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: 1738Z

Calculation Name: 5CUS-H-Xray372

Preferred Name: Receptor tyrosine-protein kinase erbB-3

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 5CUS

Chain ID: H

ChEMBL ID: CHEMBL5838

UniProt ID: P21860

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1673683.202923
FMO2-HF: Nuclear repulsion 1604190.072379
FMO2-HF: Total energy -69493.130544
FMO2-MP2: Total energy -69694.115609


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-77.112-78.31217.072-8.554-7.3190.086
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.810 / q_NPA : -0.901
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].
3H3GLN0-0.049-0.0281.704-35.148-37.47317.055-8.086-6.6440.086
4H4LEU0-0.013-0.0224.379-8.656-8.5600.001-0.064-0.0330.000
5H5LEU00.0100.0217.037-0.385-0.3850.0000.0000.0000.000
6H6GLU-1-0.808-0.9238.66019.31619.3160.0000.0000.0000.000
7H7SER0-0.041-0.02612.318-0.050-0.0500.0000.0000.0000.000
8H8GLY00.0400.01015.502-0.383-0.3830.0000.0000.0000.000
9H9GLY00.0040.01418.464-0.834-0.8340.0000.0000.0000.000
10H10GLY0-0.007-0.00720.2550.0710.0710.0000.0000.0000.000
11H11LEU0-0.051-0.01923.050-0.215-0.2150.0000.0000.0000.000
12H12VAL0-0.0070.00126.671-0.122-0.1220.0000.0000.0000.000
13H13GLN0-0.002-0.00129.285-0.249-0.2490.0000.0000.0000.000
14H14PRO00.020-0.00732.5410.1450.1450.0000.0000.0000.000
15H15GLY0-0.0290.00034.224-0.209-0.2090.0000.0000.0000.000
16H16GLY0-0.0010.00731.782-0.009-0.0090.0000.0000.0000.000
17H17SER0-0.041-0.03529.227-0.062-0.0620.0000.0000.0000.000
18H18LEU0-0.0070.00223.8020.0260.0260.0000.0000.0000.000
19H19ARG10.8780.95320.839-14.293-14.2930.0000.0000.0000.000
20H20LEU00.0030.02818.1130.4700.4700.0000.0000.0000.000
21H21SER0-0.004-0.02215.777-0.573-0.5730.0000.0000.0000.000
22H22CYS0-0.059-0.01512.3110.5800.5800.0000.0000.0000.000
23H23ALA00.0310.03910.081-1.051-1.0510.0000.0000.0000.000
24H24ALA00.0090.0038.2642.1122.1120.0000.0000.0000.000
25H25SER0-0.021-0.0192.953-2.135-1.4150.012-0.305-0.4270.000
26H26GLY00.0310.0093.7881.7171.8740.005-0.083-0.0790.000
27H27PHE0-0.001-0.0044.566-3.524-3.372-0.001-0.016-0.1360.000
28H28THR00.0210.0138.2750.3570.3570.0000.0000.0000.000
29H29PHE00.0630.03411.428-1.531-1.5310.0000.0000.0000.000
30H30SER0-0.002-0.02212.892-0.728-0.7280.0000.0000.0000.000
31H31TYR00.0040.00115.298-0.922-0.9220.0000.0000.0000.000
32H32TYR00.0050.03312.625-0.203-0.2030.0000.0000.0000.000
33H33TYR00.0540.03317.021-0.111-0.1110.0000.0000.0000.000
34H34MET0-0.040-0.00512.8511.1061.1060.0000.0000.0000.000
35H35GLN00.0470.01016.884-1.661-1.6610.0000.0000.0000.000
36H36TRP00.008-0.00615.9501.0761.0760.0000.0000.0000.000
37H37VAL0-0.009-0.00318.413-1.039-1.0390.0000.0000.0000.000
38H38ARG10.8020.87019.125-11.135-11.1350.0000.0000.0000.000
39H39GLN00.0050.00220.7170.3340.3340.0000.0000.0000.000
40H40ALA00.0470.03522.8530.1650.1650.0000.0000.0000.000
41H41PRO0-0.003-0.00625.6430.1020.1020.0000.0000.0000.000
42H42GLY00.0220.01226.528-0.461-0.4610.0000.0000.0000.000
43H43LYS10.8840.94826.841-10.294-10.2940.0000.0000.0000.000
44H44GLY00.0510.02525.0130.3860.3860.0000.0000.0000.000
45H45LEU0-0.012-0.00619.4870.0020.0020.0000.0000.0000.000
46H46GLU-1-0.796-0.85223.17810.82510.8250.0000.0000.0000.000
47H47TRP0-0.005-0.00322.0460.2030.2030.0000.0000.0000.000
48H48VAL0-0.010-0.00122.583-0.566-0.5660.0000.0000.0000.000
49H49SER0-0.011-0.04022.864-0.523-0.5230.0000.0000.0000.000
50H50TYR0-0.026-0.00921.5670.7660.7660.0000.0000.0000.000
51H51ILE0-0.011-0.00520.262-0.645-0.6450.0000.0000.0000.000
52H52GLY00.0520.02521.1690.6200.6200.0000.0000.0000.000
53H53SER0-0.031-0.02619.4890.2090.2090.0000.0000.0000.000
54H54SER00.006-0.00420.1620.3810.3810.0000.0000.0000.000
55H55GLY0-0.030-0.01322.377-0.412-0.4120.0000.0000.0000.000
56H56GLY0-0.018-0.00223.663-0.220-0.2200.0000.0000.0000.000
57H57VAL00.0050.01326.490-0.328-0.3280.0000.0000.0000.000
58H58THR00.0500.02225.7210.4520.4520.0000.0000.0000.000
59H59ASN0-0.035-0.00926.328-0.531-0.5310.0000.0000.0000.000
60H60TYR00.0500.03326.3840.5440.5440.0000.0000.0000.000
61H61ALA00.0710.04627.635-0.418-0.4180.0000.0000.0000.000
62H62ASP-1-0.830-0.92129.3809.2639.2630.0000.0000.0000.000
63H63SER0-0.029-0.01328.968-0.231-0.2310.0000.0000.0000.000
64H64VAL0-0.006-0.00826.836-0.054-0.0540.0000.0000.0000.000
65H65LYS10.8110.90230.064-9.398-9.3980.0000.0000.0000.000
66H66GLY0-0.0030.00731.755-0.283-0.2830.0000.0000.0000.000
67H67ARG10.7310.83830.270-10.194-10.1940.0000.0000.0000.000
68H68PHE00.015-0.00325.2670.2150.2150.0000.0000.0000.000
69H69THR0-0.044-0.03326.474-0.396-0.3960.0000.0000.0000.000
70H70ILE0-0.0040.02120.2070.3880.3880.0000.0000.0000.000
71H71SER0-0.015-0.01921.791-0.448-0.4480.0000.0000.0000.000
72H72ARG10.8090.89016.464-16.162-16.1620.0000.0000.0000.000
73H73ASP-1-0.759-0.83317.71814.43614.4360.0000.0000.0000.000
74H74ASN00.0370.00216.3571.5761.5760.0000.0000.0000.000
75H75SER0-0.084-0.05216.2770.2970.2970.0000.0000.0000.000
76H76LYS10.8420.89514.628-14.892-14.8920.0000.0000.0000.000
77H77ASN0-0.0210.00610.8010.8670.8670.0000.0000.0000.000
78H78THR00.0350.01111.7132.0262.0260.0000.0000.0000.000
79H79LEU0-0.022-0.00314.208-1.533-1.5330.0000.0000.0000.000
80H80TYR00.001-0.02416.5000.2740.2740.0000.0000.0000.000
81H81LEU00.0240.00819.203-0.403-0.4030.0000.0000.0000.000
82H82GLN0-0.031-0.01121.7550.4420.4420.0000.0000.0000.000
83H83MET0-0.018-0.00223.001-0.132-0.1320.0000.0000.0000.000
84H84ASN00.0820.03126.7610.1360.1360.0000.0000.0000.000
85H85SER0-0.010-0.00330.459-0.174-0.1740.0000.0000.0000.000
86H86LEU0-0.0050.01026.955-0.072-0.0720.0000.0000.0000.000
87H87ARG10.8930.92831.082-9.475-9.4750.0000.0000.0000.000
88H88ALA00.0550.02330.9980.3070.3070.0000.0000.0000.000
89H89GLU-1-0.864-0.92830.7319.6219.6210.0000.0000.0000.000
90H90ASP-1-0.750-0.82327.19810.95210.9520.0000.0000.0000.000
91H91THR0-0.026-0.00725.9250.5980.5980.0000.0000.0000.000
92H92ALA0-0.023-0.01623.242-0.258-0.2580.0000.0000.0000.000
93H93VAL00.0530.03417.5790.2140.2140.0000.0000.0000.000
94H94TYR0-0.058-0.04618.373-0.811-0.8110.0000.0000.0000.000
95H95TYR00.0270.00414.2570.8980.8980.0000.0000.0000.000
96H97ALA00.027-0.00113.0781.4271.4270.0000.0000.0000.000
97H98ARG10.8030.87310.313-25.499-25.4990.0000.0000.0000.000
98H99VAL0-0.031-0.00714.004-0.115-0.1150.0000.0000.0000.000
99H100GLY00.0550.02515.0950.7530.7530.0000.0000.0000.000
100H101LEU0-0.053-0.03815.744-0.946-0.9460.0000.0000.0000.000
101H102GLY00.0090.00418.314-0.043-0.0430.0000.0000.0000.000
102H103ASP-1-0.931-0.96719.82413.23813.2380.0000.0000.0000.000
103H104ALA0-0.0030.00417.7870.1370.1370.0000.0000.0000.000
104H105PHE0-0.040-0.02715.9000.6210.6210.0000.0000.0000.000
105H106ASP-1-0.770-0.85112.42122.58722.5870.0000.0000.0000.000
106H107ILE0-0.033-0.0037.0831.9511.9510.0000.0000.0000.000
107H108TRP0-0.010-0.0289.683-2.881-2.8810.0000.0000.0000.000
108H109GLY00.0340.0269.0233.1763.1760.0000.0000.0000.000
109H110GLN00.004-0.0039.3620.5970.5970.0000.0000.0000.000
110H111GLY00.005-0.00211.112-1.264-1.2640.0000.0000.0000.000
111H112THR0-0.053-0.03914.437-1.538-1.5380.0000.0000.0000.000
112H113MET0-0.0050.01716.338-0.704-0.7040.0000.0000.0000.000
113H114VAL00.0180.01919.832-0.120-0.1200.0000.0000.0000.000
114H115THR0-0.070-0.04823.051-0.295-0.2950.0000.0000.0000.000
115H116VAL00.0290.02126.600-0.039-0.0390.0000.0000.0000.000
116H117SER00.005-0.00329.916-0.389-0.3890.0000.0000.0000.000
117H118SER00.0470.00132.8390.0800.0800.0000.0000.0000.000
118H119ALA0-0.0420.00535.125-0.210-0.2100.0000.0000.0000.000
119H120SER00.0370.01134.5130.3560.3560.0000.0000.0000.000
120H121THR0-0.062-0.04033.955-0.081-0.0810.0000.0000.0000.000
121H122LYS10.8480.91535.455-8.012-8.0120.0000.0000.0000.000
122H123GLY00.0640.03337.4050.1810.1810.0000.0000.0000.000
123H124PRO0-0.029-0.01737.481-0.142-0.1420.0000.0000.0000.000
124H125SER0-0.011-0.00439.724-0.223-0.2230.0000.0000.0000.000
125H126VAL00.0270.01741.1190.0100.0100.0000.0000.0000.000
126H127PHE0-0.012-0.00643.649-0.223-0.2230.0000.0000.0000.000
127H128PRO00.0080.00845.6410.1360.1360.0000.0000.0000.000
128H129LEU0-0.018-0.00844.557-0.107-0.1070.0000.0000.0000.000
129H130ALA00.0190.01148.591-0.071-0.0710.0000.0000.0000.000
130H131PRO0-0.0040.00450.6890.0650.0650.0000.0000.0000.000
131H144GLY00.0740.03844.1560.0130.0130.0000.0000.0000.000
132H201CYS0-0.117-0.05641.158-0.252-0.2520.0000.0000.0000.000
133H146LEU00.0240.02641.1570.1900.1900.0000.0000.0000.000
134H147VAL0-0.015-0.01137.382-0.141-0.1410.0000.0000.0000.000
135H148LYS10.8750.92238.906-7.321-7.3210.0000.0000.0000.000
136H149ASP-1-0.857-0.92039.3207.6557.6550.0000.0000.0000.000
137H150TYR00.012-0.00832.421-0.283-0.2830.0000.0000.0000.000
138H151PHE00.0520.02631.2500.1770.1770.0000.0000.0000.000
139H152PRO00.0340.02029.012-0.212-0.2120.0000.0000.0000.000
140H153GLU-1-0.788-0.87728.00210.27910.2790.0000.0000.0000.000
141H154PRO0-0.026-0.00426.5020.2300.2300.0000.0000.0000.000
142H155VAL0-0.005-0.02329.275-0.176-0.1760.0000.0000.0000.000
143H156THR0-0.034-0.00730.8270.2420.2420.0000.0000.0000.000
144H157VAL0-0.018-0.02032.490-0.274-0.2740.0000.0000.0000.000
145H158SER00.0220.01934.5820.1730.1730.0000.0000.0000.000
146H159TRP00.0410.00737.063-0.342-0.3420.0000.0000.0000.000
147H160ASN00.0180.02440.0760.2320.2320.0000.0000.0000.000
148H161SER0-0.015-0.00338.1670.0970.0970.0000.0000.0000.000
149H169HIS00.0180.01834.6610.1970.1970.0000.0000.0000.000
150H170THR0-0.038-0.03133.888-0.347-0.3470.0000.0000.0000.000
151H171PHE0-0.0030.00433.6470.2570.2570.0000.0000.0000.000
152H172PRO00.028-0.00230.3970.0480.0480.0000.0000.0000.000
153H173ALA0-0.0100.00731.744-0.336-0.3360.0000.0000.0000.000
154H174VAL0-0.030-0.01033.0450.1570.1570.0000.0000.0000.000
155H175LEU0-0.016-0.00831.705-0.049-0.0490.0000.0000.0000.000
156H176GLN0-0.012-0.02034.637-0.303-0.3030.0000.0000.0000.000
157H177SER00.014-0.00437.4340.1070.1070.0000.0000.0000.000
158H178SER0-0.011-0.00339.8690.0220.0220.0000.0000.0000.000
159H179GLY00.0020.00335.4000.0220.0220.0000.0000.0000.000
160H180LEU0-0.048-0.01534.4650.2620.2620.0000.0000.0000.000
161H181TYR00.0550.03329.2380.0550.0550.0000.0000.0000.000
162H182SER0-0.045-0.02935.359-0.420-0.4200.0000.0000.0000.000
163H183LEU00.0520.05133.0120.0830.0830.0000.0000.0000.000
164H184SER00.0260.00336.759-0.342-0.3420.0000.0000.0000.000
165H185SER0-0.022-0.01637.4540.1760.1760.0000.0000.0000.000
166H186VAL00.0250.01339.236-0.267-0.2670.0000.0000.0000.000
167H187VAL00.0360.03040.4710.1170.1170.0000.0000.0000.000
168H202ASN0-0.035-0.04438.3710.0560.0560.0000.0000.0000.000
169H203VAL0-0.016-0.01437.4590.2610.2610.0000.0000.0000.000
170H204ASN0-0.029-0.02034.484-0.037-0.0370.0000.0000.0000.000
171H205HIS00.020-0.00832.8290.1400.1400.0000.0000.0000.000
172H206LYS10.9670.97229.153-10.970-10.9700.0000.0000.0000.000
173H207PRO00.0270.02329.508-0.105-0.1050.0000.0000.0000.000
174H208SER00.0310.03631.962-0.141-0.1410.0000.0000.0000.000
175H209ASN0-0.056-0.03234.132-0.214-0.2140.0000.0000.0000.000
176H210THR0-0.0360.00036.220-0.278-0.2780.0000.0000.0000.000
177H211LYS10.9360.96136.001-8.637-8.6370.0000.0000.0000.000
178H212VAL00.0010.00439.516-0.214-0.2140.0000.0000.0000.000
179H213ASP-1-0.819-0.89541.5187.9427.9420.0000.0000.0000.000
180H214LYS10.8600.92443.828-6.987-6.9870.0000.0000.0000.000