Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 39M1L

Calculation Name: 5WJ7-A-Xray372

Preferred Name: Cardiac myosin

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 5WJ7

Chain ID: A

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1758715.456063
FMO2-HF: Nuclear repulsion 1679735.150611
FMO2-HF: Total energy -78980.305452
FMO2-MP2: Total energy -79205.860695


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(A:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-12.905-8.4880.531-2.727-2.219-0.009
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.012
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].
3A2GLU-1-0.952-0.9622.547-8.954-4.5960.533-2.691-2.200-0.009
4A3ARG10.8060.8635.299-0.158-0.133-0.001-0.001-0.0220.000
5A4LYS10.9490.9838.4080.4110.4110.0000.0000.0000.000
6A5ILE00.0140.01411.9470.0210.0210.0000.0000.0000.000
7A6SER0-0.015-0.00914.6720.0050.0050.0000.0000.0000.000
8A7ARG10.9360.96918.1480.0900.0900.0000.0000.0000.000
9A8ILE00.0050.01121.516-0.023-0.0230.0000.0000.0000.000
10A9HIS00.0200.00324.1050.0310.0310.0000.0000.0000.000
11A10LEU0-0.0090.00425.914-0.015-0.0150.0000.0000.0000.000
12A11VAL00.013-0.00129.0720.0110.0110.0000.0000.0000.000
13A12SER0-0.015-0.00932.1540.0050.0050.0000.0000.0000.000
14A13GLU-1-0.898-0.95830.884-0.044-0.0440.0000.0000.0000.000
15A14PRO00.0110.01331.189-0.002-0.0020.0000.0000.0000.000
16A15SER0-0.032-0.01132.8120.0000.0000.0000.0000.0000.000
17A16ILE0-0.019-0.00229.0910.0070.0070.0000.0000.0000.000
18A17THR0-0.043-0.02224.460-0.009-0.0090.0000.0000.0000.000
19A18HIS0-0.0140.00023.8030.0180.0180.0000.0000.0000.000
20A19PHE0-0.014-0.01719.095-0.008-0.0080.0000.0000.0000.000
21A20LEU00.004-0.00117.7950.0110.0110.0000.0000.0000.000
22A21GLN00.0400.01212.3980.0440.0440.0000.0000.0000.000
23A22VAL00.0030.00312.7860.0030.0030.0000.0000.0000.000
24A23SER00.0210.0108.2220.0830.0830.0000.0000.0000.000
25A24TRP0-0.011-0.0168.0490.4080.4080.0000.0000.0000.000
26A25GLU-1-0.859-0.9224.285-7.284-7.250-0.001-0.0350.0030.000
27A26LYS10.9751.0046.1121.1891.1890.0000.0000.0000.000
28A27THR0-0.082-0.0718.1430.3150.3150.0000.0000.0000.000
29A28LEU00.0440.02211.751-0.058-0.0580.0000.0000.0000.000
30A29GLU-1-0.891-0.94313.366-0.690-0.6900.0000.0000.0000.000
31A30SER0-0.026-0.01011.5870.0080.0080.0000.0000.0000.000
32A31GLY00.0480.02913.3900.0190.0190.0000.0000.0000.000
33A32PHE0-0.065-0.04112.074-0.245-0.2450.0000.0000.0000.000
34A33VAL00.0110.02011.6980.1560.1560.0000.0000.0000.000
35A34ILE0-0.005-0.00613.379-0.047-0.0470.0000.0000.0000.000
36A35THR0-0.008-0.01315.1390.0800.0800.0000.0000.0000.000
37A36LEU0-0.021-0.00117.299-0.010-0.0100.0000.0000.0000.000
38A37THR0-0.018-0.02419.7290.0350.0350.0000.0000.0000.000
39A38ASP-1-0.794-0.91322.138-0.015-0.0150.0000.0000.0000.000
40A39GLY0-0.0220.00123.6720.0060.0060.0000.0000.0000.000
41A40HIS0-0.049-0.01824.7860.0230.0230.0000.0000.0000.000
42A41SER0-0.062-0.04125.2880.0130.0130.0000.0000.0000.000
43A42ALA00.0250.01020.0450.0010.0010.0000.0000.0000.000
44A43TRP0-0.017-0.01221.3150.0110.0110.0000.0000.0000.000
45A44THR00.0450.02215.981-0.007-0.0070.0000.0000.0000.000
46A45GLY00.0470.02317.7450.0250.0250.0000.0000.0000.000
47A46THR0-0.031-0.02015.172-0.057-0.0570.0000.0000.0000.000
48A47VAL00.0150.03316.4250.0570.0570.0000.0000.0000.000
49A48SER0-0.007-0.00316.304-0.122-0.1220.0000.0000.0000.000
50A49GLU-1-0.892-0.96416.020-0.806-0.8060.0000.0000.0000.000
51A50SER0-0.022-0.01717.7920.0390.0390.0000.0000.0000.000
52A51GLU-1-0.856-0.93720.806-0.377-0.3770.0000.0000.0000.000
53A52ILE0-0.0270.00017.1990.0250.0250.0000.0000.0000.000
54A53SER0-0.091-0.06221.4060.0170.0170.0000.0000.0000.000
55A54GLN0-0.047-0.02223.3220.0230.0230.0000.0000.0000.000
56A55GLU-1-0.875-0.93124.916-0.280-0.2800.0000.0000.0000.000
57A56ALA0-0.115-0.07424.4320.0160.0160.0000.0000.0000.000
58A57ASP-1-0.943-0.97726.503-0.291-0.2910.0000.0000.0000.000
59A58ASP-1-0.908-0.92029.290-0.248-0.2480.0000.0000.0000.000
60A59MET0-0.116-0.04729.1290.0170.0170.0000.0000.0000.000
61A60ALA00.009-0.00331.092-0.012-0.0120.0000.0000.0000.000
62A61MET0-0.076-0.03426.4620.0100.0100.0000.0000.0000.000
63A62GLU-1-0.834-0.89725.394-0.460-0.4600.0000.0000.0000.000
64A63LYS10.9690.97019.4170.6450.6450.0000.0000.0000.000
65A64GLY00.0280.01021.790-0.045-0.0450.0000.0000.0000.000
66A65LYS10.8810.92922.1260.2990.2990.0000.0000.0000.000
67A66TYR0-0.009-0.03022.426-0.015-0.0150.0000.0000.0000.000
68A67VAL00.0400.01717.346-0.018-0.0180.0000.0000.0000.000
69A68GLY0-0.022-0.01419.240-0.038-0.0380.0000.0000.0000.000
70A69GLU-1-0.845-0.94820.960-0.318-0.3180.0000.0000.0000.000
71A70LEU00.0270.02918.6710.0190.0190.0000.0000.0000.000
72A71ARG10.9290.97112.6011.1331.1330.0000.0000.0000.000
73A72LYS10.8640.94817.9200.3780.3780.0000.0000.0000.000
74A73ALA0-0.0020.00920.9840.0350.0350.0000.0000.0000.000
75A74LEU0-0.011-0.01817.6710.0370.0370.0000.0000.0000.000
76A75LEU0-0.050-0.01913.169-0.012-0.0120.0000.0000.0000.000
77A76SER0-0.021-0.00716.3370.0260.0260.0000.0000.0000.000
78A77GLY00.0200.00819.1070.0050.0050.0000.0000.0000.000
79A78ALA0-0.029-0.01820.190-0.009-0.0090.0000.0000.0000.000
80A79GLY00.0160.01423.8410.0240.0240.0000.0000.0000.000
81A80PRO0-0.031-0.02625.4710.0220.0220.0000.0000.0000.000
82A81ALA0-0.020-0.00428.6430.0000.0000.0000.0000.0000.000
83A82ASP-1-0.911-0.93827.246-0.249-0.2490.0000.0000.0000.000
84A83VAL0-0.026-0.02028.9060.0060.0060.0000.0000.0000.000
85A84TYR0-0.010-0.01625.459-0.008-0.0080.0000.0000.0000.000
86A85THR0-0.028-0.00227.9910.0140.0140.0000.0000.0000.000
87A86PHE00.0330.00622.585-0.015-0.0150.0000.0000.0000.000
88A87ASN0-0.0030.00027.2800.0350.0350.0000.0000.0000.000
89A88PHE00.0520.01025.690-0.016-0.0160.0000.0000.0000.000
90A89SER00.0300.03728.6880.0170.0170.0000.0000.0000.000
91A90LYS10.8570.92728.1950.0450.0450.0000.0000.0000.000
92A91GLU-1-0.966-0.97230.533-0.049-0.0490.0000.0000.0000.000
93A92SER0-0.039-0.02931.7870.0020.0020.0000.0000.0000.000
94A93CYS0-0.039-0.01026.373-0.003-0.0030.0000.0000.0000.000
95A94TYR00.0180.01726.674-0.015-0.0150.0000.0000.0000.000
96A95PHE0-0.003-0.00623.3690.0140.0140.0000.0000.0000.000
97A96PHE0-0.012-0.01226.053-0.023-0.0230.0000.0000.0000.000
98A97PHE00.0220.01222.3650.0160.0160.0000.0000.0000.000
99A98GLU-1-0.873-0.94926.870-0.188-0.1880.0000.0000.0000.000
100A99LYS10.9260.97027.8420.2520.2520.0000.0000.0000.000
101A100ASN0-0.010-0.01129.7950.0010.0010.0000.0000.0000.000
102A101LEU0-0.045-0.03132.282-0.006-0.0060.0000.0000.0000.000
103A102LYS10.9270.95735.0450.1640.1640.0000.0000.0000.000
104A103ASP-1-0.887-0.93938.450-0.113-0.1130.0000.0000.0000.000
105A104VAL0-0.093-0.03835.1480.0000.0000.0000.0000.0000.000
106A105SER0-0.003-0.01133.4740.0020.0020.0000.0000.0000.000
107A106PHE00.0290.03029.5750.0030.0030.0000.0000.0000.000
108A107ARG10.9470.97229.0790.1970.1970.0000.0000.0000.000
109A108LEU0-0.048-0.01025.002-0.008-0.0080.0000.0000.0000.000
110A109GLY00.1240.06024.567-0.025-0.0250.0000.0000.0000.000
111A110SER0-0.108-0.05525.0960.0360.0360.0000.0000.0000.000
112A111PHE00.0710.03120.989-0.029-0.0290.0000.0000.0000.000
113A112ASN0-0.005-0.00523.8250.0390.0390.0000.0000.0000.000
114A113LEU0-0.062-0.01420.311-0.017-0.0170.0000.0000.0000.000
115A114GLU-1-0.881-0.94022.031-0.111-0.1110.0000.0000.0000.000
116A115LYS10.9160.94322.3790.0070.0070.0000.0000.0000.000
117A116VAL00.0010.00319.0860.0030.0030.0000.0000.0000.000
118A117GLU-1-0.943-0.96722.2220.0880.0880.0000.0000.0000.000
119A118ASN0-0.038-0.02917.908-0.027-0.0270.0000.0000.0000.000
120A119PRO00.0250.01420.2940.0210.0210.0000.0000.0000.000
121A120ALA00.0300.00120.9590.0150.0150.0000.0000.0000.000
122A121GLU-1-0.937-0.97316.7540.4040.4040.0000.0000.0000.000
123A122VAL00.0420.02816.1130.0560.0560.0000.0000.0000.000
124A123ILE0-0.0110.00116.6260.0190.0190.0000.0000.0000.000
125A124ARG10.9210.95517.938-0.317-0.3170.0000.0000.0000.000
126A125GLU-1-0.801-0.86410.4210.8950.8950.0000.0000.0000.000
127A126LEU00.0340.02613.0950.0650.0650.0000.0000.0000.000
128A127ILE0-0.036-0.03614.650-0.010-0.0100.0000.0000.0000.000
129A128CYS0-0.045-0.02913.316-0.017-0.0170.0000.0000.0000.000
130A129TYR00.0820.0536.6670.0090.0090.0000.0000.0000.000
131A130CYS0-0.041-0.01811.544-0.087-0.0870.0000.0000.0000.000
132A131LEU0-0.047-0.02514.336-0.047-0.0470.0000.0000.0000.000
133A132ASP-1-0.902-0.95310.2911.1361.1360.0000.0000.0000.000
134A1733ASP-1-0.934-0.97811.207-0.041-0.0410.0000.0000.0000.000
135A1734LEU0-0.074-0.03012.066-0.096-0.0960.0000.0000.0000.000
136A1735SER0-0.041-0.02314.212-0.061-0.0610.0000.0000.0000.000
137A1736GLN0-0.0240.0019.9210.1890.1890.0000.0000.0000.000
138A1737LEU00.0330.01612.867-0.079-0.0790.0000.0000.0000.000
139A1738GLN0-0.052-0.03515.178-0.040-0.0400.0000.0000.0000.000
140A1739THR0-0.005-0.00315.093-0.008-0.0080.0000.0000.0000.000
141A1740GLU-1-0.836-0.92012.177-0.198-0.1980.0000.0000.0000.000
142A1741VAL0-0.060-0.01816.823-0.040-0.0400.0000.0000.0000.000
143A1742GLU-1-0.970-0.98820.2500.1580.1580.0000.0000.0000.000
144A1743GLU-1-0.950-0.97516.5250.0880.0880.0000.0000.0000.000
145A1744ALA00.0370.02220.135-0.020-0.0200.0000.0000.0000.000
146A1745VAL0-0.055-0.03521.650-0.009-0.0090.0000.0000.0000.000
147A1746GLN0-0.049-0.02523.6240.0030.0030.0000.0000.0000.000
148A1747GLU-1-0.965-0.98920.375-0.116-0.1160.0000.0000.0000.000
149A1748CYS0-0.023-0.00324.902-0.009-0.0090.0000.0000.0000.000
150A1749ARG10.9650.98427.512-0.021-0.0210.0000.0000.0000.000
151A1750ASN0-0.0020.00225.8970.0090.0090.0000.0000.0000.000
152A1751ALA0-0.033-0.01228.539-0.002-0.0020.0000.0000.0000.000
153A1752GLU-1-0.909-0.96230.319-0.030-0.0300.0000.0000.0000.000
154A1753GLU-1-0.903-0.95232.8550.0000.0000.0000.0000.0000.000
155A1754LYS10.9200.95528.7720.0510.0510.0000.0000.0000.000
156A1755ALA0-0.0010.00534.318-0.002-0.0020.0000.0000.0000.000
157A1756LYS10.9360.96936.1420.0080.0080.0000.0000.0000.000
158A1757LYS10.9050.95236.9790.0220.0220.0000.0000.0000.000
159A1758ALA00.0170.01337.7330.0000.0000.0000.0000.0000.000
160A1759ILE0-0.009-0.00539.6580.0000.0000.0000.0000.0000.000
161A1760THR0-0.035-0.02142.1920.0020.0020.0000.0000.0000.000
162A1761ASP-1-0.863-0.93841.204-0.024-0.0240.0000.0000.0000.000
163A1762ALA0-0.021-0.00743.8010.0000.0000.0000.0000.0000.000
164A1763ALA0-0.020-0.00945.4720.0000.0000.0000.0000.0000.000
165A1764MET00.013-0.00345.8220.0020.0020.0000.0000.0000.000
166A1765MET0-0.0120.00947.1930.0000.0000.0000.0000.0000.000
167A1766ALA0-0.015-0.01449.2410.0000.0000.0000.0000.0000.000
168A1767GLU-1-0.940-0.96651.649-0.014-0.0140.0000.0000.0000.000
169A1768GLU-1-0.888-0.96151.954-0.016-0.0160.0000.0000.0000.000
170A1769LEU0-0.037-0.00452.9400.0000.0000.0000.0000.0000.000
171A1770LYS10.9050.95254.9550.0240.0240.0000.0000.0000.000
172A1771LYS10.9330.96755.7950.0150.0150.0000.0000.0000.000
173A1772GLU-1-0.894-0.92757.428-0.021-0.0210.0000.0000.0000.000
174A1773GLN0-0.056-0.03857.9620.0010.0010.0000.0000.0000.000
175A1774ASP-1-0.893-0.94860.933-0.020-0.0200.0000.0000.0000.000
176A1775THR0-0.035-0.02162.1170.0020.0020.0000.0000.0000.000
177A1776SER0-0.025-0.01462.6880.0010.0010.0000.0000.0000.000
178A1777ALA00.0220.00664.5470.0000.0000.0000.0000.0000.000
179A1778HIS0-0.039-0.02666.8770.0000.0000.0000.0000.0000.000
180A1779LEU00.0320.00665.5050.0010.0010.0000.0000.0000.000
181A1780GLU-1-0.881-0.93068.819-0.022-0.0220.0000.0000.0000.000
182A1781ARG10.9240.95768.9840.0180.0180.0000.0000.0000.000
183A1782MET0-0.015-0.00671.8880.0010.0010.0000.0000.0000.000
184A1783LYS10.9260.97671.7720.0220.0220.0000.0000.0000.000
185A1784LYS10.9450.96774.4080.0190.0190.0000.0000.0000.000
186A1785ASN0-0.019-0.00576.7110.0010.0010.0000.0000.0000.000
187A1786MET0-0.022-0.01274.0750.0010.0010.0000.0000.0000.000
188A1787GLU-1-0.906-0.95876.303-0.019-0.0190.0000.0000.0000.000
189A1788GLN0-0.089-0.04780.053-0.001-0.0010.0000.0000.0000.000
190A1789THR0-0.031-0.02182.1770.0010.0010.0000.0000.0000.000
191A1790ILE0-0.009-0.01280.2030.0000.0000.0000.0000.0000.000
192A1791LYS10.9030.96384.1260.0170.0170.0000.0000.0000.000
193A1792ASP-1-0.854-0.92285.898-0.013-0.0130.0000.0000.0000.000
194A1793LEU0-0.093-0.02685.9720.0010.0010.0000.0000.0000.000
195A1794GLN0-0.053-0.01986.4910.0000.0000.0000.0000.0000.000