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: YZMJ2

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1669024.012017
FMO2-HF: Nuclear repulsion 1599531.978714
FMO2-HF: Total energy -69492.033303
FMO2-MP2: Total energy -69692.940364


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.
-43.081-37.9720.495-2.482-3.1210.007
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 : -0.903 / q_NPA : -0.968
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].
3H3GLN00.0010.0032.917-14.002-9.3950.491-2.308-2.7900.007
4H4LEU0-0.031-0.0194.393-4.022-3.9470.000-0.025-0.0500.000
5H5LEU00.0230.0297.673-1.149-1.1490.0000.0000.0000.000
6H6GLU-1-0.785-0.9389.33318.53818.5380.0000.0000.0000.000
7H7SER0-0.052-0.02912.9420.0960.0960.0000.0000.0000.000
8H8GLY00.0510.02415.776-0.488-0.4880.0000.0000.0000.000
9H9GLY00.0060.01618.829-0.801-0.8010.0000.0000.0000.000
10H10GLY00.0130.00020.6650.0710.0710.0000.0000.0000.000
11H11LEU0-0.058-0.02523.273-0.225-0.2250.0000.0000.0000.000
12H12VAL0-0.011-0.00226.894-0.142-0.1420.0000.0000.0000.000
13H13GLN00.0270.01029.388-0.270-0.2700.0000.0000.0000.000
14H14PRO00.013-0.00732.7700.1470.1470.0000.0000.0000.000
15H15GLY0-0.0260.00534.308-0.227-0.2270.0000.0000.0000.000
16H16GLY0-0.023-0.00532.066-0.003-0.0030.0000.0000.0000.000
17H17SER0-0.029-0.03229.802-0.007-0.0070.0000.0000.0000.000
18H18LEU0-0.003-0.01124.0060.0780.0780.0000.0000.0000.000
19H19ARG10.8950.97621.352-13.493-13.4930.0000.0000.0000.000
20H20LEU0-0.0110.01118.9120.3790.3790.0000.0000.0000.000
21H21SER0-0.023-0.03415.724-0.226-0.2260.0000.0000.0000.000
22H22CYS0-0.048-0.01012.8230.4290.4290.0000.0000.0000.000
23H23ALA00.0110.02010.251-0.834-0.8340.0000.0000.0000.000
24H24ALA00.0170.0088.5992.0282.0280.0000.0000.0000.000
25H25SER0-0.026-0.0154.3911.3881.587-0.001-0.023-0.1740.000
26H26GLY00.0850.0423.8742.2742.3620.006-0.1120.0180.000
27H27PHE0-0.022-0.0124.559-2.971-2.831-0.001-0.014-0.1250.000
28H28THR00.0260.0118.0330.1640.1640.0000.0000.0000.000
29H29PHE00.0710.02611.629-1.245-1.2450.0000.0000.0000.000
30H30SER0-0.002-0.02113.120-0.688-0.6880.0000.0000.0000.000
31H31TYR0-0.013-0.00915.055-0.992-0.9920.0000.0000.0000.000
32H32TYR0-0.0190.01712.4330.0330.0330.0000.0000.0000.000
33H33TYR00.0490.02716.866-0.210-0.2100.0000.0000.0000.000
34H34MET0-0.028-0.00512.4281.0401.0400.0000.0000.0000.000
35H35GLN00.0560.00816.515-1.369-1.3690.0000.0000.0000.000
36H36TRP0-0.0070.00217.0570.7830.7830.0000.0000.0000.000
37H37VAL0-0.009-0.01218.597-0.902-0.9020.0000.0000.0000.000
38H38ARG10.8010.89619.332-10.698-10.6980.0000.0000.0000.000
39H39GLN00.017-0.00420.9590.2110.2110.0000.0000.0000.000
40H40ALA00.0430.02423.2230.1630.1630.0000.0000.0000.000
41H41PRO00.0150.00525.5050.0920.0920.0000.0000.0000.000
42H42GLY00.0120.01326.374-0.478-0.4780.0000.0000.0000.000
43H43LYS10.8910.95027.669-9.880-9.8800.0000.0000.0000.000
44H44GLY00.0340.01425.5230.3300.3300.0000.0000.0000.000
45H45LEU0-0.018-0.01520.0770.0480.0480.0000.0000.0000.000
46H46GLU-1-0.796-0.87523.49310.50910.5090.0000.0000.0000.000
47H47TRP0-0.030-0.00622.2940.1830.1830.0000.0000.0000.000
48H48VAL0-0.0050.00222.827-0.532-0.5320.0000.0000.0000.000
49H49SER0-0.027-0.05922.872-0.514-0.5140.0000.0000.0000.000
50H50TYR0-0.0120.00721.2600.6520.6520.0000.0000.0000.000
51H51ILE00.0000.01420.156-0.605-0.6050.0000.0000.0000.000
52H52GLY00.0530.01521.0490.4980.4980.0000.0000.0000.000
53H53SER00.014-0.00119.7810.3870.3870.0000.0000.0000.000
54H54SER0-0.007-0.00920.4650.3490.3490.0000.0000.0000.000
55H55GLY0-0.016-0.00922.566-0.333-0.3330.0000.0000.0000.000
56H56GLY0-0.0250.00423.898-0.377-0.3770.0000.0000.0000.000
57H57VAL00.0190.00526.391-0.185-0.1850.0000.0000.0000.000
58H58THR00.0520.01625.6840.6210.6210.0000.0000.0000.000
59H59ASN0-0.051-0.01026.426-0.296-0.2960.0000.0000.0000.000
60H60TYR00.0500.04126.4030.5030.5030.0000.0000.0000.000
61H61ALA00.0700.04327.905-0.341-0.3410.0000.0000.0000.000
62H62ASP-1-0.878-0.96229.5388.9578.9570.0000.0000.0000.000
63H63SER0-0.0150.00030.355-0.300-0.3000.0000.0000.0000.000
64H64VAL0-0.0100.00227.371-0.025-0.0250.0000.0000.0000.000
65H65LYS10.9050.97130.546-9.111-9.1110.0000.0000.0000.000
66H66GLY0-0.0070.00532.138-0.290-0.2900.0000.0000.0000.000
67H67ARG10.7240.84231.091-9.908-9.9080.0000.0000.0000.000
68H68PHE00.008-0.00426.0210.2380.2380.0000.0000.0000.000
69H69THR0-0.022-0.01527.115-0.338-0.3380.0000.0000.0000.000
70H70ILE00.0070.02220.4480.3900.3900.0000.0000.0000.000
71H71SER0-0.033-0.01722.244-0.365-0.3650.0000.0000.0000.000
72H72ARG10.8190.91416.408-15.506-15.5060.0000.0000.0000.000
73H73ASP-1-0.768-0.83017.94314.04514.0450.0000.0000.0000.000
74H74ASN00.007-0.02216.4821.3841.3840.0000.0000.0000.000
75H75SER0-0.097-0.07316.1580.5000.5000.0000.0000.0000.000
76H76LYS10.8960.93315.291-14.289-14.2890.0000.0000.0000.000
77H77ASN0-0.039-0.00211.3431.3271.3270.0000.0000.0000.000
78H78THR0-0.014-0.00812.2051.3611.3610.0000.0000.0000.000
79H79LEU00.0050.00514.683-1.246-1.2460.0000.0000.0000.000
80H80TYR0-0.021-0.03116.7870.1900.1900.0000.0000.0000.000
81H81LEU00.0280.00519.743-0.362-0.3620.0000.0000.0000.000
82H82GLN0-0.055-0.04922.4050.4270.4270.0000.0000.0000.000
83H83MET0-0.0090.01023.569-0.412-0.4120.0000.0000.0000.000
84H84ASN00.1000.05327.2820.1160.1160.0000.0000.0000.000
85H85SER0-0.018-0.01230.936-0.185-0.1850.0000.0000.0000.000
86H86LEU00.0000.00827.442-0.092-0.0920.0000.0000.0000.000
87H87ARG10.9660.98031.552-9.162-9.1620.0000.0000.0000.000
88H88ALA00.0640.01931.4940.2860.2860.0000.0000.0000.000
89H89GLU-1-0.945-0.97231.4849.1959.1950.0000.0000.0000.000
90H90ASP-1-0.762-0.84828.04010.53110.5310.0000.0000.0000.000
91H91THR0-0.0350.00026.5540.5460.5460.0000.0000.0000.000
92H92ALA0-0.030-0.01723.762-0.211-0.2110.0000.0000.0000.000
93H93VAL00.0060.00117.8140.1350.1350.0000.0000.0000.000
94H94TYR0-0.075-0.05019.332-0.340-0.3400.0000.0000.0000.000
95H95TYR00.0810.04714.3960.7770.7770.0000.0000.0000.000
96H97ALA00.0360.01812.8151.5271.5270.0000.0000.0000.000
97H98ARG10.8140.88510.514-24.067-24.0670.0000.0000.0000.000
98H99VAL0-0.039-0.00813.590-0.165-0.1650.0000.0000.0000.000
99H100GLY00.0560.02015.0210.7670.7670.0000.0000.0000.000
100H101LEU0-0.042-0.03215.652-0.878-0.8780.0000.0000.0000.000
101H102GLY00.000-0.00418.0100.0490.0490.0000.0000.0000.000
102H103ASP-1-0.938-0.95919.83912.62812.6280.0000.0000.0000.000
103H104ALA0-0.0050.00617.398-0.136-0.1360.0000.0000.0000.000
104H105PHE0-0.031-0.02815.2260.5640.5640.0000.0000.0000.000
105H106ASP-1-0.789-0.86811.79421.91121.9110.0000.0000.0000.000
106H107ILE0-0.026-0.0067.1101.7731.7730.0000.0000.0000.000
107H108TRP0-0.018-0.0289.635-2.324-2.3240.0000.0000.0000.000
108H109GLY00.0480.0259.2052.4722.4720.0000.0000.0000.000
109H110GLN0-0.0010.0099.3931.2031.2030.0000.0000.0000.000
110H111GLY0-0.021-0.02311.105-1.144-1.1440.0000.0000.0000.000
111H112THR0-0.031-0.01014.865-1.131-1.1310.0000.0000.0000.000
112H113MET00.0020.01616.727-0.488-0.4880.0000.0000.0000.000
113H114VAL0-0.011-0.00120.216-0.140-0.1400.0000.0000.0000.000
114H115THR0-0.005-0.02123.229-0.319-0.3190.0000.0000.0000.000
115H116VAL00.0250.01626.606-0.073-0.0730.0000.0000.0000.000
116H117SER0-0.012-0.00730.035-0.346-0.3460.0000.0000.0000.000
117H118SER00.036-0.00532.810-0.041-0.0410.0000.0000.0000.000
118H119ALA0-0.0340.00635.825-0.159-0.1590.0000.0000.0000.000
119H120SER00.0330.02534.7270.3690.3690.0000.0000.0000.000
120H121THR0-0.037-0.02334.064-0.033-0.0330.0000.0000.0000.000
121H122LYS10.9430.97035.597-7.877-7.8770.0000.0000.0000.000
122H123GLY00.0140.01337.3010.1970.1970.0000.0000.0000.000
123H124PRO0-0.011-0.01537.264-0.126-0.1260.0000.0000.0000.000
124H125SER0-0.0210.00139.471-0.198-0.1980.0000.0000.0000.000
125H126VAL00.0170.00741.1570.0500.0500.0000.0000.0000.000
126H127PHE0-0.045-0.03743.637-0.198-0.1980.0000.0000.0000.000
127H128PRO0-0.032-0.01045.7980.1080.1080.0000.0000.0000.000
128H129LEU00.0050.00744.463-0.143-0.1430.0000.0000.0000.000
129H130ALA00.0120.01048.402-0.083-0.0830.0000.0000.0000.000
130H131PRO00.0050.00950.1930.0730.0730.0000.0000.0000.000
131H144GLY00.0590.03143.3670.0020.0020.0000.0000.0000.000
132H201CYS0-0.133-0.07140.287-0.228-0.2280.0000.0000.0000.000
133H146LEU00.0220.01240.9000.1180.1180.0000.0000.0000.000
134H147VAL0-0.015-0.00236.672-0.125-0.1250.0000.0000.0000.000
135H148LYS10.9950.98338.758-7.039-7.0390.0000.0000.0000.000
136H149ASP-1-0.949-0.97139.0067.5597.5590.0000.0000.0000.000
137H150TYR00.004-0.00632.028-0.004-0.0040.0000.0000.0000.000
138H151PHE00.0330.02931.0040.2080.2080.0000.0000.0000.000
139H152PRO00.0340.00328.913-0.207-0.2070.0000.0000.0000.000
140H153GLU-1-0.890-0.94728.04910.64610.6460.0000.0000.0000.000
141H154PRO00.006-0.00725.7920.2210.2210.0000.0000.0000.000
142H155VAL0-0.005-0.01828.891-0.146-0.1460.0000.0000.0000.000
143H156THR0-0.031-0.01730.0610.1240.1240.0000.0000.0000.000
144H157VAL0-0.008-0.00831.787-0.218-0.2180.0000.0000.0000.000
145H158SER00.0040.01133.5590.1320.1320.0000.0000.0000.000
146H159TRP00.0300.00436.094-0.282-0.2820.0000.0000.0000.000
147H160ASN0-0.0090.01839.0740.2270.2270.0000.0000.0000.000
148H161SER00.0280.00937.122-0.032-0.0320.0000.0000.0000.000
149H169HIS0-0.011-0.01433.5770.2550.2550.0000.0000.0000.000
150H170THR0-0.023-0.01433.108-0.348-0.3480.0000.0000.0000.000
151H171PHE00.0050.00532.9710.2710.2710.0000.0000.0000.000
152H172PRO00.0360.00529.971-0.031-0.0310.0000.0000.0000.000
153H173ALA0-0.0200.00031.809-0.309-0.3090.0000.0000.0000.000
154H174VAL00.0080.02232.7470.1870.1870.0000.0000.0000.000
155H175LEU00.018-0.00331.5020.0190.0190.0000.0000.0000.000
156H176GLN0-0.031-0.02334.497-0.272-0.2720.0000.0000.0000.000
157H177SER00.0270.01137.3040.1050.1050.0000.0000.0000.000
158H178SER0-0.032-0.01639.7420.0160.0160.0000.0000.0000.000
159H179GLY00.0110.00835.4890.0250.0250.0000.0000.0000.000
160H180LEU0-0.067-0.01434.6720.2220.2220.0000.0000.0000.000
161H181TYR00.0680.03929.5160.0420.0420.0000.0000.0000.000
162H182SER0-0.058-0.04635.386-0.321-0.3210.0000.0000.0000.000
163H183LEU00.0090.02432.7080.0610.0610.0000.0000.0000.000
164H184SER00.0300.00536.444-0.342-0.3420.0000.0000.0000.000
165H185SER0-0.006-0.00437.0220.1810.1810.0000.0000.0000.000
166H186VAL00.0300.01938.837-0.240-0.2400.0000.0000.0000.000
167H187VAL00.0220.01939.9930.1000.1000.0000.0000.0000.000
168H202ASN0-0.064-0.04837.555-0.026-0.0260.0000.0000.0000.000
169H203VAL00.0090.00236.6270.2740.2740.0000.0000.0000.000
170H204ASN0-0.014-0.00733.995-0.248-0.2480.0000.0000.0000.000
171H205HIS00.011-0.01032.3540.0820.0820.0000.0000.0000.000
172H206LYS10.9560.96328.777-10.843-10.8430.0000.0000.0000.000
173H207PRO00.0270.02229.317-0.087-0.0870.0000.0000.0000.000
174H208SER00.0240.01331.732-0.172-0.1720.0000.0000.0000.000
175H209ASN0-0.075-0.02633.934-0.173-0.1730.0000.0000.0000.000
176H210THR0-0.031-0.00336.046-0.285-0.2850.0000.0000.0000.000
177H211LYS10.9520.96735.936-8.417-8.4170.0000.0000.0000.000
178H212VAL00.0360.02339.199-0.185-0.1850.0000.0000.0000.000
179H213ASP-1-0.817-0.88541.3887.8127.8120.0000.0000.0000.000
180H214LYS10.9200.96243.460-6.764-6.7640.0000.0000.0000.000