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: 49K5N

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1649372.2365
FMO2-HF: Nuclear repulsion 1578920.025409
FMO2-HF: Total energy -70452.211091
FMO2-MP2: Total energy -70658.119096


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.
-7.268-2.5310.533-2.216-3.055-0.009
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 : -0.014 / q_NPA : -0.018
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].
3L4LEU0-0.022-0.0143.8030.9662.255-0.027-0.622-0.6400.000
4L5THR0-0.050-0.0306.8530.2730.2730.0000.0000.0000.000
5L6GLN00.017-0.0169.784-0.257-0.2570.0000.0000.0000.000
6L7PRO0-0.0120.01213.1060.0950.0950.0000.0000.0000.000
7L8PRO00.0950.05416.071-0.070-0.0700.0000.0000.0000.000
8L9SER0-0.006-0.00417.110-0.042-0.0420.0000.0000.0000.000
9L10ALA00.0030.00420.6890.0170.0170.0000.0000.0000.000
10L11SER00.0070.00722.968-0.010-0.0100.0000.0000.0000.000
11L12GLY00.0110.01026.7320.0040.0040.0000.0000.0000.000
12L13THR0-0.027-0.02529.686-0.004-0.0040.0000.0000.0000.000
13L14PRO00.017-0.01933.004-0.003-0.0030.0000.0000.0000.000
14L15GLY00.0480.04233.4020.0030.0030.0000.0000.0000.000
15L16GLN0-0.0100.02430.6680.0000.0000.0000.0000.0000.000
16L17ARG10.9230.94526.2590.0400.0400.0000.0000.0000.000
17L18VAL00.0060.01824.6680.0150.0150.0000.0000.0000.000
18L19THR0-0.036-0.03121.974-0.016-0.0160.0000.0000.0000.000
19L20ILE0-0.0130.00016.7550.0280.0280.0000.0000.0000.000
20L21SER00.0090.01016.302-0.045-0.0450.0000.0000.0000.000
21L22CYS0-0.055-0.03311.372-0.001-0.0010.0000.0000.0000.000
22L23SER00.0100.00510.246-0.080-0.0800.0000.0000.0000.000
23L24GLY00.0940.0347.313-0.171-0.1710.0000.0000.0000.000
24L25SER0-0.048-0.0276.3490.5630.5630.0000.0000.0000.000
25L26LEU00.012-0.0138.214-0.267-0.2670.0000.0000.0000.000
26L27SER0-0.0050.0096.2970.0610.0610.0000.0000.0000.000
27L28ASN00.0890.0564.1790.0790.159-0.001-0.011-0.0680.000
28L29ILE00.012-0.0037.3380.1040.1040.0000.0000.0000.000
29L30GLY0-0.071-0.05010.4060.0560.0560.0000.0000.0000.000
30L31LEU0-0.045-0.00511.4210.0910.0910.0000.0000.0000.000
31L32ASN0-0.0170.0109.5670.0320.0320.0000.0000.0000.000
32L33TYR0-0.033-0.02212.4770.1300.1300.0000.0000.0000.000
33L34VAL00.0300.01712.111-0.110-0.1100.0000.0000.0000.000
34L35SER0-0.059-0.02012.8850.0950.0950.0000.0000.0000.000
35L36TRP00.0180.00213.789-0.084-0.0840.0000.0000.0000.000
36L37TYR00.014-0.00813.3030.0580.0580.0000.0000.0000.000
37L38GLN0-0.005-0.00617.3100.0140.0140.0000.0000.0000.000
38L39GLN00.007-0.01417.918-0.049-0.0490.0000.0000.0000.000
39L40LEU00.0290.02020.7610.0290.0290.0000.0000.0000.000
40L41PRO00.0460.01823.758-0.020-0.0200.0000.0000.0000.000
41L42GLY00.0110.01924.1450.0100.0100.0000.0000.0000.000
42L43THR0-0.074-0.03924.003-0.006-0.0060.0000.0000.0000.000
43L44ALA00.0370.01720.797-0.017-0.0170.0000.0000.0000.000
44L45PRO0-0.0040.00316.5070.0310.0310.0000.0000.0000.000
45L46LYS10.9580.98819.3530.2440.2440.0000.0000.0000.000
46L47LEU0-0.010-0.01717.684-0.011-0.0110.0000.0000.0000.000
47L48LEU0-0.067-0.01419.4280.0460.0460.0000.0000.0000.000
48L49ILE0-0.009-0.02018.6020.0400.0400.0000.0000.0000.000
49L50SER00.0180.01817.783-0.075-0.0750.0000.0000.0000.000
50L51ARG10.9740.97217.2710.4150.4150.0000.0000.0000.000
51L52ASN00.0380.02416.5440.0120.0120.0000.0000.0000.000
52L53ASN0-0.026-0.01918.2930.0050.0050.0000.0000.0000.000
53L54GLN0-0.043-0.00421.4070.0350.0350.0000.0000.0000.000
54L55ARG10.9130.96222.3640.1540.1540.0000.0000.0000.000
55L56PRO00.0200.02423.2230.0150.0150.0000.0000.0000.000
56L57SER00.026-0.01026.0780.0140.0140.0000.0000.0000.000
57L58GLY00.0290.01829.207-0.004-0.0040.0000.0000.0000.000
58L59VAL0-0.083-0.02024.3210.0090.0090.0000.0000.0000.000
59L60PRO0-0.0010.00327.6760.0050.0050.0000.0000.0000.000
60L61ASP-1-0.894-0.97028.503-0.125-0.1250.0000.0000.0000.000
61L62ARG10.7770.88929.5650.1200.1200.0000.0000.0000.000
62L63PHE00.0080.00123.9020.0050.0050.0000.0000.0000.000
63L64SER0-0.010-0.01624.3410.0000.0000.0000.0000.0000.000
64L65GLY00.0020.02220.2870.0130.0130.0000.0000.0000.000
65L66SER0-0.029-0.02219.5620.0180.0180.0000.0000.0000.000
66L67LYS10.8740.92414.2470.3670.3670.0000.0000.0000.000
67L68SER0-0.0050.00517.0740.0030.0030.0000.0000.0000.000
68L69GLY00.0200.02016.3190.0430.0430.0000.0000.0000.000
69L70THR00.012-0.00510.913-0.085-0.0850.0000.0000.0000.000
70L71SER0-0.030-0.00311.4840.0740.0740.0000.0000.0000.000
71L72ALA00.018-0.00313.552-0.051-0.0510.0000.0000.0000.000
72L73SER0-0.031-0.02115.3610.0460.0460.0000.0000.0000.000
73L74LEU00.0220.01818.018-0.039-0.0390.0000.0000.0000.000
74L75ALA0-0.028-0.00919.9860.0310.0310.0000.0000.0000.000
75L76ILE00.0370.01322.777-0.020-0.0200.0000.0000.0000.000
76L77SER00.0010.00026.1490.0230.0230.0000.0000.0000.000
77L78GLY00.0340.02229.667-0.007-0.0070.0000.0000.0000.000
78L79LEU0-0.045-0.00627.516-0.010-0.0100.0000.0000.0000.000
79L80ARG10.9180.94630.3690.1070.1070.0000.0000.0000.000
80L81SER00.0300.00530.564-0.002-0.0020.0000.0000.0000.000
81L82GLU-1-0.844-0.90630.253-0.116-0.1160.0000.0000.0000.000
82L83ASP-1-0.784-0.88526.580-0.135-0.1350.0000.0000.0000.000
83L84GLU-1-0.860-0.91525.512-0.078-0.0780.0000.0000.0000.000
84L85ALA0-0.005-0.00322.848-0.008-0.0080.0000.0000.0000.000
85L86ASP-1-0.807-0.87318.109-0.138-0.1380.0000.0000.0000.000
86L87TYR0-0.073-0.06117.848-0.048-0.0480.0000.0000.0000.000
87L88TYR00.0360.04212.6180.0480.0480.0000.0000.0000.000
88L90ALA00.0260.0009.158-0.140-0.1400.0000.0000.0000.000
89L91ALA00.020-0.0018.0190.4390.4390.0000.0000.0000.000
90L92TRP00.0340.0496.830-0.706-0.7060.0000.0000.0000.000
91L93ASP-1-0.818-0.9433.044-4.418-2.8240.143-0.890-0.847-0.009
92L94ASP-1-0.853-0.9165.834-0.951-0.9510.0000.0000.0000.000
93L95SER0-0.028-0.0346.792-0.031-0.0310.0000.0000.0000.000
94L96PRO0-0.077-0.0132.471-0.6400.6470.415-0.615-1.0880.000
95L97PRO00.003-0.0104.316-1.808-1.651-0.001-0.019-0.1370.000
96L98GLY00.0130.0145.531-0.046-0.0460.0000.0000.0000.000
97L99GLU-1-0.914-0.9525.905-1.772-1.7720.0000.0000.0000.000
98L100ALA0-0.0010.0013.539-1.251-1.0190.005-0.052-0.1850.000
99L101PHE00.017-0.0054.6101.5131.611-0.001-0.007-0.0900.000
100L102GLY00.0330.0336.595-0.091-0.0910.0000.0000.0000.000
101L103GLY0-0.036-0.0169.237-0.027-0.0270.0000.0000.0000.000
102L104GLY00.0060.00310.647-0.032-0.0320.0000.0000.0000.000
103L105THR0-0.067-0.04014.0550.0820.0820.0000.0000.0000.000
104L106LYS10.8690.90717.2420.0640.0640.0000.0000.0000.000
105L107LEU0-0.042-0.01920.5780.0330.0330.0000.0000.0000.000
106L108THR0-0.041-0.02923.317-0.007-0.0070.0000.0000.0000.000
107L109VAL0-0.005-0.01026.6770.0110.0110.0000.0000.0000.000
108L110LEU00.0280.00329.8240.0000.0000.0000.0000.0000.000
109L111GLY00.0030.00332.806-0.007-0.0070.0000.0000.0000.000
110L112GLN0-0.036-0.01335.9150.0040.0040.0000.0000.0000.000
111L113PRO00.0060.01137.3410.0050.0050.0000.0000.0000.000
112L114LYS10.8240.90234.609-0.046-0.0460.0000.0000.0000.000
113L115ALA0-0.0120.00437.7540.0000.0000.0000.0000.0000.000
114L116ALA0-0.009-0.02337.8980.0030.0030.0000.0000.0000.000
115L117PRO0-0.0180.01036.419-0.003-0.0030.0000.0000.0000.000
116L118SER0-0.004-0.01238.9220.0030.0030.0000.0000.0000.000
117L119VAL0-0.035-0.01739.021-0.003-0.0030.0000.0000.0000.000
118L120THR0-0.0010.00541.172-0.001-0.0010.0000.0000.0000.000
119L121LEU0-0.033-0.02040.636-0.001-0.0010.0000.0000.0000.000
120L122PHE00.002-0.00642.786-0.001-0.0010.0000.0000.0000.000
121L123PRO0-0.019-0.02443.7310.0020.0020.0000.0000.0000.000
122L124PRO00.0100.01443.693-0.003-0.0030.0000.0000.0000.000
123L125SER00.0100.00445.045-0.001-0.0010.0000.0000.0000.000
124L126SER00.004-0.00647.5460.0010.0010.0000.0000.0000.000
125L127GLU-1-0.870-0.92349.4550.0000.0000.0000.0000.0000.000
126L128GLU-1-0.787-0.86342.4480.0100.0100.0000.0000.0000.000
127L129LEU0-0.031-0.01747.0140.0020.0020.0000.0000.0000.000
128L130GLN0-0.114-0.05348.5380.0030.0030.0000.0000.0000.000
129L131ALA0-0.009-0.01046.899-0.001-0.0010.0000.0000.0000.000
130L132ASN0-0.047-0.02545.4430.0000.0000.0000.0000.0000.000
131L133LYS10.8700.93038.025-0.026-0.0260.0000.0000.0000.000
132L134ALA00.021-0.01042.494-0.001-0.0010.0000.0000.0000.000
133L135THR0-0.084-0.05138.4160.0040.0040.0000.0000.0000.000
134L136LEU0-0.0050.00139.404-0.002-0.0020.0000.0000.0000.000
135L137VAL00.0330.01438.584-0.001-0.0010.0000.0000.0000.000
136L138CYS0-0.038-0.00336.964-0.001-0.0010.0000.0000.0000.000
137L139LEU00.0270.01336.981-0.001-0.0010.0000.0000.0000.000
138L140ILE00.000-0.01033.5770.0030.0030.0000.0000.0000.000
139L141SER00.0410.00536.740-0.008-0.0080.0000.0000.0000.000
140L142ASP-1-0.800-0.88138.187-0.013-0.0130.0000.0000.0000.000
141L143PHE00.0120.01531.5830.0050.0050.0000.0000.0000.000
142L144TYR00.0020.01532.601-0.007-0.0070.0000.0000.0000.000
143L145PRO00.037-0.00430.0600.0040.0040.0000.0000.0000.000
144L146GLY00.034-0.00529.9620.0070.0070.0000.0000.0000.000
145L147ALA0-0.043-0.02427.757-0.001-0.0010.0000.0000.0000.000
146L148VAL0-0.0130.00128.9990.0050.0050.0000.0000.0000.000
147L149THR0-0.0030.01827.2370.0010.0010.0000.0000.0000.000
148L150VAL00.0320.03029.9970.0040.0040.0000.0000.0000.000
149L164GLU-1-0.910-0.96028.8970.0400.0400.0000.0000.0000.000
150L165THR0-0.055-0.02528.366-0.001-0.0010.0000.0000.0000.000
151L166THR00.0000.01527.6190.0030.0030.0000.0000.0000.000
152L167THR00.0390.01923.7660.0080.0080.0000.0000.0000.000
153L168PRO0-0.031-0.03226.577-0.007-0.0070.0000.0000.0000.000
154L169SER0-0.021-0.00628.615-0.014-0.0140.0000.0000.0000.000
155L170LYS10.8770.93630.7360.0830.0830.0000.0000.0000.000
156L171GLN0-0.030-0.03032.502-0.004-0.0040.0000.0000.0000.000
157L172SER00.0510.01236.101-0.003-0.0030.0000.0000.0000.000
158L173ASN0-0.032-0.01738.675-0.002-0.0020.0000.0000.0000.000
159L174ASN0-0.032-0.02036.3540.0000.0000.0000.0000.0000.000
160L175LYS10.8390.94835.9530.0250.0250.0000.0000.0000.000
161L176TYR0-0.0030.00329.347-0.010-0.0100.0000.0000.0000.000
162L177ALA00.0190.01033.4780.0060.0060.0000.0000.0000.000
163L178ALA0-0.014-0.01331.709-0.003-0.0030.0000.0000.0000.000
164L179SER00.0210.01632.534-0.003-0.0030.0000.0000.0000.000
165L180SER0-0.044-0.02532.2690.0020.0020.0000.0000.0000.000
166L181TYR00.0360.01633.176-0.003-0.0030.0000.0000.0000.000
167L182LEU00.0280.01333.9770.0070.0070.0000.0000.0000.000
168L183SER00.0530.02234.974-0.006-0.0060.0000.0000.0000.000
169L184LEU0-0.025-0.01036.7650.0070.0070.0000.0000.0000.000
170L185THR0-0.016-0.02239.437-0.003-0.0030.0000.0000.0000.000
171L186PRO00.0820.03442.5430.0020.0020.0000.0000.0000.000
172L187GLU-1-0.820-0.90345.4190.0350.0350.0000.0000.0000.000
173L188GLN0-0.0130.00341.7000.0030.0030.0000.0000.0000.000
174L189TRP00.0670.04044.6600.0030.0030.0000.0000.0000.000
175L190LYS10.8080.90945.595-0.033-0.0330.0000.0000.0000.000
176L191SER00.0110.01246.1540.0000.0000.0000.0000.0000.000
177L192HIS0-0.018-0.01044.0590.0010.0010.0000.0000.0000.000
178L193ARG10.8670.92747.889-0.043-0.0430.0000.0000.0000.000
179L194SER0-0.010-0.00844.5510.0010.0010.0000.0000.0000.000
180L195TYR00.0570.03144.559-0.003-0.0030.0000.0000.0000.000
181L196SER00.0020.00141.0090.0020.0020.0000.0000.0000.000
182L197CYS00.0190.00840.117-0.001-0.0010.0000.0000.0000.000
183L198GLN0-0.011-0.00136.2510.0010.0010.0000.0000.0000.000
184L199VAL00.0560.01134.796-0.003-0.0030.0000.0000.0000.000
185L200THR0-0.052-0.01932.4630.0030.0030.0000.0000.0000.000
186L201HIS10.8750.93032.582-0.035-0.0350.0000.0000.0000.000
187L202GLU-1-0.820-0.89431.3030.0440.0440.0000.0000.0000.000
188L203GLY00.0530.03133.988-0.004-0.0040.0000.0000.0000.000
189L204SER0-0.045-0.02036.843-0.005-0.0050.0000.0000.0000.000