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: 85QYY

Calculation Name: 5WLZ-C-Xray372

Preferred Name: Cardiac myosin

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 5WLZ

Chain ID: C

ChEMBL ID: CHEMBL3831286

UniProt ID: P12883

Base Structure: X-ray

Registration Date: 2023-06-22

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1847249.426924
FMO2-HF: Nuclear repulsion 1765884.770533
FMO2-HF: Total energy -81364.656392
FMO2-MP2: Total energy -81604.054025


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(C:-1:GLY)


Summations of interaction energy for fragment #1(C:-1:GLY)
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.
-7.217-5.5170.062-0.84-0.9220.005
Interaction energy analysis for fragmet #1(C:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.013
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].
3C1GLY00.0180.0063.8211.9732.814-0.002-0.369-0.4710.001
4C2GLU-1-0.951-0.9526.1430.0150.0150.0000.0000.0000.000
5C3ARG10.8590.9138.4920.5520.5520.0000.0000.0000.000
6C4LYS10.9100.96711.7870.1120.1120.0000.0000.0000.000
7C5ILE00.0370.01314.9910.0240.0240.0000.0000.0000.000
8C6SER0-0.038-0.02018.1660.0010.0010.0000.0000.0000.000
9C7ARG10.9650.99821.3860.0660.0660.0000.0000.0000.000
10C8ILE0-0.021-0.00924.7810.0090.0090.0000.0000.0000.000
11C9HIS00.0140.00027.390-0.007-0.0070.0000.0000.0000.000
12C10LEU0-0.018-0.00329.1780.0070.0070.0000.0000.0000.000
13C11VAL00.0330.00032.566-0.001-0.0010.0000.0000.0000.000
14C12SER0-0.064-0.02534.8030.0000.0000.0000.0000.0000.000
15C13GLU-1-0.884-0.95434.619-0.039-0.0390.0000.0000.0000.000
16C14PRO0-0.038-0.00734.872-0.003-0.0030.0000.0000.0000.000
17C15SER0-0.047-0.01435.980-0.002-0.0020.0000.0000.0000.000
18C16ILE00.0380.02231.326-0.003-0.0030.0000.0000.0000.000
19C17THR0-0.038-0.02628.2550.0020.0020.0000.0000.0000.000
20C18HIS00.0210.02427.675-0.010-0.0100.0000.0000.0000.000
21C19PHE0-0.008-0.01122.890-0.001-0.0010.0000.0000.0000.000
22C20LEU0-0.004-0.00721.3010.0030.0030.0000.0000.0000.000
23C21GLN00.0470.01316.155-0.052-0.0520.0000.0000.0000.000
24C22VAL0-0.004-0.00515.7970.0230.0230.0000.0000.0000.000
25C23SER00.0010.00111.201-0.040-0.0400.0000.0000.0000.000
26C24TRP0-0.015-0.02411.168-0.016-0.0160.0000.0000.0000.000
27C25GLU-1-0.837-0.9117.3571.2341.2340.0000.0000.0000.000
28C26LYS11.0041.0212.964-8.405-7.5460.064-0.471-0.4510.004
29C27THR0-0.086-0.0628.983-0.284-0.2840.0000.0000.0000.000
30C28LEU00.0470.01812.800-0.012-0.0120.0000.0000.0000.000
31C29LYS10.9500.95115.366-0.394-0.3940.0000.0000.0000.000
32C30SER00.0100.00013.996-0.006-0.0060.0000.0000.0000.000
33C31GLY0-0.0100.01116.103-0.009-0.0090.0000.0000.0000.000
34C32PHE0-0.037-0.02414.9120.0390.0390.0000.0000.0000.000
35C33VAL00.0010.00015.606-0.004-0.0040.0000.0000.0000.000
36C34ILE0-0.044-0.01017.331-0.021-0.0210.0000.0000.0000.000
37C35THR00.0130.00818.984-0.008-0.0080.0000.0000.0000.000
38C36LEU0-0.0130.00521.116-0.004-0.0040.0000.0000.0000.000
39C37THR00.009-0.00323.426-0.006-0.0060.0000.0000.0000.000
40C38ASP-1-0.755-0.90225.920-0.065-0.0650.0000.0000.0000.000
41C39GLY0-0.0250.00527.7250.0010.0010.0000.0000.0000.000
42C40HIS0-0.040-0.00828.755-0.006-0.0060.0000.0000.0000.000
43C41SER0-0.028-0.01329.133-0.001-0.0010.0000.0000.0000.000
44C42ALA00.022-0.01124.147-0.006-0.0060.0000.0000.0000.000
45C43TRP0-0.015-0.00325.2440.0060.0060.0000.0000.0000.000
46C44THR00.0420.01719.872-0.013-0.0130.0000.0000.0000.000
47C45GLY00.0090.00321.4880.0090.0090.0000.0000.0000.000
48C46THR00.0240.01218.407-0.003-0.0030.0000.0000.0000.000
49C47VAL0-0.029-0.00719.652-0.001-0.0010.0000.0000.0000.000
50C48SER00.0830.03119.1970.0200.0200.0000.0000.0000.000
51C49GLU-1-0.843-0.93418.6750.2960.2960.0000.0000.0000.000
52C50SER0-0.023-0.02320.403-0.009-0.0090.0000.0000.0000.000
53C51LYS10.8600.93523.297-0.088-0.0880.0000.0000.0000.000
54C52ILE0-0.0010.02119.489-0.010-0.0100.0000.0000.0000.000
55C53SER0-0.014-0.01523.8680.0000.0000.0000.0000.0000.000
56C54GLN00.0440.04026.034-0.003-0.0030.0000.0000.0000.000
57C55GLU-1-0.921-0.97326.9670.0570.0570.0000.0000.0000.000
58C56ALA0-0.039-0.01926.458-0.005-0.0050.0000.0000.0000.000
59C57ALA0-0.012-0.00928.536-0.004-0.0040.0000.0000.0000.000
60C58THR0-0.043-0.01731.619-0.007-0.0070.0000.0000.0000.000
61C59MET0-0.052-0.02030.329-0.006-0.0060.0000.0000.0000.000
62C60ALA00.0160.02832.941-0.002-0.0020.0000.0000.0000.000
63C61MET0-0.050-0.01229.5330.0030.0030.0000.0000.0000.000
64C62ASN00.0490.01526.5750.0120.0120.0000.0000.0000.000
65C63LYS10.9780.98221.707-0.214-0.2140.0000.0000.0000.000
66C64GLY00.0080.00922.5010.0080.0080.0000.0000.0000.000
67C65LYS10.9780.98223.102-0.087-0.0870.0000.0000.0000.000
68C66TYR00.0340.02024.625-0.001-0.0010.0000.0000.0000.000
69C67VAL00.013-0.00618.745-0.004-0.0040.0000.0000.0000.000
70C68GLY0-0.004-0.00420.807-0.001-0.0010.0000.0000.0000.000
71C69GLU-1-0.871-0.95722.1780.0510.0510.0000.0000.0000.000
72C70LEU0-0.015-0.01021.376-0.012-0.0120.0000.0000.0000.000
73C71ARG10.9080.95113.414-0.224-0.2240.0000.0000.0000.000
74C72LYS10.8590.94020.058-0.069-0.0690.0000.0000.0000.000
75C73ALA00.0760.06623.004-0.011-0.0110.0000.0000.0000.000
76C74LEU00.0010.04020.153-0.014-0.0140.0000.0000.0000.000
77C75LEU0-0.061-0.01915.403-0.019-0.0190.0000.0000.0000.000
78C76SER0-0.061-0.04019.0670.0070.0070.0000.0000.0000.000
79C77GLY00.0720.05520.9170.0100.0100.0000.0000.0000.000
80C78ALA0-0.007-0.02124.219-0.009-0.0090.0000.0000.0000.000
81C79GLY00.0070.00727.2800.0000.0000.0000.0000.0000.000
82C80PRO0-0.002-0.01529.8120.0020.0020.0000.0000.0000.000
83C81ALA0-0.0290.01130.0530.0030.0030.0000.0000.0000.000
84C82ASP-1-0.883-0.95028.0930.0330.0330.0000.0000.0000.000
85C83VAL0-0.0190.00330.347-0.006-0.0060.0000.0000.0000.000
86C84TYR0-0.034-0.07125.0400.0040.0040.0000.0000.0000.000
87C85THR0-0.044-0.03630.678-0.003-0.0030.0000.0000.0000.000
88C86PHE00.0550.01330.1060.0040.0040.0000.0000.0000.000
89C87ASN0-0.0390.00032.348-0.002-0.0020.0000.0000.0000.000
90C88PHE00.1070.05332.2710.0010.0010.0000.0000.0000.000
91C89SER0-0.016-0.01135.1010.0000.0000.0000.0000.0000.000
92C90LYS10.8870.92936.4630.0050.0050.0000.0000.0000.000
93C91GLU-1-0.862-0.92131.735-0.014-0.0140.0000.0000.0000.000
94C92SER00.0250.02730.9630.0030.0030.0000.0000.0000.000
95C93ARG10.8680.91631.139-0.021-0.0210.0000.0000.0000.000
96C94TYR00.0550.03025.315-0.001-0.0010.0000.0000.0000.000
97C95PHE0-0.038-0.02028.6260.0080.0080.0000.0000.0000.000
98C96PHE00.0480.02425.237-0.005-0.0050.0000.0000.0000.000
99C97PHE0-0.056-0.03130.2970.0070.0070.0000.0000.0000.000
100C98LYS10.9840.99229.639-0.041-0.0410.0000.0000.0000.000
101C99LYS10.9110.96932.514-0.006-0.0060.0000.0000.0000.000
102C100ASN00.0130.00535.059-0.003-0.0030.0000.0000.0000.000
103C101LEU00.0300.00336.783-0.002-0.0020.0000.0000.0000.000
104C102LYS10.9110.94340.253-0.019-0.0190.0000.0000.0000.000
105C103ASP-1-0.892-0.92841.5570.0120.0120.0000.0000.0000.000
106C104VAL0-0.0270.01437.8070.0010.0010.0000.0000.0000.000
107C105SER0-0.016-0.04436.753-0.002-0.0020.0000.0000.0000.000
108C106PHE00.0140.01531.4060.0000.0000.0000.0000.0000.000
109C107ARG10.9210.95032.410-0.027-0.0270.0000.0000.0000.000
110C108LEU00.0180.03026.6580.0050.0050.0000.0000.0000.000
111C109GLY00.0760.02727.3730.0100.0100.0000.0000.0000.000
112C110SER0-0.013-0.03428.234-0.012-0.0120.0000.0000.0000.000
113C111PHE0-0.013-0.00224.3140.0090.0090.0000.0000.0000.000
114C112ASN0-0.022-0.01327.329-0.012-0.0120.0000.0000.0000.000
115C113LEU0-0.023-0.00424.2500.0060.0060.0000.0000.0000.000
116C114GLU-1-0.854-0.91425.990-0.009-0.0090.0000.0000.0000.000
117C115LYS10.9050.95326.2790.0370.0370.0000.0000.0000.000
118C116VAL0-0.022-0.00323.2400.0020.0020.0000.0000.0000.000
119C117GLU-1-0.911-0.95626.179-0.056-0.0560.0000.0000.0000.000
120C118ASN0-0.025-0.01324.4650.0040.0040.0000.0000.0000.000
121C119PRO00.0040.00524.485-0.012-0.0120.0000.0000.0000.000
122C120ALA00.0470.01424.786-0.011-0.0110.0000.0000.0000.000
123C121GLU-1-0.960-0.99320.405-0.196-0.1960.0000.0000.0000.000
124C122VAL00.0280.01820.009-0.024-0.0240.0000.0000.0000.000
125C123ILE0-0.0110.00120.235-0.021-0.0210.0000.0000.0000.000
126C124ARG10.9460.97521.3110.1650.1650.0000.0000.0000.000
127C125GLU-1-0.819-0.88714.639-0.412-0.4120.0000.0000.0000.000
128C126LEU0-0.0180.00216.435-0.041-0.0410.0000.0000.0000.000
129C127ILE0-0.052-0.05217.741-0.018-0.0180.0000.0000.0000.000
130C128ASP-1-0.898-0.95316.201-0.406-0.4060.0000.0000.0000.000
131C129TYR00.0120.0119.798-0.045-0.0450.0000.0000.0000.000
132C130ALA0-0.072-0.04314.358-0.021-0.0210.0000.0000.0000.000
133C131LEU0-0.033-0.02916.9340.0200.0200.0000.0000.0000.000
134C132ASP-1-0.887-0.92410.862-0.807-0.8070.0000.0000.0000.000
135C1677ARG10.9490.97011.6370.3820.3820.0000.0000.0000.000
136C1678ASN0-0.042-0.01413.7410.0550.0550.0000.0000.0000.000
137C1679ASN00.0030.00315.2160.0710.0710.0000.0000.0000.000
138C1680LEU0-0.0110.0059.2310.0160.0160.0000.0000.0000.000
139C1681LEU0-0.006-0.02413.2930.0450.0450.0000.0000.0000.000
140C1682GLN0-0.046-0.02015.6890.0560.0560.0000.0000.0000.000
141C1683ALA00.0440.02314.7230.0270.0270.0000.0000.0000.000
142C1684GLU-1-0.924-0.96712.479-0.267-0.2670.0000.0000.0000.000
143C1685LEU0-0.055-0.02715.9760.0390.0390.0000.0000.0000.000
144C1686GLU-1-0.969-0.98819.697-0.154-0.1540.0000.0000.0000.000
145C1687GLU-1-0.897-0.93516.625-0.114-0.1140.0000.0000.0000.000
146C1688LEU0-0.024-0.02917.2210.0250.0250.0000.0000.0000.000
147C1689ARG10.8780.93720.5940.1340.1340.0000.0000.0000.000
148C1690ALA00.0700.05022.3990.0110.0110.0000.0000.0000.000
149C1691VAL0-0.002-0.00420.2240.0120.0120.0000.0000.0000.000
150C1692VAL0-0.0270.01723.5930.0120.0120.0000.0000.0000.000
151C1693GLU-1-0.892-0.94326.266-0.061-0.0610.0000.0000.0000.000
152C1694GLN0-0.023-0.01124.0070.0130.0130.0000.0000.0000.000
153C1695THR0-0.033-0.04925.8490.0080.0080.0000.0000.0000.000
154C1696GLU-1-0.856-0.93328.457-0.015-0.0150.0000.0000.0000.000
155C1697ARG10.8870.95531.1070.0330.0330.0000.0000.0000.000
156C1698SER0-0.012-0.02230.0060.0030.0030.0000.0000.0000.000
157C1699ARG10.9080.96432.5340.0160.0160.0000.0000.0000.000
158C1700LYS10.9480.96834.0920.0230.0230.0000.0000.0000.000
159C1701LEU0-0.047-0.01135.5630.0010.0010.0000.0000.0000.000
160C1702ALA00.0610.02435.8810.0010.0010.0000.0000.0000.000
161C1703GLU-1-0.948-0.96537.752-0.003-0.0030.0000.0000.0000.000
162C1704GLN0-0.060-0.04639.878-0.001-0.0010.0000.0000.0000.000
163C1705GLU-1-0.909-0.94340.004-0.003-0.0030.0000.0000.0000.000
164C1706LEU0-0.0160.00641.3240.0020.0020.0000.0000.0000.000
165C1707ILE0-0.0080.00743.1720.0010.0010.0000.0000.0000.000
166C1708GLU-1-0.893-0.92545.691-0.004-0.0040.0000.0000.0000.000
167C1709THR0-0.044-0.04044.4410.0010.0010.0000.0000.0000.000
168C1710SER0-0.092-0.08446.5040.0010.0010.0000.0000.0000.000
169C1711GLU-1-0.895-0.94048.079-0.003-0.0030.0000.0000.0000.000
170C1712ARG10.9580.97850.090-0.002-0.0020.0000.0000.0000.000
171C1713VAL0-0.016-0.00848.1310.0010.0010.0000.0000.0000.000
172C1714GLN00.0340.02151.4360.0010.0010.0000.0000.0000.000
173C1715LEU0-0.017-0.01153.8770.0000.0000.0000.0000.0000.000
174C1716LEU0-0.030-0.01353.2400.0000.0000.0000.0000.0000.000
175C1717HIS00.0220.00153.9450.0000.0000.0000.0000.0000.000
176C1718SER0-0.016-0.01156.4550.0000.0000.0000.0000.0000.000
177C1719GLN00.0020.00059.3580.0000.0000.0000.0000.0000.000
178C1720ASN00.0090.01157.2480.0000.0000.0000.0000.0000.000
179C1721THR0-0.013-0.00959.4290.0000.0000.0000.0000.0000.000
180C1722SER0-0.0110.00261.9780.0000.0000.0000.0000.0000.000
181C1723LEU00.0360.01062.8230.0000.0000.0000.0000.0000.000
182C1724ILE0-0.026-0.00760.5870.0000.0000.0000.0000.0000.000
183C1725ASN0-0.006-0.00964.9970.0010.0010.0000.0000.0000.000
184C1726GLN0-0.014-0.00167.8140.0000.0000.0000.0000.0000.000
185C1727LYS10.9310.97865.814-0.009-0.0090.0000.0000.0000.000
186C1728LYS10.8960.95167.267-0.009-0.0090.0000.0000.0000.000
187C1729LYS10.9560.97570.344-0.004-0.0040.0000.0000.0000.000
188C1730MET00.0100.00571.8890.0000.0000.0000.0000.0000.000
189C1731ASP-1-0.863-0.93770.5790.0080.0080.0000.0000.0000.000
190C1732ALA0-0.061-0.02774.0760.0000.0000.0000.0000.0000.000
191C1733ASP-1-0.901-0.96476.5800.0050.0050.0000.0000.0000.000
192C1734LEU0-0.031-0.01575.3420.0000.0000.0000.0000.0000.000
193C1735SER0-0.016-0.01278.7440.0000.0000.0000.0000.0000.000
194C1736GLN00.0080.02480.6800.0000.0000.0000.0000.0000.000
195C1737LEU00.0350.01881.9260.0000.0000.0000.0000.0000.000
196C1738GLN0-0.040-0.00281.6560.0000.0000.0000.0000.0000.000
197C1739THR0-0.028-0.05483.5720.0000.0000.0000.0000.0000.000
198C1740GLU-1-0.902-0.93985.9840.0050.0050.0000.0000.0000.000
199C1741VAL0-0.061-0.02786.4500.0000.0000.0000.0000.0000.000
200C1742GLU-1-0.991-0.99686.2490.0070.0070.0000.0000.0000.000
201C1743GLU-1-0.875-0.96689.1600.0060.0060.0000.0000.0000.000
202C1744ALA0-0.042-0.00191.6560.0000.0000.0000.0000.0000.000
203C1745VAL0-0.067-0.03391.1780.0000.0000.0000.0000.0000.000
204C1746GLN0-0.097-0.04090.7860.0000.0000.0000.0000.0000.000
205C1747GLU-1-0.921-0.95894.8920.0050.0050.0000.0000.0000.000
206C1748CYS0-0.141-0.05397.7650.0000.0000.0000.0000.0000.000