Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4N4RN

Calculation Name: 1AZ4-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AZ4

Chain ID: A

ChEMBL ID:

UniProt ID: P04390

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 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2380817.526063
FMO2-HF: Nuclear repulsion 2299999.605671
FMO2-HF: Total energy -80817.920392
FMO2-MP2: Total energy -81060.928925


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:SER )


Summations of interaction energy for fragment #1(A:2:SER )
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.
-11.673-8.0479.41-6.25-6.7850.021
Interaction energy analysis for fragmet #1(A:2:SER )
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 : 0.012
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].
3A4ARG 10.8590.9183.233-4.162-1.5120.118-1.222-1.5460.006
4A5SER 0-0.003-0.0111.837-4.741-5.8618.718-4.143-3.4540.007
5A6ASP -1-0.863-0.9283.908-2.455-1.4610.028-0.304-0.7190.001
6A7LEU 0-0.030-0.0045.6810.1290.1290.0000.0000.0000.000
7A8ILE 00.0390.0196.402-0.254-0.2540.0000.0000.0000.000
8A9ASN 00.019-0.0016.8790.0180.0180.0000.0000.0000.000
9A10ALA 00.003-0.0019.3450.0080.0080.0000.0000.0000.000
10A11LEU 00.0030.01011.1350.0270.0270.0000.0000.0000.000
11A12TYR 0-0.054-0.03811.562-0.013-0.0130.0000.0000.0000.000
12A13ASP -1-0.942-0.95613.513-0.158-0.1580.0000.0000.0000.000
13A14GLU -1-0.847-0.94115.2880.0310.0310.0000.0000.0000.000
14A15ASN 0-0.054-0.02017.1240.0380.0380.0000.0000.0000.000
15A16GLN 0-0.048-0.03518.7700.0260.0260.0000.0000.0000.000
16A17LYS 10.8640.93218.5290.0580.0580.0000.0000.0000.000
17A18TYR 0-0.025-0.01716.5310.0290.0290.0000.0000.0000.000
18A19ASP -1-0.909-0.91523.2830.0070.0070.0000.0000.0000.000
19A20VAL 00.0490.02126.7550.0040.0040.0000.0000.0000.000
20A21CYS 0-0.035-0.02229.376-0.002-0.0020.0000.0000.0000.000
21A22GLY 00.0450.01632.893-0.002-0.0020.0000.0000.0000.000
22A23ILE 0-0.0200.00933.2980.0030.0030.0000.0000.0000.000
23A24ILE 0-0.004-0.00434.061-0.004-0.0040.0000.0000.0000.000
24A25SER 0-0.072-0.03436.6170.0040.0040.0000.0000.0000.000
25A26ALA 00.0600.01439.362-0.002-0.0020.0000.0000.0000.000
26A27GLU -1-0.962-0.97440.2910.0250.0250.0000.0000.0000.000
27A28GLY 00.0240.00340.118-0.003-0.0030.0000.0000.0000.000
28A29LYS 10.9010.96440.763-0.031-0.0310.0000.0000.0000.000
29A30ILE 00.0400.03037.0210.0040.0040.0000.0000.0000.000
30A31TYR 0-0.012-0.02338.587-0.003-0.0030.0000.0000.0000.000
31A32PRO 00.0350.03937.3270.0030.0030.0000.0000.0000.000
32A33LEU 0-0.019-0.02130.8790.0040.0040.0000.0000.0000.000
33A34NME 0-0.0170.00635.4960.0000.0000.0000.0000.0000.000
34A40ACE 00.002-0.01229.648-0.002-0.0020.0000.0000.0000.000
35A41SER 0-0.012-0.01626.051-0.004-0.0040.0000.0000.0000.000
36A42THR 00.0750.05625.5710.0070.0070.0000.0000.0000.000
37A43ILE 00.009-0.00425.4990.0130.0130.0000.0000.0000.000
38A44PHE 00.0540.01621.5260.0040.0040.0000.0000.0000.000
39A45GLU -1-0.874-0.93621.0140.2130.2130.0000.0000.0000.000
40A46LEU 0-0.079-0.05121.2500.0220.0220.0000.0000.0000.000
41A47PHE 00.0150.02620.2580.0040.0040.0000.0000.0000.000
42A48SER 00.0370.02716.5890.0060.0060.0000.0000.0000.000
43A49ARG 10.9150.98016.716-0.198-0.1980.0000.0000.0000.000
44A50PRO 0-0.0060.02417.2500.0420.0420.0000.0000.0000.000
45A51ILE 00.0080.00513.0090.0190.0190.0000.0000.0000.000
46A52ILE 0-0.028-0.02612.5910.0480.0480.0000.0000.0000.000
47A53ASN 0-0.040-0.05212.3930.1230.1230.0000.0000.0000.000
48A54LYS 10.9921.01311.527-0.027-0.0270.0000.0000.0000.000
49A55ILE 0-0.036-0.0227.373-0.039-0.0390.0000.0000.0000.000
50A56ALA 00.0700.0308.9500.1890.1890.0000.0000.0000.000
51A57GLU -1-0.912-0.94210.5570.4600.4600.0000.0000.0000.000
52A58LYS 10.8740.9556.7810.1750.1750.0000.0000.0000.000
53A59HIS 0-0.098-0.0692.824-1.195-0.0930.546-0.581-1.0660.007
54A60GLY 0-0.020-0.0098.4450.0790.0790.0000.0000.0000.000
55A61TYR 0-0.071-0.0396.9050.1550.1550.0000.0000.0000.000
56A62ILE 00.0110.01712.195-0.080-0.0800.0000.0000.0000.000
57A63VAL 00.005-0.00813.9610.0600.0600.0000.0000.0000.000
58A64GLU -1-0.802-0.87516.3360.3100.3100.0000.0000.0000.000
59A65GLU -1-0.806-0.89319.3020.2860.2860.0000.0000.0000.000
60A66PRO 0-0.0050.00121.647-0.012-0.0120.0000.0000.0000.000
61A67LYS 10.8030.87723.543-0.302-0.3020.0000.0000.0000.000
62A68GLN 00.0180.01527.819-0.022-0.0220.0000.0000.0000.000
63A69GLN 0-0.018-0.00428.2310.0080.0080.0000.0000.0000.000
64A70ASN 0-0.028-0.02628.0210.0080.0080.0000.0000.0000.000
65A71HIS 0-0.039-0.02425.413-0.005-0.0050.0000.0000.0000.000
66A72TYR 0-0.0410.00617.3280.0080.0080.0000.0000.0000.000
67A73PRO 00.013-0.01817.562-0.003-0.0030.0000.0000.0000.000
68A74ASP -1-0.770-0.88918.9930.2900.2900.0000.0000.0000.000
69A75PHE 0-0.002-0.01715.769-0.011-0.0110.0000.0000.0000.000
70A76THR 0-0.026-0.01215.8570.0400.0400.0000.0000.0000.000
71A77LEU 0-0.017-0.01610.189-0.010-0.0100.0000.0000.0000.000
72A78TYR 00.000-0.00212.6030.0630.0630.0000.0000.0000.000
73A79LYS 10.9791.0199.207-1.456-1.4560.0000.0000.0000.000
74A80PRO 00.022-0.00913.580-0.043-0.0430.0000.0000.0000.000
75A81SER 00.0010.00215.756-0.029-0.0290.0000.0000.0000.000
76A82GLU -1-0.879-0.92013.1720.5570.5570.0000.0000.0000.000
77A83PRO 00.0240.01415.1410.0600.0600.0000.0000.0000.000
78A84ASN 0-0.003-0.01117.443-0.004-0.0040.0000.0000.0000.000
79A85LYS 10.8700.91511.961-0.628-0.6280.0000.0000.0000.000
80A86LYS 10.8050.94712.250-0.344-0.3440.0000.0000.0000.000
81A87ILE 0-0.0200.0077.8630.0010.0010.0000.0000.0000.000
82A88ALA 00.0050.00112.241-0.091-0.0910.0000.0000.0000.000
83A89ILE 0-0.0120.00411.1280.0610.0610.0000.0000.0000.000
84A90ASP -1-0.847-0.95214.8250.2420.2420.0000.0000.0000.000
85A91ILE 0-0.0160.00616.6380.0120.0120.0000.0000.0000.000
86A92LYS 10.8670.94618.748-0.259-0.2590.0000.0000.0000.000
87A93ALA 00.026-0.00520.229-0.008-0.0080.0000.0000.0000.000
88A94THR 0-0.0180.00422.921-0.007-0.0070.0000.0000.0000.000
89A95TYR 00.008-0.01025.669-0.008-0.0080.0000.0000.0000.000
90A96THR 0-0.0210.00226.823-0.005-0.0050.0000.0000.0000.000
91A97ASN 0-0.038-0.03229.360-0.004-0.0040.0000.0000.0000.000
92A98LYS 10.8190.93032.4790.0070.0070.0000.0000.0000.000
93A99GLU -1-0.881-0.95430.268-0.016-0.0160.0000.0000.0000.000
94A100ASN 00.0810.06626.982-0.003-0.0030.0000.0000.0000.000
95A101GLU -1-0.761-0.90028.1460.0110.0110.0000.0000.0000.000
96A102LYS 10.9811.00327.845-0.001-0.0010.0000.0000.0000.000
97A103ILE 00.029-0.01123.3760.0040.0040.0000.0000.0000.000
98A104LYS 10.8660.95524.955-0.070-0.0700.0000.0000.0000.000
99A105PHE 00.0200.02120.9890.0030.0030.0000.0000.0000.000
100A106THR 0-0.0220.00424.249-0.011-0.0110.0000.0000.0000.000
101A107LEU 0-0.049-0.05119.7340.0220.0220.0000.0000.0000.000
102A108GLY 00.0280.03023.0970.0090.0090.0000.0000.0000.000
103A109GLY 00.0560.01124.512-0.020-0.0200.0000.0000.0000.000
104A110TYR 00.0050.01126.1570.0150.0150.0000.0000.0000.000
105A111THR 00.0310.02827.817-0.006-0.0060.0000.0000.0000.000
106A112SER 00.015-0.00928.176-0.001-0.0010.0000.0000.0000.000
107A113PHE 00.0410.01822.077-0.006-0.0060.0000.0000.0000.000
108A114ILE 00.0960.07023.9740.0090.0090.0000.0000.0000.000
109A115ARG 10.8770.94125.445-0.143-0.1430.0000.0000.0000.000
110A116ASN 0-0.053-0.01328.590-0.015-0.0150.0000.0000.0000.000
111A117ASN 00.0470.03423.9670.0160.0160.0000.0000.0000.000
112A118THR 00.0490.02525.3640.0130.0130.0000.0000.0000.000
113A119LYS 10.8490.92227.866-0.180-0.1800.0000.0000.0000.000
114A120ASN 00.022-0.01027.4870.0040.0040.0000.0000.0000.000
115A121ILE 0-0.0040.02620.7460.0030.0030.0000.0000.0000.000
116A122VAL 0-0.026-0.00121.440-0.021-0.0210.0000.0000.0000.000
117A123TYR 0-0.051-0.05520.034-0.012-0.0120.0000.0000.0000.000
118A124PRO 0-0.002-0.02322.311-0.007-0.0070.0000.0000.0000.000
119A125PHE 00.0850.02520.7260.0340.0340.0000.0000.0000.000
120A126ASP -1-0.912-0.94919.7140.3270.3270.0000.0000.0000.000
121A127GLN 0-0.055-0.05018.4080.0300.0300.0000.0000.0000.000
122A128TYR 0-0.045-0.03015.4380.0590.0590.0000.0000.0000.000
123A129ILE 00.0040.01910.023-0.035-0.0350.0000.0000.0000.000
124A130ALA 00.0260.01210.5620.0570.0570.0000.0000.0000.000
125A131HIS 00.0310.03312.514-0.054-0.0540.0000.0000.0000.000
126A132TRP 00.005-0.0156.4290.1980.1980.0000.0000.0000.000
127A133ILE 0-0.050-0.00912.993-0.067-0.0670.0000.0000.0000.000
128A134ILE 0-0.002-0.00312.3020.0330.0330.0000.0000.0000.000
129A135GLY 00.0100.00415.216-0.028-0.0280.0000.0000.0000.000
130A136TYR 0-0.017-0.02417.677-0.033-0.0330.0000.0000.0000.000
131A137VAL 0-0.015-0.01320.4790.0020.0020.0000.0000.0000.000
132A138TYR 00.0010.01623.234-0.014-0.0140.0000.0000.0000.000
133A139THR 0-0.025-0.01125.958-0.003-0.0030.0000.0000.0000.000
134A140ARG 10.8690.93729.437-0.023-0.0230.0000.0000.0000.000
135A141VAL 00.0600.01132.382-0.007-0.0070.0000.0000.0000.000
136A142NME 00.0100.03535.9000.0010.0010.0000.0000.0000.000
137A148ACE 00.015-0.00445.4830.0000.0000.0000.0000.0000.000
138A149LYS 10.8350.92344.584-0.015-0.0150.0000.0000.0000.000
139A150THR 00.0000.01142.6440.0010.0010.0000.0000.0000.000
140A151TYR 00.0150.01541.339-0.001-0.0010.0000.0000.0000.000
141A152ASN 00.0680.01242.0560.0020.0020.0000.0000.0000.000
142A153ILE 00.0600.01236.504-0.001-0.0010.0000.0000.0000.000
143A154ASN 0-0.017-0.00539.714-0.004-0.0040.0000.0000.0000.000
144A155GLU -1-0.864-0.94441.9780.0100.0100.0000.0000.0000.000
145A156LEU 0-0.043-0.01935.1310.0000.0000.0000.0000.0000.000
146A157ASN 0-0.031-0.00837.860-0.002-0.0020.0000.0000.0000.000
147A158GLU -1-0.903-0.96239.207-0.003-0.0030.0000.0000.0000.000
148A159ILE 0-0.078-0.02137.2700.0030.0030.0000.0000.0000.000
149A160PRO 0-0.027-0.00537.308-0.001-0.0010.0000.0000.0000.000
150A161LYS 10.8810.92631.202-0.001-0.0010.0000.0000.0000.000
151A162PRO 0-0.0150.01630.6590.0000.0000.0000.0000.0000.000
152A163TYR 0-0.095-0.12826.3520.0030.0030.0000.0000.0000.000
153A164LYS 10.8460.91530.0830.0030.0030.0000.0000.0000.000
154A165GLY 00.0360.02926.761-0.004-0.0040.0000.0000.0000.000
155A166VAL 00.025-0.00821.6740.0120.0120.0000.0000.0000.000
156A167LYS 10.8680.96120.0640.0290.0290.0000.0000.0000.000
157A168VAL 00.0700.02714.9540.0220.0220.0000.0000.0000.000
158A169PHE 0-0.0070.01313.654-0.059-0.0590.0000.0000.0000.000
159A170LEU 00.0300.0338.0260.0480.0480.0000.0000.0000.000
160A171GLN 00.0000.00810.9580.0260.0260.0000.0000.0000.000
161A172ASP -1-0.806-0.89910.6170.7510.7510.0000.0000.0000.000
162A173LYS 10.9040.93613.088-0.417-0.4170.0000.0000.0000.000
163A174TRP 00.0210.02313.635-0.063-0.0630.0000.0000.0000.000
164A175VAL 0-0.0240.02113.041-0.035-0.0350.0000.0000.0000.000
165A176ILE 0-0.028-0.00616.341-0.044-0.0440.0000.0000.0000.000
166A177ALA 0-0.006-0.03018.7170.0160.0160.0000.0000.0000.000
167A178GLY 0-0.024-0.01421.795-0.012-0.0120.0000.0000.0000.000
168A179ASP -1-0.870-0.92125.2310.0610.0610.0000.0000.0000.000
169A180LEU 00.0700.02428.9580.0070.0070.0000.0000.0000.000
170A181ALA 0-0.107-0.03430.127-0.001-0.0010.0000.0000.0000.000
171A182GLY 00.0960.03530.970-0.007-0.0070.0000.0000.0000.000
172A183SER 0-0.024-0.00733.209-0.001-0.0010.0000.0000.0000.000
173A184GLY 00.0100.02231.029-0.001-0.0010.0000.0000.0000.000
174A185ASN 0-0.059-0.03431.9410.0070.0070.0000.0000.0000.000
175A186THR 00.0180.00233.663-0.004-0.0040.0000.0000.0000.000
176A187THR 00.007-0.00331.8320.0060.0060.0000.0000.0000.000
177A188ASN 0-0.045-0.02227.5660.0110.0110.0000.0000.0000.000
178A189ILE 00.0130.00924.241-0.010-0.0100.0000.0000.0000.000
179A190GLY 0-0.0240.01325.3080.0130.0130.0000.0000.0000.000
180A191SER 0-0.023-0.02021.741-0.001-0.0010.0000.0000.0000.000
181A192ILE 00.0800.04520.582-0.009-0.0090.0000.0000.0000.000
182A193HIS 00.019-0.00924.1120.0110.0110.0000.0000.0000.000
183A194ALA 0-0.0010.00322.358-0.010-0.0100.0000.0000.0000.000
184A195HIS 0-0.024-0.02723.6060.0040.0040.0000.0000.0000.000
185A196TYR 00.0380.00016.361-0.026-0.0260.0000.0000.0000.000
186A197LYS 10.7740.85516.1110.2170.2170.0000.0000.0000.000
187A198ASP -1-0.805-0.90719.000-0.063-0.0630.0000.0000.0000.000
188A199PHE 00.019-0.01016.995-0.003-0.0030.0000.0000.0000.000
189A200VAL 0-0.015-0.01013.6690.0290.0290.0000.0000.0000.000
190A201GLU -1-0.870-0.91712.887-0.306-0.3060.0000.0000.0000.000
191A202GLY 0-0.058-0.02814.767-0.017-0.0170.0000.0000.0000.000
192A203LYS 10.8990.92815.2880.1790.1790.0000.0000.0000.000
193A204GLY 00.0620.05118.9000.0110.0110.0000.0000.0000.000
194A205ILE 0-0.088-0.05620.370-0.016-0.0160.0000.0000.0000.000
195A206PHE 0-0.0200.01620.7710.0000.0000.0000.0000.0000.000
196A207ASP -1-0.865-0.92520.4110.0120.0120.0000.0000.0000.000
197A208SER 0-0.059-0.04018.3240.0020.0020.0000.0000.0000.000
198A209GLU -1-0.942-0.98416.0220.4050.4050.0000.0000.0000.000
199A210ASP -1-0.904-0.96518.7350.1860.1860.0000.0000.0000.000
200A211GLU -1-0.870-0.94821.9650.0550.0550.0000.0000.0000.000
201A212PHE 0-0.058-0.01120.0310.0090.0090.0000.0000.0000.000
202A213LEU 0-0.043-0.05121.025-0.001-0.0010.0000.0000.0000.000
203A214ASP -1-1.004-0.98723.9720.0890.0890.0000.0000.0000.000
204A215TYR 00.0420.01026.374-0.014-0.0140.0000.0000.0000.000
205A216TRP 0-0.044-0.02424.535-0.002-0.0020.0000.0000.0000.000
206A217ARG 10.8480.92723.915-0.188-0.1880.0000.0000.0000.000
207A1NME 0-0.0010.01029.221-0.009-0.0090.0000.0000.0000.000