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: JL189

Calculation Name: 1AZZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AZZ

Chain ID: A

ChEMBL ID:

UniProt ID: P00771

Base Structure: X-ray

Registration Date: 2023-09-20

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541907.54818
FMO2-HF: Nuclear repulsion 2458372.182963
FMO2-HF: Total energy -83535.365218
FMO2-MP2: Total energy -83776.250647


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:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
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.
-32.85-22.7338.006-17.73-30.396-0.122
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.038
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].
3A18GLY00.024-0.0053.639-0.0991.8690.018-0.834-1.1520.004
4A19GLY00.0190.0032.742-0.5800.0720.240-0.301-0.5900.001
5A20VAL0-0.106-0.0503.596-0.577-0.616-0.0020.149-0.1080.000
6A21GLU-1-0.868-0.9274.9871.2091.294-0.001-0.003-0.0820.000
7A22ALA00.0190.0156.682-0.158-0.1580.0000.0000.0000.000
8A23VAL0-0.007-0.0098.365-0.084-0.0840.0000.0000.0000.000
9A24PRO00.0490.02611.522-0.008-0.0080.0000.0000.0000.000
10A25ASN00.007-0.00312.486-0.036-0.0360.0000.0000.0000.000
11A26SER0-0.069-0.03810.930-0.027-0.0270.0000.0000.0000.000
12A27TRP0-0.009-0.0147.777-0.090-0.0900.0000.0000.0000.000
13A28PRO00.0010.00210.928-0.028-0.0280.0000.0000.0000.000
14A29HIS00.0240.0209.643-0.018-0.0180.0000.0000.0000.000
15A30GLN0-0.035-0.0016.564-0.049-0.0490.0000.0000.0000.000
16A31ALA0-0.005-0.00610.5200.0340.0340.0000.0000.0000.000
17A32ALA00.0250.02110.177-0.078-0.0780.0000.0000.0000.000
18A33LEU0-0.034-0.02211.3720.0460.0460.0000.0000.0000.000
19A34PHE00.0370.00813.080-0.057-0.0570.0000.0000.0000.000
20A35ILE0-0.032-0.02414.7030.0250.0250.0000.0000.0000.000
21A37ASP-1-0.743-0.86217.349-0.168-0.1680.0000.0000.0000.000
22A38ASP-1-0.934-0.96719.285-0.094-0.0940.0000.0000.0000.000
23A39MET0-0.118-0.05517.849-0.001-0.0010.0000.0000.0000.000
24A40TYR0-0.054-0.03013.931-0.037-0.0370.0000.0000.0000.000
25A41PHE0-0.0080.0037.4560.0690.0690.0000.0000.0000.000
26A42CYS0-0.130-0.0559.186-0.201-0.2010.0000.0000.0000.000
27A43GLY00.0750.0467.8440.1170.1170.0000.0000.0000.000
28A44GLY00.025-0.0038.8890.0030.0030.0000.0000.0000.000
29A45SER0-0.0270.00310.3170.0550.0550.0000.0000.0000.000
30A46LEU0-0.0130.01212.276-0.010-0.0100.0000.0000.0000.000
31A47ILE00.0180.00015.4530.0200.0200.0000.0000.0000.000
32A48SER00.008-0.01917.6070.0100.0100.0000.0000.0000.000
33A49PRO00.014-0.01720.494-0.006-0.0060.0000.0000.0000.000
34A50GLU-1-0.815-0.86522.562-0.016-0.0160.0000.0000.0000.000
35A51TRP00.0110.01220.186-0.010-0.0100.0000.0000.0000.000
36A52ILE00.0260.02114.3430.0130.0130.0000.0000.0000.000
37A53LEU0-0.0090.00113.837-0.004-0.0040.0000.0000.0000.000
38A54THR00.032-0.00611.848-0.024-0.0240.0000.0000.0000.000
39A55ALA00.0250.01011.8570.0240.0240.0000.0000.0000.000
40A56ALA0-0.0100.00213.7360.0060.0060.0000.0000.0000.000
41A57HIS10.8200.87911.6010.5580.5580.0000.0000.0000.000
42A59MET0-0.002-0.00315.2220.0330.0330.0000.0000.0000.000
43A60ASP-1-0.908-0.95218.577-0.180-0.1800.0000.0000.0000.000
44A61GLY0-0.046-0.01721.2460.0180.0180.0000.0000.0000.000
45A61ALA0-0.058-0.01520.0990.0060.0060.0000.0000.0000.000
46A61GLY0-0.027-0.01722.1780.0150.0150.0000.0000.0000.000
47A62PHE0-0.092-0.05721.8700.0100.0100.0000.0000.0000.000
48A63VAL0-0.001-0.00216.967-0.020-0.0200.0000.0000.0000.000
49A64ASP-1-0.805-0.88718.467-0.039-0.0390.0000.0000.0000.000
50A65VAL0-0.003-0.01215.929-0.017-0.0170.0000.0000.0000.000
51A66VAL0-0.019-0.01514.3680.0180.0180.0000.0000.0000.000
52A68LEU0-0.044-0.03114.2270.0010.0010.0000.0000.0000.000
53A69GLY00.0700.03015.0310.0050.0050.0000.0000.0000.000
54A70ALA0-0.0140.00812.4440.0020.0020.0000.0000.0000.000
55A71HIS0-0.066-0.0559.435-0.003-0.0030.0000.0000.0000.000
56A72ASN00.020-0.02010.5650.1100.1100.0000.0000.0000.000
57A73ILE0-0.021-0.02410.039-0.085-0.0850.0000.0000.0000.000
58A74ARG10.8710.94511.621-0.134-0.1340.0000.0000.0000.000
59A75GLU-1-0.968-0.97615.8370.2220.2220.0000.0000.0000.000
60A76ASP-1-0.929-0.94717.8690.0770.0770.0000.0000.0000.000
61A77GLU-1-0.778-0.87215.2250.2990.2990.0000.0000.0000.000
62A78ALA0-0.019-0.02919.537-0.014-0.0140.0000.0000.0000.000
63A79THR0-0.083-0.06317.093-0.008-0.0080.0000.0000.0000.000
64A80GLN0-0.053-0.02215.913-0.035-0.0350.0000.0000.0000.000
65A81VAL0-0.0210.00018.616-0.012-0.0120.0000.0000.0000.000
66A82THR00.0460.02818.677-0.001-0.0010.0000.0000.0000.000
67A83ILE0-0.076-0.04019.8970.0020.0020.0000.0000.0000.000
68A84GLN0-0.047-0.03020.614-0.007-0.0070.0000.0000.0000.000
69A85SER0-0.054-0.05221.7060.0070.0070.0000.0000.0000.000
70A86THR00.015-0.00623.033-0.007-0.0070.0000.0000.0000.000
71A87ASP-1-0.978-0.96924.355-0.064-0.0640.0000.0000.0000.000
72A88PHE00.0410.00620.695-0.001-0.0010.0000.0000.0000.000
73A89THR0-0.0360.00321.8590.0020.0020.0000.0000.0000.000
74A90VAL00.0240.00619.952-0.010-0.0100.0000.0000.0000.000
75A91HIS00.0230.01020.8800.0110.0110.0000.0000.0000.000
76A92GLU-1-0.817-0.90022.704-0.095-0.0950.0000.0000.0000.000
77A93ASN0-0.074-0.04125.0740.0020.0020.0000.0000.0000.000
78A94TYR0-0.0010.01218.450-0.018-0.0180.0000.0000.0000.000
79A95ASN0-0.014-0.00722.1000.0010.0010.0000.0000.0000.000
80A96SER00.0520.01820.720-0.007-0.0070.0000.0000.0000.000
81A97PHE0-0.096-0.03821.244-0.016-0.0160.0000.0000.0000.000
82A98VAL0-0.020-0.02421.755-0.007-0.0070.0000.0000.0000.000
83A99ILE00.0190.02315.654-0.005-0.0050.0000.0000.0000.000
84A100SER00.0290.02617.965-0.002-0.0020.0000.0000.0000.000
85A101ASN0-0.062-0.06719.2940.0050.0050.0000.0000.0000.000
86A102ASP-1-0.703-0.79014.209-0.365-0.3650.0000.0000.0000.000
87A103ILE0-0.041-0.00615.243-0.016-0.0160.0000.0000.0000.000
88A104ALA00.0290.01416.3640.0120.0120.0000.0000.0000.000
89A105VAL0-0.0320.00016.869-0.004-0.0040.0000.0000.0000.000
90A106ILE00.0330.00316.321-0.004-0.0040.0000.0000.0000.000
91A107ARG10.8500.91219.9190.0420.0420.0000.0000.0000.000
92A108LEU0-0.044-0.01319.268-0.002-0.0020.0000.0000.0000.000
93A109PRO00.003-0.00923.1680.0040.0040.0000.0000.0000.000
94A110VAL0-0.029-0.01325.9580.0030.0030.0000.0000.0000.000
95A111PRO0-0.039-0.01125.0260.0000.0000.0000.0000.0000.000
96A112VAL00.0250.01521.0400.0040.0040.0000.0000.0000.000
97A113THR0-0.047-0.02424.0200.0010.0010.0000.0000.0000.000
98A114LEU00.0070.00521.2070.0050.0050.0000.0000.0000.000
99A115THR0-0.028-0.01921.0390.0050.0050.0000.0000.0000.000
100A116ALA0-0.049-0.03320.6270.0010.0010.0000.0000.0000.000
101A117ALA00.0110.00216.9310.0150.0150.0000.0000.0000.000
102A118ILE00.0150.03516.0610.0080.0080.0000.0000.0000.000
103A119ALA0-0.015-0.01316.767-0.012-0.0120.0000.0000.0000.000
104A120THR00.0120.02116.502-0.001-0.0010.0000.0000.0000.000
105A121VAL0-0.0090.00312.5160.0180.0180.0000.0000.0000.000
106A122GLY0-0.041-0.01115.652-0.017-0.0170.0000.0000.0000.000
107A123LEU00.0410.01316.0650.0010.0010.0000.0000.0000.000
108A124PRO00.0360.02415.9060.0080.0080.0000.0000.0000.000
109A125SER0-0.010-0.01218.893-0.009-0.0090.0000.0000.0000.000
110A127THR0-0.039-0.02421.410-0.005-0.0050.0000.0000.0000.000
111A128ASP-1-0.762-0.84317.705-0.006-0.0060.0000.0000.0000.000
112A129VAL0-0.0140.00414.7330.0050.0050.0000.0000.0000.000
113A130GLY0-0.022-0.00517.795-0.012-0.0120.0000.0000.0000.000
114A132VAL00.0400.02117.1960.0150.0150.0000.0000.0000.000
115A133GLY0-0.039-0.01216.3480.0000.0000.0000.0000.0000.000
116A134THR0-0.076-0.05414.1290.0210.0210.0000.0000.0000.000
117A135VAL0-0.029-0.00410.273-0.011-0.0110.0000.0000.0000.000
118A136VAL0-0.022-0.0118.209-0.020-0.0200.0000.0000.0000.000
119A137THR00.016-0.0225.4770.0300.0300.0000.0000.0000.000
120A138PRO0-0.0250.0102.613-1.214-0.3110.552-0.358-1.0960.003
121A139THR0-0.020-0.0282.719-1.3480.2431.210-0.917-1.884-0.008
122A140GLY00.010-0.0082.606-2.235-1.2371.256-0.468-1.787-0.007
123A141TRP0-0.028-0.0283.2001.0981.9070.157-0.162-0.805-0.003
124A142GLY00.0290.0233.160-0.0060.4720.051-0.171-0.3580.001
125A143LEU0-0.008-0.0273.4082.2223.1200.185-0.439-0.644-0.001
126A144PRO0-0.0060.0051.892-5.219-8.4098.732-3.116-2.426-0.024
127A145SER0-0.023-0.0323.906-0.1120.002-0.001-0.017-0.0960.000
128A146ASP-1-0.774-0.8846.405-1.157-1.1570.0000.0000.0000.000
129A147SER0-0.095-0.0458.5500.1070.1070.0000.0000.0000.000
130A148ALA0-0.059-0.0117.2220.1800.1800.0000.0000.0000.000
131A149LEU00.004-0.0189.132-0.026-0.0260.0000.0000.0000.000
132A150GLY0-0.030-0.0109.5050.0170.0170.0000.0000.0000.000
133A151ILE0-0.037-0.0116.576-0.083-0.0830.0000.0000.0000.000
134A152SER0-0.068-0.0375.286-0.048-0.0480.0000.0000.0000.000
135A153ASP-1-0.875-0.9407.1930.3700.3700.0000.0000.0000.000
136A154VAL0-0.0100.0187.700-0.074-0.0740.0000.0000.0000.000
137A155LEU0-0.0480.0174.9320.5090.5090.0000.0000.0000.000
138A156ARG10.9280.9602.300-3.898-3.0231.853-0.813-1.9150.001
139A157GLN00.0650.0312.731-3.347-1.3731.169-0.803-2.340-0.011
140A158VAL0-0.009-0.0082.4000.508-0.0084.720-0.560-3.6440.001
141A159ASP-1-0.881-0.9073.7580.3030.4380.0090.049-0.1930.000
142A160VAL0-0.013-0.0096.210-0.041-0.0410.0000.0000.0000.000
143A161PRO00.0010.0048.692-0.022-0.0220.0000.0000.0000.000
144A162ILE00.0210.02211.793-0.034-0.0340.0000.0000.0000.000
145A163MET00.0010.01513.368-0.003-0.0030.0000.0000.0000.000
146A164SER0-0.073-0.07415.840-0.006-0.0060.0000.0000.0000.000
147A165ASN00.035-0.01218.0570.0000.0000.0000.0000.0000.000
148A166ALA00.0040.01219.062-0.014-0.0140.0000.0000.0000.000
149A167ASP-1-0.826-0.89018.665-0.049-0.0490.0000.0000.0000.000
150A168CYS0-0.042-0.02811.908-0.065-0.0650.0000.0000.0000.000
151A169ASP-1-0.844-0.93017.427-0.158-0.1580.0000.0000.0000.000
152A170ALA0-0.060-0.01820.265-0.005-0.0050.0000.0000.0000.000
153A171VAL0-0.076-0.02616.658-0.002-0.0020.0000.0000.0000.000
154A172TYR0-0.053-0.07312.630-0.022-0.0220.0000.0000.0000.000
155A174GLY0-0.042-0.00319.283-0.006-0.0060.0000.0000.0000.000
156A175ILE0-0.035-0.01717.9460.0110.0110.0000.0000.0000.000
157A176VAL0-0.046-0.01616.994-0.010-0.0100.0000.0000.0000.000
158A177THR0-0.014-0.01319.3230.0230.0230.0000.0000.0000.000
159A178ASP-1-0.919-0.97619.678-0.071-0.0710.0000.0000.0000.000
160A179GLY00.0060.01319.3390.0090.0090.0000.0000.0000.000
161A180ASN0-0.030-0.01015.120-0.001-0.0010.0000.0000.0000.000
162A181ILE00.0100.01912.2990.0290.0290.0000.0000.0000.000
163A183ILE00.0110.0187.3160.0550.0550.0000.0000.0000.000
164A184ASP-1-0.819-0.89710.689-0.084-0.0840.0000.0000.0000.000
165A185SER00.026-0.0178.3360.0830.0830.0000.0000.0000.000
166A186THR0-0.042-0.0559.588-0.036-0.0360.0000.0000.0000.000
167A187GLY0-0.037-0.02410.9080.0670.0670.0000.0000.0000.000
168A188GLY00.0040.0248.9760.0610.0610.0000.0000.0000.000
169A188LYS10.8050.8995.360-0.293-0.2930.0000.0000.0000.000
170A189GLY00.0580.0173.710-0.368-0.0190.000-0.107-0.2410.000
171A190THR0-0.045-0.0032.274-2.067-0.6096.669-3.910-4.217-0.025
172A191CYS0-0.052-0.0282.7480.4721.3920.166-0.048-1.0380.002
173A192ASN00.028-0.0164.347-0.483-0.312-0.001-0.016-0.1540.000
174A193GLY00.0390.0295.480-0.145-0.1450.0000.0000.0000.000
175A194ASP-1-0.712-0.8601.903-15.610-16.18111.025-4.881-5.573-0.056
176A195SER0-0.072-0.0465.0410.6280.686-0.001-0.004-0.0530.000
177A196GLY00.0350.0118.3580.0420.0420.0000.0000.0000.000
178A197GLY0-0.0020.0116.0590.1360.1360.0000.0000.0000.000
179A198PRO0-0.032-0.0055.7330.0300.0300.0000.0000.0000.000
180A199LEU00.0110.0295.7120.0770.0770.0000.0000.0000.000
181A200ASN0-0.035-0.0296.694-0.128-0.1280.0000.0000.0000.000
182A201TYR00.039-0.0029.5950.0430.0430.0000.0000.0000.000
183A202ASN0-0.035-0.02412.506-0.024-0.0240.0000.0000.0000.000
184A203GLY00.0240.01614.393-0.021-0.0210.0000.0000.0000.000
185A204LEU0-0.041-0.00514.818-0.019-0.0190.0000.0000.0000.000
186A209THR00.0380.01110.6110.0370.0370.0000.0000.0000.000
187A210TYR00.000-0.03111.571-0.016-0.0160.0000.0000.0000.000
188A211GLY0-0.009-0.01510.777-0.012-0.0120.0000.0000.0000.000
189A212ILE0-0.0120.0189.5700.0150.0150.0000.0000.0000.000
190A213THR0-0.023-0.0035.0210.1760.1760.0000.0000.0000.000
191A214SER0-0.046-0.0447.942-0.042-0.0420.0000.0000.0000.000
192A215PHE00.005-0.00810.902-0.067-0.0670.0000.0000.0000.000
193A216GLY00.1050.04710.0780.0230.0230.0000.0000.0000.000
194A217ALA0-0.0210.00111.0380.0540.0540.0000.0000.0000.000
195A217ALA0-0.001-0.01412.176-0.083-0.0830.0000.0000.0000.000
196A218ALA0-0.090-0.04313.953-0.013-0.0130.0000.0000.0000.000
197A219GLY00.0330.02710.7150.0450.0450.0000.0000.0000.000
198A221GLU-1-0.900-0.9607.753-0.556-0.5560.0000.0000.0000.000
199A222ALA0-0.073-0.0309.4490.1650.1650.0000.0000.0000.000
200A223GLY0-0.021-0.00211.0160.0700.0700.0000.0000.0000.000
201A224TYR0-0.033-0.00612.0930.0710.0710.0000.0000.0000.000
202A225PRO00.0300.03211.140-0.031-0.0310.0000.0000.0000.000
203A226ASP-1-0.800-0.8596.451-0.817-0.8170.0000.0000.0000.000
204A227ALA0-0.004-0.0199.4690.1250.1250.0000.0000.0000.000
205A228PHE00.016-0.0085.640-0.098-0.0980.0000.0000.0000.000
206A229THR0-0.032-0.03511.1620.0300.0300.0000.0000.0000.000
207A230ARG10.8050.89213.1610.0600.0600.0000.0000.0000.000
208A231VAL00.0370.00413.527-0.002-0.0020.0000.0000.0000.000
209A232THR0-0.040-0.06116.208-0.004-0.0040.0000.0000.0000.000
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