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: 17Y2Z

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2635283.220626
FMO2-HF: Nuclear repulsion 2551663.945422
FMO2-HF: Total energy -83619.275204
FMO2-MP2: Total energy -83864.232973


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.
-226.58-223.68839.607-18.999-23.5-0.204
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 : 0.816 / q_NPA : 0.898
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].
3A5ILE00.0100.0033.483-4.888-2.4380.014-1.256-1.2070.005
4A6VAL00.0110.0204.8913.0323.0320.0000.0000.0000.000
5A7VAL0-0.051-0.0296.7680.7720.7720.0000.0000.0000.000
6A8ALA00.0090.00410.5100.4360.4360.0000.0000.0000.000
7A9PRO00.011-0.00612.3740.4170.4170.0000.0000.0000.000
8A10SER0-0.031-0.03316.1170.1070.1070.0000.0000.0000.000
9A11ILE00.0240.00318.1500.6890.6890.0000.0000.0000.000
10A12LEU0-0.020-0.00920.8720.6600.6600.0000.0000.0000.000
11A13SER0-0.061-0.02922.0610.5120.5120.0000.0000.0000.000
12A14ALA0-0.0010.01823.3290.2520.2520.0000.0000.0000.000
13A15ASP-1-0.768-0.84925.153-9.336-9.3360.0000.0000.0000.000
14A16PHE0-0.003-0.02024.594-0.005-0.0050.0000.0000.0000.000
15A17SER0-0.110-0.06529.2780.1880.1880.0000.0000.0000.000
16A18ARG10.7860.86228.83110.14710.1470.0000.0000.0000.000
17A19LEU00.0120.01524.318-0.283-0.2830.0000.0000.0000.000
18A20GLY00.021-0.00425.585-0.464-0.4640.0000.0000.0000.000
19A21GLU-1-0.852-0.91925.838-9.917-9.9170.0000.0000.0000.000
20A22GLU-1-0.806-0.87524.362-11.546-11.5460.0000.0000.0000.000
21A23ILE00.004-0.00620.702-0.594-0.5940.0000.0000.0000.000
22A24LYS10.8170.89420.86012.42112.4210.0000.0000.0000.000
23A25ALA00.0040.01821.999-0.275-0.2750.0000.0000.0000.000
24A26VAL00.001-0.01517.975-0.337-0.3370.0000.0000.0000.000
25A27ASP-1-0.838-0.88117.345-16.139-16.1390.0000.0000.0000.000
26A28GLU-1-0.886-0.95017.331-12.894-12.8940.0000.0000.0000.000
27A29ALA0-0.040-0.00219.4230.0940.0940.0000.0000.0000.000
28A30GLY0-0.006-0.00115.419-0.197-0.1970.0000.0000.0000.000
29A31ALA0-0.010-0.00213.305-1.167-1.1670.0000.0000.0000.000
30A32ASP-1-0.814-0.8738.771-24.903-24.9030.0000.0000.0000.000
31A33TRP0-0.020-0.0295.7210.0890.0890.0000.0000.0000.000
32A34ILE00.0230.01312.4130.9260.9260.0000.0000.0000.000
33A35HIS10.8150.90012.99819.18119.1810.0000.0000.0000.000
34A36VAL00.004-0.01515.2431.2041.2040.0000.0000.0000.000
35A37ASP-1-0.768-0.85918.199-16.332-16.3320.0000.0000.0000.000
36A38VAL00.0110.02919.9050.8340.8340.0000.0000.0000.000
37A39MET0-0.0060.00822.249-0.063-0.0630.0000.0000.0000.000
38A40ASP-1-0.691-0.84725.170-11.046-11.0460.0000.0000.0000.000
39A41GLY0-0.0040.01028.2700.4210.4210.0000.0000.0000.000
40A42ARG10.7630.87229.1909.8349.8340.0000.0000.0000.000
41A43PHE0-0.026-0.01222.2150.0640.0640.0000.0000.0000.000
42A44VAL00.0080.00224.313-0.140-0.1400.0000.0000.0000.000
43A45PRO0-0.033-0.01027.4720.1960.1960.0000.0000.0000.000
44A46ASN0-0.014-0.03326.5820.5200.5200.0000.0000.0000.000
45A47ILE0-0.0030.00828.472-0.216-0.2160.0000.0000.0000.000
46A48THR0-0.036-0.03024.0490.1600.1600.0000.0000.0000.000
47A49ILE00.0110.00922.2810.3600.3600.0000.0000.0000.000
48A50GLY00.0530.02525.146-0.270-0.2700.0000.0000.0000.000
49A51PRO00.015-0.00623.692-0.116-0.1160.0000.0000.0000.000
50A52LEU00.0370.01424.617-0.245-0.2450.0000.0000.0000.000
51A53ILE0-0.003-0.00123.8510.1790.1790.0000.0000.0000.000
52A54VAL0-0.033-0.01319.455-0.299-0.2990.0000.0000.0000.000
53A55ASP-1-0.911-0.95822.224-11.503-11.5030.0000.0000.0000.000
54A56ALA0-0.015-0.01124.707-0.010-0.0100.0000.0000.0000.000
55A57ILE0-0.016-0.01720.0430.1200.1200.0000.0000.0000.000
56A58ARG10.7630.88315.96716.24916.2490.0000.0000.0000.000
57A59PRO0-0.019-0.01321.579-0.317-0.3170.0000.0000.0000.000
58A60LEU0-0.0440.00223.4180.1010.1010.0000.0000.0000.000
59A61THR00.004-0.01918.013-0.341-0.3410.0000.0000.0000.000
60A62LYS10.9300.96517.45213.68613.6860.0000.0000.0000.000
61A63LYS10.8140.91913.26716.71416.7140.0000.0000.0000.000
62A64THR0-0.0050.0069.6230.2300.2300.0000.0000.0000.000
63A65LEU00.0180.00612.8450.3290.3290.0000.0000.0000.000
64A66ASP-1-0.781-0.85611.435-24.720-24.7200.0000.0000.0000.000
65A67VAL00.0200.01113.1780.9990.9990.0000.0000.0000.000
66A68HIS00.019-0.00415.196-0.911-0.9110.0000.0000.0000.000
67A69LEU00.0150.00616.9461.0101.0100.0000.0000.0000.000
68A70MET0-0.061-0.01919.572-0.252-0.2520.0000.0000.0000.000
69A71ILE0-0.024-0.01721.3060.6390.6390.0000.0000.0000.000
70A72VAL00.002-0.01423.442-0.362-0.3620.0000.0000.0000.000
71A73GLU-1-0.828-0.88325.618-10.523-10.5230.0000.0000.0000.000
72A74PRO00.0520.03320.5350.0790.0790.0000.0000.0000.000
73A75GLU-1-0.844-0.93422.187-13.466-13.4660.0000.0000.0000.000
74A76LYS10.7720.87623.06110.37410.3740.0000.0000.0000.000
75A77TYR00.0130.00223.9980.3620.3620.0000.0000.0000.000
76A78VAL0-0.027-0.00518.711-0.247-0.2470.0000.0000.0000.000
77A79GLU-1-0.830-0.91620.336-12.322-12.3220.0000.0000.0000.000
78A80ASP-1-0.870-0.93622.627-11.447-11.4470.0000.0000.0000.000
79A81PHE00.012-0.00819.3710.0590.0590.0000.0000.0000.000
80A82ALA00.0130.01118.596-0.412-0.4120.0000.0000.0000.000
81A83LYS10.7880.88719.56311.70711.7070.0000.0000.0000.000
82A84ALA0-0.025-0.00322.0940.1750.1750.0000.0000.0000.000
83A85GLY00.0220.00419.381-0.006-0.0060.0000.0000.0000.000
84A86ALA0-0.015-0.00416.261-0.665-0.6650.0000.0000.0000.000
85A87ASP-1-0.860-0.92311.989-19.507-19.5070.0000.0000.0000.000
86A88ILE0-0.031-0.0167.825-1.618-1.6180.0000.0000.0000.000
87A89ILE00.0070.01511.5941.6991.6990.0000.0000.0000.000
88A90SER0-0.017-0.00112.224-0.604-0.6040.0000.0000.0000.000
89A91VAL00.0150.00113.9871.4031.4030.0000.0000.0000.000
90A92HIS10.8100.89216.09615.07815.0780.0000.0000.0000.000
91A93VAL00.0250.01415.8680.4360.4360.0000.0000.0000.000
92A94GLU-1-0.723-0.81118.764-14.734-14.7340.0000.0000.0000.000
93A95HIS00.0680.01622.2680.0610.0610.0000.0000.0000.000
94A96ASN0-0.031-0.01125.1620.0600.0600.0000.0000.0000.000
95A97ALA0-0.028-0.01222.2920.2540.2540.0000.0000.0000.000
96A98SER00.015-0.01220.1710.2290.2290.0000.0000.0000.000
97A99PRO0-0.0010.00221.942-0.431-0.4310.0000.0000.0000.000
98A100HIS0-0.006-0.00423.358-0.089-0.0890.0000.0000.0000.000
99A101LEU00.0360.01716.132-0.307-0.3070.0000.0000.0000.000
100A102HIS00.0530.02816.821-0.893-0.8930.0000.0000.0000.000
101A103ARG10.8720.93418.10512.84012.8400.0000.0000.0000.000
102A104THR00.0220.00418.5230.0500.0500.0000.0000.0000.000
103A105LEU0-0.003-0.00512.864-0.318-0.3180.0000.0000.0000.000
104A106CYS0-0.029-0.02415.221-0.930-0.9300.0000.0000.0000.000
105A107GLN00.0130.01317.228-0.180-0.1800.0000.0000.0000.000
106A108ILE0-0.020-0.01113.7440.3340.3340.0000.0000.0000.000
107A109ARG10.8550.9289.03727.38927.3890.0000.0000.0000.000
108A110GLU-1-0.945-0.96214.825-15.445-15.4450.0000.0000.0000.000
109A111LEU0-0.063-0.02417.9510.5920.5920.0000.0000.0000.000
110A112GLY0-0.0040.00515.5920.1570.1570.0000.0000.0000.000
111A113LYS10.8310.93413.05717.26017.2600.0000.0000.0000.000
112A114LYS10.7680.8657.45628.17028.1700.0000.0000.0000.000
113A115ALA00.0510.02610.3121.3511.3510.0000.0000.0000.000
114A116GLY00.002-0.0089.794-2.961-2.9610.0000.0000.0000.000
115A117ALA00.0340.02410.8132.2502.2500.0000.0000.0000.000
116A118VAL0-0.022-0.01712.178-1.323-1.3230.0000.0000.0000.000
117A119LEU00.0040.01014.1921.0791.0790.0000.0000.0000.000
118A120ASN00.023-0.00716.884-0.597-0.5970.0000.0000.0000.000
119A121PRO00.0210.00719.563-0.256-0.2560.0000.0000.0000.000
120A122SER00.0000.01020.838-0.099-0.0990.0000.0000.0000.000
121A123THR0-0.079-0.05419.4360.5380.5380.0000.0000.0000.000
122A124PRO00.0240.03019.210-0.849-0.8490.0000.0000.0000.000
123A125LEU00.042-0.00513.963-0.208-0.2080.0000.0000.0000.000
124A126ASP-1-0.844-0.91916.895-15.182-15.1820.0000.0000.0000.000
125A127PHE0-0.058-0.04018.1650.1780.1780.0000.0000.0000.000
126A128LEU0-0.012-0.01912.122-0.437-0.4370.0000.0000.0000.000
127A129GLU-1-0.828-0.88714.696-17.566-17.5660.0000.0000.0000.000
128A130TYR0-0.070-0.05116.332-0.344-0.3440.0000.0000.0000.000
129A131VAL0-0.021-0.01114.2140.2410.2410.0000.0000.0000.000
130A132LEU00.0530.0279.462-1.253-1.2530.0000.0000.0000.000
131A133PRO00.003-0.0019.792-2.488-2.4880.0000.0000.0000.000
132A134VAL0-0.051-0.03310.886-0.521-0.5210.0000.0000.0000.000
133A135CYS0-0.051-0.0088.8381.5901.5900.0000.0000.0000.000
134A136ASP-1-0.786-0.8706.474-35.238-35.2380.0000.0000.0000.000
135A137LEU0-0.052-0.0214.820-9.304-9.157-0.001-0.005-0.1410.000
136A138ILE00.0150.0076.7213.7193.7190.0000.0000.0000.000
137A139LEU0-0.020-0.0018.776-1.820-1.8200.0000.0000.0000.000
138A140ILE0-0.016-0.00411.5221.8141.8140.0000.0000.0000.000
139A141MET0-0.0150.00814.015-0.209-0.2090.0000.0000.0000.000
140A142SER00.013-0.01816.6460.1200.1200.0000.0000.0000.000
141A143VAL0-0.0570.01118.2500.6450.6450.0000.0000.0000.000
142A144ASN0-0.0110.00221.115-0.713-0.7130.0000.0000.0000.000
143A145PRO00.0330.02522.5920.3540.3540.0000.0000.0000.000
144A146GLY00.046-0.01019.553-0.072-0.0720.0000.0000.0000.000
145A147PHE0-0.008-0.03020.282-0.075-0.0750.0000.0000.0000.000
146A148GLY00.0120.01423.0360.4230.4230.0000.0000.0000.000
147A149GLY00.0540.01626.4150.3320.3320.0000.0000.0000.000
148A150GLN0-0.040-0.03024.400-0.265-0.2650.0000.0000.0000.000
149A151SER0-0.044-0.01723.842-0.211-0.2110.0000.0000.0000.000
150A152PHE0-0.007-0.01216.4720.0140.0140.0000.0000.0000.000
151A153ILE00.0230.02221.3270.4690.4690.0000.0000.0000.000
152A154PRO0-0.006-0.01120.777-0.757-0.7570.0000.0000.0000.000
153A155GLU-1-0.853-0.93920.841-13.106-13.1060.0000.0000.0000.000
154A156VAL0-0.033-0.01416.703-0.404-0.4040.0000.0000.0000.000
155A157LEU0-0.028-0.00416.144-1.167-1.1670.0000.0000.0000.000
156A158PRO00.000-0.01216.254-0.956-0.9560.0000.0000.0000.000
157A159LYS10.8390.92015.91215.93415.9340.0000.0000.0000.000
158A160ILE00.0250.01010.944-0.936-0.9360.0000.0000.0000.000
159A161ARG10.8530.93412.01917.89517.8950.0000.0000.0000.000
160A162ALA00.0040.00413.544-0.816-0.8160.0000.0000.0000.000
161A163LEU00.0230.0109.432-0.099-0.0990.0000.0000.0000.000
162A164ARG10.7940.8844.04445.65545.769-0.001-0.006-0.1080.000
163A165GLN0-0.032-0.02110.050-1.594-1.5940.0000.0000.0000.000
164A166MET0-0.035-0.01412.9310.0750.0750.0000.0000.0000.000
165A167CYS0-0.079-0.0367.642-0.464-0.4640.0000.0000.0000.000
166A168ASP-1-0.798-0.9008.585-34.261-34.2610.0000.0000.0000.000
167A169GLU-1-0.858-0.91610.373-18.138-18.1380.0000.0000.0000.000
168A170ARG10.7380.86411.54722.13722.1370.0000.0000.0000.000
169A171GLY0-0.0150.00910.2930.2130.2130.0000.0000.0000.000
170A172LEU0-0.064-0.0316.753-2.136-2.1360.0000.0000.0000.000
171A173ASP-1-0.752-0.8581.655-115.437-119.53619.351-9.163-6.089-0.097
172A174PRO00.0100.0231.802-40.991-43.42911.332-4.741-4.154-0.060
173A175TRP0-0.011-0.0262.532-23.128-17.5667.131-3.279-9.414-0.048
174A176ILE0-0.0030.0043.3928.4918.4830.0240.175-0.1900.000
175A177GLH0-0.012-0.0466.4361.2611.2610.0000.0000.0000.000
176A178VAL0-0.009-0.0158.5271.4881.4880.0000.0000.0000.000
177A179ASP-1-0.822-0.91712.056-17.519-17.5190.0000.0000.0000.000
178A180GLY00.1190.04515.1150.6580.6580.0000.0000.0000.000
179A181GLY00.0110.00518.656-0.132-0.1320.0000.0000.0000.000
180A182LEU0-0.064-0.01313.9060.4140.4140.0000.0000.0000.000
181A183LYS10.9110.93517.76513.40113.4010.0000.0000.0000.000
182A184PRO00.0570.03717.522-0.344-0.3440.0000.0000.0000.000
183A185ASN00.0090.02318.569-0.280-0.2800.0000.0000.0000.000
184A186ASN0-0.004-0.00519.1770.5270.5270.0000.0000.0000.000
185A187THR00.0570.02112.681-0.366-0.3660.0000.0000.0000.000
186A188TRP00.0140.00613.969-1.152-1.1520.0000.0000.0000.000
187A189GLN0-0.0150.00814.928-0.555-0.5550.0000.0000.0000.000
188A190VAL00.0520.01312.185-0.190-0.1900.0000.0000.0000.000
189A191LEU0-0.0090.0148.958-1.580-1.5800.0000.0000.0000.000
190A192GLU-1-0.805-0.86710.626-17.172-17.1720.0000.0000.0000.000
191A193ALA0-0.062-0.02413.3000.1200.1200.0000.0000.0000.000
192A194GLY00.0420.0189.2540.2330.2330.0000.0000.0000.000
193A195ALA0-0.022-0.0077.574-3.586-3.5860.0000.0000.0000.000
194A196ASN00.001-0.0062.4671.9513.0051.758-0.711-2.102-0.004
195A197ALA00.0280.0224.491-1.624-1.514-0.001-0.013-0.0950.000
196A198ILE0-0.038-0.0196.8621.8221.8220.0000.0000.0000.000
197A199VAL00.0240.03110.5490.4500.4500.0000.0000.0000.000
198A200ALA0-0.012-0.01213.5700.5870.5870.0000.0000.0000.000
199A201GLY00.0740.03216.671-0.034-0.0340.0000.0000.0000.000
200A202SER00.0330.01120.249-0.160-0.1600.0000.0000.0000.000
201A203ALA0-0.068-0.03519.5580.2550.2550.0000.0000.0000.000
202A204VAL0-0.004-0.00417.182-0.102-0.1020.0000.0000.0000.000
203A205PHE00.0490.01619.6010.3250.3250.0000.0000.0000.000
204A206ASN0-0.045-0.02223.3980.4410.4410.0000.0000.0000.000
205A207ALA0-0.0290.00623.1320.3390.3390.0000.0000.0000.000
206A208PRO0-0.009-0.01225.0770.0510.0510.0000.0000.0000.000
207A209ASN00.008-0.02123.500-0.098-0.0980.0000.0000.0000.000
208A210TYR0-0.018-0.03020.547-0.415-0.4150.0000.0000.0000.000
209A211ALA00.0570.03518.850-0.676-0.6760.0000.0000.0000.000
210A212GLU-1-0.908-0.93918.455-11.952-11.9520.0000.0000.0000.000
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