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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: V56J1

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 OptHSide
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 -1669980.918823
FMO2-HF: Nuclear repulsion 1600488.284975
FMO2-HF: Total energy -69492.633849
FMO2-MP2: Total energy -69693.540424


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.
-64.622-64.75313.645-7.058-6.4570.064
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 : -0.856 / q_NPA : -0.935
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].
3H3GLN0-0.059-0.0341.734-30.910-31.63613.641-6.837-6.0790.064
4H4LEU0-0.018-0.0124.698-5.427-5.375-0.001-0.029-0.0210.000
5H5LEU00.0220.0277.271-1.440-1.4400.0000.0000.0000.000
6H6GLU-1-0.751-0.9048.82419.12519.1250.0000.0000.0000.000
7H7SER0-0.041-0.02912.4760.0590.0590.0000.0000.0000.000
8H8GLY00.0410.02015.383-0.509-0.5090.0000.0000.0000.000
9H9GLY0-0.0050.01318.483-0.831-0.8310.0000.0000.0000.000
10H10GLY00.0180.00320.3280.0680.0680.0000.0000.0000.000
11H11LEU0-0.059-0.02623.017-0.229-0.2290.0000.0000.0000.000
12H12VAL0-0.005-0.00126.657-0.154-0.1540.0000.0000.0000.000
13H13GLN00.0220.01329.083-0.229-0.2290.0000.0000.0000.000
14H14PRO00.022-0.00432.4050.1410.1410.0000.0000.0000.000
15H15GLY0-0.0350.00133.902-0.234-0.2340.0000.0000.0000.000
16H16GLY0-0.018-0.00331.673-0.002-0.0020.0000.0000.0000.000
17H17SER0-0.031-0.03329.332-0.005-0.0050.0000.0000.0000.000
18H18LEU0-0.005-0.00723.7850.0810.0810.0000.0000.0000.000
19H19ARG10.8730.96321.262-13.744-13.7440.0000.0000.0000.000
20H20LEU0-0.0070.01618.3620.3900.3900.0000.0000.0000.000
21H21SER0-0.024-0.03715.814-0.299-0.2990.0000.0000.0000.000
22H22CYS0-0.057-0.01913.0410.3300.3300.0000.0000.0000.000
23H23ALA00.0060.02410.248-0.969-0.9690.0000.0000.0000.000
24H24ALA00.0190.0118.5762.3172.3170.0000.0000.0000.000
25H25SER00.0290.0083.422-1.254-0.9770.000-0.063-0.2150.000
26H26GLY00.0370.0263.8582.8983.0150.006-0.113-0.0100.000
27H27PHE0-0.017-0.0144.536-3.185-3.036-0.001-0.016-0.1320.000
28H28THR00.0180.0128.0210.1910.1910.0000.0000.0000.000
29H29PHE00.0740.03211.611-1.200-1.2000.0000.0000.0000.000
30H30SER0-0.008-0.02113.060-0.720-0.7200.0000.0000.0000.000
31H31TYR0-0.020-0.01815.045-0.949-0.9490.0000.0000.0000.000
32H32TYR0-0.0040.02212.4060.0910.0910.0000.0000.0000.000
33H33TYR00.0470.03116.958-0.284-0.2840.0000.0000.0000.000
34H34MET0-0.034-0.00612.8431.1141.1140.0000.0000.0000.000
35H35GLN00.0450.00616.676-1.525-1.5250.0000.0000.0000.000
36H36TRP0-0.002-0.00516.4420.8210.8210.0000.0000.0000.000
37H37VAL0-0.023-0.01518.643-0.957-0.9570.0000.0000.0000.000
38H38ARG10.8150.89419.199-10.880-10.8800.0000.0000.0000.000
39H39GLN00.0270.00920.5520.3150.3150.0000.0000.0000.000
40H40ALA00.0340.02122.8950.1570.1570.0000.0000.0000.000
41H41PRO00.0190.00625.3320.0810.0810.0000.0000.0000.000
42H42GLY00.0120.01226.201-0.490-0.4900.0000.0000.0000.000
43H43LYS10.8900.95027.349-9.976-9.9760.0000.0000.0000.000
44H44GLY00.0430.01825.4260.3380.3380.0000.0000.0000.000
45H45LEU0-0.016-0.01119.9600.0330.0330.0000.0000.0000.000
46H46GLU-1-0.791-0.86323.51910.66410.6640.0000.0000.0000.000
47H47TRP0-0.023-0.00522.2950.1890.1890.0000.0000.0000.000
48H48VAL0-0.0110.00122.942-0.530-0.5300.0000.0000.0000.000
49H49SER0-0.022-0.05223.040-0.551-0.5510.0000.0000.0000.000
50H50TYR0-0.021-0.01521.3980.7490.7490.0000.0000.0000.000
51H51ILE0-0.0250.00220.458-0.633-0.6330.0000.0000.0000.000
52H52GLY00.0560.02321.2290.5150.5150.0000.0000.0000.000
53H53SER00.0220.01019.6560.3470.3470.0000.0000.0000.000
54H54SER0-0.017-0.01020.4100.3960.3960.0000.0000.0000.000
55H55GLY0-0.018-0.00622.526-0.337-0.3370.0000.0000.0000.000
56H56GLY0-0.0250.00323.851-0.385-0.3850.0000.0000.0000.000
57H57VAL00.0200.00926.539-0.197-0.1970.0000.0000.0000.000
58H58THR00.0320.00825.8820.4170.4170.0000.0000.0000.000
59H59ASN0-0.0140.01526.608-0.358-0.3580.0000.0000.0000.000
60H60TYR00.0630.04626.6620.5260.5260.0000.0000.0000.000
61H61ALA00.0800.04828.011-0.359-0.3590.0000.0000.0000.000
62H62ASP-1-0.836-0.92529.6919.0649.0640.0000.0000.0000.000
63H63SER0-0.0190.00129.665-0.216-0.2160.0000.0000.0000.000
64H64VAL0-0.006-0.01027.265-0.029-0.0290.0000.0000.0000.000
65H65LYS10.8060.90530.458-9.255-9.2550.0000.0000.0000.000
66H66GLY00.0040.00932.181-0.304-0.3040.0000.0000.0000.000
67H67ARG10.7250.83430.661-10.051-10.0510.0000.0000.0000.000
68H68PHE00.015-0.00425.7380.2590.2590.0000.0000.0000.000
69H69THR0-0.013-0.01126.911-0.325-0.3250.0000.0000.0000.000
70H70ILE0-0.0110.02020.7040.3960.3960.0000.0000.0000.000
71H71SER0-0.015-0.01722.231-0.397-0.3970.0000.0000.0000.000
72H72ARG10.8200.89116.549-15.828-15.8280.0000.0000.0000.000
73H73ASP-1-0.750-0.83118.00214.27414.2740.0000.0000.0000.000
74H74ASN00.024-0.01216.4261.4211.4210.0000.0000.0000.000
75H75SER0-0.093-0.05216.0860.4520.4520.0000.0000.0000.000
76H76LYS10.8620.90515.214-14.499-14.4990.0000.0000.0000.000
77H77ASN0-0.041-0.00711.3241.3601.3600.0000.0000.0000.000
78H78THR00.0020.00312.1621.6011.6010.0000.0000.0000.000
79H79LEU0-0.0130.00314.648-1.377-1.3770.0000.0000.0000.000
80H80TYR0-0.005-0.02816.7650.0820.0820.0000.0000.0000.000
81H81LEU00.0330.00819.729-0.371-0.3710.0000.0000.0000.000
82H82GLN0-0.056-0.04822.1390.4030.4030.0000.0000.0000.000
83H83MET00.0000.01423.043-0.391-0.3910.0000.0000.0000.000
84H84ASN00.0830.04126.7570.1330.1330.0000.0000.0000.000
85H85SER0-0.014-0.00730.415-0.181-0.1810.0000.0000.0000.000
86H86LEU0-0.0080.00826.946-0.092-0.0920.0000.0000.0000.000
87H87ARG10.9260.94131.106-9.337-9.3370.0000.0000.0000.000
88H88ALA00.0610.01631.1080.2960.2960.0000.0000.0000.000
89H89GLU-1-0.917-0.94331.1559.3939.3930.0000.0000.0000.000
90H90ASP-1-0.744-0.82227.55910.69810.6980.0000.0000.0000.000
91H91THR0-0.0160.01126.2220.6000.6000.0000.0000.0000.000
92H92ALA0-0.034-0.02023.491-0.225-0.2250.0000.0000.0000.000
93H93VAL00.0210.00417.5330.1360.1360.0000.0000.0000.000
94H94TYR0-0.076-0.05218.912-0.360-0.3600.0000.0000.0000.000
95H95TYR00.0670.03514.3680.8350.8350.0000.0000.0000.000
96H97ALA00.0310.01112.9871.6431.6430.0000.0000.0000.000
97H98ARG10.8190.89510.762-24.419-24.4190.0000.0000.0000.000
98H99VAL0-0.024-0.00913.681-0.151-0.1510.0000.0000.0000.000
99H100GLY00.0470.02014.9410.7940.7940.0000.0000.0000.000
100H101LEU0-0.045-0.03315.587-0.929-0.9290.0000.0000.0000.000
101H102GLY0-0.003-0.00618.0950.0460.0460.0000.0000.0000.000
102H103ASP-1-0.942-0.96019.72912.95612.9560.0000.0000.0000.000
103H104ALA0-0.0050.00717.267-0.139-0.1390.0000.0000.0000.000
104H105PHE0-0.035-0.02915.2180.6480.6480.0000.0000.0000.000
105H106ASP-1-0.785-0.87411.69422.13222.1320.0000.0000.0000.000
106H107ILE0-0.026-0.0046.9651.8461.8460.0000.0000.0000.000
107H108TRP0-0.005-0.0229.642-2.498-2.4980.0000.0000.0000.000
108H109GLY00.0460.0339.3062.7562.7560.0000.0000.0000.000
109H110GLN0-0.008-0.0119.0721.1271.1270.0000.0000.0000.000
110H111GLY0-0.043-0.03410.848-1.306-1.3060.0000.0000.0000.000
111H112THR0-0.022-0.01014.594-1.204-1.2040.0000.0000.0000.000
112H113MET0-0.0070.01516.435-0.513-0.5130.0000.0000.0000.000
113H114VAL0-0.0030.00119.964-0.153-0.1530.0000.0000.0000.000
114H115THR0-0.024-0.02422.911-0.349-0.3490.0000.0000.0000.000
115H116VAL00.0220.01326.333-0.076-0.0760.0000.0000.0000.000
116H117SER0-0.003-0.00129.724-0.353-0.3530.0000.0000.0000.000
117H118SER00.041-0.00632.5530.0830.0830.0000.0000.0000.000
118H119ALA0-0.0420.00135.611-0.167-0.1670.0000.0000.0000.000
119H120SER00.0350.01834.5450.3740.3740.0000.0000.0000.000
120H121THR0-0.034-0.01334.007-0.015-0.0150.0000.0000.0000.000
121H122LYS10.9300.96435.508-7.937-7.9370.0000.0000.0000.000
122H123GLY00.0240.02037.2950.1960.1960.0000.0000.0000.000
123H124PRO0-0.015-0.01437.484-0.121-0.1210.0000.0000.0000.000
124H125SER0-0.021-0.00239.529-0.196-0.1960.0000.0000.0000.000
125H126VAL00.0350.01841.2010.0460.0460.0000.0000.0000.000
126H127PHE0-0.022-0.01443.759-0.214-0.2140.0000.0000.0000.000
127H128PRO0-0.027-0.01045.9440.1060.1060.0000.0000.0000.000
128H129LEU00.0140.01144.550-0.140-0.1400.0000.0000.0000.000
129H130ALA00.0110.01148.581-0.083-0.0830.0000.0000.0000.000
130H131PRO00.0090.01050.4110.0720.0720.0000.0000.0000.000
131H144GLY00.0620.03243.6140.0020.0020.0000.0000.0000.000
132H201CYS0-0.134-0.07040.550-0.212-0.2120.0000.0000.0000.000
133H146LEU00.0300.01441.0450.1180.1180.0000.0000.0000.000
134H147VAL0-0.021-0.00936.931-0.126-0.1260.0000.0000.0000.000
135H148LYS10.9030.94438.839-7.290-7.2900.0000.0000.0000.000
136H149ASP-1-0.902-0.95138.9537.5647.5640.0000.0000.0000.000
137H150TYR0-0.024-0.03631.985-0.197-0.1970.0000.0000.0000.000
138H151PHE00.0360.03430.9910.2110.2110.0000.0000.0000.000
139H152PRO00.0380.00728.837-0.216-0.2160.0000.0000.0000.000
140H153GLU-1-0.827-0.90027.79010.42110.4210.0000.0000.0000.000
141H154PRO0-0.004-0.00426.0690.2320.2320.0000.0000.0000.000
142H155VAL00.014-0.01828.986-0.148-0.1480.0000.0000.0000.000
143H156THR0-0.028-0.01030.2360.1270.1270.0000.0000.0000.000
144H157VAL0-0.011-0.01332.020-0.226-0.2260.0000.0000.0000.000
145H158SER00.0080.01433.8630.1220.1220.0000.0000.0000.000
146H159TRP00.0240.00036.410-0.294-0.2940.0000.0000.0000.000
147H160ASN00.0170.02039.4340.2520.2520.0000.0000.0000.000
148H161SER00.0130.01537.8570.0790.0790.0000.0000.0000.000
149H169HIS00.0300.02834.1480.2120.2120.0000.0000.0000.000
150H170THR0-0.047-0.04333.530-0.344-0.3440.0000.0000.0000.000
151H171PHE00.0040.00633.2010.2760.2760.0000.0000.0000.000
152H172PRO00.0350.00430.055-0.027-0.0270.0000.0000.0000.000
153H173ALA0-0.0080.00831.930-0.311-0.3110.0000.0000.0000.000
154H174VAL0-0.0110.00632.7800.1940.1940.0000.0000.0000.000
155H175LEU00.009-0.00331.3370.0170.0170.0000.0000.0000.000
156H176GLN0-0.036-0.02934.422-0.273-0.2730.0000.0000.0000.000
157H177SER00.0270.00937.1720.1020.1020.0000.0000.0000.000
158H178SER0-0.026-0.01339.6060.0140.0140.0000.0000.0000.000
159H179GLY00.0130.00835.3310.0250.0250.0000.0000.0000.000
160H180LEU0-0.062-0.02034.5460.2180.2180.0000.0000.0000.000
161H181TYR00.0730.04229.2670.0510.0510.0000.0000.0000.000
162H182SER0-0.051-0.03935.369-0.341-0.3410.0000.0000.0000.000
163H183LEU00.0340.04132.9100.0400.0400.0000.0000.0000.000
164H184SER00.0320.01036.550-0.344-0.3440.0000.0000.0000.000
165H185SER0-0.022-0.02137.2120.1870.1870.0000.0000.0000.000
166H186VAL00.0190.01339.063-0.245-0.2450.0000.0000.0000.000
167H187VAL00.0290.02540.2920.1020.1020.0000.0000.0000.000
168H202ASN0-0.047-0.04537.7470.0440.0440.0000.0000.0000.000
169H203VAL0-0.005-0.00336.9300.2830.2830.0000.0000.0000.000
170H204ASN0-0.026-0.01334.320-0.140-0.1400.0000.0000.0000.000
171H205HIS00.000-0.01832.4000.0860.0860.0000.0000.0000.000
172H206LYS10.9700.96728.578-11.012-11.0120.0000.0000.0000.000
173H207PRO00.0220.02229.327-0.074-0.0740.0000.0000.0000.000
174H208SER00.0280.01931.761-0.153-0.1530.0000.0000.0000.000
175H209ASN0-0.077-0.03133.880-0.175-0.1750.0000.0000.0000.000
176H210THR0-0.040-0.01136.141-0.301-0.3010.0000.0000.0000.000
177H211LYS10.9650.97735.909-8.561-8.5610.0000.0000.0000.000
178H212VAL00.0200.01739.382-0.195-0.1950.0000.0000.0000.000
179H213ASP-1-0.833-0.89941.5867.8597.8590.0000.0000.0000.000
180H214LYS10.8630.92443.687-6.883-6.8830.0000.0000.0000.000