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: 379GL

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 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 212
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1931260.717079
FMO2-HF: Nuclear repulsion 1845249.753416
FMO2-HF: Total energy -86010.963663
FMO2-MP2: Total energy -86260.225523


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.
-5.77-3.3910.005-1.314-1.0680.003
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 : -0.022 / q_NPA : -0.011
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-1-0.903-0.9433.444-0.9991.4010.006-1.299-1.1060.003
4A3ARG10.7950.8306.1751.3781.3780.0000.0000.0000.000
5A4MLY10.8610.9609.5950.3740.3740.0000.0000.0000.000
6A5ILE00.0180.00713.028-0.028-0.0280.0000.0000.0000.000
7A6SER0-0.032-0.01315.8940.0580.0580.0000.0000.0000.000
8A7ARG10.9420.97419.3030.1580.1580.0000.0000.0000.000
9A8ILE0-0.012-0.00122.8240.0170.0170.0000.0000.0000.000
10A9HIS00.0290.01225.372-0.009-0.0090.0000.0000.0000.000
11A10LEU00.0070.01227.0710.0020.0020.0000.0000.0000.000
12A11VAL00.0150.00030.3390.0080.0080.0000.0000.0000.000
13A12SER0-0.021-0.01433.4460.0060.0060.0000.0000.0000.000
14A13GLU-1-0.932-0.97631.980-0.150-0.1500.0000.0000.0000.000
15A14PRO00.0290.01532.534-0.006-0.0060.0000.0000.0000.000
16A15SER0-0.034-0.01533.729-0.002-0.0020.0000.0000.0000.000
17A16ILE0-0.0070.00329.653-0.001-0.0010.0000.0000.0000.000
18A17THR0-0.059-0.02625.7280.0020.0020.0000.0000.0000.000
19A18HIS0-0.029-0.01825.154-0.012-0.0120.0000.0000.0000.000
20A19PHE0-0.013-0.01820.1640.0150.0150.0000.0000.0000.000
21A20LEU00.0210.01619.167-0.007-0.0070.0000.0000.0000.000
22A21GLN00.0310.01613.554-0.013-0.0130.0000.0000.0000.000
23A22VAL00.0170.01013.906-0.012-0.0120.0000.0000.0000.000
24A23SER00.0370.0098.9370.0130.0130.0000.0000.0000.000
25A24TRP0-0.063-0.0448.684-0.085-0.0850.0000.0000.0000.000
26A25GLU-1-0.888-0.9394.575-3.336-3.357-0.001-0.0150.0380.000
27A26MLY10.9250.9635.6730.1710.1710.0000.0000.0000.000
28A27THR00.0130.0027.7410.0440.0440.0000.0000.0000.000
29A28LEU00.0400.01711.221-0.109-0.1090.0000.0000.0000.000
30A29GLU-1-0.869-0.94113.5830.0390.0390.0000.0000.0000.000
31A30SER0-0.014-0.01011.0960.0390.0390.0000.0000.0000.000
32A31GLY00.0120.01713.082-0.047-0.0470.0000.0000.0000.000
33A32PHE0-0.070-0.04411.767-0.041-0.0410.0000.0000.0000.000
34A33VAL00.0060.01711.6250.0570.0570.0000.0000.0000.000
35A34ILE0-0.003-0.01213.756-0.012-0.0120.0000.0000.0000.000
36A35THR00.0350.02516.1990.0240.0240.0000.0000.0000.000
37A36LEU0-0.0170.01318.3240.0170.0170.0000.0000.0000.000
38A37THR0-0.020-0.03420.390-0.017-0.0170.0000.0000.0000.000
39A38ASP-1-0.748-0.87022.989-0.229-0.2290.0000.0000.0000.000
40A39GLY0-0.039-0.03024.524-0.023-0.0230.0000.0000.0000.000
41A40HIS0-0.047-0.01326.057-0.008-0.0080.0000.0000.0000.000
42A41SER0-0.051-0.03825.776-0.003-0.0030.0000.0000.0000.000
43A42ALA00.0210.00320.760-0.009-0.0090.0000.0000.0000.000
44A43TRP0-0.014-0.00222.2500.0160.0160.0000.0000.0000.000
45A44THR0-0.004-0.03016.281-0.014-0.0140.0000.0000.0000.000
46A45GLY00.0460.03218.5560.0350.0350.0000.0000.0000.000
47A46THR0-0.052-0.03314.389-0.106-0.1060.0000.0000.0000.000
48A47VAL0-0.0110.01716.0050.0550.0550.0000.0000.0000.000
49A48SER0-0.035-0.05515.666-0.019-0.0190.0000.0000.0000.000
50A49GLU-1-0.863-0.95015.4300.0020.0020.0000.0000.0000.000
51A50SER0-0.055-0.02917.1050.0380.0380.0000.0000.0000.000
52A51GLU-1-0.789-0.86119.752-0.243-0.2430.0000.0000.0000.000
53A52ILE0-0.0170.00416.7310.0130.0130.0000.0000.0000.000
54A53SER0-0.075-0.06320.2920.0300.0300.0000.0000.0000.000
55A54GLN0-0.070-0.03622.5430.0140.0140.0000.0000.0000.000
56A55GLU-1-0.846-0.92724.113-0.114-0.1140.0000.0000.0000.000
57A56ALA0-0.083-0.04424.3740.0090.0090.0000.0000.0000.000
58A57ASP-1-0.958-0.97926.303-0.013-0.0130.0000.0000.0000.000
59A58ASP-1-0.866-0.91628.584-0.067-0.0670.0000.0000.0000.000
60A59MET0-0.098-0.03628.844-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.059-0.01531.2400.0060.0060.0000.0000.0000.000
62A61MET0-0.066-0.01927.1060.0050.0050.0000.0000.0000.000
63A62GLU-1-0.845-0.93025.5570.0560.0560.0000.0000.0000.000
64A63MLY10.9540.96420.031-0.042-0.0420.0000.0000.0000.000
65A64GLY00.0380.02121.713-0.005-0.0050.0000.0000.0000.000
66A65MLY10.8540.91722.332-0.041-0.0410.0000.0000.0000.000
67A66TYR00.035-0.00222.492-0.007-0.0070.0000.0000.0000.000
68A67VAL00.0350.01417.494-0.016-0.0160.0000.0000.0000.000
69A68GLY0-0.017-0.01019.753-0.005-0.0050.0000.0000.0000.000
70A69GLU-1-0.783-0.87121.518-0.037-0.0370.0000.0000.0000.000
71A70LEU00.0270.03019.148-0.017-0.0170.0000.0000.0000.000
72A71ARG10.9090.95513.005-0.167-0.1670.0000.0000.0000.000
73A72MLY10.8410.93418.920-0.021-0.0210.0000.0000.0000.000
74A73ALA00.0000.00721.912-0.009-0.0090.0000.0000.0000.000
75A74LEU00.004-0.00318.679-0.014-0.0140.0000.0000.0000.000
76A75LEU0-0.024-0.00414.258-0.038-0.0380.0000.0000.0000.000
77A76SER0-0.040-0.02317.6350.0090.0090.0000.0000.0000.000
78A77GLY00.0080.00620.3330.0110.0110.0000.0000.0000.000
79A78ALA0-0.032-0.01320.9790.0210.0210.0000.0000.0000.000
80A79GLY00.002-0.00724.8090.0040.0040.0000.0000.0000.000
81A80PRO0-0.0100.00226.8130.0000.0000.0000.0000.0000.000
82A81ALA0-0.036-0.04326.4640.0030.0030.0000.0000.0000.000
83A82ASP-1-0.906-0.94228.406-0.073-0.0730.0000.0000.0000.000
84A83VAL0-0.0020.01728.886-0.001-0.0010.0000.0000.0000.000
85A84TYR0-0.019-0.03926.1210.0040.0040.0000.0000.0000.000
86A85THR00.0210.03128.632-0.005-0.0050.0000.0000.0000.000
87A86PHE00.0290.00623.939-0.004-0.0040.0000.0000.0000.000
88A87ASN0-0.026-0.01028.5980.0110.0110.0000.0000.0000.000
89A88PHE00.0460.00626.376-0.011-0.0110.0000.0000.0000.000
90A89SER00.0040.03629.7430.0090.0090.0000.0000.0000.000
91A90MLY10.8800.94829.9980.1800.1800.0000.0000.0000.000
92A91GLU-1-0.919-0.96730.949-0.160-0.1600.0000.0000.0000.000
93A92SER0-0.040-0.03232.028-0.001-0.0010.0000.0000.0000.000
94A93CYS0-0.030-0.00226.789-0.011-0.0110.0000.0000.0000.000
95A94TYR00.0170.02726.935-0.009-0.0090.0000.0000.0000.000
96A95PHE00.006-0.00623.7410.0040.0040.0000.0000.0000.000
97A96PHE0-0.005-0.01026.5590.0020.0020.0000.0000.0000.000
98A97PHE00.0180.00723.0300.0000.0000.0000.0000.0000.000
99A98GLU-1-0.845-0.93028.088-0.084-0.0840.0000.0000.0000.000
100A99MLY10.8140.90428.3880.0290.0290.0000.0000.0000.000
101A100ASN0-0.046-0.05130.7500.0050.0050.0000.0000.0000.000
102A101LEU0-0.039-0.01233.5290.0050.0050.0000.0000.0000.000
103A102MLY10.8880.92236.0550.0170.0170.0000.0000.0000.000
104A103ASP-1-0.877-0.94739.016-0.045-0.0450.0000.0000.0000.000
105A104VAL0-0.0280.00938.244-0.002-0.0020.0000.0000.0000.000
106A105SER00.0020.00634.8960.0020.0020.0000.0000.0000.000
107A106PHE0-0.006-0.00730.4240.0050.0050.0000.0000.0000.000
108A107ARG10.9480.98529.8040.1070.1070.0000.0000.0000.000
109A108LEU0-0.053-0.01925.1720.0080.0080.0000.0000.0000.000
110A109GLY00.1050.04525.0040.0030.0030.0000.0000.0000.000
111A110SER0-0.092-0.04325.2380.0020.0020.0000.0000.0000.000
112A111PHE00.0430.01120.987-0.013-0.0130.0000.0000.0000.000
113A112ASN00.0230.01823.9220.0200.0200.0000.0000.0000.000
114A113LEU0-0.062-0.03220.742-0.027-0.0270.0000.0000.0000.000
115A114GLU-1-0.871-0.93422.006-0.298-0.2980.0000.0000.0000.000
116A115MLY10.9000.95122.3760.2040.2040.0000.0000.0000.000
117A116VAL00.0310.02119.1880.0040.0040.0000.0000.0000.000
118A117GLU-1-0.923-0.96422.429-0.336-0.3360.0000.0000.0000.000
119A118ASN0-0.068-0.04418.2050.0270.0270.0000.0000.0000.000
120A119PRO00.0560.02620.682-0.044-0.0440.0000.0000.0000.000
121A120ALA00.0140.00020.974-0.025-0.0250.0000.0000.0000.000
122A121GLU-1-0.891-0.93717.332-0.488-0.4880.0000.0000.0000.000
123A122VAL00.0580.02616.134-0.059-0.0590.0000.0000.0000.000
124A123ILE0-0.0010.00616.640-0.049-0.0490.0000.0000.0000.000
125A124ARG10.8800.93518.2480.4160.4160.0000.0000.0000.000
126A125GLU-1-0.796-0.84410.564-1.360-1.3600.0000.0000.0000.000
127A126LEU00.0410.02613.621-0.050-0.0500.0000.0000.0000.000
128A127ILE0-0.007-0.01115.2560.0190.0190.0000.0000.0000.000
129A128CYS0-0.040-0.03014.0790.0640.0640.0000.0000.0000.000
130A129TYR00.0820.0557.762-0.025-0.0250.0000.0000.0000.000
131A130CYS0-0.052-0.02412.6390.0730.0730.0000.0000.0000.000
132A131LEU0-0.030-0.01115.3110.0720.0720.0000.0000.0000.000
133A132ASP-1-0.868-0.93111.852-0.552-0.5520.0000.0000.0000.000
134A133THR0-0.028-0.02411.9300.0740.0740.0000.0000.0000.000
135A134THR0-0.096-0.06413.1190.1000.1000.0000.0000.0000.000
136A135ALA00.0220.01415.6000.0530.0530.0000.0000.0000.000
137A136GLU-1-0.930-0.9639.861-0.221-0.2210.0000.0000.0000.000
138A137ASN0-0.039-0.03314.4620.1060.1060.0000.0000.0000.000
139A138GLN0-0.040-0.00716.5670.0160.0160.0000.0000.0000.000
140A139ALA00.0570.03516.7890.0250.0250.0000.0000.0000.000
141A140MLY10.8850.93912.338-0.045-0.0450.0000.0000.0000.000
142A141ASN0-0.013-0.01518.2580.0310.0310.0000.0000.0000.000
143A142GLU-1-0.882-0.93421.433-0.007-0.0070.0000.0000.0000.000
144A143HIS0-0.028-0.03320.211-0.003-0.0030.0000.0000.0000.000
145A1590HIS00.006-0.00418.8230.0080.0080.0000.0000.0000.000
146A1591LEU00.0110.00123.4030.0010.0010.0000.0000.0000.000
147A1592ARG10.9410.99221.698-0.073-0.0730.0000.0000.0000.000
148A1593VAL0-0.026-0.00523.5180.0030.0030.0000.0000.0000.000
149A1594VAL00.004-0.00526.7260.0010.0010.0000.0000.0000.000
150A1595ASP-1-0.906-0.93929.0880.0530.0530.0000.0000.0000.000
151A1596SER00.0210.01929.6910.0020.0020.0000.0000.0000.000
152A1597LEU0-0.019-0.02228.153-0.001-0.0010.0000.0000.0000.000
153A1598GLN0-0.021-0.02032.109-0.005-0.0050.0000.0000.0000.000
154A1599THR00.0020.01034.660-0.005-0.0050.0000.0000.0000.000
155A1600SER0-0.025-0.02334.058-0.001-0.0010.0000.0000.0000.000
156A1601LEU00.0160.00535.234-0.002-0.0020.0000.0000.0000.000
157A1602ASP-1-0.832-0.86737.9760.0420.0420.0000.0000.0000.000
158A1603ALA00.0140.00539.934-0.003-0.0030.0000.0000.0000.000
159A1604GLU-1-0.908-0.95938.9980.0730.0730.0000.0000.0000.000
160A1605THR0-0.058-0.02941.836-0.003-0.0030.0000.0000.0000.000
161A1606ARG10.7820.84743.928-0.044-0.0440.0000.0000.0000.000
162A1607SER00.0360.02744.969-0.003-0.0030.0000.0000.0000.000
163A1608ARG10.9300.97143.761-0.054-0.0540.0000.0000.0000.000
164A1609ASN0-0.014-0.02747.432-0.001-0.0010.0000.0000.0000.000
165A1610GLU-1-0.874-0.92149.4780.0380.0380.0000.0000.0000.000
166A1611ALA00.0200.00750.195-0.002-0.0020.0000.0000.0000.000
167A1612LEU0-0.0050.00150.698-0.001-0.0010.0000.0000.0000.000
168A1613ARG10.8270.90453.472-0.037-0.0370.0000.0000.0000.000
169A1614VAL00.0080.00155.076-0.001-0.0010.0000.0000.0000.000
170A1615MLY10.8540.92054.519-0.042-0.0420.0000.0000.0000.000
171A1616MLY10.9810.98557.090-0.031-0.0310.0000.0000.0000.000
172A1617MLY10.8380.91059.749-0.033-0.0330.0000.0000.0000.000
173A1618MET00.0010.00157.5230.0000.0000.0000.0000.0000.000
174A1619GLU-1-0.811-0.88658.9560.0390.0390.0000.0000.0000.000
175A1620GLY0-0.0040.00362.811-0.001-0.0010.0000.0000.0000.000
176A1621ASP-1-0.824-0.90764.3940.0310.0310.0000.0000.0000.000
177A1622LEU0-0.0100.00063.729-0.001-0.0010.0000.0000.0000.000
178A1623ASN00.0290.01166.643-0.001-0.0010.0000.0000.0000.000
179A1624GLU-1-0.882-0.92968.7870.0240.0240.0000.0000.0000.000
180A1625MET0-0.021-0.02267.229-0.001-0.0010.0000.0000.0000.000
181A1626GLU-1-0.920-0.94668.4630.0310.0310.0000.0000.0000.000
182A1627ILE0-0.030-0.01772.361-0.001-0.0010.0000.0000.0000.000
183A1628GLN0-0.085-0.05674.414-0.001-0.0010.0000.0000.0000.000
184A1629LEU0-0.0040.00173.639-0.001-0.0010.0000.0000.0000.000
185A1630SER0-0.040-0.01176.498-0.001-0.0010.0000.0000.0000.000
186A1631HIS0-0.016-0.02078.272-0.001-0.0010.0000.0000.0000.000
187A1632ALA00.0360.02179.696-0.001-0.0010.0000.0000.0000.000
188A1633ASN00.005-0.00777.735-0.001-0.0010.0000.0000.0000.000
189A1634ARG10.9480.97181.825-0.021-0.0210.0000.0000.0000.000
190A1635MET0-0.0070.00584.303-0.001-0.0010.0000.0000.0000.000
191A1636ALA0-0.0100.00584.7000.0000.0000.0000.0000.0000.000
192A1637ALA00.0150.00485.6320.0000.0000.0000.0000.0000.000
193A1638GLU-1-0.811-0.89287.4980.0180.0180.0000.0000.0000.000
194A1639ALA00.0330.01289.823-0.001-0.0010.0000.0000.0000.000
195A1640GLN00.003-0.00888.810-0.001-0.0010.0000.0000.0000.000
196A1641MLY10.8170.90488.454-0.019-0.0190.0000.0000.0000.000
197A1642GLN00.0000.00893.7490.0000.0000.0000.0000.0000.000
198A1643VAL00.0190.00493.5560.0000.0000.0000.0000.0000.000
199A1644MLY10.9590.98594.672-0.018-0.0180.0000.0000.0000.000
200A1645SER0-0.032-0.02797.1510.0000.0000.0000.0000.0000.000
201A1646LEU00.0140.00798.4140.0000.0000.0000.0000.0000.000
202A1647GLN0-0.004-0.00396.3410.0000.0000.0000.0000.0000.000
203A1648SER0-0.030-0.024101.3140.0000.0000.0000.0000.0000.000
204A1649LEU00.0360.023103.1920.0000.0000.0000.0000.0000.000
205A1650LEU0-0.0220.013103.6300.0000.0000.0000.0000.0000.000
206A1651MLY10.9340.971100.007-0.017-0.0170.0000.0000.0000.000
207A1652ASP-1-0.870-0.939106.9350.0140.0140.0000.0000.0000.000
208A1653THR0-0.054-0.036109.0850.0000.0000.0000.0000.0000.000
209A1654GLN0-0.033-0.037106.6910.0000.0000.0000.0000.0000.000
210A1655ILE0-0.036-0.003110.3200.0000.0000.0000.0000.0000.000
211A1656GLN0-0.080-0.034112.7300.0000.0000.0000.0000.0000.000
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