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: Z6J2N

Calculation Name: 3V6M-C-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: C

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2552363.719971
FMO2-HF: Nuclear repulsion 2467864.552331
FMO2-HF: Total energy -84499.16764
FMO2-MP2: Total energy -84740.648016


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(C:31:PHE)


Summations of interaction energy for fragment #1(C: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.
2.1344.533-0.016-0.965-1.4170.004
Interaction energy analysis for fragmet #1(C:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.006
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].
3C33PRO00.0230.0173.8590.0562.338-0.015-0.961-1.3060.004
4C34ALA00.0250.0055.0230.6770.794-0.001-0.004-0.1110.000
5C35GLU-1-0.806-0.8565.7341.5251.5250.0000.0000.0000.000
6C36LYS10.8920.9287.9210.1430.1430.0000.0000.0000.000
7C37TYR00.019-0.01910.4460.0950.0950.0000.0000.0000.000
8C38LYS10.8320.91612.357-0.161-0.1610.0000.0000.0000.000
9C39MET0-0.040-0.02114.8340.0020.0020.0000.0000.0000.000
10C40ASP-1-0.825-0.89517.3750.0350.0350.0000.0000.0000.000
11C41HIS0-0.040-0.02016.9680.0400.0400.0000.0000.0000.000
12C42ARG10.9090.94621.736-0.057-0.0570.0000.0000.0000.000
13C43ARG10.7320.82524.663-0.052-0.0520.0000.0000.0000.000
14C44ARG10.8340.91321.4640.0640.0640.0000.0000.0000.000
15C45GLY00.0270.00322.4490.0060.0060.0000.0000.0000.000
16C46ILE0-0.038-0.01824.696-0.008-0.0080.0000.0000.0000.000
17C47ALA00.0170.01025.462-0.002-0.0020.0000.0000.0000.000
18C48LEU0-0.0040.00327.3940.0000.0000.0000.0000.0000.000
19C49ILE0-0.016-0.01228.836-0.006-0.0060.0000.0000.0000.000
20C50PHE00.0530.01329.8200.0030.0030.0000.0000.0000.000
21C51ASN0-0.004-0.01033.377-0.006-0.0060.0000.0000.0000.000
22C52HIS00.0260.01335.0890.0060.0060.0000.0000.0000.000
23C53GLU-1-0.805-0.89438.488-0.029-0.0290.0000.0000.0000.000
24C54ARG10.7800.86141.3990.0170.0170.0000.0000.0000.000
25C55PHE0-0.014-0.01438.9410.0000.0000.0000.0000.0000.000
26C56PHE00.0110.00844.2350.0000.0000.0000.0000.0000.000
27C57TRP00.0340.00746.7370.0000.0000.0000.0000.0000.000
28C58HIS00.0210.00849.024-0.001-0.0010.0000.0000.0000.000
29C59LEU0-0.037-0.00342.2320.0000.0000.0000.0000.0000.000
30C60THR0-0.055-0.02645.340-0.001-0.0010.0000.0000.0000.000
31C61LEU0-0.0130.01240.681-0.002-0.0020.0000.0000.0000.000
32C62PRO0-0.0050.00343.0400.0010.0010.0000.0000.0000.000
33C63GLU-1-0.770-0.86743.364-0.022-0.0220.0000.0000.0000.000
34C64ARG10.8200.92235.3600.0320.0320.0000.0000.0000.000
35C65ARG10.8450.88541.0360.0230.0230.0000.0000.0000.000
36C66GLY00.0860.04740.820-0.002-0.0020.0000.0000.0000.000
37C67THR0-0.033-0.01336.938-0.003-0.0030.0000.0000.0000.000
38C68CYS0-0.026-0.01537.4540.0000.0000.0000.0000.0000.000
39C69ALA00.0000.00839.3800.0000.0000.0000.0000.0000.000
40C70ASP-1-0.782-0.86834.381-0.058-0.0580.0000.0000.0000.000
41C71ARG10.8530.91134.1450.0260.0260.0000.0000.0000.000
42C72ASP-1-0.792-0.84734.497-0.035-0.0350.0000.0000.0000.000
43C73ASN00.0060.00034.241-0.003-0.0030.0000.0000.0000.000
44C74LEU00.0420.00728.763-0.004-0.0040.0000.0000.0000.000
45C75THR0-0.014-0.02830.7560.0010.0010.0000.0000.0000.000
46C76ARG10.7970.90732.7540.0460.0460.0000.0000.0000.000
47C77ARG10.8830.94428.7060.0780.0780.0000.0000.0000.000
48C78PHE00.009-0.00323.951-0.005-0.0050.0000.0000.0000.000
49C79SER0-0.003-0.01628.3500.0050.0050.0000.0000.0000.000
50C80ASP-1-0.871-0.93229.999-0.064-0.0640.0000.0000.0000.000
51C81LEU0-0.042-0.00624.167-0.007-0.0070.0000.0000.0000.000
52C82GLY00.000-0.00125.5410.0000.0000.0000.0000.0000.000
53C83PHE0-0.014-0.01821.8570.0080.0080.0000.0000.0000.000
54C84GLU-1-0.801-0.90427.4290.0120.0120.0000.0000.0000.000
55C85VAL0-0.017-0.01629.8540.0040.0040.0000.0000.0000.000
56C86LYS10.8990.95831.202-0.010-0.0100.0000.0000.0000.000
57C87CYS00.0010.02232.861-0.002-0.0020.0000.0000.0000.000
58C88PHE00.011-0.00533.8110.0040.0040.0000.0000.0000.000
59C89ASN00.0260.00236.786-0.005-0.0050.0000.0000.0000.000
60C90ASP-1-0.778-0.88339.553-0.014-0.0140.0000.0000.0000.000
61C91LEU00.0050.02636.1560.0020.0020.0000.0000.0000.000
62C92LYS10.9420.95239.600-0.005-0.0050.0000.0000.0000.000
63C93ALA0-0.007-0.01837.7920.0010.0010.0000.0000.0000.000
64C94GLU-1-0.920-0.95837.3430.0170.0170.0000.0000.0000.000
65C95GLU-1-0.852-0.92638.1090.0070.0070.0000.0000.0000.000
66C96LEU0-0.037-0.01332.7410.0010.0010.0000.0000.0000.000
67C97LEU00.0180.00032.7040.0020.0020.0000.0000.0000.000
68C98LEU00.0130.00933.4470.0040.0040.0000.0000.0000.000
69C99LYS10.7810.88633.402-0.013-0.0130.0000.0000.0000.000
70C100ILE0-0.015-0.01427.3870.0010.0010.0000.0000.0000.000
71C101HIS00.0200.01829.2570.0010.0010.0000.0000.0000.000
72C102GLU-1-0.787-0.85730.0040.0280.0280.0000.0000.0000.000
73C103VAL0-0.025-0.02527.0110.0050.0050.0000.0000.0000.000
74C104SER0-0.072-0.04325.7040.0050.0050.0000.0000.0000.000
75C105THR00.0290.01725.6920.0110.0110.0000.0000.0000.000
76C106VAL0-0.0380.00327.5460.0040.0040.0000.0000.0000.000
77C107SER00.000-0.00325.5870.0080.0080.0000.0000.0000.000
78C108HIS10.9110.94321.847-0.067-0.0670.0000.0000.0000.000
79C109ALA00.0520.03720.9830.0030.0030.0000.0000.0000.000
80C110ASP-1-0.806-0.86221.0600.0730.0730.0000.0000.0000.000
81C111ALA00.006-0.00122.155-0.014-0.0140.0000.0000.0000.000
82C112ASP-1-0.734-0.85318.8730.0170.0170.0000.0000.0000.000
83C113CYS0-0.079-0.02717.8030.0020.0020.0000.0000.0000.000
84C114PHE0-0.016-0.00919.4920.0090.0090.0000.0000.0000.000
85C115VAL00.0220.02920.844-0.011-0.0110.0000.0000.0000.000
86C116CYS0-0.037-0.00623.5170.0100.0100.0000.0000.0000.000
87C117VAL0-0.002-0.00125.615-0.006-0.0060.0000.0000.0000.000
88C118PHE00.009-0.00526.8850.0070.0070.0000.0000.0000.000
89C119LEU0-0.030-0.01230.466-0.006-0.0060.0000.0000.0000.000
90C120SER00.005-0.01833.3900.0030.0030.0000.0000.0000.000
91C121HIS00.0270.00235.369-0.006-0.0060.0000.0000.0000.000
92C122GLY00.015-0.01233.4190.0020.0020.0000.0000.0000.000
93C123GLU-1-0.812-0.88234.007-0.012-0.0120.0000.0000.0000.000
94C124GLY00.0490.03232.3400.0040.0040.0000.0000.0000.000
95C125ASN0-0.037-0.02328.392-0.006-0.0060.0000.0000.0000.000
96C126HIS0-0.023-0.01529.7700.0070.0070.0000.0000.0000.000
97C127ILE0-0.033-0.01330.896-0.006-0.0060.0000.0000.0000.000
98C128TYR00.005-0.00832.9050.0050.0050.0000.0000.0000.000
99C129ALA00.0140.03536.157-0.002-0.0020.0000.0000.0000.000
100C130TYR00.006-0.00737.830-0.001-0.0010.0000.0000.0000.000
101C131ASP-1-0.777-0.90141.3810.0020.0020.0000.0000.0000.000
102C132ALA00.0130.01339.8470.0010.0010.0000.0000.0000.000
103C133LYS10.7980.90636.1200.0040.0040.0000.0000.0000.000
104C134ILE00.0230.00231.7760.0040.0040.0000.0000.0000.000
105C135GLU-1-0.850-0.90029.7330.0070.0070.0000.0000.0000.000
106C136ILE00.0430.01325.0470.0050.0050.0000.0000.0000.000
107C137GLN0-0.0030.00522.0380.0090.0090.0000.0000.0000.000
108C138THR0-0.026-0.02025.4660.0070.0070.0000.0000.0000.000
109C139LEU0-0.0050.00427.5280.0050.0050.0000.0000.0000.000
110C140THR0-0.030-0.03821.9060.0050.0050.0000.0000.0000.000
111C141GLY00.0240.00922.6300.0070.0070.0000.0000.0000.000
112C142LEU0-0.023-0.01423.5510.0120.0120.0000.0000.0000.000
113C143PHE00.013-0.01121.2000.0080.0080.0000.0000.0000.000
114C144LYS10.8700.95318.666-0.069-0.0690.0000.0000.0000.000
115C145GLY00.0330.01016.6010.0050.0050.0000.0000.0000.000
116C146ASP-1-0.839-0.92917.5870.1260.1260.0000.0000.0000.000
117C147LYS10.8230.90620.405-0.097-0.0970.0000.0000.0000.000
118C148CYS00.0000.01721.217-0.006-0.0060.0000.0000.0000.000
119C149HIS00.0420.01419.2570.0020.0020.0000.0000.0000.000
120C150SER0-0.041-0.02118.5450.0130.0130.0000.0000.0000.000
121C151LEU00.016-0.00318.028-0.007-0.0070.0000.0000.0000.000
122C152VAL00.0010.01313.375-0.015-0.0150.0000.0000.0000.000
123C153GLY00.0090.01711.1760.0280.0280.0000.0000.0000.000
124C154LYS10.7870.90612.071-0.125-0.1250.0000.0000.0000.000
125C155PRO00.0040.00514.095-0.009-0.0090.0000.0000.0000.000
126C156LYS10.7880.89714.442-0.062-0.0620.0000.0000.0000.000
127C157ILE00.0070.00517.897-0.012-0.0120.0000.0000.0000.000
128C158PHE00.020-0.00519.7370.0140.0140.0000.0000.0000.000
129C159ILE0-0.009-0.00822.317-0.013-0.0130.0000.0000.0000.000
130C160ILE00.0040.00225.0030.0090.0090.0000.0000.0000.000
131C161GLN0-0.023-0.00627.684-0.005-0.0050.0000.0000.0000.000
132C162ALA00.021-0.00530.8230.0050.0050.0000.0000.0000.000
133C163CYS0-0.0190.00632.662-0.002-0.0020.0000.0000.0000.000
134C198TYR00.0570.03720.700-0.006-0.0060.0000.0000.0000.000
135C199THR0-0.057-0.04723.3760.0120.0120.0000.0000.0000.000
136C200LEU00.0320.02618.786-0.008-0.0080.0000.0000.0000.000
137C201PRO00.006-0.01415.9430.0130.0130.0000.0000.0000.000
138C202ALA00.0520.04117.6610.0070.0070.0000.0000.0000.000
139C203GLY0-0.008-0.00815.3510.0260.0260.0000.0000.0000.000
140C204ALA00.0470.01610.687-0.029-0.0290.0000.0000.0000.000
141C205ASP-1-0.788-0.88210.7130.1200.1200.0000.0000.0000.000
142C206PHE0-0.0260.00012.556-0.004-0.0040.0000.0000.0000.000
143C207LEU0-0.028-0.01414.574-0.030-0.0300.0000.0000.0000.000
144C208MET0-0.0220.02116.8500.0170.0170.0000.0000.0000.000
145C209CYS0-0.010-0.00520.123-0.022-0.0220.0000.0000.0000.000
146C210TYR00.017-0.01522.1400.0160.0160.0000.0000.0000.000
147C211SER00.0230.00125.639-0.008-0.0080.0000.0000.0000.000
148C212VAL0-0.031-0.01127.365-0.001-0.0010.0000.0000.0000.000
149C222THR00.023-0.00241.0670.0000.0000.0000.0000.0000.000
150C223VAL00.0170.00241.2440.0000.0000.0000.0000.0000.000
151C224ASN0-0.0040.00141.5720.0030.0030.0000.0000.0000.000
152C225GLY00.0120.01937.686-0.003-0.0030.0000.0000.0000.000
153C226SER0-0.045-0.05434.497-0.002-0.0020.0000.0000.0000.000
154C227TRP00.012-0.01334.255-0.004-0.0040.0000.0000.0000.000
155C228TYR00.0700.03224.6090.0000.0000.0000.0000.0000.000
156C229ILE00.0270.02029.560-0.006-0.0060.0000.0000.0000.000
157C230GLN00.0180.00431.342-0.006-0.0060.0000.0000.0000.000
158C231ASP-1-0.748-0.85629.733-0.102-0.1020.0000.0000.0000.000
159C232LEU00.0000.00324.705-0.008-0.0080.0000.0000.0000.000
160C233CYS0-0.029-0.01627.720-0.003-0.0030.0000.0000.0000.000
161C234GLU-1-0.821-0.88230.264-0.109-0.1090.0000.0000.0000.000
162C235MET0-0.027-0.01125.465-0.008-0.0080.0000.0000.0000.000
163C236LEU00.016-0.00223.881-0.009-0.0090.0000.0000.0000.000
164C237GLY0-0.018-0.01226.6610.0000.0000.0000.0000.0000.000
165C238LYS10.8200.90428.5670.1190.1190.0000.0000.0000.000
166C239TYR00.0380.00223.700-0.002-0.0020.0000.0000.0000.000
167C240GLY00.0310.02123.103-0.015-0.0150.0000.0000.0000.000
168C241SER0-0.023-0.00822.555-0.007-0.0070.0000.0000.0000.000
169C242SER0-0.018-0.02421.665-0.004-0.0040.0000.0000.0000.000
170C243LEU00.0160.01219.421-0.022-0.0220.0000.0000.0000.000
171C244GLU-1-0.769-0.84613.200-0.325-0.3250.0000.0000.0000.000
172C245PHE00.017-0.01616.6060.0170.0170.0000.0000.0000.000
173C246THR0-0.018-0.03813.9790.0110.0110.0000.0000.0000.000
174C247GLU-1-0.819-0.89216.561-0.348-0.3480.0000.0000.0000.000
175C248LEU0-0.038-0.01218.1300.0240.0240.0000.0000.0000.000
176C249LEU00.011-0.00918.8830.0190.0190.0000.0000.0000.000
177C250THR0-0.036-0.02618.8010.0130.0130.0000.0000.0000.000
178C251LEU0-0.042-0.01821.4440.0130.0130.0000.0000.0000.000
179C252VAL0-0.038-0.01224.3290.0140.0140.0000.0000.0000.000
180C253ASN00.0220.00221.8680.0210.0210.0000.0000.0000.000
181C254ARG10.9550.98725.1100.1850.1850.0000.0000.0000.000
182C255LYS10.7570.86227.5030.1190.1190.0000.0000.0000.000
183C256VAL00.000-0.00529.4300.0090.0090.0000.0000.0000.000
184C257GLU-1-0.845-0.91329.599-0.113-0.1130.0000.0000.0000.000
185C258GLN0-0.012-0.01630.550-0.003-0.0030.0000.0000.0000.000
186C259ARG10.7890.91233.4060.0880.0880.0000.0000.0000.000
187C260ARG10.8250.91734.1440.0980.0980.0000.0000.0000.000
188C275VAL00.0240.01327.0980.0000.0000.0000.0000.0000.000
189C276PRO0-0.060-0.01926.3420.0030.0030.0000.0000.0000.000
190C277CYS0-0.018-0.01322.178-0.016-0.0160.0000.0000.0000.000
191C278PHE0-0.002-0.01216.0300.0130.0130.0000.0000.0000.000
192C279ALA00.0340.02017.227-0.013-0.0130.0000.0000.0000.000
193C280SER00.003-0.00812.3280.0280.0280.0000.0000.0000.000
194C281MET00.0030.00711.1090.0020.0020.0000.0000.0000.000
195C282LEU0-0.044-0.00910.3060.0420.0420.0000.0000.0000.000
196C283THR0-0.011-0.0136.001-0.063-0.0630.0000.0000.0000.000
197C284LYS10.7810.8875.244-0.949-0.9490.0000.0000.0000.000
198C285LYS10.8210.9047.7520.9570.9570.0000.0000.0000.000
199C286LEU0-0.034-0.02610.9860.0870.0870.0000.0000.0000.000
200C287HIS00.0050.00514.338-0.062-0.0620.0000.0000.0000.000
201C288PHE0-0.021-0.02217.5490.0260.0260.0000.0000.0000.000
202C289PHE00.0190.01616.8400.0110.0110.0000.0000.0000.000
203C290PRO00.0050.00422.1760.0180.0180.0000.0000.0000.000
204C291LYS10.7960.89721.7530.0060.0060.0000.0000.0000.000
205C292SER00.0110.01424.842-0.003-0.0030.0000.0000.0000.000