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: QYR8Y

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 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 -2532726.110898
FMO2-HF: Nuclear repulsion 2448326.245467
FMO2-HF: Total energy -84399.865431
FMO2-MP2: Total energy -84641.006165


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.
1.173.123-0.021-0.651-1.280.001
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 : -0.031 / q_NPA : -0.032
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].
3A33PRO00.0450.0383.805-0.0071.761-0.020-0.646-1.1020.001
4A34ALA0-0.064-0.0785.6840.4080.4080.0000.0000.0000.000
5A35GLU-1-0.904-0.9475.186-0.408-0.223-0.001-0.005-0.1780.000
6A36LYS10.9390.9657.8950.4160.4160.0000.0000.0000.000
7A37TYR0-0.021-0.04210.831-0.009-0.0090.0000.0000.0000.000
8A38LYS10.8220.88512.6090.1880.1880.0000.0000.0000.000
9A39MET0-0.034-0.00214.7120.0150.0150.0000.0000.0000.000
10A40ASP-1-0.838-0.89417.960-0.168-0.1680.0000.0000.0000.000
11A41HIS0-0.063-0.01918.016-0.002-0.0020.0000.0000.0000.000
12A42ARG10.9150.95521.9040.0810.0810.0000.0000.0000.000
13A43ARG10.8530.90625.0480.0880.0880.0000.0000.0000.000
14A44ARG10.8680.93421.6840.1220.1220.0000.0000.0000.000
15A45GLY00.013-0.00722.912-0.007-0.0070.0000.0000.0000.000
16A46ILE0-0.031-0.01125.1230.0030.0030.0000.0000.0000.000
17A47ALA0-0.001-0.00226.065-0.006-0.0060.0000.0000.0000.000
18A48LEU0-0.006-0.00728.0690.0050.0050.0000.0000.0000.000
19A49ILE00.0220.01329.498-0.003-0.0030.0000.0000.0000.000
20A50PHE0-0.006-0.00930.7010.0040.0040.0000.0000.0000.000
21A51ASN00.005-0.01634.244-0.002-0.0020.0000.0000.0000.000
22A52HIS00.0130.01035.9090.0030.0030.0000.0000.0000.000
23A53GLU-1-0.927-0.96439.160-0.037-0.0370.0000.0000.0000.000
24A54ARG10.8720.93942.2760.0290.0290.0000.0000.0000.000
25A55PHE0-0.024-0.01539.505-0.001-0.0010.0000.0000.0000.000
26A56PHE00.0250.00544.9980.0010.0010.0000.0000.0000.000
27A57TRP00.016-0.00847.2660.0000.0000.0000.0000.0000.000
28A58HIS00.0030.00549.7760.0000.0000.0000.0000.0000.000
29A59LEU0-0.0350.00142.6620.0000.0000.0000.0000.0000.000
30A60THR0-0.057-0.01745.8410.0000.0000.0000.0000.0000.000
31A61LEU0-0.0180.00241.235-0.001-0.0010.0000.0000.0000.000
32A62PRO0-0.014-0.00543.4650.0000.0000.0000.0000.0000.000
33A63GLU-1-0.824-0.91343.922-0.031-0.0310.0000.0000.0000.000
34A64ARG10.8300.92636.1730.0460.0460.0000.0000.0000.000
35A65ARG10.9840.98442.2480.0330.0330.0000.0000.0000.000
36A66GLY00.002-0.00741.969-0.001-0.0010.0000.0000.0000.000
37A67THR00.0530.02937.772-0.003-0.0030.0000.0000.0000.000
38A68CYS0-0.010-0.00138.119-0.003-0.0030.0000.0000.0000.000
39A69ALA00.0310.02739.598-0.001-0.0010.0000.0000.0000.000
40A70ASP-1-0.773-0.87234.917-0.056-0.0560.0000.0000.0000.000
41A71ARG10.8410.90535.0100.0430.0430.0000.0000.0000.000
42A72ASP-1-0.836-0.89335.367-0.050-0.0500.0000.0000.0000.000
43A73ASN0-0.049-0.04034.961-0.003-0.0030.0000.0000.0000.000
44A74LEU00.0460.00129.380-0.003-0.0030.0000.0000.0000.000
45A75THR0-0.016-0.02831.516-0.004-0.0040.0000.0000.0000.000
46A76ARG10.9190.97233.2780.0530.0530.0000.0000.0000.000
47A77ARG10.9100.96329.7210.0670.0670.0000.0000.0000.000
48A78PHE00.0630.02124.678-0.004-0.0040.0000.0000.0000.000
49A79SER00.0030.00728.948-0.003-0.0030.0000.0000.0000.000
50A80ASP-1-0.914-0.94130.842-0.072-0.0720.0000.0000.0000.000
51A81LEU0-0.061-0.01524.960-0.004-0.0040.0000.0000.0000.000
52A82GLY0-0.044-0.03026.168-0.009-0.0090.0000.0000.0000.000
53A83PHE0-0.061-0.03922.763-0.002-0.0020.0000.0000.0000.000
54A84GLU-1-0.910-0.95128.358-0.062-0.0620.0000.0000.0000.000
55A85VAL0-0.017-0.01530.354-0.002-0.0020.0000.0000.0000.000
56A86LYS10.9290.97332.0650.0630.0630.0000.0000.0000.000
57A87CYS0-0.033-0.01133.526-0.003-0.0030.0000.0000.0000.000
58A88PHE00.0300.00734.1190.0020.0020.0000.0000.0000.000
59A89ASN00.0160.01637.555-0.003-0.0030.0000.0000.0000.000
60A90ASP-1-0.759-0.88040.077-0.036-0.0360.0000.0000.0000.000
61A91LEU0-0.0480.00036.9760.0010.0010.0000.0000.0000.000
62A92LYS11.0080.99640.2060.0280.0280.0000.0000.0000.000
63A93ALA00.009-0.01438.314-0.002-0.0020.0000.0000.0000.000
64A94GLU-1-0.913-0.95737.915-0.031-0.0310.0000.0000.0000.000
65A95GLU-1-0.859-0.93438.758-0.036-0.0360.0000.0000.0000.000
66A96LEU0-0.009-0.00532.987-0.002-0.0020.0000.0000.0000.000
67A97LEU00.0300.00333.251-0.003-0.0030.0000.0000.0000.000
68A98LEU00.0100.00133.989-0.002-0.0020.0000.0000.0000.000
69A99LYS10.8200.90934.7230.0430.0430.0000.0000.0000.000
70A100ILE0-0.009-0.00328.072-0.003-0.0030.0000.0000.0000.000
71A101HIS00.0150.00129.789-0.004-0.0040.0000.0000.0000.000
72A102GLU-1-0.836-0.87530.727-0.050-0.0500.0000.0000.0000.000
73A103VAL00.0330.00927.632-0.003-0.0030.0000.0000.0000.000
74A104SER0-0.067-0.02826.152-0.005-0.0050.0000.0000.0000.000
75A105THR0-0.074-0.06426.238-0.002-0.0020.0000.0000.0000.000
76A106VAL00.0030.02927.8420.0020.0020.0000.0000.0000.000
77A107SER00.0110.00126.017-0.006-0.0060.0000.0000.0000.000
78A108HIS10.8580.90722.3930.0900.0900.0000.0000.0000.000
79A109ALA00.0580.02721.492-0.009-0.0090.0000.0000.0000.000
80A110ASP-1-0.831-0.89021.568-0.091-0.0910.0000.0000.0000.000
81A111ALA0-0.019-0.02022.3530.0030.0030.0000.0000.0000.000
82A112ASP-1-0.690-0.83819.216-0.150-0.1500.0000.0000.0000.000
83A113CYS0-0.045-0.01218.064-0.012-0.0120.0000.0000.0000.000
84A114PHE0-0.038-0.02119.9120.0120.0120.0000.0000.0000.000
85A115VAL00.0410.03821.696-0.007-0.0070.0000.0000.0000.000
86A116CYS0-0.0290.00124.2330.0090.0090.0000.0000.0000.000
87A117VAL0-0.020-0.01326.129-0.003-0.0030.0000.0000.0000.000
88A118PHE0-0.007-0.00527.5090.0040.0040.0000.0000.0000.000
89A119LEU0-0.015-0.00331.133-0.001-0.0010.0000.0000.0000.000
90A120SER00.005-0.01633.9970.0030.0030.0000.0000.0000.000
91A121HIS00.008-0.00335.700-0.002-0.0020.0000.0000.0000.000
92A122GLY00.018-0.01733.782-0.001-0.0010.0000.0000.0000.000
93A123GLU-1-0.844-0.87834.805-0.032-0.0320.0000.0000.0000.000
94A124GLY00.0530.02432.9840.0010.0010.0000.0000.0000.000
95A125ASN0-0.001-0.00128.868-0.002-0.0020.0000.0000.0000.000
96A126HIS0-0.008-0.01330.303-0.001-0.0010.0000.0000.0000.000
97A127ILE0-0.035-0.01131.002-0.001-0.0010.0000.0000.0000.000
98A128TYR00.003-0.00233.5810.0020.0020.0000.0000.0000.000
99A129ALA0-0.0180.01137.064-0.002-0.0020.0000.0000.0000.000
100A130TYR00.0340.00438.4140.0020.0020.0000.0000.0000.000
101A131ASP-1-0.795-0.92341.990-0.031-0.0310.0000.0000.0000.000
102A132ALA00.0160.00940.5880.0010.0010.0000.0000.0000.000
103A133LYS10.8180.91736.5810.0300.0300.0000.0000.0000.000
104A134ILE00.0130.00032.2760.0010.0010.0000.0000.0000.000
105A135GLU-1-0.902-0.94230.302-0.041-0.0410.0000.0000.0000.000
106A136ILE00.016-0.01125.808-0.002-0.0020.0000.0000.0000.000
107A137GLN00.0200.01722.728-0.006-0.0060.0000.0000.0000.000
108A138THR0-0.020-0.01026.159-0.002-0.0020.0000.0000.0000.000
109A139LEU00.0130.01228.099-0.001-0.0010.0000.0000.0000.000
110A140THR00.011-0.01022.414-0.002-0.0020.0000.0000.0000.000
111A141GLY00.015-0.00223.064-0.006-0.0060.0000.0000.0000.000
112A142LEU0-0.0080.00023.786-0.001-0.0010.0000.0000.0000.000
113A143PHE00.001-0.02321.509-0.001-0.0010.0000.0000.0000.000
114A144LYS10.8800.94619.0760.0580.0580.0000.0000.0000.000
115A145GLY00.0570.01517.2990.0030.0030.0000.0000.0000.000
116A146ASP-1-0.882-0.93118.239-0.066-0.0660.0000.0000.0000.000
117A147LYS10.8420.93820.9920.0710.0710.0000.0000.0000.000
118A148CYS0-0.068-0.02821.6340.0010.0010.0000.0000.0000.000
119A149HIS00.1000.05019.823-0.012-0.0120.0000.0000.0000.000
120A150SER0-0.012-0.00819.071-0.010-0.0100.0000.0000.0000.000
121A151LEU00.017-0.01218.788-0.005-0.0050.0000.0000.0000.000
122A152VAL0-0.0140.00513.741-0.013-0.0130.0000.0000.0000.000
123A153GLY00.0030.01411.805-0.004-0.0040.0000.0000.0000.000
124A154LYS10.7460.89312.6090.1250.1250.0000.0000.0000.000
125A155PRO00.0120.01014.6280.0070.0070.0000.0000.0000.000
126A156LYS10.8350.93315.4520.1710.1710.0000.0000.0000.000
127A157ILE00.0230.00818.560-0.003-0.0030.0000.0000.0000.000
128A158PHE0-0.002-0.01320.4890.0100.0100.0000.0000.0000.000
129A159ILE00.0000.00323.171-0.003-0.0030.0000.0000.0000.000
130A160ILE0-0.008-0.01625.6100.0060.0060.0000.0000.0000.000
131A161GLN0-0.0220.00328.087-0.001-0.0010.0000.0000.0000.000
132A162ALA00.009-0.01631.1480.0030.0030.0000.0000.0000.000
133A163CYS00.0070.02933.3150.0010.0010.0000.0000.0000.000
134A199THR00.0580.03223.9910.0050.0050.0000.0000.0000.000
135A200LEU0-0.032-0.01919.337-0.007-0.0070.0000.0000.0000.000
136A201PRO00.005-0.01516.5350.0050.0050.0000.0000.0000.000
137A202ALA00.0190.01318.3760.0020.0020.0000.0000.0000.000
138A203GLY00.004-0.00315.7370.0100.0100.0000.0000.0000.000
139A204ALA00.0300.00811.034-0.008-0.0080.0000.0000.0000.000
140A205ASP-1-0.827-0.89410.840-0.261-0.2610.0000.0000.0000.000
141A206PHE0-0.026-0.00213.1000.0190.0190.0000.0000.0000.000
142A207LEU0-0.018-0.01015.249-0.013-0.0130.0000.0000.0000.000
143A208MET0-0.036-0.00117.3730.0090.0090.0000.0000.0000.000
144A209CYS00.0010.00220.615-0.007-0.0070.0000.0000.0000.000
145A210TYR00.014-0.00222.2010.0080.0080.0000.0000.0000.000
146A211SER00.001-0.01725.992-0.002-0.0020.0000.0000.0000.000
147A212VAL0-0.0130.01227.3380.0030.0030.0000.0000.0000.000
148A222THR00.0420.01041.7610.0000.0000.0000.0000.0000.000
149A223VAL00.011-0.00542.124-0.001-0.0010.0000.0000.0000.000
150A224ASN0-0.020-0.01042.1350.0000.0000.0000.0000.0000.000
151A225GLY00.0310.04138.307-0.002-0.0020.0000.0000.0000.000
152A226SER0-0.050-0.04834.9160.0000.0000.0000.0000.0000.000
153A227TRP00.024-0.00334.665-0.002-0.0020.0000.0000.0000.000
154A228TYR00.0760.03925.162-0.001-0.0010.0000.0000.0000.000
155A229ILE00.0080.01130.409-0.005-0.0050.0000.0000.0000.000
156A230GLN0-0.033-0.04032.144-0.003-0.0030.0000.0000.0000.000
157A231ASP-1-0.772-0.88330.818-0.063-0.0630.0000.0000.0000.000
158A232LEU0-0.015-0.00925.354-0.004-0.0040.0000.0000.0000.000
159A233CYS0-0.032-0.01328.440-0.004-0.0040.0000.0000.0000.000
160A234GLU-1-0.967-0.97830.889-0.064-0.0640.0000.0000.0000.000
161A235MET0-0.044-0.02926.635-0.002-0.0020.0000.0000.0000.000
162A236LEU0-0.0040.00025.000-0.005-0.0050.0000.0000.0000.000
163A237GLY0-0.022-0.00827.546-0.002-0.0020.0000.0000.0000.000
164A238LYS10.9160.96429.6860.0700.0700.0000.0000.0000.000
165A239TYR00.031-0.00224.7360.0020.0020.0000.0000.0000.000
166A240GLY00.0360.03624.182-0.010-0.0100.0000.0000.0000.000
167A241SER0-0.007-0.00423.454-0.009-0.0090.0000.0000.0000.000
168A242SER0-0.011-0.02623.093-0.003-0.0030.0000.0000.0000.000
169A243LEU0-0.030-0.02520.524-0.011-0.0110.0000.0000.0000.000
170A244GLU-1-0.767-0.81414.105-0.241-0.2410.0000.0000.0000.000
171A245PHE00.030-0.01017.4750.0130.0130.0000.0000.0000.000
172A246THR0-0.035-0.07314.5980.0120.0120.0000.0000.0000.000
173A247GLU-1-0.830-0.90317.369-0.174-0.1740.0000.0000.0000.000
174A248LEU0-0.044-0.02018.9180.0170.0170.0000.0000.0000.000
175A249LEU00.004-0.01319.2450.0130.0130.0000.0000.0000.000
176A250THR0-0.025-0.01419.4210.0100.0100.0000.0000.0000.000
177A251LEU0-0.042-0.02422.0680.0110.0110.0000.0000.0000.000
178A252VAL0-0.0230.00625.0540.0090.0090.0000.0000.0000.000
179A253ASN00.0330.01522.6830.0090.0090.0000.0000.0000.000
180A254ARG10.9680.99325.2880.0910.0910.0000.0000.0000.000
181A255LYS10.9000.94828.0620.0710.0710.0000.0000.0000.000
182A256VAL0-0.003-0.01330.1270.0050.0050.0000.0000.0000.000
183A257GLU-1-0.961-0.96229.938-0.056-0.0560.0000.0000.0000.000
184A258GLN0-0.044-0.01831.9200.0020.0020.0000.0000.0000.000
185A259ARG10.7880.89134.2490.0570.0570.0000.0000.0000.000
186A260ARG10.9480.98835.8420.0450.0450.0000.0000.0000.000
187A274GLN00.0100.00333.062-0.001-0.0010.0000.0000.0000.000
188A275VAL0-0.026-0.04127.476-0.001-0.0010.0000.0000.0000.000
189A276PRO0-0.0030.01426.7210.0000.0000.0000.0000.0000.000
190A277CYS00.017-0.00123.024-0.005-0.0050.0000.0000.0000.000
191A278PHE0-0.022-0.00616.1690.0000.0000.0000.0000.0000.000
192A279ALA00.0340.01817.752-0.003-0.0030.0000.0000.0000.000
193A280SER00.005-0.00812.5050.0020.0020.0000.0000.0000.000
194A281MET0-0.0080.01111.876-0.003-0.0030.0000.0000.0000.000
195A282LEU0-0.035-0.00811.039-0.011-0.0110.0000.0000.0000.000
196A283THR0-0.029-0.0246.277-0.031-0.0310.0000.0000.0000.000
197A284LYS10.9100.9726.0870.3690.3690.0000.0000.0000.000
198A285LYS10.8820.9838.5610.5060.5060.0000.0000.0000.000
199A286LEU0-0.020-0.01311.6050.0040.0040.0000.0000.0000.000
200A287HIS0-0.0060.00114.914-0.014-0.0140.0000.0000.0000.000
201A288PHE00.014-0.01318.1110.0000.0000.0000.0000.0000.000
202A289PHE0-0.0360.00717.4130.0090.0090.0000.0000.0000.000
203A290PRO00.0410.01322.3360.0000.0000.0000.0000.0000.000
204A291LYS10.8110.90922.4090.1230.1230.0000.0000.0000.000
205A292SER00.0090.01625.0040.0090.0090.0000.0000.0000.000