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: YZ582

Calculation Name: 3K7E-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3K7E

Chain ID: B

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2544411.23033
FMO2-HF: Nuclear repulsion 2459662.940895
FMO2-HF: Total energy -84748.289434
FMO2-MP2: Total energy -84990.320566


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(B:32:ASP)


Summations of interaction energy for fragment #1(B:32:ASP)
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.
-82.172-79.0280.126-1.335-1.9350.005
Interaction energy analysis for fragmet #1(B:32:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.851 / q_NPA : -0.937
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].
3B34ALA0-0.079-0.0573.745-12.432-10.546-0.010-0.860-1.0170.004
4B35GLU-1-0.844-0.9132.83234.13835.3230.136-0.459-0.8610.001
5B36LYS10.8980.9554.460-29.176-29.1030.000-0.016-0.0570.000
6B37TYR00.005-0.0138.1501.0021.0020.0000.0000.0000.000
7B38LYS10.8090.8946.829-29.010-29.0100.0000.0000.0000.000
8B39MET0-0.041-0.03212.484-1.086-1.0860.0000.0000.0000.000
9B40ASP-1-0.926-0.94015.38016.67916.6790.0000.0000.0000.000
10B41HIS0-0.0260.01215.904-0.303-0.3030.0000.0000.0000.000
11B42ARG10.8460.90320.010-10.899-10.8990.0000.0000.0000.000
12B43ARG10.8040.86523.393-11.221-11.2210.0000.0000.0000.000
13B44ARG10.8740.96519.061-13.248-13.2480.0000.0000.0000.000
14B45GLY00.0490.00421.7930.4950.4950.0000.0000.0000.000
15B46ILE0-0.038-0.00924.383-0.325-0.3250.0000.0000.0000.000
16B47ALA00.0000.02326.3440.3270.3270.0000.0000.0000.000
17B48LEU0-0.027-0.01427.889-0.432-0.4320.0000.0000.0000.000
18B49ILE00.0070.00230.1580.1630.1630.0000.0000.0000.000
19B50PHE0-0.024-0.01432.792-0.301-0.3010.0000.0000.0000.000
20B51ASN0-0.040-0.04534.6710.1390.1390.0000.0000.0000.000
21B52HIS10.7810.89237.654-7.909-7.9090.0000.0000.0000.000
22B53GLU-1-0.870-0.93939.3407.2017.2010.0000.0000.0000.000
23B54ARG10.8310.90241.241-7.530-7.5300.0000.0000.0000.000
24B55PHE0-0.009-0.01743.9890.0920.0920.0000.0000.0000.000
25B56PHE0-0.0010.03644.847-0.006-0.0060.0000.0000.0000.000
26B57TRP00.028-0.00246.883-0.057-0.0570.0000.0000.0000.000
27B58HIS00.0160.01749.8720.0700.0700.0000.0000.0000.000
28B59LEU00.0540.03745.5960.0730.0730.0000.0000.0000.000
29B60THR00.0490.01648.852-0.064-0.0640.0000.0000.0000.000
30B61LEU00.039-0.00248.9460.1010.1010.0000.0000.0000.000
31B62PRO00.0150.00146.9100.0810.0810.0000.0000.0000.000
32B63GLU-1-0.730-0.84344.2417.1787.1780.0000.0000.0000.000
33B64ARG10.9430.97844.070-6.106-6.1060.0000.0000.0000.000
34B65ARG10.9400.95742.512-6.946-6.9460.0000.0000.0000.000
35B66GLY00.0710.04042.6720.1100.1100.0000.0000.0000.000
36B67THR00.0210.01039.5990.2210.2210.0000.0000.0000.000
37B68CYS0-0.106-0.05539.5230.1320.1320.0000.0000.0000.000
38B69ALA0-0.0090.01139.8760.1020.1020.0000.0000.0000.000
39B70ASP-1-0.764-0.88735.8368.4978.4970.0000.0000.0000.000
40B71ARG10.9550.98135.254-7.444-7.4440.0000.0000.0000.000
41B72ASP-1-0.909-0.94535.6197.8057.8050.0000.0000.0000.000
42B73ASN0-0.066-0.03634.6460.1930.1930.0000.0000.0000.000
43B74LEU00.048-0.00830.1450.2340.2340.0000.0000.0000.000
44B75THR0-0.032-0.03431.0010.3050.3050.0000.0000.0000.000
45B76ARG10.9480.97932.137-8.123-8.1230.0000.0000.0000.000
46B77ARG10.9360.97228.739-9.325-9.3250.0000.0000.0000.000
47B78PHE00.0280.00424.4060.3230.3230.0000.0000.0000.000
48B79SER00.0100.00627.3040.2500.2500.0000.0000.0000.000
49B80ASP-1-0.938-0.94728.6319.7259.7250.0000.0000.0000.000
50B81LEU0-0.044-0.01522.8630.3080.3080.0000.0000.0000.000
51B82GLY00.010-0.00123.7590.5470.5470.0000.0000.0000.000
52B83PHE0-0.041-0.03121.8270.1390.1390.0000.0000.0000.000
53B84GLU-1-0.875-0.92326.9079.6919.6910.0000.0000.0000.000
54B85VAL0-0.018-0.02029.9300.0390.0390.0000.0000.0000.000
55B86LYS10.9100.96531.644-9.352-9.3520.0000.0000.0000.000
56B87CYS00.0160.02133.7300.1610.1610.0000.0000.0000.000
57B88PHE0-0.011-0.01834.078-0.219-0.2190.0000.0000.0000.000
58B89ASN00.0630.02737.9140.1490.1490.0000.0000.0000.000
59B90ASP-1-0.673-0.79240.0317.5277.5270.0000.0000.0000.000
60B91LEU0-0.033-0.01541.556-0.121-0.1210.0000.0000.0000.000
61B92LYS10.8250.92243.193-7.043-7.0430.0000.0000.0000.000
62B93ALA00.0290.00643.4750.1550.1550.0000.0000.0000.000
63B94GLU-1-0.885-0.93244.1006.7406.7400.0000.0000.0000.000
64B95GLU-1-0.776-0.89242.3797.1747.1740.0000.0000.0000.000
65B96LEU0-0.030-0.01537.6460.1840.1840.0000.0000.0000.000
66B97LEU00.0310.02338.7760.2550.2550.0000.0000.0000.000
67B98LEU00.0850.03338.8030.2250.2250.0000.0000.0000.000
68B99LYS10.8900.94637.246-7.424-7.4240.0000.0000.0000.000
69B100ILE0-0.043-0.02233.9810.2720.2720.0000.0000.0000.000
70B101HIS00.0180.00333.8700.4130.4130.0000.0000.0000.000
71B102GLU-1-0.935-0.95034.6038.6978.6970.0000.0000.0000.000
72B103VAL0-0.050-0.03429.6790.2870.2870.0000.0000.0000.000
73B104SER0-0.085-0.04629.6260.3380.3380.0000.0000.0000.000
74B105THR0-0.022-0.02029.3630.2920.2920.0000.0000.0000.000
75B106VAL00.0010.03029.2260.1670.1670.0000.0000.0000.000
76B107SER00.000-0.00627.4150.5120.5120.0000.0000.0000.000
77B108HIS10.9110.93323.553-11.246-11.2460.0000.0000.0000.000
78B109ALA00.0530.02522.4230.5430.5430.0000.0000.0000.000
79B110ASP-1-0.817-0.87321.80311.56311.5630.0000.0000.0000.000
80B111ALA0-0.023-0.01822.078-0.111-0.1110.0000.0000.0000.000
81B112ASP-1-0.734-0.86117.68915.18215.1820.0000.0000.0000.000
82B113CYS0-0.069-0.03117.7620.6570.6570.0000.0000.0000.000
83B114PHE0-0.008-0.00719.873-0.739-0.7390.0000.0000.0000.000
84B115VAL00.0240.02422.2070.4050.4050.0000.0000.0000.000
85B116CYS0-0.042-0.01024.626-0.592-0.5920.0000.0000.0000.000
86B117VAL00.0120.00227.3490.2060.2060.0000.0000.0000.000
87B118PHE0-0.009-0.00329.790-0.346-0.3460.0000.0000.0000.000
88B119LEU00.0350.00632.2970.0660.0660.0000.0000.0000.000
89B120SER0-0.068-0.06135.264-0.215-0.2150.0000.0000.0000.000
90B121HIS10.8330.90838.133-7.285-7.2850.0000.0000.0000.000
91B122GLY00.0340.01240.6650.1050.1050.0000.0000.0000.000
92B123GLU-1-0.902-0.95042.2256.3996.3990.0000.0000.0000.000
93B124GLY0-0.015-0.01643.173-0.025-0.0250.0000.0000.0000.000
94B125ASN00.0120.01744.1310.0570.0570.0000.0000.0000.000
95B126HIS00.1100.02344.6330.2500.2500.0000.0000.0000.000
96B127ILE00.0080.01243.9190.1590.1590.0000.0000.0000.000
97B128TYR0-0.036-0.02541.0070.1950.1950.0000.0000.0000.000
98B129ALA00.0530.02040.2290.2040.2040.0000.0000.0000.000
99B130TYR0-0.065-0.04039.1100.2970.2970.0000.0000.0000.000
100B131ASP-1-0.761-0.86939.3097.7097.7090.0000.0000.0000.000
101B132ALA00.0150.01236.4590.1790.1790.0000.0000.0000.000
102B133LYS10.9640.98234.631-7.749-7.7490.0000.0000.0000.000
103B134ILE00.0180.01734.2310.2640.2640.0000.0000.0000.000
104B135GLH0-0.011-0.05135.0730.2300.2300.0000.0000.0000.000
105B136ILE00.0330.02429.5760.2180.2180.0000.0000.0000.000
106B137GLN0-0.0170.03030.3060.2870.2870.0000.0000.0000.000
107B138THR0-0.036-0.01530.3440.2460.2460.0000.0000.0000.000
108B139LEU00.000-0.00229.9820.2250.2250.0000.0000.0000.000
109B140THR0-0.043-0.06025.9710.2660.2660.0000.0000.0000.000
110B141GLY0-0.028-0.01326.1620.4280.4280.0000.0000.0000.000
111B142LEU0-0.030-0.02127.6460.1710.1710.0000.0000.0000.000
112B143PHE00.0250.00023.7140.0740.0740.0000.0000.0000.000
113B144LYS10.8970.95722.664-11.308-11.3080.0000.0000.0000.000
114B145GLY00.002-0.00620.826-0.233-0.2330.0000.0000.0000.000
115B146ASP-1-0.902-0.96021.67810.80910.8090.0000.0000.0000.000
116B147LYS10.8520.94724.768-10.466-10.4660.0000.0000.0000.000
117B148CYS0-0.0170.00323.882-0.241-0.2410.0000.0000.0000.000
118B149HIS00.1030.03222.4450.9300.9300.0000.0000.0000.000
119B150SER0-0.040-0.01221.4300.4300.4300.0000.0000.0000.000
120B151LEU00.015-0.00420.1790.3300.3300.0000.0000.0000.000
121B152VAL00.0110.02316.8130.7090.7090.0000.0000.0000.000
122B153GLY0-0.0150.00213.8800.1340.1340.0000.0000.0000.000
123B154LYS10.7700.89113.692-13.585-13.5850.0000.0000.0000.000
124B155PRO00.0200.00614.650-0.409-0.4090.0000.0000.0000.000
125B156LYS10.8640.95216.836-16.321-16.3210.0000.0000.0000.000
126B157ILE00.002-0.00218.9530.2120.2120.0000.0000.0000.000
127B158PHE00.005-0.00921.601-0.624-0.6240.0000.0000.0000.000
128B159ILE00.0110.00224.6680.2110.2110.0000.0000.0000.000
129B160ILE00.012-0.00126.861-0.428-0.4280.0000.0000.0000.000
130B161GLN0-0.002-0.00729.7600.0370.0370.0000.0000.0000.000
131B162ALA00.0090.02532.876-0.219-0.2190.0000.0000.0000.000
132B163CYS0-0.0010.01134.563-0.238-0.2380.0000.0000.0000.000
133B202ALA00.0430.02720.862-0.072-0.0720.0000.0000.0000.000
134B203GLY0-0.010-0.02919.964-0.586-0.5860.0000.0000.0000.000
135B204ALA00.0520.02614.4900.2170.2170.0000.0000.0000.000
136B205ASP-1-0.836-0.91712.71220.37120.3710.0000.0000.0000.000
137B206PHE0-0.0380.00315.196-0.754-0.7540.0000.0000.0000.000
138B207LEU0-0.012-0.00317.4740.6700.6700.0000.0000.0000.000
139B208MET0-0.039-0.00819.285-0.592-0.5920.0000.0000.0000.000
140B209CYS00.0040.00722.7290.3850.3850.0000.0000.0000.000
141B210TYR00.0260.00824.611-0.466-0.4660.0000.0000.0000.000
142B211SER00.043-0.00728.0140.0290.0290.0000.0000.0000.000
143B212VAL0-0.078-0.03431.011-0.074-0.0740.0000.0000.0000.000
144B213ALA00.0260.02429.5500.1220.1220.0000.0000.0000.000
145B214GLU-1-0.834-0.89829.78110.04310.0430.0000.0000.0000.000
146B215GLY0-0.037-0.02932.991-0.116-0.1160.0000.0000.0000.000
147B216TYR0-0.143-0.09032.054-0.275-0.2750.0000.0000.0000.000
148B217TYR0-0.015-0.00537.256-0.122-0.1220.0000.0000.0000.000
149B218SER00.0110.00437.273-0.044-0.0440.0000.0000.0000.000
150B219HIS00.0290.02639.671-0.161-0.1610.0000.0000.0000.000
151B220ARG10.7390.85442.181-6.392-6.3920.0000.0000.0000.000
152B221GLU-1-0.781-0.88539.1257.8007.8000.0000.0000.0000.000
153B222THR00.0000.00441.674-0.268-0.2680.0000.0000.0000.000
154B223VAL0-0.001-0.00843.3110.0570.0570.0000.0000.0000.000
155B224ASN0-0.036-0.03141.343-0.134-0.1340.0000.0000.0000.000
156B225GLY00.0240.04839.0350.1830.1830.0000.0000.0000.000
157B226SER0-0.023-0.00736.173-0.016-0.0160.0000.0000.0000.000
158B227TRP00.013-0.00935.6500.2080.2080.0000.0000.0000.000
159B228TYR00.0710.04426.6250.0910.0910.0000.0000.0000.000
160B229ILE00.0090.01231.4070.3340.3340.0000.0000.0000.000
161B230GLN0-0.032-0.04532.6150.1740.1740.0000.0000.0000.000
162B231ASP-1-0.813-0.91931.0369.3859.3850.0000.0000.0000.000
163B232LEU0-0.022-0.00525.8320.2960.2960.0000.0000.0000.000
164B233CYS0-0.035-0.01528.0420.3060.3060.0000.0000.0000.000
165B234GLU-1-0.954-0.96630.0239.4249.4240.0000.0000.0000.000
166B235MET0-0.055-0.04025.7810.2060.2060.0000.0000.0000.000
167B236LEU00.0050.00824.0610.3160.3160.0000.0000.0000.000
168B237GLY0-0.030-0.01425.9760.1770.1770.0000.0000.0000.000
169B238LYS10.8850.96127.596-10.052-10.0520.0000.0000.0000.000
170B239TYR00.020-0.02322.695-0.054-0.0540.0000.0000.0000.000
171B240GLY00.0290.02721.8140.6260.6260.0000.0000.0000.000
172B241SER00.0020.00020.7340.5360.5360.0000.0000.0000.000
173B242SER0-0.047-0.02819.2320.4800.4800.0000.0000.0000.000
174B243LEU0-0.009-0.00617.6600.7640.7640.0000.0000.0000.000
175B244GLU-1-0.784-0.83412.57320.18720.1870.0000.0000.0000.000
176B245PHE00.0620.00115.624-0.834-0.8340.0000.0000.0000.000
177B246THR0-0.042-0.07015.382-0.734-0.7340.0000.0000.0000.000
178B247GLU-1-0.901-0.95616.63816.33016.3300.0000.0000.0000.000
179B248LEU0-0.039-0.01318.444-0.903-0.9030.0000.0000.0000.000
180B249LEU0-0.001-0.01420.078-0.770-0.7700.0000.0000.0000.000
181B250THR00.0150.01320.082-0.683-0.6830.0000.0000.0000.000
182B251LEU0-0.043-0.02722.572-0.609-0.6090.0000.0000.0000.000
183B252VAL0-0.014-0.00425.137-0.563-0.5630.0000.0000.0000.000
184B253ASN00.0220.00724.314-0.586-0.5860.0000.0000.0000.000
185B254ARG10.9400.98225.167-12.016-12.0160.0000.0000.0000.000
186B255LYS10.9330.95029.040-10.182-10.1820.0000.0000.0000.000
187B256VAL00.0330.02030.726-0.328-0.3280.0000.0000.0000.000
188B257SER0-0.108-0.03831.133-0.297-0.2970.0000.0000.0000.000
189B258GLN0-0.037-0.01432.816-0.129-0.1290.0000.0000.0000.000
190B259ARG10.8670.95935.338-8.786-8.7860.0000.0000.0000.000
191B275VAL0-0.008-0.02029.270-0.061-0.0610.0000.0000.0000.000
192B276PRO0-0.0110.01427.7120.0180.0180.0000.0000.0000.000
193B277CYS0-0.0120.00125.4110.3780.3780.0000.0000.0000.000
194B278PHE0-0.009-0.01817.905-0.086-0.0860.0000.0000.0000.000
195B279ALA00.0350.02920.5700.3510.3510.0000.0000.0000.000
196B280SER0-0.007-0.01314.472-0.105-0.1050.0000.0000.0000.000
197B281MET00.002-0.00515.075-0.091-0.0910.0000.0000.0000.000
198B282LEU0-0.020-0.00512.5450.3060.3060.0000.0000.0000.000
199B283THR0-0.031-0.0168.4141.0551.0550.0000.0000.0000.000
200B284LYS10.8980.9606.760-25.743-25.7430.0000.0000.0000.000
201B285LYS10.9160.9787.918-32.041-32.0410.0000.0000.0000.000
202B286LEU00.001-0.00110.316-0.101-0.1010.0000.0000.0000.000
203B287HIS00.0420.03211.7220.5000.5000.0000.0000.0000.000
204B288PHE00.0220.00015.2620.0020.0020.0000.0000.0000.000
205B289PHE00.0200.01213.583-0.602-0.6020.0000.0000.0000.000
206B290PRO00.0360.02118.9420.1160.1160.0000.0000.0000.000