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: LZ1L9

Calculation Name: 3V6M-F-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: F

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2494619.619251
FMO2-HF: Nuclear repulsion 2411124.80512
FMO2-HF: Total energy -83494.814131
FMO2-MP2: Total energy -83733.272264


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(F:32:ASP)


Summations of interaction energy for fragment #1(F:32:ASP)
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.
-136.237-129.23111.482-9.037-9.4510.098
Interaction energy analysis for fragmet #1(F:32:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.805 / q_NPA : -0.916
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].
3F34ALA0-0.063-0.0831.860-38.734-35.5439.687-7.156-5.7220.081
4F35GLU-1-0.900-0.9422.41232.89736.2471.718-1.722-3.3460.013
5F36LYS10.9380.9653.601-51.179-50.7140.077-0.159-0.3830.004
6F37TYR0-0.011-0.0367.0060.0580.0580.0000.0000.0000.000
7F38LYS10.8230.8979.662-23.511-23.5110.0000.0000.0000.000
8F39MET0-0.0110.00311.497-1.785-1.7850.0000.0000.0000.000
9F40ASP-1-0.827-0.88814.18720.21820.2180.0000.0000.0000.000
10F41HIS0-0.037-0.01015.360-0.983-0.9830.0000.0000.0000.000
11F42ARG10.8840.93518.719-11.985-11.9850.0000.0000.0000.000
12F43ARG10.8780.92522.264-12.288-12.2880.0000.0000.0000.000
13F44ARG10.8680.94416.915-15.832-15.8320.0000.0000.0000.000
14F45GLY00.0470.00320.9290.4970.4970.0000.0000.0000.000
15F46ILE0-0.037-0.01323.608-0.269-0.2690.0000.0000.0000.000
16F47ALA0-0.002-0.00325.5410.4440.4440.0000.0000.0000.000
17F48LEU00.000-0.00227.379-0.434-0.4340.0000.0000.0000.000
18F49ILE00.0030.00830.1320.2090.2090.0000.0000.0000.000
19F50PHE0-0.012-0.01232.466-0.329-0.3290.0000.0000.0000.000
20F51ASN00.0190.00035.5350.1900.1900.0000.0000.0000.000
21F52HIS00.0130.00937.836-0.095-0.0950.0000.0000.0000.000
22F53GLU-1-0.916-0.96140.8667.2787.2780.0000.0000.0000.000
23F54ARG10.9510.99043.650-6.487-6.4870.0000.0000.0000.000
24F55PHE0-0.031-0.02242.0550.1270.1270.0000.0000.0000.000
25F56PHE00.022-0.00247.608-0.172-0.1720.0000.0000.0000.000
26F57TRP00.032-0.00250.1540.0090.0090.0000.0000.0000.000
27F58HIS0-0.054-0.01953.0060.0190.0190.0000.0000.0000.000
28F59LEU0-0.0140.01045.976-0.001-0.0010.0000.0000.0000.000
29F60THR0-0.058-0.01949.3810.0010.0010.0000.0000.0000.000
30F61LEU0-0.0130.00844.3320.0550.0550.0000.0000.0000.000
31F62PRO0-0.023-0.01046.341-0.089-0.0890.0000.0000.0000.000
32F63GLU-1-0.898-0.95746.3716.6806.6800.0000.0000.0000.000
33F64ARG10.8290.92037.602-8.247-8.2470.0000.0000.0000.000
34F65ARG10.9690.97143.211-6.639-6.6390.0000.0000.0000.000
35F66GLY00.0280.02041.9530.0960.0960.0000.0000.0000.000
36F67THR00.0350.00838.5680.3060.3060.0000.0000.0000.000
37F68CYS0-0.0060.00138.1510.2600.2600.0000.0000.0000.000
38F69ALA00.0350.02838.6780.1280.1280.0000.0000.0000.000
39F70ASP-1-0.766-0.87834.8979.2599.2590.0000.0000.0000.000
40F71ARG10.8380.91134.047-7.842-7.8420.0000.0000.0000.000
41F72ASP-1-0.846-0.91134.1888.6218.6210.0000.0000.0000.000
42F73ASN0-0.025-0.00932.7080.3480.3480.0000.0000.0000.000
43F74LEU00.052-0.00528.7350.3450.3450.0000.0000.0000.000
44F75THR00.006-0.00229.4790.3780.3780.0000.0000.0000.000
45F76ARG10.9010.94930.675-9.308-9.3080.0000.0000.0000.000
46F77ARG10.8950.95626.807-10.573-10.5730.0000.0000.0000.000
47F78PHE00.0580.01523.2110.4620.4620.0000.0000.0000.000
48F79SER00.0090.01425.6940.3160.3160.0000.0000.0000.000
49F80ASP-1-0.908-0.93526.63511.22011.2200.0000.0000.0000.000
50F81LEU0-0.056-0.01620.8630.5230.5230.0000.0000.0000.000
51F82GLY0-0.049-0.03521.9390.8070.8070.0000.0000.0000.000
52F83PHE0-0.052-0.03820.8740.1080.1080.0000.0000.0000.000
53F84GLU-1-0.908-0.95025.5619.9469.9460.0000.0000.0000.000
54F85VAL0-0.015-0.01328.7050.1420.1420.0000.0000.0000.000
55F86LYS10.9020.95930.511-9.980-9.9800.0000.0000.0000.000
56F87CYS0-0.031-0.00933.2910.1950.1950.0000.0000.0000.000
57F88PHE00.0190.00034.499-0.210-0.2100.0000.0000.0000.000
58F89ASN00.0380.02138.3230.2570.2570.0000.0000.0000.000
59F90ASP-1-0.780-0.88741.0417.2447.2440.0000.0000.0000.000
60F91LEU0-0.0320.01238.613-0.115-0.1150.0000.0000.0000.000
61F92LYS11.0010.98942.279-6.498-6.4980.0000.0000.0000.000
62F93ALA00.001-0.02041.2470.1740.1740.0000.0000.0000.000
63F94GLU-1-0.919-0.95640.7107.0297.0290.0000.0000.0000.000
64F95GLU-1-0.856-0.93141.2447.3067.3060.0000.0000.0000.000
65F96LEU0-0.014-0.00335.5270.2140.2140.0000.0000.0000.000
66F97LEU00.016-0.00536.0610.3080.3080.0000.0000.0000.000
67F98LEU00.0320.01336.5320.2410.2410.0000.0000.0000.000
68F99LYS10.8610.93535.965-8.332-8.3320.0000.0000.0000.000
69F100ILE0-0.054-0.02430.5540.3070.3070.0000.0000.0000.000
70F101HIS00.019-0.00531.9780.4120.4120.0000.0000.0000.000
71F102GLU-1-0.824-0.89533.0428.9428.9420.0000.0000.0000.000
72F103VAL0-0.006-0.01128.8290.2780.2780.0000.0000.0000.000
73F104SER0-0.104-0.04128.3040.4330.4330.0000.0000.0000.000
74F105THR0-0.014-0.01328.5370.2870.2870.0000.0000.0000.000
75F106VAL0-0.0300.00828.706-0.055-0.0550.0000.0000.0000.000
76F107SER00.0150.00826.5080.4580.4580.0000.0000.0000.000
77F108HIS10.8680.90422.789-12.179-12.1790.0000.0000.0000.000
78F109ALA00.0570.02921.6900.6810.6810.0000.0000.0000.000
79F110ASP-1-0.830-0.87820.76012.65912.6590.0000.0000.0000.000
80F111ALA0-0.010-0.01621.369-0.191-0.1910.0000.0000.0000.000
81F112ASP-1-0.699-0.83416.84317.79617.7960.0000.0000.0000.000
82F113CYS0-0.053-0.00617.1650.7630.7630.0000.0000.0000.000
83F114PHE0-0.028-0.02019.415-0.769-0.7690.0000.0000.0000.000
84F115VAL00.0320.02522.2160.4310.4310.0000.0000.0000.000
85F116CYS0-0.040-0.00824.505-0.641-0.6410.0000.0000.0000.000
86F117VAL0-0.008-0.00727.7630.1950.1950.0000.0000.0000.000
87F118PHE0-0.013-0.01229.984-0.328-0.3280.0000.0000.0000.000
88F119LEU0-0.005-0.00132.9440.1340.1340.0000.0000.0000.000
89F120SER00.017-0.01535.700-0.316-0.3160.0000.0000.0000.000
90F121HIS0-0.006-0.01038.3340.2430.2430.0000.0000.0000.000
91F122GLY00.026-0.01237.2980.1010.1010.0000.0000.0000.000
92F123GLU-1-0.851-0.88638.3257.4457.4450.0000.0000.0000.000
93F124GLY00.0520.02037.270-0.021-0.0210.0000.0000.0000.000
94F125ASN0-0.0040.00133.2140.0420.0420.0000.0000.0000.000
95F126HIS0-0.006-0.01034.4860.0820.0820.0000.0000.0000.000
96F127ILE0-0.027-0.00934.3950.0880.0880.0000.0000.0000.000
97F128TYR0-0.004-0.00136.938-0.190-0.1900.0000.0000.0000.000
98F129ALA0-0.0060.02439.9280.1520.1520.0000.0000.0000.000
99F130TYR00.011-0.01141.295-0.175-0.1750.0000.0000.0000.000
100F131ASP-1-0.791-0.91344.7796.9356.9350.0000.0000.0000.000
101F132ALA00.0170.00844.007-0.120-0.1200.0000.0000.0000.000
102F133LYS10.8130.91440.463-7.339-7.3390.0000.0000.0000.000
103F134ILE00.0250.01035.719-0.079-0.0790.0000.0000.0000.000
104F135GLU-1-0.912-0.95034.4418.7238.7230.0000.0000.0000.000
105F136ILE00.0210.00329.5400.1280.1280.0000.0000.0000.000
106F137GLN00.0180.00827.0650.4190.4190.0000.0000.0000.000
107F138THR0-0.032-0.02129.9680.1800.1800.0000.0000.0000.000
108F139LEU00.0300.02031.3080.0470.0470.0000.0000.0000.000
109F140THR00.013-0.00525.8650.1440.1440.0000.0000.0000.000
110F141GLY00.001-0.01026.2360.4490.4490.0000.0000.0000.000
111F142LEU0-0.034-0.01227.4370.1130.1130.0000.0000.0000.000
112F143PHE0-0.005-0.02324.0260.0890.0890.0000.0000.0000.000
113F144LYS10.8650.94322.513-10.820-10.8200.0000.0000.0000.000
114F145GLY00.0540.00720.973-0.173-0.1730.0000.0000.0000.000
115F146ASP-1-0.895-0.93521.79611.44811.4480.0000.0000.0000.000
116F147LYS10.9170.97924.913-10.579-10.5790.0000.0000.0000.000
117F148CYS0-0.046-0.01924.414-0.163-0.1630.0000.0000.0000.000
118F149HIS00.1050.04622.6610.5380.5380.0000.0000.0000.000
119F150SER0-0.023-0.00621.3900.5720.5720.0000.0000.0000.000
120F151LEU00.022-0.00920.0520.4010.4010.0000.0000.0000.000
121F152VAL0-0.0190.00216.5870.6480.6480.0000.0000.0000.000
122F153GLY00.0040.01514.0210.2950.2950.0000.0000.0000.000
123F154LYS10.7620.89513.555-14.513-14.5130.0000.0000.0000.000
124F155PRO00.0100.00714.468-0.755-0.7550.0000.0000.0000.000
125F156LYS10.8310.92816.854-16.587-16.5870.0000.0000.0000.000
126F157ILE00.0210.01518.4830.1010.1010.0000.0000.0000.000
127F158PHE00.006-0.01022.043-0.606-0.6060.0000.0000.0000.000
128F159ILE00.0130.01124.7440.2080.2080.0000.0000.0000.000
129F160ILE0-0.004-0.01027.407-0.413-0.4130.0000.0000.0000.000
130F161GLN0-0.023-0.00330.6820.1080.1080.0000.0000.0000.000
131F162ALA00.012-0.01433.366-0.226-0.2260.0000.0000.0000.000
132F163CYS00.0060.03036.2360.0190.0190.0000.0000.0000.000
133F198TYR0-0.002-0.00825.6360.0390.0390.0000.0000.0000.000
134F199THR00.0180.01128.427-0.308-0.3080.0000.0000.0000.000
135F200LEU00.0210.01824.1860.3300.3300.0000.0000.0000.000
136F201PRO00.010-0.01120.673-0.305-0.3050.0000.0000.0000.000
137F202ALA00.0030.00722.785-0.005-0.0050.0000.0000.0000.000
138F203GLY00.0140.00120.236-0.301-0.3010.0000.0000.0000.000
139F204ALA00.0190.00114.7770.2590.2590.0000.0000.0000.000
140F205ASP-1-0.817-0.88813.12720.25020.2500.0000.0000.0000.000
141F206PHE0-0.0100.00415.748-0.497-0.4970.0000.0000.0000.000
142F207LEU0-0.032-0.01818.2900.5780.5780.0000.0000.0000.000
143F208MET0-0.034-0.00119.990-0.451-0.4510.0000.0000.0000.000
144F209CYS0-0.0140.00423.3390.4470.4470.0000.0000.0000.000
145F210TYR00.001-0.03325.420-0.513-0.5130.0000.0000.0000.000
146F211SER0-0.012-0.02328.7750.1540.1540.0000.0000.0000.000
147F212VAL00.0040.01231.038-0.214-0.2140.0000.0000.0000.000
148F222THR00.0350.00542.008-0.025-0.0250.0000.0000.0000.000
149F223VAL00.022-0.00442.0820.1080.1080.0000.0000.0000.000
150F224ASN0-0.008-0.00140.663-0.058-0.0580.0000.0000.0000.000
151F225GLY00.0360.04637.6950.2340.2340.0000.0000.0000.000
152F226SER0-0.061-0.04435.489-0.037-0.0370.0000.0000.0000.000
153F227TRP00.034-0.00235.0220.2200.2200.0000.0000.0000.000
154F228TYR00.0720.03726.4540.1240.1240.0000.0000.0000.000
155F229ILE00.0080.01130.5400.3990.3990.0000.0000.0000.000
156F230GLN0-0.017-0.03131.0670.3060.3060.0000.0000.0000.000
157F231ASP-1-0.781-0.88929.88810.25910.2590.0000.0000.0000.000
158F232LEU0-0.0050.00024.5690.4530.4530.0000.0000.0000.000
159F233CYS0-0.036-0.01426.5960.4150.4150.0000.0000.0000.000
160F234GLU-1-0.966-0.97928.18610.51010.5100.0000.0000.0000.000
161F235MET0-0.046-0.03024.1770.3380.3380.0000.0000.0000.000
162F236LEU00.0110.00722.6300.5430.5430.0000.0000.0000.000
163F237GLY0-0.041-0.02024.0760.3110.3110.0000.0000.0000.000
164F238LYS10.9190.96825.283-11.342-11.3420.0000.0000.0000.000
165F239TYR00.033-0.00320.574-0.107-0.1070.0000.0000.0000.000
166F240GLY00.0430.03719.6580.9800.9800.0000.0000.0000.000
167F241SER0-0.014-0.00518.8220.8470.8470.0000.0000.0000.000
168F242SER0-0.025-0.02916.8970.5720.5720.0000.0000.0000.000
169F243LEU0-0.035-0.03415.2451.3461.3460.0000.0000.0000.000
170F244GLU-1-0.765-0.83111.34823.85823.8580.0000.0000.0000.000
171F245PHE00.029-0.00914.212-1.474-1.4740.0000.0000.0000.000
172F246THR0-0.023-0.04115.005-1.305-1.3050.0000.0000.0000.000
173F247GLU-1-0.836-0.90615.00120.63720.6370.0000.0000.0000.000
174F248LEU0-0.041-0.01617.741-1.179-1.1790.0000.0000.0000.000
175F249LEU0-0.003-0.01620.147-1.023-1.0230.0000.0000.0000.000
176F250THR0-0.020-0.02219.606-0.824-0.8240.0000.0000.0000.000
177F251LEU0-0.050-0.02521.661-0.779-0.7790.0000.0000.0000.000
178F252VAL0-0.020-0.00324.064-0.650-0.6500.0000.0000.0000.000
179F253ASN00.0220.01224.455-0.752-0.7520.0000.0000.0000.000
180F254ARG10.9740.99723.950-13.100-13.1000.0000.0000.0000.000
181F255LYS10.8750.94528.082-11.043-11.0430.0000.0000.0000.000
182F256VAL00.000-0.01730.119-0.405-0.4050.0000.0000.0000.000
183F257GLU-1-1.000-0.99130.9309.9879.9870.0000.0000.0000.000
184F258GLN0-0.0120.01032.402-0.129-0.1290.0000.0000.0000.000
185F259ARG10.7860.90534.247-9.595-9.5950.0000.0000.0000.000
186F275VAL0-0.005-0.01629.504-0.093-0.0930.0000.0000.0000.000
187F276PRO0-0.0270.01228.4760.0230.0230.0000.0000.0000.000
188F277CYS00.010-0.01026.2300.4060.4060.0000.0000.0000.000
189F278PHE0-0.0060.00218.567-0.063-0.0630.0000.0000.0000.000
190F279ALA00.0170.00921.3660.1260.1260.0000.0000.0000.000
191F280SER00.020-0.00115.305-0.042-0.0420.0000.0000.0000.000
192F281MET0-0.0100.01716.010-0.083-0.0830.0000.0000.0000.000
193F282LEU0-0.034-0.00913.0950.1340.1340.0000.0000.0000.000
194F283THR0-0.031-0.0269.1750.8730.8730.0000.0000.0000.000
195F284LYS10.9000.9706.818-28.499-28.4990.0000.0000.0000.000
196F285LYS10.8780.9825.830-50.456-50.4560.0000.0000.0000.000
197F286LEU0-0.018-0.0189.5920.5420.5420.0000.0000.0000.000
198F287HIS0-0.016-0.00310.6241.5141.5140.0000.0000.0000.000
199F288PHE00.008-0.00713.687-0.240-0.2400.0000.0000.0000.000
200F289PHE0-0.0120.00711.009-0.542-0.5420.0000.0000.0000.000
201F290PRO00.0240.01216.506-0.236-0.2360.0000.0000.0000.000
202F291LYS10.7470.84517.356-16.145-16.1450.0000.0000.0000.000
203F292SER00.0030.01519.825-0.793-0.7930.0000.0000.0000.000