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: JL1M9

Calculation Name: 3V6M-I-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: I

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2527086.138433
FMO2-HF: Nuclear repulsion 2443114.733278
FMO2-HF: Total energy -83971.405155
FMO2-MP2: Total energy -84211.299782


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(I:31:PHE)


Summations of interaction energy for fragment #1(I: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.
1.774.15-0.018-0.964-1.3980.004
Interaction energy analysis for fragmet #1(I:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.007
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].
3I33PRO00.0220.0153.8700.2182.481-0.017-0.960-1.2860.004
4I34ALA0-0.034-0.0275.3510.3530.470-0.001-0.004-0.1120.000
5I35GLU-1-0.803-0.8715.5230.9570.9570.0000.0000.0000.000
6I36LYS10.8470.9187.6900.4390.4390.0000.0000.0000.000
7I37TYR00.006-0.02210.6290.0660.0660.0000.0000.0000.000
8I38LYS10.8090.89412.379-0.103-0.1030.0000.0000.0000.000
9I39MET0-0.010-0.00314.8930.0090.0090.0000.0000.0000.000
10I40ASP-1-0.816-0.90017.3500.0220.0220.0000.0000.0000.000
11I41HIS0-0.042-0.00616.9450.0330.0330.0000.0000.0000.000
12I42ARG10.8940.93621.687-0.042-0.0420.0000.0000.0000.000
13I43ARG10.7730.84524.732-0.036-0.0360.0000.0000.0000.000
14I44ARG10.8370.91121.4080.0640.0640.0000.0000.0000.000
15I45GLY00.0580.01622.2090.0040.0040.0000.0000.0000.000
16I46ILE0-0.040-0.01124.397-0.006-0.0060.0000.0000.0000.000
17I47ALA00.0100.00325.561-0.003-0.0030.0000.0000.0000.000
18I48LEU00.0080.01027.7120.0010.0010.0000.0000.0000.000
19I49ILE0-0.014-0.01529.277-0.006-0.0060.0000.0000.0000.000
20I50PHE00.0290.01830.4770.0030.0030.0000.0000.0000.000
21I51ASN00.0150.00833.783-0.007-0.0070.0000.0000.0000.000
22I52HIS00.0200.00536.5210.0010.0010.0000.0000.0000.000
23I53GLU-1-0.739-0.86639.298-0.031-0.0310.0000.0000.0000.000
24I54ARG10.8760.93741.9980.0120.0120.0000.0000.0000.000
25I55PHE00.005-0.00339.3040.0000.0000.0000.0000.0000.000
26I56PHE0-0.008-0.00944.8040.0000.0000.0000.0000.0000.000
27I57TRP00.0590.01147.2770.0000.0000.0000.0000.0000.000
28I58HIS00.0200.01049.626-0.001-0.0010.0000.0000.0000.000
29I59LEU0-0.030-0.00142.7340.0000.0000.0000.0000.0000.000
30I60THR0-0.061-0.02845.728-0.001-0.0010.0000.0000.0000.000
31I61LEU0-0.0090.01241.093-0.002-0.0020.0000.0000.0000.000
32I62PRO0-0.0150.00043.3590.0010.0010.0000.0000.0000.000
33I63GLU-1-0.879-0.95143.655-0.020-0.0200.0000.0000.0000.000
34I64ARG10.7840.90735.2700.0310.0310.0000.0000.0000.000
35I65ARG10.9020.94241.2570.0300.0300.0000.0000.0000.000
36I66GLY0-0.016-0.01441.326-0.002-0.0020.0000.0000.0000.000
37I67THR0-0.009-0.00237.172-0.003-0.0030.0000.0000.0000.000
38I68CYS0-0.029-0.01237.7090.0000.0000.0000.0000.0000.000
39I69ALA00.0140.01738.963-0.001-0.0010.0000.0000.0000.000
40I70ASP-1-0.780-0.86734.420-0.055-0.0550.0000.0000.0000.000
41I71ARG10.8100.85034.2470.0240.0240.0000.0000.0000.000
42I72ASP-1-0.801-0.84734.704-0.031-0.0310.0000.0000.0000.000
43I73ASN0-0.017-0.00534.674-0.002-0.0020.0000.0000.0000.000
44I74LEU00.0500.00728.879-0.004-0.0040.0000.0000.0000.000
45I75THR0-0.009-0.02431.1120.0000.0000.0000.0000.0000.000
46I76ARG10.8610.93832.8900.0580.0580.0000.0000.0000.000
47I77ARG10.8200.92729.0940.0730.0730.0000.0000.0000.000
48I78PHE00.0270.00524.431-0.005-0.0050.0000.0000.0000.000
49I79SER00.001-0.01528.6510.0030.0030.0000.0000.0000.000
50I80ASP-1-0.860-0.92530.158-0.060-0.0600.0000.0000.0000.000
51I81LEU0-0.047-0.01024.375-0.006-0.0060.0000.0000.0000.000
52I82GLY00.0010.00225.637-0.001-0.0010.0000.0000.0000.000
53I83PHE0-0.036-0.03022.2290.0070.0070.0000.0000.0000.000
54I84GLU-1-0.834-0.90227.6310.0090.0090.0000.0000.0000.000
55I85VAL0-0.014-0.01930.0450.0030.0030.0000.0000.0000.000
56I86LYS10.8430.92431.426-0.003-0.0030.0000.0000.0000.000
57I87CYS0-0.0200.00133.157-0.001-0.0010.0000.0000.0000.000
58I88PHE00.0220.00134.0350.0030.0030.0000.0000.0000.000
59I89ASN00.0290.01937.233-0.004-0.0040.0000.0000.0000.000
60I90ASP-1-0.829-0.93639.993-0.015-0.0150.0000.0000.0000.000
61I91LEU0-0.0360.01536.9800.0020.0020.0000.0000.0000.000
62I92LYS10.9230.94240.157-0.002-0.0020.0000.0000.0000.000
63I93ALA00.016-0.00838.3120.0010.0010.0000.0000.0000.000
64I94GLU-1-0.908-0.95437.7580.0120.0120.0000.0000.0000.000
65I95GLU-1-0.804-0.88838.5310.0020.0020.0000.0000.0000.000
66I96LEU0-0.013-0.00632.9810.0010.0010.0000.0000.0000.000
67I97LEU00.0320.00833.1270.0010.0010.0000.0000.0000.000
68I98LEU00.0130.01433.8890.0030.0030.0000.0000.0000.000
69I99LYS10.7920.88134.502-0.009-0.0090.0000.0000.0000.000
70I100ILE00.0100.00427.9120.0010.0010.0000.0000.0000.000
71I101HIS0-0.014-0.01429.5640.0060.0060.0000.0000.0000.000
72I102GLU-1-0.807-0.85030.4060.0210.0210.0000.0000.0000.000
73I103VAL00.004-0.00927.2110.0040.0040.0000.0000.0000.000
74I104SER0-0.078-0.04026.0160.0030.0030.0000.0000.0000.000
75I105THR0-0.020-0.02126.1640.0080.0080.0000.0000.0000.000
76I106VAL0-0.0250.00727.7800.0050.0050.0000.0000.0000.000
77I107SER0-0.020-0.00925.8890.0060.0060.0000.0000.0000.000
78I108HIS00.0500.00722.209-0.013-0.0130.0000.0000.0000.000
79I109ALA00.0140.01421.3680.0020.0020.0000.0000.0000.000
80I110ASP-1-0.808-0.86921.3870.0510.0510.0000.0000.0000.000
81I111ALA00.0070.00022.282-0.011-0.0110.0000.0000.0000.000
82I112ASP-1-0.719-0.83918.5690.0010.0010.0000.0000.0000.000
83I113CYS0-0.087-0.03317.541-0.002-0.0020.0000.0000.0000.000
84I114PHE00.0250.01319.3620.0070.0070.0000.0000.0000.000
85I115VAL00.0040.01821.185-0.011-0.0110.0000.0000.0000.000
86I116CYS0-0.040-0.00523.9490.0090.0090.0000.0000.0000.000
87I117VAL0-0.020-0.00925.967-0.006-0.0060.0000.0000.0000.000
88I118PHE00.014-0.00427.3730.0060.0060.0000.0000.0000.000
89I119LEU0-0.022-0.00530.911-0.005-0.0050.0000.0000.0000.000
90I120SER00.034-0.00633.7710.0030.0030.0000.0000.0000.000
91I121HIS00.025-0.00135.510-0.005-0.0050.0000.0000.0000.000
92I122GLY00.011-0.00933.6940.0020.0020.0000.0000.0000.000
93I123GLU-1-0.797-0.85434.215-0.015-0.0150.0000.0000.0000.000
94I124GLY00.0420.02732.2160.0030.0030.0000.0000.0000.000
95I125ASN0-0.029-0.01829.421-0.006-0.0060.0000.0000.0000.000
96I126HIS0-0.037-0.02030.3570.0060.0060.0000.0000.0000.000
97I127ILE0-0.011-0.00631.363-0.005-0.0050.0000.0000.0000.000
98I128TYR0-0.032-0.03833.5400.0050.0050.0000.0000.0000.000
99I129ALA0-0.0050.02736.750-0.002-0.0020.0000.0000.0000.000
100I130TYR0-0.015-0.00638.563-0.001-0.0010.0000.0000.0000.000
101I131ASP-1-0.795-0.91642.026-0.002-0.0020.0000.0000.0000.000
102I132ALA00.0220.01440.9550.0010.0010.0000.0000.0000.000
103I133LYS10.8320.91636.7280.0070.0070.0000.0000.0000.000
104I134ILE00.0140.00532.5420.0030.0030.0000.0000.0000.000
105I135GLU-1-0.859-0.91230.350-0.001-0.0010.0000.0000.0000.000
106I136ILE00.0100.00625.9260.0030.0030.0000.0000.0000.000
107I137GLN00.0600.03022.4620.0040.0040.0000.0000.0000.000
108I138THR0-0.060-0.04426.2350.0060.0060.0000.0000.0000.000
109I139LEU0-0.0070.00928.0430.0040.0040.0000.0000.0000.000
110I140THR00.008-0.01122.4420.0020.0020.0000.0000.0000.000
111I141GLY00.009-0.00222.9070.0050.0050.0000.0000.0000.000
112I142LEU0-0.066-0.04423.9810.0110.0110.0000.0000.0000.000
113I143PHE00.0420.00321.3750.0070.0070.0000.0000.0000.000
114I144LYS10.8280.92418.935-0.067-0.0670.0000.0000.0000.000
115I145GLY00.0430.01517.1440.0050.0050.0000.0000.0000.000
116I146ASP-1-0.817-0.91418.1100.0980.0980.0000.0000.0000.000
117I147LYS10.8520.94021.011-0.055-0.0550.0000.0000.0000.000
118I148CYS0-0.0010.02021.637-0.005-0.0050.0000.0000.0000.000
119I149HIS00.0280.00819.802-0.002-0.0020.0000.0000.0000.000
120I150SER0-0.035-0.01719.0300.0100.0100.0000.0000.0000.000
121I151LEU00.0280.01418.269-0.002-0.0020.0000.0000.0000.000
122I152VAL00.0020.00813.878-0.016-0.0160.0000.0000.0000.000
123I153GLY00.0100.01511.4430.0230.0230.0000.0000.0000.000
124I154LYS10.7890.91012.357-0.091-0.0910.0000.0000.0000.000
125I155PRO0-0.005-0.00114.375-0.006-0.0060.0000.0000.0000.000
126I156LYS10.7860.89814.538-0.021-0.0210.0000.0000.0000.000
127I157ILE0-0.0050.00018.345-0.011-0.0110.0000.0000.0000.000
128I158PHE00.027-0.00420.2270.0120.0120.0000.0000.0000.000
129I159ILE0-0.011-0.00822.677-0.011-0.0110.0000.0000.0000.000
130I160ILE0-0.003-0.00125.3120.0080.0080.0000.0000.0000.000
131I161GLN0-0.026-0.01228.065-0.005-0.0050.0000.0000.0000.000
132I162ALA00.026-0.00131.1370.0040.0040.0000.0000.0000.000
133I163CYS0-0.020-0.00132.946-0.002-0.0020.0000.0000.0000.000
134I198TYR00.0300.02325.1270.0000.0000.0000.0000.0000.000
135I199THR0-0.024-0.02824.0090.0020.0020.0000.0000.0000.000
136I200LEU00.0330.03019.378-0.009-0.0090.0000.0000.0000.000
137I201PRO00.017-0.01616.4780.0110.0110.0000.0000.0000.000
138I202ALA00.0070.01218.4650.0050.0050.0000.0000.0000.000
139I203GLY00.012-0.00215.8100.0210.0210.0000.0000.0000.000
140I204ALA00.0290.00610.898-0.024-0.0240.0000.0000.0000.000
141I205ASP-1-0.789-0.88210.7910.0390.0390.0000.0000.0000.000
142I206PHE0-0.0160.00512.9890.0030.0030.0000.0000.0000.000
143I207LEU0-0.034-0.01715.013-0.027-0.0270.0000.0000.0000.000
144I208MET0-0.0120.02517.2060.0150.0150.0000.0000.0000.000
145I209CYS0-0.018-0.01020.164-0.020-0.0200.0000.0000.0000.000
146I210TYR00.005-0.02322.5690.0140.0140.0000.0000.0000.000
147I211SER00.0260.00125.776-0.007-0.0070.0000.0000.0000.000
148I212VAL0-0.030-0.00827.3210.0000.0000.0000.0000.0000.000
149I222THR00.0190.00940.9090.0010.0010.0000.0000.0000.000
150I223VAL00.006-0.00641.6190.0000.0000.0000.0000.0000.000
151I224ASN00.0150.00841.7160.0030.0030.0000.0000.0000.000
152I225GLY00.0300.02737.846-0.003-0.0030.0000.0000.0000.000
153I226SER0-0.059-0.06434.448-0.001-0.0010.0000.0000.0000.000
154I227TRP00.002-0.01134.100-0.003-0.0030.0000.0000.0000.000
155I228TYR00.0860.03924.6500.0010.0010.0000.0000.0000.000
156I229ILE00.0290.02529.615-0.006-0.0060.0000.0000.0000.000
157I230GLN00.0080.00031.403-0.005-0.0050.0000.0000.0000.000
158I231ASP-1-0.746-0.85729.632-0.091-0.0910.0000.0000.0000.000
159I232LEU00.0110.01024.750-0.007-0.0070.0000.0000.0000.000
160I233CYS0-0.041-0.02227.807-0.003-0.0030.0000.0000.0000.000
161I234GLU-1-0.826-0.88630.416-0.097-0.0970.0000.0000.0000.000
162I235MET0-0.022-0.01125.469-0.007-0.0070.0000.0000.0000.000
163I236LEU00.024-0.00223.896-0.007-0.0070.0000.0000.0000.000
164I237GLY0-0.042-0.02726.5750.0000.0000.0000.0000.0000.000
165I238LYS10.8200.90728.6700.1080.1080.0000.0000.0000.000
166I239TYR00.0370.00123.884-0.002-0.0020.0000.0000.0000.000
167I240GLY00.0400.02623.027-0.012-0.0120.0000.0000.0000.000
168I241SER0-0.025-0.00922.499-0.006-0.0060.0000.0000.0000.000
169I242SER0-0.017-0.02221.990-0.004-0.0040.0000.0000.0000.000
170I243LEU00.0160.01119.787-0.019-0.0190.0000.0000.0000.000
171I244GLU-1-0.796-0.86412.966-0.279-0.2790.0000.0000.0000.000
172I245PHE00.027-0.00916.6390.0120.0120.0000.0000.0000.000
173I246THR0-0.007-0.03113.7590.0070.0070.0000.0000.0000.000
174I247GLU-1-0.831-0.89816.673-0.298-0.2980.0000.0000.0000.000
175I248LEU0-0.031-0.01118.2880.0190.0190.0000.0000.0000.000
176I249LEU00.003-0.01018.7600.0150.0150.0000.0000.0000.000
177I250THR0-0.031-0.02618.7520.0100.0100.0000.0000.0000.000
178I251LEU0-0.050-0.02321.4200.0100.0100.0000.0000.0000.000
179I252VAL0-0.038-0.01524.2830.0110.0110.0000.0000.0000.000
180I253ASN00.0210.00221.7250.0180.0180.0000.0000.0000.000
181I254ARG10.9811.00524.8240.1650.1650.0000.0000.0000.000
182I255LYS10.7590.85927.5970.1070.1070.0000.0000.0000.000
183I256VAL0-0.011-0.01129.3540.0080.0080.0000.0000.0000.000
184I257GLU-1-0.946-0.97028.753-0.119-0.1190.0000.0000.0000.000
185I258GLN0-0.048-0.02531.048-0.003-0.0030.0000.0000.0000.000
186I259ARG10.7850.90933.6140.0810.0810.0000.0000.0000.000
187I275VAL0-0.008-0.01426.7220.0020.0020.0000.0000.0000.000
188I276PRO0-0.0310.00826.3470.0020.0020.0000.0000.0000.000
189I277CYS0-0.013-0.01422.324-0.013-0.0130.0000.0000.0000.000
190I278PHE0-0.009-0.01215.9070.0090.0090.0000.0000.0000.000
191I279ALA00.0250.01517.260-0.011-0.0110.0000.0000.0000.000
192I280SER00.000-0.00912.4180.0230.0230.0000.0000.0000.000
193I281MET00.0040.00711.4850.0000.0000.0000.0000.0000.000
194I282LEU0-0.043-0.00810.6930.0240.0240.0000.0000.0000.000
195I283THR0-0.020-0.0176.223-0.058-0.0580.0000.0000.0000.000
196I284LYS10.7810.8865.701-0.532-0.5320.0000.0000.0000.000
197I285LYS10.8670.9288.0630.6800.6800.0000.0000.0000.000
198I286LEU0-0.017-0.01710.8890.0570.0570.0000.0000.0000.000
199I287HIS00.0500.03214.429-0.061-0.0610.0000.0000.0000.000
200I288PHE0-0.010-0.01317.7280.0200.0200.0000.0000.0000.000
201I289PHE00.0190.01516.4640.0070.0070.0000.0000.0000.000
202I290PRO00.0000.00322.0140.0140.0140.0000.0000.0000.000
203I291LYS10.8040.90121.9170.0120.0120.0000.0000.0000.000
204I292SER00.0040.01024.4160.0010.0010.0000.0000.0000.000