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

tag_button

FMODB ID: JQYG9

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 OptAll
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 -2663439.310262
FMO2-HF: Nuclear repulsion 2577774.746855
FMO2-HF: Total energy -85664.563407
FMO2-MP2: Total energy -85919.273702


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.
-147.822-155.25634.22-15.943-10.844-0.172
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 : 0.837 / 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-1-0.851-0.9133.866-37.771-35.433-0.021-1.203-1.114-0.001
4A4SER0-0.086-0.0476.3073.0453.0450.0000.0000.0000.000
5A5GLU-1-0.801-0.8701.746-153.647-163.41934.241-14.740-9.730-0.171
6A6ASN00.0780.0275.9774.1104.1100.0000.0000.0000.000
7A7ILE0-0.013-0.0068.2992.4872.4870.0000.0000.0000.000
8A8LYS10.8790.9487.70834.68334.6830.0000.0000.0000.000
9A9ASP-1-0.832-0.9117.037-38.412-38.4120.0000.0000.0000.000
10A10VAL0-0.044-0.01810.1502.5792.5790.0000.0000.0000.000
11A11LYS10.7620.89713.31321.76621.7660.0000.0000.0000.000
12A12LEU00.0300.01610.5531.6011.6010.0000.0000.0000.000
13A13GLN0-0.045-0.02313.4720.9890.9890.0000.0000.0000.000
14A14LEU0-0.0200.00015.8931.3391.3390.0000.0000.0000.000
15A15ASN00.001-0.01017.7641.1191.1190.0000.0000.0000.000
16A16TYR00.0080.00417.8941.0391.0390.0000.0000.0000.000
17A17ALA0-0.050-0.01919.6350.9130.9130.0000.0000.0000.000
18A18TYR00.038-0.00921.8860.6420.6420.0000.0000.0000.000
19A19GLU-1-0.853-0.89522.150-12.631-12.6310.0000.0000.0000.000
20A20ILE0-0.099-0.04524.7080.0400.0400.0000.0000.0000.000
21A21ILE00.0150.00527.6170.2180.2180.0000.0000.0000.000
22A22PRO0-0.0080.00431.451-0.059-0.0590.0000.0000.0000.000
23A23VAL0-0.023-0.02533.2530.2500.2500.0000.0000.0000.000
24A24ASP-1-0.833-0.91936.205-8.160-8.1600.0000.0000.0000.000
25A25TYR00.0120.00738.7210.1550.1550.0000.0000.0000.000
26A26THR00.0250.00642.4070.0310.0310.0000.0000.0000.000
27A27ASN00.0140.01645.6430.0890.0890.0000.0000.0000.000
28A28CYS0-0.0120.01445.3820.0560.0560.0000.0000.0000.000
29A29ASN0-0.004-0.01847.5690.1380.1380.0000.0000.0000.000
30A30ILE00.0090.00846.638-0.137-0.1370.0000.0000.0000.000
31A31ASP-1-0.825-0.89348.045-6.309-6.3090.0000.0000.0000.000
32A32TYR0-0.046-0.05046.9760.2170.2170.0000.0000.0000.000
33A33LEU00.0000.01745.637-0.136-0.1360.0000.0000.0000.000
34A34THR0-0.013-0.02042.3170.1430.1430.0000.0000.0000.000
35A35THR0-0.009-0.01942.2710.0890.0890.0000.0000.0000.000
36A36HIS0-0.033-0.01238.594-0.003-0.0030.0000.0000.0000.000
37A37ASP-1-0.749-0.80639.005-8.278-8.2780.0000.0000.0000.000
38A38PHE0-0.019-0.01940.6390.2780.2780.0000.0000.0000.000
39A39TYR0-0.054-0.03840.284-0.139-0.1390.0000.0000.0000.000
40A40ILE0-0.026-0.01142.8390.1960.1960.0000.0000.0000.000
41A41ASP-1-0.749-0.85444.276-6.785-6.7850.0000.0000.0000.000
42A42ILE0-0.011-0.01441.051-0.059-0.0590.0000.0000.0000.000
43A43SER00.040-0.00545.534-0.065-0.0650.0000.0000.0000.000
44A44SER0-0.058-0.01347.7220.0230.0230.0000.0000.0000.000
45A45TYR0-0.039-0.03445.1930.0460.0460.0000.0000.0000.000
46A46LYS10.8340.90639.3047.9827.9820.0000.0000.0000.000
47A47LYS10.8480.92845.7376.4206.4200.0000.0000.0000.000
48A48LYS10.8540.92042.5197.5077.5070.0000.0000.0000.000
49A49ASN0-0.006-0.00846.0930.0270.0270.0000.0000.0000.000
50A50PHE0-0.010-0.01738.577-0.132-0.1320.0000.0000.0000.000
51A51SER0-0.0080.00642.5370.0950.0950.0000.0000.0000.000
52A52VAL0-0.019-0.01837.938-0.224-0.2240.0000.0000.0000.000
53A53ASH0-0.026-0.02637.5640.1300.1300.0000.0000.0000.000
54A54SER0-0.059-0.04336.998-0.226-0.2260.0000.0000.0000.000
55A55GLU-1-0.710-0.82633.167-9.479-9.4790.0000.0000.0000.000
56A56VAL0-0.028-0.03035.416-0.224-0.2240.0000.0000.0000.000
57A57GLU-1-0.896-0.96733.804-9.354-9.3540.0000.0000.0000.000
58A58SER00.014-0.00537.5020.1660.1660.0000.0000.0000.000
59A59TYR0-0.014-0.00440.889-0.064-0.0640.0000.0000.0000.000
60A60ILE00.0130.01238.8740.1390.1390.0000.0000.0000.000
61A61THR00.008-0.01242.2460.1170.1170.0000.0000.0000.000
62A62THR00.008-0.00844.4550.0910.0910.0000.0000.0000.000
63A63LYS10.8400.95141.9077.6977.6970.0000.0000.0000.000
64A64PHE0-0.032-0.01043.9130.0460.0460.0000.0000.0000.000
65A65THR00.0100.00048.8310.1000.1000.0000.0000.0000.000
66A66LYS10.9690.97950.2756.0636.0630.0000.0000.0000.000
67A67ASN0-0.015-0.00951.6920.0570.0570.0000.0000.0000.000
68A68GLN00.0280.03549.8210.0930.0930.0000.0000.0000.000
69A69LYS10.8740.93350.0256.0036.0030.0000.0000.0000.000
70A70VAL0-0.012-0.01344.9120.0030.0030.0000.0000.0000.000
71A71ASN0-0.038-0.03243.2870.1100.1100.0000.0000.0000.000
72A72ILE0-0.009-0.01338.395-0.050-0.0500.0000.0000.0000.000
73A73PHE00.009-0.00333.052-0.008-0.0080.0000.0000.0000.000
74A74GLY00.0010.01033.858-0.077-0.0770.0000.0000.0000.000
75A75LEU0-0.0140.00227.8810.0900.0900.0000.0000.0000.000
76A76PRO0-0.029-0.00830.317-0.022-0.0220.0000.0000.0000.000
77A77TYR0-0.030-0.04027.630-0.491-0.4910.0000.0000.0000.000
78A78ILE0-0.047-0.01227.282-0.438-0.4380.0000.0000.0000.000
79A79PHE00.0100.00628.7040.3610.3610.0000.0000.0000.000
80A80THR00.0230.00431.820-0.016-0.0160.0000.0000.0000.000
81A81ARG10.9290.95734.5208.1918.1910.0000.0000.0000.000
82A82TYR00.0310.01437.3980.2090.2090.0000.0000.0000.000
83A83ASP-1-0.773-0.86138.534-7.767-7.7670.0000.0000.0000.000
84A84VAL0-0.023-0.01838.1850.2030.2030.0000.0000.0000.000
85A85TYR0-0.0030.01735.358-0.157-0.1570.0000.0000.0000.000
86A86TYR00.0270.01332.9720.2490.2490.0000.0000.0000.000
87A87ILE0-0.021-0.00532.568-0.338-0.3380.0000.0000.0000.000
88A88TYR00.0210.00927.9850.2370.2370.0000.0000.0000.000
89A89GLY00.0630.02333.114-0.063-0.0630.0000.0000.0000.000
90A90GLY0-0.0020.00936.146-0.009-0.0090.0000.0000.0000.000
91A91VAL0-0.011-0.00636.9300.1320.1320.0000.0000.0000.000
92A92THR0-0.017-0.00940.7810.0130.0130.0000.0000.0000.000
93A93PRO00.016-0.00143.5470.0720.0720.0000.0000.0000.000
94A94SER0-0.0130.01647.420-0.070-0.0700.0000.0000.0000.000
95A95VAL0-0.019-0.01948.8220.1370.1370.0000.0000.0000.000
96A96ASN0-0.020-0.02250.3630.0540.0540.0000.0000.0000.000
97A97SER00.0060.00351.388-0.030-0.0300.0000.0000.0000.000
98A98ASN0-0.0240.00746.672-0.106-0.1060.0000.0000.0000.000
99A99SER00.0350.00647.335-0.048-0.0480.0000.0000.0000.000
100A100GLU-1-0.868-0.92746.038-6.469-6.4690.0000.0000.0000.000
101A101ASN0-0.040-0.04546.556-0.222-0.2220.0000.0000.0000.000
102A102SER00.0080.01745.1890.0930.0930.0000.0000.0000.000
103A103LYS10.9300.98143.7727.0917.0910.0000.0000.0000.000
104A104ILE00.0310.02538.106-0.004-0.0040.0000.0000.0000.000
105A105VAL0-0.033-0.03639.794-0.048-0.0480.0000.0000.0000.000
106A106GLY00.0750.02436.6590.0090.0090.0000.0000.0000.000
107A107ASN0-0.069-0.02734.9340.2170.2170.0000.0000.0000.000
108A108LEU00.0060.01227.472-0.223-0.2230.0000.0000.0000.000
109A109LEU00.0260.01830.1230.1000.1000.0000.0000.0000.000
110A110ILE0-0.013-0.02024.262-0.472-0.4720.0000.0000.0000.000
111A111ASP-1-0.803-0.89222.769-13.595-13.5950.0000.0000.0000.000
112A112GLY00.0230.01525.6750.2310.2310.0000.0000.0000.000
113A113VAL0-0.0170.00229.0590.4620.4620.0000.0000.0000.000
114A114GLN00.0300.00630.479-0.532-0.5320.0000.0000.0000.000
115A115GLN0-0.044-0.01928.7170.1160.1160.0000.0000.0000.000
116A116LYS10.9350.95832.1959.4489.4480.0000.0000.0000.000
117A117THR00.0070.01334.523-0.105-0.1050.0000.0000.0000.000
118A118LEU0-0.082-0.03832.2130.0600.0600.0000.0000.0000.000
119A119ILE00.010-0.02436.9320.2030.2030.0000.0000.0000.000
120A120ASN00.000-0.00339.156-0.042-0.0420.0000.0000.0000.000
121A121PRO0-0.0080.01333.8100.0060.0060.0000.0000.0000.000
122A122ILE00.0050.00533.504-0.234-0.2340.0000.0000.0000.000
123A123LYS10.8330.90936.4297.4547.4540.0000.0000.0000.000
124A124ILE0-0.005-0.00636.990-0.181-0.1810.0000.0000.0000.000
125A125ASP-1-0.815-0.88740.763-7.256-7.2560.0000.0000.0000.000
126A126LYS10.8070.90539.7408.2068.2060.0000.0000.0000.000
127A127PRO00.0190.01144.064-0.141-0.1410.0000.0000.0000.000
128A128ILE0-0.011-0.00543.9330.0040.0040.0000.0000.0000.000
129A129PHE00.0160.01538.296-0.019-0.0190.0000.0000.0000.000
130A130THR00.0680.03636.438-0.062-0.0620.0000.0000.0000.000
131A131ILE00.022-0.00332.464-0.067-0.0670.0000.0000.0000.000
132A132GLN00.0110.01031.390-0.426-0.4260.0000.0000.0000.000
133A133GLU-1-0.754-0.86032.190-8.549-8.5490.0000.0000.0000.000
134A134PHE00.008-0.00833.421-0.097-0.0970.0000.0000.0000.000
135A135ASP-1-0.770-0.85528.178-11.770-11.7700.0000.0000.0000.000
136A136PHE00.0120.00428.373-0.292-0.2920.0000.0000.0000.000
137A137LYS10.7970.89329.2008.4158.4150.0000.0000.0000.000
138A138ILE00.0000.00029.529-0.103-0.1030.0000.0000.0000.000
139A139ARG10.7910.87323.10612.65512.6550.0000.0000.0000.000
140A140GLN00.023-0.00626.104-0.193-0.1930.0000.0000.0000.000
141A141TYR00.0340.02527.591-0.177-0.1770.0000.0000.0000.000
142A142LEU00.000-0.00625.314-0.083-0.0830.0000.0000.0000.000
143A143MET0-0.040-0.00622.298-0.354-0.3540.0000.0000.0000.000
144A144GLN0-0.022-0.01923.923-0.037-0.0370.0000.0000.0000.000
145A145THR0-0.076-0.02426.5680.0800.0800.0000.0000.0000.000
146A146TYR0-0.032-0.03424.8440.0410.0410.0000.0000.0000.000
147A147LYS10.9140.95720.24512.33712.3370.0000.0000.0000.000
148A148ILE0-0.0020.02419.477-1.046-1.0460.0000.0000.0000.000
149A149TYR0-0.008-0.02317.635-0.409-0.4090.0000.0000.0000.000
150A150ASP-1-0.788-0.87615.984-19.765-19.7650.0000.0000.0000.000
151A151PRO0-0.017-0.02310.913-0.170-0.1700.0000.0000.0000.000
152A152ASN0-0.055-0.04912.298-2.528-2.5280.0000.0000.0000.000
153A153SER0-0.038-0.01214.3080.5180.5180.0000.0000.0000.000
154A154PRO00.000-0.01215.786-0.953-0.9530.0000.0000.0000.000
155A155TYR0-0.007-0.00516.954-0.142-0.1420.0000.0000.0000.000
156A156ILE00.0190.01413.819-0.868-0.8680.0000.0000.0000.000
157A157LYS10.9560.97616.76516.54516.5450.0000.0000.0000.000
158A158GLY00.0440.00919.7700.2360.2360.0000.0000.0000.000
159A159GLN00.0090.01723.301-0.193-0.1930.0000.0000.0000.000
160A160LEU00.0100.01126.5300.1120.1120.0000.0000.0000.000
161A161GLU-1-0.821-0.86729.503-9.956-9.9560.0000.0000.0000.000
162A162ILE0-0.029-0.03032.8980.1030.1030.0000.0000.0000.000
163A163ALA00.0390.03836.2520.0960.0960.0000.0000.0000.000
164A164ILE0-0.029-0.01639.4480.1880.1880.0000.0000.0000.000
165A165ASN0-0.026-0.03842.1110.1110.1110.0000.0000.0000.000
166A166GLY0-0.026-0.01445.5770.0100.0100.0000.0000.0000.000
167A167ASN0-0.026-0.02842.756-0.094-0.0940.0000.0000.0000.000
168A168LYS10.9590.99740.8087.1047.1040.0000.0000.0000.000
169A169HIS00.0450.01736.912-0.109-0.1090.0000.0000.0000.000
170A170GLU-1-0.820-0.88435.061-9.261-9.2610.0000.0000.0000.000
171A171SER0-0.040-0.04630.871-0.219-0.2190.0000.0000.0000.000
172A172PHE00.0050.00328.056-0.067-0.0670.0000.0000.0000.000
173A173ASN00.000-0.00820.687-0.149-0.1490.0000.0000.0000.000
174A174LEU00.0120.01123.3610.0520.0520.0000.0000.0000.000
175A175TYR0-0.024-0.02417.141-0.159-0.1590.0000.0000.0000.000
176A176ASP-1-0.808-0.87219.137-14.310-14.3100.0000.0000.0000.000
177A177ALA00.0240.01117.1440.5020.5020.0000.0000.0000.000
178A178THR00.0260.01614.478-0.602-0.6020.0000.0000.0000.000
179A179SER00.0480.0159.9061.8711.8710.0000.0000.0000.000
180A180SER0-0.020-0.01712.017-0.688-0.6880.0000.0000.0000.000
181A181SER0-0.049-0.00714.6481.4211.4210.0000.0000.0000.000
182A182THR00.009-0.02117.887-0.138-0.1380.0000.0000.0000.000
183A183ARG10.8960.93620.32613.26013.2600.0000.0000.0000.000
184A184SER00.0490.03423.2190.4980.4980.0000.0000.0000.000
185A185ASP-1-0.831-0.87621.425-13.498-13.4980.0000.0000.0000.000
186A186ILE00.0610.02618.7230.3010.3010.0000.0000.0000.000
187A187PHE0-0.006-0.01123.0810.3360.3360.0000.0000.0000.000
188A188LYS10.8670.92425.35712.47412.4740.0000.0000.0000.000
189A189LYS10.7910.88024.73112.94712.9470.0000.0000.0000.000
190A190TYR0-0.028-0.02828.1170.1370.1370.0000.0000.0000.000
191A191LYS10.8200.91731.7619.7249.7240.0000.0000.0000.000
192A192ASP-1-0.793-0.89833.807-9.074-9.0740.0000.0000.0000.000
193A193ASN0-0.036-0.03535.5660.1520.1520.0000.0000.0000.000
194A194LYS10.8040.91034.2419.5689.5680.0000.0000.0000.000
195A195THR0-0.045-0.03937.453-0.102-0.1020.0000.0000.0000.000
196A196ILE0-0.0290.00237.8560.0890.0890.0000.0000.0000.000
197A197ASN0-0.032-0.02641.8370.0470.0470.0000.0000.0000.000
198A198MET00.0130.00241.994-0.052-0.0520.0000.0000.0000.000
199A199LYS10.8220.89545.1726.5476.5470.0000.0000.0000.000
200A200ASP-1-0.776-0.86545.317-6.687-6.6870.0000.0000.0000.000
201A201PHE0-0.0280.00638.272-0.112-0.1120.0000.0000.0000.000
202A202SER0-0.044-0.00842.3920.2410.2410.0000.0000.0000.000
203A203HIS0-0.048-0.04238.0650.2800.2800.0000.0000.0000.000
204A204PHE0-0.0060.00333.405-0.070-0.0700.0000.0000.0000.000
205A205ASP-1-0.785-0.87333.538-8.831-8.8310.0000.0000.0000.000
206A206ILE0-0.025-0.01227.682-0.229-0.2290.0000.0000.0000.000
207A207TYR0-0.021-0.01627.3830.1050.1050.0000.0000.0000.000
208A208LEU0-0.0180.00122.932-0.514-0.5140.0000.0000.0000.000
209A209TRP00.001-0.01221.4760.3640.3640.0000.0000.0000.000
210A210THR0-0.012-0.02318.390-0.762-0.7620.0000.0000.0000.000
211A211LYS10.8190.91517.49813.43013.4300.0000.0000.0000.000