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: 85LJY

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2515406.044305
FMO2-HF: Nuclear repulsion 2431436.369226
FMO2-HF: Total energy -83969.675079
FMO2-MP2: Total energy -84209.718596


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.
-2.5290.134-0.028-0.828-1.8070.001
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 : -0.026 / q_NPA : -0.031
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].
3I33PRO00.0330.0373.808-1.5420.713-0.026-0.812-1.4180.001
4I34ALA0-0.059-0.0735.726-0.316-0.189-0.001-0.007-0.1190.000
5I35GLU-1-0.925-0.9594.706-0.2010.080-0.001-0.009-0.2700.000
6I36LYS10.9480.9717.506-0.293-0.2930.0000.0000.0000.000
7I37TYR0-0.013-0.0509.9880.0290.0290.0000.0000.0000.000
8I38LYS10.7970.88611.479-0.193-0.1930.0000.0000.0000.000
9I39MET0-0.0200.00214.082-0.036-0.0360.0000.0000.0000.000
10I40ASP-1-0.855-0.91917.2870.1820.1820.0000.0000.0000.000
11I41HIS0-0.0240.00116.5030.0180.0180.0000.0000.0000.000
12I42ARG10.9150.95321.395-0.053-0.0530.0000.0000.0000.000
13I43ARG10.8420.89824.435-0.030-0.0300.0000.0000.0000.000
14I44ARG10.8700.92520.345-0.016-0.0160.0000.0000.0000.000
15I45GLY00.0300.00622.055-0.006-0.0060.0000.0000.0000.000
16I46ILE0-0.015-0.00624.4400.0010.0010.0000.0000.0000.000
17I47ALA0-0.0040.00025.277-0.006-0.0060.0000.0000.0000.000
18I48LEU00.005-0.00127.3150.0040.0040.0000.0000.0000.000
19I49ILE00.0040.00129.028-0.006-0.0060.0000.0000.0000.000
20I50PHE0-0.003-0.00630.3830.0040.0040.0000.0000.0000.000
21I51ASN00.011-0.00333.952-0.005-0.0050.0000.0000.0000.000
22I52HIS00.0080.01336.2150.0020.0020.0000.0000.0000.000
23I53GLU-1-0.923-0.96639.083-0.021-0.0210.0000.0000.0000.000
24I54ARG10.9360.96742.1460.0160.0160.0000.0000.0000.000
25I55PHE0-0.030-0.02439.543-0.001-0.0010.0000.0000.0000.000
26I56PHE0-0.0210.00045.1440.0010.0010.0000.0000.0000.000
27I57TRP00.0750.01047.431-0.001-0.0010.0000.0000.0000.000
28I58HIS0-0.006-0.00550.166-0.001-0.0010.0000.0000.0000.000
29I59LEU0-0.0280.00743.018-0.001-0.0010.0000.0000.0000.000
30I60THR0-0.057-0.01846.209-0.001-0.0010.0000.0000.0000.000
31I61LEU0-0.0180.00341.511-0.001-0.0010.0000.0000.0000.000
32I62PRO0-0.015-0.00143.5090.0010.0010.0000.0000.0000.000
33I63GLU-1-0.875-0.95043.990-0.020-0.0200.0000.0000.0000.000
34I64ARG10.8260.92036.0560.0340.0340.0000.0000.0000.000
35I65ARG10.9780.97842.0710.0210.0210.0000.0000.0000.000
36I66GLY00.0120.00041.605-0.001-0.0010.0000.0000.0000.000
37I67THR00.0540.03337.549-0.002-0.0020.0000.0000.0000.000
38I68CYS0-0.010-0.00237.7900.0000.0000.0000.0000.0000.000
39I69ALA00.0390.02639.1000.0010.0010.0000.0000.0000.000
40I70ASP-1-0.774-0.86234.578-0.036-0.0360.0000.0000.0000.000
41I71ARG10.8310.90834.4240.0160.0160.0000.0000.0000.000
42I72ASP-1-0.831-0.90734.754-0.014-0.0140.0000.0000.0000.000
43I73ASN0-0.035-0.01934.4010.0040.0040.0000.0000.0000.000
44I74LEU00.0490.00128.8290.0000.0000.0000.0000.0000.000
45I75THR00.012-0.00530.6410.0010.0010.0000.0000.0000.000
46I76ARG10.8750.94032.3640.0190.0190.0000.0000.0000.000
47I77ARG10.8900.95628.7660.0230.0230.0000.0000.0000.000
48I78PHE00.0590.01923.9180.0010.0010.0000.0000.0000.000
49I79SER00.0150.01127.8350.0040.0040.0000.0000.0000.000
50I80ASP-1-0.923-0.94229.5600.0020.0020.0000.0000.0000.000
51I81LEU0-0.064-0.02423.8340.0030.0030.0000.0000.0000.000
52I82GLY0-0.030-0.01924.8280.0030.0030.0000.0000.0000.000
53I83PHE0-0.054-0.04421.7260.0030.0030.0000.0000.0000.000
54I84GLU-1-0.912-0.95027.2480.0110.0110.0000.0000.0000.000
55I85VAL0-0.028-0.01829.451-0.004-0.0040.0000.0000.0000.000
56I86LYS10.9250.96931.2760.0020.0020.0000.0000.0000.000
57I87CYS0-0.033-0.01032.886-0.004-0.0040.0000.0000.0000.000
58I88PHE00.0160.00033.5700.0030.0030.0000.0000.0000.000
59I89ASN00.0290.02037.195-0.004-0.0040.0000.0000.0000.000
60I90ASP-1-0.795-0.90339.738-0.019-0.0190.0000.0000.0000.000
61I91LEU0-0.0490.00436.6860.0010.0010.0000.0000.0000.000
62I92LYS10.9940.97840.0380.0110.0110.0000.0000.0000.000
63I93ALA00.010-0.00638.4740.0000.0000.0000.0000.0000.000
64I94GLU-1-0.918-0.95638.022-0.013-0.0130.0000.0000.0000.000
65I95GLU-1-0.865-0.94338.545-0.012-0.0120.0000.0000.0000.000
66I96LEU0-0.011-0.00532.9410.0000.0000.0000.0000.0000.000
67I97LEU00.0300.00433.288-0.001-0.0010.0000.0000.0000.000
68I98LEU00.0250.00434.0650.0010.0010.0000.0000.0000.000
69I99LYS10.8190.91534.3230.0090.0090.0000.0000.0000.000
70I100ILE0-0.023-0.01128.0920.0010.0010.0000.0000.0000.000
71I101HIS0-0.002-0.01429.795-0.001-0.0010.0000.0000.0000.000
72I102GLU-1-0.824-0.87930.867-0.002-0.0020.0000.0000.0000.000
73I103VAL0-0.004-0.01527.3660.0020.0020.0000.0000.0000.000
74I104SER0-0.086-0.04026.2980.0010.0010.0000.0000.0000.000
75I105THR0-0.039-0.01626.3170.0020.0020.0000.0000.0000.000
76I106VAL0-0.0070.02127.8250.0050.0050.0000.0000.0000.000
77I107SER0-0.020-0.01726.156-0.001-0.0010.0000.0000.0000.000
78I108HIS00.011-0.01222.227-0.001-0.0010.0000.0000.0000.000
79I109ALA00.0190.00521.6190.0010.0010.0000.0000.0000.000
80I110ASP-1-0.809-0.86721.4580.0510.0510.0000.0000.0000.000
81I111ALA0-0.022-0.02022.1220.0020.0020.0000.0000.0000.000
82I112ASP-1-0.714-0.85318.3590.0500.0500.0000.0000.0000.000
83I113CYS0-0.063-0.01717.340-0.015-0.0150.0000.0000.0000.000
84I114PHE00.0170.00619.1690.0130.0130.0000.0000.0000.000
85I115VAL00.0060.01721.040-0.013-0.0130.0000.0000.0000.000
86I116CYS0-0.033-0.00323.6190.0100.0100.0000.0000.0000.000
87I117VAL0-0.010-0.01025.869-0.007-0.0070.0000.0000.0000.000
88I118PHE0-0.005-0.00527.4460.0050.0050.0000.0000.0000.000
89I119LEU0-0.020-0.01331.089-0.004-0.0040.0000.0000.0000.000
90I120SER00.023-0.01133.9540.0040.0040.0000.0000.0000.000
91I121HIS00.000-0.00235.653-0.005-0.0050.0000.0000.0000.000
92I122GLY00.020-0.01334.0630.0000.0000.0000.0000.0000.000
93I123GLU-1-0.836-0.88535.095-0.038-0.0380.0000.0000.0000.000
94I124GLY00.0180.00333.3390.0010.0010.0000.0000.0000.000
95I125ASN0-0.0020.00529.769-0.002-0.0020.0000.0000.0000.000
96I126HIS0-0.007-0.01530.8450.0020.0020.0000.0000.0000.000
97I127ILE0-0.0080.00731.480-0.002-0.0020.0000.0000.0000.000
98I128TYR0-0.026-0.01833.9840.0030.0030.0000.0000.0000.000
99I129ALA0-0.0150.00737.2920.0000.0000.0000.0000.0000.000
100I130TYR00.0040.00438.6130.0000.0000.0000.0000.0000.000
101I131ASP-1-0.796-0.92442.170-0.020-0.0200.0000.0000.0000.000
102I132ALA00.0100.00840.9790.0000.0000.0000.0000.0000.000
103I133LYS10.8710.95837.1740.0360.0360.0000.0000.0000.000
104I134ILE00.0150.00232.6020.0020.0020.0000.0000.0000.000
105I135GLU-1-0.914-0.95230.933-0.048-0.0480.0000.0000.0000.000
106I136ILE00.0280.00226.3090.0010.0010.0000.0000.0000.000
107I137GLN00.0090.00623.552-0.001-0.0010.0000.0000.0000.000
108I138THR0-0.045-0.02526.6300.0010.0010.0000.0000.0000.000
109I139LEU00.0150.01528.2800.0030.0030.0000.0000.0000.000
110I140THR00.021-0.00222.7000.0020.0020.0000.0000.0000.000
111I141GLY00.003-0.00523.192-0.003-0.0030.0000.0000.0000.000
112I142LEU0-0.056-0.02824.2300.0030.0030.0000.0000.0000.000
113I143PHE00.0340.00121.5080.0050.0050.0000.0000.0000.000
114I144LYS10.9120.97319.3330.0640.0640.0000.0000.0000.000
115I145GLY00.0490.01118.0300.0090.0090.0000.0000.0000.000
116I146ASP-1-0.917-0.96218.911-0.032-0.0320.0000.0000.0000.000
117I147LYS10.8840.94021.8980.0340.0340.0000.0000.0000.000
118I148CYS0-0.0010.02621.9430.0050.0050.0000.0000.0000.000
119I149HIS00.0330.01620.533-0.001-0.0010.0000.0000.0000.000
120I150SER0-0.009-0.00819.5750.0000.0000.0000.0000.0000.000
121I151LEU00.0490.01318.7820.0040.0040.0000.0000.0000.000
122I152VAL0-0.038-0.01114.384-0.024-0.0240.0000.0000.0000.000
123I153GLY0-0.0080.00611.9020.0220.0220.0000.0000.0000.000
124I154LYS10.7650.89912.320-0.036-0.0360.0000.0000.0000.000
125I155PRO0-0.010-0.00313.571-0.014-0.0140.0000.0000.0000.000
126I156LYS10.8700.95615.3710.1300.1300.0000.0000.0000.000
127I157ILE00.0040.00517.872-0.017-0.0170.0000.0000.0000.000
128I158PHE00.017-0.00420.1680.0150.0150.0000.0000.0000.000
129I159ILE0-0.0030.00223.075-0.009-0.0090.0000.0000.0000.000
130I160ILE00.006-0.00625.5090.0080.0080.0000.0000.0000.000
131I161GLN0-0.0100.04628.140-0.007-0.0070.0000.0000.0000.000
132I162ALA00.021-0.01231.0920.0040.0040.0000.0000.0000.000
133I163CYS0-0.0020.02533.361-0.002-0.0020.0000.0000.0000.000
134I198TYR00.0210.00025.7580.0020.0020.0000.0000.0000.000
135I199THR0-0.003-0.00424.4150.0020.0020.0000.0000.0000.000
136I200LEU0-0.0040.01519.635-0.005-0.0050.0000.0000.0000.000
137I201PRO00.020-0.01016.8250.0120.0120.0000.0000.0000.000
138I202ALA00.0270.01419.102-0.002-0.0020.0000.0000.0000.000
139I203GLY0-0.011-0.01516.5060.0110.0110.0000.0000.0000.000
140I204ALA00.0280.00611.276-0.011-0.0110.0000.0000.0000.000
141I205ASP-1-0.817-0.87110.522-0.268-0.2680.0000.0000.0000.000
142I206PHE0-0.0050.00612.9670.0380.0380.0000.0000.0000.000
143I207LEU0-0.031-0.01915.407-0.030-0.0300.0000.0000.0000.000
144I208MET0-0.0210.00917.4430.0220.0220.0000.0000.0000.000
145I209CYS0-0.015-0.00520.512-0.012-0.0120.0000.0000.0000.000
146I210TYR0-0.002-0.01822.2320.0140.0140.0000.0000.0000.000
147I211SER0-0.034-0.07225.778-0.003-0.0030.0000.0000.0000.000
148I212VAL00.0060.01727.2710.0020.0020.0000.0000.0000.000
149I222THR00.0410.01141.2440.0010.0010.0000.0000.0000.000
150I223VAL00.016-0.00541.6650.0000.0000.0000.0000.0000.000
151I224ASN0-0.020-0.01141.5070.0020.0020.0000.0000.0000.000
152I225GLY00.0400.04837.8010.0000.0000.0000.0000.0000.000
153I226SER0-0.059-0.06834.579-0.002-0.0020.0000.0000.0000.000
154I227TRP00.0330.00233.9570.0000.0000.0000.0000.0000.000
155I228TYR00.0690.03524.7270.0020.0020.0000.0000.0000.000
156I229ILE00.0160.01729.990-0.002-0.0020.0000.0000.0000.000
157I230GLN0-0.026-0.04131.5850.0000.0000.0000.0000.0000.000
158I231ASP-1-0.786-0.89129.966-0.048-0.0480.0000.0000.0000.000
159I232LEU0-0.002-0.00324.882-0.001-0.0010.0000.0000.0000.000
160I233CYS0-0.032-0.01227.7890.0020.0020.0000.0000.0000.000
161I234GLU-1-0.965-0.97430.193-0.032-0.0320.0000.0000.0000.000
162I235MET0-0.046-0.02725.7540.0020.0020.0000.0000.0000.000
163I236LEU0-0.001-0.00424.2080.0020.0020.0000.0000.0000.000
164I237GLY0-0.030-0.01526.7160.0050.0050.0000.0000.0000.000
165I238LYS10.9140.96828.7370.0340.0340.0000.0000.0000.000
166I239TYR00.037-0.00123.8150.0040.0040.0000.0000.0000.000
167I240GLY00.0440.03623.243-0.002-0.0020.0000.0000.0000.000
168I241SER0-0.011-0.00322.209-0.002-0.0020.0000.0000.0000.000
169I242SER0-0.034-0.03421.9890.0100.0100.0000.0000.0000.000
170I243LEU0-0.021-0.02219.6580.0050.0050.0000.0000.0000.000
171I244GLU-1-0.767-0.82313.245-0.208-0.2080.0000.0000.0000.000
172I245PHE00.029-0.01216.549-0.005-0.0050.0000.0000.0000.000
173I246THR0-0.035-0.05814.003-0.004-0.0040.0000.0000.0000.000
174I247GLU-1-0.833-0.91216.615-0.113-0.1130.0000.0000.0000.000
175I248LEU0-0.046-0.01818.0760.0130.0130.0000.0000.0000.000
176I249LEU00.011-0.01018.7060.0080.0080.0000.0000.0000.000
177I250THR0-0.027-0.01118.5050.0010.0010.0000.0000.0000.000
178I251LEU0-0.051-0.03021.1900.0070.0070.0000.0000.0000.000
179I252VAL0-0.0250.00024.1320.0070.0070.0000.0000.0000.000
180I253ASN00.0330.01521.9830.0110.0110.0000.0000.0000.000
181I254ARG10.9610.99724.5990.0880.0880.0000.0000.0000.000
182I255LYS10.9020.94627.3410.0520.0520.0000.0000.0000.000
183I256VAL00.001-0.01029.3080.0040.0040.0000.0000.0000.000
184I257GLU-1-0.994-0.98629.193-0.076-0.0760.0000.0000.0000.000
185I258GLN0-0.054-0.02631.1550.0020.0020.0000.0000.0000.000
186I259ARG10.8080.92633.5480.0470.0470.0000.0000.0000.000
187I275VAL0-0.001-0.01726.5820.0020.0020.0000.0000.0000.000
188I276PRO0-0.045-0.00126.106-0.002-0.0020.0000.0000.0000.000
189I277CYS00.011-0.01122.797-0.011-0.0110.0000.0000.0000.000
190I278PHE0-0.0090.00215.5710.0060.0060.0000.0000.0000.000
191I279ALA00.0240.01417.542-0.011-0.0110.0000.0000.0000.000
192I280SER00.013-0.00412.3150.0140.0140.0000.0000.0000.000
193I281MET0-0.0190.00212.270-0.011-0.0110.0000.0000.0000.000
194I282LEU0-0.034-0.00710.903-0.003-0.0030.0000.0000.0000.000
195I283THR0-0.032-0.0215.941-0.063-0.0630.0000.0000.0000.000
196I284LYS10.9090.9715.388-0.132-0.1320.0000.0000.0000.000
197I285LYS10.8770.9757.5100.3270.3270.0000.0000.0000.000
198I286LEU0-0.017-0.01610.4830.0510.0510.0000.0000.0000.000
199I287HIS0-0.014-0.00413.787-0.007-0.0070.0000.0000.0000.000
200I288PHE00.004-0.01016.7720.0090.0090.0000.0000.0000.000
201I289PHE0-0.0140.01016.9210.0040.0040.0000.0000.0000.000
202I290PRO00.0250.01421.4150.0010.0010.0000.0000.0000.000
203I291LYS10.7990.89921.409-0.051-0.0510.0000.0000.0000.000
204I292SER00.0090.01524.802-0.005-0.0050.0000.0000.0000.000