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: MVZRZ

Calculation Name: 2A22-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A22

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CYJ7

Base Structure: X-ray

Registration Date: 2023-06-26

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2183768.282319
FMO2-HF: Nuclear repulsion 2108172.281207
FMO2-HF: Total energy -75596.001111
FMO2-MP2: Total energy -75815.221858


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
40.3442.9830.004-1.451-1.1960.007
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.862 / q_NPA : -0.926
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].
3A6GLY0-0.018-0.0173.905-6.110-3.4160.005-1.441-1.2580.007
4A7ASP-1-0.840-0.8945.02728.98828.937-0.001-0.0100.0620.000
5A8LEU0-0.055-0.0417.725-0.742-0.7420.0000.0000.0000.000
6A9VAL00.0180.00710.506-0.471-0.4710.0000.0000.0000.000
7A10LEU00.0030.01313.393-0.632-0.6320.0000.0000.0000.000
8A11LEU0-0.004-0.00516.403-0.396-0.3960.0000.0000.0000.000
9A12ILE00.0400.00019.663-0.290-0.2900.0000.0000.0000.000
10A13GLY00.0880.03422.5150.0400.0400.0000.0000.0000.000
11A14ASP-1-0.720-0.87025.8089.5689.5680.0000.0000.0000.000
12A15LEU0-0.0110.02625.376-0.150-0.1500.0000.0000.0000.000
13A16LYS10.8560.91529.626-9.075-9.0750.0000.0000.0000.000
14A17ILE0-0.0050.05229.578-0.290-0.2900.0000.0000.0000.000
15A18PRO0-0.004-0.02533.2400.0700.0700.0000.0000.0000.000
16A19TYR0-0.072-0.05435.987-0.194-0.1940.0000.0000.0000.000
17A20GLY00.0070.00736.333-0.227-0.2270.0000.0000.0000.000
18A21ALA0-0.019-0.00333.2730.0520.0520.0000.0000.0000.000
19A22LYS10.8190.86634.533-8.774-8.7740.0000.0000.0000.000
20A23GLU-1-0.781-0.85330.1429.1269.1260.0000.0000.0000.000
21A24LEU00.0260.01124.119-0.054-0.0540.0000.0000.0000.000
22A25PRO00.0090.00727.306-0.098-0.0980.0000.0000.0000.000
23A26SER00.0380.01726.6870.4320.4320.0000.0000.0000.000
24A27ASN0-0.023-0.01326.3740.3280.3280.0000.0000.0000.000
25A28PHE00.006-0.00823.1750.3120.3120.0000.0000.0000.000
26A29ARG10.8940.94621.941-11.826-11.8260.0000.0000.0000.000
27A30GLU-1-0.827-0.91919.51413.56713.5670.0000.0000.0000.000
28A31LEU0-0.064-0.02217.9810.8930.8930.0000.0000.0000.000
29A32LEU0-0.008-0.01317.2130.8510.8510.0000.0000.0000.000
30A33ALA0-0.0090.00317.2160.0700.0700.0000.0000.0000.000
31A34THR0-0.044-0.00112.8151.2391.2390.0000.0000.0000.000
32A35ASP-1-0.861-0.94910.37023.13923.1390.0000.0000.0000.000
33A36LYS10.8920.9437.546-32.573-32.5730.0000.0000.0000.000
34A37ILE0-0.0010.0208.5611.1841.1840.0000.0000.0000.000
35A38ASN00.005-0.0015.557-1.862-1.8620.0000.0000.0000.000
36A39TYR00.002-0.0028.412-1.415-1.4150.0000.0000.0000.000
37A40VAL00.0040.00711.914-0.111-0.1110.0000.0000.0000.000
38A41LEU0-0.018-0.00515.703-0.347-0.3470.0000.0000.0000.000
39A42CYS0-0.040-0.00918.468-0.473-0.4730.0000.0000.0000.000
40A43THR00.0320.00021.745-0.129-0.1290.0000.0000.0000.000
41A44GLY00.0830.04724.939-0.427-0.4270.0000.0000.0000.000
42A45ASN0-0.136-0.09427.120-0.048-0.0480.0000.0000.0000.000
43A46VAL00.0150.00325.4830.0270.0270.0000.0000.0000.000
44A47CYS0-0.087-0.03328.525-0.075-0.0750.0000.0000.0000.000
45A48SER00.0290.02730.554-0.242-0.2420.0000.0000.0000.000
46A49GLN00.041-0.00327.9200.2100.2100.0000.0000.0000.000
47A50GLU-1-0.909-0.94627.80410.09910.0990.0000.0000.0000.000
48A51TYR00.012-0.01926.0640.5250.5250.0000.0000.0000.000
49A52VAL00.0020.01024.4990.5130.5130.0000.0000.0000.000
50A53GLU-1-0.872-0.92923.15511.01811.0180.0000.0000.0000.000
51A54MET0-0.0290.00521.1280.5350.5350.0000.0000.0000.000
52A55LEU00.019-0.00820.2970.6980.6980.0000.0000.0000.000
53A56LYS10.7550.85218.599-12.640-12.6400.0000.0000.0000.000
54A57ASN0-0.068-0.04018.0730.6680.6680.0000.0000.0000.000
55A58ILE0-0.0310.00514.6520.5620.5620.0000.0000.0000.000
56A59THR0-0.015-0.01910.5901.2601.2600.0000.0000.0000.000
57A60LYS10.9200.97010.816-21.115-21.1150.0000.0000.0000.000
58A61ASN0-0.056-0.0319.009-1.636-1.6360.0000.0000.0000.000
59A62VAL00.0350.02713.1320.1070.1070.0000.0000.0000.000
60A63TYR00.001-0.00214.317-0.376-0.3760.0000.0000.0000.000
61A64ILE0-0.005-0.00919.0650.1050.1050.0000.0000.0000.000
62A65VAL0-0.0460.00122.615-0.122-0.1220.0000.0000.0000.000
63A66SER00.0030.00025.681-0.056-0.0560.0000.0000.0000.000
64A67GLY0-0.011-0.03729.325-0.035-0.0350.0000.0000.0000.000
65A68ASP-1-0.874-0.93331.3278.2658.2650.0000.0000.0000.000
66A69LEU00.0230.00434.089-0.251-0.2510.0000.0000.0000.000
67A70ASP-1-0.754-0.85929.7459.7709.7700.0000.0000.0000.000
68A71SER0-0.036-0.02432.965-0.118-0.1180.0000.0000.0000.000
69A72ALA0-0.029-0.00934.278-0.206-0.2060.0000.0000.0000.000
70A73ILE0-0.045-0.00928.4320.1300.1300.0000.0000.0000.000
71A74PHE0-0.0170.00328.775-0.229-0.2290.0000.0000.0000.000
72A75ASN0-0.010-0.02023.7440.5560.5560.0000.0000.0000.000
73A76PRO0-0.010-0.00822.893-0.185-0.1850.0000.0000.0000.000
74A77ASP-1-0.806-0.87820.90813.07813.0780.0000.0000.0000.000
75A78PRO00.0040.00822.712-0.407-0.4070.0000.0000.0000.000
76A79GLU-1-0.888-0.95724.81810.51010.5100.0000.0000.0000.000
77A80SER0-0.078-0.03925.675-0.420-0.4200.0000.0000.0000.000
78A81ASN0-0.082-0.04627.541-0.493-0.4930.0000.0000.0000.000
79A82GLY00.0630.03428.940-0.315-0.3150.0000.0000.0000.000
80A83VAL0-0.049-0.01629.763-0.004-0.0040.0000.0000.0000.000
81A84PHE00.0490.01724.0150.4050.4050.0000.0000.0000.000
82A85PRO0-0.0130.00424.220-0.357-0.3570.0000.0000.0000.000
83A86GLU-1-0.839-0.91427.4048.9378.9370.0000.0000.0000.000
84A87TYR0-0.033-0.04225.545-0.058-0.0580.0000.0000.0000.000
85A88VAL0-0.003-0.00119.647-0.010-0.0100.0000.0000.0000.000
86A89VAL0-0.028-0.02120.147-0.045-0.0450.0000.0000.0000.000
87A90VAL0-0.023-0.00514.291-0.056-0.0560.0000.0000.0000.000
88A91GLN0-0.054-0.02112.831-0.955-0.9550.0000.0000.0000.000
89A92ILE0-0.022-0.01510.3350.6690.6690.0000.0000.0000.000
90A93GLY00.0580.0369.322-0.437-0.4370.0000.0000.0000.000
91A94GLU-1-0.944-0.97910.21320.92820.9280.0000.0000.0000.000
92A95PHE0-0.049-0.01313.518-1.396-1.3960.0000.0000.0000.000
93A96LYS10.9040.96815.153-11.815-11.8150.0000.0000.0000.000
94A97ILE0-0.009-0.00715.228-0.760-0.7600.0000.0000.0000.000
95A98GLY00.0200.00318.525-0.106-0.1060.0000.0000.0000.000
96A99LEU0-0.015-0.00320.2250.1030.1030.0000.0000.0000.000
97A100MET00.015-0.00222.907-0.223-0.2230.0000.0000.0000.000
98A101HIS0-0.0110.01926.489-0.242-0.2420.0000.0000.0000.000
99A102GLY00.0560.01628.8700.0710.0710.0000.0000.0000.000
100A103ASN0-0.022-0.01931.064-0.019-0.0190.0000.0000.0000.000
101A104GLN00.031-0.00531.620-0.132-0.1320.0000.0000.0000.000
102A105VAL0-0.0560.00031.401-0.075-0.0750.0000.0000.0000.000
103A106LEU0-0.0190.00134.496-0.165-0.1650.0000.0000.0000.000
104A107PRO00.0420.00138.231-0.043-0.0430.0000.0000.0000.000
105A108TRP00.0460.01835.6100.1420.1420.0000.0000.0000.000
106A109ASP-1-0.765-0.85431.7089.3489.3480.0000.0000.0000.000
107A110ASP-1-0.834-0.90033.9438.2368.2360.0000.0000.0000.000
108A111PRO00.001-0.01233.0970.1830.1830.0000.0000.0000.000
109A112GLY00.0140.02233.3530.1910.1910.0000.0000.0000.000
110A113SER0-0.004-0.01834.8290.1710.1710.0000.0000.0000.000
111A114LEU00.015-0.00229.0920.1430.1430.0000.0000.0000.000
112A115GLU-1-0.737-0.85930.1629.3349.3340.0000.0000.0000.000
113A116GLN0-0.045-0.03130.9320.1370.1370.0000.0000.0000.000
114A117TRP00.0230.00029.4960.0930.0930.0000.0000.0000.000
115A118GLN00.009-0.01125.712-0.141-0.1410.0000.0000.0000.000
116A119ARG10.8100.89926.822-8.891-8.8910.0000.0000.0000.000
117A120ARG10.8730.94829.025-8.675-8.6750.0000.0000.0000.000
118A121LEU0-0.016-0.01524.835-0.010-0.0100.0000.0000.0000.000
119A122ASP-1-0.911-0.95024.40911.82511.8250.0000.0000.0000.000
120A123CYS0-0.0470.00121.5630.2050.2050.0000.0000.0000.000
121A124ASP-1-0.798-0.90519.18713.34213.3420.0000.0000.0000.000
122A125ILE00.003-0.00217.352-0.179-0.1790.0000.0000.0000.000
123A126LEU0-0.0110.00021.3460.0110.0110.0000.0000.0000.000
124A127VAL0-0.024-0.00620.167-0.068-0.0680.0000.0000.0000.000
125A128THR0-0.001-0.00823.628-0.239-0.2390.0000.0000.0000.000
126A129GLY00.0520.02026.9190.1750.1750.0000.0000.0000.000
127A130HIS10.7760.90828.751-8.827-8.8270.0000.0000.0000.000
128A131THR0-0.061-0.08332.288-0.173-0.1730.0000.0000.0000.000
129A132HIS00.0160.04131.470-0.233-0.2330.0000.0000.0000.000
130A133LYS10.9510.98032.346-8.469-8.4690.0000.0000.0000.000
131A134LEU0-0.0080.00626.2870.1600.1600.0000.0000.0000.000
132A135ARG10.7690.87428.032-9.826-9.8260.0000.0000.0000.000
133A136VAL00.0500.02124.4370.3660.3660.0000.0000.0000.000
134A137PHE0-0.066-0.02826.888-0.396-0.3960.0000.0000.0000.000
135A138GLU-1-0.836-0.91725.97411.29111.2910.0000.0000.0000.000
136A139LYS10.8230.90427.726-9.498-9.4980.0000.0000.0000.000
137A140ASN0-0.053-0.02228.937-0.058-0.0580.0000.0000.0000.000
138A141GLY00.0000.01026.195-0.001-0.0010.0000.0000.0000.000
139A142LYS10.7970.90623.090-11.604-11.6040.0000.0000.0000.000
140A143LEU00.0030.00720.432-0.298-0.2980.0000.0000.0000.000
141A144PHE0-0.032-0.01924.1180.0620.0620.0000.0000.0000.000
142A145LEU0-0.008-0.01020.731-0.010-0.0100.0000.0000.0000.000
143A146ASN00.0330.00624.9000.0420.0420.0000.0000.0000.000
144A147PRO00.0340.01523.221-0.010-0.0100.0000.0000.0000.000
145A148GLY00.0360.03425.272-0.011-0.0110.0000.0000.0000.000
146A149THR0-0.015-0.01728.927-0.088-0.0880.0000.0000.0000.000
147A150ALA00.0120.00525.5540.0190.0190.0000.0000.0000.000
148A151THR0-0.054-0.05727.1600.1640.1640.0000.0000.0000.000
149A152GLY0-0.0090.00830.419-0.173-0.1730.0000.0000.0000.000
150A153ALA00.0030.02732.928-0.314-0.3140.0000.0000.0000.000
151A154PHE00.009-0.00934.9390.0350.0350.0000.0000.0000.000
152A155SER00.0330.00236.398-0.059-0.0590.0000.0000.0000.000
153A156ALA00.002-0.00538.324-0.016-0.0160.0000.0000.0000.000
154A157LEU0-0.080-0.02636.915-0.100-0.1000.0000.0000.0000.000
155A158THR0-0.053-0.04234.8950.0490.0490.0000.0000.0000.000
156A159PRO0-0.030-0.00137.3240.1320.1320.0000.0000.0000.000
157A160ASP-1-0.911-0.96938.5317.6157.6150.0000.0000.0000.000
158A161ALA0-0.0260.00133.4380.1210.1210.0000.0000.0000.000
159A162PRO0-0.018-0.00431.401-0.021-0.0210.0000.0000.0000.000
160A163PRO0-0.0030.00029.3810.1680.1680.0000.0000.0000.000
161A164SER0-0.057-0.05526.638-0.016-0.0160.0000.0000.0000.000
162A165PHE0-0.028-0.00819.2460.0360.0360.0000.0000.0000.000
163A166MET0-0.040-0.01620.239-0.009-0.0090.0000.0000.0000.000
164A167LEU00.0070.02014.5080.2810.2810.0000.0000.0000.000
165A168MET00.0010.00314.811-0.339-0.3390.0000.0000.0000.000
166A169ALA00.0180.02111.3130.9600.9600.0000.0000.0000.000
167A170LEU0-0.026-0.01110.669-1.796-1.7960.0000.0000.0000.000
168A171GLN0-0.014-0.0227.151-0.434-0.4340.0000.0000.0000.000
169A172GLY00.0540.0409.867-1.276-1.2760.0000.0000.0000.000
170A173ASN0-0.009-0.02211.625-1.875-1.8750.0000.0000.0000.000
171A174LYS10.8080.89213.705-18.823-18.8230.0000.0000.0000.000
172A175VAL00.0550.03313.9901.1891.1890.0000.0000.0000.000
173A176VAL0-0.013-0.01414.647-1.001-1.0010.0000.0000.0000.000
174A177LEU0-0.0080.00215.8400.7520.7520.0000.0000.0000.000
175A178TYR00.003-0.00615.507-0.823-0.8230.0000.0000.0000.000
176A179VAL00.0410.01619.6230.1410.1410.0000.0000.0000.000
177A180TYR00.008-0.00417.919-0.090-0.0900.0000.0000.0000.000
178A181ASP-1-0.780-0.87024.12810.05410.0540.0000.0000.0000.000
179A182LEU00.0040.00827.6850.2290.2290.0000.0000.0000.000
180A183ARG10.8780.91530.006-9.890-9.8900.0000.0000.0000.000
181A184ASP-1-0.896-0.95133.4688.7278.7270.0000.0000.0000.000
182A185GLY0-0.0200.00134.340-0.055-0.0550.0000.0000.0000.000
183A186LYS10.8490.91328.931-10.496-10.4960.0000.0000.0000.000
184A187THR00.0350.01324.488-0.226-0.2260.0000.0000.0000.000
185A188ASN0-0.119-0.06527.155-0.048-0.0480.0000.0000.0000.000
186A189VAL00.0400.01021.0440.2630.2630.0000.0000.0000.000
187A190ALA0-0.024-0.00123.974-0.354-0.3540.0000.0000.0000.000
188A191MET0-0.0140.01319.6400.3860.3860.0000.0000.0000.000
189A192SER0-0.052-0.03521.061-0.947-0.9470.0000.0000.0000.000
190A193GLU-1-0.843-0.90618.56217.03117.0310.0000.0000.0000.000
191A194PHE00.0120.00219.581-0.907-0.9070.0000.0000.0000.000
192A195SER0-0.003-0.01218.8460.9570.9570.0000.0000.0000.000
193A196LYS10.9500.99518.806-13.708-13.7080.0000.0000.0000.000