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

tag_button

FMODB ID: Z6JNN

Calculation Name: 4IYR-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4IYR

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200944.509651
FMO2-HF: Nuclear repulsion 2123445.620664
FMO2-HF: Total energy -77498.888986
FMO2-MP2: Total energy -77718.733818


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:31:PHE)


Summations of interaction energy for fragment #1(B: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.
-1.0092.0110.013-0.926-2.1060.002
Interaction energy analysis for fragmet #1(B:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.026
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].
3B33PRO00.0180.0233.214-0.9091.7260.014-0.900-1.7490.002
4B34ALA0-0.069-0.0354.498-0.283-0.1200.000-0.021-0.1410.000
5B35GLU-1-0.878-0.9384.9691.5101.732-0.001-0.005-0.2160.000
6B36LYS10.9050.9527.842-0.422-0.4220.0000.0000.0000.000
7B37TYR0-0.049-0.07511.0970.0900.0900.0000.0000.0000.000
8B38LYS10.9340.97610.865-0.706-0.7060.0000.0000.0000.000
9B39MET0-0.044-0.02014.923-0.052-0.0520.0000.0000.0000.000
10B40ASP-1-0.906-0.95617.6250.2880.2880.0000.0000.0000.000
11B41HIS0-0.048-0.01517.4030.0060.0060.0000.0000.0000.000
12B42ARG10.8780.92322.328-0.106-0.1060.0000.0000.0000.000
13B43ARG10.8780.93625.168-0.092-0.0920.0000.0000.0000.000
14B44ARG10.9030.95621.150-0.084-0.0840.0000.0000.0000.000
15B45GLY00.023-0.00123.1070.0030.0030.0000.0000.0000.000
16B46ILE0-0.0130.00125.534-0.003-0.0030.0000.0000.0000.000
17B47ALA0-0.002-0.00126.359-0.001-0.0010.0000.0000.0000.000
18B48LEU0-0.033-0.01528.4390.0000.0000.0000.0000.0000.000
19B49ILE00.0240.01230.238-0.004-0.0040.0000.0000.0000.000
20B50PHE00.004-0.00831.0910.0020.0020.0000.0000.0000.000
21B51ASN00.039-0.00534.767-0.004-0.0040.0000.0000.0000.000
22B52HIS0-0.0010.01137.4680.0020.0020.0000.0000.0000.000
23B66GLY00.0390.01842.3110.0000.0000.0000.0000.0000.000
24B67THR00.0720.01639.1450.0000.0000.0000.0000.0000.000
25B68CYS0-0.011-0.00538.8620.0010.0010.0000.0000.0000.000
26B69ALA00.0500.03139.5830.0010.0010.0000.0000.0000.000
27B70ASP-1-0.775-0.89735.166-0.009-0.0090.0000.0000.0000.000
28B71ARG10.8940.94135.065-0.005-0.0050.0000.0000.0000.000
29B72ASP-1-0.818-0.89335.5180.0100.0100.0000.0000.0000.000
30B73ASN0-0.034-0.02034.6720.0050.0050.0000.0000.0000.000
31B74LEU00.046-0.00329.4270.0010.0010.0000.0000.0000.000
32B75THR0-0.016-0.01231.4640.0040.0040.0000.0000.0000.000
33B76ARG10.9000.95433.030-0.006-0.0060.0000.0000.0000.000
34B77ARG10.9130.97029.381-0.004-0.0040.0000.0000.0000.000
35B78PHE00.0610.01824.9470.0020.0020.0000.0000.0000.000
36B79SER00.0210.00628.7150.0070.0070.0000.0000.0000.000
37B80ASP-1-0.927-0.94630.4670.0320.0320.0000.0000.0000.000
38B81LEU0-0.066-0.02624.4090.0040.0040.0000.0000.0000.000
39B82GLY0-0.038-0.01925.9660.0100.0100.0000.0000.0000.000
40B83PHE0-0.072-0.04422.6760.0040.0040.0000.0000.0000.000
41B84GLU-1-0.914-0.94428.1980.0460.0460.0000.0000.0000.000
42B85VAL0-0.027-0.02530.460-0.001-0.0010.0000.0000.0000.000
43B86LYS10.9320.97832.383-0.034-0.0340.0000.0000.0000.000
44B87CYS0-0.022-0.01234.049-0.002-0.0020.0000.0000.0000.000
45B88PHE00.000-0.00333.7450.0020.0020.0000.0000.0000.000
46B89ASN0-0.055-0.06038.455-0.001-0.0010.0000.0000.0000.000
47B90ASP-1-0.845-0.89440.9210.0020.0020.0000.0000.0000.000
48B91LEU00.0100.01437.7700.0010.0010.0000.0000.0000.000
49B92LYS10.9420.95841.194-0.006-0.0060.0000.0000.0000.000
50B93ALA00.030-0.00439.2750.0010.0010.0000.0000.0000.000
51B94GLU-1-0.962-0.97838.9600.0090.0090.0000.0000.0000.000
52B95GLU-1-0.848-0.92939.9210.0150.0150.0000.0000.0000.000
53B96LEU0-0.078-0.03534.0250.0020.0020.0000.0000.0000.000
54B97LEU0-0.019-0.02534.4430.0010.0010.0000.0000.0000.000
55B98LEU00.0390.03634.9440.0020.0020.0000.0000.0000.000
56B99LYS10.9510.97935.718-0.018-0.0180.0000.0000.0000.000
57B100ILE0-0.019-0.01029.1830.0030.0030.0000.0000.0000.000
58B101HIS00.0200.01430.8210.0030.0030.0000.0000.0000.000
59B102GLU-1-0.856-0.92631.7050.0290.0290.0000.0000.0000.000
60B103VAL0-0.087-0.03928.5800.0050.0050.0000.0000.0000.000
61B104SER0-0.094-0.06727.2400.0050.0050.0000.0000.0000.000
62B105THR0-0.011-0.01327.3410.0050.0050.0000.0000.0000.000
63B106VAL0-0.0110.02829.0480.0040.0040.0000.0000.0000.000
64B107SER00.002-0.00926.7650.0040.0040.0000.0000.0000.000
65B108HIS10.8880.94523.136-0.060-0.0600.0000.0000.0000.000
66B109ALA00.0350.01722.6320.0080.0080.0000.0000.0000.000
67B110ASP-1-0.789-0.87922.3090.1160.1160.0000.0000.0000.000
68B111ALA0-0.041-0.03123.036-0.003-0.0030.0000.0000.0000.000
69B112ASP-1-0.704-0.84319.4800.1590.1590.0000.0000.0000.000
70B113CYS0-0.066-0.02518.453-0.001-0.0010.0000.0000.0000.000
71B114PHE0-0.0050.00120.3070.0010.0010.0000.0000.0000.000
72B115VAL00.0320.03122.092-0.008-0.0080.0000.0000.0000.000
73B116CYS0-0.049-0.01524.6030.0040.0040.0000.0000.0000.000
74B117VAL00.0130.00726.647-0.006-0.0060.0000.0000.0000.000
75B118PHE0-0.006-0.01028.2660.0030.0030.0000.0000.0000.000
76B119LEU0-0.0370.01331.726-0.004-0.0040.0000.0000.0000.000
77B120SER00.0540.02134.1210.0030.0030.0000.0000.0000.000
78B121ALA0-0.020-0.00634.3110.0010.0010.0000.0000.0000.000
79B122GLY00.0330.01532.871-0.001-0.0010.0000.0000.0000.000
80B123GLU-1-0.898-0.95233.926-0.025-0.0250.0000.0000.0000.000
81B124GLY0-0.019-0.01831.8990.0010.0010.0000.0000.0000.000
82B125ASN0-0.005-0.00729.5750.0000.0000.0000.0000.0000.000
83B126HIS00.009-0.00430.7680.0040.0040.0000.0000.0000.000
84B127ILE00.0170.00131.570-0.002-0.0020.0000.0000.0000.000
85B128TYR0-0.040-0.02634.4730.0000.0000.0000.0000.0000.000
86B129ALA00.0160.01537.7650.0010.0010.0000.0000.0000.000
87B130TYR0-0.037-0.03639.586-0.001-0.0010.0000.0000.0000.000
88B131ASP-1-0.803-0.89643.1370.0010.0010.0000.0000.0000.000
89B132ALA00.0040.01040.980-0.001-0.0010.0000.0000.0000.000
90B133LYS10.8820.96437.2290.0150.0150.0000.0000.0000.000
91B134ILE00.016-0.00133.5700.0010.0010.0000.0000.0000.000
92B135GLU-1-0.875-0.93031.427-0.018-0.0180.0000.0000.0000.000
93B136ILE00.0490.02926.9180.0020.0020.0000.0000.0000.000
94B137GLN0-0.027-0.03126.4580.0010.0010.0000.0000.0000.000
95B138THR00.0060.00827.2760.0020.0020.0000.0000.0000.000
96B139LEU0-0.0090.01129.1710.0040.0040.0000.0000.0000.000
97B140THR0-0.034-0.02223.6340.0020.0020.0000.0000.0000.000
98B141GLY00.0340.01024.1010.0030.0030.0000.0000.0000.000
99B142LEU0-0.027-0.00824.6490.0030.0030.0000.0000.0000.000
100B143PHE00.016-0.01422.3530.0070.0070.0000.0000.0000.000
101B144LYS10.9070.95519.9900.0290.0290.0000.0000.0000.000
102B145GLY0-0.002-0.01818.1650.0060.0060.0000.0000.0000.000
103B146ASP-1-0.920-0.97819.1330.0240.0240.0000.0000.0000.000
104B147LYS10.9350.98821.798-0.002-0.0020.0000.0000.0000.000
105B148CYS0-0.0370.00422.5400.0060.0060.0000.0000.0000.000
106B149HIS00.0790.03319.9870.0000.0000.0000.0000.0000.000
107B150SER00.0190.00120.0120.0070.0070.0000.0000.0000.000
108B151LEU00.016-0.00619.5400.0100.0100.0000.0000.0000.000
109B152VAL0-0.0110.01815.128-0.010-0.0100.0000.0000.0000.000
110B153GLY0-0.030-0.00212.6330.0280.0280.0000.0000.0000.000
111B154LYS10.7730.89113.054-0.125-0.1250.0000.0000.0000.000
112B155PRO00.0000.00414.706-0.024-0.0240.0000.0000.0000.000
113B156LYS10.8100.92616.349-0.012-0.0120.0000.0000.0000.000
114B157ILE0-0.007-0.01418.942-0.015-0.0150.0000.0000.0000.000
115B158PHE00.0230.00421.0750.0080.0080.0000.0000.0000.000
116B159ILE0-0.013-0.00923.518-0.008-0.0080.0000.0000.0000.000
117B160ILE00.0040.01125.9880.0050.0050.0000.0000.0000.000
118B161GLN0-0.032-0.03928.650-0.002-0.0020.0000.0000.0000.000
119B162ALA00.0350.01831.4200.0020.0020.0000.0000.0000.000
120B163CYS0-0.034-0.00433.6410.0020.0020.0000.0000.0000.000
121B200LEU00.001-0.01220.6140.0020.0020.0000.0000.0000.000
122B201PRO0-0.0170.00223.485-0.001-0.0010.0000.0000.0000.000
123B202ALA00.022-0.00218.834-0.008-0.0080.0000.0000.0000.000
124B203GLY0-0.013-0.01917.8650.0130.0130.0000.0000.0000.000
125B204ALA00.0260.01812.556-0.011-0.0110.0000.0000.0000.000
126B205ASP-1-0.805-0.85211.642-0.007-0.0070.0000.0000.0000.000
127B206PHE00.0050.00613.9530.0260.0260.0000.0000.0000.000
128B207LEU0-0.0030.00115.802-0.020-0.0200.0000.0000.0000.000
129B208MET0-0.0380.00017.9040.0150.0150.0000.0000.0000.000
130B209CYS0-0.006-0.00120.937-0.010-0.0100.0000.0000.0000.000
131B210TYR00.0690.02122.8710.0090.0090.0000.0000.0000.000
132B211SER00.0540.01826.158-0.002-0.0020.0000.0000.0000.000
133B212VAL0-0.059-0.02629.006-0.001-0.0010.0000.0000.0000.000
134B213ALA00.0160.02726.8850.0010.0010.0000.0000.0000.000
135B222THR00.0480.03240.844-0.001-0.0010.0000.0000.0000.000
136B223VAL0-0.015-0.02341.9440.0010.0010.0000.0000.0000.000
137B224ASN0-0.063-0.03441.0050.0010.0010.0000.0000.0000.000
138B225GLY00.0360.03138.0030.0000.0000.0000.0000.0000.000
139B226SER0-0.018-0.01835.002-0.002-0.0020.0000.0000.0000.000
140B227TRP00.0340.00134.0830.0000.0000.0000.0000.0000.000
141B228TYR00.0670.03125.1100.0020.0020.0000.0000.0000.000
142B229ILE00.0230.02830.3010.0000.0000.0000.0000.0000.000
143B230GLN00.0110.00131.6510.0020.0020.0000.0000.0000.000
144B231ASP-1-0.791-0.90329.976-0.026-0.0260.0000.0000.0000.000
145B232LEU00.0100.01325.0830.0000.0000.0000.0000.0000.000
146B233CYS0-0.034-0.01927.8640.0040.0040.0000.0000.0000.000
147B234GLU-1-0.873-0.91730.474-0.017-0.0170.0000.0000.0000.000
148B235MET0-0.041-0.02425.5840.0000.0000.0000.0000.0000.000
149B236LEU00.0080.00424.4640.0030.0030.0000.0000.0000.000
150B237GLY0-0.045-0.02026.8740.0060.0060.0000.0000.0000.000
151B238LYS10.8340.90828.8030.0200.0200.0000.0000.0000.000
152B239TYR00.0330.00123.7490.0000.0000.0000.0000.0000.000
153B240GLY00.0300.02523.3040.0020.0020.0000.0000.0000.000
154B241SER0-0.020-0.00122.5790.0040.0040.0000.0000.0000.000
155B242SER0-0.021-0.03321.6760.0090.0090.0000.0000.0000.000
156B243LEU00.0020.00319.5230.0020.0020.0000.0000.0000.000
157B244GLU-1-0.818-0.87713.142-0.062-0.0620.0000.0000.0000.000
158B245PHE00.0620.00316.572-0.015-0.0150.0000.0000.0000.000
159B246THR0-0.027-0.04514.369-0.013-0.0130.0000.0000.0000.000
160B247GLU-1-0.878-0.92016.612-0.110-0.1100.0000.0000.0000.000
161B248LEU0-0.023-0.01718.0130.0030.0030.0000.0000.0000.000
162B249LEU0-0.007-0.01518.8800.0030.0030.0000.0000.0000.000
163B250THR0-0.014-0.00718.722-0.003-0.0030.0000.0000.0000.000
164B251LEU0-0.028-0.01821.3420.0030.0030.0000.0000.0000.000
165B252VAL0-0.0380.00024.2330.0030.0030.0000.0000.0000.000
166B253ASN00.0150.00522.1680.0080.0080.0000.0000.0000.000
167B254ARG10.9540.98424.0340.0720.0720.0000.0000.0000.000
168B255LYS10.8380.90127.2980.0310.0310.0000.0000.0000.000
169B256VAL0-0.0130.00129.3050.0030.0030.0000.0000.0000.000
170B257SER0-0.090-0.03328.9460.0000.0000.0000.0000.0000.000
171B258GLN0-0.046-0.00930.9680.0020.0020.0000.0000.0000.000
172B259ARG10.8940.95733.4890.0290.0290.0000.0000.0000.000
173B274GLN0-0.025-0.03531.2900.0020.0020.0000.0000.0000.000
174B275VAL00.0330.00826.845-0.001-0.0010.0000.0000.0000.000
175B276PRO0-0.0180.01125.9980.0000.0000.0000.0000.0000.000
176B277CYS0-0.030-0.01122.648-0.005-0.0050.0000.0000.0000.000
177B278PHE00.0190.00615.8740.0100.0100.0000.0000.0000.000
178B279ALA00.0110.01218.078-0.011-0.0110.0000.0000.0000.000
179B280SER00.018-0.01112.5660.0170.0170.0000.0000.0000.000
180B281MET0-0.022-0.00412.706-0.010-0.0100.0000.0000.0000.000
181B282LEU0-0.024-0.00111.4750.0070.0070.0000.0000.0000.000
182B283THR0-0.017-0.0186.852-0.039-0.0390.0000.0000.0000.000
183B284LYS10.8560.9436.380-0.539-0.5390.0000.0000.0000.000
184B285LYS10.8790.9448.2260.1220.1220.0000.0000.0000.000
185B286LEU00.0110.00010.8400.0630.0630.0000.0000.0000.000
186B287HIS00.0000.00614.3170.0040.0040.0000.0000.0000.000
187B288PHE00.014-0.00317.2970.0180.0180.0000.0000.0000.000
188B289PHE0-0.0050.00817.179-0.004-0.0040.0000.0000.0000.000
189B290PRO00.019-0.00522.1780.0070.0070.0000.0000.0000.000
190B291LYS10.8300.92422.457-0.129-0.1290.0000.0000.0000.000
191B292SER00.0120.01825.272-0.001-0.0010.0000.0000.0000.000