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: K9ZJ3

Calculation Name: 5CUS-L-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: L

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1647831.026381
FMO2-HF: Nuclear repulsion 1577379.445879
FMO2-HF: Total energy -70451.580502
FMO2-MP2: Total energy -70657.468373


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(L:2:SER)


Summations of interaction energy for fragment #1(L:2:SER)
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.
-11.298-6.21.196-2.825-3.47-0.003
Interaction energy analysis for fragmet #1(L:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.006
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].
3L4LEU0-0.027-0.0223.803-1.1440.505-0.031-0.855-0.7630.003
4L5THR0-0.044-0.0236.8620.5520.5520.0000.0000.0000.000
5L6GLN00.008-0.0379.810-0.225-0.2250.0000.0000.0000.000
6L7PRO0-0.0120.01213.1260.1040.1040.0000.0000.0000.000
7L8PRO00.0930.05215.832-0.033-0.0330.0000.0000.0000.000
8L9SER0-0.038-0.02017.176-0.016-0.0160.0000.0000.0000.000
9L10ALA00.0380.02120.689-0.013-0.0130.0000.0000.0000.000
10L11SER00.0020.00822.9680.0070.0070.0000.0000.0000.000
11L12GLY00.0170.01226.732-0.009-0.0090.0000.0000.0000.000
12L13THR0-0.023-0.01329.6860.0050.0050.0000.0000.0000.000
13L14PRO00.015-0.01733.004-0.007-0.0070.0000.0000.0000.000
14L15GLY00.0470.04233.4140.0030.0030.0000.0000.0000.000
15L16GLN0-0.0180.00830.2890.0020.0020.0000.0000.0000.000
16L17ARG10.9320.95226.0100.1390.1390.0000.0000.0000.000
17L18VAL00.0040.01724.6660.0080.0080.0000.0000.0000.000
18L19THR0-0.047-0.03822.015-0.016-0.0160.0000.0000.0000.000
19L20ILE00.0000.00616.7130.0270.0270.0000.0000.0000.000
20L21SER0-0.014-0.00216.442-0.044-0.0440.0000.0000.0000.000
21L22CYS0-0.049-0.03011.181-0.032-0.0320.0000.0000.0000.000
22L23SER0-0.004-0.00210.472-0.115-0.1150.0000.0000.0000.000
23L24GLY00.1170.0397.322-0.142-0.1420.0000.0000.0000.000
24L25SER0-0.057-0.0356.4180.2780.2780.0000.0000.0000.000
25L26LEU00.014-0.0118.212-0.125-0.1250.0000.0000.0000.000
26L27SER0-0.0070.0046.2580.2400.2400.0000.0000.0000.000
27L28ASN00.1320.1164.5280.6410.698-0.001-0.004-0.0520.000
28L29ILE00.023-0.0117.5020.4320.4320.0000.0000.0000.000
29L30GLY0-0.086-0.05610.3760.2120.2120.0000.0000.0000.000
30L31LEU0-0.053-0.00711.6000.2150.2150.0000.0000.0000.000
31L32ASN00.0150.0269.8520.2210.2210.0000.0000.0000.000
32L33TYR0-0.070-0.03812.5610.1190.1190.0000.0000.0000.000
33L34VAL00.0410.01912.338-0.123-0.1230.0000.0000.0000.000
34L35SER0-0.064-0.02512.6480.1580.1580.0000.0000.0000.000
35L36TRP00.0350.01013.601-0.066-0.0660.0000.0000.0000.000
36L37TYR00.016-0.00812.6690.0920.0920.0000.0000.0000.000
37L38GLN00.0100.01217.0860.0130.0130.0000.0000.0000.000
38L39GLN00.017-0.00318.103-0.013-0.0130.0000.0000.0000.000
39L40LEU00.0320.02520.9180.0240.0240.0000.0000.0000.000
40L41PRO00.0300.02923.8810.0030.0030.0000.0000.0000.000
41L42GLY00.0100.01824.228-0.001-0.0010.0000.0000.0000.000
42L43THR0-0.071-0.05824.103-0.011-0.0110.0000.0000.0000.000
43L44ALA00.0300.00720.9390.0060.0060.0000.0000.0000.000
44L45PRO0-0.007-0.00116.7060.0000.0000.0000.0000.0000.000
45L46LYS10.9860.99619.5320.1670.1670.0000.0000.0000.000
46L47LEU0-0.017-0.01717.493-0.017-0.0170.0000.0000.0000.000
47L48LEU0-0.065-0.01419.1900.0330.0330.0000.0000.0000.000
48L49ILE0-0.013-0.01618.4270.0220.0220.0000.0000.0000.000
49L50SER00.0250.01617.635-0.060-0.0600.0000.0000.0000.000
50L51ARG10.9830.97417.1580.4550.4550.0000.0000.0000.000
51L52ASN00.0370.02716.438-0.010-0.0100.0000.0000.0000.000
52L53ASN0-0.034-0.03218.2450.0140.0140.0000.0000.0000.000
53L54GLN0-0.0230.01321.3150.0570.0570.0000.0000.0000.000
54L55ARG10.9140.96222.2230.1920.1920.0000.0000.0000.000
55L56PRO00.0210.02723.0100.0130.0130.0000.0000.0000.000
56L57SER00.031-0.01025.8910.0100.0100.0000.0000.0000.000
57L58GLY00.0200.01328.9720.0060.0060.0000.0000.0000.000
58L59VAL0-0.095-0.02324.0910.0120.0120.0000.0000.0000.000
59L60PRO0-0.005-0.00127.462-0.002-0.0020.0000.0000.0000.000
60L61ASP-1-0.903-0.97328.325-0.150-0.1500.0000.0000.0000.000
61L62ARG10.8110.91529.2320.1110.1110.0000.0000.0000.000
62L63PHE00.0040.00423.777-0.004-0.0040.0000.0000.0000.000
63L64SER0-0.016-0.01724.3940.0000.0000.0000.0000.0000.000
64L65GLY00.0180.02320.1850.0060.0060.0000.0000.0000.000
65L66SER0-0.026-0.01919.5400.0140.0140.0000.0000.0000.000
66L67LYS10.9070.94014.4950.7960.7960.0000.0000.0000.000
67L68SER0-0.037-0.00817.0550.0310.0310.0000.0000.0000.000
68L69GLY00.0500.03416.3080.0170.0170.0000.0000.0000.000
69L70THR00.003-0.00710.909-0.044-0.0440.0000.0000.0000.000
70L71SER0-0.023-0.00311.484-0.002-0.0020.0000.0000.0000.000
71L72ALA00.011-0.00413.5500.0080.0080.0000.0000.0000.000
72L73SER0-0.036-0.02315.3520.0490.0490.0000.0000.0000.000
73L74LEU00.0250.02318.014-0.023-0.0230.0000.0000.0000.000
74L75ALA0-0.043-0.02119.9790.0360.0360.0000.0000.0000.000
75L76ILE00.0460.02022.994-0.010-0.0100.0000.0000.0000.000
76L77SER0-0.012-0.00326.1440.0210.0210.0000.0000.0000.000
77L78GLY00.0300.01729.662-0.002-0.0020.0000.0000.0000.000
78L79LEU0-0.049-0.01027.347-0.004-0.0040.0000.0000.0000.000
79L80ARG10.9580.96830.3830.0980.0980.0000.0000.0000.000
80L81SER00.0160.00030.564-0.003-0.0030.0000.0000.0000.000
81L82GLU-1-0.863-0.92830.161-0.085-0.0850.0000.0000.0000.000
82L83ASP-1-0.813-0.90826.602-0.114-0.1140.0000.0000.0000.000
83L84GLU-1-0.935-0.97125.512-0.018-0.0180.0000.0000.0000.000
84L85ALA0-0.020-0.01422.8490.0040.0040.0000.0000.0000.000
85L86ASP-1-0.887-0.92618.1050.0160.0160.0000.0000.0000.000
86L87TYR0-0.056-0.05017.848-0.045-0.0450.0000.0000.0000.000
87L88TYR00.0220.03612.4240.0280.0280.0000.0000.0000.000
88L90ALA00.0340.0028.949-0.062-0.0620.0000.0000.0000.000
89L91ALA00.008-0.0067.8480.3420.3420.0000.0000.0000.000
90L92TRP00.0280.0466.741-0.635-0.6350.0000.0000.0000.000
91L93ASP-1-0.867-0.9733.239-10.774-8.9720.076-1.014-0.864-0.008
92L94ASP-1-0.865-0.9295.958-1.139-1.1390.0000.0000.0000.000
93L95SER0-0.055-0.0465.9690.3510.3510.0000.0000.0000.000
94L96PRO0-0.063-0.0212.1130.2541.3411.148-0.859-1.3760.002
95L97PRO00.000-0.0024.204-1.681-1.527-0.001-0.030-0.1230.000
96L98GLY00.0160.0165.5240.6670.6670.0000.0000.0000.000
97L99GLU-1-0.921-0.9535.793-2.211-2.2110.0000.0000.0000.000
98L100ALA0-0.0010.0003.532-0.748-0.4930.006-0.054-0.2070.000
99L101PHE00.013-0.0054.3931.2271.321-0.001-0.009-0.0850.000
100L102GLY00.0350.0326.595-0.084-0.0840.0000.0000.0000.000
101L103GLY0-0.040-0.0189.2370.1540.1540.0000.0000.0000.000
102L104GLY00.0110.00910.7630.0240.0240.0000.0000.0000.000
103L105THR0-0.069-0.03114.0550.0270.0270.0000.0000.0000.000
104L106LYS10.9580.97917.242-0.082-0.0820.0000.0000.0000.000
105L107LEU0-0.040-0.02020.5780.0100.0100.0000.0000.0000.000
106L108THR0-0.036-0.02623.3170.0070.0070.0000.0000.0000.000
107L109VAL0-0.016-0.01026.677-0.003-0.0030.0000.0000.0000.000
108L110LEU00.0260.01029.8240.0060.0060.0000.0000.0000.000
109L111GLY00.0080.00032.806-0.003-0.0030.0000.0000.0000.000
110L112GLN0-0.035-0.01535.8700.0020.0020.0000.0000.0000.000
111L113PRO00.0010.01037.3450.0020.0020.0000.0000.0000.000
112L114LYS10.8270.90835.124-0.047-0.0470.0000.0000.0000.000
113L115ALA0-0.028-0.01038.058-0.001-0.0010.0000.0000.0000.000
114L116ALA0-0.012-0.02238.2480.0040.0040.0000.0000.0000.000
115L117PRO0-0.0160.00936.857-0.003-0.0030.0000.0000.0000.000
116L118SER00.001-0.00739.3820.0000.0000.0000.0000.0000.000
117L119VAL0-0.029-0.01539.4550.0010.0010.0000.0000.0000.000
118L120THR00.0050.00741.762-0.005-0.0050.0000.0000.0000.000
119L121LEU0-0.040-0.02041.3210.0030.0030.0000.0000.0000.000
120L122PHE0-0.006-0.00643.478-0.004-0.0040.0000.0000.0000.000
121L123PRO0-0.020-0.02744.4510.0050.0050.0000.0000.0000.000
122L124PRO00.0420.01944.761-0.002-0.0020.0000.0000.0000.000
123L125SER00.0220.03346.037-0.005-0.0050.0000.0000.0000.000
124L126SER00.010-0.00648.3490.0010.0010.0000.0000.0000.000
125L127GLU-1-0.866-0.91750.3540.0540.0540.0000.0000.0000.000
126L128GLU-1-0.813-0.87843.2190.0850.0850.0000.0000.0000.000
127L129LEU0-0.036-0.02147.8660.0020.0020.0000.0000.0000.000
128L130GLN0-0.114-0.05149.3630.0000.0000.0000.0000.0000.000
129L131ALA0-0.011-0.01147.663-0.001-0.0010.0000.0000.0000.000
130L132ASN0-0.034-0.02146.0540.0020.0020.0000.0000.0000.000
131L133LYS10.8550.92438.926-0.106-0.1060.0000.0000.0000.000
132L134ALA00.022-0.01043.305-0.005-0.0050.0000.0000.0000.000
133L135THR0-0.084-0.06538.9640.0030.0030.0000.0000.0000.000
134L136LEU0-0.016-0.00440.161-0.006-0.0060.0000.0000.0000.000
135L137VAL00.0340.01739.3340.0050.0050.0000.0000.0000.000
136L138CYS0-0.025-0.00537.649-0.008-0.0080.0000.0000.0000.000
137L139LEU00.0180.00837.6550.0050.0050.0000.0000.0000.000
138L140ILE00.001-0.00834.254-0.003-0.0030.0000.0000.0000.000
139L141SER00.047-0.00237.345-0.001-0.0010.0000.0000.0000.000
140L142ASP-1-0.886-0.92338.7850.0310.0310.0000.0000.0000.000
141L143PHE0-0.0260.00132.0560.0010.0010.0000.0000.0000.000
142L144TYR0-0.011-0.00132.6900.0000.0000.0000.0000.0000.000
143L145PRO00.0600.01130.319-0.002-0.0020.0000.0000.0000.000
144L146GLY00.041-0.00730.3920.0070.0070.0000.0000.0000.000
145L147ALA0-0.032-0.02128.0830.0080.0080.0000.0000.0000.000
146L148VAL0-0.0120.00229.405-0.004-0.0040.0000.0000.0000.000
147L149THR0-0.048-0.00427.7750.0100.0100.0000.0000.0000.000
148L150VAL00.0650.04030.467-0.005-0.0050.0000.0000.0000.000
149L164GLU-1-0.898-0.95829.5640.1680.1680.0000.0000.0000.000
150L165THR0-0.068-0.03429.104-0.018-0.0180.0000.0000.0000.000
151L166THR0-0.048-0.00728.3370.0090.0090.0000.0000.0000.000
152L167THR00.0150.00224.4190.0020.0020.0000.0000.0000.000
153L168PRO0-0.007-0.01727.071-0.009-0.0090.0000.0000.0000.000
154L169SER00.0060.00529.201-0.004-0.0040.0000.0000.0000.000
155L170LYS10.9570.98431.1150.0050.0050.0000.0000.0000.000
156L171GLN0-0.0010.00032.8730.0010.0010.0000.0000.0000.000
157L172SER00.0400.00536.311-0.003-0.0030.0000.0000.0000.000
158L173ASN0-0.021-0.01438.823-0.007-0.0070.0000.0000.0000.000
159L174ASN0-0.032-0.02036.557-0.002-0.0020.0000.0000.0000.000
160L175LYS10.9210.98736.258-0.018-0.0180.0000.0000.0000.000
161L176TYR0-0.018-0.00529.654-0.001-0.0010.0000.0000.0000.000
162L177ALA00.0510.02134.0610.0000.0000.0000.0000.0000.000
163L178ALA0-0.027-0.01432.3120.0050.0050.0000.0000.0000.000
164L179SER00.0160.01633.206-0.004-0.0040.0000.0000.0000.000
165L180SER0-0.015-0.00732.9920.0080.0080.0000.0000.0000.000
166L181TYR00.0400.02134.016-0.011-0.0110.0000.0000.0000.000
167L182LEU00.0210.01534.7110.0090.0090.0000.0000.0000.000
168L183SER00.0460.01035.517-0.011-0.0110.0000.0000.0000.000
169L184LEU0-0.017-0.00237.5280.0060.0060.0000.0000.0000.000
170L185THR00.0130.00840.205-0.001-0.0010.0000.0000.0000.000
171L186PRO00.0740.03243.321-0.001-0.0010.0000.0000.0000.000
172L187GLU-1-0.849-0.93246.4920.0860.0860.0000.0000.0000.000
173L188GLN0-0.034-0.01342.392-0.002-0.0020.0000.0000.0000.000
174L189TRP00.0390.03345.082-0.001-0.0010.0000.0000.0000.000
175L190LYS10.8750.93746.305-0.071-0.0710.0000.0000.0000.000
176L191SER0-0.0070.00046.808-0.002-0.0020.0000.0000.0000.000
177L192HIS00.0020.00044.633-0.005-0.0050.0000.0000.0000.000
178L193ARG10.8600.92648.499-0.069-0.0690.0000.0000.0000.000
179L194SER0-0.007-0.00745.0050.0000.0000.0000.0000.0000.000
180L195TYR00.0460.03045.172-0.001-0.0010.0000.0000.0000.000
181L196SER00.0000.00041.667-0.002-0.0020.0000.0000.0000.000
182L197CYS00.0030.00440.7490.0030.0030.0000.0000.0000.000
183L198GLN00.0040.00836.804-0.003-0.0030.0000.0000.0000.000
184L199VAL00.023-0.01235.2830.0030.0030.0000.0000.0000.000
185L200THR0-0.0060.00532.724-0.004-0.0040.0000.0000.0000.000
186L201HIS10.8780.93433.217-0.058-0.0580.0000.0000.0000.000
187L202GLU-1-0.832-0.91331.6660.0550.0550.0000.0000.0000.000
188L203GLY00.0290.01234.091-0.007-0.0070.0000.0000.0000.000
189L204SER0-0.0130.01737.207-0.002-0.0020.0000.0000.0000.000