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: 2JYKR

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2539818.362912
FMO2-HF: Nuclear repulsion 2455320.822995
FMO2-HF: Total energy -84497.539917
FMO2-MP2: Total energy -84739.141825


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.
1.4483.426-0.019-0.678-1.280.001
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 : -0.024 / q_NPA : -0.030
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].
3C33PRO00.0450.0373.8310.0191.809-0.018-0.673-1.0990.001
4C34ALA0-0.058-0.0665.4340.4830.4830.0000.0000.0000.000
5C35GLU-1-0.920-0.9525.151-0.1370.051-0.001-0.005-0.1810.000
6C36LYS10.9250.9597.8450.3540.3540.0000.0000.0000.000
7C37TYR0-0.007-0.04010.6900.0100.0100.0000.0000.0000.000
8C38LYS10.8400.90012.5540.1710.1710.0000.0000.0000.000
9C39MET0-0.070-0.03114.6840.0130.0130.0000.0000.0000.000
10C40ASP-1-0.821-0.89317.914-0.165-0.1650.0000.0000.0000.000
11C41HIS0-0.032-0.01116.8770.0110.0110.0000.0000.0000.000
12C42ARG10.9130.94721.8640.0720.0720.0000.0000.0000.000
13C43ARG10.7800.87524.9290.0830.0830.0000.0000.0000.000
14C44ARG10.8400.91821.6380.1230.1230.0000.0000.0000.000
15C45GLY00.0290.00322.808-0.008-0.0080.0000.0000.0000.000
16C46ILE0-0.022-0.00625.0360.0030.0030.0000.0000.0000.000
17C47ALA00.0000.00325.784-0.006-0.0060.0000.0000.0000.000
18C48LEU00.0010.00027.7990.0050.0050.0000.0000.0000.000
19C49ILE00.0070.00429.268-0.003-0.0030.0000.0000.0000.000
20C50PHE00.007-0.00330.3820.0040.0040.0000.0000.0000.000
21C51ASN0-0.001-0.02633.935-0.002-0.0020.0000.0000.0000.000
22C52HIS0-0.0060.00736.0990.0030.0030.0000.0000.0000.000
23C53GLU-1-0.877-0.93638.920-0.037-0.0370.0000.0000.0000.000
24C54ARG10.8420.90842.0480.0340.0340.0000.0000.0000.000
25C55PHE0-0.032-0.01639.241-0.001-0.0010.0000.0000.0000.000
26C56PHE0-0.0020.01044.7770.0010.0010.0000.0000.0000.000
27C57TRP00.0710.01447.0890.0000.0000.0000.0000.0000.000
28C58HIS0-0.007-0.00749.315-0.001-0.0010.0000.0000.0000.000
29C59LEU0-0.0310.00642.4650.0000.0000.0000.0000.0000.000
30C60THR0-0.055-0.02145.7890.0000.0000.0000.0000.0000.000
31C61LEU0-0.0110.00640.984-0.001-0.0010.0000.0000.0000.000
32C62PRO0-0.016-0.00243.3790.0000.0000.0000.0000.0000.000
33C63GLU-1-0.767-0.86943.742-0.032-0.0320.0000.0000.0000.000
34C64ARG10.8360.91535.9980.0450.0450.0000.0000.0000.000
35C65ARG10.8660.90241.9800.0290.0290.0000.0000.0000.000
36C66GLY00.0350.02141.715-0.001-0.0010.0000.0000.0000.000
37C67THR00.0460.02837.505-0.003-0.0030.0000.0000.0000.000
38C68CYS0-0.0010.00237.886-0.003-0.0030.0000.0000.0000.000
39C69ALA00.0220.01939.301-0.001-0.0010.0000.0000.0000.000
40C70ASP-1-0.765-0.87034.612-0.058-0.0580.0000.0000.0000.000
41C71ARG10.8500.92034.6980.0460.0460.0000.0000.0000.000
42C72ASP-1-0.804-0.85935.094-0.053-0.0530.0000.0000.0000.000
43C73ASN00.001-0.00634.776-0.003-0.0030.0000.0000.0000.000
44C74LEU00.042-0.00229.114-0.003-0.0030.0000.0000.0000.000
45C75THR0-0.029-0.03531.209-0.003-0.0030.0000.0000.0000.000
46C76ARG10.8550.91333.0400.0530.0530.0000.0000.0000.000
47C77ARG10.9320.97829.4550.0710.0710.0000.0000.0000.000
48C78PHE00.0480.01324.436-0.005-0.0050.0000.0000.0000.000
49C79SER0-0.0080.00128.643-0.003-0.0030.0000.0000.0000.000
50C80ASP-1-0.919-0.94430.595-0.075-0.0750.0000.0000.0000.000
51C81LEU0-0.065-0.01824.621-0.005-0.0050.0000.0000.0000.000
52C82GLY0-0.028-0.02425.863-0.009-0.0090.0000.0000.0000.000
53C83PHE0-0.043-0.02822.3820.0000.0000.0000.0000.0000.000
54C84GLU-1-0.803-0.90428.051-0.077-0.0770.0000.0000.0000.000
55C85VAL0-0.012-0.01030.238-0.001-0.0010.0000.0000.0000.000
56C86LYS10.9310.96831.8490.0610.0610.0000.0000.0000.000
57C87CYS0-0.034-0.00133.230-0.002-0.0020.0000.0000.0000.000
58C88PHE00.0260.00133.8630.0020.0020.0000.0000.0000.000
59C89ASN0-0.002-0.00737.267-0.003-0.0030.0000.0000.0000.000
60C90ASP-1-0.776-0.88939.752-0.035-0.0350.0000.0000.0000.000
61C91LEU0-0.0450.00236.7170.0010.0010.0000.0000.0000.000
62C92LYS10.9880.99439.8400.0270.0270.0000.0000.0000.000
63C93ALA0-0.002-0.02238.101-0.002-0.0020.0000.0000.0000.000
64C94GLU-1-0.904-0.95137.722-0.028-0.0280.0000.0000.0000.000
65C95GLU-1-0.847-0.93938.413-0.034-0.0340.0000.0000.0000.000
66C96LEU0-0.032-0.00733.021-0.002-0.0020.0000.0000.0000.000
67C97LEU00.040-0.00232.792-0.003-0.0030.0000.0000.0000.000
68C98LEU00.0210.01533.904-0.002-0.0020.0000.0000.0000.000
69C99LYS10.8150.92233.7950.0420.0420.0000.0000.0000.000
70C100ILE0-0.037-0.01827.916-0.003-0.0030.0000.0000.0000.000
71C101HIS00.0360.01929.619-0.004-0.0040.0000.0000.0000.000
72C102GLU-1-0.809-0.89430.460-0.047-0.0470.0000.0000.0000.000
73C103VAL0-0.034-0.03127.506-0.003-0.0030.0000.0000.0000.000
74C104SER0-0.083-0.03826.110-0.005-0.0050.0000.0000.0000.000
75C105THR0-0.0040.00026.105-0.001-0.0010.0000.0000.0000.000
76C106VAL0-0.0400.00327.5550.0020.0020.0000.0000.0000.000
77C107SER00.002-0.00325.928-0.005-0.0050.0000.0000.0000.000
78C108HIS10.8660.91722.2810.0820.0820.0000.0000.0000.000
79C109ALA00.0540.02121.371-0.009-0.0090.0000.0000.0000.000
80C110ASP-1-0.821-0.87721.418-0.087-0.0870.0000.0000.0000.000
81C111ALA00.002-0.00922.2210.0020.0020.0000.0000.0000.000
82C112ASP-1-0.724-0.84419.109-0.146-0.1460.0000.0000.0000.000
83C113CYS0-0.056-0.01617.879-0.012-0.0120.0000.0000.0000.000
84C114PHE0-0.011-0.00219.8240.0110.0110.0000.0000.0000.000
85C115VAL00.0280.03021.339-0.007-0.0070.0000.0000.0000.000
86C116CYS0-0.029-0.00323.8790.0090.0090.0000.0000.0000.000
87C117VAL00.001-0.00125.853-0.003-0.0030.0000.0000.0000.000
88C118PHE0-0.005-0.00627.2370.0040.0040.0000.0000.0000.000
89C119LEU0-0.013-0.00630.941-0.002-0.0020.0000.0000.0000.000
90C120SER0-0.002-0.02533.7800.0030.0030.0000.0000.0000.000
91C121HIS00.012-0.00235.412-0.003-0.0030.0000.0000.0000.000
92C122GLY00.015-0.01633.671-0.001-0.0010.0000.0000.0000.000
93C123GLU-1-0.852-0.88534.697-0.029-0.0290.0000.0000.0000.000
94C124GLY00.0540.02132.8910.0010.0010.0000.0000.0000.000
95C125ASN0-0.006-0.00228.763-0.002-0.0020.0000.0000.0000.000
96C126HIS0-0.012-0.01430.1960.0000.0000.0000.0000.0000.000
97C127ILE0-0.020-0.00530.897-0.002-0.0020.0000.0000.0000.000
98C128TYR0-0.018-0.00833.4440.0030.0030.0000.0000.0000.000
99C129ALA00.0330.04036.908-0.002-0.0020.0000.0000.0000.000
100C130TYR0-0.018-0.02338.1800.0010.0010.0000.0000.0000.000
101C131ASP-1-0.789-0.91341.752-0.029-0.0290.0000.0000.0000.000
102C132ALA00.0130.00840.3290.0020.0020.0000.0000.0000.000
103C133LYS10.8230.92436.4870.0270.0270.0000.0000.0000.000
104C134ILE00.0180.00632.0630.0010.0010.0000.0000.0000.000
105C135GLU-1-0.903-0.95030.169-0.036-0.0360.0000.0000.0000.000
106C136ILE00.022-0.00425.656-0.002-0.0020.0000.0000.0000.000
107C137GLN00.0060.00222.541-0.005-0.0050.0000.0000.0000.000
108C138THR0-0.036-0.01625.941-0.001-0.0010.0000.0000.0000.000
109C139LEU00.0200.01927.844-0.001-0.0010.0000.0000.0000.000
110C140THR00.014-0.00822.210-0.002-0.0020.0000.0000.0000.000
111C141GLY0-0.015-0.01622.851-0.005-0.0050.0000.0000.0000.000
112C142LEU00.0000.00223.6810.0010.0010.0000.0000.0000.000
113C143PHE00.005-0.01621.392-0.001-0.0010.0000.0000.0000.000
114C144LYS10.9210.98218.9340.0470.0470.0000.0000.0000.000
115C145GLY00.0590.02017.1630.0030.0030.0000.0000.0000.000
116C146ASP-1-0.899-0.95718.099-0.050-0.0500.0000.0000.0000.000
117C147LYS10.8300.91020.8140.0490.0490.0000.0000.0000.000
118C148CYS00.0160.04121.488-0.001-0.0010.0000.0000.0000.000
119C149HIS00.0610.02419.719-0.011-0.0110.0000.0000.0000.000
120C150SER0-0.030-0.01618.936-0.009-0.0090.0000.0000.0000.000
121C151LEU00.034-0.00418.625-0.005-0.0050.0000.0000.0000.000
122C152VAL0-0.0110.00513.589-0.013-0.0130.0000.0000.0000.000
123C153GLY0-0.0050.00811.643-0.003-0.0030.0000.0000.0000.000
124C154LYS10.7640.89512.4410.1110.1110.0000.0000.0000.000
125C155PRO0-0.0080.00214.2020.0080.0080.0000.0000.0000.000
126C156LYS10.8380.93215.2800.1560.1560.0000.0000.0000.000
127C157ILE00.0190.00618.275-0.004-0.0040.0000.0000.0000.000
128C158PHE00.003-0.01020.2250.0100.0100.0000.0000.0000.000
129C159ILE0-0.0030.00122.907-0.004-0.0040.0000.0000.0000.000
130C160ILE00.006-0.00925.3580.0060.0060.0000.0000.0000.000
131C161GLN0-0.0050.02927.872-0.002-0.0020.0000.0000.0000.000
132C162ALA00.011-0.01630.9470.0030.0030.0000.0000.0000.000
133C163CYS00.0100.03033.1800.0000.0000.0000.0000.0000.000
134C198TYR00.015-0.00421.128-0.004-0.0040.0000.0000.0000.000
135C199THR00.0080.01023.8400.0080.0080.0000.0000.0000.000
136C200LEU00.0120.01018.964-0.006-0.0060.0000.0000.0000.000
137C201PRO00.013-0.00616.3990.0060.0060.0000.0000.0000.000
138C202ALA00.0070.00118.1820.0040.0040.0000.0000.0000.000
139C203GLY0-0.008-0.01015.6040.0120.0120.0000.0000.0000.000
140C204ALA00.0350.01410.952-0.010-0.0100.0000.0000.0000.000
141C205ASP-1-0.817-0.88410.558-0.238-0.2380.0000.0000.0000.000
142C206PHE0-0.0100.00412.8230.0170.0170.0000.0000.0000.000
143C207LEU0-0.027-0.01614.997-0.016-0.0160.0000.0000.0000.000
144C208MET0-0.0220.00717.1670.0100.0100.0000.0000.0000.000
145C209CYS0-0.017-0.00120.433-0.008-0.0080.0000.0000.0000.000
146C210TYR00.015-0.01222.0980.0080.0080.0000.0000.0000.000
147C211SER0-0.032-0.05025.803-0.002-0.0020.0000.0000.0000.000
148C212VAL00.0120.01927.5860.0030.0030.0000.0000.0000.000
149C222THR00.0250.00041.5980.0000.0000.0000.0000.0000.000
150C223VAL00.0410.01041.950-0.001-0.0010.0000.0000.0000.000
151C224ASN0-0.020-0.00841.8700.0000.0000.0000.0000.0000.000
152C225GLY00.0380.04038.036-0.002-0.0020.0000.0000.0000.000
153C226SER0-0.065-0.05534.7790.0010.0010.0000.0000.0000.000
154C227TRP00.030-0.00334.527-0.003-0.0030.0000.0000.0000.000
155C228TYR00.0780.03824.988-0.001-0.0010.0000.0000.0000.000
156C229ILE00.0070.01330.143-0.005-0.0050.0000.0000.0000.000
157C230GLN0-0.004-0.02331.844-0.003-0.0030.0000.0000.0000.000
158C231ASP-1-0.793-0.89130.636-0.068-0.0680.0000.0000.0000.000
159C232LEU0-0.021-0.01025.126-0.005-0.0050.0000.0000.0000.000
160C233CYS0-0.037-0.01328.186-0.005-0.0050.0000.0000.0000.000
161C234GLU-1-0.957-0.97430.639-0.069-0.0690.0000.0000.0000.000
162C235MET0-0.049-0.03126.350-0.003-0.0030.0000.0000.0000.000
163C236LEU00.000-0.00424.707-0.006-0.0060.0000.0000.0000.000
164C237GLY0-0.023-0.00927.348-0.003-0.0030.0000.0000.0000.000
165C238LYS10.9200.96629.3640.0770.0770.0000.0000.0000.000
166C239TYR00.029-0.00224.3800.0020.0020.0000.0000.0000.000
167C240GLY00.0300.03323.957-0.011-0.0110.0000.0000.0000.000
168C241SER00.0020.00223.152-0.010-0.0100.0000.0000.0000.000
169C242SER0-0.022-0.02822.902-0.004-0.0040.0000.0000.0000.000
170C243LEU0-0.010-0.01820.175-0.012-0.0120.0000.0000.0000.000
171C244GLU-1-0.781-0.84113.846-0.266-0.2660.0000.0000.0000.000
172C245PHE00.042-0.00917.2160.0160.0160.0000.0000.0000.000
173C246THR0-0.034-0.04814.4410.0140.0140.0000.0000.0000.000
174C247GLU-1-0.829-0.90317.067-0.201-0.2010.0000.0000.0000.000
175C248LEU0-0.033-0.01018.6240.0190.0190.0000.0000.0000.000
176C249LEU00.008-0.01619.0230.0150.0150.0000.0000.0000.000
177C250THR0-0.025-0.01819.1030.0120.0120.0000.0000.0000.000
178C251LEU0-0.046-0.02521.7720.0130.0130.0000.0000.0000.000
179C252VAL0-0.032-0.00524.7130.0100.0100.0000.0000.0000.000
180C253ASN00.0250.01122.5210.0110.0110.0000.0000.0000.000
181C254ARG10.9821.00225.0340.1020.1020.0000.0000.0000.000
182C255LYS10.8860.94527.8500.0780.0780.0000.0000.0000.000
183C256VAL00.007-0.01129.9020.0050.0050.0000.0000.0000.000
184C257GLU-1-0.977-0.96929.722-0.061-0.0610.0000.0000.0000.000
185C258GLN0-0.041-0.02931.7060.0020.0020.0000.0000.0000.000
186C259ARG10.7920.91134.0700.0610.0610.0000.0000.0000.000
187C260ARG10.9530.98935.7180.0490.0490.0000.0000.0000.000
188C275VAL0-0.015-0.02327.1640.0010.0010.0000.0000.0000.000
189C276PRO0-0.0260.00626.4770.0000.0000.0000.0000.0000.000
190C277CYS00.0110.00221.439-0.003-0.0030.0000.0000.0000.000
191C278PHE0-0.029-0.01016.0940.0020.0020.0000.0000.0000.000
192C279ALA00.0370.00317.678-0.003-0.0030.0000.0000.0000.000
193C280SER00.008-0.00212.4090.0050.0050.0000.0000.0000.000
194C281MET0-0.0140.00811.7550.0010.0010.0000.0000.0000.000
195C282LEU0-0.033-0.00910.799-0.006-0.0060.0000.0000.0000.000
196C283THR0-0.031-0.0265.975-0.032-0.0320.0000.0000.0000.000
197C284LYS10.9130.9735.7520.2540.2540.0000.0000.0000.000
198C285LYS10.8820.9808.2270.6160.6160.0000.0000.0000.000
199C286LEU0-0.022-0.01711.3780.0140.0140.0000.0000.0000.000
200C287HIS0-0.015-0.00114.627-0.018-0.0180.0000.0000.0000.000
201C288PHE0-0.027-0.02117.8400.0030.0030.0000.0000.0000.000
202C289PHE0-0.0030.01217.3140.0090.0090.0000.0000.0000.000
203C290PRO00.0230.00822.3230.0010.0010.0000.0000.0000.000
204C291LYS10.7900.90022.3650.1190.1190.0000.0000.0000.000
205C292SER00.0120.01724.9770.0090.0090.0000.0000.0000.000