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: YZ162

Calculation Name: 1TQJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TQJ

Chain ID: A

ChEMBL ID:

UniProt ID: P74061

Base Structure: X-ray

Registration Date: 2023-06-22

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2626078.351912
FMO2-HF: Nuclear repulsion 2542460.45333
FMO2-HF: Total energy -83617.898582
FMO2-MP2: Total energy -83862.816565


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-210.116-191.24711.908-11.769-19.007-0.136
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.936
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].
3A5ILE00.003-0.0053.504-4.619-2.7980.006-0.880-0.9460.002
4A6VAL0-0.0020.0095.1512.3902.3900.0000.0000.0000.000
5A7VAL0-0.034-0.0157.0410.7050.7050.0000.0000.0000.000
6A8ALA00.004-0.00510.7530.1620.1620.0000.0000.0000.000
7A9PRO0-0.004-0.01112.5570.5540.5540.0000.0000.0000.000
8A10SER00.0110.00016.3100.0090.0090.0000.0000.0000.000
9A11ILE00.0410.01218.2640.7090.7090.0000.0000.0000.000
10A12LEU0-0.029-0.00921.0730.6840.6840.0000.0000.0000.000
11A13SER0-0.054-0.03222.4580.5320.5320.0000.0000.0000.000
12A14ALA0-0.055-0.00723.4350.2720.2720.0000.0000.0000.000
13A15ASP-1-0.771-0.86525.237-9.411-9.4110.0000.0000.0000.000
14A16PHE0-0.017-0.03124.596-0.066-0.0660.0000.0000.0000.000
15A17SER0-0.103-0.05529.3910.1910.1910.0000.0000.0000.000
16A18ARG10.8310.90329.30610.06210.0620.0000.0000.0000.000
17A19LEU00.0510.02924.140-0.286-0.2860.0000.0000.0000.000
18A20GLY00.014-0.00925.628-0.458-0.4580.0000.0000.0000.000
19A21GLU-1-0.871-0.93726.026-9.873-9.8730.0000.0000.0000.000
20A22GLU-1-0.766-0.84924.257-11.775-11.7750.0000.0000.0000.000
21A23ILE0-0.039-0.01620.576-0.607-0.6070.0000.0000.0000.000
22A24LYS10.8970.94021.11212.13212.1320.0000.0000.0000.000
23A25ALA00.0360.02922.235-0.287-0.2870.0000.0000.0000.000
24A26VAL0-0.009-0.01518.272-0.313-0.3130.0000.0000.0000.000
25A27ASP-1-0.895-0.92517.330-16.482-16.4820.0000.0000.0000.000
26A28GLU-1-0.944-0.98417.529-12.657-12.6570.0000.0000.0000.000
27A29ALA0-0.067-0.01819.4210.0450.0450.0000.0000.0000.000
28A30GLY00.006-0.00115.372-0.134-0.1340.0000.0000.0000.000
29A31ALA0-0.036-0.00613.448-1.264-1.2640.0000.0000.0000.000
30A32ASP-1-0.814-0.8969.194-24.699-24.6990.0000.0000.0000.000
31A33TRP0-0.034-0.0335.453-0.170-0.1700.0000.0000.0000.000
32A34ILE00.0100.00312.3021.0351.0350.0000.0000.0000.000
33A35HIS10.8150.89713.05719.36319.3630.0000.0000.0000.000
34A36VAL00.011-0.00615.3571.2541.2540.0000.0000.0000.000
35A37ASP-1-0.802-0.89617.991-16.965-16.9650.0000.0000.0000.000
36A38VAL00.0100.02019.9060.8090.8090.0000.0000.0000.000
37A39MET0-0.032-0.00622.108-0.105-0.1050.0000.0000.0000.000
38A40ASP-1-0.692-0.86724.884-11.180-11.1800.0000.0000.0000.000
39A41GLY0-0.037-0.01527.8760.4370.4370.0000.0000.0000.000
40A42ARG10.8240.91428.9079.8489.8480.0000.0000.0000.000
41A43PHE0-0.025-0.00721.8990.0600.0600.0000.0000.0000.000
42A44VAL0-0.002-0.00924.045-0.155-0.1550.0000.0000.0000.000
43A45PRO0-0.011-0.00427.1470.1490.1490.0000.0000.0000.000
44A46ASN0-0.001-0.01627.1410.5590.5590.0000.0000.0000.000
45A47ILE00.0010.01428.225-0.270-0.2700.0000.0000.0000.000
46A48THR0-0.036-0.02823.9660.2240.2240.0000.0000.0000.000
47A49ILE00.001-0.00222.6540.3920.3920.0000.0000.0000.000
48A50GLY00.0470.01424.616-0.381-0.3810.0000.0000.0000.000
49A51PRO00.020-0.00823.428-0.150-0.1500.0000.0000.0000.000
50A52LEU00.0300.02024.489-0.206-0.2060.0000.0000.0000.000
51A53ILE00.0320.02123.4340.1380.1380.0000.0000.0000.000
52A54VAL0-0.028-0.01619.463-0.258-0.2580.0000.0000.0000.000
53A55ASP-1-0.931-0.96821.985-11.636-11.6360.0000.0000.0000.000
54A56ALA0-0.0120.00024.4100.0810.0810.0000.0000.0000.000
55A57ILE0-0.012-0.02419.3890.0820.0820.0000.0000.0000.000
56A58ARG10.7800.90015.59916.78216.7820.0000.0000.0000.000
57A59PRO0-0.019-0.00621.040-0.380-0.3800.0000.0000.0000.000
58A60LEU0-0.050-0.00822.9030.2680.2680.0000.0000.0000.000
59A61THR0-0.009-0.01717.777-0.291-0.2910.0000.0000.0000.000
60A62LYS10.9350.96917.16914.18814.1880.0000.0000.0000.000
61A63LYS10.8190.92913.45116.95416.9540.0000.0000.0000.000
62A64THR0-0.006-0.0039.1771.2161.2160.0000.0000.0000.000
63A65LEU00.0060.01412.2770.4900.4900.0000.0000.0000.000
64A66ASP-1-0.801-0.86911.085-25.606-25.6060.0000.0000.0000.000
65A67VAL00.0080.00012.8371.2051.2050.0000.0000.0000.000
66A68HIS00.0330.02015.138-0.536-0.5360.0000.0000.0000.000
67A69LEU00.0060.00716.3531.0391.0390.0000.0000.0000.000
68A70MET0-0.065-0.03119.205-0.099-0.0990.0000.0000.0000.000
69A71ILE0-0.012-0.00521.2990.6210.6210.0000.0000.0000.000
70A72VAL0-0.010-0.01423.251-0.386-0.3860.0000.0000.0000.000
71A73GLU-1-0.973-0.97325.362-10.671-10.6710.0000.0000.0000.000
72A74PRO00.0260.01220.1980.0100.0100.0000.0000.0000.000
73A75GLU-1-0.894-0.97121.873-13.201-13.2010.0000.0000.0000.000
74A76LYS10.9200.97822.81510.38310.3830.0000.0000.0000.000
75A77TYR00.015-0.00923.4590.4160.4160.0000.0000.0000.000
76A78VAL0-0.0050.01018.312-0.283-0.2830.0000.0000.0000.000
77A79GLU-1-0.894-0.95120.250-12.917-12.9170.0000.0000.0000.000
78A80ASP-1-0.902-0.96222.431-11.706-11.7060.0000.0000.0000.000
79A81PHE00.015-0.00819.0690.0620.0620.0000.0000.0000.000
80A82ALA00.0280.01318.062-0.445-0.4450.0000.0000.0000.000
81A83LYS10.8360.92319.06511.96811.9680.0000.0000.0000.000
82A84ALA0-0.028-0.00621.6670.2100.2100.0000.0000.0000.000
83A85GLY00.0130.00418.8570.2290.2290.0000.0000.0000.000
84A86ALA0-0.0150.00615.806-0.679-0.6790.0000.0000.0000.000
85A87ASP-1-0.824-0.91511.525-20.310-20.3100.0000.0000.0000.000
86A88ILE0-0.033-0.0167.655-1.954-1.9540.0000.0000.0000.000
87A89ILE00.0160.01811.2891.8371.8370.0000.0000.0000.000
88A90SER0-0.019-0.00211.891-0.607-0.6070.0000.0000.0000.000
89A91VAL00.0360.01413.6261.4551.4550.0000.0000.0000.000
90A92HIS10.7900.87215.77215.10515.1050.0000.0000.0000.000
91A93VAL00.0530.03216.1090.2770.2770.0000.0000.0000.000
92A94GLU-1-0.724-0.81818.910-14.727-14.7270.0000.0000.0000.000
93A95HIS00.0850.02222.369-0.064-0.0640.0000.0000.0000.000
94A96ASN0-0.066-0.03325.173-0.007-0.0070.0000.0000.0000.000
95A97ALA0-0.0110.00521.9810.2580.2580.0000.0000.0000.000
96A98SER0-0.026-0.03119.8450.2620.2620.0000.0000.0000.000
97A99PRO00.0110.01221.836-0.472-0.4720.0000.0000.0000.000
98A100HIS0-0.021-0.01323.020-0.119-0.1190.0000.0000.0000.000
99A101LEU00.0660.03115.911-0.234-0.2340.0000.0000.0000.000
100A102HIS00.0430.02117.102-1.010-1.0100.0000.0000.0000.000
101A103ARG10.9380.98017.94613.05713.0570.0000.0000.0000.000
102A104THR00.0390.00617.8920.0360.0360.0000.0000.0000.000
103A105LEU00.0220.01712.548-0.335-0.3350.0000.0000.0000.000
104A106CYS0-0.029-0.02714.811-1.024-1.0240.0000.0000.0000.000
105A107GLN00.0080.01416.567-0.243-0.2430.0000.0000.0000.000
106A108ILE0-0.021-0.00913.2990.3070.3070.0000.0000.0000.000
107A109ARG10.8900.9408.57028.43928.4390.0000.0000.0000.000
108A110GLU-1-0.964-0.96014.030-16.504-16.5040.0000.0000.0000.000
109A111LEU0-0.063-0.02817.2110.6870.6870.0000.0000.0000.000
110A112GLY0-0.016-0.00314.5290.2450.2450.0000.0000.0000.000
111A113LYS10.8320.93512.74717.71417.7140.0000.0000.0000.000
112A114LYS10.9360.9736.16734.84934.8490.0000.0000.0000.000
113A115ALA00.0400.0149.8371.9891.9890.0000.0000.0000.000
114A116GLY0-0.015-0.0179.216-3.215-3.2150.0000.0000.0000.000
115A117ALA00.0340.02110.6572.3322.3320.0000.0000.0000.000
116A118VAL0-0.032-0.01512.126-1.396-1.3960.0000.0000.0000.000
117A119LEU0-0.011-0.00314.3750.9990.9990.0000.0000.0000.000
118A120ASN00.022-0.00817.081-0.580-0.5800.0000.0000.0000.000
119A121PRO00.0180.00119.911-0.205-0.2050.0000.0000.0000.000
120A122SER0-0.0190.00521.053-0.279-0.2790.0000.0000.0000.000
121A123THR0-0.057-0.04519.7030.5150.5150.0000.0000.0000.000
122A124PRO00.0270.03719.696-0.803-0.8030.0000.0000.0000.000
123A125LEU00.045-0.00814.607-0.301-0.3010.0000.0000.0000.000
124A126ASP-1-0.807-0.89517.315-15.127-15.1270.0000.0000.0000.000
125A127PHE0-0.067-0.03718.6580.1080.1080.0000.0000.0000.000
126A128LEU0-0.036-0.03012.353-0.397-0.3970.0000.0000.0000.000
127A129GLU-1-0.952-0.96914.969-16.617-16.6170.0000.0000.0000.000
128A130TYR0-0.019-0.01917.147-0.332-0.3320.0000.0000.0000.000
129A131VAL0-0.012-0.00613.6940.1470.1470.0000.0000.0000.000
130A132LEU00.0430.0319.681-1.264-1.2640.0000.0000.0000.000
131A133PRO0-0.008-0.0099.836-2.808-2.8080.0000.0000.0000.000
132A134VAL0-0.050-0.02210.318-0.979-0.9790.0000.0000.0000.000
133A135CYS0-0.059-0.0168.8191.9561.9560.0000.0000.0000.000
134A136ASP-1-0.818-0.9115.661-41.274-41.2740.0000.0000.0000.000
135A137LEU0-0.055-0.0244.213-10.732-10.521-0.001-0.025-0.1860.000
136A138ILE00.0180.0136.4524.2284.2280.0000.0000.0000.000
137A139LEU0-0.021-0.0019.070-1.457-1.4570.0000.0000.0000.000
138A140ILE0-0.024-0.01611.6581.7661.7660.0000.0000.0000.000
139A141MET00.0140.04514.032-0.152-0.1520.0000.0000.0000.000
140A142SER0-0.018-0.04016.9280.0880.0880.0000.0000.0000.000
141A143VAL0-0.0570.05618.6550.5920.5920.0000.0000.0000.000
142A144ASN0-0.0380.01021.151-0.649-0.6490.0000.0000.0000.000
143A145PRO00.0610.03323.0400.3640.3640.0000.0000.0000.000
144A146GLY00.059-0.08419.651-0.138-0.1380.0000.0000.0000.000
145A147PHE00.007-0.01920.460-0.022-0.0220.0000.0000.0000.000
146A148GLY00.0140.01023.1820.2990.2990.0000.0000.0000.000
147A149GLY00.0460.00425.4950.5230.5230.0000.0000.0000.000
148A150GLN0-0.054-0.02524.375-0.249-0.2490.0000.0000.0000.000
149A151SER0-0.030-0.01424.093-0.126-0.1260.0000.0000.0000.000
150A152PHE0-0.001-0.00716.9690.0510.0510.0000.0000.0000.000
151A153ILE0-0.0140.00921.3950.5390.5390.0000.0000.0000.000
152A154PRO00.018-0.00221.045-0.724-0.7240.0000.0000.0000.000
153A155GLU-1-0.872-0.94921.558-12.601-12.6010.0000.0000.0000.000
154A156VAL0-0.045-0.01317.075-0.320-0.3200.0000.0000.0000.000
155A157LEU0-0.012-0.00516.651-1.056-1.0560.0000.0000.0000.000
156A158PRO0-0.005-0.01616.747-0.971-0.9710.0000.0000.0000.000
157A159LYS10.8440.92116.08216.08716.0870.0000.0000.0000.000
158A160ILE00.0090.00811.349-0.940-0.9400.0000.0000.0000.000
159A161ARG10.9360.97112.34216.86816.8680.0000.0000.0000.000
160A162ALA00.0000.00413.914-0.656-0.6560.0000.0000.0000.000
161A163LEU00.0270.0159.878-0.157-0.1570.0000.0000.0000.000
162A164ARG10.8920.9434.78340.56540.638-0.001-0.001-0.0710.000
163A165GLN0-0.010-0.01110.387-1.608-1.6080.0000.0000.0000.000
164A166MET0-0.035-0.00712.9640.0560.0560.0000.0000.0000.000
165A167CYS0-0.084-0.0477.961-0.935-0.9350.0000.0000.0000.000
166A168ASP-1-0.878-0.9339.473-30.942-30.9420.0000.0000.0000.000
167A169GLU-1-0.921-0.95511.040-18.073-18.0730.0000.0000.0000.000
168A170ARG10.8330.92511.43522.40122.4010.0000.0000.0000.000
169A171GLY0-0.0080.01410.0930.1650.1650.0000.0000.0000.000
170A172LEU0-0.072-0.0406.933-2.051-2.0510.0000.0000.0000.000
171A173ASP-1-0.871-0.9552.612-98.627-91.5781.050-4.380-3.719-0.050
172A174PRO0-0.0140.0102.039-41.594-38.8564.689-3.670-3.756-0.050
173A175TRP0-0.016-0.0232.733-16.880-11.2195.886-2.447-9.099-0.038
174A176ILE00.0070.0053.6487.1707.2850.0160.025-0.1570.000
175A177GLH0-0.027-0.0616.8130.9360.9360.0000.0000.0000.000
176A178VAL0-0.013-0.0108.7631.4891.4890.0000.0000.0000.000
177A179ASP-1-0.866-0.94212.306-17.322-17.3220.0000.0000.0000.000
178A180GLY00.1100.03415.3400.5580.5580.0000.0000.0000.000
179A181GLY00.0240.02118.809-0.023-0.0230.0000.0000.0000.000
180A182LEU0-0.054-0.00514.2330.3870.3870.0000.0000.0000.000
181A183LYS10.9200.94218.06412.69212.6920.0000.0000.0000.000
182A184PRO00.0630.02917.942-0.402-0.4020.0000.0000.0000.000
183A185ASN00.0090.01518.960-0.465-0.4650.0000.0000.0000.000
184A186ASN0-0.016-0.01419.369-0.071-0.0710.0000.0000.0000.000
185A187THR00.0830.04013.252-0.432-0.4320.0000.0000.0000.000
186A188TRP00.0360.01914.460-1.032-1.0320.0000.0000.0000.000
187A189GLN0-0.032-0.01215.257-0.623-0.6230.0000.0000.0000.000
188A190VAL00.0410.00712.212-0.241-0.2410.0000.0000.0000.000
189A191LEU0-0.0120.0099.300-1.365-1.3650.0000.0000.0000.000
190A192GLU-1-0.851-0.90610.893-16.736-16.7360.0000.0000.0000.000
191A193ALA0-0.092-0.04413.195-0.127-0.1270.0000.0000.0000.000
192A194GLY00.0560.0289.263-0.052-0.0520.0000.0000.0000.000
193A195ALA0-0.0110.0047.791-3.761-3.7610.0000.0000.0000.000
194A196ASN00.015-0.0112.9112.1423.2940.264-0.389-1.0270.000
195A197ALA00.0310.0315.150-1.419-1.370-0.001-0.002-0.0460.000
196A198ILE0-0.036-0.0187.2681.6271.6270.0000.0000.0000.000
197A199VAL00.0220.03510.8860.2920.2920.0000.0000.0000.000
198A200ALA0-0.006-0.01113.7800.7640.7640.0000.0000.0000.000
199A201GLY00.0740.03516.899-0.078-0.0780.0000.0000.0000.000
200A202SER00.0180.01120.257-0.078-0.0780.0000.0000.0000.000
201A203ALA0-0.049-0.02319.7840.3150.3150.0000.0000.0000.000
202A204VAL00.005-0.00117.3940.0550.0550.0000.0000.0000.000
203A205PHE00.0500.00419.9110.3040.3040.0000.0000.0000.000
204A206ASN0-0.047-0.01423.5290.4040.4040.0000.0000.0000.000
205A207ALA0-0.047-0.00923.5060.4070.4070.0000.0000.0000.000
206A208PRO00.0150.00425.4200.0710.0710.0000.0000.0000.000
207A209ASN00.0560.02323.612-0.266-0.2660.0000.0000.0000.000
208A210TYR0-0.034-0.04920.846-0.401-0.4010.0000.0000.0000.000
209A211ALA00.0560.03019.231-0.592-0.5920.0000.0000.0000.000
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