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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: 492NN

Calculation Name: 3V6M-A-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: A

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 -2544308.43013
FMO2-HF: Nuclear repulsion 2459906.852832
FMO2-HF: Total energy -84401.577297
FMO2-MP2: Total energy -84642.719379


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(A:31:PHE)


Summations of interaction energy for fragment #1(A: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.
2.5694.822-0.018-0.933-1.3010.004
Interaction energy analysis for fragmet #1(A:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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].
3A33PRO00.0240.0183.8660.2602.405-0.017-0.930-1.1980.004
4A34ALA0-0.035-0.0285.2670.6110.719-0.001-0.003-0.1030.000
5A35GLU-1-0.797-0.8675.5621.4771.4770.0000.0000.0000.000
6A36LYS10.8460.9177.7290.4760.4760.0000.0000.0000.000
7A37TYR00.000-0.02910.5740.0960.0960.0000.0000.0000.000
8A38LYS10.8260.90512.764-0.159-0.1590.0000.0000.0000.000
9A39MET0-0.023-0.01114.8330.0050.0050.0000.0000.0000.000
10A40ASP-1-0.823-0.89317.4220.0490.0490.0000.0000.0000.000
11A41HIS0-0.0160.00118.1160.0250.0250.0000.0000.0000.000
12A42ARG10.8750.91621.741-0.064-0.0640.0000.0000.0000.000
13A43ARG10.8080.89025.022-0.050-0.0500.0000.0000.0000.000
14A44ARG10.8520.91921.5690.0560.0560.0000.0000.0000.000
15A45GLY00.0440.00722.5230.0070.0070.0000.0000.0000.000
16A46ILE0-0.042-0.01024.642-0.006-0.0060.0000.0000.0000.000
17A47ALA00.0170.00625.684-0.002-0.0020.0000.0000.0000.000
18A48LEU00.0050.00827.7210.0000.0000.0000.0000.0000.000
19A49ILE0-0.012-0.01229.107-0.006-0.0060.0000.0000.0000.000
20A50PHE00.0290.01830.3200.0030.0030.0000.0000.0000.000
21A51ASN00.0150.00333.717-0.007-0.0070.0000.0000.0000.000
22A52HIS00.0430.02335.6690.0030.0030.0000.0000.0000.000
23A53GLU-1-0.787-0.89139.103-0.030-0.0300.0000.0000.0000.000
24A54ARG10.8160.89441.9270.0130.0130.0000.0000.0000.000
25A55PHE00.0130.00739.2980.0000.0000.0000.0000.0000.000
26A56PHE00.0360.01344.7410.0000.0000.0000.0000.0000.000
27A57TRP00.016-0.00747.151-0.001-0.0010.0000.0000.0000.000
28A58HIS00.0280.01349.242-0.002-0.0020.0000.0000.0000.000
29A59LEU0-0.0270.00242.4400.0000.0000.0000.0000.0000.000
30A60THR0-0.062-0.02845.492-0.001-0.0010.0000.0000.0000.000
31A61LEU0-0.0120.01140.920-0.002-0.0020.0000.0000.0000.000
32A62PRO0-0.0080.00343.2900.0010.0010.0000.0000.0000.000
33A63GLU-1-0.832-0.90743.651-0.019-0.0190.0000.0000.0000.000
34A64ARG10.8080.91335.8130.0300.0300.0000.0000.0000.000
35A65ARG10.9070.94541.2980.0290.0290.0000.0000.0000.000
36A66GLY00.0160.00241.218-0.002-0.0020.0000.0000.0000.000
37A67THR0-0.014-0.00837.205-0.003-0.0030.0000.0000.0000.000
38A68CYS0-0.020-0.00537.7280.0000.0000.0000.0000.0000.000
39A69ALA00.0160.01638.9910.0000.0000.0000.0000.0000.000
40A70ASP-1-0.775-0.85934.463-0.054-0.0540.0000.0000.0000.000
41A71ARG10.8350.86834.3430.0220.0220.0000.0000.0000.000
42A72ASP-1-0.816-0.86334.715-0.029-0.0290.0000.0000.0000.000
43A73ASN0-0.031-0.02234.3260.0000.0000.0000.0000.0000.000
44A74LEU00.0360.00728.918-0.004-0.0040.0000.0000.0000.000
45A75THR0-0.010-0.02531.0990.0010.0010.0000.0000.0000.000
46A76ARG10.8800.95833.0830.0480.0480.0000.0000.0000.000
47A77ARG10.8610.93229.1880.0720.0720.0000.0000.0000.000
48A78PHE00.007-0.00224.298-0.005-0.0050.0000.0000.0000.000
49A79SER00.003-0.01328.6610.0050.0050.0000.0000.0000.000
50A80ASP-1-0.877-0.92730.259-0.058-0.0580.0000.0000.0000.000
51A81LEU0-0.048-0.01224.501-0.007-0.0070.0000.0000.0000.000
52A82GLY0-0.0010.00125.7890.0010.0010.0000.0000.0000.000
53A83PHE0-0.042-0.03422.2020.0090.0090.0000.0000.0000.000
54A84GLU-1-0.833-0.90027.8370.0170.0170.0000.0000.0000.000
55A85VAL0-0.010-0.01830.2320.0030.0030.0000.0000.0000.000
56A86LYS10.8290.91231.351-0.007-0.0070.0000.0000.0000.000
57A87CYS0-0.0170.00333.148-0.001-0.0010.0000.0000.0000.000
58A88PHE00.0120.00134.0980.0040.0040.0000.0000.0000.000
59A89ASN00.0300.02137.020-0.005-0.0050.0000.0000.0000.000
60A90ASP-1-0.794-0.90739.814-0.013-0.0130.0000.0000.0000.000
61A91LEU0-0.0460.00736.6670.0020.0020.0000.0000.0000.000
62A92LYS10.9500.94939.844-0.005-0.0050.0000.0000.0000.000
63A93ALA00.010-0.01237.9100.0010.0010.0000.0000.0000.000
64A94GLU-1-0.911-0.95437.4940.0150.0150.0000.0000.0000.000
65A95GLU-1-0.827-0.90038.4140.0050.0050.0000.0000.0000.000
66A96LEU0-0.023-0.01132.6650.0010.0010.0000.0000.0000.000
67A97LEU00.0270.00332.8560.0020.0020.0000.0000.0000.000
68A98LEU00.0000.00533.7800.0040.0040.0000.0000.0000.000
69A99LYS10.8340.90234.464-0.013-0.0130.0000.0000.0000.000
70A100ILE00.0000.00127.6720.0020.0020.0000.0000.0000.000
71A101HIS00.0450.02329.5790.0060.0060.0000.0000.0000.000
72A102GLU-1-0.832-0.86830.2730.0280.0280.0000.0000.0000.000
73A103VAL00.0230.00227.3850.0050.0050.0000.0000.0000.000
74A104SER0-0.063-0.03126.0730.0060.0060.0000.0000.0000.000
75A105THR0-0.052-0.04026.2240.0080.0080.0000.0000.0000.000
76A106VAL00.0010.02527.9490.0050.0050.0000.0000.0000.000
77A107SER0-0.005-0.00525.9080.0070.0070.0000.0000.0000.000
78A108HIS10.8970.93222.211-0.060-0.0600.0000.0000.0000.000
79A109ALA00.0390.02221.3530.0030.0030.0000.0000.0000.000
80A110ASP-1-0.819-0.88221.4220.0710.0710.0000.0000.0000.000
81A111ALA00.0120.00022.455-0.013-0.0130.0000.0000.0000.000
82A112ASP-1-0.705-0.83718.8510.0240.0240.0000.0000.0000.000
83A113CYS0-0.092-0.03017.8750.0030.0030.0000.0000.0000.000
84A114PHE0-0.026-0.01919.7290.0070.0070.0000.0000.0000.000
85A115VAL00.0240.03121.103-0.010-0.0100.0000.0000.0000.000
86A116CYS0-0.041-0.00723.7880.0090.0090.0000.0000.0000.000
87A117VAL0-0.015-0.00725.767-0.007-0.0070.0000.0000.0000.000
88A118PHE00.011-0.00127.1360.0070.0070.0000.0000.0000.000
89A119LEU0-0.025-0.00830.762-0.006-0.0060.0000.0000.0000.000
90A120SER00.005-0.02733.6960.0030.0030.0000.0000.0000.000
91A121HIS00.0190.00135.649-0.006-0.0060.0000.0000.0000.000
92A122GLY00.015-0.01333.6500.0020.0020.0000.0000.0000.000
93A123GLU-1-0.811-0.88034.208-0.014-0.0140.0000.0000.0000.000
94A124GLY00.0540.03832.5800.0030.0030.0000.0000.0000.000
95A125ASN0-0.043-0.02628.533-0.006-0.0060.0000.0000.0000.000
96A126HIS0-0.022-0.01729.9650.0060.0060.0000.0000.0000.000
97A127ILE0-0.034-0.01631.176-0.005-0.0050.0000.0000.0000.000
98A128TYR00.008-0.00433.2080.0040.0040.0000.0000.0000.000
99A129ALA0-0.0080.02636.470-0.002-0.0020.0000.0000.0000.000
100A130TYR00.029-0.00138.259-0.001-0.0010.0000.0000.0000.000
101A131ASP-1-0.807-0.92241.6290.0000.0000.0000.0000.0000.000
102A132ALA00.0190.01340.3350.0000.0000.0000.0000.0000.000
103A133LYS10.8010.90336.3500.0060.0060.0000.0000.0000.000
104A134ILE00.0200.00432.0150.0030.0030.0000.0000.0000.000
105A135GLU-1-0.845-0.90330.1520.0020.0020.0000.0000.0000.000
106A136ILE00.0140.00125.7560.0040.0040.0000.0000.0000.000
107A137GLN00.0220.00921.8980.0070.0070.0000.0000.0000.000
108A138THR0-0.025-0.02525.6740.0070.0070.0000.0000.0000.000
109A139LEU0-0.0120.00227.7510.0050.0050.0000.0000.0000.000
110A140THR00.000-0.01221.9960.0020.0020.0000.0000.0000.000
111A141GLY00.0300.00722.7230.0070.0070.0000.0000.0000.000
112A142LEU0-0.017-0.00623.6220.0110.0110.0000.0000.0000.000
113A143PHE00.020-0.00621.4310.0070.0070.0000.0000.0000.000
114A144LYS10.8550.93718.896-0.075-0.0750.0000.0000.0000.000
115A145GLY00.0290.00716.9080.0050.0050.0000.0000.0000.000
116A146ASP-1-0.824-0.91417.8930.1100.1100.0000.0000.0000.000
117A147LYS10.8270.91820.647-0.064-0.0640.0000.0000.0000.000
118A148CYS0-0.068-0.02821.429-0.009-0.0090.0000.0000.0000.000
119A149HIS00.0670.03119.4820.0000.0000.0000.0000.0000.000
120A150SER0-0.045-0.02118.7520.0120.0120.0000.0000.0000.000
121A151LEU00.013-0.00418.230-0.004-0.0040.0000.0000.0000.000
122A152VAL00.0170.01813.554-0.015-0.0150.0000.0000.0000.000
123A153GLY00.0060.01711.3650.0240.0240.0000.0000.0000.000
124A154LYS10.7920.91712.250-0.113-0.1130.0000.0000.0000.000
125A155PRO00.0050.00614.493-0.010-0.0100.0000.0000.0000.000
126A156LYS10.7840.89514.653-0.057-0.0570.0000.0000.0000.000
127A157ILE00.0060.00518.155-0.011-0.0110.0000.0000.0000.000
128A158PHE00.020-0.00619.9960.0120.0120.0000.0000.0000.000
129A159ILE0-0.016-0.01222.609-0.012-0.0120.0000.0000.0000.000
130A160ILE00.002-0.00125.2490.0080.0080.0000.0000.0000.000
131A161GLN0-0.031-0.01027.946-0.005-0.0050.0000.0000.0000.000
132A162ALA00.0270.00031.1230.0050.0050.0000.0000.0000.000
133A163CYS0-0.0250.00232.906-0.003-0.0030.0000.0000.0000.000
134A199THR00.0510.02623.1820.0050.0050.0000.0000.0000.000
135A200LEU0-0.009-0.00418.979-0.010-0.0100.0000.0000.0000.000
136A201PRO00.000-0.02416.1560.0120.0120.0000.0000.0000.000
137A202ALA00.0170.01918.0990.0040.0040.0000.0000.0000.000
138A203GLY00.0090.00015.3490.0200.0200.0000.0000.0000.000
139A204ALA00.0300.00610.865-0.025-0.0250.0000.0000.0000.000
140A205ASP-1-0.791-0.88310.9920.1190.1190.0000.0000.0000.000
141A206PHE0-0.0270.00012.824-0.003-0.0030.0000.0000.0000.000
142A207LEU0-0.028-0.01514.821-0.027-0.0270.0000.0000.0000.000
143A208MET0-0.0100.02717.0940.0150.0150.0000.0000.0000.000
144A209CYS0-0.017-0.00920.191-0.022-0.0220.0000.0000.0000.000
145A210TYR00.016-0.00922.4700.0150.0150.0000.0000.0000.000
146A211SER00.0240.00025.878-0.008-0.0080.0000.0000.0000.000
147A212VAL0-0.032-0.01227.040-0.002-0.0020.0000.0000.0000.000
148A222THR00.0420.00841.2260.0000.0000.0000.0000.0000.000
149A223VAL0-0.019-0.00941.7360.0000.0000.0000.0000.0000.000
150A224ASN00.0130.00741.9620.0040.0040.0000.0000.0000.000
151A225GLY00.0140.01537.994-0.003-0.0030.0000.0000.0000.000
152A226SER0-0.057-0.06134.530-0.002-0.0020.0000.0000.0000.000
153A227TRP00.008-0.01434.490-0.003-0.0030.0000.0000.0000.000
154A228TYR00.0740.03624.7730.0000.0000.0000.0000.0000.000
155A229ILE00.0270.02429.749-0.006-0.0060.0000.0000.0000.000
156A230GLN00.0080.00331.592-0.005-0.0050.0000.0000.0000.000
157A231ASP-1-0.742-0.85629.945-0.095-0.0950.0000.0000.0000.000
158A232LEU0-0.0020.00324.939-0.008-0.0080.0000.0000.0000.000
159A233CYS0-0.027-0.01628.034-0.002-0.0020.0000.0000.0000.000
160A234GLU-1-0.822-0.88230.615-0.102-0.1020.0000.0000.0000.000
161A235MET0-0.024-0.01125.699-0.008-0.0080.0000.0000.0000.000
162A236LEU00.017-0.00224.177-0.008-0.0080.0000.0000.0000.000
163A237GLY0-0.015-0.01226.9440.0000.0000.0000.0000.0000.000
164A238LYS10.8190.90428.7290.1110.1110.0000.0000.0000.000
165A239TYR00.0390.00323.883-0.003-0.0030.0000.0000.0000.000
166A240GLY00.0290.02023.370-0.013-0.0130.0000.0000.0000.000
167A241SER0-0.019-0.00722.831-0.006-0.0060.0000.0000.0000.000
168A242SER0-0.012-0.02121.965-0.004-0.0040.0000.0000.0000.000
169A243LEU00.0170.01119.688-0.021-0.0210.0000.0000.0000.000
170A244GLU-1-0.794-0.86113.268-0.292-0.2920.0000.0000.0000.000
171A245PHE00.024-0.01016.8230.0140.0140.0000.0000.0000.000
172A246THR0-0.012-0.03314.1250.0070.0070.0000.0000.0000.000
173A247GLU-1-0.829-0.89716.795-0.324-0.3240.0000.0000.0000.000
174A248LEU0-0.030-0.00918.3390.0210.0210.0000.0000.0000.000
175A249LEU00.006-0.00919.0330.0160.0160.0000.0000.0000.000
176A250THR0-0.033-0.02818.9250.0100.0100.0000.0000.0000.000
177A251LEU0-0.061-0.02521.5750.0100.0100.0000.0000.0000.000
178A252VAL0-0.031-0.01024.5450.0120.0120.0000.0000.0000.000
179A253ASN00.0230.00122.0630.0190.0190.0000.0000.0000.000
180A254ARG10.9770.99724.4920.1780.1780.0000.0000.0000.000
181A255LYS10.7770.87427.6900.1110.1110.0000.0000.0000.000
182A256VAL0-0.007-0.00929.6140.0080.0080.0000.0000.0000.000
183A257GLU-1-0.826-0.90529.700-0.108-0.1080.0000.0000.0000.000
184A258GLN0-0.045-0.01931.4880.0010.0010.0000.0000.0000.000
185A259ARG10.7910.90333.5290.0820.0820.0000.0000.0000.000
186A260ARG10.8220.91634.1550.0940.0940.0000.0000.0000.000
187A274GLN00.0200.00933.0160.0010.0010.0000.0000.0000.000
188A275VAL0-0.012-0.02427.076-0.004-0.0040.0000.0000.0000.000
189A276PRO0-0.0300.01426.5060.0030.0030.0000.0000.0000.000
190A277CYS0-0.022-0.01822.523-0.014-0.0140.0000.0000.0000.000
191A278PHE00.000-0.00816.2340.0110.0110.0000.0000.0000.000
192A279ALA00.0270.01717.408-0.013-0.0130.0000.0000.0000.000
193A280SER00.002-0.00912.4830.0280.0280.0000.0000.0000.000
194A281MET00.0090.01011.325-0.003-0.0030.0000.0000.0000.000
195A282LEU0-0.049-0.01010.5460.0360.0360.0000.0000.0000.000
196A283THR0-0.015-0.0156.322-0.058-0.0580.0000.0000.0000.000
197A284LYS10.7880.8905.531-0.824-0.8240.0000.0000.0000.000
198A285LYS10.8670.9288.0450.8450.8450.0000.0000.0000.000
199A286LEU0-0.018-0.01711.1390.0760.0760.0000.0000.0000.000
200A287HIS00.0510.03314.563-0.076-0.0760.0000.0000.0000.000
201A288PHE0-0.006-0.01417.8870.0250.0250.0000.0000.0000.000
202A289PHE00.0200.01616.4850.0080.0080.0000.0000.0000.000
203A290PRO00.0000.00521.9800.0170.0170.0000.0000.0000.000
204A291LYS10.7920.89321.974-0.003-0.0030.0000.0000.0000.000
205A292SER00.0110.01424.5250.0000.0000.0000.0000.0000.000