Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 724RK

Calculation Name: 3WSQ-L-Xray372

Preferred Name: Receptor protein-tyrosine kinase erbB-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3WSQ

Chain ID: L

ChEMBL ID: CHEMBL1824

UniProt ID: P04626

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062661.270737
FMO2-HF: Nuclear repulsion 1983031.900002
FMO2-HF: Total energy -79629.370735
FMO2-MP2: Total energy -79861.335085


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:1:GLN)


Summations of interaction energy for fragment #1(L:1:GLN)
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.
-68.355-63.70425.087-13.455-16.278-0.002
Interaction energy analysis for fragmet #1(L:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.010
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].
3L3VAL00.0200.0073.8882.5354.209-0.014-0.877-0.7820.002
4L4LEU00.0020.0086.925-0.478-0.4780.0000.0000.0000.000
5L5THR00.012-0.01110.5330.1460.1460.0000.0000.0000.000
6L6GLN0-0.0600.00413.712-0.042-0.0420.0000.0000.0000.000
7L7PRO00.0330.02116.6740.0350.0350.0000.0000.0000.000
8L8PRO00.0380.00318.734-0.020-0.0200.0000.0000.0000.000
9L9SER0-0.042-0.02219.620-0.048-0.0480.0000.0000.0000.000
10L10ALA0-0.007-0.00522.8820.0400.0400.0000.0000.0000.000
11L11SER0-0.004-0.01924.771-0.031-0.0310.0000.0000.0000.000
12L12GLY0-0.0070.00928.2950.0210.0210.0000.0000.0000.000
13L13THR0-0.017-0.00930.123-0.012-0.0120.0000.0000.0000.000
14L14PRO00.0540.01032.5170.0020.0020.0000.0000.0000.000
15L15GLY0-0.037-0.01533.6630.0080.0080.0000.0000.0000.000
16L16GLN00.0020.02429.913-0.001-0.0010.0000.0000.0000.000
17L17THR00.0200.01527.775-0.009-0.0090.0000.0000.0000.000
18L18VAL0-0.025-0.01223.9000.0120.0120.0000.0000.0000.000
19L19THR0-0.040-0.03319.7950.0160.0160.0000.0000.0000.000
20L20LEU0-0.0020.02218.279-0.007-0.0070.0000.0000.0000.000
21L21SER0-0.040-0.03315.2430.0560.0560.0000.0000.0000.000
22L22CYS00.0230.00810.050-0.008-0.0080.0000.0000.0000.000
23L23SER0-0.013-0.0049.3050.0680.0680.0000.0000.0000.000
24L24GLY00.0330.0065.433-0.073-0.0730.0000.0000.0000.000
25L25SER0-0.021-0.0252.807-2.454-0.9520.249-0.805-0.946-0.008
26L26ARG10.8720.9261.859-39.297-41.63913.827-5.067-6.4170.061
27L27THR00.004-0.0024.4410.2560.312-0.001-0.003-0.0510.000
28L28ASN00.0160.0223.323-3.055-2.2730.028-0.396-0.4140.004
29L29ALA00.0790.0404.958-0.193-0.196-0.001-0.0030.0080.000
30L30GLY00.0260.0107.9040.1160.1160.0000.0000.0000.000
31L31ARG10.6680.8007.841-1.342-1.3420.0000.0000.0000.000
32L32ASP-1-0.847-0.90710.8450.0410.0410.0000.0000.0000.000
33L33PRO0-0.0150.0016.945-0.138-0.1380.0000.0000.0000.000
34L34VAL0-0.036-0.0208.281-0.236-0.2360.0000.0000.0000.000
35L35SER0-0.0030.00010.099-0.083-0.0830.0000.0000.0000.000
36L36TRP0-0.017-0.01212.194-0.059-0.0590.0000.0000.0000.000
37L37TYR0-0.016-0.00812.613-0.053-0.0530.0000.0000.0000.000
38L38GLN00.0370.01917.3550.0800.0800.0000.0000.0000.000
39L39GLN0-0.056-0.05220.264-0.113-0.1130.0000.0000.0000.000
40L40LEU00.0210.02022.1150.0340.0340.0000.0000.0000.000
41L41PRO00.0870.03925.762-0.041-0.0410.0000.0000.0000.000
42L42GLY00.0060.00827.8420.0000.0000.0000.0000.0000.000
43L43THR0-0.058-0.02126.763-0.003-0.0030.0000.0000.0000.000
44L44ALA0-0.0020.00023.644-0.028-0.0280.0000.0000.0000.000
45L45PRO00.0060.01919.2170.0410.0410.0000.0000.0000.000
46L46LYS10.9130.94920.8090.3560.3560.0000.0000.0000.000
47L47LEU0-0.0090.00215.8720.0060.0060.0000.0000.0000.000
48L48LEU0-0.039-0.01518.1920.0420.0420.0000.0000.0000.000
49L49THR0-0.044-0.04516.9780.0320.0320.0000.0000.0000.000
50L50SER00.0240.00314.635-0.103-0.1030.0000.0000.0000.000
51L51THR0-0.014-0.01313.9000.0440.0440.0000.0000.0000.000
52L52ALA00.0330.01313.1720.0860.0860.0000.0000.0000.000
53L53PRO0-0.0080.00614.991-0.043-0.0430.0000.0000.0000.000
54L54GLN0-0.0120.01118.118-0.014-0.0140.0000.0000.0000.000
55L55GLY00.0550.03219.279-0.048-0.0480.0000.0000.0000.000
56L56PRO0-0.0040.00820.5290.0010.0010.0000.0000.0000.000
57L57SER00.012-0.01722.8360.0350.0350.0000.0000.0000.000
58L58GLY0-0.037-0.02426.503-0.019-0.0190.0000.0000.0000.000
59L59VAL0-0.059-0.00822.446-0.005-0.0050.0000.0000.0000.000
60L60PRO0-0.014-0.01325.6830.0140.0140.0000.0000.0000.000
61L61ASP-1-0.834-0.92126.597-0.100-0.1000.0000.0000.0000.000
62L62ARG10.7560.86927.2710.1410.1410.0000.0000.0000.000
63L63PHE0-0.005-0.00122.4830.0150.0150.0000.0000.0000.000
64L64SER00.0480.02221.319-0.017-0.0170.0000.0000.0000.000
65L65GLY00.0100.02017.3810.0140.0140.0000.0000.0000.000
66L66SER0-0.022-0.01516.2980.0250.0250.0000.0000.0000.000
67L67LYN00.0620.0157.6540.0060.0060.0000.0000.0000.000
68L68SER00.0100.02413.353-0.062-0.0620.0000.0000.0000.000
69L69GLY00.0380.03812.4820.0980.0980.0000.0000.0000.000
70L70THR0-0.026-0.0097.032-0.192-0.1920.0000.0000.0000.000
71L71SER0-0.053-0.0228.3990.2700.2700.0000.0000.0000.000
72L72SER0-0.004-0.01610.885-0.123-0.1230.0000.0000.0000.000
73L73SER00.007-0.01712.6250.0110.0110.0000.0000.0000.000
74L74LEU0-0.0280.01916.144-0.024-0.0240.0000.0000.0000.000
75L75ALA00.015-0.00718.3650.0270.0270.0000.0000.0000.000
76L76ILE00.0040.00022.002-0.032-0.0320.0000.0000.0000.000
77L77SER0-0.001-0.00625.3530.0150.0150.0000.0000.0000.000
78L78GLY00.0710.01628.4960.0130.0130.0000.0000.0000.000
79L79LEU0-0.0610.00627.392-0.015-0.0150.0000.0000.0000.000
80L80GLN0-0.042-0.04330.2590.0020.0020.0000.0000.0000.000
81L81SER00.019-0.00531.731-0.003-0.0030.0000.0000.0000.000
82L82GLY00.012-0.00131.520-0.004-0.0040.0000.0000.0000.000
83L83ASP-1-0.787-0.84627.208-0.135-0.1350.0000.0000.0000.000
84L84GLU-1-0.852-0.90426.915-0.120-0.1200.0000.0000.0000.000
85L85ALA0-0.001-0.00723.306-0.026-0.0260.0000.0000.0000.000
86L86ASP-1-0.869-0.93620.289-0.250-0.2500.0000.0000.0000.000
87L87TYR0-0.055-0.04118.580-0.048-0.0480.0000.0000.0000.000
88L88TYR0-0.009-0.00113.997-0.005-0.0050.0000.0000.0000.000
89L90THR00.0610.0118.190-0.174-0.1740.0000.0000.0000.000
90L91VAL0-0.040-0.0133.3710.0510.7470.064-0.254-0.5060.001
91L92TRP0-0.0120.0044.352-2.301-2.185-0.001-0.018-0.0970.000
92L93ASP-1-0.844-0.9283.2000.4280.9060.027-0.148-0.357-0.001
93L94SER0-0.053-0.0303.145-1.701-0.5800.075-0.420-0.775-0.003
94L95VAL0-0.0020.0194.531-1.246-1.064-0.001-0.023-0.1580.000
95L96PRO00.000-0.0082.758-0.5560.9800.321-0.554-1.3030.001
96L97GLY00.0420.0141.820-21.477-22.88410.510-4.863-4.240-0.059
97L98ALA0-0.031-0.0023.8282.3612.6210.004-0.024-0.2400.000
98L99SER00.0290.0135.9720.7510.7510.0000.0000.0000.000
99L100VAL00.001-0.0108.8540.0160.0160.0000.0000.0000.000
100L101PHE0-0.014-0.02211.305-0.064-0.0640.0000.0000.0000.000
101L102GLY00.0530.04714.5680.0220.0220.0000.0000.0000.000
102L103SER0-0.018-0.01716.5930.0960.0960.0000.0000.0000.000
103L104GLY00.0220.03318.882-0.013-0.0130.0000.0000.0000.000
104L105THR0-0.034-0.01422.3710.0410.0410.0000.0000.0000.000
105L106PHE00.009-0.00225.418-0.020-0.0200.0000.0000.0000.000
106L107LEU00.0380.03129.1740.0220.0220.0000.0000.0000.000
107L108THR00.000-0.00832.2560.0010.0010.0000.0000.0000.000
108L109VAL0-0.0090.00634.3950.0110.0110.0000.0000.0000.000
109L110THR0-0.040-0.02537.9100.0030.0030.0000.0000.0000.000
110L111VAL0-0.031-0.00235.170-0.006-0.0060.0000.0000.0000.000
111L112ALA00.0110.01537.4860.0020.0020.0000.0000.0000.000
112L113ALA00.0230.00838.074-0.003-0.0030.0000.0000.0000.000
113L114PRO00.0070.00537.204-0.005-0.0050.0000.0000.0000.000
114L115SER0-0.007-0.00439.8060.0070.0070.0000.0000.0000.000
115L116VAL0-0.015-0.00139.935-0.007-0.0070.0000.0000.0000.000
116L117PHE0-0.030-0.01542.4160.0070.0070.0000.0000.0000.000
117L118ILE0-0.018-0.01542.123-0.002-0.0020.0000.0000.0000.000
118L119PHE00.0020.00243.9290.0020.0020.0000.0000.0000.000
119L120PRO00.0110.01644.936-0.003-0.0030.0000.0000.0000.000
120L121PRO00.0030.00545.226-0.004-0.0040.0000.0000.0000.000
121L122SER00.0500.01846.8890.0040.0040.0000.0000.0000.000
122L123ASP-1-0.851-0.94250.046-0.052-0.0520.0000.0000.0000.000
123L124GLU-1-0.892-0.91951.395-0.067-0.0670.0000.0000.0000.000
124L125GLN00.0620.01642.8320.0030.0030.0000.0000.0000.000
125L126LEU00.0340.02047.660-0.001-0.0010.0000.0000.0000.000
126L127LYS10.7630.85949.6940.0670.0670.0000.0000.0000.000
127L128SER00.0000.01947.339-0.001-0.0010.0000.0000.0000.000
128L129GLY0-0.019-0.01547.018-0.006-0.0060.0000.0000.0000.000
129L130THR0-0.044-0.01641.9290.0010.0010.0000.0000.0000.000
130L131ALA00.000-0.00543.0880.0050.0050.0000.0000.0000.000
131L132SER0-0.0090.00340.154-0.005-0.0050.0000.0000.0000.000
132L133VAL0-0.0170.01141.1840.0030.0030.0000.0000.0000.000
133L134VAL00.0180.01239.880-0.004-0.0040.0000.0000.0000.000
134L135CYS0-0.054-0.02638.5970.0080.0080.0000.0000.0000.000
135L136LEU0-0.0170.01138.655-0.007-0.0070.0000.0000.0000.000
136L137LEU00.003-0.00135.5020.0110.0110.0000.0000.0000.000
137L138ASN0-0.006-0.02938.862-0.011-0.0110.0000.0000.0000.000
138L139ASN00.006-0.00340.0670.0090.0090.0000.0000.0000.000
139L140PHE0-0.0100.01832.7630.0070.0070.0000.0000.0000.000
140L141TYR00.0320.01032.508-0.005-0.0050.0000.0000.0000.000
141L142PRO0-0.021-0.01930.0330.0120.0120.0000.0000.0000.000
142L143ARG10.9880.98625.5960.2000.2000.0000.0000.0000.000
143L144GLU-1-0.910-0.93526.038-0.027-0.0270.0000.0000.0000.000
144L145ALA00.0230.00328.8390.0110.0110.0000.0000.0000.000
145L146LYS10.9070.96729.290-0.047-0.0470.0000.0000.0000.000
146L147VAL00.0260.01031.0080.0120.0120.0000.0000.0000.000
147L148GLN0-0.072-0.04732.0920.0060.0060.0000.0000.0000.000
148L149TRP00.0320.00334.2530.0060.0060.0000.0000.0000.000
149L150LYS10.8140.88236.477-0.028-0.0280.0000.0000.0000.000
150L151VAL00.0250.02139.2780.0010.0010.0000.0000.0000.000
151L152ASP-1-0.782-0.88741.7770.0000.0000.0000.0000.0000.000
152L153ASN0-0.045-0.03641.7500.0060.0060.0000.0000.0000.000
153L154ALA0-0.0040.01339.0190.0080.0080.0000.0000.0000.000
154L155LEU0-0.014-0.00331.609-0.009-0.0090.0000.0000.0000.000
155L156GLN0-0.0230.00334.939-0.008-0.0080.0000.0000.0000.000
156L157SER0-0.007-0.02629.7840.0090.0090.0000.0000.0000.000
157L158GLY00.0000.02429.4290.0010.0010.0000.0000.0000.000
158L159ASN0-0.011-0.02130.301-0.016-0.0160.0000.0000.0000.000
159L160SER00.030-0.00332.4130.0110.0110.0000.0000.0000.000
160L161GLN0-0.065-0.01029.960-0.006-0.0060.0000.0000.0000.000
161L162GLU-1-0.907-0.96229.801-0.085-0.0850.0000.0000.0000.000
162L163SER0-0.007-0.00231.072-0.024-0.0240.0000.0000.0000.000
163L164VAL0-0.001-0.00829.8800.0190.0190.0000.0000.0000.000
164L165THR0-0.040-0.01832.610-0.013-0.0130.0000.0000.0000.000
165L166GLU-1-0.862-0.93931.100-0.238-0.2380.0000.0000.0000.000
166L167GLN0-0.0070.01132.7440.0140.0140.0000.0000.0000.000
167L168ASP-1-0.743-0.84234.959-0.106-0.1060.0000.0000.0000.000
168L169SER0-0.027-0.02338.6910.0050.0050.0000.0000.0000.000
169L170LYS10.7230.83540.3030.1010.1010.0000.0000.0000.000
170L171ASP-1-0.811-0.88441.174-0.074-0.0740.0000.0000.0000.000
171L172SER0-0.030-0.00436.5330.0040.0040.0000.0000.0000.000
172L173THR0-0.094-0.06236.415-0.001-0.0010.0000.0000.0000.000
173L174TYR0-0.004-0.02031.075-0.016-0.0160.0000.0000.0000.000
174L175SER0-0.006-0.01436.1970.0150.0150.0000.0000.0000.000
175L176LEU0-0.0130.00031.888-0.013-0.0130.0000.0000.0000.000
176L177SER0-0.002-0.00235.3910.0140.0140.0000.0000.0000.000
177L178SER00.0410.02433.937-0.011-0.0110.0000.0000.0000.000
178L179THR0-0.005-0.02135.3000.0090.0090.0000.0000.0000.000
179L180LEU00.0070.02935.901-0.008-0.0080.0000.0000.0000.000
180L181THR00.005-0.01836.7610.0030.0030.0000.0000.0000.000
181L182LEU0-0.028-0.00937.9250.0030.0030.0000.0000.0000.000
182L183SER00.0540.02540.681-0.003-0.0030.0000.0000.0000.000
183L184LYS10.9380.94743.4520.0600.0600.0000.0000.0000.000
184L185ALA0-0.024-0.01845.6820.0050.0050.0000.0000.0000.000
185L186ASP-1-0.823-0.89342.983-0.026-0.0260.0000.0000.0000.000
186L187TYR00.0490.01945.0220.0060.0060.0000.0000.0000.000
187L188GLU-1-0.814-0.90746.108-0.031-0.0310.0000.0000.0000.000
188L189LYS10.7800.88844.6130.0320.0320.0000.0000.0000.000
189L190HIS10.8040.90743.1970.0220.0220.0000.0000.0000.000
190L191LYS10.8380.90747.4330.0030.0030.0000.0000.0000.000
191L192VAL00.0240.02245.098-0.003-0.0030.0000.0000.0000.000
192L193TYR00.002-0.01442.708-0.001-0.0010.0000.0000.0000.000
193L194ALA00.0190.01741.951-0.004-0.0040.0000.0000.0000.000
194L196GLU-1-0.824-0.89537.1780.0350.0350.0000.0000.0000.000
195L197VAL00.0670.03935.7940.0040.0040.0000.0000.0000.000
196L198THR0-0.022-0.00932.8280.0140.0140.0000.0000.0000.000
197L199HIS00.0380.01832.8720.0000.0000.0000.0000.0000.000
198L200GLN00.007-0.01128.6720.0050.0050.0000.0000.0000.000
199L201GLY00.0480.00633.3860.0000.0000.0000.0000.0000.000
200L202LEU0-0.069-0.02436.898-0.003-0.0030.0000.0000.0000.000
201L203SER0-0.031-0.01737.5610.0040.0040.0000.0000.0000.000
202L204SER0-0.003-0.00738.5850.0110.0110.0000.0000.0000.000
203L205PRO0-0.035-0.01535.788-0.007-0.0070.0000.0000.0000.000
204L206VAL00.0070.01938.1050.0020.0020.0000.0000.0000.000
205L207THR0-0.011-0.01140.203-0.007-0.0070.0000.0000.0000.000
206L208LYS10.8840.93742.2100.0210.0210.0000.0000.0000.000
207L209SER00.0450.01543.570-0.001-0.0010.0000.0000.0000.000
208L210PHE0-0.0170.00245.4280.0000.0000.0000.0000.0000.000
209L211ASN0-0.005-0.02048.7510.0040.0040.0000.0000.0000.000
210L212ARG10.7650.85949.4460.0240.0240.0000.0000.0000.000
211L213GLY00.0260.01751.3400.0030.0030.0000.0000.0000.000
212L214GLU-1-0.855-0.89554.429-0.009-0.0090.0000.0000.0000.000
213L215CYS0-0.023-0.00852.945-0.001-0.0010.0000.0000.0000.000