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: K9YR3

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 OptHSide
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 -2533960.610068
FMO2-HF: Nuclear repulsion 2449559.628287
FMO2-HF: Total energy -84400.981781
FMO2-MP2: Total energy -84642.169108


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.
2.324.649-0.026-0.998-1.3050.004
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 : -0.005 / q_NPA : -0.002
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].
3A33PRO00.0320.0253.805-0.0702.259-0.026-0.998-1.3050.004
4A34ALA0-0.054-0.0335.5400.6720.6720.0000.0000.0000.000
5A35GLU-1-0.816-0.8865.7421.0281.0280.0000.0000.0000.000
6A36LYS10.8610.9297.8850.4790.4790.0000.0000.0000.000
7A37TYR0-0.009-0.03910.7240.0750.0750.0000.0000.0000.000
8A38LYS10.8280.90012.656-0.100-0.1000.0000.0000.0000.000
9A39MET0-0.034-0.00614.6970.0100.0100.0000.0000.0000.000
10A40ASP-1-0.839-0.90217.4650.0140.0140.0000.0000.0000.000
11A41HIS0-0.030-0.00517.9280.0210.0210.0000.0000.0000.000
12A42ARG10.8920.92621.886-0.040-0.0400.0000.0000.0000.000
13A43ARG10.8520.91925.004-0.023-0.0230.0000.0000.0000.000
14A44ARG10.8770.93521.7810.0800.0800.0000.0000.0000.000
15A45GLY00.013-0.00622.9110.0020.0020.0000.0000.0000.000
16A46ILE0-0.043-0.01825.108-0.004-0.0040.0000.0000.0000.000
17A47ALA00.0070.00325.905-0.004-0.0040.0000.0000.0000.000
18A48LEU0-0.003-0.00927.8440.0030.0030.0000.0000.0000.000
19A49ILE00.0170.01029.300-0.006-0.0060.0000.0000.0000.000
20A50PHE00.002-0.00430.3400.0040.0040.0000.0000.0000.000
21A51ASN00.015-0.01134.058-0.007-0.0070.0000.0000.0000.000
22A52HIS00.0130.00735.7600.0040.0040.0000.0000.0000.000
23A53GLU-1-0.842-0.90639.016-0.036-0.0360.0000.0000.0000.000
24A54ARG10.8640.92442.1490.0200.0200.0000.0000.0000.000
25A55PHE0-0.009-0.00839.4620.0000.0000.0000.0000.0000.000
26A56PHE00.0290.00644.8570.0010.0010.0000.0000.0000.000
27A57TRP00.016-0.00847.111-0.001-0.0010.0000.0000.0000.000
28A58HIS00.0000.00149.509-0.002-0.0020.0000.0000.0000.000
29A59LEU0-0.0260.00342.4860.0000.0000.0000.0000.0000.000
30A60THR0-0.067-0.02445.741-0.001-0.0010.0000.0000.0000.000
31A61LEU0-0.0090.00841.037-0.002-0.0020.0000.0000.0000.000
32A62PRO0-0.015-0.00443.4480.0010.0010.0000.0000.0000.000
33A63GLU-1-0.821-0.90243.837-0.026-0.0260.0000.0000.0000.000
34A64ARG10.8100.91635.8230.0410.0410.0000.0000.0000.000
35A65ARG10.9900.98842.1670.0360.0360.0000.0000.0000.000
36A66GLY0-0.003-0.01041.908-0.002-0.0020.0000.0000.0000.000
37A67THR00.0290.01837.710-0.004-0.0040.0000.0000.0000.000
38A68CYS0-0.044-0.02938.010-0.001-0.0010.0000.0000.0000.000
39A69ALA00.0180.01539.479-0.001-0.0010.0000.0000.0000.000
40A70ASP-1-0.776-0.86534.901-0.065-0.0650.0000.0000.0000.000
41A71ARG10.8120.87634.9060.0320.0320.0000.0000.0000.000
42A72ASP-1-0.823-0.87835.228-0.039-0.0390.0000.0000.0000.000
43A73ASN0-0.023-0.01834.940-0.001-0.0010.0000.0000.0000.000
44A74LEU00.0340.00229.411-0.004-0.0040.0000.0000.0000.000
45A75THR0-0.004-0.01731.3790.0000.0000.0000.0000.0000.000
46A76ARG10.8810.95733.1200.0570.0570.0000.0000.0000.000
47A77ARG10.8850.96129.6440.0800.0800.0000.0000.0000.000
48A78PHE00.0430.01224.432-0.005-0.0050.0000.0000.0000.000
49A79SER0-0.008-0.01128.7750.0030.0030.0000.0000.0000.000
50A80ASP-1-0.872-0.92430.664-0.067-0.0670.0000.0000.0000.000
51A81LEU0-0.049-0.00925.016-0.006-0.0060.0000.0000.0000.000
52A82GLY0-0.045-0.03125.989-0.002-0.0020.0000.0000.0000.000
53A83PHE0-0.049-0.03522.4850.0070.0070.0000.0000.0000.000
54A84GLU-1-0.861-0.91828.248-0.004-0.0040.0000.0000.0000.000
55A85VAL0-0.007-0.01430.2640.0010.0010.0000.0000.0000.000
56A86LYS10.8600.93631.8510.0100.0100.0000.0000.0000.000
57A87CYS0-0.026-0.00833.303-0.003-0.0030.0000.0000.0000.000
58A88PHE00.0300.00734.2370.0040.0040.0000.0000.0000.000
59A89ASN00.0120.01137.362-0.005-0.0050.0000.0000.0000.000
60A90ASP-1-0.773-0.88739.886-0.023-0.0230.0000.0000.0000.000
61A91LEU0-0.0400.00836.5530.0020.0020.0000.0000.0000.000
62A92LYS11.0230.99740.0080.0050.0050.0000.0000.0000.000
63A93ALA00.001-0.01838.1020.0010.0010.0000.0000.0000.000
64A94GLU-1-0.921-0.95737.6800.0030.0030.0000.0000.0000.000
65A95GLU-1-0.847-0.92338.542-0.006-0.0060.0000.0000.0000.000
66A96LEU0-0.015-0.01032.7540.0000.0000.0000.0000.0000.000
67A97LEU00.0140.00233.0460.0010.0010.0000.0000.0000.000
68A98LEU00.0030.00033.8630.0030.0030.0000.0000.0000.000
69A99LYS10.8370.90434.5890.0010.0010.0000.0000.0000.000
70A100ILE0-0.013-0.00527.8450.0010.0010.0000.0000.0000.000
71A101HIS00.0220.00629.7330.0040.0040.0000.0000.0000.000
72A102GLU-1-0.818-0.85630.6320.0110.0110.0000.0000.0000.000
73A103VAL00.0250.00327.6790.0040.0040.0000.0000.0000.000
74A104SER0-0.074-0.03326.1100.0050.0050.0000.0000.0000.000
75A105THR0-0.067-0.05526.1280.0070.0070.0000.0000.0000.000
76A106VAL00.0000.02827.7780.0040.0040.0000.0000.0000.000
77A107SER00.0000.00025.8760.0060.0060.0000.0000.0000.000
78A108HIS10.8810.90822.268-0.026-0.0260.0000.0000.0000.000
79A109ALA00.0600.03221.353-0.001-0.0010.0000.0000.0000.000
80A110ASP-1-0.839-0.89221.4360.0410.0410.0000.0000.0000.000
81A111ALA00.003-0.00322.234-0.010-0.0100.0000.0000.0000.000
82A112ASP-1-0.706-0.83219.194-0.015-0.0150.0000.0000.0000.000
83A113CYS0-0.052-0.00818.044-0.003-0.0030.0000.0000.0000.000
84A114PHE0-0.035-0.01719.9100.0080.0080.0000.0000.0000.000
85A115VAL00.0330.03121.469-0.010-0.0100.0000.0000.0000.000
86A116CYS0-0.0300.00524.0230.0110.0110.0000.0000.0000.000
87A117VAL0-0.009-0.01425.960-0.007-0.0070.0000.0000.0000.000
88A118PHE00.0030.00127.6160.0070.0070.0000.0000.0000.000
89A119LEU0-0.017-0.00430.988-0.006-0.0060.0000.0000.0000.000
90A120SER00.014-0.01833.8800.0040.0040.0000.0000.0000.000
91A121HIS00.0170.00235.612-0.006-0.0060.0000.0000.0000.000
92A122GLY00.021-0.01433.7030.0020.0020.0000.0000.0000.000
93A123GLU-1-0.835-0.88034.722-0.026-0.0260.0000.0000.0000.000
94A124GLY00.0610.03632.9390.0030.0030.0000.0000.0000.000
95A125ASN0-0.037-0.01528.593-0.005-0.0050.0000.0000.0000.000
96A126HIS0-0.008-0.02330.2140.0060.0060.0000.0000.0000.000
97A127ILE0-0.044-0.01531.212-0.005-0.0050.0000.0000.0000.000
98A128TYR00.015-0.00133.4490.0050.0050.0000.0000.0000.000
99A129ALA0-0.0270.01136.912-0.002-0.0020.0000.0000.0000.000
100A130TYR00.0400.00538.2400.0000.0000.0000.0000.0000.000
101A131ASP-1-0.804-0.93141.789-0.010-0.0100.0000.0000.0000.000
102A132ALA00.0120.01440.2880.0010.0010.0000.0000.0000.000
103A133LYS10.8030.91436.4470.0180.0180.0000.0000.0000.000
104A134ILE00.007-0.00332.2940.0030.0030.0000.0000.0000.000
105A135GLU-1-0.873-0.92530.169-0.015-0.0150.0000.0000.0000.000
106A136ILE00.021-0.00725.8340.0030.0030.0000.0000.0000.000
107A137GLN00.0350.02522.3840.0040.0040.0000.0000.0000.000
108A138THR0-0.036-0.02525.9480.0050.0050.0000.0000.0000.000
109A139LEU00.0050.01127.9640.0040.0040.0000.0000.0000.000
110A140THR00.008-0.00822.2200.0020.0020.0000.0000.0000.000
111A141GLY00.023-0.00122.8140.0040.0040.0000.0000.0000.000
112A142LEU0-0.008-0.00123.6840.0100.0100.0000.0000.0000.000
113A143PHE00.010-0.01421.5440.0070.0070.0000.0000.0000.000
114A144LYS10.8720.94219.003-0.039-0.0390.0000.0000.0000.000
115A145GLY00.0620.01717.1530.0060.0060.0000.0000.0000.000
116A146ASP-1-0.876-0.92818.0980.0680.0680.0000.0000.0000.000
117A147LYS10.8350.92120.823-0.034-0.0340.0000.0000.0000.000
118A148CYS0-0.081-0.02821.495-0.005-0.0050.0000.0000.0000.000
119A149HIS00.0910.04319.634-0.002-0.0020.0000.0000.0000.000
120A150SER0-0.027-0.01318.8980.0050.0050.0000.0000.0000.000
121A151LEU00.015-0.00718.707-0.004-0.0040.0000.0000.0000.000
122A152VAL00.0000.01213.739-0.015-0.0150.0000.0000.0000.000
123A153GLY0-0.0010.01111.7080.0210.0210.0000.0000.0000.000
124A154LYS10.7770.91312.507-0.066-0.0660.0000.0000.0000.000
125A155PRO00.0050.00514.366-0.005-0.0050.0000.0000.0000.000
126A156LYS10.8150.92215.1760.0170.0170.0000.0000.0000.000
127A157ILE00.0120.00018.256-0.013-0.0130.0000.0000.0000.000
128A158PHE00.002-0.00720.3150.0120.0120.0000.0000.0000.000
129A159ILE0-0.003-0.00123.057-0.011-0.0110.0000.0000.0000.000
130A160ILE0-0.014-0.01625.5010.0100.0100.0000.0000.0000.000
131A161GLN0-0.0170.00027.993-0.006-0.0060.0000.0000.0000.000
132A162ALA00.012-0.01631.0810.0050.0050.0000.0000.0000.000
133A163CYS00.0170.03233.253-0.002-0.0020.0000.0000.0000.000
134A199THR00.0730.03923.7800.0050.0050.0000.0000.0000.000
135A200LEU0-0.044-0.02019.309-0.009-0.0090.0000.0000.0000.000
136A201PRO00.010-0.01616.4090.0130.0130.0000.0000.0000.000
137A202ALA00.0150.01518.2350.0050.0050.0000.0000.0000.000
138A203GLY00.004-0.00315.5390.0170.0170.0000.0000.0000.000
139A204ALA00.0240.00710.780-0.022-0.0220.0000.0000.0000.000
140A205ASP-1-0.824-0.89110.686-0.003-0.0030.0000.0000.0000.000
141A206PHE0-0.030-0.00212.8630.0110.0110.0000.0000.0000.000
142A207LEU0-0.021-0.00915.114-0.026-0.0260.0000.0000.0000.000
143A208MET0-0.0310.00417.2560.0180.0180.0000.0000.0000.000
144A209CYS00.0010.00120.528-0.020-0.0200.0000.0000.0000.000
145A210TYR00.018-0.00422.4880.0150.0150.0000.0000.0000.000
146A211SER00.000-0.02125.967-0.007-0.0070.0000.0000.0000.000
147A212VAL0-0.0090.00327.4730.0000.0000.0000.0000.0000.000
148A222THR00.0680.02041.7570.0010.0010.0000.0000.0000.000
149A223VAL0-0.033-0.02242.0880.0000.0000.0000.0000.0000.000
150A224ASN0-0.012-0.00742.0650.0030.0030.0000.0000.0000.000
151A225GLY00.0350.03538.269-0.003-0.0030.0000.0000.0000.000
152A226SER0-0.051-0.05334.822-0.002-0.0020.0000.0000.0000.000
153A227TRP00.017-0.01134.864-0.003-0.0030.0000.0000.0000.000
154A228TYR00.0890.04625.2090.0000.0000.0000.0000.0000.000
155A229ILE00.0190.01830.227-0.006-0.0060.0000.0000.0000.000
156A230GLN0-0.004-0.00532.107-0.005-0.0050.0000.0000.0000.000
157A231ASP-1-0.752-0.86730.577-0.102-0.1020.0000.0000.0000.000
158A232LEU0-0.001-0.00125.181-0.008-0.0080.0000.0000.0000.000
159A233CYS0-0.030-0.01728.414-0.003-0.0030.0000.0000.0000.000
160A234GLU-1-0.839-0.89530.846-0.106-0.1060.0000.0000.0000.000
161A235MET0-0.025-0.01426.495-0.007-0.0070.0000.0000.0000.000
162A236LEU00.0050.00524.711-0.007-0.0070.0000.0000.0000.000
163A237GLY0-0.013-0.01327.503-0.001-0.0010.0000.0000.0000.000
164A238LYS10.8300.91329.4500.1150.1150.0000.0000.0000.000
165A239TYR00.036-0.00424.5460.0000.0000.0000.0000.0000.000
166A240GLY00.0280.03224.088-0.015-0.0150.0000.0000.0000.000
167A241SER0-0.026-0.01023.383-0.008-0.0080.0000.0000.0000.000
168A242SER00.005-0.01822.982-0.004-0.0040.0000.0000.0000.000
169A243LEU0-0.018-0.01620.355-0.020-0.0200.0000.0000.0000.000
170A244GLU-1-0.789-0.85313.855-0.323-0.3230.0000.0000.0000.000
171A245PHE00.038-0.00617.4120.0110.0110.0000.0000.0000.000
172A246THR0-0.018-0.04514.4980.0100.0100.0000.0000.0000.000
173A247GLU-1-0.833-0.90217.234-0.330-0.3300.0000.0000.0000.000
174A248LEU0-0.043-0.01618.7570.0210.0210.0000.0000.0000.000
175A249LEU00.009-0.00719.1600.0180.0180.0000.0000.0000.000
176A250THR0-0.036-0.02219.2890.0110.0110.0000.0000.0000.000
177A251LEU0-0.027-0.01921.9320.0130.0130.0000.0000.0000.000
178A252VAL0-0.0280.00424.8990.0140.0140.0000.0000.0000.000
179A253ASN00.0250.00722.4220.0200.0200.0000.0000.0000.000
180A254ARG10.9740.99625.0920.1840.1840.0000.0000.0000.000
181A255LYS10.7750.86727.9690.1190.1190.0000.0000.0000.000
182A256VAL0-0.022-0.02230.0250.0080.0080.0000.0000.0000.000
183A257GLU-1-0.954-0.96229.936-0.120-0.1200.0000.0000.0000.000
184A258GLN0-0.026-0.01331.8250.0010.0010.0000.0000.0000.000
185A259ARG10.7690.87734.1660.0900.0900.0000.0000.0000.000
186A260ARG10.9480.99635.2920.0970.0970.0000.0000.0000.000
187A274GLN00.004-0.00333.1970.0010.0010.0000.0000.0000.000
188A275VAL0-0.027-0.03627.367-0.004-0.0040.0000.0000.0000.000
189A276PRO0-0.0120.02526.7920.0020.0020.0000.0000.0000.000
190A277CYS00.019-0.00722.920-0.013-0.0130.0000.0000.0000.000
191A278PHE0-0.024-0.00516.4030.0100.0100.0000.0000.0000.000
192A279ALA00.0320.01917.771-0.013-0.0130.0000.0000.0000.000
193A280SER00.011-0.01012.7140.0260.0260.0000.0000.0000.000
194A281MET0-0.0030.01211.787-0.008-0.0080.0000.0000.0000.000
195A282LEU0-0.044-0.01010.9060.0250.0250.0000.0000.0000.000
196A283THR0-0.023-0.0236.101-0.048-0.0480.0000.0000.0000.000
197A284LYS10.8120.9035.936-0.411-0.4110.0000.0000.0000.000
198A285LYS10.8850.9418.4290.8930.8930.0000.0000.0000.000
199A286LEU0-0.014-0.01611.5510.0640.0640.0000.0000.0000.000
200A287HIS00.0420.02614.808-0.068-0.0680.0000.0000.0000.000
201A288PHE00.011-0.01518.0130.0240.0240.0000.0000.0000.000
202A289PHE0-0.0200.01117.0560.0120.0120.0000.0000.0000.000
203A290PRO00.0330.01022.3210.0130.0130.0000.0000.0000.000
204A291LYS10.7880.88622.1380.0280.0280.0000.0000.0000.000
205A292SER00.0040.01224.9890.0010.0010.0000.0000.0000.000