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: 94R12

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 OptAll
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 -1761264.467317
FMO2-HF: Nuclear repulsion 1682282.766719
FMO2-HF: Total energy -78981.700597
FMO2-MP2: Total energy -79207.29407


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.
-17.319-13.7833.331-3.87-2.999-0.031
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 : -0.029 / q_NPA : -0.018
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-1-0.882-0.9152.058-15.686-12.3593.332-3.799-2.861-0.031
4A3ARG10.7720.8194.9000.5400.581-0.001-0.005-0.0360.000
5A4LYS10.8700.9528.0860.5570.5570.0000.0000.0000.000
6A5ILE00.0520.03811.6660.0620.0620.0000.0000.0000.000
7A6SER0-0.030-0.02714.270-0.018-0.0180.0000.0000.0000.000
8A7ARG10.9430.98317.8370.1590.1590.0000.0000.0000.000
9A8ILE00.0070.00421.235-0.023-0.0230.0000.0000.0000.000
10A9HIS00.0270.02023.8370.0370.0370.0000.0000.0000.000
11A10LEU00.0110.02325.657-0.018-0.0180.0000.0000.0000.000
12A11VAL00.013-0.00628.8310.0120.0120.0000.0000.0000.000
13A12SER0-0.013-0.00431.1730.0060.0060.0000.0000.0000.000
14A13GLU-1-0.844-0.92430.114-0.058-0.0580.0000.0000.0000.000
15A14PRO00.0090.00630.726-0.002-0.0020.0000.0000.0000.000
16A15SER0-0.055-0.02732.058-0.003-0.0030.0000.0000.0000.000
17A16ILE0-0.009-0.00229.1570.0090.0090.0000.0000.0000.000
18A17THR0-0.050-0.03924.046-0.009-0.0090.0000.0000.0000.000
19A18HIS00.0220.02923.6140.0230.0230.0000.0000.0000.000
20A19PHE0-0.030-0.02318.951-0.019-0.0190.0000.0000.0000.000
21A20LEU00.0170.00617.1020.0240.0240.0000.0000.0000.000
22A21GLN00.0180.01911.081-0.028-0.0280.0000.0000.0000.000
23A22VAL00.006-0.00212.6610.0360.0360.0000.0000.0000.000
24A23SER00.0170.0097.8460.0300.0300.0000.0000.0000.000
25A24TRP00.004-0.0017.6290.6740.6740.0000.0000.0000.000
26A25GLU-1-0.818-0.9124.092-6.342-6.1740.000-0.066-0.1020.000
27A26LYS10.9270.9666.6712.0422.0420.0000.0000.0000.000
28A27THR0-0.109-0.0688.1960.4420.4420.0000.0000.0000.000
29A28LEU00.0480.01911.505-0.071-0.0710.0000.0000.0000.000
30A29GLU-1-0.828-0.90113.186-0.689-0.6890.0000.0000.0000.000
31A30SER0-0.016-0.00611.6920.0230.0230.0000.0000.0000.000
32A31GLY00.0040.01013.2010.0170.0170.0000.0000.0000.000
33A32PHE0-0.072-0.04611.862-0.266-0.2660.0000.0000.0000.000
34A33VAL00.0200.01911.3070.1840.1840.0000.0000.0000.000
35A34ILE0-0.029-0.01912.654-0.108-0.1080.0000.0000.0000.000
36A35THR00.010-0.01115.0930.0740.0740.0000.0000.0000.000
37A36LEU0-0.0120.00516.794-0.035-0.0350.0000.0000.0000.000
38A37THR0-0.024-0.04319.3950.0460.0460.0000.0000.0000.000
39A38ASP-1-0.761-0.89221.742-0.036-0.0360.0000.0000.0000.000
40A39GLY0-0.0050.01223.4900.0040.0040.0000.0000.0000.000
41A40HIS0-0.044-0.01824.5060.0280.0280.0000.0000.0000.000
42A41SER0-0.053-0.02125.1840.0160.0160.0000.0000.0000.000
43A42ALA00.0210.01919.918-0.010-0.0100.0000.0000.0000.000
44A43TRP00.005-0.00321.0280.0220.0220.0000.0000.0000.000
45A44THR00.0400.02015.780-0.026-0.0260.0000.0000.0000.000
46A45GLY00.0650.04517.5180.0330.0330.0000.0000.0000.000
47A46THR0-0.047-0.02614.518-0.045-0.0450.0000.0000.0000.000
48A47VAL00.0080.02416.1400.0620.0620.0000.0000.0000.000
49A48SER0-0.019-0.04716.277-0.130-0.1300.0000.0000.0000.000
50A49GLU-1-0.772-0.89316.175-0.814-0.8140.0000.0000.0000.000
51A50SER0-0.036-0.00217.9050.0350.0350.0000.0000.0000.000
52A51GLU-1-0.816-0.86220.364-0.369-0.3690.0000.0000.0000.000
53A52ILE0-0.037-0.01016.9010.0190.0190.0000.0000.0000.000
54A53SER0-0.076-0.07721.3360.0310.0310.0000.0000.0000.000
55A54GLN0-0.042-0.01323.2230.0160.0160.0000.0000.0000.000
56A55GLU-1-0.811-0.91224.498-0.285-0.2850.0000.0000.0000.000
57A56ALA0-0.087-0.05324.2480.0130.0130.0000.0000.0000.000
58A57ASP-1-0.960-0.97726.350-0.286-0.2860.0000.0000.0000.000
59A58ASP-1-0.881-0.93629.432-0.230-0.2300.0000.0000.0000.000
60A59MET0-0.142-0.05328.1460.0170.0170.0000.0000.0000.000
61A60ALA00.014-0.00530.724-0.015-0.0150.0000.0000.0000.000
62A61MET0-0.085-0.02126.4090.0080.0080.0000.0000.0000.000
63A62GLU-1-0.823-0.89725.566-0.489-0.4890.0000.0000.0000.000
64A63LYS10.8720.91519.1350.6840.6840.0000.0000.0000.000
65A64GLY00.0560.02121.469-0.047-0.0470.0000.0000.0000.000
66A65LYS10.8320.90321.8910.3480.3480.0000.0000.0000.000
67A66TYR00.000-0.02621.824-0.021-0.0210.0000.0000.0000.000
68A67VAL00.0430.01417.169-0.019-0.0190.0000.0000.0000.000
69A68GLY0-0.023-0.01319.070-0.049-0.0490.0000.0000.0000.000
70A69GLU-1-0.820-0.91121.088-0.365-0.3650.0000.0000.0000.000
71A70LEU00.0230.02318.3280.0150.0150.0000.0000.0000.000
72A71ARG10.9250.96312.4771.3071.3070.0000.0000.0000.000
73A72LYS10.7530.87618.0350.3950.3950.0000.0000.0000.000
74A73ALA00.0030.00421.1830.0230.0230.0000.0000.0000.000
75A74LEU0-0.0060.00017.5280.0370.0370.0000.0000.0000.000
76A75LEU0-0.037-0.02112.867-0.004-0.0040.0000.0000.0000.000
77A76SER0-0.018-0.01316.2760.0180.0180.0000.0000.0000.000
78A77GLY00.0270.02119.3510.0260.0260.0000.0000.0000.000
79A78ALA0-0.033-0.02020.3380.0190.0190.0000.0000.0000.000
80A79GLY00.0120.01123.5410.0280.0280.0000.0000.0000.000
81A80PRO0-0.029-0.02225.2570.0280.0280.0000.0000.0000.000
82A81ALA0-0.028-0.01728.4340.0060.0060.0000.0000.0000.000
83A82ASP-1-0.788-0.85927.025-0.294-0.2940.0000.0000.0000.000
84A83VAL0-0.019-0.01227.983-0.006-0.0060.0000.0000.0000.000
85A84TYR0-0.005-0.02525.305-0.013-0.0130.0000.0000.0000.000
86A85THR0-0.032-0.02128.0130.0180.0180.0000.0000.0000.000
87A86PHE00.0200.00922.633-0.015-0.0150.0000.0000.0000.000
88A87ASN0-0.0130.00027.1140.0350.0350.0000.0000.0000.000
89A88PHE00.0350.00625.348-0.014-0.0140.0000.0000.0000.000
90A89SER0-0.011-0.00228.4870.0110.0110.0000.0000.0000.000
91A90LYS10.7780.86127.1700.0610.0610.0000.0000.0000.000
92A91GLU-1-0.887-0.92030.292-0.059-0.0590.0000.0000.0000.000
93A92SER0-0.060-0.04531.6240.0000.0000.0000.0000.0000.000
94A93CYS0-0.064-0.01926.1180.0010.0010.0000.0000.0000.000
95A94TYR00.0530.02926.173-0.013-0.0130.0000.0000.0000.000
96A95PHE0-0.018-0.01422.7630.0100.0100.0000.0000.0000.000
97A96PHE0-0.019-0.02025.788-0.018-0.0180.0000.0000.0000.000
98A97PHE00.0150.01022.2320.0090.0090.0000.0000.0000.000
99A98GLU-1-0.797-0.88726.215-0.207-0.2070.0000.0000.0000.000
100A99LYS10.8490.91727.7530.2750.2750.0000.0000.0000.000
101A100ASN0-0.027-0.00929.7640.0040.0040.0000.0000.0000.000
102A101LEU0-0.027-0.02632.237-0.011-0.0110.0000.0000.0000.000
103A102LYS10.9670.96734.9300.1720.1720.0000.0000.0000.000
104A103ASP-1-0.861-0.91538.498-0.131-0.1310.0000.0000.0000.000
105A104VAL0-0.091-0.05235.298-0.001-0.0010.0000.0000.0000.000
106A105SER0-0.021-0.01933.597-0.001-0.0010.0000.0000.0000.000
107A106PHE00.0360.04029.8130.0030.0030.0000.0000.0000.000
108A107ARG10.8610.91728.5290.2050.2050.0000.0000.0000.000
109A108LEU0-0.025-0.00524.968-0.007-0.0070.0000.0000.0000.000
110A109GLY00.0650.02924.494-0.026-0.0260.0000.0000.0000.000
111A110SER0-0.135-0.05225.1480.0340.0340.0000.0000.0000.000
112A111PHE00.0690.03620.430-0.027-0.0270.0000.0000.0000.000
113A112ASN00.001-0.00223.5280.0310.0310.0000.0000.0000.000
114A113LEU0-0.054-0.01619.933-0.023-0.0230.0000.0000.0000.000
115A114GLU-1-0.905-0.95121.699-0.056-0.0560.0000.0000.0000.000
116A115LYS10.8610.91722.223-0.012-0.0120.0000.0000.0000.000
117A116VAL0-0.0070.00019.1210.0110.0110.0000.0000.0000.000
118A117GLU-1-0.930-0.96422.1430.1480.1480.0000.0000.0000.000
119A118ASN0-0.030-0.02518.645-0.032-0.0320.0000.0000.0000.000
120A119PRO00.0270.01420.7430.0270.0270.0000.0000.0000.000
121A120ALA00.027-0.00720.6270.0060.0060.0000.0000.0000.000
122A121GLU-1-0.868-0.90117.1600.4460.4460.0000.0000.0000.000
123A122VAL00.0350.01615.7720.0530.0530.0000.0000.0000.000
124A123ILE0-0.020-0.00216.1830.0000.0000.0000.0000.0000.000
125A124ARG10.8610.91017.475-0.368-0.3680.0000.0000.0000.000
126A125GLU-1-0.807-0.86710.2710.7180.7180.0000.0000.0000.000
127A126LEU00.0400.02212.8150.0390.0390.0000.0000.0000.000
128A127ILE0-0.009-0.01014.059-0.040-0.0400.0000.0000.0000.000
129A128CYS0-0.068-0.04112.957-0.019-0.0190.0000.0000.0000.000
130A129TYR00.0680.0256.0550.1260.1260.0000.0000.0000.000
131A130CYS0-0.053-0.03011.155-0.130-0.1300.0000.0000.0000.000
132A131LEU0-0.042-0.01814.183-0.053-0.0530.0000.0000.0000.000
133A132ASP-1-0.898-0.93310.0901.0271.0270.0000.0000.0000.000
134A1733ASP-1-0.935-0.96411.081-0.353-0.3530.0000.0000.0000.000
135A1734LEU0-0.060-0.03812.108-0.051-0.0510.0000.0000.0000.000
136A1735SER0-0.071-0.04314.139-0.025-0.0250.0000.0000.0000.000
137A1736GLN0-0.039-0.02710.3650.1490.1490.0000.0000.0000.000
138A1737LEU00.0370.01513.334-0.046-0.0460.0000.0000.0000.000
139A1738GLN0-0.057-0.03215.678-0.006-0.0060.0000.0000.0000.000
140A1739THR00.0200.01015.4670.0110.0110.0000.0000.0000.000
141A1740GLU-1-0.852-0.90612.867-0.432-0.4320.0000.0000.0000.000
142A1741VAL0-0.060-0.02617.487-0.021-0.0210.0000.0000.0000.000
143A1742GLU-1-0.961-0.98320.8640.0800.0800.0000.0000.0000.000
144A1743GLU-1-0.950-0.97716.990-0.051-0.0510.0000.0000.0000.000
145A1744ALA00.0260.01420.999-0.008-0.0080.0000.0000.0000.000
146A1745VAL0-0.047-0.02622.5730.0020.0020.0000.0000.0000.000
147A1746GLN0-0.051-0.03424.4360.0120.0120.0000.0000.0000.000
148A1747GLU-1-0.966-0.99221.425-0.198-0.1980.0000.0000.0000.000
149A1748CYS0-0.086-0.04025.324-0.005-0.0050.0000.0000.0000.000
150A1749ARG11.0111.01028.2440.0370.0370.0000.0000.0000.000
151A1750ASN0-0.025-0.00725.4600.0190.0190.0000.0000.0000.000
152A1751ALA0-0.038-0.01729.159-0.002-0.0020.0000.0000.0000.000
153A1752GLU-1-0.848-0.93030.887-0.069-0.0690.0000.0000.0000.000
154A1753GLU-1-0.841-0.90833.431-0.037-0.0370.0000.0000.0000.000
155A1754LYS10.9110.96528.5410.1070.1070.0000.0000.0000.000
156A1755ALA00.0190.01434.7530.0010.0010.0000.0000.0000.000
157A1756LYS10.8470.90836.7120.0490.0490.0000.0000.0000.000
158A1757LYS10.8630.91637.8190.0540.0540.0000.0000.0000.000
159A1758ALA00.0270.01237.9810.0020.0020.0000.0000.0000.000
160A1759ILE0-0.006-0.00539.9690.0010.0010.0000.0000.0000.000
161A1760THR0-0.021-0.01742.6100.0040.0040.0000.0000.0000.000
162A1761ASP-1-0.843-0.90841.135-0.051-0.0510.0000.0000.0000.000
163A1762ALA0-0.014-0.00543.9830.0010.0010.0000.0000.0000.000
164A1763ALA0-0.014-0.00345.6660.0010.0010.0000.0000.0000.000
165A1764MET00.0130.00445.5780.0030.0030.0000.0000.0000.000
166A1765MET0-0.0140.00147.3940.0010.0010.0000.0000.0000.000
167A1766ALA0-0.006-0.01049.4170.0010.0010.0000.0000.0000.000
168A1767GLU-1-0.886-0.93051.744-0.030-0.0300.0000.0000.0000.000
169A1768GLU-1-0.852-0.92252.246-0.032-0.0320.0000.0000.0000.000
170A1769LEU0-0.033-0.00652.6030.0010.0010.0000.0000.0000.000
171A1770LYS10.7850.88054.9830.0380.0380.0000.0000.0000.000
172A1771LYS10.8390.88755.0840.0330.0330.0000.0000.0000.000
173A1772GLU-1-0.889-0.92757.625-0.034-0.0340.0000.0000.0000.000
174A1773GLN0-0.027-0.01557.7830.0020.0020.0000.0000.0000.000
175A1774ASP-1-0.819-0.89660.976-0.034-0.0340.0000.0000.0000.000
176A1775THR0-0.034-0.02462.2790.0020.0020.0000.0000.0000.000
177A1776SER0-0.008-0.00262.5300.0010.0010.0000.0000.0000.000
178A1777ALA00.0160.00064.5810.0010.0010.0000.0000.0000.000
179A1778HIS0-0.005-0.00466.9330.0000.0000.0000.0000.0000.000
180A1779LEU00.0350.00965.4950.0010.0010.0000.0000.0000.000
181A1780GLU-1-0.806-0.87468.817-0.031-0.0310.0000.0000.0000.000
182A1781ARG10.8720.93268.3000.0290.0290.0000.0000.0000.000
183A1782MET0-0.023-0.01271.8180.0010.0010.0000.0000.0000.000
184A1783LYS10.8190.89471.4610.0310.0310.0000.0000.0000.000
185A1784LYS10.8200.89974.3250.0280.0280.0000.0000.0000.000
186A1785ASN00.0130.00776.6810.0010.0010.0000.0000.0000.000
187A1786MET0-0.015-0.00473.9230.0010.0010.0000.0000.0000.000
188A1787GLU-1-0.775-0.86975.867-0.027-0.0270.0000.0000.0000.000
189A1788GLN0-0.049-0.00679.9960.0000.0000.0000.0000.0000.000
190A1789THR0-0.030-0.02881.9560.0010.0010.0000.0000.0000.000
191A1790ILE0-0.017-0.01880.1310.0010.0010.0000.0000.0000.000
192A1791LYS10.7990.89784.0990.0220.0220.0000.0000.0000.000
193A1792ASP-1-0.765-0.89285.864-0.020-0.0200.0000.0000.0000.000
194A1793LEU0-0.071-0.01285.9230.0010.0010.0000.0000.0000.000
195A1794GLN0-0.093-0.04187.0430.0000.0000.0000.0000.0000.000