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

tag_button

FMODB ID: J2LK9

Calculation Name: 5CHX-A-Xray372

Preferred Name: Cardiac myosin

Target Type: PROTEIN COMPLEX

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 5CHX

Chain ID: A

ChEMBL ID: CHEMBL3831286

UniProt ID: P12883

Base Structure: X-ray

Registration Date: 2023-09-26

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 212
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1929415.688735
FMO2-HF: Nuclear repulsion 1843405.630618
FMO2-HF: Total energy -86010.058117
FMO2-MP2: Total energy -86259.263224


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.
-7.18-5.173-0.001-1.083-0.9210
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 : -0.025 / q_NPA : -0.031
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-1-0.952-0.9723.405-6.394-4.3310.001-1.068-0.9950.000
4A3ARG10.8070.8605.7892.4842.4840.0000.0000.0000.000
5A4MLY10.8860.9669.5210.5880.5880.0000.0000.0000.000
6A5ILE00.0150.01112.9510.0510.0510.0000.0000.0000.000
7A6SER0-0.029-0.01916.0190.0070.0070.0000.0000.0000.000
8A7ARG10.9460.97919.3270.3280.3280.0000.0000.0000.000
9A8ILE0-0.013-0.00522.6410.0140.0140.0000.0000.0000.000
10A9HIS00.0120.00725.303-0.010-0.0100.0000.0000.0000.000
11A10LEU0-0.0020.00327.0680.0050.0050.0000.0000.0000.000
12A11VAL00.0130.00430.1910.0050.0050.0000.0000.0000.000
13A12SER0-0.050-0.02933.3510.0030.0030.0000.0000.0000.000
14A13GLU-1-0.944-0.97832.065-0.148-0.1480.0000.0000.0000.000
15A14PRO00.0220.01232.620-0.011-0.0110.0000.0000.0000.000
16A15SER0-0.054-0.02533.841-0.008-0.0080.0000.0000.0000.000
17A16ILE00.0100.01029.749-0.008-0.0080.0000.0000.0000.000
18A17THR0-0.049-0.01325.8580.0000.0000.0000.0000.0000.000
19A18HIS0-0.016-0.01024.997-0.003-0.0030.0000.0000.0000.000
20A19PHE0-0.012-0.02120.245-0.002-0.0020.0000.0000.0000.000
21A20LEU00.0120.01219.1100.0160.0160.0000.0000.0000.000
22A21GLN00.0310.01413.593-0.098-0.0980.0000.0000.0000.000
23A22VAL00.0250.01313.2110.0470.0470.0000.0000.0000.000
24A23SER0-0.009-0.0098.948-0.161-0.1610.0000.0000.0000.000
25A24TRP00.018-0.0058.0920.1530.1530.0000.0000.0000.000
26A25GLU-1-0.879-0.9325.0211.8811.836-0.001-0.0090.0560.000
27A26MLY10.9350.9714.986-2.342-2.353-0.001-0.0060.0180.000
28A27THR0-0.012-0.0187.144-0.487-0.4870.0000.0000.0000.000
29A28LEU00.0290.01310.4310.0320.0320.0000.0000.0000.000
30A29GLU-1-0.924-0.97912.7320.2850.2850.0000.0000.0000.000
31A30SER0-0.008-0.00511.1000.0890.0890.0000.0000.0000.000
32A31GLY00.0230.02113.5060.0510.0510.0000.0000.0000.000
33A32PHE0-0.069-0.04511.9630.0150.0150.0000.0000.0000.000
34A33VAL00.0220.02911.2480.0470.0470.0000.0000.0000.000
35A34ILE0-0.011-0.02213.561-0.090-0.0900.0000.0000.0000.000
36A35THR00.003-0.01916.3940.0150.0150.0000.0000.0000.000
37A36LEU0-0.030-0.00518.101-0.016-0.0160.0000.0000.0000.000
38A37THR0-0.085-0.09820.5200.0050.0050.0000.0000.0000.000
39A38ASP-1-0.740-0.85822.976-0.249-0.2490.0000.0000.0000.000
40A39GLY0-0.0130.01824.510-0.027-0.0270.0000.0000.0000.000
41A40HIS0-0.063-0.01526.044-0.010-0.0100.0000.0000.0000.000
42A41SER0-0.046-0.04625.7470.0070.0070.0000.0000.0000.000
43A42ALA00.0280.01120.606-0.019-0.0190.0000.0000.0000.000
44A43TRP0-0.016-0.00322.0890.0190.0190.0000.0000.0000.000
45A44THR00.0230.02116.119-0.058-0.0580.0000.0000.0000.000
46A45GLY00.0320.03018.2850.0360.0360.0000.0000.0000.000
47A46THR0-0.052-0.03214.278-0.072-0.0720.0000.0000.0000.000
48A47VAL0-0.0170.01415.9720.0240.0240.0000.0000.0000.000
49A48SER0-0.003-0.03015.8380.0400.0400.0000.0000.0000.000
50A49GLU-1-0.878-0.95915.9440.4650.4650.0000.0000.0000.000
51A50SER0-0.044-0.02517.582-0.016-0.0160.0000.0000.0000.000
52A51GLU-1-0.794-0.87019.4810.0250.0250.0000.0000.0000.000
53A52ILE0-0.042-0.00916.767-0.025-0.0250.0000.0000.0000.000
54A53SER0-0.091-0.06520.629-0.005-0.0050.0000.0000.0000.000
55A54GLN0-0.050-0.01622.6430.0050.0050.0000.0000.0000.000
56A55GLU-1-0.862-0.92824.098-0.012-0.0120.0000.0000.0000.000
57A56ALA0-0.085-0.04223.940-0.009-0.0090.0000.0000.0000.000
58A57ASP-1-0.987-0.99225.9430.0890.0890.0000.0000.0000.000
59A58ASP-1-0.862-0.93028.5940.0430.0430.0000.0000.0000.000
60A59MET0-0.085-0.03828.435-0.013-0.0130.0000.0000.0000.000
61A60ALA0-0.071-0.01730.834-0.004-0.0040.0000.0000.0000.000
62A61MET0-0.057-0.01926.688-0.007-0.0070.0000.0000.0000.000
63A62GLU-1-0.871-0.94324.7490.1240.1240.0000.0000.0000.000
64A63MLY11.0231.00720.489-0.259-0.2590.0000.0000.0000.000
65A64GLY00.0370.02020.894-0.007-0.0070.0000.0000.0000.000
66A65MLY10.8860.93421.405-0.064-0.0640.0000.0000.0000.000
67A66TYR00.0470.01922.011-0.023-0.0230.0000.0000.0000.000
68A67VAL00.0320.01316.604-0.031-0.0310.0000.0000.0000.000
69A68GLY0-0.022-0.01318.732-0.034-0.0340.0000.0000.0000.000
70A69GLU-1-0.777-0.83320.455-0.091-0.0910.0000.0000.0000.000
71A70LEU00.0300.02818.509-0.033-0.0330.0000.0000.0000.000
72A71ARG10.9140.96411.886-0.023-0.0230.0000.0000.0000.000
73A72MLY10.8890.95017.8310.0250.0250.0000.0000.0000.000
74A73ALA00.0000.00820.968-0.020-0.0200.0000.0000.0000.000
75A74LEU00.0120.00017.875-0.022-0.0220.0000.0000.0000.000
76A75LEU0-0.026-0.00513.342-0.058-0.0580.0000.0000.0000.000
77A76SER0-0.043-0.02317.033-0.036-0.0360.0000.0000.0000.000
78A77GLY0-0.0070.00219.549-0.014-0.0140.0000.0000.0000.000
79A78ALA0-0.036-0.01220.2690.0290.0290.0000.0000.0000.000
80A79GLY0-0.007-0.01224.062-0.008-0.0080.0000.0000.0000.000
81A80PRO0-0.0170.00326.2910.0060.0060.0000.0000.0000.000
82A81ALA0-0.028-0.04226.0390.0080.0080.0000.0000.0000.000
83A82ASP-1-0.899-0.94227.915-0.144-0.1440.0000.0000.0000.000
84A83VAL0-0.0120.01028.1160.0060.0060.0000.0000.0000.000
85A84TYR0-0.033-0.07125.0880.0060.0060.0000.0000.0000.000
86A85THR00.0320.03427.933-0.011-0.0110.0000.0000.0000.000
87A86PHE00.015-0.00123.3240.0040.0040.0000.0000.0000.000
88A87ASN0-0.009-0.00128.1460.0020.0020.0000.0000.0000.000
89A88PHE00.0550.00926.048-0.005-0.0050.0000.0000.0000.000
90A89SER0-0.0230.04529.5090.0070.0070.0000.0000.0000.000
91A90MLY10.9820.98429.8290.1710.1710.0000.0000.0000.000
92A91GLU-1-0.926-0.96330.739-0.119-0.1190.0000.0000.0000.000
93A92SER0-0.055-0.06331.7740.0030.0030.0000.0000.0000.000
94A93CYS0-0.0190.00226.429-0.002-0.0020.0000.0000.0000.000
95A94TYR00.0120.02526.664-0.004-0.0040.0000.0000.0000.000
96A95PHE00.015-0.00423.441-0.010-0.0100.0000.0000.0000.000
97A96PHE0-0.006-0.00726.5090.0130.0130.0000.0000.0000.000
98A97PHE00.0230.01022.480-0.013-0.0130.0000.0000.0000.000
99A98GLU-1-0.897-0.95427.469-0.057-0.0570.0000.0000.0000.000
100A99MLY10.8090.88327.4590.0430.0430.0000.0000.0000.000
101A100ASN0-0.041-0.03029.8120.0140.0140.0000.0000.0000.000
102A101LEU0-0.046-0.02232.645-0.002-0.0020.0000.0000.0000.000
103A102MLY10.8810.92335.1150.0420.0420.0000.0000.0000.000
104A103ASP-1-0.861-0.94538.178-0.053-0.0530.0000.0000.0000.000
105A104VAL0-0.0360.01436.8610.0010.0010.0000.0000.0000.000
106A105SER00.0210.01134.129-0.001-0.0010.0000.0000.0000.000
107A106PHE0-0.002-0.00629.4580.0070.0070.0000.0000.0000.000
108A107ARG10.9680.99129.6060.0490.0490.0000.0000.0000.000
109A108LEU0-0.058-0.01824.3670.0090.0090.0000.0000.0000.000
110A109GLY00.1030.03324.6620.0140.0140.0000.0000.0000.000
111A110SER0-0.091-0.04425.210-0.011-0.0110.0000.0000.0000.000
112A111PHE00.0540.01320.6730.0020.0020.0000.0000.0000.000
113A112ASN00.0040.00523.689-0.009-0.0090.0000.0000.0000.000
114A113LEU0-0.062-0.02820.531-0.007-0.0070.0000.0000.0000.000
115A114GLU-1-0.862-0.93121.780-0.134-0.1340.0000.0000.0000.000
116A115MLY10.9060.94722.1920.1560.1560.0000.0000.0000.000
117A116VAL00.0190.01819.0450.0080.0080.0000.0000.0000.000
118A117GLU-1-0.915-0.96122.319-0.230-0.2300.0000.0000.0000.000
119A118ASN0-0.061-0.04018.0790.0320.0320.0000.0000.0000.000
120A119PRO00.0470.02220.668-0.044-0.0440.0000.0000.0000.000
121A120ALA00.016-0.00420.967-0.036-0.0360.0000.0000.0000.000
122A121GLU-1-0.936-0.95817.011-0.483-0.4830.0000.0000.0000.000
123A122VAL00.0540.03016.269-0.069-0.0690.0000.0000.0000.000
124A123ILE0-0.0030.00216.629-0.075-0.0750.0000.0000.0000.000
125A124ARG10.9300.95718.3730.4000.4000.0000.0000.0000.000
126A125GLU-1-0.801-0.86310.299-1.492-1.4920.0000.0000.0000.000
127A126LEU00.0540.03113.606-0.092-0.0920.0000.0000.0000.000
128A127ILE0-0.027-0.02715.240-0.030-0.0300.0000.0000.0000.000
129A128CYS0-0.033-0.02313.9100.0430.0430.0000.0000.0000.000
130A129TYR00.0730.0527.978-0.079-0.0790.0000.0000.0000.000
131A130CYS0-0.051-0.03012.6170.0060.0060.0000.0000.0000.000
132A131LEU0-0.040-0.02215.3020.0500.0500.0000.0000.0000.000
133A132ASP-1-0.870-0.93011.699-0.970-0.9700.0000.0000.0000.000
134A133THR0-0.017-0.01111.7730.0070.0070.0000.0000.0000.000
135A134THR0-0.087-0.04813.0770.1030.1030.0000.0000.0000.000
136A135ALA00.0210.01315.4620.0710.0710.0000.0000.0000.000
137A136GLU-1-0.930-0.9659.892-1.182-1.1820.0000.0000.0000.000
138A137ASN0-0.061-0.04914.3660.0540.0540.0000.0000.0000.000
139A138GLN0-0.0080.01016.5180.0450.0450.0000.0000.0000.000
140A139ALA00.0570.03716.6930.0470.0470.0000.0000.0000.000
141A140MLY10.9310.96912.8620.6060.6060.0000.0000.0000.000
142A141ASN0-0.023-0.02018.1850.0380.0380.0000.0000.0000.000
143A142GLU-1-0.918-0.95721.377-0.239-0.2390.0000.0000.0000.000
144A143HIS0-0.044-0.03720.1040.0260.0260.0000.0000.0000.000
145A1590HIS00.000-0.00818.9380.0460.0460.0000.0000.0000.000
146A1591LEU00.0180.00423.3480.0210.0210.0000.0000.0000.000
147A1592ARG10.9500.99221.8250.1880.1880.0000.0000.0000.000
148A1593VAL0-0.019-0.00423.5230.0160.0160.0000.0000.0000.000
149A1594VAL0-0.008-0.00926.6570.0140.0140.0000.0000.0000.000
150A1595ASP-1-0.909-0.94029.040-0.076-0.0760.0000.0000.0000.000
151A1596SER00.0050.00729.5920.0120.0120.0000.0000.0000.000
152A1597LEU0-0.027-0.02528.0590.0100.0100.0000.0000.0000.000
153A1598GLN0-0.015-0.01532.0570.0050.0050.0000.0000.0000.000
154A1599THR00.0110.01734.6000.0060.0060.0000.0000.0000.000
155A1600SER00.001-0.01334.4680.0070.0070.0000.0000.0000.000
156A1601LEU00.0230.00935.7820.0050.0050.0000.0000.0000.000
157A1602ASP-1-0.907-0.93037.936-0.037-0.0370.0000.0000.0000.000
158A1603ALA00.0180.00439.8780.0030.0030.0000.0000.0000.000
159A1604GLU-1-0.917-0.96538.871-0.007-0.0070.0000.0000.0000.000
160A1605THR0-0.099-0.05241.6380.0030.0030.0000.0000.0000.000
161A1606ARG10.8550.91643.8930.0380.0380.0000.0000.0000.000
162A1607SER00.0590.03845.0010.0020.0020.0000.0000.0000.000
163A1608ARG10.9730.99943.5890.0220.0220.0000.0000.0000.000
164A1609ASN0-0.036-0.03947.3990.0030.0030.0000.0000.0000.000
165A1610GLU-1-0.969-0.97749.743-0.015-0.0150.0000.0000.0000.000
166A1611ALA00.0230.00950.2390.0010.0010.0000.0000.0000.000
167A1612LEU00.0010.00451.2410.0020.0020.0000.0000.0000.000
168A1613ARG10.8950.94053.2580.0170.0170.0000.0000.0000.000
169A1614VAL00.0170.00954.9860.0010.0010.0000.0000.0000.000
170A1615MLY10.8550.90954.2690.0020.0020.0000.0000.0000.000
171A1616MLY11.0020.99957.0590.0100.0100.0000.0000.0000.000
172A1617MLY10.8480.93959.7250.0040.0040.0000.0000.0000.000
173A1618MET0-0.011-0.00657.6320.0010.0010.0000.0000.0000.000
174A1619GLU-1-0.804-0.87458.882-0.001-0.0010.0000.0000.0000.000
175A1620GLY0-0.013-0.00262.7020.0000.0000.0000.0000.0000.000
176A1621ASP-1-0.837-0.93764.799-0.002-0.0020.0000.0000.0000.000
177A1622LEU0-0.027-0.00963.4470.0010.0010.0000.0000.0000.000
178A1623ASN00.0330.01366.5150.0010.0010.0000.0000.0000.000
179A1624GLU-1-0.889-0.93368.634-0.001-0.0010.0000.0000.0000.000
180A1625MET0-0.011-0.01967.6200.0000.0000.0000.0000.0000.000
181A1626GLU-1-0.916-0.94568.4610.0040.0040.0000.0000.0000.000
182A1627ILE0-0.043-0.02572.1600.0000.0000.0000.0000.0000.000
183A1628GLN0-0.056-0.04274.2820.0010.0010.0000.0000.0000.000
184A1629LEU0-0.0120.00273.3390.0000.0000.0000.0000.0000.000
185A1630SER0-0.048-0.01576.2770.0000.0000.0000.0000.0000.000
186A1631HIS0-0.002-0.01478.0290.0000.0000.0000.0000.0000.000
187A1632ALA00.0350.02079.5710.0000.0000.0000.0000.0000.000
188A1633ASN00.007-0.00677.5840.0000.0000.0000.0000.0000.000
189A1634ARG10.9320.96481.555-0.001-0.0010.0000.0000.0000.000
190A1635MET0-0.0020.00784.0340.0000.0000.0000.0000.0000.000
191A1636ALA0-0.0100.00784.4950.0000.0000.0000.0000.0000.000
192A1637ALA00.0080.00185.3430.0000.0000.0000.0000.0000.000
193A1638GLU-1-0.840-0.91387.1740.0030.0030.0000.0000.0000.000
194A1639ALA00.0440.01789.5680.0000.0000.0000.0000.0000.000
195A1640GLN00.002-0.01088.5160.0000.0000.0000.0000.0000.000
196A1641MLY10.8400.92288.195-0.003-0.0030.0000.0000.0000.000
197A1642GLN0-0.0050.00593.3990.0000.0000.0000.0000.0000.000
198A1643VAL00.0140.00293.2990.0000.0000.0000.0000.0000.000
199A1644MLY10.9610.98694.348-0.005-0.0050.0000.0000.0000.000
200A1645SER0-0.025-0.01996.7720.0000.0000.0000.0000.0000.000
201A1646LEU00.0090.00498.2740.0000.0000.0000.0000.0000.000
202A1647GLN0-0.013-0.01296.2640.0000.0000.0000.0000.0000.000
203A1648SER0-0.024-0.016100.9510.0000.0000.0000.0000.0000.000
204A1649LEU00.0300.019102.7880.0000.0000.0000.0000.0000.000
205A1650LEU0-0.0190.009103.4780.0000.0000.0000.0000.0000.000
206A1651MLY10.9460.97299.516-0.006-0.0060.0000.0000.0000.000
207A1652ASP-1-0.887-0.948106.5300.0040.0040.0000.0000.0000.000
208A1653THR0-0.048-0.033108.7190.0000.0000.0000.0000.0000.000
209A1654GLN0-0.038-0.037106.4370.0000.0000.0000.0000.0000.000
210A1655ILE0-0.043-0.003110.1090.0000.0000.0000.0000.0000.000
211A1656GLN0-0.051-0.016112.3020.0000.0000.0000.0000.0000.000
212A1657LEU0-0.059-0.015113.5760.0000.0000.0000.0000.0000.000