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: N9LYQ

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1847864.283863
FMO2-HF: Nuclear repulsion 1766498.219436
FMO2-HF: Total energy -81366.064427
FMO2-MP2: Total energy -81605.43842


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.
-2.617-1.3210.056-0.565-0.7880.002
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 : 0.003 / q_NPA : -0.007
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].
3C1GLY00.0250.0103.8211.9402.814-0.002-0.391-0.4820.001
4C2GLU-1-0.870-0.9065.6780.1920.1920.0000.0000.0000.000
5C3ARG10.7850.8488.4900.4620.4620.0000.0000.0000.000
6C4LYS10.9140.97511.7850.0740.0740.0000.0000.0000.000
7C5ILE00.0340.01214.9910.0240.0240.0000.0000.0000.000
8C6SER0-0.037-0.02418.165-0.004-0.0040.0000.0000.0000.000
9C7ARG10.9380.99121.3860.0550.0550.0000.0000.0000.000
10C8ILE0-0.019-0.00624.7680.0070.0070.0000.0000.0000.000
11C9HIS00.0240.00427.389-0.008-0.0080.0000.0000.0000.000
12C10LEU0-0.0160.00629.3450.0060.0060.0000.0000.0000.000
13C11VAL00.031-0.00132.565-0.001-0.0010.0000.0000.0000.000
14C12SER0-0.061-0.03234.8270.0000.0000.0000.0000.0000.000
15C13GLU-1-0.855-0.93034.184-0.032-0.0320.0000.0000.0000.000
16C14PRO0-0.037-0.00834.872-0.002-0.0020.0000.0000.0000.000
17C15SER0-0.044-0.01035.980-0.001-0.0010.0000.0000.0000.000
18C16ILE00.0320.01931.399-0.003-0.0030.0000.0000.0000.000
19C17THR0-0.026-0.02528.1290.0020.0020.0000.0000.0000.000
20C18HIS0-0.012-0.00727.676-0.008-0.0080.0000.0000.0000.000
21C19PHE0-0.011-0.01322.902-0.002-0.0020.0000.0000.0000.000
22C20LEU0-0.015-0.01021.4180.0040.0040.0000.0000.0000.000
23C21GLN00.0580.02316.285-0.041-0.0410.0000.0000.0000.000
24C22VAL0-0.011-0.00916.0760.0220.0220.0000.0000.0000.000
25C23SER0-0.008-0.01311.230-0.052-0.0520.0000.0000.0000.000
26C24TRP0-0.029-0.03211.043-0.031-0.0310.0000.0000.0000.000
27C25GLU-1-0.848-0.9147.0951.4901.4900.0000.0000.0000.000
28C26LYS10.9110.9612.877-4.328-3.9060.058-0.174-0.3060.001
29C27THR0-0.071-0.0488.979-0.272-0.2720.0000.0000.0000.000
30C28LEU00.0380.01612.795-0.008-0.0080.0000.0000.0000.000
31C29LYS10.8820.90715.362-0.362-0.3620.0000.0000.0000.000
32C30SER0-0.007-0.00313.954-0.010-0.0100.0000.0000.0000.000
33C31GLY0-0.030-0.00316.103-0.007-0.0070.0000.0000.0000.000
34C32PHE0-0.032-0.02314.9120.0380.0380.0000.0000.0000.000
35C33VAL0-0.009-0.00515.630-0.007-0.0070.0000.0000.0000.000
36C34ILE0-0.028-0.00417.331-0.018-0.0180.0000.0000.0000.000
37C35THR00.012-0.00119.215-0.006-0.0060.0000.0000.0000.000
38C36LEU0-0.0210.00521.116-0.004-0.0040.0000.0000.0000.000
39C37THR00.017-0.01023.509-0.005-0.0050.0000.0000.0000.000
40C38ASP-1-0.758-0.89125.920-0.052-0.0520.0000.0000.0000.000
41C39GLY0-0.0070.01027.7410.0000.0000.0000.0000.0000.000
42C40HIS0-0.056-0.01828.755-0.005-0.0050.0000.0000.0000.000
43C41SER0-0.041-0.02129.2030.0000.0000.0000.0000.0000.000
44C42ALA00.0420.00924.235-0.005-0.0050.0000.0000.0000.000
45C43TRP0-0.022-0.00125.3080.0050.0050.0000.0000.0000.000
46C44THR00.0380.01719.886-0.008-0.0080.0000.0000.0000.000
47C45GLY00.0130.00421.5850.0070.0070.0000.0000.0000.000
48C46THR00.0110.00518.251-0.001-0.0010.0000.0000.0000.000
49C47VAL0-0.035-0.00419.746-0.003-0.0030.0000.0000.0000.000
50C48SER00.0740.03319.2730.0190.0190.0000.0000.0000.000
51C49GLU-1-0.699-0.85018.6200.2810.2810.0000.0000.0000.000
52C50SER0-0.006-0.01920.403-0.009-0.0090.0000.0000.0000.000
53C51LYS10.8900.94223.582-0.092-0.0920.0000.0000.0000.000
54C52ILE00.0070.02619.528-0.010-0.0100.0000.0000.0000.000
55C53SER0-0.004-0.00823.8630.0000.0000.0000.0000.0000.000
56C54GLN00.0230.03026.034-0.005-0.0050.0000.0000.0000.000
57C55GLU-1-0.865-0.95026.9510.0550.0550.0000.0000.0000.000
58C56ALA0-0.037-0.02026.444-0.005-0.0050.0000.0000.0000.000
59C57ALA0-0.014-0.00828.531-0.004-0.0040.0000.0000.0000.000
60C58THR0-0.053-0.02731.615-0.007-0.0070.0000.0000.0000.000
61C59MET0-0.044-0.01630.374-0.006-0.0060.0000.0000.0000.000
62C60ALA00.0090.02332.937-0.002-0.0020.0000.0000.0000.000
63C61MET0-0.048-0.00729.4800.0020.0020.0000.0000.0000.000
64C62ASN00.0440.01426.6020.0130.0130.0000.0000.0000.000
65C63LYS10.9320.95921.771-0.200-0.2000.0000.0000.0000.000
66C64GLY00.0190.01422.4970.0070.0070.0000.0000.0000.000
67C65LYS10.9680.97723.098-0.079-0.0790.0000.0000.0000.000
68C66TYR00.0160.00024.534-0.001-0.0010.0000.0000.0000.000
69C67VAL00.023-0.00318.764-0.004-0.0040.0000.0000.0000.000
70C68GLY0-0.002-0.00120.803-0.001-0.0010.0000.0000.0000.000
71C69GLU-1-0.835-0.90822.1750.0460.0460.0000.0000.0000.000
72C70LEU00.0070.00021.343-0.010-0.0100.0000.0000.0000.000
73C71ARG10.9030.95013.271-0.199-0.1990.0000.0000.0000.000
74C72LYS10.8270.90520.055-0.070-0.0700.0000.0000.0000.000
75C73ALA00.0380.04423.002-0.011-0.0110.0000.0000.0000.000
76C74LEU00.0100.01320.123-0.013-0.0130.0000.0000.0000.000
77C75LEU0-0.053-0.02115.370-0.016-0.0160.0000.0000.0000.000
78C76SER0-0.046-0.03319.0650.0020.0020.0000.0000.0000.000
79C77GLY00.0420.04020.9170.0080.0080.0000.0000.0000.000
80C78ALA00.002-0.01324.218-0.008-0.0080.0000.0000.0000.000
81C79GLY00.0110.01027.279-0.001-0.0010.0000.0000.0000.000
82C80PRO00.003-0.01329.8110.0020.0020.0000.0000.0000.000
83C81ALA0-0.0160.01730.0430.0020.0020.0000.0000.0000.000
84C82ASP-1-0.799-0.89128.2640.0360.0360.0000.0000.0000.000
85C83VAL00.0070.02030.345-0.005-0.0050.0000.0000.0000.000
86C84TYR0-0.001-0.02225.2760.0040.0040.0000.0000.0000.000
87C85THR0-0.030-0.02930.676-0.003-0.0030.0000.0000.0000.000
88C86PHE00.0530.01730.3200.0040.0040.0000.0000.0000.000
89C87ASN0-0.074-0.01832.348-0.003-0.0030.0000.0000.0000.000
90C88PHE00.1110.05332.6070.0010.0010.0000.0000.0000.000
91C89SER0-0.007-0.00835.1060.0000.0000.0000.0000.0000.000
92C90LYS10.9050.93736.686-0.001-0.0010.0000.0000.0000.000
93C91GLU-1-0.851-0.90631.385-0.007-0.0070.0000.0000.0000.000
94C92SER00.0300.02131.0490.0030.0030.0000.0000.0000.000
95C93ARG10.9000.93431.184-0.027-0.0270.0000.0000.0000.000
96C94TYR00.0470.02925.280-0.005-0.0050.0000.0000.0000.000
97C95PHE0-0.015-0.01828.6230.0080.0080.0000.0000.0000.000
98C96PHE00.0510.02425.187-0.005-0.0050.0000.0000.0000.000
99C97PHE0-0.046-0.03630.2950.0060.0060.0000.0000.0000.000
100C98LYS10.8210.88428.018-0.039-0.0390.0000.0000.0000.000
101C99LYS10.8480.93332.511-0.009-0.0090.0000.0000.0000.000
102C100ASN00.0200.00935.058-0.003-0.0030.0000.0000.0000.000
103C101LEU00.0310.00036.781-0.002-0.0020.0000.0000.0000.000
104C102LYS10.9100.93940.251-0.018-0.0180.0000.0000.0000.000
105C103ASP-1-0.842-0.89841.4410.0120.0120.0000.0000.0000.000
106C104VAL0-0.0120.02237.6610.0010.0010.0000.0000.0000.000
107C105SER0-0.010-0.03336.747-0.002-0.0020.0000.0000.0000.000
108C106PHE0-0.0030.00531.2530.0000.0000.0000.0000.0000.000
109C107ARG10.8970.95232.397-0.028-0.0280.0000.0000.0000.000
110C108LEU00.0130.02526.7180.0050.0050.0000.0000.0000.000
111C109GLY00.0690.03427.3690.0100.0100.0000.0000.0000.000
112C110SER0-0.058-0.04228.331-0.012-0.0120.0000.0000.0000.000
113C111PHE00.001-0.00324.0740.0080.0080.0000.0000.0000.000
114C112ASN0-0.023-0.01327.419-0.011-0.0110.0000.0000.0000.000
115C113LEU0-0.024-0.00424.2250.0070.0070.0000.0000.0000.000
116C114GLU-1-0.886-0.93026.0720.0000.0000.0000.0000.0000.000
117C115LYS10.8950.94526.3610.0290.0290.0000.0000.0000.000
118C116VAL0-0.015-0.00123.2600.0020.0020.0000.0000.0000.000
119C117GLU-1-0.914-0.95426.254-0.042-0.0420.0000.0000.0000.000
120C118ASN0-0.036-0.02424.739-0.001-0.0010.0000.0000.0000.000
121C119PRO00.0160.00624.550-0.010-0.0100.0000.0000.0000.000
122C120ALA00.0430.01524.852-0.010-0.0100.0000.0000.0000.000
123C121GLU-1-0.863-0.92320.630-0.168-0.1680.0000.0000.0000.000
124C122VAL00.0160.00620.087-0.021-0.0210.0000.0000.0000.000
125C123ILE0-0.013-0.00120.250-0.019-0.0190.0000.0000.0000.000
126C124ARG10.8770.92921.3110.1390.1390.0000.0000.0000.000
127C125GLU-1-0.787-0.84614.069-0.374-0.3740.0000.0000.0000.000
128C126LEU0-0.023-0.00316.435-0.036-0.0360.0000.0000.0000.000
129C127ILE0-0.044-0.04317.741-0.016-0.0160.0000.0000.0000.000
130C128ASP-1-0.906-0.95316.241-0.373-0.3730.0000.0000.0000.000
131C129TYR00.0340.0179.5990.0570.0570.0000.0000.0000.000
132C130ALA0-0.076-0.04614.359-0.021-0.0210.0000.0000.0000.000
133C131LEU0-0.013-0.01816.9350.0160.0160.0000.0000.0000.000
134C132ASP-1-0.895-0.93110.795-0.732-0.7320.0000.0000.0000.000
135C1677ARG10.9510.97211.7060.3310.3310.0000.0000.0000.000
136C1678ASN0-0.042-0.01413.7420.0400.0400.0000.0000.0000.000
137C1679ASN00.0020.00515.2060.0620.0620.0000.0000.0000.000
138C1680LEU0-0.016-0.0019.0350.0140.0140.0000.0000.0000.000
139C1681LEU0-0.002-0.01513.2930.0400.0400.0000.0000.0000.000
140C1682GLN0-0.042-0.02015.6880.0490.0490.0000.0000.0000.000
141C1683ALA00.0300.01614.7150.0240.0240.0000.0000.0000.000
142C1684GLU-1-0.910-0.96212.646-0.245-0.2450.0000.0000.0000.000
143C1685LEU0-0.060-0.02815.9750.0350.0350.0000.0000.0000.000
144C1686GLU-1-0.960-0.98519.696-0.135-0.1350.0000.0000.0000.000
145C1687GLU-1-0.895-0.93716.534-0.100-0.1000.0000.0000.0000.000
146C1688LEU0-0.017-0.02617.3480.0220.0220.0000.0000.0000.000
147C1689ARG10.8660.93320.5990.1250.1250.0000.0000.0000.000
148C1690ALA00.0600.04422.3790.0100.0100.0000.0000.0000.000
149C1691VAL00.0040.00020.2830.0110.0110.0000.0000.0000.000
150C1692VAL0-0.0250.00523.5910.0110.0110.0000.0000.0000.000
151C1693GLU-1-0.903-0.95126.270-0.056-0.0560.0000.0000.0000.000
152C1694GLN0-0.0140.00023.6910.0100.0100.0000.0000.0000.000
153C1695THR0-0.027-0.03625.8410.0070.0070.0000.0000.0000.000
154C1696GLU-1-0.830-0.91128.461-0.015-0.0150.0000.0000.0000.000
155C1697ARG10.8810.95231.1000.0320.0320.0000.0000.0000.000
156C1698SER0-0.021-0.02730.0020.0020.0020.0000.0000.0000.000
157C1699ARG10.7660.87232.5370.0160.0160.0000.0000.0000.000
158C1700LYS10.9430.96234.0960.0220.0220.0000.0000.0000.000
159C1701LEU0-0.051-0.01135.4830.0010.0010.0000.0000.0000.000
160C1702ALA00.0670.02735.8490.0010.0010.0000.0000.0000.000
161C1703GLU-1-0.855-0.90837.756-0.006-0.0060.0000.0000.0000.000
162C1704GLN0-0.034-0.03139.882-0.001-0.0010.0000.0000.0000.000
163C1705GLU-1-0.902-0.94039.641-0.006-0.0060.0000.0000.0000.000
164C1706LEU0-0.0120.00641.2830.0020.0020.0000.0000.0000.000
165C1707ILE0-0.0100.00243.1750.0010.0010.0000.0000.0000.000
166C1708GLU-1-0.913-0.93445.691-0.005-0.0050.0000.0000.0000.000
167C1709THR0-0.035-0.03344.4450.0010.0010.0000.0000.0000.000
168C1710SER0-0.084-0.07446.5160.0010.0010.0000.0000.0000.000
169C1711GLU-1-0.895-0.94248.083-0.004-0.0040.0000.0000.0000.000
170C1712ARG10.9570.97950.0720.0010.0010.0000.0000.0000.000
171C1713VAL0-0.007-0.00848.1710.0010.0010.0000.0000.0000.000
172C1714GLN00.0300.02051.4390.0010.0010.0000.0000.0000.000
173C1715LEU0-0.028-0.01153.8800.0000.0000.0000.0000.0000.000
174C1716LEU0-0.020-0.00853.4260.0000.0000.0000.0000.0000.000
175C1717HIS00.0330.01054.4370.0000.0000.0000.0000.0000.000
176C1718SER0-0.031-0.00956.4580.0000.0000.0000.0000.0000.000
177C1719GLN00.010-0.00359.3680.0000.0000.0000.0000.0000.000
178C1720ASN00.0130.00457.2850.0000.0000.0000.0000.0000.000
179C1721THR00.000-0.00659.5240.0000.0000.0000.0000.0000.000
180C1722SER0-0.018-0.00161.9810.0000.0000.0000.0000.0000.000
181C1723LEU00.0200.00862.7740.0000.0000.0000.0000.0000.000
182C1724ILE0-0.0140.00060.5210.0000.0000.0000.0000.0000.000
183C1725ASN0-0.004-0.00764.9990.0010.0010.0000.0000.0000.000
184C1726GLN0-0.019-0.00667.7490.0000.0000.0000.0000.0000.000
185C1727LYS10.9100.95166.253-0.007-0.0070.0000.0000.0000.000
186C1728LYS10.8120.89267.433-0.007-0.0070.0000.0000.0000.000
187C1729LYS10.9450.97570.346-0.003-0.0030.0000.0000.0000.000
188C1730MET00.0100.00772.2930.0000.0000.0000.0000.0000.000
189C1731ASP-1-0.810-0.88470.5500.0060.0060.0000.0000.0000.000
190C1732ALA0-0.034-0.01374.0780.0000.0000.0000.0000.0000.000
191C1733ASP-1-0.890-0.96176.5820.0040.0040.0000.0000.0000.000
192C1734LEU0-0.019-0.01375.1610.0000.0000.0000.0000.0000.000
193C1735SER00.0060.00578.7460.0000.0000.0000.0000.0000.000
194C1736GLN0-0.078-0.01680.6820.0000.0000.0000.0000.0000.000
195C1737LEU00.0350.01482.1230.0000.0000.0000.0000.0000.000
196C1738GLN0-0.067-0.02681.6790.0000.0000.0000.0000.0000.000
197C1739THR0-0.024-0.05483.6610.0000.0000.0000.0000.0000.000
198C1740GLU-1-0.866-0.91885.9860.0040.0040.0000.0000.0000.000
199C1741VAL0-0.042-0.01986.5740.0000.0000.0000.0000.0000.000
200C1742GLU-1-0.939-0.96985.6730.0060.0060.0000.0000.0000.000
201C1743GLU-1-0.863-0.94289.1620.0050.0050.0000.0000.0000.000
202C1744ALA0-0.042-0.00191.6590.0000.0000.0000.0000.0000.000
203C1745VAL0-0.063-0.03190.9800.0000.0000.0000.0000.0000.000
204C1746GLN0-0.127-0.06591.1910.0000.0000.0000.0000.0000.000
205C1747GLU-1-0.948-0.96294.8940.0030.0030.0000.0000.0000.000
206C1748CYS0-0.113-0.04997.7670.0000.0000.0000.0000.0000.000