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

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FMODB ID: 94Q62

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2058619.691944
FMO2-HF: Nuclear repulsion 1978993.01503
FMO2-HF: Total energy -79626.676914
FMO2-MP2: Total energy -79858.752087


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.
-43.596-32.02311.075-9.134-13.515-0.025
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 : 0.007 / q_NPA : -0.017
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].
3L3VAL00.0030.0083.8590.3492.306-0.025-1.084-0.8470.001
4L4LEU00.0320.0096.671-0.081-0.0810.0000.0000.0000.000
5L5THR00.0670.00710.4670.1290.1290.0000.0000.0000.000
6L6GLN0-0.0560.04113.3020.0890.0890.0000.0000.0000.000
7L7PRO00.0360.04116.3590.0230.0230.0000.0000.0000.000
8L8PRO00.0630.00018.210-0.050-0.0500.0000.0000.0000.000
9L9SER0-0.006-0.00119.156-0.017-0.0170.0000.0000.0000.000
10L10ALA00.0110.01222.1720.0470.0470.0000.0000.0000.000
11L11SER00.006-0.00623.712-0.030-0.0300.0000.0000.0000.000
12L12GLY0-0.024-0.01027.1600.0150.0150.0000.0000.0000.000
13L13THR0-0.0160.01328.981-0.001-0.0010.0000.0000.0000.000
14L14PRO00.0750.00731.463-0.005-0.0050.0000.0000.0000.000
15L15GLY0-0.036-0.00433.1670.0110.0110.0000.0000.0000.000
16L16GLN0-0.0150.00229.1420.0010.0010.0000.0000.0000.000
17L17THR00.0180.01226.760-0.008-0.0080.0000.0000.0000.000
18L18VAL0-0.0220.00122.7400.0130.0130.0000.0000.0000.000
19L19THR0-0.036-0.03218.8160.0230.0230.0000.0000.0000.000
20L20LEU00.0060.01916.879-0.006-0.0060.0000.0000.0000.000
21L21SER0-0.033-0.06814.2220.0020.0020.0000.0000.0000.000
22L22CYS0-0.019-0.0199.256-0.261-0.2610.0000.0000.0000.000
23L23SER0-0.0140.0078.8300.1140.1140.0000.0000.0000.000
24L24GLY00.0270.0214.702-0.189-0.202-0.001-0.0030.0170.000
25L25SER0-0.037-0.0223.7462.3452.9820.068-0.287-0.4170.000
26L26ARG10.9500.9562.510-22.177-18.3281.542-1.982-3.4090.019
27L27THR0-0.007-0.0104.753-1.598-1.515-0.001-0.007-0.0750.000
28L28ASN0-0.0440.0002.694-0.6630.0380.386-0.405-0.683-0.002
29L29ALA00.1180.0585.2140.5240.547-0.001-0.005-0.0170.000
30L30GLY00.0500.0208.192-0.271-0.2710.0000.0000.0000.000
31L31ARG10.6810.8066.7390.3640.3640.0000.0000.0000.000
32L32ASP-1-0.854-0.92910.626-0.355-0.3550.0000.0000.0000.000
33L33PRO0-0.0550.0066.793-0.008-0.0080.0000.0000.0000.000
34L34VAL0-0.005-0.0307.146-0.216-0.2160.0000.0000.0000.000
35L35SER0-0.023-0.0159.4790.2210.2210.0000.0000.0000.000
36L36TRP0-0.045-0.01112.068-0.301-0.3010.0000.0000.0000.000
37L37TYR0-0.003-0.00812.9650.1190.1190.0000.0000.0000.000
38L38GLN00.0170.00917.2440.0730.0730.0000.0000.0000.000
39L39GLN0-0.061-0.04020.288-0.106-0.1060.0000.0000.0000.000
40L40LEU00.0220.02122.1240.0370.0370.0000.0000.0000.000
41L41PRO00.0680.02325.750-0.048-0.0480.0000.0000.0000.000
42L42GLY00.0370.03426.4080.0310.0310.0000.0000.0000.000
43L43THR0-0.058-0.02826.1790.0250.0250.0000.0000.0000.000
44L44ALA0-0.010-0.01322.865-0.048-0.0480.0000.0000.0000.000
45L45PRO00.0190.01818.6500.0450.0450.0000.0000.0000.000
46L46LYS10.9280.96520.3700.6120.6120.0000.0000.0000.000
47L47LEU00.0140.01415.136-0.026-0.0260.0000.0000.0000.000
48L48LEU0-0.028-0.02117.8020.1040.1040.0000.0000.0000.000
49L49THR00.000-0.00416.0550.0410.0410.0000.0000.0000.000
50L50SER00.050-0.00814.318-0.182-0.1820.0000.0000.0000.000
51L51THR0-0.032-0.00513.5470.1430.1430.0000.0000.0000.000
52L52ALA00.0290.02312.7310.1090.1090.0000.0000.0000.000
53L53PRO0-0.045-0.00714.294-0.022-0.0220.0000.0000.0000.000
54L54GLN00.003-0.00817.9360.0250.0250.0000.0000.0000.000
55L55GLY00.0270.02919.229-0.079-0.0790.0000.0000.0000.000
56L56PRO00.0220.02420.8410.0240.0240.0000.0000.0000.000
57L57SER0-0.013-0.02822.7780.0520.0520.0000.0000.0000.000
58L58GLY0-0.011-0.00526.355-0.014-0.0140.0000.0000.0000.000
59L59VAL0-0.079-0.02822.088-0.015-0.0150.0000.0000.0000.000
60L60PRO0-0.011-0.01325.3020.0160.0160.0000.0000.0000.000
61L61ASP-1-0.790-0.90425.465-0.321-0.3210.0000.0000.0000.000
62L62ARG10.6730.84326.4620.3850.3850.0000.0000.0000.000
63L63PHE00.014-0.00521.660-0.017-0.0170.0000.0000.0000.000
64L64SER00.0640.02220.7410.0140.0140.0000.0000.0000.000
65L65GLY0-0.0010.01316.5990.0050.0050.0000.0000.0000.000
66L66SER0-0.0040.02115.4780.0930.0930.0000.0000.0000.000
67L67LYN00.0550.0046.659-0.174-0.1740.0000.0000.0000.000
68L68SER0-0.0020.01812.5060.0950.0950.0000.0000.0000.000
69L69GLY00.0260.03112.1140.0290.0290.0000.0000.0000.000
70L70THR0-0.034-0.0277.157-0.049-0.0490.0000.0000.0000.000
71L71SER0-0.040-0.0178.668-0.047-0.0470.0000.0000.0000.000
72L72SER00.0080.00110.2770.0040.0040.0000.0000.0000.000
73L73SER0-0.026-0.03911.7900.0120.0120.0000.0000.0000.000
74L74LEU0-0.0520.00015.3840.0250.0250.0000.0000.0000.000
75L75ALA00.0340.00017.5100.0480.0480.0000.0000.0000.000
76L76ILE00.017-0.00621.206-0.017-0.0170.0000.0000.0000.000
77L77SER0-0.030-0.00924.4720.0210.0210.0000.0000.0000.000
78L78GLY00.0830.03727.7700.0190.0190.0000.0000.0000.000
79L79LEU0-0.052-0.00626.629-0.014-0.0140.0000.0000.0000.000
80L80GLN0-0.066-0.05329.3720.0300.0300.0000.0000.0000.000
81L81SER00.028-0.00531.086-0.008-0.0080.0000.0000.0000.000
82L82GLY00.0230.02030.9690.0010.0010.0000.0000.0000.000
83L83ASP-1-0.845-0.87826.259-0.429-0.4290.0000.0000.0000.000
84L84GLU-1-0.856-0.93426.764-0.365-0.3650.0000.0000.0000.000
85L85ALA0-0.006-0.02123.021-0.020-0.0200.0000.0000.0000.000
86L86ASP-1-0.862-0.93119.865-0.711-0.7110.0000.0000.0000.000
87L87TYR0-0.044-0.04217.530-0.044-0.0440.0000.0000.0000.000
88L88TYR00.0030.00713.650-0.038-0.0380.0000.0000.0000.000
89L90THR00.035-0.0027.382-0.162-0.1620.0000.0000.0000.000
90L91VAL0-0.0270.0012.6180.0210.7810.190-0.281-0.6690.001
91L92TRP0-0.0030.0044.317-2.338-2.205-0.001-0.020-0.1130.000
92L93ASP-1-0.827-0.9093.591-0.731-0.4490.006-0.067-0.2210.000
93L94SER0-0.0200.0022.459-4.630-2.9500.930-0.971-1.640-0.003
94L95VAL0-0.0010.0384.573-2.017-1.850-0.001-0.014-0.1520.000
95L96PRO0-0.005-0.0302.0863.3432.4283.848-1.068-1.865-0.001
96L97GLY00.017-0.0232.121-17.749-15.9734.128-2.827-3.076-0.040
97L98ALA0-0.024-0.0023.6652.8373.2900.007-0.113-0.3480.000
98L99SER00.0270.0145.7410.5700.5700.0000.0000.0000.000
99L100VAL0-0.035-0.0088.561-0.081-0.0810.0000.0000.0000.000
100L101PHE0-0.031-0.04110.8420.0400.0400.0000.0000.0000.000
101L102GLY00.0170.02213.9480.1320.1320.0000.0000.0000.000
102L103SER00.0020.00915.9250.0980.0980.0000.0000.0000.000
103L104GLY00.0080.02417.818-0.025-0.0250.0000.0000.0000.000
104L105THR0-0.041-0.01021.2770.0520.0520.0000.0000.0000.000
105L106PHE0-0.003-0.01524.136-0.012-0.0120.0000.0000.0000.000
106L107LEU00.0140.01827.8890.0220.0220.0000.0000.0000.000
107L108THR0-0.031-0.03431.0770.0030.0030.0000.0000.0000.000
108L109VAL00.0100.01133.1640.0170.0170.0000.0000.0000.000
109L110THR0-0.043-0.02036.7700.0090.0090.0000.0000.0000.000
110L111VAL00.0040.00934.462-0.005-0.0050.0000.0000.0000.000
111L112ALA00.0270.03336.9770.0130.0130.0000.0000.0000.000
112L113ALA0-0.014-0.02037.775-0.010-0.0100.0000.0000.0000.000
113L114PRO00.0200.01837.1040.0010.0010.0000.0000.0000.000
114L115SER0-0.047-0.04339.3700.0160.0160.0000.0000.0000.000
115L116VAL00.0070.01139.695-0.007-0.0070.0000.0000.0000.000
116L117PHE0-0.033-0.01542.2320.0170.0170.0000.0000.0000.000
117L118ILE0-0.018-0.01842.420-0.006-0.0060.0000.0000.0000.000
118L119PHE0-0.012-0.00244.0130.0070.0070.0000.0000.0000.000
119L120PRO00.0090.01344.965-0.007-0.0070.0000.0000.0000.000
120L121PRO0-0.0150.00545.118-0.004-0.0040.0000.0000.0000.000
121L122SER00.0520.01146.8280.0070.0070.0000.0000.0000.000
122L123ASP-1-0.859-0.94849.854-0.127-0.1270.0000.0000.0000.000
123L124GLU-1-0.953-0.98051.247-0.139-0.1390.0000.0000.0000.000
124L125GLN00.0320.00143.594-0.009-0.0090.0000.0000.0000.000
125L126LEU00.0350.03347.300-0.001-0.0010.0000.0000.0000.000
126L127LYS10.7660.88649.2780.1310.1310.0000.0000.0000.000
127L128SER00.0260.02447.7320.0030.0030.0000.0000.0000.000
128L129GLY0-0.047-0.01446.566-0.009-0.0090.0000.0000.0000.000
129L130THR0-0.010-0.01241.003-0.001-0.0010.0000.0000.0000.000
130L131ALA0-0.002-0.00242.7270.0090.0090.0000.0000.0000.000
131L132SER0-0.011-0.01741.103-0.015-0.0150.0000.0000.0000.000
132L133VAL0-0.0120.01441.0890.0080.0080.0000.0000.0000.000
133L134VAL00.0410.01839.394-0.008-0.0080.0000.0000.0000.000
134L135CYS0-0.069-0.04338.4250.0060.0060.0000.0000.0000.000
135L136LEU0-0.0120.01038.677-0.009-0.0090.0000.0000.0000.000
136L137LEU0-0.0080.00035.1440.0140.0140.0000.0000.0000.000
137L138ASN00.0500.00038.848-0.022-0.0220.0000.0000.0000.000
138L139ASN00.0460.04839.2910.0040.0040.0000.0000.0000.000
139L140PHE0-0.0090.01332.3240.0130.0130.0000.0000.0000.000
140L141TYR00.0580.04531.437-0.017-0.0170.0000.0000.0000.000
141L142PRO0-0.017-0.00829.1140.0200.0200.0000.0000.0000.000
142L143ARG10.9980.98325.5850.5280.5280.0000.0000.0000.000
143L144GLU-1-0.976-0.97925.614-0.369-0.3690.0000.0000.0000.000
144L145ALA00.0240.00628.3860.0360.0360.0000.0000.0000.000
145L146LYS10.9630.99229.2770.1790.1790.0000.0000.0000.000
146L147VAL00.010-0.00731.1380.0250.0250.0000.0000.0000.000
147L148GLN00.0050.01332.006-0.013-0.0130.0000.0000.0000.000
148L149TRP00.021-0.00133.8830.0190.0190.0000.0000.0000.000
149L150LYS10.9110.94636.1600.1250.1250.0000.0000.0000.000
150L151VAL0-0.015-0.01038.8810.0060.0060.0000.0000.0000.000
151L152ASP-1-0.851-0.92941.012-0.105-0.1050.0000.0000.0000.000
152L153ASN0-0.057-0.01741.3160.0030.0030.0000.0000.0000.000
153L154ALA00.0390.03538.2540.0060.0060.0000.0000.0000.000
154L155LEU0-0.031-0.01430.891-0.008-0.0080.0000.0000.0000.000
155L156GLN0-0.0110.03334.160-0.004-0.0040.0000.0000.0000.000
156L157SER0-0.022-0.04229.088-0.004-0.0040.0000.0000.0000.000
157L158GLY00.0200.02428.9970.0060.0060.0000.0000.0000.000
158L159ASN0-0.019-0.02529.867-0.023-0.0230.0000.0000.0000.000
159L160SER00.031-0.01331.8380.0240.0240.0000.0000.0000.000
160L161GLN0-0.046-0.00329.795-0.007-0.0070.0000.0000.0000.000
161L162GLU-1-0.943-0.95928.685-0.370-0.3700.0000.0000.0000.000
162L163SER00.018-0.01031.323-0.025-0.0250.0000.0000.0000.000
163L164VAL0-0.008-0.01229.4110.0240.0240.0000.0000.0000.000
164L165THR00.0040.01132.269-0.018-0.0180.0000.0000.0000.000
165L166GLU-1-0.925-0.96531.229-0.473-0.4730.0000.0000.0000.000
166L167GLN0-0.012-0.00131.9220.0030.0030.0000.0000.0000.000
167L168ASP-1-0.829-0.89234.447-0.245-0.2450.0000.0000.0000.000
168L169SER0-0.043-0.03137.9320.0040.0040.0000.0000.0000.000
169L170LYS10.8500.90239.8510.2200.2200.0000.0000.0000.000
170L171ASP-1-0.860-0.91540.392-0.222-0.2220.0000.0000.0000.000
171L172SER0-0.039-0.00635.651-0.004-0.0040.0000.0000.0000.000
172L173THR0-0.061-0.03636.0810.0020.0020.0000.0000.0000.000
173L174TYR0-0.034-0.02830.572-0.015-0.0150.0000.0000.0000.000
174L175SER00.013-0.01935.4550.0270.0270.0000.0000.0000.000
175L176LEU0-0.043-0.00931.741-0.019-0.0190.0000.0000.0000.000
176L177SER0-0.009-0.02034.9880.0270.0270.0000.0000.0000.000
177L178SER0-0.0080.02534.562-0.017-0.0170.0000.0000.0000.000
178L179THR00.0270.00335.0480.0260.0260.0000.0000.0000.000
179L180LEU00.0050.01435.560-0.013-0.0130.0000.0000.0000.000
180L181THR00.0230.00836.4840.0080.0080.0000.0000.0000.000
181L182LEU0-0.041-0.02437.6250.0010.0010.0000.0000.0000.000
182L183SER00.0500.01840.2980.0000.0000.0000.0000.0000.000
183L184LYS10.9950.98843.1360.1330.1330.0000.0000.0000.000
184L185ALA0-0.032-0.01845.4230.0080.0080.0000.0000.0000.000
185L186ASP-1-0.840-0.93141.662-0.138-0.1380.0000.0000.0000.000
186L187TYR00.004-0.01244.7160.0070.0070.0000.0000.0000.000
187L188GLU-1-0.909-0.95646.027-0.106-0.1060.0000.0000.0000.000
188L189LYS10.8010.93444.4310.1270.1270.0000.0000.0000.000
189L190HIS10.8670.92742.1900.1270.1270.0000.0000.0000.000
190L191LYS10.9160.95946.9370.0890.0890.0000.0000.0000.000
191L192VAL00.0080.00444.547-0.003-0.0030.0000.0000.0000.000
192L193TYR00.023-0.00241.786-0.001-0.0010.0000.0000.0000.000
193L194ALA00.0150.01441.628-0.002-0.0020.0000.0000.0000.000
194L196GLU-1-0.946-0.97837.177-0.125-0.1250.0000.0000.0000.000
195L197VAL00.0330.00435.832-0.013-0.0130.0000.0000.0000.000
196L198THR0-0.064-0.03032.8810.0160.0160.0000.0000.0000.000
197L199HIS00.0760.01832.617-0.003-0.0030.0000.0000.0000.000
198L200GLN00.0760.05427.8060.0150.0150.0000.0000.0000.000
199L201GLY0-0.029-0.02732.931-0.004-0.0040.0000.0000.0000.000
200L202LEU0-0.063-0.02236.4480.0110.0110.0000.0000.0000.000
201L203SER0-0.013-0.01237.357-0.002-0.0020.0000.0000.0000.000
202L204SER00.018-0.00138.2930.0100.0100.0000.0000.0000.000
203L205PRO0-0.052-0.03735.725-0.007-0.0070.0000.0000.0000.000
204L206VAL00.0670.06838.1140.0100.0100.0000.0000.0000.000
205L207THR0-0.0160.00140.109-0.013-0.0130.0000.0000.0000.000
206L208LYS10.9010.94342.2310.1510.1510.0000.0000.0000.000
207L209SER00.040-0.00343.460-0.005-0.0050.0000.0000.0000.000
208L210PHE0-0.0260.01444.7060.0030.0030.0000.0000.0000.000
209L211ASN0-0.044-0.05248.263-0.002-0.0020.0000.0000.0000.000
210L212ARG10.8920.95349.0060.1080.1080.0000.0000.0000.000
211L213GLY00.0060.00450.8540.0060.0060.0000.0000.0000.000
212L214GLU-1-0.866-0.89853.988-0.085-0.0850.0000.0000.0000.000
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