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: V5N81

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2628056.938115
FMO2-HF: Nuclear repulsion 2544438.009877
FMO2-HF: Total energy -83618.928239
FMO2-MP2: Total energy -83863.87676


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.
-231.483-225.41133.058-17.154-21.972-0.199
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 : 0.790 / q_NPA : 0.883
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].
3A5ILE00.003-0.0093.468-5.127-3.1760.008-0.975-0.9840.003
4A6VAL00.0040.0155.2102.6062.6060.0000.0000.0000.000
5A7VAL0-0.031-0.0187.0390.6180.6180.0000.0000.0000.000
6A8ALA00.010-0.00310.7390.2420.2420.0000.0000.0000.000
7A9PRO0-0.004-0.01012.5900.5330.5330.0000.0000.0000.000
8A10SER00.001-0.00116.3330.0460.0460.0000.0000.0000.000
9A11ILE00.0310.00618.2340.6980.6980.0000.0000.0000.000
10A12LEU0-0.028-0.00721.0410.6840.6840.0000.0000.0000.000
11A13SER0-0.058-0.03422.2360.5010.5010.0000.0000.0000.000
12A14ALA0-0.048-0.00223.4200.2680.2680.0000.0000.0000.000
13A15ASP-1-0.767-0.85125.263-9.353-9.3530.0000.0000.0000.000
14A16PHE0-0.017-0.03024.585-0.070-0.0700.0000.0000.0000.000
15A17SER0-0.114-0.06629.3590.1990.1990.0000.0000.0000.000
16A18ARG10.7860.86928.80110.10610.1060.0000.0000.0000.000
17A19LEU00.0460.02324.456-0.292-0.2920.0000.0000.0000.000
18A20GLY00.013-0.00725.698-0.450-0.4500.0000.0000.0000.000
19A21GLU-1-0.849-0.91826.074-9.828-9.8280.0000.0000.0000.000
20A22GLU-1-0.795-0.88524.372-11.489-11.4890.0000.0000.0000.000
21A23ILE0-0.021-0.01420.718-0.600-0.6000.0000.0000.0000.000
22A24LYS10.8930.94421.19412.08312.0830.0000.0000.0000.000
23A25ALA00.0260.02922.283-0.289-0.2890.0000.0000.0000.000
24A26VAL0-0.009-0.02118.542-0.353-0.3530.0000.0000.0000.000
25A27ASP-1-0.860-0.88417.408-16.351-16.3510.0000.0000.0000.000
26A28GLU-1-0.947-0.99017.543-12.575-12.5750.0000.0000.0000.000
27A29ALA0-0.060-0.01319.4480.0390.0390.0000.0000.0000.000
28A30GLY00.005-0.00115.390-0.141-0.1410.0000.0000.0000.000
29A31ALA0-0.032-0.00413.479-1.260-1.2600.0000.0000.0000.000
30A32ASP-1-0.800-0.8699.247-24.163-24.1630.0000.0000.0000.000
31A33TRP0-0.025-0.0285.574-0.158-0.1580.0000.0000.0000.000
32A34ILE00.0140.00412.3430.9770.9770.0000.0000.0000.000
33A35HIS10.8200.90012.99619.08619.0860.0000.0000.0000.000
34A36VAL00.003-0.01215.3221.2131.2130.0000.0000.0000.000
35A37ASP-1-0.787-0.87718.009-16.848-16.8480.0000.0000.0000.000
36A38VAL00.0100.02119.8660.8090.8090.0000.0000.0000.000
37A39MET0-0.0220.00122.424-0.099-0.0990.0000.0000.0000.000
38A40ASP-1-0.673-0.83925.133-11.091-11.0910.0000.0000.0000.000
39A41GLY0-0.023-0.00628.1840.4350.4350.0000.0000.0000.000
40A42ARG10.7870.88829.1619.9029.9020.0000.0000.0000.000
41A43PHE0-0.016-0.00922.1920.0400.0400.0000.0000.0000.000
42A44VAL00.001-0.00524.157-0.163-0.1630.0000.0000.0000.000
43A45PRO0-0.022-0.00627.3750.1550.1550.0000.0000.0000.000
44A46ASN0-0.002-0.02026.8770.5460.5460.0000.0000.0000.000
45A47ILE0-0.0070.00828.346-0.261-0.2610.0000.0000.0000.000
46A48THR0-0.027-0.02323.9450.2260.2260.0000.0000.0000.000
47A49ILE00.0010.00422.6130.3930.3930.0000.0000.0000.000
48A50GLY00.0510.01624.871-0.374-0.3740.0000.0000.0000.000
49A51PRO00.025-0.00623.770-0.151-0.1510.0000.0000.0000.000
50A52LEU00.0200.01524.847-0.189-0.1890.0000.0000.0000.000
51A53ILE00.0290.01823.7720.1260.1260.0000.0000.0000.000
52A54VAL0-0.028-0.01719.677-0.254-0.2540.0000.0000.0000.000
53A55ASP-1-0.922-0.96122.371-11.516-11.5160.0000.0000.0000.000
54A56ALA0-0.019-0.00524.7870.0920.0920.0000.0000.0000.000
55A57ILE0-0.005-0.01919.8920.0780.0780.0000.0000.0000.000
56A58ARG10.7740.89615.81416.46916.4690.0000.0000.0000.000
57A59PRO0-0.020-0.00921.441-0.357-0.3570.0000.0000.0000.000
58A60LEU0-0.050-0.01023.2940.2560.2560.0000.0000.0000.000
59A61THR00.004-0.02718.152-0.309-0.3090.0000.0000.0000.000
60A62LYS10.9260.96617.20313.90513.9050.0000.0000.0000.000
61A63LYS10.8100.91413.38616.68416.6840.0000.0000.0000.000
62A64THR0-0.0100.0019.5540.2870.2870.0000.0000.0000.000
63A65LEU00.0200.02112.7010.3850.3850.0000.0000.0000.000
64A66ASP-1-0.804-0.87511.338-24.952-24.9520.0000.0000.0000.000
65A67VAL00.005-0.00313.2231.1261.1260.0000.0000.0000.000
66A68HIS00.0350.01215.339-0.513-0.5130.0000.0000.0000.000
67A69LEU00.0120.00616.6821.0321.0320.0000.0000.0000.000
68A70MET0-0.073-0.03419.518-0.278-0.2780.0000.0000.0000.000
69A71ILE0-0.012-0.01021.5690.6220.6220.0000.0000.0000.000
70A72VAL0-0.001-0.01323.502-0.384-0.3840.0000.0000.0000.000
71A73GLU-1-0.850-0.89125.579-10.510-10.5100.0000.0000.0000.000
72A74PRO00.0530.02620.4870.0510.0510.0000.0000.0000.000
73A75GLU-1-0.867-0.94022.153-13.215-13.2150.0000.0000.0000.000
74A76LYS10.7800.87623.09010.43710.4370.0000.0000.0000.000
75A77TYR00.0240.00023.7760.3380.3380.0000.0000.0000.000
76A78VAL0-0.0160.00518.526-0.271-0.2710.0000.0000.0000.000
77A79GLU-1-0.831-0.92020.465-12.453-12.4530.0000.0000.0000.000
78A80ASP-1-0.895-0.94622.626-11.548-11.5480.0000.0000.0000.000
79A81PHE00.017-0.00719.3480.0320.0320.0000.0000.0000.000
80A82ALA00.0190.00818.324-0.418-0.4180.0000.0000.0000.000
81A83LYS10.7860.88719.31811.84611.8460.0000.0000.0000.000
82A84ALA0-0.030-0.00421.9620.2030.2030.0000.0000.0000.000
83A85GLY00.0170.00319.1790.1950.1950.0000.0000.0000.000
84A86ALA0-0.0150.00216.166-0.694-0.6940.0000.0000.0000.000
85A87ASP-1-0.839-0.92111.892-19.716-19.7160.0000.0000.0000.000
86A88ILE0-0.027-0.0127.923-1.754-1.7540.0000.0000.0000.000
87A89ILE00.0090.01811.5841.6881.6880.0000.0000.0000.000
88A90SER0-0.020-0.00212.125-0.597-0.5970.0000.0000.0000.000
89A91VAL00.0330.01513.9231.4151.4150.0000.0000.0000.000
90A92HIS10.7890.87115.96415.01415.0140.0000.0000.0000.000
91A93VAL00.0550.03316.1840.2790.2790.0000.0000.0000.000
92A94GLU-1-0.734-0.81219.010-14.840-14.8400.0000.0000.0000.000
93A95HIS00.0900.02722.465-0.011-0.0110.0000.0000.0000.000
94A96ASN0-0.051-0.02725.275-0.076-0.0760.0000.0000.0000.000
95A97ALA0-0.031-0.00822.2860.2670.2670.0000.0000.0000.000
96A98SER0-0.017-0.03320.1250.2880.2880.0000.0000.0000.000
97A99PRO00.0150.01221.946-0.449-0.4490.0000.0000.0000.000
98A100HIS0-0.025-0.00823.130-0.152-0.1520.0000.0000.0000.000
99A101LEU00.0630.02816.053-0.234-0.2340.0000.0000.0000.000
100A102HIS00.0570.02516.665-0.985-0.9850.0000.0000.0000.000
101A103ARG10.8690.93618.06413.03113.0310.0000.0000.0000.000
102A104THR00.0550.02018.1470.0470.0470.0000.0000.0000.000
103A105LEU00.0140.01112.623-0.330-0.3300.0000.0000.0000.000
104A106CYS0-0.035-0.03115.035-0.983-0.9830.0000.0000.0000.000
105A107GLN00.0210.02016.993-0.158-0.1580.0000.0000.0000.000
106A108ILE0-0.014-0.01113.7920.3080.3080.0000.0000.0000.000
107A109ARG10.8720.9318.88328.24028.2400.0000.0000.0000.000
108A110GLU-1-0.950-0.95614.754-16.057-16.0570.0000.0000.0000.000
109A111LEU0-0.070-0.03117.7640.6890.6890.0000.0000.0000.000
110A112GLY0-0.0110.00315.1600.2350.2350.0000.0000.0000.000
111A113LYS10.8140.92212.91817.57217.5720.0000.0000.0000.000
112A114LYS10.8050.8926.78931.61131.6110.0000.0000.0000.000
113A115ALA00.0630.02410.0761.7771.7770.0000.0000.0000.000
114A116GLY0-0.012-0.0199.457-3.096-3.0960.0000.0000.0000.000
115A117ALA00.0270.02010.8872.2542.2540.0000.0000.0000.000
116A118VAL0-0.030-0.01912.256-1.421-1.4210.0000.0000.0000.000
117A119LEU00.0000.00414.5080.9830.9830.0000.0000.0000.000
118A120ASN00.016-0.01317.153-0.558-0.5580.0000.0000.0000.000
119A121PRO00.0330.01219.948-0.247-0.2470.0000.0000.0000.000
120A122SER00.0070.01521.027-0.130-0.1300.0000.0000.0000.000
121A123THR0-0.111-0.07319.6520.5400.5400.0000.0000.0000.000
122A124PRO00.0390.03419.655-0.801-0.8010.0000.0000.0000.000
123A125LEU00.044-0.00514.401-0.280-0.2800.0000.0000.0000.000
124A126ASP-1-0.820-0.90417.188-15.279-15.2790.0000.0000.0000.000
125A127PHE0-0.051-0.03418.6420.1310.1310.0000.0000.0000.000
126A128LEU0-0.036-0.02912.363-0.356-0.3560.0000.0000.0000.000
127A129GLU-1-0.910-0.94014.850-16.740-16.7400.0000.0000.0000.000
128A130TYR0-0.086-0.05816.887-0.275-0.2750.0000.0000.0000.000
129A131VAL0-0.023-0.01113.9310.1430.1430.0000.0000.0000.000
130A132LEU00.0530.0389.599-1.277-1.2770.0000.0000.0000.000
131A133PRO00.001-0.0059.658-2.778-2.7780.0000.0000.0000.000
132A134VAL0-0.055-0.03210.393-0.919-0.9190.0000.0000.0000.000
133A135CYS0-0.056-0.0118.9131.9421.9420.0000.0000.0000.000
134A136ASP-1-0.775-0.8665.819-38.591-38.5910.0000.0000.0000.000
135A137LEU0-0.043-0.0194.454-9.813-9.631-0.001-0.011-0.1690.000
136A138ILE00.0190.0126.6584.0654.0650.0000.0000.0000.000
137A139LEU0-0.023-0.0019.165-1.505-1.5050.0000.0000.0000.000
138A140ILE0-0.022-0.01611.7871.7471.7470.0000.0000.0000.000
139A141MET0-0.0070.02214.004-0.188-0.1880.0000.0000.0000.000
140A142SER0-0.008-0.03216.8990.0610.0610.0000.0000.0000.000
141A143VAL0-0.0560.00718.6320.5910.5910.0000.0000.0000.000
142A144ASN0-0.0310.02121.121-0.750-0.7500.0000.0000.0000.000
143A145PRO00.0350.01422.9670.3210.3210.0000.0000.0000.000
144A146GLY00.061-0.03519.491-0.078-0.0780.0000.0000.0000.000
145A147PHE0-0.007-0.01920.156-0.139-0.1390.0000.0000.0000.000
146A148GLY00.0260.01222.8850.3750.3750.0000.0000.0000.000
147A149GLY00.0410.01426.5280.3390.3390.0000.0000.0000.000
148A150GLN0-0.044-0.02524.593-0.209-0.2090.0000.0000.0000.000
149A151SER0-0.020-0.00924.073-0.143-0.1430.0000.0000.0000.000
150A152PHE00.004-0.00816.8780.0410.0410.0000.0000.0000.000
151A153ILE0-0.0110.01321.3690.5290.5290.0000.0000.0000.000
152A154PRO00.010-0.00821.031-0.745-0.7450.0000.0000.0000.000
153A155GLU-1-0.864-0.94321.550-12.828-12.8280.0000.0000.0000.000
154A156VAL0-0.043-0.01817.080-0.355-0.3550.0000.0000.0000.000
155A157LEU0-0.012-0.00116.644-1.111-1.1110.0000.0000.0000.000
156A158PRO0-0.003-0.01516.590-1.008-1.0080.0000.0000.0000.000
157A159LYS10.8450.92516.13016.16616.1660.0000.0000.0000.000
158A160ILE00.0160.01111.244-0.986-0.9860.0000.0000.0000.000
159A161ARG10.8900.95412.22817.73617.7360.0000.0000.0000.000
160A162ALA0-0.014-0.00213.809-0.730-0.7300.0000.0000.0000.000
161A163LEU00.0400.0199.777-0.156-0.1560.0000.0000.0000.000
162A164ARG10.8060.9034.13645.62745.729-0.001-0.003-0.0980.000
163A165GLN0-0.013-0.01010.314-1.672-1.6720.0000.0000.0000.000
164A166MET0-0.040-0.01212.9730.0940.0940.0000.0000.0000.000
165A167CYS0-0.067-0.0357.802-0.528-0.5280.0000.0000.0000.000
166A168ASP-1-0.820-0.9129.018-34.157-34.1570.0000.0000.0000.000
167A169GLU-1-0.865-0.92010.770-18.639-18.6390.0000.0000.0000.000
168A170ARG10.8000.89911.29422.75822.7580.0000.0000.0000.000
169A171GLY0-0.0100.0139.9170.2570.2570.0000.0000.0000.000
170A172LEU0-0.065-0.0336.635-2.166-2.1660.0000.0000.0000.000
171A173ASP-1-0.782-0.8901.712-121.406-122.26715.606-8.575-6.170-0.099
172A174PRO0-0.0080.0131.913-44.585-47.04711.951-4.817-4.671-0.066
173A175TRP00.000-0.0172.728-16.741-11.0124.977-2.323-8.381-0.036
174A176ILE00.0110.0093.7487.4597.5870.0130.018-0.1600.000
175A177GLH0-0.021-0.0546.7911.0531.0530.0000.0000.0000.000
176A178VAL0-0.015-0.0108.7351.4601.4600.0000.0000.0000.000
177A179ASP-1-0.845-0.93112.283-17.428-17.4280.0000.0000.0000.000
178A180GLY00.1130.03815.3130.5720.5720.0000.0000.0000.000
179A181GLY00.0250.01918.785-0.037-0.0370.0000.0000.0000.000
180A182LEU0-0.056-0.00614.1490.3850.3850.0000.0000.0000.000
181A183LYS10.9510.96017.97912.77312.7730.0000.0000.0000.000
182A184PRO00.0700.04417.832-0.406-0.4060.0000.0000.0000.000
183A185ASN0-0.0130.00718.836-0.309-0.3090.0000.0000.0000.000
184A186ASN0-0.015-0.01719.4910.0400.0400.0000.0000.0000.000
185A187THR00.0690.02913.043-0.421-0.4210.0000.0000.0000.000
186A188TRP00.0290.01414.315-1.064-1.0640.0000.0000.0000.000
187A189GLN0-0.039-0.01115.187-0.494-0.4940.0000.0000.0000.000
188A190VAL00.0430.00612.423-0.266-0.2660.0000.0000.0000.000
189A191LEU0-0.0130.0129.273-1.416-1.4160.0000.0000.0000.000
190A192GLU-1-0.814-0.86610.892-16.914-16.9140.0000.0000.0000.000
191A193ALA0-0.073-0.04313.176-0.179-0.1790.0000.0000.0000.000
192A194GLY00.0520.0229.2470.0250.0250.0000.0000.0000.000
193A195ALA0-0.0270.0027.797-3.635-3.6350.0000.0000.0000.000
194A196ASN00.015-0.0122.6732.2403.4880.506-0.466-1.287-0.001
195A197ALA00.0290.0305.076-1.280-1.225-0.001-0.002-0.0520.000
196A198ILE0-0.035-0.0207.2511.6641.6640.0000.0000.0000.000
197A199VAL00.0300.03810.8340.3550.3550.0000.0000.0000.000
198A200ALA0-0.011-0.01213.7550.7420.7420.0000.0000.0000.000
199A201GLY00.0760.03616.869-0.057-0.0570.0000.0000.0000.000
200A202SER00.0210.00920.245-0.060-0.0600.0000.0000.0000.000
201A203ALA0-0.057-0.02519.7030.3210.3210.0000.0000.0000.000
202A204VAL00.009-0.00317.3310.0580.0580.0000.0000.0000.000
203A205PHE00.0570.00919.7570.3090.3090.0000.0000.0000.000
204A206ASN0-0.047-0.01823.5290.3610.3610.0000.0000.0000.000
205A207ALA0-0.047-0.00223.4160.4010.4010.0000.0000.0000.000
206A208PRO00.011-0.00225.3860.0750.0750.0000.0000.0000.000
207A209ASN00.014-0.01423.934-0.137-0.1370.0000.0000.0000.000
208A210TYR0-0.014-0.01420.871-0.453-0.4530.0000.0000.0000.000
209A211ALA00.0640.03319.226-0.604-0.6040.0000.0000.0000.000
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