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: JLV59

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1848663.874136
FMO2-HF: Nuclear repulsion 1767297.06828
FMO2-HF: Total energy -81366.805856
FMO2-MP2: Total energy -81606.090317


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.
-2.354-1.1890.006-0.657-0.5150.003
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 : 0.030 / 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].
3C1GLY00.0340.0243.8731.0001.697-0.003-0.453-0.2410.002
4C2GLU-1-0.879-0.9146.5590.3550.3550.0000.0000.0000.000
5C3ARG10.7730.8499.1610.4140.4140.0000.0000.0000.000
6C4LYS10.8330.94712.3710.0760.0760.0000.0000.0000.000
7C5ILE00.0610.03515.7220.0060.0060.0000.0000.0000.000
8C6SER0-0.042-0.03218.6770.0080.0080.0000.0000.0000.000
9C7ARG10.9450.98422.1010.0380.0380.0000.0000.0000.000
10C8ILE0-0.0080.00025.6690.0080.0080.0000.0000.0000.000
11C9HIS00.0440.01828.327-0.007-0.0070.0000.0000.0000.000
12C10LEU0-0.0110.01529.9610.0050.0050.0000.0000.0000.000
13C11VAL00.012-0.01533.2510.0000.0000.0000.0000.0000.000
14C12SER0-0.055-0.03835.3470.0010.0010.0000.0000.0000.000
15C13GLU-1-0.848-0.91834.299-0.042-0.0420.0000.0000.0000.000
16C14PRO0-0.035-0.01035.372-0.002-0.0020.0000.0000.0000.000
17C15SER0-0.031-0.01236.7270.0000.0000.0000.0000.0000.000
18C16ILE00.0100.01231.984-0.002-0.0020.0000.0000.0000.000
19C17THR0-0.067-0.04928.2350.0020.0020.0000.0000.0000.000
20C18HIS00.0090.00128.136-0.008-0.0080.0000.0000.0000.000
21C19PHE0-0.020-0.01523.4500.0020.0020.0000.0000.0000.000
22C20LEU0-0.001-0.00122.012-0.002-0.0020.0000.0000.0000.000
23C21GLN00.0640.03716.643-0.017-0.0170.0000.0000.0000.000
24C22VAL0-0.014-0.01816.9040.0150.0150.0000.0000.0000.000
25C23SER00.013-0.01811.675-0.050-0.0500.0000.0000.0000.000
26C24TRP0-0.046-0.03811.717-0.025-0.0250.0000.0000.0000.000
27C25GLU-1-0.859-0.9166.3130.4090.4090.0000.0000.0000.000
28C26LYS10.8980.9383.583-2.677-2.2090.009-0.204-0.2740.001
29C27THR0-0.073-0.0489.264-0.209-0.2090.0000.0000.0000.000
30C28LEU00.0170.00813.007-0.037-0.0370.0000.0000.0000.000
31C29LYS10.8770.90715.545-0.276-0.2760.0000.0000.0000.000
32C30SER00.0360.02613.739-0.016-0.0160.0000.0000.0000.000
33C31GLY0-0.040-0.02915.869-0.029-0.0290.0000.0000.0000.000
34C32PHE0-0.036-0.01714.7280.0260.0260.0000.0000.0000.000
35C33VAL0-0.0040.00215.3360.0020.0020.0000.0000.0000.000
36C34ILE0-0.035-0.01117.277-0.004-0.0040.0000.0000.0000.000
37C35THR00.0220.00119.386-0.010-0.0100.0000.0000.0000.000
38C36LEU0-0.033-0.00721.2590.0030.0030.0000.0000.0000.000
39C37THR0-0.005-0.02924.032-0.005-0.0050.0000.0000.0000.000
40C38ASP-1-0.726-0.83426.395-0.065-0.0650.0000.0000.0000.000
41C39GLY00.0040.01428.2210.0030.0030.0000.0000.0000.000
42C40HIS0-0.041-0.01429.168-0.006-0.0060.0000.0000.0000.000
43C41SER0-0.080-0.07229.643-0.003-0.0030.0000.0000.0000.000
44C42ALA00.0350.01324.690-0.003-0.0030.0000.0000.0000.000
45C43TRP0-0.0100.00725.5510.0050.0050.0000.0000.0000.000
46C44THR0-0.015-0.02319.862-0.017-0.0170.0000.0000.0000.000
47C45GLY00.0470.03121.5120.0090.0090.0000.0000.0000.000
48C46THR00.0140.01817.837-0.006-0.0060.0000.0000.0000.000
49C47VAL0-0.032-0.00919.4120.0060.0060.0000.0000.0000.000
50C48SER00.0820.04218.6380.0110.0110.0000.0000.0000.000
51C49GLU-1-0.718-0.83518.3450.1930.1930.0000.0000.0000.000
52C50SER00.024-0.00820.088-0.003-0.0030.0000.0000.0000.000
53C51LYS10.8980.95123.057-0.012-0.0120.0000.0000.0000.000
54C52ILE00.0050.01919.208-0.003-0.0030.0000.0000.0000.000
55C53SER0-0.012-0.01123.5810.0060.0060.0000.0000.0000.000
56C54GLN00.0290.03325.756-0.001-0.0010.0000.0000.0000.000
57C55GLU-1-0.841-0.91226.7260.0240.0240.0000.0000.0000.000
58C56ALA0-0.011-0.00726.461-0.002-0.0020.0000.0000.0000.000
59C57ALA00.003-0.00228.500-0.002-0.0020.0000.0000.0000.000
60C58THR0-0.042-0.03631.346-0.005-0.0050.0000.0000.0000.000
61C59MET0-0.075-0.03130.495-0.004-0.0040.0000.0000.0000.000
62C60ALA00.0070.01633.0420.0000.0000.0000.0000.0000.000
63C61MET0-0.056-0.01529.7370.0040.0040.0000.0000.0000.000
64C62ASN00.0270.00727.0470.0110.0110.0000.0000.0000.000
65C63LYS10.8640.90221.511-0.129-0.1290.0000.0000.0000.000
66C64GLY00.0260.02422.9300.0060.0060.0000.0000.0000.000
67C65LYS10.9610.97123.732-0.070-0.0700.0000.0000.0000.000
68C66TYR00.006-0.00724.818-0.001-0.0010.0000.0000.0000.000
69C67VAL00.014-0.00319.122-0.006-0.0060.0000.0000.0000.000
70C68GLY00.0140.00921.4120.0010.0010.0000.0000.0000.000
71C69GLU-1-0.807-0.88822.8500.0440.0440.0000.0000.0000.000
72C70LEU00.0240.01321.922-0.010-0.0100.0000.0000.0000.000
73C71ARG10.9070.95213.760-0.211-0.2110.0000.0000.0000.000
74C72LYS10.8220.89420.625-0.068-0.0680.0000.0000.0000.000
75C73ALA00.0350.03523.672-0.009-0.0090.0000.0000.0000.000
76C74LEU00.0310.02120.936-0.011-0.0110.0000.0000.0000.000
77C75LEU0-0.020-0.00316.062-0.015-0.0150.0000.0000.0000.000
78C76SER0-0.040-0.04719.5420.0000.0000.0000.0000.0000.000
79C77GLY0-0.0180.01121.9500.0050.0050.0000.0000.0000.000
80C78ALA00.0200.00425.108-0.009-0.0090.0000.0000.0000.000
81C79GLY00.0150.00627.7060.0000.0000.0000.0000.0000.000
82C80PRO00.002-0.01630.7120.0020.0020.0000.0000.0000.000
83C81ALA0-0.0090.02130.9510.0010.0010.0000.0000.0000.000
84C82ASP-1-0.802-0.89029.1220.0270.0270.0000.0000.0000.000
85C83VAL0-0.0060.00331.236-0.004-0.0040.0000.0000.0000.000
86C84TYR0-0.005-0.01626.5490.0010.0010.0000.0000.0000.000
87C85THR00.0200.00131.328-0.002-0.0020.0000.0000.0000.000
88C86PHE00.0140.01130.7530.0010.0010.0000.0000.0000.000
89C87ASN0-0.041-0.00432.8610.0010.0010.0000.0000.0000.000
90C88PHE00.1310.05332.6460.0000.0000.0000.0000.0000.000
91C89SER0-0.005-0.00435.549-0.001-0.0010.0000.0000.0000.000
92C90LYS10.8600.91536.7410.0200.0200.0000.0000.0000.000
93C91GLU-1-0.830-0.90131.193-0.040-0.0400.0000.0000.0000.000
94C92SER00.0810.06030.777-0.001-0.0010.0000.0000.0000.000
95C93ARG10.8870.93230.9090.0030.0030.0000.0000.0000.000
96C94TYR00.0570.03926.146-0.001-0.0010.0000.0000.0000.000
97C95PHE0-0.030-0.02529.0120.0060.0060.0000.0000.0000.000
98C96PHE00.0300.01325.891-0.003-0.0030.0000.0000.0000.000
99C97PHE0-0.017-0.02231.1000.0050.0050.0000.0000.0000.000
100C98LYS10.7700.87428.485-0.033-0.0330.0000.0000.0000.000
101C99LYS10.8300.91233.500-0.005-0.0050.0000.0000.0000.000
102C100ASN00.0100.00435.6510.0000.0000.0000.0000.0000.000
103C101LEU00.0480.00537.965-0.002-0.0020.0000.0000.0000.000
104C102LYS10.8940.93241.361-0.017-0.0170.0000.0000.0000.000
105C103ASP-1-0.798-0.87142.0670.0070.0070.0000.0000.0000.000
106C104VAL00.0060.03638.8090.0000.0000.0000.0000.0000.000
107C105SER0-0.010-0.03537.729-0.002-0.0020.0000.0000.0000.000
108C106PHE0-0.0170.00231.9780.0000.0000.0000.0000.0000.000
109C107ARG10.8850.95632.542-0.007-0.0070.0000.0000.0000.000
110C108LEU00.0150.01427.5800.0030.0030.0000.0000.0000.000
111C109GLY00.0620.03427.9700.0070.0070.0000.0000.0000.000
112C110SER0-0.055-0.05228.717-0.007-0.0070.0000.0000.0000.000
113C111PHE00.0340.02024.0130.0010.0010.0000.0000.0000.000
114C112ASN0-0.012-0.01627.036-0.006-0.0060.0000.0000.0000.000
115C113LEU0-0.066-0.03024.6490.0010.0010.0000.0000.0000.000
116C114GLU-1-0.884-0.93026.113-0.040-0.0400.0000.0000.0000.000
117C115LYS10.8580.92126.6390.0520.0520.0000.0000.0000.000
118C116VAL0-0.0050.00423.297-0.001-0.0010.0000.0000.0000.000
119C117GLU-1-0.926-0.96426.379-0.077-0.0770.0000.0000.0000.000
120C118ASN0-0.042-0.02725.2040.0060.0060.0000.0000.0000.000
121C119PRO00.0110.00724.934-0.012-0.0120.0000.0000.0000.000
122C120ALA00.0410.01425.038-0.008-0.0080.0000.0000.0000.000
123C121GLU-1-0.801-0.87520.903-0.178-0.1780.0000.0000.0000.000
124C122VAL0-0.0090.00020.428-0.020-0.0200.0000.0000.0000.000
125C123ILE0-0.022-0.01020.593-0.014-0.0140.0000.0000.0000.000
126C124ARG10.8580.90521.1180.1520.1520.0000.0000.0000.000
127C125GLU-1-0.793-0.85614.231-0.396-0.3960.0000.0000.0000.000
128C126LEU0-0.014-0.00416.633-0.028-0.0280.0000.0000.0000.000
129C127ILE0-0.035-0.02418.084-0.003-0.0030.0000.0000.0000.000
130C128ASP-1-0.907-0.94916.059-0.320-0.3200.0000.0000.0000.000
131C129TYR00.0430.0179.8350.0640.0640.0000.0000.0000.000
132C130ALA0-0.071-0.04114.472-0.006-0.0060.0000.0000.0000.000
133C131LEU0-0.010-0.00817.1300.0190.0190.0000.0000.0000.000
134C132ASP-1-0.916-0.95210.957-0.562-0.5620.0000.0000.0000.000
135C1677ARG10.9590.97511.9030.2680.2680.0000.0000.0000.000
136C1678ASN0-0.046-0.02013.9530.0370.0370.0000.0000.0000.000
137C1679ASN0-0.012-0.00315.7160.0500.0500.0000.0000.0000.000
138C1680LEU0-0.0190.0049.4870.0200.0200.0000.0000.0000.000
139C1681LEU00.0270.00213.5440.0370.0370.0000.0000.0000.000
140C1682GLN0-0.052-0.01615.8400.0380.0380.0000.0000.0000.000
141C1683ALA00.0390.01815.2580.0190.0190.0000.0000.0000.000
142C1684GLU-1-0.915-0.96612.402-0.109-0.1090.0000.0000.0000.000
143C1685LEU0-0.044-0.03515.9460.0260.0260.0000.0000.0000.000
144C1686GLU-1-0.917-0.94819.370-0.068-0.0680.0000.0000.0000.000
145C1687GLU-1-0.891-0.94016.642-0.007-0.0070.0000.0000.0000.000
146C1688LEU0-0.027-0.02917.5060.0140.0140.0000.0000.0000.000
147C1689ARG10.8090.90520.6420.0610.0610.0000.0000.0000.000
148C1690ALA00.0740.04822.4090.0060.0060.0000.0000.0000.000
149C1691VAL0-0.006-0.00719.8930.0060.0060.0000.0000.0000.000
150C1692VAL0-0.0140.00823.2710.0060.0060.0000.0000.0000.000
151C1693GLU-1-0.922-0.96226.083-0.012-0.0120.0000.0000.0000.000
152C1694GLN0-0.017-0.00523.3250.0060.0060.0000.0000.0000.000
153C1695THR0-0.022-0.01425.7430.0050.0050.0000.0000.0000.000
154C1696GLU-1-0.824-0.90928.2900.0160.0160.0000.0000.0000.000
155C1697ARG10.8900.95331.173-0.003-0.0030.0000.0000.0000.000
156C1698SER0-0.024-0.02829.6530.0000.0000.0000.0000.0000.000
157C1699ARG10.7480.84132.219-0.016-0.0160.0000.0000.0000.000
158C1700LYS10.9390.95433.890-0.007-0.0070.0000.0000.0000.000
159C1701LEU0-0.0400.00235.164-0.001-0.0010.0000.0000.0000.000
160C1702ALA00.0760.03135.5670.0000.0000.0000.0000.0000.000
161C1703GLU-1-0.869-0.90737.4970.0170.0170.0000.0000.0000.000
162C1704GLN0-0.024-0.02339.610-0.001-0.0010.0000.0000.0000.000
163C1705GLU-1-0.918-0.95338.9940.0180.0180.0000.0000.0000.000
164C1706LEU0-0.0150.00441.0410.0000.0000.0000.0000.0000.000
165C1707ILE00.0180.01542.9270.0000.0000.0000.0000.0000.000
166C1708GLU-1-0.903-0.94045.8710.0120.0120.0000.0000.0000.000
167C1709THR0-0.051-0.03844.1810.0000.0000.0000.0000.0000.000
168C1710SER0-0.063-0.04946.4780.0000.0000.0000.0000.0000.000
169C1711GLU-1-0.905-0.94648.0950.0110.0110.0000.0000.0000.000
170C1712ARG10.9560.97749.583-0.015-0.0150.0000.0000.0000.000
171C1713VAL0-0.013-0.01548.1030.0000.0000.0000.0000.0000.000
172C1714GLN00.0260.01751.2950.0010.0010.0000.0000.0000.000
173C1715LEU0-0.023-0.01053.7820.0000.0000.0000.0000.0000.000
174C1716LEU0-0.0010.00653.0400.0000.0000.0000.0000.0000.000
175C1717HIS00.0530.01554.3470.0000.0000.0000.0000.0000.000
176C1718SER0-0.0150.01156.3720.0000.0000.0000.0000.0000.000
177C1719GLN0-0.004-0.00559.2800.0000.0000.0000.0000.0000.000
178C1720ASN0-0.010-0.01357.1330.0000.0000.0000.0000.0000.000
179C1721THR0-0.017-0.02459.1370.0000.0000.0000.0000.0000.000
180C1722SER0-0.0100.00861.6490.0000.0000.0000.0000.0000.000
181C1723LEU00.0200.00062.5080.0000.0000.0000.0000.0000.000
182C1724ILE0-0.021-0.00160.1440.0000.0000.0000.0000.0000.000
183C1725ASN0-0.007-0.01164.6600.0000.0000.0000.0000.0000.000
184C1726GLN0-0.037-0.01267.3860.0000.0000.0000.0000.0000.000
185C1727LYS10.8940.92966.346-0.014-0.0140.0000.0000.0000.000
186C1728LYS10.7900.87767.384-0.014-0.0140.0000.0000.0000.000
187C1729LYS10.9280.97870.061-0.010-0.0100.0000.0000.0000.000
188C1730MET00.0160.01072.2290.0000.0000.0000.0000.0000.000
189C1731ASP-1-0.781-0.86470.3580.0130.0130.0000.0000.0000.000
190C1732ALA0-0.033-0.01073.8860.0000.0000.0000.0000.0000.000
191C1733ASP-1-0.833-0.93876.6890.0100.0100.0000.0000.0000.000
192C1734LEU0-0.021-0.01974.7470.0000.0000.0000.0000.0000.000
193C1735SER0-0.0210.00578.4800.0000.0000.0000.0000.0000.000
194C1736GLN0-0.052-0.01380.1030.0000.0000.0000.0000.0000.000
195C1737LEU00.0120.00081.8120.0000.0000.0000.0000.0000.000
196C1738GLN0-0.067-0.03481.4650.0000.0000.0000.0000.0000.000
197C1739THR0-0.005-0.03283.4630.0000.0000.0000.0000.0000.000
198C1740GLU-1-0.875-0.92085.7710.0080.0080.0000.0000.0000.000
199C1741VAL0-0.051-0.02586.3610.0000.0000.0000.0000.0000.000
200C1742GLU-1-0.930-0.95785.3230.0100.0100.0000.0000.0000.000
201C1743GLU-1-0.856-0.93688.7840.0090.0090.0000.0000.0000.000
202C1744ALA0-0.024-0.00991.4270.0000.0000.0000.0000.0000.000
203C1745VAL0-0.063-0.02390.9590.0000.0000.0000.0000.0000.000
204C1746GLN0-0.100-0.06291.6540.0000.0000.0000.0000.0000.000
205C1747GLU-1-0.995-0.97794.8170.0070.0070.0000.0000.0000.000
206C1748CYS0-0.124-0.05797.3220.0000.0000.0000.0000.0000.000