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: 729JK

Calculation Name: 3V6M-D-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: D

ChEMBL ID: CHEMBL3308

UniProt ID: P55212

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2515131.208473
FMO2-HF: Nuclear repulsion 2431160.919226
FMO2-HF: Total energy -83970.289247
FMO2-MP2: Total energy -84210.075398


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(D:31:PHE)


Summations of interaction energy for fragment #1(D:31:PHE)
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.
1.2113.187-0.021-0.773-1.1830
Interaction energy analysis for fragmet #1(D:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.035
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].
3D33PRO00.0150.0183.824-0.1761.800-0.021-0.773-1.1830.000
4D34ALA0-0.050-0.0265.4810.4340.4340.0000.0000.0000.000
5D35GLU-1-0.953-0.9755.208-0.027-0.0270.0000.0000.0000.000
6D36LYS10.9340.9617.8720.4630.4630.0000.0000.0000.000
7D37TYR0-0.029-0.05810.8160.0040.0040.0000.0000.0000.000
8D38LYS10.8430.90412.6350.1790.1790.0000.0000.0000.000
9D39MET0-0.047-0.02014.7040.0180.0180.0000.0000.0000.000
10D40ASP-1-0.841-0.89917.853-0.171-0.1710.0000.0000.0000.000
11D41HIS0-0.046-0.01416.9970.0120.0120.0000.0000.0000.000
12D42ARG10.9790.98521.9040.0770.0770.0000.0000.0000.000
13D43ARG10.9480.97524.9370.0850.0850.0000.0000.0000.000
14D44ARG10.8790.94321.6600.1290.1290.0000.0000.0000.000
15D45GLY00.003-0.01322.857-0.006-0.0060.0000.0000.0000.000
16D46ILE0-0.021-0.00825.1630.0020.0020.0000.0000.0000.000
17D47ALA00.0090.00725.931-0.006-0.0060.0000.0000.0000.000
18D48LEU0-0.020-0.01927.8790.0050.0050.0000.0000.0000.000
19D49ILE00.0190.00929.416-0.003-0.0030.0000.0000.0000.000
20D50PHE00.0110.00630.5390.0040.0040.0000.0000.0000.000
21D51ASN0-0.005-0.02634.121-0.002-0.0020.0000.0000.0000.000
22D52HIS00.0260.02436.0760.0030.0030.0000.0000.0000.000
23D53GLU-1-0.856-0.92639.056-0.038-0.0380.0000.0000.0000.000
24D54ARG10.9200.96242.1690.0340.0340.0000.0000.0000.000
25D55PHE0-0.023-0.01339.335-0.001-0.0010.0000.0000.0000.000
26D56PHE00.0130.01044.8750.0010.0010.0000.0000.0000.000
27D57TRP00.0550.01147.1210.0000.0000.0000.0000.0000.000
28D58HIS0-0.006-0.00149.6620.0000.0000.0000.0000.0000.000
29D59LEU0-0.036-0.00542.5480.0000.0000.0000.0000.0000.000
30D60THR0-0.057-0.01745.7800.0000.0000.0000.0000.0000.000
31D61LEU0-0.0190.00041.109-0.001-0.0010.0000.0000.0000.000
32D62PRO0-0.018-0.00343.3990.0000.0000.0000.0000.0000.000
33D63GLU-1-0.812-0.90543.841-0.032-0.0320.0000.0000.0000.000
34D64ARG10.8400.92836.1130.0470.0470.0000.0000.0000.000
35D65ARG10.8030.86142.1150.0340.0340.0000.0000.0000.000
36D66GLY00.0260.01741.828-0.001-0.0010.0000.0000.0000.000
37D67THR00.0530.02837.655-0.003-0.0030.0000.0000.0000.000
38D68CYS0-0.025-0.01438.014-0.003-0.0030.0000.0000.0000.000
39D69ALA00.0480.03439.496-0.001-0.0010.0000.0000.0000.000
40D70ASP-1-0.780-0.86734.811-0.060-0.0600.0000.0000.0000.000
41D71ARG10.8340.90434.8130.0440.0440.0000.0000.0000.000
42D72ASP-1-0.837-0.90335.164-0.053-0.0530.0000.0000.0000.000
43D73ASN0-0.054-0.03534.861-0.003-0.0030.0000.0000.0000.000
44D74LEU00.0480.00029.176-0.003-0.0030.0000.0000.0000.000
45D75THR0-0.010-0.02231.314-0.004-0.0040.0000.0000.0000.000
46D76ARG10.9280.97633.1230.0570.0570.0000.0000.0000.000
47D77ARG10.9170.97129.5280.0730.0730.0000.0000.0000.000
48D78PHE00.0460.01424.542-0.005-0.0050.0000.0000.0000.000
49D79SER00.0080.00528.760-0.003-0.0030.0000.0000.0000.000
50D80ASP-1-0.924-0.94730.743-0.078-0.0780.0000.0000.0000.000
51D81LEU0-0.075-0.02624.789-0.005-0.0050.0000.0000.0000.000
52D82GLY0-0.018-0.01625.956-0.009-0.0090.0000.0000.0000.000
53D83PHE0-0.052-0.03722.563-0.001-0.0010.0000.0000.0000.000
54D84GLU-1-0.910-0.95128.266-0.061-0.0610.0000.0000.0000.000
55D85VAL0-0.015-0.00830.263-0.002-0.0020.0000.0000.0000.000
56D86LYS10.9160.96132.0030.0620.0620.0000.0000.0000.000
57D87CYS0-0.025-0.00333.370-0.002-0.0020.0000.0000.0000.000
58D88PHE00.0250.00134.0320.0020.0020.0000.0000.0000.000
59D89ASN00.0100.02137.457-0.003-0.0030.0000.0000.0000.000
60D90ASP-1-0.758-0.89039.921-0.036-0.0360.0000.0000.0000.000
61D91LEU0-0.058-0.00536.8760.0010.0010.0000.0000.0000.000
62D92LYS10.9920.99140.0940.0270.0270.0000.0000.0000.000
63D93ALA00.006-0.02138.202-0.002-0.0020.0000.0000.0000.000
64D94GLU-1-0.904-0.94937.864-0.028-0.0280.0000.0000.0000.000
65D95GLU-1-0.872-0.93938.658-0.034-0.0340.0000.0000.0000.000
66D96LEU0-0.029-0.01432.839-0.002-0.0020.0000.0000.0000.000
67D97LEU00.027-0.00132.993-0.003-0.0030.0000.0000.0000.000
68D98LEU00.0210.01234.003-0.002-0.0020.0000.0000.0000.000
69D99LYS10.8290.91934.4440.0410.0410.0000.0000.0000.000
70D100ILE0-0.020-0.01328.104-0.003-0.0030.0000.0000.0000.000
71D101HIS00.0370.02029.836-0.004-0.0040.0000.0000.0000.000
72D102GLU-1-0.835-0.88830.569-0.048-0.0480.0000.0000.0000.000
73D103VAL0-0.002-0.01027.623-0.003-0.0030.0000.0000.0000.000
74D104SER0-0.092-0.03826.165-0.005-0.0050.0000.0000.0000.000
75D105THR0-0.009-0.01826.232-0.001-0.0010.0000.0000.0000.000
76D106VAL0-0.0330.00927.7910.0020.0020.0000.0000.0000.000
77D107SER00.004-0.00326.112-0.006-0.0060.0000.0000.0000.000
78D108HIS10.8520.90622.3920.0840.0840.0000.0000.0000.000
79D109ALA00.0470.02521.531-0.009-0.0090.0000.0000.0000.000
80D110ASP-1-0.909-0.94621.523-0.094-0.0940.0000.0000.0000.000
81D111ALA0-0.085-0.05922.4090.0020.0020.0000.0000.0000.000
82D112ASP-1-0.692-0.83719.220-0.151-0.1510.0000.0000.0000.000
83D113CYS0-0.054-0.00918.011-0.012-0.0120.0000.0000.0000.000
84D114PHE0-0.025-0.01019.8900.0110.0110.0000.0000.0000.000
85D115VAL00.0330.03421.553-0.007-0.0070.0000.0000.0000.000
86D116CYS0-0.0290.00124.0600.0090.0090.0000.0000.0000.000
87D117VAL0-0.008-0.00926.019-0.003-0.0030.0000.0000.0000.000
88D118PHE0-0.002-0.00127.3850.0050.0050.0000.0000.0000.000
89D119LEU0-0.011-0.00531.035-0.002-0.0020.0000.0000.0000.000
90D120SER0-0.003-0.01733.8830.0030.0030.0000.0000.0000.000
91D121HIS00.0110.00235.517-0.003-0.0030.0000.0000.0000.000
92D122GLY00.017-0.01533.759-0.001-0.0010.0000.0000.0000.000
93D123GLU-1-0.843-0.88234.782-0.030-0.0300.0000.0000.0000.000
94D124GLY00.0550.02132.9590.0010.0010.0000.0000.0000.000
95D125ASN0-0.016-0.00428.803-0.002-0.0020.0000.0000.0000.000
96D126HIS0-0.005-0.01430.2490.0000.0000.0000.0000.0000.000
97D127ILE0-0.029-0.00630.985-0.002-0.0020.0000.0000.0000.000
98D128TYR0-0.004-0.00433.5030.0030.0030.0000.0000.0000.000
99D129ALA00.0000.00636.951-0.002-0.0020.0000.0000.0000.000
100D130TYR00.0170.00038.3270.0010.0010.0000.0000.0000.000
101D131ASP-1-0.793-0.91941.899-0.030-0.0300.0000.0000.0000.000
102D132ALA00.0240.01540.6370.0010.0010.0000.0000.0000.000
103D133LYS10.8110.91636.5220.0280.0280.0000.0000.0000.000
104D134ILE00.0170.00432.1770.0010.0010.0000.0000.0000.000
105D135GLU-1-0.898-0.94130.244-0.037-0.0370.0000.0000.0000.000
106D136ILE00.021-0.00325.743-0.002-0.0020.0000.0000.0000.000
107D137GLN00.0170.00622.561-0.006-0.0060.0000.0000.0000.000
108D138THR0-0.031-0.01426.081-0.001-0.0010.0000.0000.0000.000
109D139LEU00.0150.01427.995-0.001-0.0010.0000.0000.0000.000
110D140THR00.020-0.00422.332-0.002-0.0020.0000.0000.0000.000
111D141GLY0-0.0040.00122.921-0.005-0.0050.0000.0000.0000.000
112D142LEU00.0190.01023.8460.0010.0010.0000.0000.0000.000
113D143PHE00.020-0.00821.525-0.001-0.0010.0000.0000.0000.000
114D144LYS10.8280.93618.6880.0570.0570.0000.0000.0000.000
115D145GLY00.061-0.00117.3130.0030.0030.0000.0000.0000.000
116D146DAS-1-0.888-0.95218.271-0.053-0.0530.0000.0000.0000.000
117D147LYS10.8380.92520.9030.0580.0580.0000.0000.0000.000
118D148CYS0-0.0340.01921.657-0.001-0.0010.0000.0000.0000.000
119D149HIS00.0770.03618.936-0.011-0.0110.0000.0000.0000.000
120D150SER00.0100.00219.075-0.009-0.0090.0000.0000.0000.000
121D151LEU00.024-0.01218.829-0.006-0.0060.0000.0000.0000.000
122D152VAL0-0.031-0.00313.802-0.013-0.0130.0000.0000.0000.000
123D153GLY00.0110.01511.774-0.002-0.0020.0000.0000.0000.000
124D154LYS10.7660.90112.5680.1120.1120.0000.0000.0000.000
125D155PRO00.0060.00914.4010.0080.0080.0000.0000.0000.000
126D156LYS10.8330.93015.4050.1560.1560.0000.0000.0000.000
127D157ILE00.0200.00618.428-0.004-0.0040.0000.0000.0000.000
128D158PHE00.008-0.00920.3690.0100.0100.0000.0000.0000.000
129D159ILE0-0.0070.00522.935-0.004-0.0040.0000.0000.0000.000
130D160ILE00.015-0.00725.4540.0060.0060.0000.0000.0000.000
131D161GLN0-0.0290.00127.974-0.001-0.0010.0000.0000.0000.000
132D162ALA00.014-0.01431.0420.0030.0030.0000.0000.0000.000
133D163CYS00.0080.03133.2600.0010.0010.0000.0000.0000.000
134D198TYR00.0250.00725.3090.0010.0010.0000.0000.0000.000
135D199THR0-0.0010.00223.8050.0070.0070.0000.0000.0000.000
136D200LEU00.0140.01319.282-0.008-0.0080.0000.0000.0000.000
137D201PRO00.011-0.01016.4470.0060.0060.0000.0000.0000.000
138D202ALA00.0320.02118.2920.0040.0040.0000.0000.0000.000
139D203GLY0-0.024-0.02415.7050.0130.0130.0000.0000.0000.000
140D204ALA00.0390.01510.995-0.010-0.0100.0000.0000.0000.000
141D205ASP-1-0.813-0.87010.781-0.237-0.2370.0000.0000.0000.000
142D206PHE0-0.034-0.00512.9960.0170.0170.0000.0000.0000.000
143D207LEU0-0.006-0.00615.151-0.015-0.0150.0000.0000.0000.000
144D208MET0-0.0330.00517.2940.0100.0100.0000.0000.0000.000
145D209CYS0-0.019-0.00820.541-0.008-0.0080.0000.0000.0000.000
146D210TYR00.006-0.02222.1090.0090.0090.0000.0000.0000.000
147D211SER0-0.016-0.02825.851-0.002-0.0020.0000.0000.0000.000
148D212VAL00.0020.01027.8150.0030.0030.0000.0000.0000.000
149D222THR00.0320.00541.6860.0000.0000.0000.0000.0000.000
150D223VAL00.0430.01442.023-0.001-0.0010.0000.0000.0000.000
151D224ASN0-0.010-0.00141.8600.0000.0000.0000.0000.0000.000
152D225GLY00.0140.02938.193-0.003-0.0030.0000.0000.0000.000
153D226SER0-0.051-0.05834.8960.0000.0000.0000.0000.0000.000
154D227TRP00.0460.00534.572-0.003-0.0030.0000.0000.0000.000
155D228TYR00.0710.03525.045-0.001-0.0010.0000.0000.0000.000
156D229ILE00.0080.01130.262-0.005-0.0050.0000.0000.0000.000
157D230GLN0-0.038-0.04331.943-0.004-0.0040.0000.0000.0000.000
158D231ASP-1-0.785-0.89130.648-0.072-0.0720.0000.0000.0000.000
159D232LEU0-0.004-0.00625.162-0.005-0.0050.0000.0000.0000.000
160D233CYS0-0.043-0.01728.276-0.005-0.0050.0000.0000.0000.000
161D234GLU-1-0.966-0.97830.689-0.072-0.0720.0000.0000.0000.000
162D235MET0-0.048-0.03226.465-0.003-0.0030.0000.0000.0000.000
163D236LEU0-0.010-0.00624.833-0.006-0.0060.0000.0000.0000.000
164D237GLY0-0.023-0.01227.405-0.003-0.0030.0000.0000.0000.000
165D238LYS10.9160.96929.3830.0800.0800.0000.0000.0000.000
166D239TYR00.035-0.00324.4370.0020.0020.0000.0000.0000.000
167D240GLY00.0300.03224.033-0.012-0.0120.0000.0000.0000.000
168D241SER0-0.004-0.00123.196-0.010-0.0100.0000.0000.0000.000
169D242SER0-0.017-0.02622.957-0.004-0.0040.0000.0000.0000.000
170D243LEU0-0.022-0.02120.229-0.013-0.0130.0000.0000.0000.000
171D244GLU-1-0.817-0.85513.892-0.281-0.2810.0000.0000.0000.000
172D245PHE00.050-0.00217.2550.0150.0150.0000.0000.0000.000
173D246THR0-0.023-0.04514.5050.0130.0130.0000.0000.0000.000
174D247GLU-1-0.841-0.91117.126-0.210-0.2100.0000.0000.0000.000
175D248LEU0-0.040-0.01718.6770.0190.0190.0000.0000.0000.000
176D249LEU00.009-0.01019.0920.0140.0140.0000.0000.0000.000
177D250THR0-0.018-0.01119.0990.0120.0120.0000.0000.0000.000
178D251LEU0-0.041-0.02521.8060.0130.0130.0000.0000.0000.000
179D252VAL0-0.0210.00624.7290.0100.0100.0000.0000.0000.000
180D253ASN00.0230.01022.6250.0110.0110.0000.0000.0000.000
181D254ARG10.9740.99425.1380.1060.1060.0000.0000.0000.000
182D255LYS10.8820.94127.8750.0800.0800.0000.0000.0000.000
183D256VAL00.002-0.01329.9290.0050.0050.0000.0000.0000.000
184D257GLU-1-0.997-0.98929.729-0.064-0.0640.0000.0000.0000.000
185D258GLN0-0.041-0.01631.7140.0060.0060.0000.0000.0000.000
186D259ARG10.8180.93734.0800.0630.0630.0000.0000.0000.000
187D275VAL0-0.005-0.01727.1860.0010.0010.0000.0000.0000.000
188D276PRO0-0.0300.00926.5520.0000.0000.0000.0000.0000.000
189D277CYS00.019-0.00222.954-0.006-0.0060.0000.0000.0000.000
190D278PHE0-0.020-0.00616.0860.0010.0010.0000.0000.0000.000
191D279ALA00.0360.01917.656-0.003-0.0030.0000.0000.0000.000
192D280SER00.008-0.00712.4180.0070.0070.0000.0000.0000.000
193D281MET0-0.0060.01311.828-0.001-0.0010.0000.0000.0000.000
194D282LEU0-0.038-0.01210.898-0.005-0.0050.0000.0000.0000.000
195D283THR0-0.030-0.0246.114-0.034-0.0340.0000.0000.0000.000
196D284LYS10.9210.9795.9170.2900.2900.0000.0000.0000.000
197D285LYS10.9300.9818.3640.4100.4100.0000.0000.0000.000
198D286LEU0-0.016-0.01811.4260.0130.0130.0000.0000.0000.000
199D287HIS0-0.007-0.00114.717-0.024-0.0240.0000.0000.0000.000
200D288PHE0-0.002-0.01217.8990.0020.0020.0000.0000.0000.000
201D289PHE0-0.0110.01017.3430.0080.0080.0000.0000.0000.000
202D290PRO00.0300.00622.3360.0010.0010.0000.0000.0000.000
203D291LYS10.8070.90522.3410.1260.1260.0000.0000.0000.000
204D292SER00.0130.01925.0180.0060.0060.0000.0000.0000.000