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: QYRNY

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2208804.695555
FMO2-HF: Nuclear repulsion 2131304.32959
FMO2-HF: Total energy -77500.365965
FMO2-MP2: Total energy -77720.344277


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.
0.7934.2250.098-1.252-2.2790.005
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 : 0.021 / q_NPA : 0.010
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].
3B33PRO00.0060.0103.097-0.6792.5860.094-1.239-2.1210.005
4B34ALA0-0.047-0.0323.9590.2220.3890.004-0.013-0.1580.000
5B35GLU-1-0.798-0.8655.5491.0281.0280.0000.0000.0000.000
6B36LYS10.8610.9197.7110.3330.3330.0000.0000.0000.000
7B37TYR00.000-0.02410.7720.0620.0620.0000.0000.0000.000
8B38LYS10.8420.90812.447-0.042-0.0420.0000.0000.0000.000
9B39MET0-0.022-0.01014.8380.0100.0100.0000.0000.0000.000
10B40ASP-1-0.815-0.89517.123-0.027-0.0270.0000.0000.0000.000
11B41HIS0-0.0380.00217.4120.0300.0300.0000.0000.0000.000
12B42ARG10.8640.91921.772-0.033-0.0330.0000.0000.0000.000
13B43ARG10.8300.89225.238-0.027-0.0270.0000.0000.0000.000
14B44ARG10.8660.91821.5180.0690.0690.0000.0000.0000.000
15B45GLY00.0470.01122.8030.0060.0060.0000.0000.0000.000
16B46ILE0-0.035-0.00925.146-0.005-0.0050.0000.0000.0000.000
17B47ALA00.0040.00126.258-0.002-0.0020.0000.0000.0000.000
18B48LEU0-0.005-0.00528.2750.0000.0000.0000.0000.0000.000
19B49ILE0-0.001-0.01329.838-0.005-0.0050.0000.0000.0000.000
20B50PHE00.0150.00031.0780.0020.0020.0000.0000.0000.000
21B51ASN0-0.020-0.02434.613-0.004-0.0040.0000.0000.0000.000
22B52HIS00.0100.01137.1950.0030.0030.0000.0000.0000.000
23B66GLY00.0530.01841.3580.0010.0010.0000.0000.0000.000
24B67THR00.0420.00738.431-0.003-0.0030.0000.0000.0000.000
25B68CYS0-0.017-0.00138.2920.0010.0010.0000.0000.0000.000
26B69ALA00.0380.02439.042-0.001-0.0010.0000.0000.0000.000
27B70ASP-1-0.743-0.85234.689-0.045-0.0450.0000.0000.0000.000
28B71ARG10.8820.91134.4530.0200.0200.0000.0000.0000.000
29B72ASP-1-0.794-0.85335.092-0.028-0.0280.0000.0000.0000.000
30B73ASN0-0.006-0.00434.801-0.003-0.0030.0000.0000.0000.000
31B74LEU00.0400.01029.154-0.004-0.0040.0000.0000.0000.000
32B75THR00.002-0.01531.3410.0000.0000.0000.0000.0000.000
33B76ARG10.8710.94533.0180.0540.0540.0000.0000.0000.000
34B77ARG10.8240.91629.1960.0700.0700.0000.0000.0000.000
35B78PHE00.014-0.00125.078-0.005-0.0050.0000.0000.0000.000
36B79SER00.008-0.01328.6970.0020.0020.0000.0000.0000.000
37B80ASP-1-0.862-0.92230.008-0.060-0.0600.0000.0000.0000.000
38B81LEU0-0.037-0.00624.147-0.006-0.0060.0000.0000.0000.000
39B82GLY00.0020.01225.859-0.002-0.0020.0000.0000.0000.000
40B83PHE0-0.059-0.03922.3550.0050.0050.0000.0000.0000.000
41B84GLU-1-0.854-0.91928.0080.0040.0040.0000.0000.0000.000
42B85VAL0-0.013-0.01630.5360.0030.0030.0000.0000.0000.000
43B86LYS10.8400.91732.0470.0010.0010.0000.0000.0000.000
44B87CYS0-0.032-0.00133.685-0.001-0.0010.0000.0000.0000.000
45B88PHE00.0300.00733.4610.0030.0030.0000.0000.0000.000
46B89ASN00.014-0.01338.098-0.004-0.0040.0000.0000.0000.000
47B90ASP-1-0.855-0.90740.650-0.009-0.0090.0000.0000.0000.000
48B91LEU0-0.0070.01637.5430.0020.0020.0000.0000.0000.000
49B92LYS10.8810.92741.196-0.009-0.0090.0000.0000.0000.000
50B93ALA00.022-0.01438.7190.0010.0010.0000.0000.0000.000
51B94GLU-1-0.895-0.93338.3160.0140.0140.0000.0000.0000.000
52B95GLU-1-0.821-0.91439.3950.0120.0120.0000.0000.0000.000
53B96LEU0-0.034-0.01433.7620.0010.0010.0000.0000.0000.000
54B97LEU0-0.009-0.02233.6570.0010.0010.0000.0000.0000.000
55B98LEU0-0.0080.01634.5380.0030.0030.0000.0000.0000.000
56B99LYS10.8230.90335.356-0.011-0.0110.0000.0000.0000.000
57B100ILE0-0.035-0.02128.7360.0010.0010.0000.0000.0000.000
58B101HIS00.0210.01830.4750.0010.0010.0000.0000.0000.000
59B102GLU-1-0.788-0.87431.4420.0220.0220.0000.0000.0000.000
60B103VAL0-0.014-0.01428.3810.0030.0030.0000.0000.0000.000
61B104SER0-0.081-0.04827.0790.0030.0030.0000.0000.0000.000
62B105THR00.005-0.01027.0150.0070.0070.0000.0000.0000.000
63B106VAL0-0.0230.00829.2000.0050.0050.0000.0000.0000.000
64B107SER0-0.019-0.01326.8110.0040.0040.0000.0000.0000.000
65B108HIS10.8810.93022.928-0.053-0.0530.0000.0000.0000.000
66B109ALA00.0330.02322.3050.0010.0010.0000.0000.0000.000
67B110ASP-1-0.781-0.85122.2250.0370.0370.0000.0000.0000.000
68B111ALA0-0.006-0.01023.055-0.012-0.0120.0000.0000.0000.000
69B112ASP-1-0.746-0.86019.288-0.008-0.0080.0000.0000.0000.000
70B113CYS0-0.086-0.03318.2250.0010.0010.0000.0000.0000.000
71B114PHE00.0140.00520.0270.0060.0060.0000.0000.0000.000
72B115VAL00.0250.02921.824-0.008-0.0080.0000.0000.0000.000
73B116CYS0-0.050-0.00224.4330.0080.0080.0000.0000.0000.000
74B117VAL0-0.015-0.00126.380-0.005-0.0050.0000.0000.0000.000
75B118PHE00.0250.00527.9890.0050.0050.0000.0000.0000.000
76B119LEU0-0.057-0.01431.579-0.004-0.0040.0000.0000.0000.000
77B120SER00.0530.02834.0980.0020.0020.0000.0000.0000.000
78B121ALA00.011-0.01034.4510.0020.0020.0000.0000.0000.000
79B122GLY00.0230.00032.8470.0010.0010.0000.0000.0000.000
80B123GLU-1-0.882-0.93033.932-0.024-0.0240.0000.0000.0000.000
81B124GLY00.0380.02932.1430.0040.0040.0000.0000.0000.000
82B125ASN0-0.040-0.02129.206-0.005-0.0050.0000.0000.0000.000
83B126HIS0-0.027-0.03030.2970.0030.0030.0000.0000.0000.000
84B127ILE00.0060.00631.056-0.004-0.0040.0000.0000.0000.000
85B128TYR0-0.016-0.02833.8110.0030.0030.0000.0000.0000.000
86B129ALA00.0260.01837.085-0.001-0.0010.0000.0000.0000.000
87B130TYR0-0.021-0.02039.5420.0000.0000.0000.0000.0000.000
88B131ASP-1-0.800-0.89042.8450.0050.0050.0000.0000.0000.000
89B132ALA0-0.0150.00140.5940.0010.0010.0000.0000.0000.000
90B133LYS10.8640.94936.2220.0040.0040.0000.0000.0000.000
91B134ILE00.006-0.00633.3010.0030.0030.0000.0000.0000.000
92B135GLU-1-0.765-0.85631.3410.0090.0090.0000.0000.0000.000
93B136ILE00.0510.02526.5220.0030.0030.0000.0000.0000.000
94B137GLN0-0.050-0.03826.275-0.002-0.0020.0000.0000.0000.000
95B138THR0-0.021-0.01526.9850.0060.0060.0000.0000.0000.000
96B139LEU0-0.0180.00328.8340.0040.0040.0000.0000.0000.000
97B140THR0-0.025-0.03323.4140.0030.0030.0000.0000.0000.000
98B141GLY00.0140.00623.7570.0050.0050.0000.0000.0000.000
99B142LEU0-0.027-0.01124.6150.0090.0090.0000.0000.0000.000
100B143PHE00.023-0.00322.1220.0050.0050.0000.0000.0000.000
101B144LYS10.8940.95419.766-0.049-0.0490.0000.0000.0000.000
102B145GLY00.009-0.00718.0250.0030.0030.0000.0000.0000.000
103B146ASP-1-0.889-0.96118.9820.0990.0990.0000.0000.0000.000
104B147LYS10.8720.94821.925-0.068-0.0680.0000.0000.0000.000
105B148CYS0-0.0260.00222.313-0.006-0.0060.0000.0000.0000.000
106B149HIS00.0720.03420.376-0.013-0.0130.0000.0000.0000.000
107B150SER00.003-0.00519.8270.0060.0060.0000.0000.0000.000
108B151LEU00.001-0.00419.055-0.008-0.0080.0000.0000.0000.000
109B152VAL00.0180.01814.853-0.011-0.0110.0000.0000.0000.000
110B153GLY00.0070.01412.2370.0190.0190.0000.0000.0000.000
111B154LYS10.7920.91713.057-0.084-0.0840.0000.0000.0000.000
112B155PRO0-0.0040.00614.654-0.003-0.0030.0000.0000.0000.000
113B156LYS10.7740.89115.787-0.043-0.0430.0000.0000.0000.000
114B157ILE0-0.0060.00018.800-0.008-0.0080.0000.0000.0000.000
115B158PHE00.0290.00020.7830.0080.0080.0000.0000.0000.000
116B159ILE0-0.020-0.01123.421-0.007-0.0070.0000.0000.0000.000
117B160ILE00.0190.00725.7320.0060.0060.0000.0000.0000.000
118B161GLN0-0.039-0.04128.448-0.003-0.0030.0000.0000.0000.000
119B162ALA00.0320.02731.4240.0030.0030.0000.0000.0000.000
120B163CYS0-0.068-0.02933.6020.0000.0000.0000.0000.0000.000
121B200LEU00.0220.01820.548-0.002-0.0020.0000.0000.0000.000
122B201PRO0-0.037-0.01323.3780.0080.0080.0000.0000.0000.000
123B202ALA00.035-0.00818.688-0.009-0.0090.0000.0000.0000.000
124B203GLY0-0.012-0.02817.5350.0160.0160.0000.0000.0000.000
125B204ALA00.0440.02312.713-0.019-0.0190.0000.0000.0000.000
126B205ASP-1-0.788-0.87111.4130.0680.0680.0000.0000.0000.000
127B206PHE00.0010.00213.699-0.002-0.0020.0000.0000.0000.000
128B207LEU0-0.020-0.01315.524-0.022-0.0220.0000.0000.0000.000
129B208MET0-0.0020.03417.6490.0090.0090.0000.0000.0000.000
130B209CYS0-0.029-0.02020.412-0.017-0.0170.0000.0000.0000.000
131B210TYR00.0680.02022.2840.0120.0120.0000.0000.0000.000
132B211SER00.0510.01426.037-0.005-0.0050.0000.0000.0000.000
133B212VAL0-0.035-0.01128.800-0.003-0.0030.0000.0000.0000.000
134B213ALA0-0.027-0.00326.5840.0070.0070.0000.0000.0000.000
135B222THR00.0110.00640.1300.0010.0010.0000.0000.0000.000
136B223VAL00.0320.00541.5590.0000.0000.0000.0000.0000.000
137B224ASN0-0.034-0.01740.8530.0010.0010.0000.0000.0000.000
138B225GLY00.0370.03237.619-0.003-0.0030.0000.0000.0000.000
139B226SER0-0.050-0.06634.318-0.001-0.0010.0000.0000.0000.000
140B227TRP00.023-0.00733.971-0.003-0.0030.0000.0000.0000.000
141B228TYR00.0600.03224.868-0.001-0.0010.0000.0000.0000.000
142B229ILE00.0160.01929.760-0.005-0.0050.0000.0000.0000.000
143B230GLN00.0210.00831.664-0.004-0.0040.0000.0000.0000.000
144B231ASP-1-0.739-0.85229.334-0.080-0.0800.0000.0000.0000.000
145B232LEU00.0190.00924.824-0.007-0.0070.0000.0000.0000.000
146B233CYS0-0.029-0.01227.713-0.003-0.0030.0000.0000.0000.000
147B234GLU-1-0.836-0.89530.363-0.090-0.0900.0000.0000.0000.000
148B235MET0-0.020-0.00825.070-0.008-0.0080.0000.0000.0000.000
149B236LEU00.015-0.00523.919-0.008-0.0080.0000.0000.0000.000
150B237GLY0-0.039-0.02826.374-0.001-0.0010.0000.0000.0000.000
151B238LYS10.8230.90628.1410.0980.0980.0000.0000.0000.000
152B239TYR00.0430.00623.377-0.004-0.0040.0000.0000.0000.000
153B240GLY00.0360.02822.792-0.013-0.0130.0000.0000.0000.000
154B241SER0-0.021-0.00722.070-0.006-0.0060.0000.0000.0000.000
155B242SER0-0.019-0.01821.142-0.008-0.0080.0000.0000.0000.000
156B243LEU0-0.002-0.01019.138-0.027-0.0270.0000.0000.0000.000
157B244GLU-1-0.812-0.86412.579-0.259-0.2590.0000.0000.0000.000
158B245PHE00.0550.00216.2530.0110.0110.0000.0000.0000.000
159B246THR00.002-0.02413.5550.0090.0090.0000.0000.0000.000
160B247GLU-1-0.762-0.87116.395-0.197-0.1970.0000.0000.0000.000
161B248LEU0-0.056-0.01618.1440.0190.0190.0000.0000.0000.000
162B249LEU00.021-0.00418.6330.0140.0140.0000.0000.0000.000
163B250THR0-0.031-0.02118.5700.0150.0150.0000.0000.0000.000
164B251LEU0-0.048-0.02621.2730.0090.0090.0000.0000.0000.000
165B252VAL0-0.043-0.00524.0610.0100.0100.0000.0000.0000.000
166B253ASN00.015-0.00121.5030.0150.0150.0000.0000.0000.000
167B254ARG10.8590.94721.9990.1700.1700.0000.0000.0000.000
168B255LYS10.8060.88926.8470.0930.0930.0000.0000.0000.000
169B256VAL0-0.032-0.01529.1410.0060.0060.0000.0000.0000.000
170B257SER0-0.020-0.02428.3910.0040.0040.0000.0000.0000.000
171B258GLN0-0.084-0.02430.6160.0000.0000.0000.0000.0000.000
172B259ARG10.8040.90733.1540.0680.0680.0000.0000.0000.000
173B274GLN0-0.018-0.03231.3130.0020.0020.0000.0000.0000.000
174B275VAL00.0580.02026.705-0.005-0.0050.0000.0000.0000.000
175B276PRO0-0.039-0.00125.9950.0050.0050.0000.0000.0000.000
176B277CYS0-0.033-0.00522.516-0.004-0.0040.0000.0000.0000.000
177B278PHE00.004-0.00715.8400.0070.0070.0000.0000.0000.000
178B279ALA00.0150.01117.711-0.007-0.0070.0000.0000.0000.000
179B280SER0-0.002-0.00612.3630.0200.0200.0000.0000.0000.000
180B281MET0-0.0150.01312.5370.0070.0070.0000.0000.0000.000
181B282LEU0-0.052-0.01311.0210.0290.0290.0000.0000.0000.000
182B283THR0-0.022-0.0216.883-0.041-0.0410.0000.0000.0000.000
183B284LYS10.7820.8885.986-0.664-0.6640.0000.0000.0000.000
184B285LYS10.8640.9247.1730.6720.6720.0000.0000.0000.000
185B286LEU0-0.011-0.01410.4230.0570.0570.0000.0000.0000.000
186B287HIS00.0640.04014.110-0.034-0.0340.0000.0000.0000.000
187B288PHE0-0.003-0.00517.1990.0180.0180.0000.0000.0000.000
188B289PHE00.0190.00916.680-0.001-0.0010.0000.0000.0000.000
189B290PRO00.0100.00721.9500.0140.0140.0000.0000.0000.000
190B291LYS10.8120.89721.9710.0230.0230.0000.0000.0000.000
191B292SER00.0020.00924.8050.0000.0000.0000.0000.0000.000