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: ZY7GN

Calculation Name: 1AZ4-A-Xray372

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: 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2365188.582658
FMO2-HF: Nuclear repulsion 2284730.20002
FMO2-HF: Total energy -80458.382638
FMO2-MP2: Total energy -80700.079322


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.
-13.899-6.9514.637-4.982-6.6010.027
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 : 0.008
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].
3A4ARG10.8720.9173.037-4.722-1.7330.222-1.402-1.8090.008
4A5SER0-0.009-0.0022.275-6.720-4.9004.078-2.708-3.1890.011
5A6ASP-1-0.816-0.8933.823-1.309-0.3400.022-0.315-0.6760.001
6A7LEU0-0.0050.0115.734-0.021-0.0210.0000.0000.0000.000
7A8ILE00.0430.0246.267-0.288-0.2880.0000.0000.0000.000
8A9ASN0-0.008-0.0146.507-0.055-0.0550.0000.0000.0000.000
9A10ALA00.0200.0069.323-0.026-0.0260.0000.0000.0000.000
10A11LEU0-0.0060.00811.0590.0030.0030.0000.0000.0000.000
11A12TYR0-0.059-0.05111.476-0.032-0.0320.0000.0000.0000.000
12A13ASP-1-0.891-0.92813.582-0.037-0.0370.0000.0000.0000.000
13A14GLU-1-0.866-0.93215.4260.0960.0960.0000.0000.0000.000
14A15ASN0-0.041-0.01917.1480.0160.0160.0000.0000.0000.000
15A16GLN0-0.020-0.01318.8290.0010.0010.0000.0000.0000.000
16A17LYS10.7580.85918.246-0.028-0.0280.0000.0000.0000.000
17A18TYR0-0.016-0.00216.3110.0250.0250.0000.0000.0000.000
18A19ASP-1-0.837-0.89223.2480.0300.0300.0000.0000.0000.000
19A20VAL00.0300.00826.7630.0050.0050.0000.0000.0000.000
20A21CYS0-0.019-0.02329.329-0.003-0.0030.0000.0000.0000.000
21A22GLY00.0240.01032.837-0.004-0.0040.0000.0000.0000.000
22A23ILE0-0.0160.00833.1030.0050.0050.0000.0000.0000.000
23A24ILE0-0.008-0.00434.132-0.006-0.0060.0000.0000.0000.000
24A25SER0-0.054-0.02936.7020.0040.0040.0000.0000.0000.000
25A26ALA00.0630.01839.447-0.002-0.0020.0000.0000.0000.000
26A27GLU-1-0.942-0.97140.3800.0390.0390.0000.0000.0000.000
27A28GLY00.0160.00540.194-0.004-0.0040.0000.0000.0000.000
28A29LYS10.8820.95840.838-0.041-0.0410.0000.0000.0000.000
29A30ILE00.0310.02036.9130.0050.0050.0000.0000.0000.000
30A31TYR00.008-0.00938.522-0.004-0.0040.0000.0000.0000.000
31A32PRO00.0440.04937.2560.0040.0040.0000.0000.0000.000
32A33LEU0-0.060-0.02830.9420.0030.0030.0000.0000.0000.000
33A41SER00.013-0.00625.925-0.007-0.0070.0000.0000.0000.000
34A42THR00.0570.03225.4430.0090.0090.0000.0000.0000.000
35A43ILE00.003-0.00525.3780.0150.0150.0000.0000.0000.000
36A44PHE00.0440.02021.4350.0060.0060.0000.0000.0000.000
37A45GLU-1-0.843-0.92220.9050.2360.2360.0000.0000.0000.000
38A46LEU0-0.093-0.05721.1240.0280.0280.0000.0000.0000.000
39A47PHE00.0260.01420.1880.0080.0080.0000.0000.0000.000
40A48SER00.0150.00616.5330.0120.0120.0000.0000.0000.000
41A49ARG10.8320.90016.716-0.227-0.2270.0000.0000.0000.000
42A50PRO00.0120.02017.2500.0480.0480.0000.0000.0000.000
43A51ILE0-0.0100.00513.0260.0280.0280.0000.0000.0000.000
44A52ILE0-0.007-0.02412.5850.0660.0660.0000.0000.0000.000
45A53ASN0-0.034-0.04112.3930.1300.1300.0000.0000.0000.000
46A54LYS10.9951.01711.954-0.170-0.1700.0000.0000.0000.000
47A55ILE0-0.026-0.0147.419-0.003-0.0030.0000.0000.0000.000
48A56ALA00.0560.0219.0630.2250.2250.0000.0000.0000.000
49A57GLU-1-0.912-0.93810.5570.5490.5490.0000.0000.0000.000
50A58LYS10.8230.8997.029-0.153-0.1530.0000.0000.0000.000
51A59HIS0-0.093-0.0692.957-1.0420.1280.315-0.557-0.9270.007
52A60GLY0-0.032-0.0148.4450.0390.0390.0000.0000.0000.000
53A61TYR0-0.071-0.0386.6340.1350.1350.0000.0000.0000.000
54A62ILE00.0070.01912.138-0.064-0.0640.0000.0000.0000.000
55A63VAL00.013-0.00313.9850.0580.0580.0000.0000.0000.000
56A64GLU-1-0.776-0.86216.2980.3150.3150.0000.0000.0000.000
57A65GLU-1-0.748-0.82519.2810.3210.3210.0000.0000.0000.000
58A66PRO00.0120.01321.627-0.012-0.0120.0000.0000.0000.000
59A67LYS10.7880.86523.513-0.308-0.3080.0000.0000.0000.000
60A68GLN00.0210.01927.806-0.022-0.0220.0000.0000.0000.000
61A69GLN0-0.016-0.00428.2260.0090.0090.0000.0000.0000.000
62A70ASN0-0.024-0.02127.8020.0070.0070.0000.0000.0000.000
63A71HIS0-0.043-0.02825.430-0.009-0.0090.0000.0000.0000.000
64A72TYR0-0.0300.02817.3270.0080.0080.0000.0000.0000.000
65A73PRO00.008-0.01017.602-0.009-0.0090.0000.0000.0000.000
66A74ASP-1-0.777-0.90018.8450.3010.3010.0000.0000.0000.000
67A75PHE00.002-0.01715.870-0.007-0.0070.0000.0000.0000.000
68A76THR0-0.0100.01515.8780.0420.0420.0000.0000.0000.000
69A77LEU00.002-0.01110.070-0.004-0.0040.0000.0000.0000.000
70A78TYR0-0.013-0.02412.5950.0530.0530.0000.0000.0000.000
71A79LYS10.9711.0168.361-1.617-1.6170.0000.0000.0000.000
72A80PRO00.022-0.00613.527-0.048-0.0480.0000.0000.0000.000
73A81SER0-0.0020.00715.482-0.028-0.0280.0000.0000.0000.000
74A82GLU-1-0.865-0.91013.4150.4840.4840.0000.0000.0000.000
75A83PRO00.0350.02015.1070.0600.0600.0000.0000.0000.000
76A84ASN0-0.021-0.00917.422-0.001-0.0010.0000.0000.0000.000
77A85LYS10.8620.90711.973-0.537-0.5370.0000.0000.0000.000
78A86LYS10.7890.92412.231-0.331-0.3310.0000.0000.0000.000
79A87ILE0-0.033-0.0017.831-0.006-0.0060.0000.0000.0000.000
80A88ALA00.0030.01012.243-0.074-0.0740.0000.0000.0000.000
81A89ILE0-0.017-0.00610.7560.0550.0550.0000.0000.0000.000
82A90ASP-1-0.765-0.87314.6350.2410.2410.0000.0000.0000.000
83A91ILE0-0.020-0.00516.5360.0130.0130.0000.0000.0000.000
84A92LYS10.8420.91618.611-0.288-0.2880.0000.0000.0000.000
85A93ALA00.0310.00520.116-0.004-0.0040.0000.0000.0000.000
86A94THR0-0.032-0.01022.811-0.008-0.0080.0000.0000.0000.000
87A95TYR0-0.003-0.00325.573-0.005-0.0050.0000.0000.0000.000
88A96THR0-0.041-0.01526.661-0.003-0.0030.0000.0000.0000.000
89A97ASN0-0.029-0.03229.267-0.003-0.0030.0000.0000.0000.000
90A98LYS10.8580.92132.462-0.014-0.0140.0000.0000.0000.000
91A99GLU-1-0.798-0.89330.878-0.005-0.0050.0000.0000.0000.000
92A100ASN0-0.0270.01527.264-0.005-0.0050.0000.0000.0000.000
93A101GLU-1-0.770-0.87528.0870.0150.0150.0000.0000.0000.000
94A102LYS10.9851.00327.7710.0030.0030.0000.0000.0000.000
95A103ILE00.006-0.02623.2630.0050.0050.0000.0000.0000.000
96A104LYS10.9020.97724.733-0.055-0.0550.0000.0000.0000.000
97A105PHE00.0060.01520.8970.0050.0050.0000.0000.0000.000
98A106THR0-0.003-0.00324.048-0.012-0.0120.0000.0000.0000.000
99A107LEU0-0.044-0.03219.4890.0200.0200.0000.0000.0000.000
100A108GLY00.0600.04622.9340.0060.0060.0000.0000.0000.000
101A109GLY00.0440.01024.331-0.019-0.0190.0000.0000.0000.000
102A110TYR00.0070.01325.9670.0130.0130.0000.0000.0000.000
103A111THR0-0.015-0.03027.633-0.008-0.0080.0000.0000.0000.000
104A112SER00.0290.00927.9310.0010.0010.0000.0000.0000.000
105A113PHE00.0480.03022.274-0.006-0.0060.0000.0000.0000.000
106A114ILE00.0630.05223.7250.0080.0080.0000.0000.0000.000
107A115ARG10.8840.96625.247-0.119-0.1190.0000.0000.0000.000
108A116ASN0-0.044-0.01828.475-0.011-0.0110.0000.0000.0000.000
109A117ASN00.003-0.00524.1090.0140.0140.0000.0000.0000.000
110A118THR00.0460.02025.3730.0140.0140.0000.0000.0000.000
111A119LYS10.8520.91527.871-0.168-0.1680.0000.0000.0000.000
112A120ASN00.027-0.00127.4990.0020.0020.0000.0000.0000.000
113A121ILE00.0010.02720.7260.0040.0040.0000.0000.0000.000
114A122VAL0-0.039-0.00621.477-0.020-0.0200.0000.0000.0000.000
115A123TYR0-0.047-0.05420.090-0.014-0.0140.0000.0000.0000.000
116A124PRO00.011-0.01222.304-0.007-0.0070.0000.0000.0000.000
117A125PHE00.0780.02420.0740.0330.0330.0000.0000.0000.000
118A126ASP-1-0.870-0.91319.7300.2950.2950.0000.0000.0000.000
119A127GLN0-0.045-0.04318.4450.0250.0250.0000.0000.0000.000
120A128TYR0-0.050-0.04215.4390.0500.0500.0000.0000.0000.000
121A129ILE0-0.0070.01310.272-0.044-0.0440.0000.0000.0000.000
122A130ALA00.0120.00610.3520.0350.0350.0000.0000.0000.000
123A131HIS00.0550.03812.325-0.005-0.0050.0000.0000.0000.000
124A132TRP0-0.007-0.0276.1110.2700.2700.0000.0000.0000.000
125A133ILE0-0.027-0.00312.815-0.054-0.0540.0000.0000.0000.000
126A134ILE0-0.012-0.00512.2990.0280.0280.0000.0000.0000.000
127A135GLY00.0170.00815.094-0.027-0.0270.0000.0000.0000.000
128A136TYR0-0.019-0.02017.703-0.032-0.0320.0000.0000.0000.000
129A137VAL0-0.014-0.01820.402-0.001-0.0010.0000.0000.0000.000
130A138TYR00.0120.02023.134-0.012-0.0120.0000.0000.0000.000
131A139THR00.0200.00225.897-0.006-0.0060.0000.0000.0000.000
132A140ARG10.8880.96029.367-0.025-0.0250.0000.0000.0000.000
133A141VAL00.0540.03432.324-0.006-0.0060.0000.0000.0000.000
134A149LYS10.8470.91044.730-0.027-0.0270.0000.0000.0000.000
135A150THR0-0.039-0.02042.7110.0010.0010.0000.0000.0000.000
136A151TYR00.0290.02041.273-0.004-0.0040.0000.0000.0000.000
137A152ASN00.035-0.00942.1310.0020.0020.0000.0000.0000.000
138A153ILE00.0540.00736.660-0.001-0.0010.0000.0000.0000.000
139A154ASN0-0.020-0.00739.773-0.003-0.0030.0000.0000.0000.000
140A155GLU-1-0.821-0.89641.9570.0230.0230.0000.0000.0000.000
141A156LEU0-0.040-0.00734.7950.0000.0000.0000.0000.0000.000
142A157ASN0-0.041-0.02737.8170.0000.0000.0000.0000.0000.000
143A158GLU-1-0.888-0.94839.1700.0110.0110.0000.0000.0000.000
144A159ILE0-0.073-0.01937.1550.0020.0020.0000.0000.0000.000
145A160PRO0-0.019-0.00137.281-0.001-0.0010.0000.0000.0000.000
146A161LYS10.8380.88931.215-0.024-0.0240.0000.0000.0000.000
147A162PRO00.0010.02130.579-0.001-0.0010.0000.0000.0000.000
148A163TYR0-0.084-0.08826.2010.0020.0020.0000.0000.0000.000
149A164LYS10.8240.89730.0510.0040.0040.0000.0000.0000.000
150A165GLY00.0060.01526.757-0.005-0.0050.0000.0000.0000.000
151A166VAL00.018-0.01521.7400.0090.0090.0000.0000.0000.000
152A167LYS10.9060.97720.0110.0150.0150.0000.0000.0000.000
153A168VAL00.0660.02715.1300.0180.0180.0000.0000.0000.000
154A169PHE00.0100.03313.580-0.060-0.0600.0000.0000.0000.000
155A170LEU00.0200.0288.1330.0530.0530.0000.0000.0000.000
156A171GLN0-0.032-0.01110.720-0.024-0.0240.0000.0000.0000.000
157A172ASP-1-0.800-0.89310.4670.6060.6060.0000.0000.0000.000
158A173LYS10.8310.87412.829-0.390-0.3900.0000.0000.0000.000
159A174TRP00.0070.00913.344-0.053-0.0530.0000.0000.0000.000
160A175VAL0-0.0110.03112.836-0.033-0.0330.0000.0000.0000.000
161A176ILE0-0.026-0.00715.953-0.034-0.0340.0000.0000.0000.000
162A177ALA00.010-0.02018.5150.0210.0210.0000.0000.0000.000
163A178GLY0-0.030-0.02221.566-0.014-0.0140.0000.0000.0000.000
164A179ASP-1-0.857-0.91325.0080.0470.0470.0000.0000.0000.000
165A180LEU00.0480.01628.7350.0060.0060.0000.0000.0000.000
166A181ALA0-0.085-0.02129.8850.0000.0000.0000.0000.0000.000
167A182GLY00.0660.02730.725-0.008-0.0080.0000.0000.0000.000
168A183SER0-0.037-0.02832.991-0.001-0.0010.0000.0000.0000.000
169A184GLY00.007-0.00632.5970.0050.0050.0000.0000.0000.000
170A185ASN0-0.0270.00227.1320.0000.0000.0000.0000.0000.000
171A186THR00.0420.01929.9790.0030.0030.0000.0000.0000.000
172A187THR0-0.006-0.02130.8800.0000.0000.0000.0000.0000.000
173A188ASN0-0.038-0.02027.0280.0190.0190.0000.0000.0000.000
174A189ILE00.0100.02324.098-0.009-0.0090.0000.0000.0000.000
175A190GLY0-0.0020.01925.0710.0130.0130.0000.0000.0000.000
176A191SER0-0.014-0.00921.3790.0020.0020.0000.0000.0000.000
177A192ILE00.0310.03920.383-0.008-0.0080.0000.0000.0000.000
178A193HIS00.003-0.03623.9290.0090.0090.0000.0000.0000.000
179A194ALA0-0.0080.00122.310-0.010-0.0100.0000.0000.0000.000
180A195HIS0-0.022-0.02323.5310.0050.0050.0000.0000.0000.000
181A196TYR00.009-0.01416.595-0.023-0.0230.0000.0000.0000.000
182A197LYS10.8030.86916.3920.2220.2220.0000.0000.0000.000
183A198ASP-1-0.813-0.90418.800-0.084-0.0840.0000.0000.0000.000
184A199PHE00.022-0.00516.885-0.010-0.0100.0000.0000.0000.000
185A200VAL00.0100.00913.5880.0200.0200.0000.0000.0000.000
186A201GLU-1-0.859-0.90312.839-0.334-0.3340.0000.0000.0000.000
187A202GLY0-0.040-0.01714.642-0.030-0.0300.0000.0000.0000.000
188A203LYS10.8550.88815.1670.2280.2280.0000.0000.0000.000
189A204GLY00.0660.05018.7810.0160.0160.0000.0000.0000.000
190A205ILE0-0.096-0.05220.210-0.015-0.0150.0000.0000.0000.000
191A206PHE0-0.0300.00620.5040.0020.0020.0000.0000.0000.000
192A207ASP-1-0.876-0.94120.223-0.045-0.0450.0000.0000.0000.000
193A208SER0-0.089-0.07018.106-0.012-0.0120.0000.0000.0000.000
194A209GLU-1-0.935-0.97715.2280.3350.3350.0000.0000.0000.000
195A210ASP-1-0.884-0.94118.4730.1120.1120.0000.0000.0000.000
196A211GLU-1-0.842-0.92021.7030.0230.0230.0000.0000.0000.000
197A212PHE0-0.043-0.00419.6410.0120.0120.0000.0000.0000.000
198A213LEU0-0.054-0.05120.4840.0050.0050.0000.0000.0000.000
199A214ASP-1-0.989-0.97923.6860.0660.0660.0000.0000.0000.000
200A215TYR00.0300.00026.154-0.013-0.0130.0000.0000.0000.000
201A216TRP0-0.049-0.01624.2750.0030.0030.0000.0000.0000.000
202A217ARG10.8610.93223.975-0.159-0.1590.0000.0000.0000.000