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: 171KZ

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2550604.62026
FMO2-HF: Nuclear repulsion 2465854.459287
FMO2-HF: Total energy -84750.160973
FMO2-MP2: Total energy -84992.103828


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.
-98.565-95.0491.054-2.154-2.4160.007
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 : -0.864 / q_NPA : -0.939
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].
3B34ALA0-0.055-0.0393.448-14.344-12.1200.007-1.086-1.1450.005
4B35GLU-1-0.810-0.8742.27731.82033.0241.046-1.037-1.2130.002
5B36LYS10.9070.9434.200-30.651-30.5630.001-0.031-0.0580.000
6B37TYR0-0.018-0.0407.8260.7580.7580.0000.0000.0000.000
7B38LYS10.8160.9137.417-27.719-27.7190.0000.0000.0000.000
8B39MET0-0.052-0.02612.467-1.041-1.0410.0000.0000.0000.000
9B40ASP-1-0.859-0.94014.06817.90417.9040.0000.0000.0000.000
10B41HIS0-0.069-0.02415.781-0.497-0.4970.0000.0000.0000.000
11B42ARG10.8390.90419.664-10.939-10.9390.0000.0000.0000.000
12B43ARG10.7790.85222.718-11.427-11.4270.0000.0000.0000.000
13B44ARG10.8840.94318.704-13.838-13.8380.0000.0000.0000.000
14B45GLY00.0550.01621.4040.4900.4900.0000.0000.0000.000
15B46ILE0-0.049-0.02524.038-0.313-0.3130.0000.0000.0000.000
16B47ALA00.0150.00925.6460.4140.4140.0000.0000.0000.000
17B48LEU0-0.010-0.00327.531-0.429-0.4290.0000.0000.0000.000
18B49ILE0-0.006-0.00929.8630.1830.1830.0000.0000.0000.000
19B50PHE0-0.004-0.00732.561-0.288-0.2880.0000.0000.0000.000
20B51ASN0-0.034-0.03534.5320.1360.1360.0000.0000.0000.000
21B52HIS10.8180.89837.344-8.051-8.0510.0000.0000.0000.000
22B53GLU-1-0.819-0.89139.0267.4857.4850.0000.0000.0000.000
23B54ARG10.8040.86140.267-7.794-7.7940.0000.0000.0000.000
24B55PHE00.002-0.01143.6740.1070.1070.0000.0000.0000.000
25B56PHE00.0010.02744.471-0.003-0.0030.0000.0000.0000.000
26B57TRP00.020-0.00246.603-0.091-0.0910.0000.0000.0000.000
27B58HIS00.0430.02749.4730.0730.0730.0000.0000.0000.000
28B59LEU00.0580.04845.4760.0720.0720.0000.0000.0000.000
29B60THR00.0730.03548.845-0.072-0.0720.0000.0000.0000.000
30B61LEU00.017-0.00348.5520.1160.1160.0000.0000.0000.000
31B62PRO00.0460.01346.6880.0880.0880.0000.0000.0000.000
32B63GLU-1-0.668-0.81043.4707.3427.3420.0000.0000.0000.000
33B64ARG10.8790.94843.610-6.216-6.2160.0000.0000.0000.000
34B65ARG10.8620.93541.957-7.166-7.1660.0000.0000.0000.000
35B66GLY00.0940.05041.7260.1180.1180.0000.0000.0000.000
36B67THR0-0.007-0.02539.2460.2500.2500.0000.0000.0000.000
37B68CYS0-0.111-0.04239.0650.1240.1240.0000.0000.0000.000
38B69ALA00.0120.00739.1380.1440.1440.0000.0000.0000.000
39B70ASP-1-0.731-0.84735.3608.8668.8660.0000.0000.0000.000
40B71ARG10.9200.94434.563-7.568-7.5680.0000.0000.0000.000
41B72ASP-1-0.808-0.89035.0957.8767.8760.0000.0000.0000.000
42B73ASN0-0.045-0.02433.7070.1780.1780.0000.0000.0000.000
43B74LEU00.0560.01629.5510.2310.2310.0000.0000.0000.000
44B75THR0-0.025-0.02830.5710.2670.2670.0000.0000.0000.000
45B76ARG10.9290.98731.899-8.409-8.4090.0000.0000.0000.000
46B77ARG10.8580.93728.097-9.677-9.6770.0000.0000.0000.000
47B78PHE00.0250.00523.6680.3570.3570.0000.0000.0000.000
48B79SER0-0.011-0.01926.9490.2060.2060.0000.0000.0000.000
49B80ASP-1-0.889-0.94928.1619.9239.9230.0000.0000.0000.000
50B81LEU0-0.046-0.01422.4040.2670.2670.0000.0000.0000.000
51B82GLY00.0080.00923.4140.4990.4990.0000.0000.0000.000
52B83PHE0-0.038-0.02921.1980.1490.1490.0000.0000.0000.000
53B84GLU-1-0.817-0.88926.2299.6939.6930.0000.0000.0000.000
54B85VAL0-0.010-0.00329.1730.0730.0730.0000.0000.0000.000
55B86LYS10.8270.91330.710-9.760-9.7600.0000.0000.0000.000
56B87CYS00.0010.01433.1740.2050.2050.0000.0000.0000.000
57B88PHE00.005-0.01534.353-0.237-0.2370.0000.0000.0000.000
58B89ASN00.0360.01437.6800.1360.1360.0000.0000.0000.000
59B90ASP-1-0.679-0.78039.2627.5997.5990.0000.0000.0000.000
60B91LEU0-0.008-0.00541.051-0.107-0.1070.0000.0000.0000.000
61B92LYS10.8320.92542.858-7.201-7.2010.0000.0000.0000.000
62B93ALA00.010-0.00543.4180.1220.1220.0000.0000.0000.000
63B94GLU-1-0.859-0.91943.2356.8966.8960.0000.0000.0000.000
64B95GLU-1-0.781-0.88541.5867.3707.3700.0000.0000.0000.000
65B96LEU0-0.042-0.01837.5280.2040.2040.0000.0000.0000.000
66B97LEU00.0170.01738.3060.2630.2630.0000.0000.0000.000
67B98LEU00.0470.02038.5720.2090.2090.0000.0000.0000.000
68B99LYS10.8540.91536.526-7.617-7.6170.0000.0000.0000.000
69B100ILE0-0.034-0.01633.2480.2940.2940.0000.0000.0000.000
70B101HIS00.0380.02833.3090.3250.3250.0000.0000.0000.000
71B102GLU-1-0.896-0.93133.6848.9798.9790.0000.0000.0000.000
72B103VAL0-0.042-0.03129.4340.2990.2990.0000.0000.0000.000
73B104SER0-0.067-0.04529.1160.4190.4190.0000.0000.0000.000
74B105THR0-0.037-0.02928.9260.2630.2630.0000.0000.0000.000
75B106VAL00.0040.02829.1040.1290.1290.0000.0000.0000.000
76B107SER00.0230.01326.8260.5660.5660.0000.0000.0000.000
77B108HIS10.8610.90123.255-11.606-11.6060.0000.0000.0000.000
78B109ALA00.0490.03122.0880.5690.5690.0000.0000.0000.000
79B110ASP-1-0.779-0.84621.19511.89911.8990.0000.0000.0000.000
80B111ALA0-0.003-0.01321.783-0.195-0.1950.0000.0000.0000.000
81B112ASP-1-0.715-0.83617.51215.59715.5970.0000.0000.0000.000
82B113CYS0-0.085-0.03817.2520.8150.8150.0000.0000.0000.000
83B114PHE0-0.005-0.00819.445-0.809-0.8090.0000.0000.0000.000
84B115VAL00.0180.02621.7090.4910.4910.0000.0000.0000.000
85B116CYS0-0.061-0.01024.289-0.609-0.6090.0000.0000.0000.000
86B117VAL00.0230.00326.9010.2500.2500.0000.0000.0000.000
87B118PHE0-0.0010.00529.451-0.409-0.4090.0000.0000.0000.000
88B119LEU00.005-0.00632.1620.0870.0870.0000.0000.0000.000
89B120SER0-0.075-0.06735.150-0.241-0.2410.0000.0000.0000.000
90B121HIS10.8030.87237.916-7.456-7.4560.0000.0000.0000.000
91B122GLY00.0360.01740.9410.0770.0770.0000.0000.0000.000
92B123GLU-1-0.847-0.90342.3546.5226.5220.0000.0000.0000.000
93B124GLY0-0.0020.00342.651-0.062-0.0620.0000.0000.0000.000
94B125ASN0-0.012-0.00543.3150.0240.0240.0000.0000.0000.000
95B126HIS00.0830.02244.2640.2350.2350.0000.0000.0000.000
96B127ILE00.0170.02243.7320.1440.1440.0000.0000.0000.000
97B128TYR0-0.028-0.03440.3850.2080.2080.0000.0000.0000.000
98B129ALA00.0670.03239.9050.2320.2320.0000.0000.0000.000
99B130TYR0-0.0260.00839.0940.2730.2730.0000.0000.0000.000
100B131ASP-1-0.744-0.86038.8147.9257.9250.0000.0000.0000.000
101B132ALA00.0130.00736.3260.1840.1840.0000.0000.0000.000
102B133LYS10.8950.94034.372-8.007-8.0070.0000.0000.0000.000
103B134ILE00.0340.02433.9170.2650.2650.0000.0000.0000.000
104B135GLH0-0.010-0.03834.7640.1840.1840.0000.0000.0000.000
105B136ILE00.0250.02329.3020.2500.2500.0000.0000.0000.000
106B137GLN0-0.0200.00129.8320.2220.2220.0000.0000.0000.000
107B138THR0-0.028-0.02630.2180.2370.2370.0000.0000.0000.000
108B139LEU0-0.026-0.01429.5610.2080.2080.0000.0000.0000.000
109B140THR0-0.042-0.04025.6610.3380.3380.0000.0000.0000.000
110B141GLY0-0.014-0.01325.6430.4680.4680.0000.0000.0000.000
111B142LEU0-0.017-0.01127.0930.2190.2190.0000.0000.0000.000
112B143PHE00.006-0.00323.4900.0340.0340.0000.0000.0000.000
113B144LYS10.8500.92122.203-11.641-11.6410.0000.0000.0000.000
114B145GLY00.0110.00020.592-0.240-0.2400.0000.0000.0000.000
115B146ASP-1-0.807-0.88821.37211.17111.1710.0000.0000.0000.000
116B147LYS10.8010.90524.627-11.169-11.1690.0000.0000.0000.000
117B148CYS0-0.0020.00723.716-0.173-0.1730.0000.0000.0000.000
118B149HIS00.0610.01222.0670.9240.9240.0000.0000.0000.000
119B150SER0-0.041-0.01521.1300.3720.3720.0000.0000.0000.000
120B151LEU00.0000.00219.3320.1550.1550.0000.0000.0000.000
121B152VAL00.0020.00116.2770.7190.7190.0000.0000.0000.000
122B153GLY00.0130.01613.1410.1160.1160.0000.0000.0000.000
123B154LYS10.7920.91413.194-14.051-14.0510.0000.0000.0000.000
124B155PRO00.0260.00114.401-0.395-0.3950.0000.0000.0000.000
125B156LYS10.7800.90716.511-17.574-17.5740.0000.0000.0000.000
126B157ILE0-0.0060.00318.5930.1350.1350.0000.0000.0000.000
127B158PHE00.015-0.00721.275-0.688-0.6880.0000.0000.0000.000
128B159ILE00.002-0.00224.3310.2110.2110.0000.0000.0000.000
129B160ILE0-0.021-0.01326.704-0.443-0.4430.0000.0000.0000.000
130B161GLN00.0140.01429.8200.0060.0060.0000.0000.0000.000
131B162ALA00.0230.02532.553-0.255-0.2550.0000.0000.0000.000
132B163CYS0-0.0070.01634.297-0.243-0.2430.0000.0000.0000.000
133B202ALA00.0230.02120.891-0.206-0.2060.0000.0000.0000.000
134B203GLY00.0450.01619.473-0.520-0.5200.0000.0000.0000.000
135B204ALA00.0550.02614.3570.3500.3500.0000.0000.0000.000
136B205ASP-1-0.799-0.87012.47020.34220.3420.0000.0000.0000.000
137B206PHE0-0.0010.00014.845-0.846-0.8460.0000.0000.0000.000
138B207LEU0-0.021-0.00916.9330.9120.9120.0000.0000.0000.000
139B208MET0-0.0080.02218.966-0.594-0.5940.0000.0000.0000.000
140B209CYS0-0.002-0.00322.2170.5250.5250.0000.0000.0000.000
141B210TYR00.0350.00824.429-0.457-0.4570.0000.0000.0000.000
142B211SER00.042-0.00127.9750.1270.1270.0000.0000.0000.000
143B212VAL0-0.081-0.03330.896-0.118-0.1180.0000.0000.0000.000
144B213ALA00.0460.02528.9790.1840.1840.0000.0000.0000.000
145B214GLU-1-0.856-0.90829.21010.38310.3830.0000.0000.0000.000
146B215GLY0-0.031-0.02532.537-0.187-0.1870.0000.0000.0000.000
147B216TYR0-0.128-0.08231.630-0.241-0.2410.0000.0000.0000.000
148B217TYR0-0.023-0.00736.823-0.131-0.1310.0000.0000.0000.000
149B218SER0-0.001-0.01436.642-0.064-0.0640.0000.0000.0000.000
150B219HIS00.0290.02539.153-0.158-0.1580.0000.0000.0000.000
151B220ARG10.6530.77541.674-6.505-6.5050.0000.0000.0000.000
152B221GLU-1-0.752-0.84638.5608.0158.0150.0000.0000.0000.000
153B222THR0-0.039-0.03341.456-0.257-0.2570.0000.0000.0000.000
154B223VAL0-0.006-0.00842.4590.1030.1030.0000.0000.0000.000
155B224ASN0-0.029-0.02141.095-0.101-0.1010.0000.0000.0000.000
156B225GLY00.0010.01938.3550.1700.1700.0000.0000.0000.000
157B226SER0-0.061-0.05835.505-0.004-0.0040.0000.0000.0000.000
158B227TRP00.024-0.01235.6300.2440.2440.0000.0000.0000.000
159B228TYR00.0560.03626.4720.0940.0940.0000.0000.0000.000
160B229ILE00.0110.01230.7370.3500.3500.0000.0000.0000.000
161B230GLN00.0400.01931.7980.2220.2220.0000.0000.0000.000
162B231ASP-1-0.724-0.82730.3359.6469.6460.0000.0000.0000.000
163B232LEU00.0010.00625.2420.3460.3460.0000.0000.0000.000
164B233CYS0-0.042-0.02527.4860.3050.3050.0000.0000.0000.000
165B234GLU-1-0.874-0.92229.8209.7489.7480.0000.0000.0000.000
166B235MET0-0.010-0.00824.9740.2980.2980.0000.0000.0000.000
167B236LEU00.001-0.00523.2840.3860.3860.0000.0000.0000.000
168B237GLY0-0.012-0.01125.4390.1570.1570.0000.0000.0000.000
169B238LYS10.8790.95727.094-10.627-10.6270.0000.0000.0000.000
170B239TYR00.041-0.00722.141-0.137-0.1370.0000.0000.0000.000
171B240GLY00.0430.02521.2780.6870.6870.0000.0000.0000.000
172B241SER0-0.0180.00120.2360.6220.6220.0000.0000.0000.000
173B242SER0-0.050-0.03318.9730.2470.2470.0000.0000.0000.000
174B243LEU0-0.027-0.01117.3940.6190.6190.0000.0000.0000.000
175B244GLU-1-0.790-0.86512.32921.71521.7150.0000.0000.0000.000
176B245PHE00.0450.00415.349-1.094-1.0940.0000.0000.0000.000
177B246THR0-0.022-0.04014.987-0.767-0.7670.0000.0000.0000.000
178B247GLU-1-0.846-0.90516.46117.15417.1540.0000.0000.0000.000
179B248LEU0-0.028-0.01218.189-0.972-0.9720.0000.0000.0000.000
180B249LEU00.012-0.00419.730-0.817-0.8170.0000.0000.0000.000
181B250THR0-0.042-0.02819.830-0.622-0.6220.0000.0000.0000.000
182B251LEU0-0.052-0.03122.013-0.641-0.6410.0000.0000.0000.000
183B252VAL0-0.020-0.00124.675-0.575-0.5750.0000.0000.0000.000
184B253ASN00.0270.00823.447-0.691-0.6910.0000.0000.0000.000
185B254ARG10.9591.00524.917-12.354-12.3540.0000.0000.0000.000
186B255LYS10.7740.86428.581-10.041-10.0410.0000.0000.0000.000
187B256VAL00.0230.00730.477-0.359-0.3590.0000.0000.0000.000
188B257SER0-0.073-0.05730.045-0.319-0.3190.0000.0000.0000.000
189B258GLN0-0.029-0.00832.0700.0220.0220.0000.0000.0000.000
190B259ARG10.7500.86834.594-9.198-9.1980.0000.0000.0000.000
191B275VAL00.005-0.01128.843-0.078-0.0780.0000.0000.0000.000
192B276PRO0-0.0340.00127.6910.0310.0310.0000.0000.0000.000
193B277CYS0-0.0130.00225.3770.4250.4250.0000.0000.0000.000
194B278PHE0-0.006-0.01217.905-0.111-0.1110.0000.0000.0000.000
195B279ALA00.0310.01720.1120.2600.2600.0000.0000.0000.000
196B280SER00.004-0.00114.223-0.276-0.2760.0000.0000.0000.000
197B281MET0-0.018-0.01614.745-0.234-0.2340.0000.0000.0000.000
198B282LEU0-0.043-0.00811.8950.2580.2580.0000.0000.0000.000
199B283THR0-0.009-0.0108.2901.4311.4310.0000.0000.0000.000
200B284LYS10.8070.9025.561-31.806-31.8060.0000.0000.0000.000
201B285LYS10.9280.9727.175-37.265-37.2650.0000.0000.0000.000
202B286LEU0-0.012-0.0199.706-0.111-0.1110.0000.0000.0000.000
203B287HIS00.0430.02911.8120.5120.5120.0000.0000.0000.000
204B288PHE00.004-0.00614.9490.1010.1010.0000.0000.0000.000
205B289PHE00.0140.01112.799-0.571-0.5710.0000.0000.0000.000
206B290PRO00.0120.02318.366-0.033-0.0330.0000.0000.0000.000