FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: QNVVY

Calculation Name: 1T72-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T72

Chain ID: A

ChEMBL ID:

UniProt ID: O67053

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2540281.933786
FMO2-HF: Nuclear repulsion 2453131.774701
FMO2-HF: Total energy -87150.159085
FMO2-MP2: Total energy -87400.28949


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-2.143-0.763-0.021-0.755-0.6040
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.017
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].
3A3GLY00.0510.0283.798-0.8220.558-0.021-0.755-0.6040.000
4A4GLY0-0.019-0.0197.042-0.086-0.0860.0000.0000.0000.000
5A5GLY00.0250.01010.3290.0350.0350.0000.0000.0000.000
6A6GLY00.0780.04810.7410.0360.0360.0000.0000.0000.000
7A7MET00.008-0.0119.5700.1240.1240.0000.0000.0000.000
8A8LYS10.7850.90213.7660.1750.1750.0000.0000.0000.000
9A9LEU00.0750.04415.3300.0280.0280.0000.0000.0000.000
10A10PHE00.0030.00816.1290.0140.0140.0000.0000.0000.000
11A11LYS10.9200.95917.0970.2130.2130.0000.0000.0000.000
12A12GLU-1-0.758-0.86419.992-0.101-0.1010.0000.0000.0000.000
13A13LEU00.0410.02520.4720.0200.0200.0000.0000.0000.000
14A14GLU-1-0.838-0.90521.420-0.198-0.1980.0000.0000.0000.000
15A15GLU-1-0.910-0.96423.564-0.099-0.0990.0000.0000.0000.000
16A16THR0-0.027-0.02625.2360.0180.0180.0000.0000.0000.000
17A17LYS10.8530.91723.6810.2020.2020.0000.0000.0000.000
18A18GLU-1-0.961-0.98128.002-0.097-0.0970.0000.0000.0000.000
19A19GLN0-0.076-0.03429.5540.0180.0180.0000.0000.0000.000
20A20VAL00.0670.02530.5470.0060.0060.0000.0000.0000.000
21A21ILE00.0000.01031.3040.0060.0060.0000.0000.0000.000
22A22LYS10.8410.91533.8620.0700.0700.0000.0000.0000.000
23A23MET00.0030.00135.8180.0030.0030.0000.0000.0000.000
24A24ALA00.0780.03637.1060.0040.0040.0000.0000.0000.000
25A25LYS10.9040.95538.7450.0610.0610.0000.0000.0000.000
26A26LEU00.0160.00440.0200.0030.0030.0000.0000.0000.000
27A27VAL00.0870.05241.3420.0030.0030.0000.0000.0000.000
28A28GLN0-0.059-0.02640.6500.0040.0040.0000.0000.0000.000
29A29GLU-1-0.963-0.97844.727-0.038-0.0380.0000.0000.0000.000
30A30ALA00.0150.01446.2620.0030.0030.0000.0000.0000.000
31A31ILE00.017-0.00246.1820.0020.0020.0000.0000.0000.000
32A32ASP-1-0.916-0.95448.988-0.039-0.0390.0000.0000.0000.000
33A33LYS10.8520.91249.3340.0360.0360.0000.0000.0000.000
34A34ALA00.0370.02752.2480.0020.0020.0000.0000.0000.000
35A35THR00.0320.01753.7620.0010.0010.0000.0000.0000.000
36A36GLU-1-0.813-0.88555.385-0.028-0.0280.0000.0000.0000.000
37A37ALA0-0.033-0.01856.7040.0010.0010.0000.0000.0000.000
38A38LEU00.0260.00458.0240.0010.0010.0000.0000.0000.000
39A39ASN0-0.047-0.02158.7600.0020.0020.0000.0000.0000.000
40A40LYS10.6910.82860.0550.0290.0290.0000.0000.0000.000
41A41GLN0-0.048-0.02863.0180.0020.0020.0000.0000.0000.000
42A42ASN0-0.0200.00660.1470.0020.0020.0000.0000.0000.000
43A43VAL00.0830.01660.059-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.967-0.96258.235-0.022-0.0220.0000.0000.0000.000
45A45LEU0-0.014-0.02954.435-0.001-0.0010.0000.0000.0000.000
46A46ALA00.0410.02755.045-0.001-0.0010.0000.0000.0000.000
47A47GLU-1-0.823-0.90354.902-0.022-0.0220.0000.0000.0000.000
48A48GLU-1-0.947-0.94752.196-0.029-0.0290.0000.0000.0000.000
49A49VAL0-0.016-0.00350.327-0.001-0.0010.0000.0000.0000.000
50A50ILE00.0110.00550.203-0.001-0.0010.0000.0000.0000.000
51A51LYS10.7450.85250.7210.0240.0240.0000.0000.0000.000
52A52GLY0-0.062-0.03647.4550.0000.0000.0000.0000.0000.000
53A53ASP-1-0.835-0.92845.866-0.042-0.0420.0000.0000.0000.000
54A54ASP-1-0.892-0.93545.092-0.030-0.0300.0000.0000.0000.000
55A55THR0-0.129-0.07141.060-0.001-0.0010.0000.0000.0000.000
56A56ILE0-0.025-0.02540.734-0.003-0.0030.0000.0000.0000.000
57A57ASP-1-0.841-0.90440.254-0.041-0.0410.0000.0000.0000.000
58A58LEU0-0.052-0.03539.075-0.002-0.0020.0000.0000.0000.000
59A59LEU0-0.074-0.03734.815-0.003-0.0030.0000.0000.0000.000
60A60GLU-1-0.724-0.84035.205-0.062-0.0620.0000.0000.0000.000
61A61VAL00.0450.02134.786-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.880-0.90731.995-0.068-0.0680.0000.0000.0000.000
63A63ILE00.017-0.00730.258-0.006-0.0060.0000.0000.0000.000
64A64GLU-1-0.799-0.86829.920-0.069-0.0690.0000.0000.0000.000
65A65ARG10.8720.91329.8970.0360.0360.0000.0000.0000.000
66A66ARG10.7770.86326.8200.0770.0770.0000.0000.0000.000
67A67CYS00.0100.01225.585-0.011-0.0110.0000.0000.0000.000
68A68ILE00.0090.00225.050-0.008-0.0080.0000.0000.0000.000
69A69ARG10.8790.94924.1770.0500.0500.0000.0000.0000.000
70A70MET0-0.025-0.00221.2170.0010.0010.0000.0000.0000.000
71A71ILE00.0150.00520.061-0.021-0.0210.0000.0000.0000.000
72A72ALA0-0.058-0.02420.373-0.004-0.0040.0000.0000.0000.000
73A73LEU0-0.072-0.03518.7600.0110.0110.0000.0000.0000.000
74A74TYR0-0.082-0.07215.3120.0050.0050.0000.0000.0000.000
75A75GLN0-0.085-0.01513.509-0.004-0.0040.0000.0000.0000.000
76A76PRO00.0220.02415.573-0.038-0.0380.0000.0000.0000.000
77A77GLU-1-0.911-0.96212.234-0.481-0.4810.0000.0000.0000.000
78A78ALA0-0.021-0.03916.8940.0100.0100.0000.0000.0000.000
79A79GLY00.0650.03918.9830.0240.0240.0000.0000.0000.000
80A80ASP-1-0.886-0.93516.549-0.349-0.3490.0000.0000.0000.000
81A81LEU0-0.038-0.02819.9220.0310.0310.0000.0000.0000.000
82A82ARG10.8480.91121.7750.2280.2280.0000.0000.0000.000
83A83MET00.0480.02923.3090.0130.0130.0000.0000.0000.000
84A84ILE0-0.0200.00021.1520.0150.0150.0000.0000.0000.000
85A85MET0-0.021-0.01225.3810.0140.0140.0000.0000.0000.000
86A86GLY00.0250.01827.6510.0100.0100.0000.0000.0000.000
87A87ILE0-0.005-0.01426.2220.0070.0070.0000.0000.0000.000
88A88TYR0-0.138-0.10429.3110.0070.0070.0000.0000.0000.000
89A89LYS10.8460.92831.1580.0820.0820.0000.0000.0000.000
90A90ILE00.0040.00032.3580.0050.0050.0000.0000.0000.000
91A91VAL0-0.046-0.02033.2230.0030.0030.0000.0000.0000.000
92A92SER00.0220.00035.1620.0030.0030.0000.0000.0000.000
93A93ASP-1-0.860-0.91238.064-0.066-0.0660.0000.0000.0000.000
94A94LEU00.017-0.01736.1240.0030.0030.0000.0000.0000.000
95A95GLU-1-0.791-0.86139.810-0.044-0.0440.0000.0000.0000.000
96A96ARG10.7150.80741.4070.0470.0470.0000.0000.0000.000
97A97MET0-0.066-0.01541.8590.0010.0010.0000.0000.0000.000
98A98GLY0-0.019-0.00744.1290.0010.0010.0000.0000.0000.000
99A99ASP-1-0.774-0.85545.632-0.035-0.0350.0000.0000.0000.000
100A100GLU-1-0.821-0.91347.678-0.037-0.0370.0000.0000.0000.000
101A101ALA0-0.032-0.02348.6660.0020.0020.0000.0000.0000.000
102A102GLU-1-0.907-0.94449.641-0.028-0.0280.0000.0000.0000.000
103A103ASN00.002-0.02051.4000.0030.0030.0000.0000.0000.000
104A104ILE0-0.069-0.03052.0200.0020.0020.0000.0000.0000.000
105A105ALA0-0.015-0.01654.0060.0020.0020.0000.0000.0000.000
106A106GLU-1-0.866-0.93855.788-0.022-0.0220.0000.0000.0000.000
107A107ARG10.8380.92157.6930.0280.0280.0000.0000.0000.000
108A108ALA0-0.0130.00058.6950.0010.0010.0000.0000.0000.000
109A109ILE00.0060.01358.8310.0010.0010.0000.0000.0000.000
110A110LEU0-0.024-0.01161.8970.0010.0010.0000.0000.0000.000
111A111LEU0-0.097-0.06361.9250.0010.0010.0000.0000.0000.000
112A112ALA00.0000.01264.1740.0000.0000.0000.0000.0000.000
113A113GLU-1-1.022-0.98566.063-0.018-0.0180.0000.0000.0000.000
114A114GLU-1-0.868-0.94469.143-0.018-0.0180.0000.0000.0000.000
115A115PRO0-0.0100.01669.412-0.001-0.0010.0000.0000.0000.000
116A116PRO00.0470.02667.3390.0000.0000.0000.0000.0000.000
117A117LEU0-0.046-0.00267.9580.0000.0000.0000.0000.0000.000
118A118LYS10.8040.87964.3740.0270.0270.0000.0000.0000.000
119A119PRO0-0.002-0.01266.4810.0000.0000.0000.0000.0000.000
120A120TYR00.0070.01961.6610.0000.0000.0000.0000.0000.000
121A121VAL00.0380.02561.502-0.001-0.0010.0000.0000.0000.000
122A122ASN00.004-0.00660.047-0.002-0.0020.0000.0000.0000.000
123A123ILE00.0430.02757.306-0.001-0.0010.0000.0000.0000.000
124A124ASN0-0.037-0.03056.373-0.002-0.0020.0000.0000.0000.000
125A125PHE0-0.028-0.02555.570-0.001-0.0010.0000.0000.0000.000
126A126MET0-0.0150.00453.718-0.001-0.0010.0000.0000.0000.000
127A127SER00.0790.03151.727-0.001-0.0010.0000.0000.0000.000
128A128GLU-1-0.905-0.93850.531-0.045-0.0450.0000.0000.0000.000
129A129ILE0-0.039-0.01349.253-0.002-0.0020.0000.0000.0000.000
130A130VAL00.0660.02447.641-0.003-0.0030.0000.0000.0000.000
131A131LYS10.7870.89246.2080.0420.0420.0000.0000.0000.000
132A132GLU-1-0.934-0.96844.823-0.063-0.0630.0000.0000.0000.000
133A133MET0-0.115-0.04543.380-0.003-0.0030.0000.0000.0000.000
134A134VAL00.0300.02641.293-0.004-0.0040.0000.0000.0000.000
135A135ASN0-0.0150.00239.921-0.006-0.0060.0000.0000.0000.000
136A136ASP-1-0.810-0.90538.535-0.077-0.0770.0000.0000.0000.000
137A137SER0-0.023-0.01337.677-0.007-0.0070.0000.0000.0000.000
138A138VAL00.0570.02534.539-0.007-0.0070.0000.0000.0000.000
139A139ILE0-0.073-0.03533.923-0.008-0.0080.0000.0000.0000.000
140A140SER0-0.075-0.05133.011-0.009-0.0090.0000.0000.0000.000
141A141PHE00.0480.01729.054-0.009-0.0090.0000.0000.0000.000
142A142ILE0-0.051-0.01428.703-0.012-0.0120.0000.0000.0000.000
143A143GLN0-0.071-0.03727.911-0.015-0.0150.0000.0000.0000.000
144A144GLN0-0.021-0.00224.9500.0000.0000.0000.0000.0000.000
145A145ASP-1-0.882-0.92430.192-0.108-0.1080.0000.0000.0000.000
146A146THR00.0540.00032.7460.0070.0070.0000.0000.0000.000
147A147LEU00.001-0.00735.0780.0070.0070.0000.0000.0000.000
148A148LEU0-0.087-0.04736.5180.0060.0060.0000.0000.0000.000
149A149ALA00.0870.04736.1880.0040.0040.0000.0000.0000.000
150A150LYS10.8600.92636.8160.0990.0990.0000.0000.0000.000
151A151LYS10.8950.96440.0690.0850.0850.0000.0000.0000.000
152A152VAL0-0.038-0.01940.5730.0040.0040.0000.0000.0000.000
153A153ILE00.0370.00740.2500.0030.0030.0000.0000.0000.000
154A154GLU-1-0.961-0.97343.840-0.061-0.0610.0000.0000.0000.000
155A155LYS10.8270.91244.3190.0660.0660.0000.0000.0000.000
156A156ASP-1-0.791-0.90746.320-0.050-0.0500.0000.0000.0000.000
157A157ASP-1-0.856-0.91348.346-0.049-0.0490.0000.0000.0000.000
158A158THR0-0.097-0.04551.0110.0030.0030.0000.0000.0000.000
159A159VAL0-0.004-0.00349.9670.0030.0030.0000.0000.0000.000
160A160ASP-1-0.794-0.88852.247-0.039-0.0390.0000.0000.0000.000
161A161GLU-1-0.974-1.00353.990-0.038-0.0380.0000.0000.0000.000
162A162LEU0-0.127-0.06455.4320.0020.0020.0000.0000.0000.000
163A163TYR0-0.019-0.04955.7580.0020.0020.0000.0000.0000.000
164A164HIS0-0.055-0.03756.5640.0040.0040.0000.0000.0000.000
165A165GLN0-0.087-0.04560.1390.0030.0030.0000.0000.0000.000
166A166LEU0-0.0110.00459.8520.0020.0020.0000.0000.0000.000
167A167GLU-1-0.687-0.78961.220-0.027-0.0270.0000.0000.0000.000
168A168ARG10.8990.95363.8330.0300.0300.0000.0000.0000.000
169A169GLU-1-0.799-0.88264.908-0.026-0.0260.0000.0000.0000.000
170A170LEU0-0.0010.00164.0130.0010.0010.0000.0000.0000.000
171A171MET0-0.042-0.00667.9050.0010.0010.0000.0000.0000.000
172A172THR0-0.023-0.02569.8460.0010.0010.0000.0000.0000.000
173A173TYR00.0410.02269.3940.0000.0000.0000.0000.0000.000
174A174VAL0-0.022-0.01970.2410.0010.0010.0000.0000.0000.000
175A175LEU0-0.064-0.04473.0660.0010.0010.0000.0000.0000.000
176A176GLU-1-0.999-0.97875.321-0.019-0.0190.0000.0000.0000.000
177A177ASP-1-0.823-0.90876.572-0.016-0.0160.0000.0000.0000.000
178A178PRO00.0110.00575.4580.0000.0000.0000.0000.0000.000
179A179ARG10.8710.93774.9200.0160.0160.0000.0000.0000.000
180A180ASN00.013-0.01172.1850.0000.0000.0000.0000.0000.000
181A181ILE0-0.045-0.01570.816-0.001-0.0010.0000.0000.0000.000
182A182LYS10.8450.91068.5750.0180.0180.0000.0000.0000.000
183A183ARG10.9200.95367.4090.0190.0190.0000.0000.0000.000
184A184ALA00.0100.00066.203-0.001-0.0010.0000.0000.0000.000
185A185MET00.0050.00664.312-0.001-0.0010.0000.0000.0000.000
186A186HIS00.0600.03362.797-0.002-0.0020.0000.0000.0000.000
187A187LEU00.0150.00461.404-0.001-0.0010.0000.0000.0000.000
188A188SER0-0.093-0.07061.015-0.001-0.0010.0000.0000.0000.000
189A189PHE0-0.042-0.03557.612-0.001-0.0010.0000.0000.0000.000
190A190VAL00.0300.03456.898-0.001-0.0010.0000.0000.0000.000
191A191ALA0-0.011-0.01655.865-0.002-0.0020.0000.0000.0000.000
192A192ARG10.8520.92755.4910.0290.0290.0000.0000.0000.000
193A193HIS00.0300.00452.4600.0000.0000.0000.0000.0000.000
194A194TYR0-0.028-0.03851.049-0.001-0.0010.0000.0000.0000.000
195A195GLU-1-0.836-0.91950.556-0.043-0.0430.0000.0000.0000.000
196A196ARG10.8930.95449.0990.0390.0390.0000.0000.0000.000
197A197ILE0-0.040-0.02146.064-0.003-0.0030.0000.0000.0000.000
198A198ALA0-0.060-0.03445.572-0.003-0.0030.0000.0000.0000.000
199A199ASP-1-0.842-0.91845.415-0.055-0.0550.0000.0000.0000.000
200A200HIS0-0.046-0.03742.1550.0000.0000.0000.0000.0000.000
201A201ALA0-0.024-0.03041.318-0.004-0.0040.0000.0000.0000.000
202A202GLU-1-0.902-0.95740.572-0.069-0.0690.0000.0000.0000.000
203A203ASN00.0640.03639.403-0.006-0.0060.0000.0000.0000.000
204A204VAL0-0.051-0.01035.468-0.007-0.0070.0000.0000.0000.000
205A205ALA00.0010.00035.768-0.008-0.0080.0000.0000.0000.000
206A206GLU-1-0.869-0.92836.501-0.084-0.0840.0000.0000.0000.000
207A207ALA0-0.063-0.04033.124-0.007-0.0070.0000.0000.0000.000
208A208ALA0-0.034-0.02332.120-0.010-0.0100.0000.0000.0000.000
209A209ILE0-0.009-0.00831.892-0.010-0.0100.0000.0000.0000.000
210A210TYR0-0.049-0.00328.508-0.010-0.0100.0000.0000.0000.000
211A211LEU0-0.013-0.01826.898-0.010-0.0100.0000.0000.0000.000
212A212SER0-0.049-0.02327.544-0.011-0.0110.0000.0000.0000.000
213A213GLU-1-0.942-0.98228.637-0.112-0.1120.0000.0000.0000.000
214A214GLY0-0.056-0.01526.760-0.002-0.0020.0000.0000.0000.000
215A215GLU-1-0.968-0.95622.209-0.261-0.2610.0000.0000.0000.000