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: JMJJ9

Calculation Name: 2AZO-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2649704.954937
FMO2-HF: Nuclear repulsion 2562367.128815
FMO2-HF: Total energy -87337.826122
FMO2-MP2: Total energy -87598.054199


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:2:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
0.4731.38-0.005-0.401-0.501-0.001
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / 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].
3A4PRO 0-0.0010.0233.8461.0161.920-0.005-0.384-0.515-0.001
4A5ARG 10.9680.9716.4620.4720.4720.0000.0000.0000.000
5A6PRO 00.0020.0169.7240.0750.0750.0000.0000.0000.000
6A7LEU 0-0.0250.03112.5840.0230.0230.0000.0000.0000.000
7A8LEU 0-0.015-0.02714.464-0.003-0.0030.0000.0000.0000.000
8A9SER 0-0.019-0.01117.1280.0030.0030.0000.0000.0000.000
9A10PRO 0-0.0250.00718.001-0.002-0.0020.0000.0000.0000.000
10A11PRO 0-0.021-0.00916.8650.0130.0130.0000.0000.0000.000
11A12GLU -1-0.881-0.94118.7480.0180.0180.0000.0000.0000.000
12A13THR 0-0.026-0.02819.3940.0040.0040.0000.0000.0000.000
13A14GLU -1-0.733-0.86318.9470.0500.0500.0000.0000.0000.000
14A15GLU -1-0.908-0.95916.8100.1000.1000.0000.0000.0000.000
15A16GLN 0-0.029-0.01314.6620.0070.0070.0000.0000.0000.000
16A17LEU 00.0150.01214.008-0.008-0.0080.0000.0000.0000.000
17A18LEU 0-0.015-0.00514.318-0.027-0.0270.0000.0000.0000.000
18A19ALA 00.0120.00710.701-0.006-0.0060.0000.0000.0000.000
19A20GLN 0-0.028-0.0219.5330.0410.0410.0000.0000.0000.000
20A21ALA 00.0050.00010.214-0.084-0.0840.0000.0000.0000.000
21A22GLN 0-0.023-0.0379.758-0.023-0.0230.0000.0000.0000.000
22A23GLN 0-0.070-0.0164.285-0.313-0.3100.000-0.0170.0140.000
23A24LEU 00.000-0.0116.860-0.319-0.3190.0000.0000.0000.000
24A25SER 0-0.037-0.0549.4580.0160.0160.0000.0000.0000.000
25A26GLY 0-0.069-0.0329.016-0.077-0.0770.0000.0000.0000.000
26A27TYR 00.0150.0205.629-0.236-0.2360.0000.0000.0000.000
27A28THR 0-0.010-0.01911.3840.1150.1150.0000.0000.0000.000
28A29LEU 0-0.020-0.02514.594-0.031-0.0310.0000.0000.0000.000
29A30GLY 00.019-0.00417.110-0.002-0.0020.0000.0000.0000.000
30A31GLU -1-0.916-0.95612.209-0.593-0.5930.0000.0000.0000.000
31A32LEU 00.0340.01110.771-0.046-0.0460.0000.0000.0000.000
32A33ALA 00.0000.00013.7630.0230.0230.0000.0000.0000.000
33A34ALA 00.0070.01615.4190.0200.0200.0000.0000.0000.000
34A35LEU 0-0.072-0.0339.6300.0110.0110.0000.0000.0000.000
35A36VAL 0-0.023-0.01913.9770.0190.0190.0000.0000.0000.000
36A37GLY 0-0.0250.01316.7490.0390.0390.0000.0000.0000.000
37A38LEU 0-0.038-0.01419.2820.0330.0330.0000.0000.0000.000
38A39VAL 00.0220.00620.569-0.017-0.0170.0000.0000.0000.000
39A40THR 0-0.031-0.01820.4720.0020.0020.0000.0000.0000.000
40A41PRO 0-0.038-0.00422.8660.0090.0090.0000.0000.0000.000
41A42GLU -1-0.870-0.95225.543-0.119-0.1190.0000.0000.0000.000
42A43ASN 0-0.052-0.05127.8420.0060.0060.0000.0000.0000.000
43A44LEU 00.0870.04625.1490.0010.0010.0000.0000.0000.000
44A45LYS 10.9060.94228.3110.0700.0700.0000.0000.0000.000
45A46ARG 10.8880.96429.8650.1050.1050.0000.0000.0000.000
46A47ASP -1-0.854-0.91627.773-0.102-0.1020.0000.0000.0000.000
47A48LYS 10.9260.95127.9970.0550.0550.0000.0000.0000.000
48A49GLY 00.013-0.00127.3880.0020.0020.0000.0000.0000.000
49A50TRP 00.0680.03319.587-0.004-0.0040.0000.0000.0000.000
50A51ILE 00.004-0.01219.881-0.008-0.0080.0000.0000.0000.000
51A52GLY 00.0030.00520.564-0.008-0.0080.0000.0000.0000.000
52A53VAL 00.0890.05221.848-0.001-0.0010.0000.0000.0000.000
53A54LEU 0-0.0210.00016.422-0.004-0.0040.0000.0000.0000.000
54A55LEU 0-0.009-0.02216.105-0.023-0.0230.0000.0000.0000.000
55A56GLU -1-0.907-0.95417.294-0.083-0.0830.0000.0000.0000.000
56A57ILE 0-0.0380.00516.6590.0040.0040.0000.0000.0000.000
57A58TRP 0-0.037-0.0289.590-0.027-0.0270.0000.0000.0000.000
58A59LEU 0-0.077-0.02414.1990.0080.0080.0000.0000.0000.000
59A60GLY 00.046-0.02016.2020.0310.0310.0000.0000.0000.000
60A61ALA 0-0.012-0.02317.4530.0000.0000.0000.0000.0000.000
61A62SER 00.0300.04120.506-0.003-0.0030.0000.0000.0000.000
62A63ALA 00.0120.00222.1930.0080.0080.0000.0000.0000.000
63A64GLY 00.0070.01025.0560.0060.0060.0000.0000.0000.000
64A65SER 0-0.035-0.02627.6800.0020.0020.0000.0000.0000.000
65A66LYS 10.9000.94529.8330.0260.0260.0000.0000.0000.000
66A67PRO 0-0.0080.01527.1270.0050.0050.0000.0000.0000.000
67A68GLU -1-0.907-0.95829.562-0.040-0.0400.0000.0000.0000.000
68A69GLN 0-0.034-0.02026.0400.0000.0000.0000.0000.0000.000
69A70ASP -1-0.798-0.88822.759-0.016-0.0160.0000.0000.0000.000
70A71PHE 0-0.036-0.05019.666-0.002-0.0020.0000.0000.0000.000
71A72ALA 0-0.0090.00123.8630.0060.0060.0000.0000.0000.000
72A73ALA 0-0.035-0.01925.6770.0050.0050.0000.0000.0000.000
73A74LEU 0-0.0130.00220.8370.0050.0050.0000.0000.0000.000
74A75GLY 0-0.0270.00824.9940.0050.0050.0000.0000.0000.000
75A76VAL 0-0.045-0.03021.8000.0030.0030.0000.0000.0000.000
76A77GLU -1-0.924-0.96024.465-0.031-0.0310.0000.0000.0000.000
77A78LEU 00.0140.01619.5050.0030.0030.0000.0000.0000.000
78A79LYS 10.8700.93522.4840.0300.0300.0000.0000.0000.000
79A80THR 00.0150.01921.128-0.004-0.0040.0000.0000.0000.000
80A81ILE 0-0.048-0.01921.6470.0080.0080.0000.0000.0000.000
81A82PRO 00.0180.01722.272-0.007-0.0070.0000.0000.0000.000
82A83VAL 0-0.009-0.01020.4820.0120.0120.0000.0000.0000.000
83A84ASP -1-0.703-0.85523.319-0.056-0.0560.0000.0000.0000.000
84A85SER 00.007-0.00220.9860.0010.0010.0000.0000.0000.000
85A86LEU 0-0.078-0.04420.7710.0020.0020.0000.0000.0000.000
86A87GLY 0-0.0180.00520.6980.0100.0100.0000.0000.0000.000
87A88ARG 10.8730.91721.3210.0350.0350.0000.0000.0000.000
88A89PRO 0-0.0090.00524.953-0.008-0.0080.0000.0000.0000.000
89A90LEU 0-0.0130.01125.9770.0040.0040.0000.0000.0000.000
90A91GLU -1-0.987-1.00628.584-0.049-0.0490.0000.0000.0000.000
91A92THR 0-0.080-0.02730.3710.0040.0040.0000.0000.0000.000
92A93THR 00.0560.02428.259-0.005-0.0050.0000.0000.0000.000
93A94PHE 0-0.020-0.00930.5520.0040.0040.0000.0000.0000.000
94A95VAL 00.0200.01530.753-0.002-0.0020.0000.0000.0000.000
95A96CYS 0-0.027-0.01732.573-0.001-0.0010.0000.0000.0000.000
96A97VAL 0-0.009-0.00635.2410.0000.0000.0000.0000.0000.000
97A98ALA 0-0.0080.01238.5940.0020.0020.0000.0000.0000.000
98A99PRO 0-0.036-0.01241.647-0.001-0.0010.0000.0000.0000.000
99A100LEU 00.024-0.01944.5830.0010.0010.0000.0000.0000.000
100A101THR 0-0.0030.01447.9990.0010.0010.0000.0000.0000.000
101A102GLY 00.013-0.00248.328-0.001-0.0010.0000.0000.0000.000
102A103ASN 00.0130.01146.0910.0000.0000.0000.0000.0000.000
103A104SER 00.0460.01847.7920.0010.0010.0000.0000.0000.000
104A105GLY 0-0.025-0.01549.3480.0000.0000.0000.0000.0000.000
105A106VAL 0-0.0230.01143.6400.0010.0010.0000.0000.0000.000
106A107THR 00.0330.01944.6620.0000.0000.0000.0000.0000.000
107A108TRP 00.0670.02536.511-0.003-0.0030.0000.0000.0000.000
108A109GLU -1-0.872-0.95639.9790.0050.0050.0000.0000.0000.000
109A110THR 0-0.048-0.02939.5800.0000.0000.0000.0000.0000.000
110A111SER 0-0.0070.02339.030-0.003-0.0030.0000.0000.0000.000
111A112HIS 00.028-0.02336.2920.0010.0010.0000.0000.0000.000
112A113VAL 00.0100.00534.791-0.001-0.0010.0000.0000.0000.000
113A114ARG 11.0361.02833.929-0.007-0.0070.0000.0000.0000.000
114A115HIS 0-0.030-0.01531.9060.0040.0040.0000.0000.0000.000
115A116LYS 10.9090.93730.6360.0220.0220.0000.0000.0000.000
116A117LEU 0-0.016-0.01029.347-0.002-0.0020.0000.0000.0000.000
117A118LYS 10.9100.98829.9330.0010.0010.0000.0000.0000.000
118A119ARG 10.8540.93022.779-0.039-0.0390.0000.0000.0000.000
119A120VAL 0-0.0290.00323.937-0.006-0.0060.0000.0000.0000.000
120A121LEU 00.0360.03017.0620.0080.0080.0000.0000.0000.000
121A122TRP 0-0.017-0.01421.048-0.020-0.0200.0000.0000.0000.000
122A123ILE 00.0540.01316.2020.0050.0050.0000.0000.0000.000
123A124PRO 0-0.006-0.01417.144-0.012-0.0120.0000.0000.0000.000
124A125VAL 00.0290.01117.582-0.022-0.0220.0000.0000.0000.000
125A126GLU -1-0.780-0.84918.893-0.131-0.1310.0000.0000.0000.000
126A127GLY 00.006-0.01721.257-0.008-0.0080.0000.0000.0000.000
127A128GLU -1-0.868-0.93224.598-0.065-0.0650.0000.0000.0000.000
128A129ARG 10.9550.96526.4580.0650.0650.0000.0000.0000.000
129A130SER 0-0.131-0.07028.402-0.007-0.0070.0000.0000.0000.000
130A131ILE 00.0610.04622.326-0.002-0.0020.0000.0000.0000.000
131A132PRO 00.0380.02924.013-0.001-0.0010.0000.0000.0000.000
132A133LEU 00.009-0.00122.608-0.009-0.0090.0000.0000.0000.000
133A134ALA 00.0530.01220.237-0.010-0.0100.0000.0000.0000.000
134A135GLN 0-0.008-0.01118.681-0.024-0.0240.0000.0000.0000.000
135A136ARG 10.8060.92719.1600.1250.1250.0000.0000.0000.000
136A137ARG 10.8630.91314.5740.1580.1580.0000.0000.0000.000
137A138VAL 0-0.0090.01612.9740.0540.0540.0000.0000.0000.000
138A139GLY 00.0040.00813.808-0.011-0.0110.0000.0000.0000.000
139A140SER 00.0090.02713.599-0.007-0.0070.0000.0000.0000.000
140A141PRO 0-0.026-0.00413.0530.0040.0040.0000.0000.0000.000
141A142LEU 00.0000.00216.0050.0230.0230.0000.0000.0000.000
142A143LEU 00.0000.00718.863-0.014-0.0140.0000.0000.0000.000
143A144TRP 0-0.034-0.04120.8460.0050.0050.0000.0000.0000.000
144A145SER 00.006-0.03924.459-0.004-0.0040.0000.0000.0000.000
145A146PRO 0-0.0660.00428.0100.0030.0030.0000.0000.0000.000
146A147ASN 00.0540.03631.1610.0000.0000.0000.0000.0000.000
147A148GLU -1-0.840-0.94632.7580.0230.0230.0000.0000.0000.000
148A149GLU -1-0.986-0.99936.1070.0240.0240.0000.0000.0000.000
149A150GLU -1-0.953-0.98831.3530.0170.0170.0000.0000.0000.000
150A151ASP -1-0.892-0.98035.0640.0080.0080.0000.0000.0000.000
151A152ARG 10.9680.99536.452-0.015-0.0150.0000.0000.0000.000
152A153GLN 00.0030.00238.1120.0000.0000.0000.0000.0000.000
153A154LEU 0-0.049-0.02933.438-0.003-0.0030.0000.0000.0000.000
154A155ARG 10.8260.92338.127-0.008-0.0080.0000.0000.0000.000
155A156GLU -1-0.907-0.95040.9780.0050.0050.0000.0000.0000.000
156A157ASP -1-0.705-0.83939.724-0.003-0.0030.0000.0000.0000.000
157A158TRP 0-0.064-0.04439.620-0.002-0.0020.0000.0000.0000.000
158A159GLU -1-0.876-0.95741.9630.0010.0010.0000.0000.0000.000
159A160GLU -1-0.859-0.90545.385-0.004-0.0040.0000.0000.0000.000
160A161LEU 0-0.044-0.04541.664-0.001-0.0010.0000.0000.0000.000
161A162MET 0-0.056-0.03443.731-0.002-0.0020.0000.0000.0000.000
162A163ASP -1-0.850-0.91146.500-0.003-0.0030.0000.0000.0000.000
163A164MET 0-0.068-0.04848.660-0.001-0.0010.0000.0000.0000.000
164A165ILE 0-0.078-0.03745.076-0.001-0.0010.0000.0000.0000.000
165A166VAL 0-0.0150.00149.398-0.001-0.0010.0000.0000.0000.000
166A167LEU 0-0.074-0.02651.8190.0000.0000.0000.0000.0000.000
167A168GLY 00.0180.02253.5090.0000.0000.0000.0000.0000.000
168A169GLN 0-0.083-0.03652.3050.0000.0000.0000.0000.0000.000
169A170VAL 00.1160.03947.6230.0000.0000.0000.0000.0000.000
170A171GLU -1-0.890-0.95848.953-0.016-0.0160.0000.0000.0000.000
171A172ARG 10.8330.91651.2490.0100.0100.0000.0000.0000.000
172A173ILE 00.0180.03045.0410.0000.0000.0000.0000.0000.000
173A174THR 0-0.102-0.03845.920-0.001-0.0010.0000.0000.0000.000
174A175ALA 0-0.013-0.03441.4730.0000.0000.0000.0000.0000.000
175A176ARG 10.8820.92242.6490.0120.0120.0000.0000.0000.000
176A177HIS 00.0900.07244.9250.0000.0000.0000.0000.0000.000
177A178GLY 00.0610.04641.670-0.001-0.0010.0000.0000.0000.000
178A179GLU -1-0.917-0.96739.525-0.002-0.0020.0000.0000.0000.000
179A180TYR 0-0.102-0.04935.2200.0000.0000.0000.0000.0000.000
180A181LEU 0-0.029-0.03135.513-0.003-0.0030.0000.0000.0000.000
181A182GLN 00.0570.01337.534-0.002-0.0020.0000.0000.0000.000
182A183ILE 00.0300.04538.766-0.002-0.0020.0000.0000.0000.000
183A184ARG 10.8750.94237.5430.0230.0230.0000.0000.0000.000
184A185PRO 00.0410.00440.722-0.001-0.0010.0000.0000.0000.000
185A186LYS 10.9180.97436.5570.0330.0330.0000.0000.0000.000
186A187ALA 0-0.057-0.04938.597-0.002-0.0020.0000.0000.0000.000
187A188ALA 0-0.0020.01238.508-0.001-0.0010.0000.0000.0000.000
188A189ASN 0-0.035-0.01041.3480.0020.0020.0000.0000.0000.000
189A190ALA 00.0580.02344.0450.0000.0000.0000.0000.0000.000
190A191LYS 10.9270.94642.7510.0350.0350.0000.0000.0000.000
191A192ALA 00.0020.02144.8600.0010.0010.0000.0000.0000.000
192A193LEU 00.006-0.01246.8370.0000.0000.0000.0000.0000.000
193A194THR 0-0.029-0.01246.513-0.001-0.0010.0000.0000.0000.000
194A195GLU -1-0.948-0.97148.861-0.014-0.0140.0000.0000.0000.000
195A196ALA 0-0.001-0.00950.5250.0000.0000.0000.0000.0000.000
196A197ILE 00.0570.03352.3490.0000.0000.0000.0000.0000.000
197A198GLY 0-0.012-0.00554.5320.0000.0000.0000.0000.0000.000
198A199ALA 00.0160.00457.0770.0010.0010.0000.0000.0000.000
199A200ARG 10.8930.94658.8690.0090.0090.0000.0000.0000.000
200A201GLY 00.0280.02158.9100.0000.0000.0000.0000.0000.000
201A202GLU -1-0.885-0.94959.477-0.010-0.0100.0000.0000.0000.000
202A203ARG 11.0031.00756.5020.0140.0140.0000.0000.0000.000
203A204ILE 0-0.035-0.00952.6550.0000.0000.0000.0000.0000.000
204A205LEU 0-0.038-0.01752.951-0.001-0.0010.0000.0000.0000.000
205A206THR 00.0490.02248.7490.0000.0000.0000.0000.0000.000
206A207LEU 00.0100.01645.332-0.001-0.0010.0000.0000.0000.000
207A208PRO 00.0380.00642.8020.0010.0010.0000.0000.0000.000
208A209ARG 10.8760.94842.0960.0160.0160.0000.0000.0000.000
209A210GLY 0-0.010-0.00738.281-0.001-0.0010.0000.0000.0000.000
210A211PHE 00.0630.03837.0390.0000.0000.0000.0000.0000.000
211A212TYR 0-0.054-0.05133.904-0.003-0.0030.0000.0000.0000.000
212A213LEU 00.0520.03130.1620.0020.0020.0000.0000.0000.000
213A214LYS 10.8890.95733.0200.0020.0020.0000.0000.0000.000
214A215LYS 10.9660.98330.6540.0260.0260.0000.0000.0000.000
215A216ASN 0-0.004-0.01630.670-0.001-0.0010.0000.0000.0000.000
216A217PHE 00.0780.05430.8760.0020.0020.0000.0000.0000.000
217A218THR 00.0400.01027.0010.0040.0040.0000.0000.0000.000
218A219SER 0-0.061-0.05026.533-0.001-0.0010.0000.0000.0000.000
219A220ALA 00.0020.00527.0270.0020.0020.0000.0000.0000.000
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