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: R5QK8

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 OptAll
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 -2367946.212616
FMO2-HF: Nuclear repulsion 2287486.145715
FMO2-HF: Total energy -80460.066901
FMO2-MP2: Total energy -80701.52352


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.
-11.013-4.6212.155-3.493-5.0550.02
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 : 0.028 / q_NPA : 0.002
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].
3A4ARG10.8290.8943.274-3.522-1.1450.106-1.067-1.4160.005
4A5SER00.0010.0042.375-6.709-4.3481.949-1.846-2.4650.011
5A6ASP-1-0.810-0.8794.012-1.290-0.6100.005-0.194-0.4920.000
6A7LEU00.0290.0225.8690.0600.0600.0000.0000.0000.000
7A8ILE00.0080.0056.335-0.185-0.1850.0000.0000.0000.000
8A9ASN0-0.015-0.0156.801-0.011-0.0110.0000.0000.0000.000
9A10ALA00.0080.0079.5680.0110.0110.0000.0000.0000.000
10A11LEU00.001-0.00311.1090.0020.0020.0000.0000.0000.000
11A12TYR0-0.032-0.02311.679-0.015-0.0150.0000.0000.0000.000
12A13ASP-1-0.831-0.89613.739-0.032-0.0320.0000.0000.0000.000
13A14GLU-1-0.811-0.89415.5860.0750.0750.0000.0000.0000.000
14A15ASN0-0.032-0.01417.2730.0180.0180.0000.0000.0000.000
15A16GLN0-0.018-0.01518.9530.0060.0060.0000.0000.0000.000
16A17LYS10.7540.85018.555-0.003-0.0030.0000.0000.0000.000
17A18TYR0-0.016-0.00816.4780.0250.0250.0000.0000.0000.000
18A19ASP-1-0.852-0.89923.4030.0240.0240.0000.0000.0000.000
19A20VAL00.0310.00926.9770.0050.0050.0000.0000.0000.000
20A21CYS0-0.014-0.01229.630-0.002-0.0020.0000.0000.0000.000
21A22GLY00.0270.01233.292-0.002-0.0020.0000.0000.0000.000
22A23ILE0-0.0190.01033.3820.0030.0030.0000.0000.0000.000
23A24ILE00.0040.00634.524-0.004-0.0040.0000.0000.0000.000
24A25SER0-0.034-0.03036.8490.0050.0050.0000.0000.0000.000
25A26ALA00.0390.00239.516-0.002-0.0020.0000.0000.0000.000
26A27GLU-1-0.907-0.94340.8550.0340.0340.0000.0000.0000.000
27A28GLY00.014-0.00541.171-0.003-0.0030.0000.0000.0000.000
28A29LYS10.8580.94841.764-0.035-0.0350.0000.0000.0000.000
29A30ILE00.0150.00837.1100.0040.0040.0000.0000.0000.000
30A31TYR00.0090.00138.823-0.004-0.0040.0000.0000.0000.000
31A32PRO00.0340.03637.5380.0030.0030.0000.0000.0000.000
32A33LEU0-0.070-0.03731.0710.0020.0020.0000.0000.0000.000
33A41SER0-0.006-0.00725.986-0.007-0.0070.0000.0000.0000.000
34A42THR00.0680.02225.2000.0030.0030.0000.0000.0000.000
35A43ILE00.0090.01025.4380.0110.0110.0000.0000.0000.000
36A44PHE00.0080.00521.4020.0010.0010.0000.0000.0000.000
37A45GLU-1-0.843-0.93220.7910.2010.2010.0000.0000.0000.000
38A46LEU0-0.083-0.04021.3790.0230.0230.0000.0000.0000.000
39A47PHE00.0190.00520.1640.0090.0090.0000.0000.0000.000
40A48SER00.0220.00416.778-0.001-0.0010.0000.0000.0000.000
41A49ARG10.8370.90216.766-0.206-0.2060.0000.0000.0000.000
42A50PRO00.0100.01217.5610.0430.0430.0000.0000.0000.000
43A51ILE0-0.0140.00213.1130.0250.0250.0000.0000.0000.000
44A52ILE00.0210.00312.5460.0550.0550.0000.0000.0000.000
45A53ASN0-0.026-0.02512.5110.1150.1150.0000.0000.0000.000
46A54LYS10.8710.93812.859-0.053-0.0530.0000.0000.0000.000
47A55ILE0-0.059-0.0247.627-0.027-0.0270.0000.0000.0000.000
48A56ALA00.010-0.0039.1960.2370.2370.0000.0000.0000.000
49A57GLU-1-0.912-0.95511.0310.5200.5200.0000.0000.0000.000
50A58LYS10.8310.9057.3610.0500.0500.0000.0000.0000.000
51A59HIS0-0.057-0.0383.095-0.0120.9620.095-0.386-0.6820.004
52A60GLY0-0.019-0.0128.4600.1230.1230.0000.0000.0000.000
53A61TYR0-0.077-0.0456.5630.1590.1590.0000.0000.0000.000
54A62ILE00.0070.01712.028-0.081-0.0810.0000.0000.0000.000
55A63VAL00.011-0.00914.2360.0720.0720.0000.0000.0000.000
56A64GLU-1-0.775-0.84216.4880.3120.3120.0000.0000.0000.000
57A65GLU-1-0.754-0.82219.1850.3040.3040.0000.0000.0000.000
58A66PRO0-0.007-0.00421.404-0.011-0.0110.0000.0000.0000.000
59A67LYS10.8160.88823.022-0.307-0.3070.0000.0000.0000.000
60A68GLN00.0200.02327.619-0.021-0.0210.0000.0000.0000.000
61A69GLN00.0040.00228.2150.0080.0080.0000.0000.0000.000
62A70ASN0-0.018-0.01828.0340.0080.0080.0000.0000.0000.000
63A71HIS0-0.062-0.04225.562-0.008-0.0080.0000.0000.0000.000
64A72TYR00.0040.02717.2600.0030.0030.0000.0000.0000.000
65A73PRO0-0.010-0.00817.262-0.008-0.0080.0000.0000.0000.000
66A74ASP-1-0.798-0.92019.0990.2800.2800.0000.0000.0000.000
67A75PHE00.003-0.01315.953-0.014-0.0140.0000.0000.0000.000
68A76THR0-0.0080.01515.7530.0470.0470.0000.0000.0000.000
69A77LEU00.0160.00910.117-0.015-0.0150.0000.0000.0000.000
70A78TYR0-0.013-0.03612.4130.0450.0450.0000.0000.0000.000
71A79LYS10.9460.9848.286-1.660-1.6600.0000.0000.0000.000
72A80PRO00.0280.00213.716-0.050-0.0500.0000.0000.0000.000
73A81SER0-0.0070.00215.271-0.028-0.0280.0000.0000.0000.000
74A82GLU-1-0.829-0.89213.2230.5620.5620.0000.0000.0000.000
75A83PRO00.0160.01815.2520.0520.0520.0000.0000.0000.000
76A84ASN0-0.013-0.00917.414-0.015-0.0150.0000.0000.0000.000
77A85LYS10.8150.89311.772-0.583-0.5830.0000.0000.0000.000
78A86LYS10.7970.91411.880-0.319-0.3190.0000.0000.0000.000
79A87ILE0-0.032-0.0097.6490.0420.0420.0000.0000.0000.000
80A88ALA00.0030.00012.006-0.083-0.0830.0000.0000.0000.000
81A89ILE0-0.025-0.00610.7700.0670.0670.0000.0000.0000.000
82A90ASP-1-0.774-0.87714.5090.2340.2340.0000.0000.0000.000
83A91ILE0-0.014-0.00616.500-0.003-0.0030.0000.0000.0000.000
84A92LYS10.8350.91818.689-0.280-0.2800.0000.0000.0000.000
85A93ALA00.0160.00920.337-0.006-0.0060.0000.0000.0000.000
86A94THR0-0.050-0.01823.081-0.007-0.0070.0000.0000.0000.000
87A95TYR00.0260.00025.434-0.005-0.0050.0000.0000.0000.000
88A96THR0-0.0200.01326.516-0.004-0.0040.0000.0000.0000.000
89A97ASN00.0100.00828.967-0.005-0.0050.0000.0000.0000.000
90A98LYS10.8480.91732.367-0.010-0.0100.0000.0000.0000.000
91A99GLU-1-0.768-0.88531.036-0.015-0.0150.0000.0000.0000.000
92A100ASN0-0.055-0.03026.708-0.002-0.0020.0000.0000.0000.000
93A101GLU-1-0.787-0.86928.4420.0040.0040.0000.0000.0000.000
94A102LYS10.9560.97427.5120.0080.0080.0000.0000.0000.000
95A103ILE0-0.019-0.01622.9590.0050.0050.0000.0000.0000.000
96A104LYS10.9220.98024.347-0.051-0.0510.0000.0000.0000.000
97A105PHE00.0060.00520.5310.0030.0030.0000.0000.0000.000
98A106THR0-0.024-0.01824.012-0.010-0.0100.0000.0000.0000.000
99A107LEU0-0.0110.00319.5490.0160.0160.0000.0000.0000.000
100A108GLY00.0620.03922.3230.0190.0190.0000.0000.0000.000
101A109GLY00.0410.00724.329-0.018-0.0180.0000.0000.0000.000
102A110TYR00.0210.01526.3160.0110.0110.0000.0000.0000.000
103A111THR00.001-0.02527.376-0.008-0.0080.0000.0000.0000.000
104A112SER00.0120.01827.554-0.002-0.0020.0000.0000.0000.000
105A113PHE00.0230.01421.753-0.004-0.0040.0000.0000.0000.000
106A114ILE00.0410.03923.2360.0050.0050.0000.0000.0000.000
107A115ARG10.9020.96524.762-0.123-0.1230.0000.0000.0000.000
108A116ASN00.0210.01028.290-0.010-0.0100.0000.0000.0000.000
109A117ASN0-0.009-0.00324.0750.0130.0130.0000.0000.0000.000
110A118THR0-0.0040.00125.0520.0150.0150.0000.0000.0000.000
111A119LYS10.8900.92627.426-0.174-0.1740.0000.0000.0000.000
112A120ASN00.0120.00127.3510.0000.0000.0000.0000.0000.000
113A121ILE0-0.0250.00720.4530.0040.0040.0000.0000.0000.000
114A122VAL0-0.030-0.00421.332-0.019-0.0190.0000.0000.0000.000
115A123TYR0-0.034-0.03920.051-0.010-0.0100.0000.0000.0000.000
116A124PRO00.007-0.00922.396-0.004-0.0040.0000.0000.0000.000
117A125PHE00.0410.01319.4550.0380.0380.0000.0000.0000.000
118A126ASP-1-0.825-0.90319.3220.3140.3140.0000.0000.0000.000
119A127GLN0-0.038-0.03218.2350.0280.0280.0000.0000.0000.000
120A128TYR0-0.053-0.04815.1510.0560.0560.0000.0000.0000.000
121A129ILE00.0130.01510.154-0.044-0.0440.0000.0000.0000.000
122A130ALA00.0080.0119.9510.0390.0390.0000.0000.0000.000
123A131HIS00.0620.03711.936-0.007-0.0070.0000.0000.0000.000
124A132TRP00.001-0.0076.1130.1980.1980.0000.0000.0000.000
125A133ILE00.0230.01112.488-0.038-0.0380.0000.0000.0000.000
126A134ILE0-0.025-0.01112.0240.0250.0250.0000.0000.0000.000
127A135GLY00.0350.01614.959-0.028-0.0280.0000.0000.0000.000
128A136TYR0-0.026-0.02417.586-0.038-0.0380.0000.0000.0000.000
129A137VAL0-0.023-0.03120.189-0.003-0.0030.0000.0000.0000.000
130A138TYR00.0180.01722.849-0.015-0.0150.0000.0000.0000.000
131A139THR0-0.024-0.02425.997-0.004-0.0040.0000.0000.0000.000
132A140ARG10.8670.93629.685-0.019-0.0190.0000.0000.0000.000
133A141VAL00.0160.02832.467-0.006-0.0060.0000.0000.0000.000
134A149LYS10.8340.89944.657-0.022-0.0220.0000.0000.0000.000
135A150THR0-0.027-0.01743.2390.0010.0010.0000.0000.0000.000
136A151TYR00.0250.01841.333-0.004-0.0040.0000.0000.0000.000
137A152ASN00.014-0.00742.4190.0020.0020.0000.0000.0000.000
138A153ILE00.0510.01737.014-0.001-0.0010.0000.0000.0000.000
139A154ASN0-0.030-0.02440.018-0.004-0.0040.0000.0000.0000.000
140A155GLU-1-0.793-0.86542.5520.0170.0170.0000.0000.0000.000
141A156LEU0-0.018-0.00834.5710.0010.0010.0000.0000.0000.000
142A157ASN0-0.073-0.05237.410-0.001-0.0010.0000.0000.0000.000
143A158GLU-1-0.852-0.92039.0060.0040.0040.0000.0000.0000.000
144A159ILE0-0.066-0.02037.2810.0020.0020.0000.0000.0000.000
145A160PRO0-0.023-0.00937.408-0.001-0.0010.0000.0000.0000.000
146A161LYS10.8620.90531.578-0.014-0.0140.0000.0000.0000.000
147A162PRO00.0150.02431.023-0.002-0.0020.0000.0000.0000.000
148A163TYR0-0.032-0.05626.3420.0030.0030.0000.0000.0000.000
149A164LYS10.8140.89230.6890.0120.0120.0000.0000.0000.000
150A165GLY00.0070.00227.233-0.008-0.0080.0000.0000.0000.000
151A166VAL0-0.026-0.02821.6780.0090.0090.0000.0000.0000.000
152A167LYS10.9270.98820.1110.0180.0180.0000.0000.0000.000
153A168VAL00.0570.03515.2030.0180.0180.0000.0000.0000.000
154A169PHE00.0170.03113.719-0.061-0.0610.0000.0000.0000.000
155A170LEU00.0160.0117.9260.0480.0480.0000.0000.0000.000
156A171GLN0-0.022-0.00210.504-0.004-0.0040.0000.0000.0000.000
157A172ASP-1-0.767-0.8759.5470.6710.6710.0000.0000.0000.000
158A173LYS10.7890.87112.405-0.403-0.4030.0000.0000.0000.000
159A174TRP00.0340.02312.998-0.055-0.0550.0000.0000.0000.000
160A175VAL0-0.0160.02012.424-0.034-0.0340.0000.0000.0000.000
161A176ILE0-0.022-0.01115.796-0.039-0.0390.0000.0000.0000.000
162A177ALA00.0050.00518.270-0.001-0.0010.0000.0000.0000.000
163A178GLY00.013-0.02021.069-0.018-0.0180.0000.0000.0000.000
164A179ASP-1-0.839-0.90624.4960.0490.0490.0000.0000.0000.000
165A180LEU00.0310.02828.2400.0060.0060.0000.0000.0000.000
166A181ALA0-0.042-0.00829.3910.0010.0010.0000.0000.0000.000
167A182GLY00.036-0.00630.653-0.007-0.0070.0000.0000.0000.000
168A183SER0-0.039-0.02332.9250.0000.0000.0000.0000.0000.000
169A184GLY00.0150.00332.4630.0050.0050.0000.0000.0000.000
170A185ASN0-0.0300.00227.077-0.001-0.0010.0000.0000.0000.000
171A186THR00.0700.02429.9090.0020.0020.0000.0000.0000.000
172A187THR00.002-0.02130.2750.0010.0010.0000.0000.0000.000
173A188ASN0-0.046-0.01126.5860.0200.0200.0000.0000.0000.000
174A189ILE00.0080.02523.412-0.009-0.0090.0000.0000.0000.000
175A190GLY00.0150.01825.0850.0110.0110.0000.0000.0000.000
176A191SER0-0.043-0.03621.5000.0080.0080.0000.0000.0000.000
177A192ILE00.0280.03120.028-0.010-0.0100.0000.0000.0000.000
178A193HIS0-0.067-0.04823.6780.0090.0090.0000.0000.0000.000
179A194ALA00.0060.01722.481-0.011-0.0110.0000.0000.0000.000
180A195HIS00.019-0.00923.4200.0020.0020.0000.0000.0000.000
181A196TYR0-0.040-0.04816.781-0.014-0.0140.0000.0000.0000.000
182A197LYS10.8640.91816.7310.2270.2270.0000.0000.0000.000
183A198ASP-1-0.779-0.90017.954-0.083-0.0830.0000.0000.0000.000
184A199PHE0-0.010-0.00317.100-0.002-0.0020.0000.0000.0000.000
185A200VAL00.0020.00113.7220.0230.0230.0000.0000.0000.000
186A201GLU-1-0.863-0.90412.987-0.319-0.3190.0000.0000.0000.000
187A202GLY00.0290.01814.262-0.029-0.0290.0000.0000.0000.000
188A203LYS10.7990.88815.1050.2010.2010.0000.0000.0000.000
189A204GLY00.0280.01018.1730.0150.0150.0000.0000.0000.000
190A205ILE0-0.091-0.04319.805-0.017-0.0170.0000.0000.0000.000
191A206PHE0-0.0080.00420.2640.0090.0090.0000.0000.0000.000
192A207ASP-1-0.876-0.93619.645-0.044-0.0440.0000.0000.0000.000
193A208SER0-0.106-0.09217.722-0.013-0.0130.0000.0000.0000.000
194A209GLU-1-0.919-0.97014.7820.3650.3650.0000.0000.0000.000
195A210ASP-1-0.847-0.90918.0220.1210.1210.0000.0000.0000.000
196A211GLU-1-0.837-0.91121.2380.0280.0280.0000.0000.0000.000
197A212PHE0-0.033-0.00919.4220.0070.0070.0000.0000.0000.000
198A213LEU0-0.065-0.05419.9090.0070.0070.0000.0000.0000.000
199A214ASP-1-0.963-0.98023.2510.0720.0720.0000.0000.0000.000
200A215TYR0-0.028-0.01925.796-0.007-0.0070.0000.0000.0000.000
201A216TRP0-0.047-0.01924.1760.0010.0010.0000.0000.0000.000
202A217ARG10.8140.91323.435-0.160-0.1600.0000.0000.0000.000