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: MVZ7Z

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2059930.481699
FMO2-HF: Nuclear repulsion 1980302.310021
FMO2-HF: Total energy -79628.171678
FMO2-MP2: Total energy -79860.142416


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.
-59.482-53.08622.259-12.936-15.717-0.031
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 : 0.023 / q_NPA : 0.004
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].
3L3VAL00.0010.0003.859-1.2101.304-0.024-1.443-1.0470.003
4L4LEU00.0200.0076.7640.1890.1890.0000.0000.0000.000
5L5THR00.0630.02810.5610.0330.0330.0000.0000.0000.000
6L6GLN0-0.0840.02113.3830.1380.1380.0000.0000.0000.000
7L7PRO00.0380.01516.4430.0220.0220.0000.0000.0000.000
8L8PRO00.052-0.00418.286-0.052-0.0520.0000.0000.0000.000
9L9SER00.0090.00219.2370.0000.0000.0000.0000.0000.000
10L10ALA00.0030.00922.2120.0400.0400.0000.0000.0000.000
11L11SER00.005-0.01623.780-0.026-0.0260.0000.0000.0000.000
12L12GLY0-0.023-0.00627.2230.0120.0120.0000.0000.0000.000
13L13THR0-0.0200.00329.0340.0030.0030.0000.0000.0000.000
14L14PRO00.0760.00631.506-0.005-0.0050.0000.0000.0000.000
15L15GLY0-0.033-0.00333.1920.0100.0100.0000.0000.0000.000
16L16GLN0-0.0090.01128.976-0.002-0.0020.0000.0000.0000.000
17L17THR00.0330.02126.756-0.006-0.0060.0000.0000.0000.000
18L18VAL0-0.023-0.00422.7320.0060.0060.0000.0000.0000.000
19L19THR0-0.039-0.03218.9340.0250.0250.0000.0000.0000.000
20L20LEU0-0.0010.02117.040-0.015-0.0150.0000.0000.0000.000
21L21SER0-0.020-0.03714.367-0.006-0.0060.0000.0000.0000.000
22L22CYS0-0.022-0.0099.136-0.276-0.2760.0000.0000.0000.000
23L23SER00.0070.0088.7290.2040.2040.0000.0000.0000.000
24L24GLY00.0180.0144.763-0.460-0.466-0.001-0.0030.0110.000
25L25SER0-0.020-0.0252.824-2.907-0.9960.252-1.091-1.072-0.011
26L26ARG10.9170.9431.867-30.547-32.22310.010-3.536-4.7980.041
27L27THR0-0.016-0.0114.304-0.999-0.925-0.001-0.003-0.0700.000
28L28ASN0-0.0210.0092.536-0.4700.1040.151-0.275-0.4500.000
29L29ALA00.0970.0535.340-0.171-0.152-0.001-0.004-0.0130.000
30L30GLY00.0570.0308.388-0.328-0.3280.0000.0000.0000.000
31L31ARG10.6440.7637.227-0.270-0.2700.0000.0000.0000.000
32L32ASP-1-0.843-0.92310.552-0.135-0.1350.0000.0000.0000.000
33L33PRO0-0.0480.0096.702-0.094-0.0940.0000.0000.0000.000
34L34VAL00.002-0.0287.047-0.321-0.3210.0000.0000.0000.000
35L35SER0-0.006-0.0129.4450.1890.1890.0000.0000.0000.000
36L36TRP0-0.037-0.00812.065-0.304-0.3040.0000.0000.0000.000
37L37TYR00.002-0.00912.8510.1360.1360.0000.0000.0000.000
38L38GLN00.0190.01117.2530.0550.0550.0000.0000.0000.000
39L39GLN0-0.061-0.04520.226-0.098-0.0980.0000.0000.0000.000
40L40LEU00.0300.01822.1410.0330.0330.0000.0000.0000.000
41L41PRO00.0740.02725.771-0.045-0.0450.0000.0000.0000.000
42L42GLY00.0240.02826.4300.0320.0320.0000.0000.0000.000
43L43THR0-0.076-0.03826.2080.0290.0290.0000.0000.0000.000
44L44ALA0-0.003-0.00222.962-0.046-0.0460.0000.0000.0000.000
45L45PRO00.0250.02618.5110.0470.0470.0000.0000.0000.000
46L46LYS10.9230.96020.4080.5930.5930.0000.0000.0000.000
47L47LEU00.0070.01115.396-0.030-0.0300.0000.0000.0000.000
48L48LEU0-0.023-0.01017.7910.0910.0910.0000.0000.0000.000
49L49THR0-0.035-0.02716.2690.0440.0440.0000.0000.0000.000
50L50SER00.0400.00514.270-0.172-0.1720.0000.0000.0000.000
51L51THR0-0.072-0.03113.4510.1270.1270.0000.0000.0000.000
52L52ALA00.0310.01312.3780.1000.1000.0000.0000.0000.000
53L53PRO0-0.0270.00114.263-0.043-0.0430.0000.0000.0000.000
54L54GLN00.0280.00817.9100.0340.0340.0000.0000.0000.000
55L55GLY00.0340.03419.189-0.071-0.0710.0000.0000.0000.000
56L56PRO00.0100.01821.0080.0260.0260.0000.0000.0000.000
57L57SER0-0.008-0.02322.7370.0470.0470.0000.0000.0000.000
58L58GLY0-0.010-0.00626.350-0.015-0.0150.0000.0000.0000.000
59L59VAL0-0.052-0.02522.182-0.019-0.0190.0000.0000.0000.000
60L60PRO0-0.019-0.01625.2850.0150.0150.0000.0000.0000.000
61L61ASP-1-0.819-0.91125.454-0.285-0.2850.0000.0000.0000.000
62L62ARG10.7280.87426.4530.3780.3780.0000.0000.0000.000
63L63PHE00.001-0.01021.786-0.020-0.0200.0000.0000.0000.000
64L64SER00.0610.02020.7370.0240.0240.0000.0000.0000.000
65L65GLY0-0.0150.01116.595-0.007-0.0070.0000.0000.0000.000
66L66SER0-0.021-0.00715.4640.0950.0950.0000.0000.0000.000
67L67LYN00.0510.0126.743-0.014-0.0140.0000.0000.0000.000
68L68SER00.0030.01912.5000.1130.1130.0000.0000.0000.000
69L69GLY00.0300.03412.119-0.034-0.0340.0000.0000.0000.000
70L70THR0-0.020-0.0147.0620.1790.1790.0000.0000.0000.000
71L71SER0-0.029-0.0118.716-0.294-0.2940.0000.0000.0000.000
72L72SER00.0080.00610.4400.0320.0320.0000.0000.0000.000
73L73SER0-0.029-0.03311.812-0.039-0.0390.0000.0000.0000.000
74L74LEU0-0.0410.00815.4100.0570.0570.0000.0000.0000.000
75L75ALA00.0330.00117.5290.0350.0350.0000.0000.0000.000
76L76ILE00.012-0.00221.223-0.010-0.0100.0000.0000.0000.000
77L77SER0-0.024-0.01624.4900.0170.0170.0000.0000.0000.000
78L78GLY00.0690.04127.7840.0140.0140.0000.0000.0000.000
79L79LEU0-0.044-0.00526.585-0.011-0.0110.0000.0000.0000.000
80L80GLN0-0.075-0.05629.4000.0330.0330.0000.0000.0000.000
81L81SER00.0410.00431.117-0.009-0.0090.0000.0000.0000.000
82L82GLY00.0080.01130.9920.0000.0000.0000.0000.0000.000
83L83ASP-1-0.837-0.89326.363-0.421-0.4210.0000.0000.0000.000
84L84GLU-1-0.850-0.91426.802-0.380-0.3800.0000.0000.0000.000
85L85ALA0-0.022-0.02023.190-0.014-0.0140.0000.0000.0000.000
86L86ASP-1-0.870-0.94019.979-0.754-0.7540.0000.0000.0000.000
87L87TYR0-0.028-0.03517.634-0.036-0.0360.0000.0000.0000.000
88L88TYR0-0.0130.00213.745-0.098-0.0980.0000.0000.0000.000
89L90THR00.0390.0017.985-0.229-0.2290.0000.0000.0000.000
90L91VAL0-0.039-0.0112.5830.1870.8030.180-0.170-0.627-0.001
91L92TRP0-0.0130.0024.320-2.019-1.875-0.001-0.020-0.1230.000
92L93ASP-1-0.806-0.8983.5383.3533.6520.007-0.068-0.2380.000
93L94SER0-0.040-0.0142.636-4.493-2.9020.749-0.824-1.515-0.006
94L95VAL0-0.0050.0314.547-1.760-1.573-0.001-0.020-0.1650.000
95L96PRO00.011-0.0172.5471.0052.4340.541-0.612-1.3590.000
96L97GLY00.032-0.0011.807-19.971-21.80610.390-4.683-3.872-0.057
97L98ALA0-0.0190.0013.6582.5153.0700.008-0.184-0.3790.000
98L99SER00.0270.0135.7700.4570.4570.0000.0000.0000.000
99L100VAL00.003-0.0048.561-0.234-0.2340.0000.0000.0000.000
100L101PHE0-0.032-0.03310.9110.1140.1140.0000.0000.0000.000
101L102GLY00.0270.02014.0120.1540.1540.0000.0000.0000.000
102L103SER0-0.0070.01015.9900.0880.0880.0000.0000.0000.000
103L104GLY00.0000.01417.883-0.010-0.0100.0000.0000.0000.000
104L105THR0-0.024-0.00521.3370.0400.0400.0000.0000.0000.000
105L106PHE0-0.003-0.01424.192-0.007-0.0070.0000.0000.0000.000
106L107LEU00.0250.02427.9440.0190.0190.0000.0000.0000.000
107L108THR0-0.040-0.02531.1270.0030.0030.0000.0000.0000.000
108L109VAL00.0130.01033.2220.0180.0180.0000.0000.0000.000
109L110THR0-0.038-0.01736.8250.0090.0090.0000.0000.0000.000
110L111VAL0-0.0020.00934.458-0.005-0.0050.0000.0000.0000.000
111L112ALA00.0270.02937.0460.0140.0140.0000.0000.0000.000
112L113ALA0-0.008-0.01537.852-0.012-0.0120.0000.0000.0000.000
113L114PRO00.0240.01236.9110.0030.0030.0000.0000.0000.000
114L115SER0-0.041-0.01539.4520.0160.0160.0000.0000.0000.000
115L116VAL0-0.0050.00139.810-0.006-0.0060.0000.0000.0000.000
116L117PHE0-0.019-0.00442.3200.0180.0180.0000.0000.0000.000
117L118ILE0-0.033-0.02842.203-0.007-0.0070.0000.0000.0000.000
118L119PHE00.0000.00543.8630.0080.0080.0000.0000.0000.000
119L120PRO00.0110.02144.988-0.007-0.0070.0000.0000.0000.000
120L121PRO0-0.015-0.00345.146-0.003-0.0030.0000.0000.0000.000
121L122SER00.0450.00946.8520.0070.0070.0000.0000.0000.000
122L123ASP-1-0.858-0.94349.879-0.139-0.1390.0000.0000.0000.000
123L124GLU-1-0.900-0.92851.661-0.140-0.1400.0000.0000.0000.000
124L125GLN00.0380.00143.976-0.004-0.0040.0000.0000.0000.000
125L126LEU00.0590.04547.471-0.001-0.0010.0000.0000.0000.000
126L127LYS10.7080.83449.3670.1390.1390.0000.0000.0000.000
127L128SER00.0110.01147.9880.0030.0030.0000.0000.0000.000
128L129GLY0-0.041-0.00846.980-0.009-0.0090.0000.0000.0000.000
129L130THR0-0.032-0.02241.331-0.002-0.0020.0000.0000.0000.000
130L131ALA00.0130.00542.8400.0090.0090.0000.0000.0000.000
131L132SER0-0.007-0.02241.012-0.017-0.0170.0000.0000.0000.000
132L133VAL0-0.0240.01541.1270.0090.0090.0000.0000.0000.000
133L134VAL00.0430.02139.538-0.010-0.0100.0000.0000.0000.000
134L135CYS0-0.064-0.04638.5380.0020.0020.0000.0000.0000.000
135L136LEU0-0.0200.01138.702-0.011-0.0110.0000.0000.0000.000
136L137LEU00.0060.00635.2270.0130.0130.0000.0000.0000.000
137L138ASN0-0.008-0.02438.926-0.015-0.0150.0000.0000.0000.000
138L139ASN00.0330.02039.3340.0150.0150.0000.0000.0000.000
139L140PHE00.0000.01832.3150.0120.0120.0000.0000.0000.000
140L141TYR00.0430.02531.460-0.017-0.0170.0000.0000.0000.000
141L142PRO0-0.017-0.01429.2030.0180.0180.0000.0000.0000.000
142L143ARG10.9970.98525.4550.5680.5680.0000.0000.0000.000
143L144GLU-1-0.954-0.96025.702-0.423-0.4230.0000.0000.0000.000
144L145ALA00.0420.02128.4670.0370.0370.0000.0000.0000.000
145L146LYS10.9400.97629.3660.2280.2280.0000.0000.0000.000
146L147VAL00.019-0.00231.1940.0280.0280.0000.0000.0000.000
147L148GLN0-0.031-0.00232.023-0.012-0.0120.0000.0000.0000.000
148L149TRP00.022-0.00533.8970.0210.0210.0000.0000.0000.000
149L150LYS10.8210.88736.1700.1660.1660.0000.0000.0000.000
150L151VAL0-0.010-0.00438.8900.0080.0080.0000.0000.0000.000
151L152ASP-1-0.807-0.90141.022-0.126-0.1260.0000.0000.0000.000
152L153ASN0-0.065-0.02141.3080.0020.0020.0000.0000.0000.000
153L154ALA00.0400.03638.3430.0050.0050.0000.0000.0000.000
154L155LEU0-0.027-0.00531.022-0.007-0.0070.0000.0000.0000.000
155L156GLN0-0.029-0.00234.169-0.001-0.0010.0000.0000.0000.000
156L157SER0-0.006-0.02929.218-0.013-0.0130.0000.0000.0000.000
157L158GLY00.0070.02029.0140.0080.0080.0000.0000.0000.000
158L159ASN0-0.011-0.01229.882-0.022-0.0220.0000.0000.0000.000
159L160SER00.026-0.00931.8560.0270.0270.0000.0000.0000.000
160L161GLN0-0.030-0.00229.745-0.010-0.0100.0000.0000.0000.000
161L162GLU-1-0.935-0.95529.159-0.397-0.3970.0000.0000.0000.000
162L163SER00.007-0.01131.354-0.021-0.0210.0000.0000.0000.000
163L164VAL0-0.022-0.02029.5120.0220.0220.0000.0000.0000.000
164L165THR00.0130.01632.269-0.015-0.0150.0000.0000.0000.000
165L166GLU-1-0.906-0.95431.062-0.487-0.4870.0000.0000.0000.000
166L167GLN0-0.0120.00032.3170.0050.0050.0000.0000.0000.000
167L168ASP-1-0.739-0.84434.501-0.249-0.2490.0000.0000.0000.000
168L169SER0-0.034-0.01637.9810.0030.0030.0000.0000.0000.000
169L170LYS10.7390.83839.8960.2420.2420.0000.0000.0000.000
170L171ASP-1-0.851-0.90740.170-0.235-0.2350.0000.0000.0000.000
171L172SER0-0.0270.00135.622-0.004-0.0040.0000.0000.0000.000
172L173THR0-0.064-0.04636.170-0.002-0.0020.0000.0000.0000.000
173L174TYR0-0.035-0.03830.635-0.014-0.0140.0000.0000.0000.000
174L175SER00.027-0.01535.5080.0290.0290.0000.0000.0000.000
175L176LEU0-0.054-0.01331.733-0.017-0.0170.0000.0000.0000.000
176L177SER0-0.001-0.00935.0080.0290.0290.0000.0000.0000.000
177L178SER00.0090.01934.590-0.018-0.0180.0000.0000.0000.000
178L179THR00.0360.00135.0720.0270.0270.0000.0000.0000.000
179L180LEU0-0.0160.01935.741-0.013-0.0130.0000.0000.0000.000
180L181THR00.0210.00336.5040.0060.0060.0000.0000.0000.000
181L182LEU0-0.034-0.01337.6450.0000.0000.0000.0000.0000.000
182L183SER00.0460.01240.3170.0010.0010.0000.0000.0000.000
183L184LYS10.9890.99043.2470.1400.1400.0000.0000.0000.000
184L185ALA0-0.022-0.01245.5230.0080.0080.0000.0000.0000.000
185L186ASP-1-0.822-0.91542.667-0.147-0.1470.0000.0000.0000.000
186L187TYR00.0260.01044.8230.0030.0030.0000.0000.0000.000
187L188GLU-1-0.826-0.91846.042-0.120-0.1200.0000.0000.0000.000
188L189LYS10.7550.89043.7770.1440.1440.0000.0000.0000.000
189L190HIS10.8470.91342.3320.1480.1480.0000.0000.0000.000
190L191LYS10.8830.92846.9470.1030.1030.0000.0000.0000.000
191L192VAL00.0220.00844.760-0.003-0.0030.0000.0000.0000.000
192L193TYR00.011-0.00141.997-0.007-0.0070.0000.0000.0000.000
193L194ALA00.0070.01041.608-0.002-0.0020.0000.0000.0000.000
194L196GLU-1-0.850-0.91037.047-0.165-0.1650.0000.0000.0000.000
195L197VAL00.0450.00735.878-0.015-0.0150.0000.0000.0000.000
196L198THR0-0.055-0.02832.7820.0130.0130.0000.0000.0000.000
197L199HIS00.0650.02132.819-0.002-0.0020.0000.0000.0000.000
198L200GLN00.0420.02228.0640.0340.0340.0000.0000.0000.000
199L201GLY0-0.031-0.02833.016-0.003-0.0030.0000.0000.0000.000
200L202LEU0-0.065-0.02136.5300.0140.0140.0000.0000.0000.000
201L203SER0-0.015-0.01137.446-0.002-0.0020.0000.0000.0000.000
202L204SER00.015-0.00238.3230.0070.0070.0000.0000.0000.000
203L205PRO0-0.045-0.03635.620-0.006-0.0060.0000.0000.0000.000
204L206VAL00.0500.06038.0840.0110.0110.0000.0000.0000.000
205L207THR0-0.0010.00240.108-0.013-0.0130.0000.0000.0000.000
206L208LYS10.8980.94842.1620.1700.1700.0000.0000.0000.000
207L209SER00.0500.00343.474-0.006-0.0060.0000.0000.0000.000
208L210PHE0-0.0140.00744.7030.0040.0040.0000.0000.0000.000
209L211ASN0-0.032-0.03448.277-0.003-0.0030.0000.0000.0000.000
210L212ARG10.8070.90649.0010.1220.1220.0000.0000.0000.000
211L213GLY00.0140.00950.8690.0060.0060.0000.0000.0000.000
212L214GLU-1-0.866-0.89354.024-0.098-0.0980.0000.0000.0000.000
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