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: QVZNY

Calculation Name: 4YZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YZE

Chain ID: A

ChEMBL ID:

UniProt ID: P67430

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2016228.172401
FMO2-HF: Nuclear repulsion 1941169.982591
FMO2-HF: Total energy -75058.189811
FMO2-MP2: Total energy -75278.431839


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:7:HIS)


Summations of interaction energy for fragment #1(A:7:HIS)
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.
-16.658-10.30.838-2.734-4.4610.019
Interaction energy analysis for fragmet #1(A:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.015
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].
3A9THR00.001-0.0032.569-0.3492.2050.278-1.148-1.6830.005
4A10ARG10.9610.9842.919-12.189-9.6220.495-1.249-1.8130.014
5A11GLU-1-0.819-0.8994.258-1.559-1.0620.001-0.092-0.4060.000
6A12HIS00.0250.0356.259-0.523-0.5230.0000.0000.0000.000
7A13LEU0-0.0080.0077.497-0.341-0.3410.0000.0000.0000.000
8A14LEU0-0.007-0.0037.251-0.390-0.3900.0000.0000.0000.000
9A15ALA0-0.0070.00310.155-0.271-0.2710.0000.0000.0000.000
10A16THR0-0.030-0.03511.996-0.185-0.1850.0000.0000.0000.000
11A17GLY0-0.002-0.01813.327-0.079-0.0790.0000.0000.0000.000
12A18GLU-1-0.843-0.91314.4960.0710.0710.0000.0000.0000.000
13A19GLN0-0.012-0.00816.386-0.048-0.0480.0000.0000.0000.000
14A20LEU00.016-0.00717.494-0.032-0.0320.0000.0000.0000.000
15A21SER00.0230.00918.307-0.016-0.0160.0000.0000.0000.000
16A22LEU0-0.038-0.00420.448-0.028-0.0280.0000.0000.0000.000
17A23GLN00.0000.00822.3650.0040.0040.0000.0000.0000.000
18A24ARG10.8350.89222.952-0.216-0.2160.0000.0000.0000.000
19A25GLY00.0140.03124.3120.0010.0010.0000.0000.0000.000
20A26PHE00.002-0.01017.2960.0440.0440.0000.0000.0000.000
21A27THR0-0.031-0.03122.0870.0460.0460.0000.0000.0000.000
22A28GLY0-0.0140.00724.6010.0050.0050.0000.0000.0000.000
23A29MET0-0.0120.02317.1240.0120.0120.0000.0000.0000.000
24A30GLY00.0290.01221.3990.0580.0580.0000.0000.0000.000
25A31LEU00.028-0.01415.496-0.008-0.0080.0000.0000.0000.000
26A32SER0-0.016-0.00217.6870.0430.0430.0000.0000.0000.000
27A33GLU-1-0.864-0.92819.2170.3270.3270.0000.0000.0000.000
28A34LEU00.0330.03713.028-0.042-0.0420.0000.0000.0000.000
29A35LEU0-0.025-0.02613.1860.0130.0130.0000.0000.0000.000
30A36LYS10.8990.96514.965-0.332-0.3320.0000.0000.0000.000
31A37THR0-0.062-0.07116.923-0.099-0.0990.0000.0000.0000.000
32A38ALA0-0.0110.00211.426-0.078-0.0780.0000.0000.0000.000
33A39GLU-1-0.939-0.95011.9870.0710.0710.0000.0000.0000.000
34A40VAL0-0.026-0.0099.0840.1420.1420.0000.0000.0000.000
35A41PRO00.0320.01210.615-0.054-0.0540.0000.0000.0000.000
36A42LYS11.0000.97412.371-0.508-0.5080.0000.0000.0000.000
37A43GLY00.003-0.00613.6800.1090.1090.0000.0000.0000.000
38A44SER00.0410.0198.423-0.036-0.0360.0000.0000.0000.000
39A45PHE00.0110.0148.9090.5610.5610.0000.0000.0000.000
40A46TYR0-0.033-0.03310.6930.1680.1680.0000.0000.0000.000
41A47HIS0-0.0450.0105.537-0.502-0.5020.0000.0000.0000.000
42A48TYR0-0.038-0.0143.0740.6601.4000.064-0.245-0.5590.000
43A49PHE0-0.006-0.0147.877-0.036-0.0360.0000.0000.0000.000
44A50ARG10.9780.99111.605-1.331-1.3310.0000.0000.0000.000
45A51SER00.010-0.01314.987-0.132-0.1320.0000.0000.0000.000
46A52LYS10.8990.95415.498-0.483-0.4830.0000.0000.0000.000
47A53GLU-1-0.814-0.91016.9400.9440.9440.0000.0000.0000.000
48A54ALA00.0380.01914.4320.0100.0100.0000.0000.0000.000
49A55PHE0-0.029-0.01610.8130.0620.0620.0000.0000.0000.000
50A56GLY00.0590.02013.3840.0120.0120.0000.0000.0000.000
51A57VAL00.0300.02415.467-0.080-0.0800.0000.0000.0000.000
52A58ALA00.0150.01210.210-0.021-0.0210.0000.0000.0000.000
53A59MET0-0.072-0.01612.061-0.086-0.0860.0000.0000.0000.000
54A60LEU0-0.016-0.00913.277-0.187-0.1870.0000.0000.0000.000
55A61GLU-1-0.942-0.97413.5400.9780.9780.0000.0000.0000.000
56A62ARG10.8560.9168.873-0.104-0.1040.0000.0000.0000.000
57A63HIS0-0.076-0.06012.007-0.261-0.2610.0000.0000.0000.000
58A64TYR0-0.014-0.04615.082-0.123-0.1230.0000.0000.0000.000
59A65ALA0-0.0140.01112.175-0.085-0.0850.0000.0000.0000.000
60A66ALA00.010-0.00212.489-0.134-0.1340.0000.0000.0000.000
61A67TYR0-0.047-0.02414.026-0.075-0.0750.0000.0000.0000.000
62A68HIS00.0360.01917.050-0.003-0.0030.0000.0000.0000.000
63A69GLN00.0020.02513.9050.0250.0250.0000.0000.0000.000
64A70ARG11.0091.00115.8070.3880.3880.0000.0000.0000.000
65A71LEU0-0.021-0.00518.9340.0050.0050.0000.0000.0000.000
66A72THR0-0.002-0.02219.6450.0320.0320.0000.0000.0000.000
67A73GLU-1-0.938-0.97017.857-0.644-0.6440.0000.0000.0000.000
68A74LEU0-0.053-0.02021.7260.0130.0130.0000.0000.0000.000
69A75LEU00.000-0.01624.6440.0170.0170.0000.0000.0000.000
70A76GLN0-0.012-0.01823.161-0.006-0.0060.0000.0000.0000.000
71A77SER0-0.098-0.06124.2480.0000.0000.0000.0000.0000.000
72A78GLY00.0280.04526.270-0.025-0.0250.0000.0000.0000.000
73A79GLU-1-0.932-0.96327.439-0.250-0.2500.0000.0000.0000.000
74A80GLY00.0270.02430.6990.0160.0160.0000.0000.0000.000
75A81ASN0-0.014-0.00732.888-0.005-0.0050.0000.0000.0000.000
76A82TYR00.0530.00129.855-0.003-0.0030.0000.0000.0000.000
77A83ARG10.8470.91533.3490.0940.0940.0000.0000.0000.000
78A84ASP-1-0.848-0.93134.044-0.145-0.1450.0000.0000.0000.000
79A85ARG10.8200.92028.7210.2060.2060.0000.0000.0000.000
80A86ILE00.0160.00730.159-0.001-0.0010.0000.0000.0000.000
81A87LEU0-0.049-0.02931.9020.0070.0070.0000.0000.0000.000
82A88ALA00.0450.02529.6400.0030.0030.0000.0000.0000.000
83A89TYR00.0220.03026.081-0.008-0.0080.0000.0000.0000.000
84A90TYR0-0.014-0.01829.0150.0040.0040.0000.0000.0000.000
85A91GLN0-0.020-0.00231.7800.0130.0130.0000.0000.0000.000
86A92GLN00.020-0.01024.5080.0090.0090.0000.0000.0000.000
87A93THR0-0.069-0.02128.1080.0010.0010.0000.0000.0000.000
88A94LEU00.004-0.00629.0540.0070.0070.0000.0000.0000.000
89A95ASN0-0.0120.00128.7340.0160.0160.0000.0000.0000.000
90A96GLN0-0.089-0.04423.315-0.044-0.0440.0000.0000.0000.000
91A97PHE00.0450.04027.1250.0160.0160.0000.0000.0000.000
92A98SER0-0.021-0.02629.1830.0180.0180.0000.0000.0000.000
93A99GLN0-0.011-0.00525.160-0.053-0.0530.0000.0000.0000.000
94A100HIS00.0210.00125.5530.0300.0300.0000.0000.0000.000
95A101GLY00.0180.02630.5960.0100.0100.0000.0000.0000.000
96A102THR0-0.044-0.01328.9350.0180.0180.0000.0000.0000.000
97A103ILE00.008-0.01629.583-0.015-0.0150.0000.0000.0000.000
98A104SER0-0.0200.00224.4190.0070.0070.0000.0000.0000.000
99A105GLY0-0.013-0.00426.5110.0020.0020.0000.0000.0000.000
100A106CYS00.0290.01724.263-0.010-0.0100.0000.0000.0000.000
101A107LEU00.0470.02218.5610.0190.0190.0000.0000.0000.000
102A108THR00.0800.05622.8090.0410.0410.0000.0000.0000.000
103A109VAL00.0400.01424.7240.0170.0170.0000.0000.0000.000
104A110LYS10.7990.93524.944-0.174-0.1740.0000.0000.0000.000
105A111LEU00.0660.01520.9080.0120.0120.0000.0000.0000.000
106A112SER0-0.016-0.02325.4570.0180.0180.0000.0000.0000.000
107A113ALA0-0.042-0.01828.5950.0100.0100.0000.0000.0000.000
108A114GLU-1-0.791-0.90324.9530.3450.3450.0000.0000.0000.000
109A115VAL0-0.045-0.01026.3820.0250.0250.0000.0000.0000.000
110A116SER0-0.036-0.02128.1690.0100.0100.0000.0000.0000.000
111A117ASP-1-0.955-0.96028.9270.2970.2970.0000.0000.0000.000
112A118LEU0-0.042-0.03422.9650.0430.0430.0000.0000.0000.000
113A119SER0-0.028-0.01121.234-0.028-0.0280.0000.0000.0000.000
114A120GLU-1-0.736-0.82124.2730.3790.3790.0000.0000.0000.000
115A121ASP-1-0.887-0.94119.9500.6820.6820.0000.0000.0000.000
116A122MET0-0.039-0.01418.8470.0220.0220.0000.0000.0000.000
117A123ARG10.8550.87621.261-0.377-0.3770.0000.0000.0000.000
118A124SER0-0.035-0.01023.124-0.044-0.0440.0000.0000.0000.000
119A125ALA00.004-0.00618.773-0.032-0.0320.0000.0000.0000.000
120A126MET0-0.030-0.01820.723-0.040-0.0400.0000.0000.0000.000
121A127ASP-1-0.921-0.94523.0050.1970.1970.0000.0000.0000.000
122A128LYS10.9240.94818.622-0.498-0.4980.0000.0000.0000.000
123A129GLY00.0030.00020.574-0.035-0.0350.0000.0000.0000.000
124A130ALA00.001-0.00221.459-0.052-0.0520.0000.0000.0000.000
125A131ARG10.9330.95824.220-0.278-0.2780.0000.0000.0000.000
126A132GLY00.0050.01621.959-0.022-0.0220.0000.0000.0000.000
127A133VAL00.0140.00322.947-0.038-0.0380.0000.0000.0000.000
128A134ILE0-0.0030.00124.566-0.024-0.0240.0000.0000.0000.000
129A135ALA0-0.002-0.00725.426-0.015-0.0150.0000.0000.0000.000
130A136LEU00.0010.00621.397-0.013-0.0130.0000.0000.0000.000
131A137LEU0-0.006-0.00726.039-0.016-0.0160.0000.0000.0000.000
132A138SER0-0.014-0.01329.195-0.008-0.0080.0000.0000.0000.000
133A139GLN00.0030.00927.9640.0080.0080.0000.0000.0000.000
134A140ALA0-0.0090.00229.284-0.009-0.0090.0000.0000.0000.000
135A141LEU0-0.041-0.02730.936-0.004-0.0040.0000.0000.0000.000
136A142GLU-1-0.899-0.94933.489-0.027-0.0270.0000.0000.0000.000
137A143ASN00.0350.01029.8480.0050.0050.0000.0000.0000.000
138A144GLY0-0.009-0.02034.179-0.005-0.0050.0000.0000.0000.000
139A145ARG10.8250.88836.3400.0220.0220.0000.0000.0000.000
140A146GLU-1-0.943-0.96036.763-0.052-0.0520.0000.0000.0000.000
141A147ASN0-0.0310.01235.5800.0030.0030.0000.0000.0000.000
142A148HIS0-0.020-0.01138.983-0.003-0.0030.0000.0000.0000.000
143A149SER0-0.028-0.04337.436-0.007-0.0070.0000.0000.0000.000
144A150LEU0-0.106-0.04935.629-0.003-0.0030.0000.0000.0000.000
145A151THR0-0.0340.00040.2500.0060.0060.0000.0000.0000.000
146A152PHE00.0290.00237.733-0.001-0.0010.0000.0000.0000.000
147A153SER0-0.0010.01142.3550.0030.0030.0000.0000.0000.000
148A154GLY00.0520.02642.0450.0020.0020.0000.0000.0000.000
149A155GLU-1-0.850-0.91938.6040.0300.0300.0000.0000.0000.000
150A156PRO00.0800.03934.7890.0020.0020.0000.0000.0000.000
151A157LEU00.0390.03131.312-0.002-0.0020.0000.0000.0000.000
152A158GLN0-0.039-0.02834.3750.0010.0010.0000.0000.0000.000
153A159GLN00.0190.01036.5030.0020.0020.0000.0000.0000.000
154A160ALA00.0250.00631.211-0.004-0.0040.0000.0000.0000.000
155A161GLN0-0.032-0.02132.3280.0090.0090.0000.0000.0000.000
156A162VAL00.0010.01633.4740.0060.0060.0000.0000.0000.000
157A163LEU00.0310.02632.963-0.001-0.0010.0000.0000.0000.000
158A164TYR00.0250.01125.8420.0050.0050.0000.0000.0000.000
159A165ALA00.014-0.00431.2860.0040.0040.0000.0000.0000.000
160A166LEU0-0.032-0.01433.8210.0020.0020.0000.0000.0000.000
161A167TRP00.004-0.01725.7390.0130.0130.0000.0000.0000.000
162A168LEU00.0040.00429.130-0.002-0.0020.0000.0000.0000.000
163A169GLY0-0.008-0.00231.6120.0040.0040.0000.0000.0000.000
164A170ALA00.0210.01734.6820.0000.0000.0000.0000.0000.000
165A171ASN00.015-0.01329.802-0.013-0.0130.0000.0000.0000.000
166A172LEU0-0.046-0.01632.5430.0010.0010.0000.0000.0000.000
167A173GLN00.0170.01234.0490.0030.0030.0000.0000.0000.000
168A174ALA00.0230.02134.276-0.002-0.0020.0000.0000.0000.000
169A175LYS10.9240.96029.524-0.093-0.0930.0000.0000.0000.000
170A176ILE0-0.071-0.03934.5140.0000.0000.0000.0000.0000.000
171A177SER0-0.054-0.03337.341-0.003-0.0030.0000.0000.0000.000
172A178ARG10.9140.96036.789-0.010-0.0100.0000.0000.0000.000
173A179SER00.0480.03938.108-0.011-0.0110.0000.0000.0000.000
174A180PHE00.0050.00235.6850.0060.0060.0000.0000.0000.000
175A181GLU-1-0.888-0.94737.352-0.029-0.0290.0000.0000.0000.000
176A182PRO00.0370.02037.373-0.001-0.0010.0000.0000.0000.000
177A183LEU0-0.036-0.02032.5700.0010.0010.0000.0000.0000.000
178A184GLU-1-0.909-0.96336.175-0.083-0.0830.0000.0000.0000.000
179A185ASN0-0.0100.00238.655-0.004-0.0040.0000.0000.0000.000
180A186ALA0-0.016-0.00936.3170.0020.0020.0000.0000.0000.000
181A187LEU0-0.019-0.01035.2690.0000.0000.0000.0000.0000.000
182A188ALA0-0.015-0.01737.446-0.003-0.0030.0000.0000.0000.000
183A189HIS00.0360.01640.190-0.001-0.0010.0000.0000.0000.000
184A190VAL00.019-0.00135.6040.0020.0020.0000.0000.0000.000
185A191LYS10.9030.96138.5940.0970.0970.0000.0000.0000.000
186A192ASN0-0.0060.00640.525-0.005-0.0050.0000.0000.0000.000
187A193ILE0-0.058-0.01540.3850.0030.0030.0000.0000.0000.000
188A194ILE0-0.0150.00236.7670.0030.0030.0000.0000.0000.000
189A195ALA00.0380.04640.023-0.010-0.0100.0000.0000.0000.000
190A196THR00.045-0.00141.694-0.003-0.0030.0000.0000.0000.000
191A197PRO0-0.028-0.00242.4140.0060.0060.0000.0000.0000.000
192A198ALA0-0.017-0.00845.624-0.003-0.0030.0000.0000.0000.000
193A199VAL00.0170.02547.210-0.001-0.0010.0000.0000.0000.000