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: 52Q4Z

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1652737.275593
FMO2-HF: Nuclear repulsion 1582284.585203
FMO2-HF: Total energy -70452.69039
FMO2-MP2: Total energy -70658.645434


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.
-5.238-1.4962.607-2.64-3.707-0.002
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 : 0.003 / q_NPA : -0.012
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].
3L4LEU0-0.031-0.0123.8731.9102.928-0.016-0.502-0.5000.001
4L5THR0-0.025-0.0146.950-0.022-0.0220.0000.0000.0000.000
5L6GLN00.035-0.00910.054-0.281-0.2810.0000.0000.0000.000
6L7PRO0-0.0130.01713.3960.0790.0790.0000.0000.0000.000
7L8PRO00.0820.05016.069-0.066-0.0660.0000.0000.0000.000
8L9SER0-0.019-0.01017.120-0.050-0.0500.0000.0000.0000.000
9L10ALA00.0030.00620.7840.0260.0260.0000.0000.0000.000
10L11SER0-0.031-0.03123.121-0.011-0.0110.0000.0000.0000.000
11L12GLY00.0130.01526.9330.0080.0080.0000.0000.0000.000
12L13THR0-0.007-0.01130.051-0.007-0.0070.0000.0000.0000.000
13L14PRO00.013-0.01433.128-0.002-0.0020.0000.0000.0000.000
14L15GLY00.0090.01434.0710.0040.0040.0000.0000.0000.000
15L16GLN00.0090.03130.428-0.002-0.0020.0000.0000.0000.000
16L17ARG10.9170.94926.116-0.007-0.0070.0000.0000.0000.000
17L18VAL0-0.0070.00225.0360.0140.0140.0000.0000.0000.000
18L19THR0-0.024-0.02821.997-0.013-0.0130.0000.0000.0000.000
19L20ILE0-0.0080.00616.8380.0250.0250.0000.0000.0000.000
20L21SER00.0230.01516.281-0.038-0.0380.0000.0000.0000.000
21L22CYS0-0.039-0.02411.173-0.007-0.0070.0000.0000.0000.000
22L23SER0-0.0040.00010.823-0.096-0.0960.0000.0000.0000.000
23L24GLY00.0760.0347.0790.0420.0420.0000.0000.0000.000
24L25SER0-0.051-0.0336.3570.5420.5420.0000.0000.0000.000
25L26LEU00.011-0.0068.273-0.286-0.2860.0000.0000.0000.000
26L27SER00.0020.0046.280-0.114-0.1140.0000.0000.0000.000
27L28ASN00.0800.0573.997-0.177-0.100-0.001-0.011-0.0650.000
28L29ILE0-0.023-0.0157.6130.0070.0070.0000.0000.0000.000
29L30GLY0-0.047-0.02910.2240.0020.0020.0000.0000.0000.000
30L31LEU0-0.0090.01111.4230.0010.0010.0000.0000.0000.000
31L32ASN0-0.039-0.0069.6300.0030.0030.0000.0000.0000.000
32L33TYR0-0.041-0.02812.6730.1320.1320.0000.0000.0000.000
33L34VAL00.0320.02111.925-0.104-0.1040.0000.0000.0000.000
34L35SER0-0.065-0.02312.7990.0640.0640.0000.0000.0000.000
35L36TRP00.0350.00313.990-0.035-0.0350.0000.0000.0000.000
36L37TYR00.008-0.00113.2630.0480.0480.0000.0000.0000.000
37L38GLN00.017-0.00317.6800.0230.0230.0000.0000.0000.000
38L39GLN00.0160.00018.305-0.042-0.0420.0000.0000.0000.000
39L40LEU00.0380.02821.2050.0280.0280.0000.0000.0000.000
40L41PRO00.0310.01124.286-0.021-0.0210.0000.0000.0000.000
41L42GLY00.0210.02324.6080.0080.0080.0000.0000.0000.000
42L43THR0-0.075-0.03924.243-0.010-0.0100.0000.0000.0000.000
43L44ALA00.0460.01920.814-0.015-0.0150.0000.0000.0000.000
44L45PRO0-0.013-0.00116.4670.0340.0340.0000.0000.0000.000
45L46LYS10.9360.97719.2820.1990.1990.0000.0000.0000.000
46L47LEU0-0.004-0.01117.8400.0020.0020.0000.0000.0000.000
47L48LEU0-0.071-0.02219.4810.0420.0420.0000.0000.0000.000
48L49ILE0-0.013-0.01918.7720.0420.0420.0000.0000.0000.000
49L50SER0-0.0010.00517.756-0.066-0.0660.0000.0000.0000.000
50L51ARG10.9590.96017.4070.3310.3310.0000.0000.0000.000
51L52ASN00.0390.01616.3380.0180.0180.0000.0000.0000.000
52L53ASN0-0.017-0.00918.1500.0040.0040.0000.0000.0000.000
53L54GLN0-0.037-0.00221.5120.0200.0200.0000.0000.0000.000
54L55ARG10.9110.95422.2940.1030.1030.0000.0000.0000.000
55L56PRO00.0350.02823.0760.0100.0100.0000.0000.0000.000
56L57SER00.033-0.00625.8950.0140.0140.0000.0000.0000.000
57L58GLY0-0.009-0.00428.9560.0010.0010.0000.0000.0000.000
58L59VAL0-0.064-0.00424.3550.0060.0060.0000.0000.0000.000
59L60PRO00.0060.00527.7150.0030.0030.0000.0000.0000.000
60L61ASP-1-0.849-0.94628.661-0.083-0.0830.0000.0000.0000.000
61L62ARG10.7560.87029.4520.0850.0850.0000.0000.0000.000
62L63PHE0-0.0170.00823.9470.0090.0090.0000.0000.0000.000
63L64SER0-0.016-0.01724.5500.0010.0010.0000.0000.0000.000
64L65GLY00.0340.02320.6070.0050.0050.0000.0000.0000.000
65L66SER0-0.045-0.03219.1740.0220.0220.0000.0000.0000.000
66L67LYS10.8740.92514.0520.1490.1490.0000.0000.0000.000
67L68SER0-0.025-0.00916.476-0.001-0.0010.0000.0000.0000.000
68L69GLY00.0540.03916.1220.0480.0480.0000.0000.0000.000
69L70THR00.0160.00610.773-0.091-0.0910.0000.0000.0000.000
70L71SER0-0.034-0.01911.2680.1010.1010.0000.0000.0000.000
71L72ALA00.0420.00613.582-0.083-0.0830.0000.0000.0000.000
72L73SER0-0.039-0.02015.2850.0520.0520.0000.0000.0000.000
73L74LEU00.0140.03317.898-0.035-0.0350.0000.0000.0000.000
74L75ALA0-0.013-0.01819.8510.0300.0300.0000.0000.0000.000
75L76ILE00.0250.02522.947-0.018-0.0180.0000.0000.0000.000
76L77SER00.003-0.00526.1890.0230.0230.0000.0000.0000.000
77L78GLY00.0290.02129.830-0.008-0.0080.0000.0000.0000.000
78L79LEU0-0.030-0.00727.611-0.011-0.0110.0000.0000.0000.000
79L80ARG10.8830.91730.5830.0790.0790.0000.0000.0000.000
80L81SER00.0640.02130.761-0.001-0.0010.0000.0000.0000.000
81L82GLU-1-0.857-0.89530.165-0.096-0.0960.0000.0000.0000.000
82L83ASP-1-0.781-0.88226.714-0.099-0.0990.0000.0000.0000.000
83L84GLU-1-0.812-0.87125.811-0.057-0.0570.0000.0000.0000.000
84L85ALA0-0.004-0.00223.248-0.011-0.0110.0000.0000.0000.000
85L86ASP-1-0.791-0.85918.528-0.105-0.1050.0000.0000.0000.000
86L87TYR0-0.064-0.04418.061-0.042-0.0420.0000.0000.0000.000
87L88TYR00.0140.01012.8350.0520.0520.0000.0000.0000.000
88L90ALA00.0140.0009.336-0.128-0.1280.0000.0000.0000.000
89L91ALA00.0220.0038.1800.4090.4090.0000.0000.0000.000
90L92TRP00.0340.0456.979-0.661-0.6610.0000.0000.0000.000
91L93ASP-1-0.817-0.9413.466-1.828-0.8690.037-0.474-0.521-0.003
92L94ASP-1-0.829-0.9126.004-0.984-0.9840.0000.0000.0000.000
93L95SER0-0.058-0.0386.9320.3100.3100.0000.0000.0000.000
94L96PRO0-0.069-0.0111.982-1.422-0.3342.582-1.506-2.1640.000
95L97PRO0-0.031-0.0264.027-2.137-1.870-0.001-0.082-0.1840.000
96L98GLY00.0430.0295.558-0.075-0.0750.0000.0000.0000.000
97L99GLU-1-0.904-0.9546.020-1.339-1.3390.0000.0000.0000.000
98L100ALA00.0050.0103.563-1.042-0.8120.007-0.058-0.1780.000
99L101PHE00.010-0.0124.6651.4771.580-0.001-0.007-0.0950.000
100L102GLY00.0200.0086.605-0.137-0.1370.0000.0000.0000.000
101L103GLY0-0.044-0.0219.168-0.067-0.0670.0000.0000.0000.000
102L104GLY0-0.0080.00410.780-0.014-0.0140.0000.0000.0000.000
103L105THR0-0.065-0.05114.1800.0860.0860.0000.0000.0000.000
104L106LYS10.8640.90817.5980.0520.0520.0000.0000.0000.000
105L107LEU0-0.044-0.01620.9450.0350.0350.0000.0000.0000.000
106L108THR0-0.004-0.01023.681-0.013-0.0130.0000.0000.0000.000
107L109VAL0-0.0050.00026.8920.0120.0120.0000.0000.0000.000
108L110LEU00.0030.00029.8730.0000.0000.0000.0000.0000.000
109L111GLY00.011-0.01133.108-0.007-0.0070.0000.0000.0000.000
110L112GLN0-0.0070.00936.2480.0020.0020.0000.0000.0000.000
111L113PRO00.0010.00837.4720.0050.0050.0000.0000.0000.000
112L114LYS10.8060.88734.673-0.050-0.0500.0000.0000.0000.000
113L115ALA00.0000.01437.7610.0000.0000.0000.0000.0000.000
114L116ALA00.013-0.01637.9270.0030.0030.0000.0000.0000.000
115L117PRO00.0040.01236.955-0.003-0.0030.0000.0000.0000.000
116L118SER00.0200.00639.1950.0020.0020.0000.0000.0000.000
117L119VAL0-0.056-0.03139.181-0.004-0.0040.0000.0000.0000.000
118L120THR0-0.0060.00841.3210.0000.0000.0000.0000.0000.000
119L121LEU0-0.036-0.02241.241-0.001-0.0010.0000.0000.0000.000
120L122PHE00.002-0.00243.308-0.001-0.0010.0000.0000.0000.000
121L123PRO0-0.013-0.02544.0570.0010.0010.0000.0000.0000.000
122L124PRO00.0100.02043.865-0.002-0.0020.0000.0000.0000.000
123L125SER0-0.010-0.01045.3110.0000.0000.0000.0000.0000.000
124L126SER0-0.017-0.02247.7890.0000.0000.0000.0000.0000.000
125L127GLU-1-0.869-0.92249.781-0.011-0.0110.0000.0000.0000.000
126L128GLU-1-0.777-0.85242.888-0.005-0.0050.0000.0000.0000.000
127L129LEU0-0.015-0.00747.3760.0010.0010.0000.0000.0000.000
128L130GLN0-0.098-0.05148.9570.0030.0030.0000.0000.0000.000
129L131ALA0-0.006-0.00147.571-0.001-0.0010.0000.0000.0000.000
130L132ASN0-0.046-0.02146.1780.0000.0000.0000.0000.0000.000
131L133LYS10.8200.90938.161-0.006-0.0060.0000.0000.0000.000
132L134ALA00.029-0.01542.7290.0000.0000.0000.0000.0000.000
133L135THR0-0.050-0.04538.9140.0030.0030.0000.0000.0000.000
134L136LEU0-0.0090.00139.9300.0000.0000.0000.0000.0000.000
135L137VAL00.0160.01239.134-0.001-0.0010.0000.0000.0000.000
136L138CYS0-0.047-0.01437.3760.0020.0020.0000.0000.0000.000
137L139LEU00.0260.01137.436-0.003-0.0030.0000.0000.0000.000
138L140ILE00.0170.00334.2210.0050.0050.0000.0000.0000.000
139L141SER00.028-0.01137.084-0.007-0.0070.0000.0000.0000.000
140L142ASP-1-0.781-0.86738.613-0.013-0.0130.0000.0000.0000.000
141L143PHE00.0160.02431.7910.0040.0040.0000.0000.0000.000
142L144TYR00.011-0.00232.566-0.008-0.0080.0000.0000.0000.000
143L145PRO00.0460.00330.4010.0050.0050.0000.0000.0000.000
144L146GLY00.0210.00129.9850.0040.0040.0000.0000.0000.000
145L147ALA0-0.040-0.02427.827-0.003-0.0030.0000.0000.0000.000
146L148VAL0-0.012-0.00929.1560.0030.0030.0000.0000.0000.000
147L149THR0-0.0060.00427.5910.0000.0000.0000.0000.0000.000
148L150VAL00.0180.03330.4340.0060.0060.0000.0000.0000.000
149L164GLU-1-0.824-0.89529.9160.0130.0130.0000.0000.0000.000
150L165THR0-0.041-0.03428.7050.0000.0000.0000.0000.0000.000
151L166THR0-0.037-0.02328.228-0.006-0.0060.0000.0000.0000.000
152L167THR00.0370.01024.4500.0070.0070.0000.0000.0000.000
153L168PRO0-0.036-0.02027.013-0.006-0.0060.0000.0000.0000.000
154L169SER0-0.024-0.00428.588-0.014-0.0140.0000.0000.0000.000
155L170LYS10.8420.90630.9500.0690.0690.0000.0000.0000.000
156L171GLN0-0.012-0.02932.737-0.004-0.0040.0000.0000.0000.000
157L172SER00.0480.00736.482-0.001-0.0010.0000.0000.0000.000
158L173ASN0-0.054-0.01838.828-0.001-0.0010.0000.0000.0000.000
159L174ASN0-0.038-0.02636.8920.0020.0020.0000.0000.0000.000
160L175LYS10.8220.93836.0230.0220.0220.0000.0000.0000.000
161L176TYR0-0.027-0.01729.389-0.009-0.0090.0000.0000.0000.000
162L177ALA00.0070.01233.9040.0060.0060.0000.0000.0000.000
163L178ALA00.001-0.00532.019-0.004-0.0040.0000.0000.0000.000
164L179SER00.0060.01232.9900.0010.0010.0000.0000.0000.000
165L180SER00.0350.02332.7730.0020.0020.0000.0000.0000.000
166L181TYR00.0010.00833.637-0.001-0.0010.0000.0000.0000.000
167L182LEU00.0360.01634.5640.0060.0060.0000.0000.0000.000
168L183SER0-0.005-0.02334.781-0.003-0.0030.0000.0000.0000.000
169L184LEU0-0.044-0.01436.9430.0020.0020.0000.0000.0000.000
170L185THR0-0.015-0.02639.498-0.003-0.0030.0000.0000.0000.000
171L186PRO00.0610.02542.7760.0030.0030.0000.0000.0000.000
172L187GLU-1-0.795-0.88445.6430.0190.0190.0000.0000.0000.000
173L188GLN0-0.0010.01741.7000.0040.0040.0000.0000.0000.000
174L189TRP00.0480.02344.8240.0030.0030.0000.0000.0000.000
175L190LYS10.8030.90945.619-0.021-0.0210.0000.0000.0000.000
176L191SER00.001-0.00746.5790.0010.0010.0000.0000.0000.000
177L192HIS0-0.0160.00544.0290.0020.0020.0000.0000.0000.000
178L193ARG10.8500.91348.094-0.032-0.0320.0000.0000.0000.000
179L194SER0-0.011-0.00744.8410.0000.0000.0000.0000.0000.000
180L195TYR00.0730.02944.853-0.003-0.0030.0000.0000.0000.000
181L196SER00.0000.00041.2030.0030.0030.0000.0000.0000.000
182L197CYS00.0290.01040.294-0.002-0.0020.0000.0000.0000.000
183L198GLN0-0.0180.00036.8220.0020.0020.0000.0000.0000.000
184L199VAL00.0490.02135.303-0.002-0.0020.0000.0000.0000.000
185L200THR0-0.043-0.01732.5720.0030.0030.0000.0000.0000.000
186L201HIS10.8560.91232.751-0.036-0.0360.0000.0000.0000.000
187L202GLU-1-0.814-0.89231.2990.0480.0480.0000.0000.0000.000
188L203GLY00.0540.02334.034-0.002-0.0020.0000.0000.0000.000
189L204SER0-0.035-0.00137.257-0.001-0.0010.0000.0000.0000.000