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: MV5MZ

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2506553.386137
FMO2-HF: Nuclear repulsion 2423056.878362
FMO2-HF: Total energy -83496.507775
FMO2-MP2: Total energy -83734.902805


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.
-141.037-136.99615.673-8.941-10.7730.104
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 : -0.818 / q_NPA : -0.921
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].
3F34ALA0-0.032-0.0261.821-35.989-34.82612.762-7.560-6.3650.081
4F35GLU-1-0.799-0.8682.27227.15729.7382.769-1.468-3.8820.016
5F36LYS10.8460.9193.421-54.770-54.4730.1420.087-0.5260.007
6F37TYR00.008-0.0216.905-0.436-0.4360.0000.0000.0000.000
7F38LYS10.8130.8939.772-23.282-23.2820.0000.0000.0000.000
8F39MET0-0.0050.00111.869-1.837-1.8370.0000.0000.0000.000
9F40ASP-1-0.810-0.89013.91620.80720.8070.0000.0000.0000.000
10F41HIS0-0.043-0.00815.355-1.049-1.0490.0000.0000.0000.000
11F42ARG10.8690.91218.691-12.048-12.0480.0000.0000.0000.000
12F43ARG10.8010.88521.982-12.336-12.3360.0000.0000.0000.000
13F44ARG10.8520.92216.818-16.139-16.1390.0000.0000.0000.000
14F45GLY00.0430.00420.4800.5700.5700.0000.0000.0000.000
15F46ILE0-0.046-0.01423.246-0.252-0.2520.0000.0000.0000.000
16F47ALA00.0180.00725.3480.4420.4420.0000.0000.0000.000
17F48LEU00.0050.00827.149-0.410-0.4100.0000.0000.0000.000
18F49ILE0-0.008-0.01029.6790.2590.2590.0000.0000.0000.000
19F50PHE00.0320.01832.269-0.348-0.3480.0000.0000.0000.000
20F51ASN00.0210.01335.0770.2690.2690.0000.0000.0000.000
21F52HIS00.0190.00637.564-0.059-0.0590.0000.0000.0000.000
22F53GLU-1-0.789-0.89140.8907.6297.6290.0000.0000.0000.000
23F54ARG10.8080.90943.402-6.706-6.7060.0000.0000.0000.000
24F55PHE00.0200.00041.8390.1340.1340.0000.0000.0000.000
25F56PHE00.0520.01547.482-0.166-0.1660.0000.0000.0000.000
26F57TRP00.002-0.00450.3220.0060.0060.0000.0000.0000.000
27F58HIS00.0080.00453.1580.0690.0690.0000.0000.0000.000
28F59LEU0-0.0120.01146.0750.0010.0010.0000.0000.0000.000
29F60THR0-0.049-0.02349.3670.0220.0220.0000.0000.0000.000
30F61LEU00.0000.02444.5300.0310.0310.0000.0000.0000.000
31F62PRO00.0190.00746.135-0.110-0.1100.0000.0000.0000.000
32F63GLU-1-0.861-0.93346.2486.7076.7070.0000.0000.0000.000
33F64ARG10.7770.90537.043-8.393-8.3930.0000.0000.0000.000
34F65ARG10.8890.92842.137-6.535-6.5350.0000.0000.0000.000
35F66GLY00.0520.02941.4440.0100.0100.0000.0000.0000.000
36F67THR0-0.034-0.01637.9480.2980.2980.0000.0000.0000.000
37F68CYS0-0.037-0.01537.7580.2260.2260.0000.0000.0000.000
38F69ALA00.0370.02538.1970.1520.1520.0000.0000.0000.000
39F70ASP-1-0.790-0.87034.4549.4299.4290.0000.0000.0000.000
40F71ARG10.8160.85433.466-7.944-7.9440.0000.0000.0000.000
41F72ASP-1-0.801-0.84733.6138.7208.7200.0000.0000.0000.000
42F73ASN0-0.019-0.00132.7820.2670.2670.0000.0000.0000.000
43F74LEU00.0450.00828.2660.3580.3580.0000.0000.0000.000
44F75THR0-0.010-0.02529.2090.3310.3310.0000.0000.0000.000
45F76ARG10.8850.95130.356-9.359-9.3590.0000.0000.0000.000
46F77ARG10.8410.92026.579-10.872-10.8720.0000.0000.0000.000
47F78PHE00.0140.00122.9920.5420.5420.0000.0000.0000.000
48F79SER00.001-0.01525.4410.3110.3110.0000.0000.0000.000
49F80ASP-1-0.871-0.92826.22211.31311.3130.0000.0000.0000.000
50F81LEU0-0.045-0.00920.5860.5090.5090.0000.0000.0000.000
51F82GLY0-0.002-0.00121.5320.8020.8020.0000.0000.0000.000
52F83PHE0-0.041-0.03320.4050.1180.1180.0000.0000.0000.000
53F84GLU-1-0.828-0.90025.08810.39110.3910.0000.0000.0000.000
54F85VAL0-0.011-0.01828.128-0.026-0.0260.0000.0000.0000.000
55F86LYS10.8380.92029.935-10.319-10.3190.0000.0000.0000.000
56F87CYS0-0.0140.00332.8110.1640.1640.0000.0000.0000.000
57F88PHE00.0130.00034.582-0.229-0.2290.0000.0000.0000.000
58F89ASN00.0300.01937.7770.2580.2580.0000.0000.0000.000
59F90ASP-1-0.796-0.92140.6187.3687.3680.0000.0000.0000.000
60F91LEU0-0.0460.01338.587-0.147-0.1470.0000.0000.0000.000
61F92LYS10.9310.94742.360-6.765-6.7650.0000.0000.0000.000
62F93ALA00.015-0.01041.1310.1940.1940.0000.0000.0000.000
63F94GLU-1-0.909-0.95340.6107.0607.0600.0000.0000.0000.000
64F95GLU-1-0.809-0.89241.1587.2357.2350.0000.0000.0000.000
65F96LEU0-0.024-0.01235.4060.1890.1890.0000.0000.0000.000
66F97LEU00.0170.00536.1050.3050.3050.0000.0000.0000.000
67F98LEU00.0190.01036.4980.2400.2400.0000.0000.0000.000
68F99LYS10.8270.89535.875-8.210-8.2100.0000.0000.0000.000
69F100ILE0-0.0080.00030.3240.3110.3110.0000.0000.0000.000
70F101HIS00.0310.01331.7720.3520.3520.0000.0000.0000.000
71F102GLU-1-0.809-0.85032.7178.8868.8860.0000.0000.0000.000
72F103VAL00.015-0.00328.5210.2750.2750.0000.0000.0000.000
73F104SER0-0.072-0.03428.1530.4500.4500.0000.0000.0000.000
74F105THR0-0.029-0.02428.6850.2140.2140.0000.0000.0000.000
75F106VAL0-0.0150.00728.641-0.027-0.0270.0000.0000.0000.000
76F107SER0-0.003-0.00226.1660.5570.5570.0000.0000.0000.000
77F108HIS10.9000.93522.468-12.416-12.4160.0000.0000.0000.000
78F109ALA00.0520.03221.4550.6910.6910.0000.0000.0000.000
79F110ASP-1-0.813-0.87620.54812.90412.9040.0000.0000.0000.000
80F111ALA0-0.005-0.01121.121-0.132-0.1320.0000.0000.0000.000
81F112ASP-1-0.716-0.84216.23917.97217.9720.0000.0000.0000.000
82F113CYS0-0.076-0.02616.9210.7430.7430.0000.0000.0000.000
83F114PHE0-0.016-0.01319.198-0.821-0.8210.0000.0000.0000.000
84F115VAL00.0240.03121.9150.4920.4920.0000.0000.0000.000
85F116CYS0-0.042-0.00824.342-0.643-0.6430.0000.0000.0000.000
86F117VAL0-0.011-0.00527.5810.1440.1440.0000.0000.0000.000
87F118PHE00.015-0.00429.629-0.328-0.3280.0000.0000.0000.000
88F119LEU0-0.022-0.00432.3000.0890.0890.0000.0000.0000.000
89F120SER00.033-0.01035.345-0.333-0.3330.0000.0000.0000.000
90F121HIS00.019-0.00338.0950.2370.2370.0000.0000.0000.000
91F122GLY00.016-0.00737.4470.1400.1400.0000.0000.0000.000
92F123GLU-1-0.819-0.88438.2067.4397.4390.0000.0000.0000.000
93F124GLY00.0540.03536.7110.0000.0000.0000.0000.0000.000
94F125ASN0-0.031-0.01333.7070.1100.1100.0000.0000.0000.000
95F126HIS0-0.030-0.02034.4810.0570.0570.0000.0000.0000.000
96F127ILE0-0.020-0.00834.5280.0700.0700.0000.0000.0000.000
97F128TYR00.005-0.00536.936-0.196-0.1960.0000.0000.0000.000
98F129ALA00.0010.03239.5900.1860.1860.0000.0000.0000.000
99F130TYR0-0.014-0.02241.412-0.160-0.1600.0000.0000.0000.000
100F131ASP-1-0.798-0.91744.7726.9846.9840.0000.0000.0000.000
101F132ALA00.0250.01744.156-0.130-0.1300.0000.0000.0000.000
102F133LYS10.8050.90540.484-7.412-7.4120.0000.0000.0000.000
103F134ILE00.0120.00335.950-0.081-0.0810.0000.0000.0000.000
104F135GLU-1-0.851-0.91134.4008.9248.9240.0000.0000.0000.000
105F136ILE00.0190.00729.5270.1640.1640.0000.0000.0000.000
106F137GLN00.0600.02626.7280.4240.4240.0000.0000.0000.000
107F138THR0-0.053-0.03930.0110.1090.1090.0000.0000.0000.000
108F139LEU0-0.0130.00631.242-0.029-0.0290.0000.0000.0000.000
109F140THR00.008-0.01225.7880.1170.1170.0000.0000.0000.000
110F141GLY00.0220.00126.2370.3960.3960.0000.0000.0000.000
111F142LEU0-0.033-0.00927.3720.1360.1360.0000.0000.0000.000
112F143PHE00.028-0.00523.9390.0280.0280.0000.0000.0000.000
113F144LYS10.8540.93622.558-10.962-10.9620.0000.0000.0000.000
114F145GLY00.0280.00620.740-0.181-0.1810.0000.0000.0000.000
115F146ASP-1-0.829-0.91521.59811.64911.6490.0000.0000.0000.000
116F147LYS10.8520.92824.798-10.914-10.9140.0000.0000.0000.000
117F148CYS0-0.070-0.02824.228-0.215-0.2150.0000.0000.0000.000
118F149HIS00.0670.03222.4500.6680.6680.0000.0000.0000.000
119F150SER0-0.048-0.02321.1530.5920.5920.0000.0000.0000.000
120F151LEU00.013-0.00119.6020.3340.3340.0000.0000.0000.000
121F152VAL00.0100.01516.3750.5180.5180.0000.0000.0000.000
122F153GLY00.0170.02013.6470.2580.2580.0000.0000.0000.000
123F154LYS10.7870.90913.425-14.932-14.9320.0000.0000.0000.000
124F155PRO00.0020.00314.407-0.803-0.8030.0000.0000.0000.000
125F156LYS10.7780.89416.826-17.152-17.1520.0000.0000.0000.000
126F157ILE0-0.0010.00318.333-0.084-0.0840.0000.0000.0000.000
127F158PHE00.030-0.00321.801-0.667-0.6670.0000.0000.0000.000
128F159ILE0-0.012-0.00824.0110.2860.2860.0000.0000.0000.000
129F160ILE00.0010.00227.203-0.417-0.4170.0000.0000.0000.000
130F161GLN0-0.022-0.01230.6370.0620.0620.0000.0000.0000.000
131F162ALA00.0310.00233.324-0.253-0.2530.0000.0000.0000.000
132F163CYS0-0.0180.00036.2320.0460.0460.0000.0000.0000.000
133F198TYR00.0550.03825.4120.0330.0330.0000.0000.0000.000
134F199THR0-0.073-0.05628.056-0.363-0.3630.0000.0000.0000.000
135F200LEU00.0400.02624.1490.3530.3530.0000.0000.0000.000
136F201PRO00.000-0.01820.512-0.325-0.3250.0000.0000.0000.000
137F202ALA00.0190.01822.640-0.024-0.0240.0000.0000.0000.000
138F203GLY00.0070.00020.102-0.329-0.3290.0000.0000.0000.000
139F204ALA00.0290.00614.6930.3010.3010.0000.0000.0000.000
140F205ASP-1-0.794-0.88513.35119.63219.6320.0000.0000.0000.000
141F206PHE0-0.0200.00415.714-0.356-0.3560.0000.0000.0000.000
142F207LEU0-0.036-0.01617.7270.6910.6910.0000.0000.0000.000
143F208MET0-0.0190.02220.054-0.396-0.3960.0000.0000.0000.000
144F209CYS0-0.012-0.00922.9480.4620.4620.0000.0000.0000.000
145F210TYR00.023-0.01025.298-0.575-0.5750.0000.0000.0000.000
146F211SER00.0390.00028.8640.1750.1750.0000.0000.0000.000
147F212VAL0-0.050-0.01330.847-0.398-0.3980.0000.0000.0000.000
148F222THR00.018-0.00641.529-0.031-0.0310.0000.0000.0000.000
149F223VAL00.0170.00141.4280.1430.1430.0000.0000.0000.000
150F224ASN0-0.014-0.00240.226-0.040-0.0400.0000.0000.0000.000
151F225GLY00.0190.02537.2710.2420.2420.0000.0000.0000.000
152F226SER0-0.052-0.05735.074-0.050-0.0500.0000.0000.0000.000
153F227TRP00.002-0.01334.5650.2680.2680.0000.0000.0000.000
154F228TYR00.0810.04026.3550.0970.0970.0000.0000.0000.000
155F229ILE00.0230.02229.7980.4540.4540.0000.0000.0000.000
156F230GLN00.0140.00230.6060.3120.3120.0000.0000.0000.000
157F231ASP-1-0.748-0.86029.07010.48310.4830.0000.0000.0000.000
158F232LEU00.0100.00724.1650.4510.4510.0000.0000.0000.000
159F233CYS0-0.033-0.01926.0870.4310.4310.0000.0000.0000.000
160F234GLU-1-0.826-0.88627.96310.88510.8850.0000.0000.0000.000
161F235MET0-0.023-0.01123.3730.3550.3550.0000.0000.0000.000
162F236LEU00.013-0.00321.7730.6230.6230.0000.0000.0000.000
163F237GLY0-0.023-0.01823.4590.2940.2940.0000.0000.0000.000
164F238LYS10.8160.90524.840-11.386-11.3860.0000.0000.0000.000
165F239TYR00.0370.00219.937-0.016-0.0160.0000.0000.0000.000
166F240GLY00.0360.02418.9640.9800.9800.0000.0000.0000.000
167F241SER0-0.026-0.01118.1600.9480.9480.0000.0000.0000.000
168F242SER0-0.015-0.02115.8300.4770.4770.0000.0000.0000.000
169F243LEU00.0190.01214.3981.5411.5410.0000.0000.0000.000
170F244GLU-1-0.797-0.86411.25825.06325.0630.0000.0000.0000.000
171F245PHE00.025-0.01113.790-1.679-1.6790.0000.0000.0000.000
172F246THR0-0.010-0.03214.589-1.336-1.3360.0000.0000.0000.000
173F247GLU-1-0.830-0.89714.76420.91720.9170.0000.0000.0000.000
174F248LEU0-0.028-0.01017.445-1.240-1.2400.0000.0000.0000.000
175F249LEU00.002-0.01119.737-1.054-1.0540.0000.0000.0000.000
176F250THR0-0.030-0.02619.497-0.872-0.8720.0000.0000.0000.000
177F251LEU0-0.061-0.02621.265-0.751-0.7510.0000.0000.0000.000
178F252VAL0-0.034-0.01323.732-0.669-0.6690.0000.0000.0000.000
179F253ASN00.0150.00024.001-0.776-0.7760.0000.0000.0000.000
180F254ARG11.0001.00723.546-13.350-13.3500.0000.0000.0000.000
181F255LYS10.7490.85727.839-11.116-11.1160.0000.0000.0000.000
182F256VAL0-0.009-0.01229.777-0.417-0.4170.0000.0000.0000.000
183F257GLU-1-0.949-0.97229.56510.67010.6700.0000.0000.0000.000
184F258GLN0-0.073-0.02432.046-0.138-0.1380.0000.0000.0000.000
185F259ARG10.7980.90633.465-9.764-9.7640.0000.0000.0000.000
186F275VAL00.001-0.01029.376-0.094-0.0940.0000.0000.0000.000
187F276PRO0-0.0280.00928.304-0.004-0.0040.0000.0000.0000.000
188F277CYS0-0.015-0.01426.3230.4240.4240.0000.0000.0000.000
189F278PHE0-0.007-0.00918.745-0.047-0.0470.0000.0000.0000.000
190F279ALA00.0240.01721.3450.1220.1220.0000.0000.0000.000
191F280SER00.000-0.01015.599-0.030-0.0300.0000.0000.0000.000
192F281MET00.0110.01215.807-0.219-0.2190.0000.0000.0000.000
193F282LEU0-0.045-0.01012.8390.2010.2010.0000.0000.0000.000
194F283THR0-0.016-0.0169.4501.0261.0260.0000.0000.0000.000
195F284LYS10.7820.8866.087-32.202-32.2020.0000.0000.0000.000
196F285LYS10.8670.9296.427-46.120-46.1200.0000.0000.0000.000
197F286LEU0-0.020-0.0189.2120.1920.1920.0000.0000.0000.000
198F287HIS00.0490.0319.9903.0003.0000.0000.0000.0000.000
199F288PHE0-0.005-0.01513.5780.0020.0020.0000.0000.0000.000
200F289PHE00.0200.01710.391-0.894-0.8940.0000.0000.0000.000
201F290PRO00.0000.00516.213-0.236-0.2360.0000.0000.0000.000
202F291LYS10.7910.89217.441-16.110-16.1100.0000.0000.0000.000
203F292SER00.0110.01619.332-0.761-0.7610.0000.0000.0000.000