SER00.003-0.01437.4170.1760.1760.0000.0000.0000.000
59A59TYR0-0.028-0.00840.736-0.059-0.0590.0000.0000.0000.000
60A60ILE00.0600.03139.3730.1000.1000.0000.0000.0000.000
61A61THR00.0330.00242.5320.1320.1320.0000.0000.0000.000
62A62THR0-0.009-0.00444.8280.0950.0950.0000.0000.0000.000
63A63LYS10.8600.95142.4227.6257.6250.0000.0000.0000.000
64A64PHE0-0.037-0.01443.9740.0570.0570.0000.0000.0000.000
65A65THR00.0120.00448.7420.1070.1070.0000.0000.0000.000
66A66LYS10.9550.96250.6265.9985.9980.0000.0000.0000.000
67A67ASN00.0010.00051.6210.0550.0550.0000.0000.0000.000
68A68GLN00.0330.04149.7640.0920.0920.0000.0000.0000.000
69A69LYS10.8720.92449.9775.9765.9760.0000.0000.0000.000
70A70VAL0-0.003-0.01644.9110.0040.0040.0000.0000.0000.000
71A71ASN0-0.051-0.03443.3070.1020.1020.0000.0000.0000.000
72A72ILE00.000-0.01238.460-0.071-0.0710.0000.0000.0000.000
73A73PHE00.0180.00733.358-0.033-0.0330.0000.0000.0000.000
74A74GLY0-0.0100.00133.996-0.081-0.0810.0000.0000.0000.000
75A75LEU0-0.0100.00528.0140.0680.0680.0000.0000.0000.000
76A76PRO0-0.0180.00030.296-0.024-0.0240.0000.0000.0000.000
77A77TYR0-0.023-0.02027.323-0.520-0.5200.0000.0000.0000.000
78A78ILE0-0.041-0.01427.168-0.422-0.4220.0000.0000.0000.000
79A79PHE00.0070.00928.6580.3570.3570.0000.0000.0000.000
80A80THR00.0210.00331.663-0.015-0.0150.0000.0000.0000.000
81A81ARG10.9410.95934.3918.1688.1680.0000.0000.0000.000
82A82TYR00.0110.00937.2840.1800.1800.0000.0000.0000.000
83A83ASP-1-0.773-0.86138.553-7.787-7.7870.0000.0000.0000.000
84A84VAL0-0.025-0.02538.5870.2090.2090.0000.0000.0000.000
85A85TYR0-0.0120.01435.444-0.142-0.1420.0000.0000.0000.000
86A86TYR00.0330.01533.1800.2180.2180.0000.0000.0000.000
87A87ILE0-0.004-0.00332.688-0.326-0.3260.0000.0000.0000.000
88A88TYR00.0380.03328.2630.1720.1720.0000.0000.0000.000
89A89GLY00.0650.03333.540-0.079-0.0790.0000.0000.0000.000
90A90GLY00.0140.01436.3200.0420.0420.0000.0000.0000.000
91A91VAL0-0.031-0.00737.1430.1530.1530.0000.0000.0000.000
92A92THR0-0.0010.00740.8570.0260.0260.0000.0000.0000.000
93A93PRO00.0300.01043.4940.0730.0730.0000.0000.0000.000
94A94SER0-0.0220.01647.166-0.078-0.0780.0000.0000.0000.000
95A95VAL0-0.011-0.02748.7140.1220.1220.0000.0000.0000.000
96A96ASN0-0.012-0.02550.4800.0400.0400.0000.0000.0000.000
97A97SER0-0.020-0.01251.394-0.032-0.0320.0000.0000.0000.000
98A98ASN0-0.038-0.00946.647-0.147-0.1470.0000.0000.0000.000
99A99SER00.0540.03247.472-0.061-0.0610.0000.0000.0000.000
100A100GLU-1-0.880-0.93446.390-6.387-6.3870.0000.0000.0000.000
101A101ASN0-0.032-0.02446.597-0.242-0.2420.0000.0000.0000.000
102A102SER00.0130.01545.2290.1360.1360.0000.0000.0000.000
103A103LYS10.9260.97243.4997.0587.0580.0000.0000.0000.000
104A104ILE00.0120.01038.115-0.004-0.0040.0000.0000.0000.000
105A105VAL0-0.024-0.02939.457-0.084-0.0840.0000.0000.0000.000
106A106GLY00.0680.01836.1390.0100.0100.0000.0000.0000.000
107A107ASN0-0.095-0.03835.1040.1930.1930.0000.0000.0000.000
108A108LEU00.0120.01827.713-0.230-0.2300.0000.0000.0000.000
109A109LEU00.0220.00630.0880.1310.1310.0000.0000.0000.000
110A110ILE00.004-0.00324.192-0.462-0.4620.0000.0000.0000.000
111A111ASP-1-0.777-0.87323.007-13.554-13.5540.0000.0000.0000.000
112A112GLY00.0130.00825.9290.2540.2540.0000.0000.0000.000
113A113VAL0-0.0180.00829.2330.4480.4480.0000.0000.0000.000
114A114GLN00.0280.00530.625-0.505-0.5050.0000.0000.0000.000
115A115GLN0-0.052-0.02828.6940.0410.0410.0000.0000.0000.000
116A116LYS10.9380.96232.1659.3019.3010.0000.0000.0000.000
117A117THR00.0220.02634.690-0.101-0.1010.0000.0000.0000.000
118A118LEU0-0.066-0.03731.7140.1060.1060.0000.0000.0000.000
119A119ILE00.012-0.01636.3560.1930.1930.0000.0000.0000.000
120A120ASN0-0.007-0.00138.968-0.008-0.0080.0000.0000.0000.000
121A121PRO0-0.0110.01433.6420.0030.0030.0000.0000.0000.000
122A122ILE00.0160.00833.272-0.175-0.1750.0000.0000.0000.000
123A123LYS10.8420.89936.2417.4857.4850.0000.0000.0000.000
124A124ILE0-0.024-0.01437.125-0.164-0.1640.0000.0000.0000.000
125A125ASP-1-0.788-0.87140.823-7.239-7.2390.0000.0000.0000.000
126A126LYS10.8370.93839.9418.1548.1540.0000.0000.0000.000
127A127PRO00.0380.01844.369-0.122-0.1220.0000.0000.0000.000
128A128ILE0-0.018-0.00843.929-0.020-0.0200.0000.0000.0000.000
129A129PHE00.0200.00138.247-0.017-0.0170.0000.0000.0000.000
130A130THR00.0770.04336.623-0.101-0.1010.0000.0000.0000.000
131A131ILE00.0300.00632.587-0.063-0.0630.0000.0000.0000.000
132A132GLN00.0240.01831.488-0.446-0.4460.0000.0000.0000.000
133A133GLU-1-0.768-0.86032.199-8.549-8.5490.0000.0000.0000.000
134A134PHE0-0.003-0.01233.453-0.129-0.1290.0000.0000.0000.000
135A135ASP-1-0.782-0.86028.238-11.737-11.7370.0000.0000.0000.000
136A136PHE00.0040.00428.379-0.270-0.2700.0000.0000.0000.000
137A137LYS10.8100.89029.3398.4248.4240.0000.0000.0000.000
138A138ILE00.0090.00929.342-0.114-0.1140.0000.0000.0000.000
139A139ARG10.8190.88823.18412.63212.6320.0000.0000.0000.000
140A140GLN00.027-0.00225.929-0.202-0.2020.0000.0000.0000.000
141A141TYR00.0230.01827.389-0.173-0.1730.0000.0000.0000.000
142A142LEU00.010-0.00625.112-0.111-0.1110.0000.0000.0000.000
143A143MET0-0.053-0.01022.130-0.383-0.3830.0000.0000.0000.000
144A144GLN0-0.025-0.02323.534-0.129-0.1290.0000.0000.0000.000
145A145THR0-0.073-0.03026.1890.1050.1050.0000.0000.0000.000
146A146TYR0-0.031-0.02424.4470.1060.1060.0000.0000.0000.000
147A147LYS10.9050.95920.03412.39512.3950.0000.0000.0000.000
148A148ILE00.0040.02319.380-1.004-1.0040.0000.0000.0000.000
149A149TYR0-0.018-0.02817.541-0.469-0.4690.0000.0000.0000.000
150A150ASP-1-0.796-0.88315.789-19.610-19.6100.0000.0000.0000.000
151A151PRO0-0.008-0.02110.884-0.177-0.1770.0000.0000.0000.000
152A152ASN0-0.078-0.05312.486-2.134-2.1340.0000.0000.0000.000
153A153SER0-0.038-0.00814.4200.6800.6800.0000.0000.0000.000
154A154PRO0-0.006-0.01815.718-1.000-1.0000.0000.0000.0000.000
155A155TYR00.003-0.00117.148-0.153-0.1530.0000.0000.0000.000
156A156ILE00.0110.01013.987-0.990-0.9900.0000.0000.0000.000
157A157LYS10.9560.97616.96916.37016.3700.0000.0000.0000.000
158A158GLY00.0450.01220.0870.2320.2320.0000.0000.0000.000
159A159GLN00.0020.02023.468-0.063-0.0630.0000.0000.0000.000
160A160LEU0-0.0050.01226.7070.1770.1770.0000.0000.0000.000
161A161GLU-1-0.820-0.90529.636-9.947-9.9470.0000.0000.0000.000
162A162ILE0-0.052-0.03732.9600.1390.1390.0000.0000.0000.000
163A163ALA00.0420.03536.1870.0830.0830.0000.0000.0000.000
164A164ILE0-0.032-0.02239.4320.1490.1490.0000.0000.0000.000
165A165ASN0-0.049-0.05042.2720.1440.1440.0000.0000.0000.000
166A166GLY0-0.002-0.00845.8080.0360.0360.0000.0000.0000.000
167A167ASN0-0.054-0.03642.902-0.064-0.0640.0000.0000.0000.000
168A168LYS10.9610.99540.7287.1827.1820.0000.0000.0000.000
169A169HIS00.0690.02636.630-0.053-0.0530.0000.0000.0000.000
170A170GLU-1-0.834-0.89334.683-9.233-9.2330.0000.0000.0000.000
171A171SER00.004-0.01530.559-0.238-0.2380.0000.0000.0000.000
172A172PHE0-0.014-0.00628.145-0.053-0.0530.0000.0000.0000.000
173A173ASN00.0210.00920.794-0.201-0.2010.0000.0000.0000.000
174A174LEU00.0170.01023.384-0.020-0.0200.0000.0000.0000.000
175A175TYR0-0.026-0.02517.221-0.164-0.1640.0000.0000.0000.000
176A176ASP-1-0.829-0.89318.893-14.308-14.3080.0000.0000.0000.000
177A177ALA00.0000.00217.3740.5000.5000.0000.0000.0000.000
178A178THR00.0220.00314.529-0.870-0.8700.0000.0000.0000.000
179A179SER00.0420.0039.9231.7431.7430.0000.0000.0000.000
180A180SER00.000-0.01012.306-0.148-0.1480.0000.0000.0000.000
181A181SER0-0.067-0.00114.8480.7390.7390.0000.0000.0000.000
182A182THR00.031-0.00318.004-0.069-0.0690.0000.0000.0000.000
183A183ARG10.9070.94120.59513.13713.1370.0000.0000.0000.000
184A184SER0-0.0010.01223.4140.4920.4920.0000.0000.0000.000
185A185ASP-1-0.825-0.89721.244-13.910-13.9100.0000.0000.0000.000
186A186ILE00.0230.01219.1090.2420.2420.0000.0000.0000.000
187A187PHE0-0.010-0.01823.3730.3230.3230.0000.0000.0000.000
188A188LYS10.9390.97526.65611.85211.8520.0000.0000.0000.000
189A189LYS10.8150.90024.80012.90612.9060.0000.0000.0000.000
190A190TYR0-0.040-0.04428.0880.1810.1810.0000.0000.0000.000
191A191LYS10.8200.91431.8819.7089.7080.0000.0000.0000.000
192A192ASP-1-0.822-0.90333.733-9.064-9.0640.0000.0000.0000.000
193A193ASN0-0.058-0.05135.5250.1570.1570.0000.0000.0000.000
194A194LYS10.8110.91034.6289.5029.5020.0000.0000.0000.000
195A195THR0-0.054-0.04537.594-0.067-0.0670.0000.0000.0000.000
196A196ILE0-0.0220.00437.7700.0670.0670.0000.0000.0000.000
197A197ASN0-0.043-0.02841.7390.0370.0370.0000.0000.0000.000
198A198MET00.0400.01841.823-0.040-0.0400.0000.0000.0000.000
199A199LYS10.8370.91044.8806.5446.5440.0000.0000.0000.000
200A200ASP-1-0.797-0.88445.302-6.693-6.6930.0000.0000.0000.000
201A201PHE0-0.0230.00838.245-0.133-0.1330.0000.0000.0000.000
202A202SER0-0.044-0.01042.2800.2230.2230.0000.0000.0000.000
203A203HIS0-0.044-0.03038.0730.2790.2790.0000.0000.0000.000
204A204PHE0-0.0100.01633.128-0.076-0.0760.0000.0000.0000.000
205A205ASP-1-0.789-0.88533.498-8.841-8.8410.0000.0000.0000.000
206A206ILE0-0.002-0.00527.607-0.219-0.2190.0000.0000.0000.000
207A207TYR0-0.0030.01027.7590.0660.0660.0000.0000.0000.000
208A208LEU0-0.016-0.00823.206-0.539-0.5390.0000.0000.0000.000
209A209TRP00.004-0.01821.7210.3270.3270.0000.0000.0000.000
210A210THR0-0.040-0.04818.710-0.756-0.7560.0000.0000.0000.000
211A211LYS10.8190.91917.66013.34813.3480.0000.0000.0000.000