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: LZVK9

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1760020.38299
FMO2-HF: Nuclear repulsion 1681039.067173
FMO2-HF: Total energy -78981.315816
FMO2-MP2: Total energy -79206.956648


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.
-12.177-7.6220.266-2.744-2.076-0.008
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 : -0.008 / 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].
3A2GLU-1-0.930-0.9512.674-9.497-4.9780.267-2.726-2.059-0.008
4A3ARG10.7810.8395.4390.0050.0050.0000.0000.0000.000
5A4LYS10.9300.9748.4120.4750.4750.0000.0000.0000.000
6A5ILE00.0160.01711.9540.0430.0430.0000.0000.0000.000
7A6SER0-0.022-0.01614.5970.0040.0040.0000.0000.0000.000
8A7ARG10.9380.97318.1090.1270.1270.0000.0000.0000.000
9A8ILE00.0030.00821.511-0.023-0.0230.0000.0000.0000.000
10A9HIS00.0240.01424.0790.0340.0340.0000.0000.0000.000
11A10LEU0-0.0030.01126.056-0.015-0.0150.0000.0000.0000.000
12A11VAL00.013-0.00229.0500.0110.0110.0000.0000.0000.000
13A12SER0-0.016-0.00432.0670.0050.0050.0000.0000.0000.000
14A13GLU-1-0.882-0.95030.793-0.056-0.0560.0000.0000.0000.000
15A14PRO00.0110.01131.119-0.003-0.0030.0000.0000.0000.000
16A15SER0-0.050-0.01632.7390.0000.0000.0000.0000.0000.000
17A16ILE00.0050.00629.2480.0060.0060.0000.0000.0000.000
18A17THR0-0.043-0.03524.352-0.009-0.0090.0000.0000.0000.000
19A18HIS0-0.0030.01723.8070.0210.0210.0000.0000.0000.000
20A19PHE0-0.014-0.01818.991-0.011-0.0110.0000.0000.0000.000
21A20LEU00.0030.00017.6980.0170.0170.0000.0000.0000.000
22A21GLN00.0460.02211.7430.0210.0210.0000.0000.0000.000
23A22VAL00.0020.00513.0820.0200.0200.0000.0000.0000.000
24A23SER00.0240.0148.2690.0510.0510.0000.0000.0000.000
25A24TRP0-0.003-0.0138.1970.4430.4430.0000.0000.0000.000
26A25GLU-1-0.867-0.9254.477-6.010-5.974-0.001-0.018-0.0170.000
27A26LYS10.9650.9896.2001.3101.3100.0000.0000.0000.000
28A27THR0-0.087-0.0628.2250.3680.3680.0000.0000.0000.000
29A28LEU00.0340.01111.838-0.061-0.0610.0000.0000.0000.000
30A29GLU-1-0.855-0.92213.653-0.663-0.6630.0000.0000.0000.000
31A30SER0-0.021-0.00611.7020.0220.0220.0000.0000.0000.000
32A31GLY00.0140.01413.3270.0210.0210.0000.0000.0000.000
33A32PHE0-0.065-0.04212.083-0.247-0.2470.0000.0000.0000.000
34A33VAL00.0080.01711.6850.1600.1600.0000.0000.0000.000
35A34ILE0-0.016-0.01313.397-0.063-0.0630.0000.0000.0000.000
36A35THR00.002-0.01315.6340.0550.0550.0000.0000.0000.000
37A36LEU0-0.029-0.00417.319-0.017-0.0170.0000.0000.0000.000
38A37THR0-0.010-0.03019.5070.0410.0410.0000.0000.0000.000
39A38ASP-1-0.779-0.91321.991-0.034-0.0340.0000.0000.0000.000
40A39GLY0-0.0150.00623.4710.0060.0060.0000.0000.0000.000
41A40HIS0-0.039-0.01324.5700.0250.0250.0000.0000.0000.000
42A41SER0-0.035-0.02225.3180.0150.0150.0000.0000.0000.000
43A42ALA00.0220.01220.081-0.003-0.0030.0000.0000.0000.000
44A43TRP0-0.017-0.00921.3230.0150.0150.0000.0000.0000.000
45A44THR00.0580.02615.971-0.021-0.0210.0000.0000.0000.000
46A45GLY00.0600.03917.7630.0280.0280.0000.0000.0000.000
47A46THR0-0.027-0.01714.875-0.054-0.0540.0000.0000.0000.000
48A47VAL0-0.0030.02016.4340.0600.0600.0000.0000.0000.000
49A48SER0-0.026-0.05416.258-0.125-0.1250.0000.0000.0000.000
50A49GLU-1-0.804-0.92216.004-0.819-0.8190.0000.0000.0000.000
51A50SER0-0.029-0.01717.7290.0320.0320.0000.0000.0000.000
52A51GLU-1-0.805-0.86120.616-0.384-0.3840.0000.0000.0000.000
53A52ILE0-0.0300.00017.1640.0220.0220.0000.0000.0000.000
54A53SER0-0.068-0.06121.3420.0330.0330.0000.0000.0000.000
55A54GLN0-0.046-0.01423.2520.0220.0220.0000.0000.0000.000
56A55GLU-1-0.876-0.94024.866-0.283-0.2830.0000.0000.0000.000
57A56ALA0-0.092-0.06324.5080.0160.0160.0000.0000.0000.000
58A57ASP-1-0.966-0.98226.529-0.282-0.2820.0000.0000.0000.000
59A58ASP-1-0.905-0.92429.250-0.237-0.2370.0000.0000.0000.000
60A59MET0-0.131-0.05428.9950.0180.0180.0000.0000.0000.000
61A60ALA00.016-0.00131.232-0.011-0.0110.0000.0000.0000.000
62A61MET0-0.080-0.02926.6820.0080.0080.0000.0000.0000.000
63A62GLU-1-0.837-0.89725.767-0.462-0.4620.0000.0000.0000.000
64A63LYS10.9090.94119.2610.6630.6630.0000.0000.0000.000
65A64GLY00.0360.00321.950-0.045-0.0450.0000.0000.0000.000
66A65LYS10.8350.91422.4540.3260.3260.0000.0000.0000.000
67A66TYR0-0.006-0.04322.501-0.018-0.0180.0000.0000.0000.000
68A67VAL00.0460.01917.663-0.017-0.0170.0000.0000.0000.000
69A68GLY0-0.027-0.01419.510-0.042-0.0420.0000.0000.0000.000
70A69GLU-1-0.817-0.93321.240-0.339-0.3390.0000.0000.0000.000
71A70LEU00.0340.03218.8390.0190.0190.0000.0000.0000.000
72A71ARG10.9220.96912.6471.2041.2040.0000.0000.0000.000
73A72LYS10.7830.90618.1310.3740.3740.0000.0000.0000.000
74A73ALA0-0.0140.00221.1640.0340.0340.0000.0000.0000.000
75A74LEU0-0.014-0.02017.8030.0370.0370.0000.0000.0000.000
76A75LEU0-0.042-0.01513.191-0.017-0.0170.0000.0000.0000.000
77A76SER0-0.038-0.02016.4510.0230.0230.0000.0000.0000.000
78A77GLY00.0330.02119.1970.0010.0010.0000.0000.0000.000
79A78ALA0-0.016-0.01220.330-0.004-0.0040.0000.0000.0000.000
80A79GLY00.0080.01023.9670.0260.0260.0000.0000.0000.000
81A80PRO0-0.028-0.02725.6510.0230.0230.0000.0000.0000.000
82A81ALA0-0.024-0.00928.7910.0000.0000.0000.0000.0000.000
83A82ASP-1-0.762-0.85627.402-0.277-0.2770.0000.0000.0000.000
84A83VAL0-0.031-0.01229.0170.0050.0050.0000.0000.0000.000
85A84TYR00.000-0.00725.413-0.008-0.0080.0000.0000.0000.000
86A85THR0-0.033-0.00728.0970.0150.0150.0000.0000.0000.000
87A86PHE00.0310.00622.708-0.015-0.0150.0000.0000.0000.000
88A87ASN0-0.015-0.00327.3270.0350.0350.0000.0000.0000.000
89A88PHE00.0550.01425.798-0.016-0.0160.0000.0000.0000.000
90A89SER00.0280.04328.6840.0150.0150.0000.0000.0000.000
91A90LYS10.8060.88127.8370.0580.0580.0000.0000.0000.000
92A91GLU-1-0.968-0.97530.550-0.054-0.0540.0000.0000.0000.000
93A92SER0-0.039-0.03531.800-0.001-0.0010.0000.0000.0000.000
94A93CYS0-0.058-0.01826.318-0.001-0.0010.0000.0000.0000.000
95A94TYR00.0370.01626.687-0.013-0.0130.0000.0000.0000.000
96A95PHE0-0.017-0.01023.0990.0110.0110.0000.0000.0000.000
97A96PHE00.002-0.00826.122-0.022-0.0220.0000.0000.0000.000
98A97PHE00.0190.01022.6560.0150.0150.0000.0000.0000.000
99A98GLU-1-0.812-0.89826.977-0.197-0.1970.0000.0000.0000.000
100A99LYS10.8500.92227.8570.2610.2610.0000.0000.0000.000
101A100ASN0-0.022-0.01729.9530.0020.0020.0000.0000.0000.000
102A101LEU0-0.026-0.01832.307-0.006-0.0060.0000.0000.0000.000
103A102LYS10.9420.95835.2170.1660.1660.0000.0000.0000.000
104A103ASP-1-0.892-0.93938.569-0.121-0.1210.0000.0000.0000.000
105A104VAL0-0.091-0.03835.4350.0010.0010.0000.0000.0000.000
106A105SER0-0.003-0.01233.6180.0020.0020.0000.0000.0000.000
107A106PHE00.0380.03130.0320.0050.0050.0000.0000.0000.000
108A107ARG10.8740.92229.1930.1980.1980.0000.0000.0000.000
109A108LEU0-0.032-0.01025.158-0.007-0.0070.0000.0000.0000.000
110A109GLY00.0990.05824.742-0.024-0.0240.0000.0000.0000.000
111A110SER0-0.100-0.04825.2460.0360.0360.0000.0000.0000.000
112A111PHE00.0680.03121.024-0.029-0.0290.0000.0000.0000.000
113A112ASN00.0000.00123.8740.0320.0320.0000.0000.0000.000
114A113LEU0-0.067-0.02120.336-0.015-0.0150.0000.0000.0000.000
115A114GLU-1-0.891-0.94222.048-0.095-0.0950.0000.0000.0000.000
116A115LYS10.8750.92822.3900.0010.0010.0000.0000.0000.000
117A116VAL0-0.0070.00019.2370.0070.0070.0000.0000.0000.000
118A117GLU-1-0.933-0.96422.2320.1050.1050.0000.0000.0000.000
119A118ASN0-0.045-0.03518.024-0.026-0.0260.0000.0000.0000.000
120A119PRO00.0310.01420.3060.0200.0200.0000.0000.0000.000
121A120ALA00.0270.00620.9760.0110.0110.0000.0000.0000.000
122A121GLU-1-0.889-0.93817.0280.4120.4120.0000.0000.0000.000
123A122VAL00.0530.02816.1910.0540.0540.0000.0000.0000.000
124A123ILE0-0.020-0.00516.5100.0100.0100.0000.0000.0000.000
125A124ARG10.8720.93017.805-0.350-0.3500.0000.0000.0000.000
126A125GLU-1-0.814-0.86610.5450.8240.8240.0000.0000.0000.000
127A126LEU00.0310.02512.9570.0450.0450.0000.0000.0000.000
128A127ILE0-0.011-0.01714.385-0.026-0.0260.0000.0000.0000.000
129A128CYS0-0.053-0.03613.214-0.023-0.0230.0000.0000.0000.000
130A129TYR00.0970.0556.1610.0570.0570.0000.0000.0000.000
131A130CYS0-0.043-0.02111.309-0.108-0.1080.0000.0000.0000.000
132A131LEU0-0.045-0.02514.082-0.045-0.0450.0000.0000.0000.000
133A132ASP-1-0.904-0.95110.0671.1221.1220.0000.0000.0000.000
134A1733ASP-1-0.950-0.98310.995-0.257-0.2570.0000.0000.0000.000
135A1734LEU0-0.064-0.03011.845-0.081-0.0810.0000.0000.0000.000
136A1735SER0-0.055-0.03213.897-0.046-0.0460.0000.0000.0000.000
137A1736GLN0-0.046-0.0239.6290.1770.1770.0000.0000.0000.000
138A1737LEU00.0230.00312.677-0.066-0.0660.0000.0000.0000.000
139A1738GLN0-0.052-0.03515.052-0.023-0.0230.0000.0000.0000.000
140A1739THR00.0390.02314.7290.0100.0100.0000.0000.0000.000
141A1740GLU-1-0.858-0.90512.133-0.345-0.3450.0000.0000.0000.000
142A1741VAL0-0.054-0.02016.763-0.030-0.0300.0000.0000.0000.000
143A1742GLU-1-0.954-0.97920.1790.1160.1160.0000.0000.0000.000
144A1743GLU-1-0.952-0.97816.3400.0170.0170.0000.0000.0000.000
145A1744ALA00.0230.01620.127-0.015-0.0150.0000.0000.0000.000
146A1745VAL0-0.052-0.03421.659-0.002-0.0020.0000.0000.0000.000
147A1746GLN0-0.054-0.03423.6700.0090.0090.0000.0000.0000.000
148A1747GLU-1-0.952-0.98120.866-0.162-0.1620.0000.0000.0000.000
149A1748CYS0-0.040-0.01224.943-0.006-0.0060.0000.0000.0000.000
150A1749ARG10.9950.99927.5530.0090.0090.0000.0000.0000.000
151A1750ASN0-0.022-0.00225.8200.0150.0150.0000.0000.0000.000
152A1751ALA0-0.032-0.01528.6020.0000.0000.0000.0000.0000.000
153A1752GLU-1-0.883-0.94930.403-0.050-0.0500.0000.0000.0000.000
154A1753GLU-1-0.837-0.90332.891-0.018-0.0180.0000.0000.0000.000
155A1754LYS10.9170.96128.4210.0770.0770.0000.0000.0000.000
156A1755ALA00.0020.00434.355-0.001-0.0010.0000.0000.0000.000
157A1756LYS10.8490.90536.2460.0280.0280.0000.0000.0000.000
158A1757LYS10.8560.90737.4060.0380.0380.0000.0000.0000.000
159A1758ALA00.0180.01137.6920.0010.0010.0000.0000.0000.000
160A1759ILE0-0.005-0.00339.6570.0000.0000.0000.0000.0000.000
161A1760THR0-0.030-0.02342.2800.0030.0030.0000.0000.0000.000
162A1761ASP-1-0.835-0.90041.018-0.036-0.0360.0000.0000.0000.000
163A1762ALA0-0.011-0.00243.7790.0000.0000.0000.0000.0000.000
164A1763ALA0-0.018-0.00745.4560.0010.0010.0000.0000.0000.000
165A1764MET00.0140.00045.6120.0030.0030.0000.0000.0000.000
166A1765MET0-0.0160.00547.1740.0010.0010.0000.0000.0000.000
167A1766ALA0-0.014-0.01249.1980.0000.0000.0000.0000.0000.000
168A1767GLU-1-0.891-0.93451.617-0.021-0.0210.0000.0000.0000.000
169A1768GLU-1-0.841-0.91652.115-0.023-0.0230.0000.0000.0000.000
170A1769LEU0-0.035-0.00352.8040.0000.0000.0000.0000.0000.000
171A1770LYS10.8180.88854.9110.0300.0300.0000.0000.0000.000
172A1771LYS10.8500.89655.1930.0230.0230.0000.0000.0000.000
173A1772GLU-1-0.901-0.93057.465-0.027-0.0270.0000.0000.0000.000
174A1773GLN0-0.038-0.02757.6460.0010.0010.0000.0000.0000.000
175A1774ASP-1-0.842-0.90360.889-0.026-0.0260.0000.0000.0000.000
176A1775THR0-0.027-0.01962.0290.0020.0020.0000.0000.0000.000
177A1776SER0-0.024-0.01162.5520.0000.0000.0000.0000.0000.000
178A1777ALA00.0230.00464.5130.0010.0010.0000.0000.0000.000
179A1778HIS0-0.003-0.00866.8370.0000.0000.0000.0000.0000.000
180A1779LEU00.0360.00865.5050.0010.0010.0000.0000.0000.000
181A1780GLU-1-0.823-0.88968.795-0.025-0.0250.0000.0000.0000.000
182A1781ARG10.8930.94768.6740.0230.0230.0000.0000.0000.000
183A1782MET0-0.016-0.00871.8090.0010.0010.0000.0000.0000.000
184A1783LYS10.8290.90571.5870.0260.0260.0000.0000.0000.000
185A1784LYS10.8220.90974.3810.0230.0230.0000.0000.0000.000
186A1785ASN0-0.0010.00076.6760.0010.0010.0000.0000.0000.000
187A1786MET0-0.004-0.01074.0370.0010.0010.0000.0000.0000.000
188A1787GLU-1-0.792-0.88575.971-0.023-0.0230.0000.0000.0000.000
189A1788GLN0-0.083-0.05280.027-0.001-0.0010.0000.0000.0000.000
190A1789THR0-0.024-0.01682.1490.0010.0010.0000.0000.0000.000
191A1790ILE0-0.006-0.01280.1160.0000.0000.0000.0000.0000.000
192A1791LYS10.8790.95284.1110.0190.0190.0000.0000.0000.000
193A1792ASP-1-0.837-0.91685.871-0.016-0.0160.0000.0000.0000.000
194A1793LEU0-0.086-0.02185.9160.0010.0010.0000.0000.0000.000
195A1794GLN0-0.061-0.01786.6020.0000.0000.0000.0000.0000.000