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: LJGQ9

Calculation Name: 2AZO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AZO

Chain ID: A

ChEMBL ID:

UniProt ID: P06722

Base Structure: X-ray

Registration Date: 2023-03-13

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2643590.314908
FMO2-HF: Nuclear repulsion 2556401.810247
FMO2-HF: Total energy -87188.504661
FMO2-MP2: Total energy -87448.189677


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:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-11.845-9.9689.02-5.129-5.7680.016
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.022
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].
3A5ARG10.9690.9713.2790.2112.7540.030-1.400-1.1720.000
4A6PRO00.0090.0236.0030.5710.5710.0000.0000.0000.000
5A7LEU0-0.0140.0219.659-0.174-0.1740.0000.0000.0000.000
6A8LEU0-0.018-0.02411.4950.0790.0790.0000.0000.0000.000
7A9SER0-0.027-0.01114.3920.0690.0690.0000.0000.0000.000
8A10PRO0-0.0050.01816.787-0.052-0.0520.0000.0000.0000.000
9A11PRO0-0.020-0.01116.269-0.003-0.0030.0000.0000.0000.000
10A12GLU-1-0.893-0.94517.941-0.299-0.2990.0000.0000.0000.000
11A13THR0-0.060-0.06519.2540.0290.0290.0000.0000.0000.000
12A14GLU-1-0.717-0.84018.604-0.019-0.0190.0000.0000.0000.000
13A15GLU-1-0.840-0.90717.191-0.057-0.0570.0000.0000.0000.000
14A16GLN0-0.028-0.00914.544-0.032-0.0320.0000.0000.0000.000
15A17LEU00.0140.01113.595-0.068-0.0680.0000.0000.0000.000
16A18LEU0-0.022-0.01014.1030.0200.0200.0000.0000.0000.000
17A19ALA00.0080.00510.9670.0980.0980.0000.0000.0000.000
18A20GLN0-0.027-0.0248.725-0.029-0.0290.0000.0000.0000.000
19A21ALA00.0110.0019.3870.1050.1050.0000.0000.0000.000
20A22GLN0-0.032-0.03510.1170.1630.1630.0000.0000.0000.000
21A23GLN0-0.066-0.0114.110-0.621-0.540-0.001-0.028-0.0520.000
22A24LEU0-0.016-0.0165.9210.8720.8720.0000.0000.0000.000
23A25SER0-0.024-0.0318.3080.1020.1020.0000.0000.0000.000
24A26GLY0-0.069-0.0338.4400.6420.6420.0000.0000.0000.000
25A27TYR0-0.010-0.0021.817-10.825-12.3088.296-3.365-3.4490.015
26A28THR0-0.047-0.0688.294-0.749-0.7490.0000.0000.0000.000
27A29LEU0-0.023-0.0269.592-0.133-0.1330.0000.0000.0000.000
28A30GLY00.023-0.00211.104-0.192-0.1920.0000.0000.0000.000
29A31GLU-1-0.868-0.8985.5941.8571.8570.0000.0000.0000.000
30A32LEU00.0240.0076.300-0.740-0.7400.0000.0000.0000.000
31A33ALA00.0040.0068.044-0.376-0.3760.0000.0000.0000.000
32A34ALA00.0090.0147.374-0.169-0.1690.0000.0000.0000.000
33A35LEU0-0.064-0.0322.650-1.456-0.7200.695-0.336-1.0950.001
34A36VAL0-0.026-0.0186.646-0.208-0.2080.0000.0000.0000.000
35A37GLY0-0.0200.01310.0810.1880.1880.0000.0000.0000.000
36A38LEU0-0.036-0.01212.0130.2060.2060.0000.0000.0000.000
37A39VAL00.0170.00312.905-0.029-0.0290.0000.0000.0000.000
38A40THR0-0.020-0.01713.7810.0330.0330.0000.0000.0000.000
39A41PRO0-0.046-0.00615.8860.0200.0200.0000.0000.0000.000
40A42GLU-1-0.759-0.87118.884-0.052-0.0520.0000.0000.0000.000
41A43ASN0-0.050-0.04620.9950.0470.0470.0000.0000.0000.000
42A44LEU00.0780.04520.356-0.024-0.0240.0000.0000.0000.000
43A45LYS10.9130.94122.927-0.064-0.0640.0000.0000.0000.000
44A46ARG10.7910.89022.8110.1010.1010.0000.0000.0000.000
45A47ASP-1-0.846-0.92121.780-0.223-0.2230.0000.0000.0000.000
46A48LYS10.9330.95322.8610.0290.0290.0000.0000.0000.000
47A49GLY00.001-0.00423.4700.0280.0280.0000.0000.0000.000
48A50TRP00.0570.03413.5810.0250.0250.0000.0000.0000.000
49A51ILE0-0.007-0.01516.579-0.033-0.0330.0000.0000.0000.000
50A52GLY0-0.0010.00217.348-0.001-0.0010.0000.0000.0000.000
51A53VAL00.0840.04718.196-0.023-0.0230.0000.0000.0000.000
52A54LEU0-0.0170.00511.350-0.067-0.0670.0000.0000.0000.000
53A55LEU0-0.003-0.01913.691-0.077-0.0770.0000.0000.0000.000
54A56GLU-1-0.916-0.95615.383-0.301-0.3010.0000.0000.0000.000
55A57ILE0-0.034-0.00312.890-0.062-0.0620.0000.0000.0000.000
56A58TRP0-0.049-0.0295.540-0.112-0.1120.0000.0000.0000.000
57A59LEU0-0.070-0.02712.344-0.103-0.1030.0000.0000.0000.000
58A60GLY00.047-0.01214.1940.0490.0490.0000.0000.0000.000
59A61ALA0-0.012-0.01815.5360.0620.0620.0000.0000.0000.000
60A62SER0-0.0150.03217.5260.0620.0620.0000.0000.0000.000
61A63ALA00.0350.00118.7480.0510.0510.0000.0000.0000.000
62A64GLY00.0080.00921.6870.0370.0370.0000.0000.0000.000
63A65SER0-0.033-0.02423.7370.0230.0230.0000.0000.0000.000
64A66LYS10.9060.94726.8500.3020.3020.0000.0000.0000.000
65A67PRO0-0.0040.02224.6240.0240.0240.0000.0000.0000.000
66A68GLU-1-0.904-0.96127.358-0.189-0.1890.0000.0000.0000.000
67A69GLN0-0.049-0.02524.4290.0170.0170.0000.0000.0000.000
68A70ASP-1-0.793-0.88821.501-0.320-0.3200.0000.0000.0000.000
69A71PHE0-0.049-0.05218.3600.0390.0390.0000.0000.0000.000
70A72ALA0-0.014-0.00222.9260.0310.0310.0000.0000.0000.000
71A73ALA0-0.026-0.01424.8060.0190.0190.0000.0000.0000.000
72A74LEU0-0.012-0.00319.9670.0210.0210.0000.0000.0000.000
73A75GLY0-0.0160.01224.4210.0220.0220.0000.0000.0000.000
74A76VAL0-0.040-0.03421.3030.0270.0270.0000.0000.0000.000
75A77GLU-1-0.832-0.91223.728-0.049-0.0490.0000.0000.0000.000
76A78LEU00.0260.01818.6070.0350.0350.0000.0000.0000.000
77A79LYS10.8210.90321.739-0.033-0.0330.0000.0000.0000.000
78A80THR00.0200.02119.0880.0170.0170.0000.0000.0000.000
79A81ILE0-0.033-0.01720.647-0.022-0.0220.0000.0000.0000.000
80A82PRO00.0040.01821.2310.0540.0540.0000.0000.0000.000
81A83VAL0-0.011-0.01119.834-0.018-0.0180.0000.0000.0000.000
82A84ASP-1-0.714-0.85121.7950.4440.4440.0000.0000.0000.000
83A85SER0-0.014-0.00619.7440.0210.0210.0000.0000.0000.000
84A86LEU0-0.052-0.03720.2420.0610.0610.0000.0000.0000.000
85A87GLY0-0.0030.00620.5360.0080.0080.0000.0000.0000.000
86A88ARG10.8690.91321.221-0.438-0.4380.0000.0000.0000.000
87A89PRO00.0230.01624.8350.0020.0020.0000.0000.0000.000
88A90LEU0-0.027-0.00223.985-0.011-0.0110.0000.0000.0000.000
89A91GLU-1-0.979-1.00427.4500.1210.1210.0000.0000.0000.000
90A92THR0-0.090-0.02629.6020.0010.0010.0000.0000.0000.000
91A93THR00.0490.01927.3910.0040.0040.0000.0000.0000.000
92A94PHE0-0.0050.00029.584-0.011-0.0110.0000.0000.0000.000
93A95VAL00.0180.01929.741-0.001-0.0010.0000.0000.0000.000
94A96CYS0-0.034-0.02831.563-0.015-0.0150.0000.0000.0000.000
95A97VAL0-0.019-0.01634.1570.0080.0080.0000.0000.0000.000
96A98ALA00.0230.02437.285-0.002-0.0020.0000.0000.0000.000
97A99PRO0-0.035-0.00640.5380.0000.0000.0000.0000.0000.000
98A100LEU00.029-0.01543.3520.0040.0040.0000.0000.0000.000
99A101THR00.0070.01246.7870.0010.0010.0000.0000.0000.000
100A102GLY00.008-0.00147.129-0.002-0.0020.0000.0000.0000.000
101A103ASN0-0.025-0.00745.517-0.004-0.0040.0000.0000.0000.000
102A104SER00.0700.03346.9330.0020.0020.0000.0000.0000.000
103A105GLY0-0.036-0.02348.566-0.003-0.0030.0000.0000.0000.000
104A106VAL0-0.0320.00542.779-0.002-0.0020.0000.0000.0000.000
105A107THR0-0.013-0.02844.0500.0030.0030.0000.0000.0000.000
106A108TRP00.0720.03436.205-0.004-0.0040.0000.0000.0000.000
107A109GLU-1-0.800-0.88339.5640.0050.0050.0000.0000.0000.000
108A110THR0-0.021-0.01139.118-0.004-0.0040.0000.0000.0000.000
109A111SER00.0090.02838.505-0.003-0.0030.0000.0000.0000.000
110A112HIS00.019-0.02835.357-0.002-0.0020.0000.0000.0000.000
111A113VAL0-0.006-0.00334.087-0.001-0.0010.0000.0000.0000.000
112A114ARG10.9991.01433.4030.0020.0020.0000.0000.0000.000
113A115HIS00.0410.02531.009-0.003-0.0030.0000.0000.0000.000
114A116LYS10.8710.93129.9520.0360.0360.0000.0000.0000.000
115A117LEU0-0.024-0.01828.7810.0080.0080.0000.0000.0000.000
116A118LYS10.8600.95829.2250.0490.0490.0000.0000.0000.000
117A119ARG10.8110.86323.069-0.040-0.0400.0000.0000.0000.000
118A120VAL0-0.039-0.00423.667-0.020-0.0200.0000.0000.0000.000
119A121LEU00.0470.03516.5610.0260.0260.0000.0000.0000.000
120A122TRP0-0.027-0.01520.630-0.018-0.0180.0000.0000.0000.000
121A123ILE00.0540.01115.1620.0470.0470.0000.0000.0000.000
122A124PRO0-0.012-0.01316.965-0.025-0.0250.0000.0000.0000.000
123A125VAL00.0290.01216.0000.0650.0650.0000.0000.0000.000
124A126GLU-1-0.773-0.82416.4650.7340.7340.0000.0000.0000.000
125A127GLY00.011-0.01719.181-0.043-0.0430.0000.0000.0000.000
126A128GLU-1-0.803-0.88422.0670.1990.1990.0000.0000.0000.000
127A129ARG10.9010.95122.796-0.145-0.1450.0000.0000.0000.000
128A130SER0-0.109-0.10023.859-0.007-0.0070.0000.0000.0000.000
129A131ILE00.0450.03818.419-0.008-0.0080.0000.0000.0000.000
130A132PRO00.0440.03118.114-0.032-0.0320.0000.0000.0000.000
131A133LEU00.016-0.00417.1300.0590.0590.0000.0000.0000.000
132A134ALA00.0420.00713.5880.0400.0400.0000.0000.0000.000
133A135GLN00.003-0.00612.807-0.002-0.0020.0000.0000.0000.000
134A136ARG10.7720.93214.649-0.163-0.1630.0000.0000.0000.000
135A137ARG10.8580.89611.994-1.157-1.1570.0000.0000.0000.000
136A138VAL0-0.0120.00911.518-0.240-0.2400.0000.0000.0000.000
137A139GLY0-0.0090.00512.8510.2400.2400.0000.0000.0000.000
138A140SER00.0250.01613.3520.1170.1170.0000.0000.0000.000
139A141PRO0-0.036-0.00813.003-0.084-0.0840.0000.0000.0000.000
140A142LEU00.001-0.00515.8910.0260.0260.0000.0000.0000.000
141A143LEU0-0.0120.01218.784-0.027-0.0270.0000.0000.0000.000
142A144TRP0-0.036-0.03720.8920.0180.0180.0000.0000.0000.000
143A145SER00.0390.00624.551-0.024-0.0240.0000.0000.0000.000
144A146PRO0-0.0670.00128.0930.0140.0140.0000.0000.0000.000
145A147ASN0-0.008-0.00431.301-0.016-0.0160.0000.0000.0000.000
146A148GLU-1-0.866-0.95233.1210.0520.0520.0000.0000.0000.000
147A149GLU-1-0.947-0.98036.3340.0990.0990.0000.0000.0000.000
148A150GLU-1-0.919-0.97331.4900.1390.1390.0000.0000.0000.000
149A151ASP-1-0.901-0.97435.1370.0390.0390.0000.0000.0000.000
150A152ARG10.8950.95436.524-0.076-0.0760.0000.0000.0000.000
151A153GLN00.0090.00538.215-0.001-0.0010.0000.0000.0000.000
152A154LEU0-0.035-0.02033.347-0.001-0.0010.0000.0000.0000.000
153A155ARG10.7770.87238.008-0.027-0.0270.0000.0000.0000.000
154A156GLU-1-0.840-0.91840.8170.0580.0580.0000.0000.0000.000
155A157ASP-1-0.721-0.84139.1380.0740.0740.0000.0000.0000.000
156A158TRP0-0.046-0.03739.088-0.005-0.0050.0000.0000.0000.000
157A159GLU-1-0.828-0.91841.5770.0190.0190.0000.0000.0000.000
158A160GLU-1-0.851-0.91145.0700.0500.0500.0000.0000.0000.000
159A161LEU0-0.038-0.04141.300-0.004-0.0040.0000.0000.0000.000
160A162MET0-0.042-0.02643.355-0.004-0.0040.0000.0000.0000.000
161A163ASP-1-0.869-0.91645.9180.0160.0160.0000.0000.0000.000
162A164MET0-0.090-0.05148.124-0.001-0.0010.0000.0000.0000.000
163A165ILE0-0.072-0.03644.201-0.002-0.0020.0000.0000.0000.000
164A166VAL0-0.0070.00248.611-0.003-0.0030.0000.0000.0000.000
165A167LEU0-0.056-0.01751.095-0.002-0.0020.0000.0000.0000.000
166A168GLY00.0100.02152.7040.0010.0010.0000.0000.0000.000
167A169GLN0-0.078-0.04651.8000.0040.0040.0000.0000.0000.000
168A170VAL00.1200.04046.5410.0040.0040.0000.0000.0000.000
169A171GLU-1-0.796-0.85247.9340.0240.0240.0000.0000.0000.000
170A172ARG10.8220.90350.139-0.028-0.0280.0000.0000.0000.000
171A173ILE00.0080.03144.3500.0040.0040.0000.0000.0000.000
172A174THR0-0.058-0.03045.0750.0040.0040.0000.0000.0000.000
173A175ALA0-0.028-0.02841.0960.0000.0000.0000.0000.0000.000
174A176ARG10.8940.92442.351-0.072-0.0720.0000.0000.0000.000
175A177HIS00.0650.06344.5960.0020.0020.0000.0000.0000.000
176A178GLY00.0830.05641.414-0.001-0.0010.0000.0000.0000.000
177A179GLU-1-0.892-0.96239.7610.1100.1100.0000.0000.0000.000
178A180TYR0-0.055-0.02735.0520.0150.0150.0000.0000.0000.000
179A181LEU0-0.044-0.03534.9320.0040.0040.0000.0000.0000.000
180A182GLN00.0380.03137.2080.0050.0050.0000.0000.0000.000
181A183ILE00.0550.04438.091-0.004-0.0040.0000.0000.0000.000
182A184ARG10.8510.92836.370-0.091-0.0910.0000.0000.0000.000
183A185PRO00.031-0.00439.419-0.006-0.0060.0000.0000.0000.000
184A186LYS10.9080.97334.8520.0160.0160.0000.0000.0000.000
185A187ALA0-0.054-0.04935.844-0.008-0.0080.0000.0000.0000.000
186A188ALA00.0100.03036.0260.0090.0090.0000.0000.0000.000
187A189ASN0-0.030-0.02036.681-0.005-0.0050.0000.0000.0000.000
188A190ALA00.0710.03440.365-0.002-0.0020.0000.0000.0000.000
189A191LYS10.8770.91938.824-0.005-0.0050.0000.0000.0000.000
190A192ALA00.0170.03041.614-0.003-0.0030.0000.0000.0000.000
191A193LEU0-0.001-0.01343.4850.0060.0060.0000.0000.0000.000
192A194THR0-0.019-0.01444.435-0.007-0.0070.0000.0000.0000.000
193A195GLU-1-0.858-0.91646.513-0.014-0.0140.0000.0000.0000.000
194A196ALA0-0.016-0.01548.9370.0000.0000.0000.0000.0000.000
195A197ILE00.0490.02750.922-0.002-0.0020.0000.0000.0000.000
196A198GLY0-0.018-0.00153.3920.0030.0030.0000.0000.0000.000
197A199ALA00.0320.00755.9020.0000.0000.0000.0000.0000.000
198A200ARG10.8340.90257.901-0.005-0.0050.0000.0000.0000.000
199A201GLY00.0290.02557.862-0.001-0.0010.0000.0000.0000.000
200A202GLU-1-0.849-0.91258.1840.0040.0040.0000.0000.0000.000
201A203ARG10.9090.94553.7180.0140.0140.0000.0000.0000.000
202A204ILE0-0.026-0.01251.8460.0010.0010.0000.0000.0000.000
203A205LEU0-0.011-0.00350.530-0.003-0.0030.0000.0000.0000.000
204A206THR00.004-0.03746.8130.0040.0040.0000.0000.0000.000
205A207LEU00.0110.02043.026-0.004-0.0040.0000.0000.0000.000
206A208PRO00.0410.01140.4620.0020.0020.0000.0000.0000.000
207A209ARG10.8370.91540.656-0.018-0.0180.0000.0000.0000.000
208A210GLY0-0.007-0.00936.982-0.009-0.0090.0000.0000.0000.000
209A211PHE00.0650.04036.3140.0070.0070.0000.0000.0000.000
210A212TYR0-0.050-0.05032.809-0.007-0.0070.0000.0000.0000.000
211A213LEU00.0480.03230.032-0.002-0.0020.0000.0000.0000.000
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213A215LYS10.9450.96629.573-0.234-0.2340.0000.0000.0000.000
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