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: R9ZY8

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 OptHSide
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 -2202632.917908
FMO2-HF: Nuclear repulsion 2125133.184322
FMO2-HF: Total energy -77499.733587
FMO2-MP2: Total energy -77719.649354


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.
0.3863.9280.021-1.369-2.1960.006
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 : 0.014 / q_NPA : 0.008
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].
3B33PRO00.0120.0153.127-1.0162.3650.020-1.349-2.0530.006
4B34ALA0-0.060-0.0304.3140.1670.3280.001-0.020-0.1430.000
5B35GLU-1-0.826-0.8945.7910.7540.7540.0000.0000.0000.000
6B36LYS10.8640.9337.8510.3000.3000.0000.0000.0000.000
7B37TYR0-0.012-0.02911.0930.0550.0550.0000.0000.0000.000
8B38LYS10.8550.92312.659-0.014-0.0140.0000.0000.0000.000
9B39MET0-0.051-0.02414.9230.0070.0070.0000.0000.0000.000
10B40ASP-1-0.817-0.89917.355-0.022-0.0220.0000.0000.0000.000
11B41HIS0-0.039-0.00317.5480.0280.0280.0000.0000.0000.000
12B42ARG10.8740.92522.324-0.022-0.0220.0000.0000.0000.000
13B43ARG10.8620.90625.285-0.012-0.0120.0000.0000.0000.000
14B44ARG10.8830.93421.2650.0810.0810.0000.0000.0000.000
15B45GLY00.0280.00123.2450.0030.0030.0000.0000.0000.000
16B46ILE0-0.024-0.00725.655-0.003-0.0030.0000.0000.0000.000
17B47ALA00.0070.00626.461-0.004-0.0040.0000.0000.0000.000
18B48LEU0-0.024-0.01528.3960.0030.0030.0000.0000.0000.000
19B49ILE00.0220.00830.056-0.005-0.0050.0000.0000.0000.000
20B50PHE00.007-0.00731.0430.0040.0040.0000.0000.0000.000
21B51ASN0-0.015-0.02734.608-0.005-0.0050.0000.0000.0000.000
22B52HIS00.0240.01337.3120.0030.0030.0000.0000.0000.000
23B66GLY00.0420.01142.2650.0010.0010.0000.0000.0000.000
24B67THR00.0760.02738.881-0.003-0.0030.0000.0000.0000.000
25B68CYS0-0.036-0.01538.7590.0000.0000.0000.0000.0000.000
26B69ALA00.0440.02839.485-0.001-0.0010.0000.0000.0000.000
27B70ASP-1-0.755-0.87135.158-0.055-0.0550.0000.0000.0000.000
28B71ARG10.8840.92534.9760.0280.0280.0000.0000.0000.000
29B72ASP-1-0.805-0.87535.403-0.036-0.0360.0000.0000.0000.000
30B73ASN0-0.012-0.00734.881-0.002-0.0020.0000.0000.0000.000
31B74LEU00.0370.00129.517-0.004-0.0040.0000.0000.0000.000
32B75THR0-0.010-0.01031.356-0.001-0.0010.0000.0000.0000.000
33B76ARG10.8780.94732.9100.0590.0590.0000.0000.0000.000
34B77ARG10.8670.95729.2940.0750.0750.0000.0000.0000.000
35B78PHE00.0350.01025.044-0.005-0.0050.0000.0000.0000.000
36B79SER00.026-0.00228.5870.0020.0020.0000.0000.0000.000
37B80ASP-1-0.907-0.93830.113-0.065-0.0650.0000.0000.0000.000
38B81LEU0-0.062-0.02724.380-0.006-0.0060.0000.0000.0000.000
39B82GLY0-0.031-0.01325.843-0.002-0.0020.0000.0000.0000.000
40B83PHE0-0.069-0.04122.4150.0050.0050.0000.0000.0000.000
41B84GLU-1-0.851-0.90728.211-0.010-0.0100.0000.0000.0000.000
42B85VAL0-0.023-0.02730.5580.0010.0010.0000.0000.0000.000
43B86LYS10.8540.93432.4520.0120.0120.0000.0000.0000.000
44B87CYS0-0.025-0.00733.963-0.002-0.0020.0000.0000.0000.000
45B88PHE00.0180.00333.5390.0030.0030.0000.0000.0000.000
46B89ASN0-0.032-0.04838.291-0.004-0.0040.0000.0000.0000.000
47B90ASP-1-0.840-0.88840.726-0.017-0.0170.0000.0000.0000.000
48B91LEU00.0060.01837.6540.0020.0020.0000.0000.0000.000
49B92LYS10.9390.95941.0130.0010.0010.0000.0000.0000.000
50B93ALA00.023-0.01139.2240.0000.0000.0000.0000.0000.000
51B94GLU-1-0.967-0.97738.9580.0050.0050.0000.0000.0000.000
52B95GLU-1-0.826-0.92039.9060.0020.0020.0000.0000.0000.000
53B96LEU0-0.032-0.01433.8510.0000.0000.0000.0000.0000.000
54B97LEU0-0.018-0.02534.1860.0000.0000.0000.0000.0000.000
55B98LEU00.0000.01734.9210.0020.0020.0000.0000.0000.000
56B99LYS10.8280.90635.9050.0000.0000.0000.0000.0000.000
57B100ILE0-0.019-0.01029.2010.0010.0010.0000.0000.0000.000
58B101HIS00.0150.01330.8160.0000.0000.0000.0000.0000.000
59B102GLU-1-0.775-0.87331.6640.0090.0090.0000.0000.0000.000
60B103VAL0-0.053-0.02828.6490.0020.0020.0000.0000.0000.000
61B104SER0-0.093-0.06427.2240.0030.0030.0000.0000.0000.000
62B105THR0-0.002-0.01127.2930.0050.0050.0000.0000.0000.000
63B106VAL0-0.0150.02329.2510.0040.0040.0000.0000.0000.000
64B107SER0-0.009-0.00826.7730.0020.0020.0000.0000.0000.000
65B108HIS10.8790.93323.122-0.027-0.0270.0000.0000.0000.000
66B109ALA00.0380.02022.592-0.001-0.0010.0000.0000.0000.000
67B110ASP-1-0.787-0.85522.3110.0230.0230.0000.0000.0000.000
68B111ALA0-0.023-0.02023.079-0.009-0.0090.0000.0000.0000.000
69B112ASP-1-0.718-0.84019.585-0.026-0.0260.0000.0000.0000.000
70B113CYS0-0.069-0.02818.565-0.004-0.0040.0000.0000.0000.000
71B114PHE00.0040.00520.4220.0070.0070.0000.0000.0000.000
72B115VAL00.0260.03122.055-0.008-0.0080.0000.0000.0000.000
73B116CYS0-0.047-0.01124.4550.0090.0090.0000.0000.0000.000
74B117VAL0-0.002-0.00126.475-0.006-0.0060.0000.0000.0000.000
75B118PHE00.016-0.00128.2630.0050.0050.0000.0000.0000.000
76B119LEU0-0.0550.00931.571-0.004-0.0040.0000.0000.0000.000
77B120SER00.0630.02133.9950.0020.0020.0000.0000.0000.000
78B121ALA0-0.017-0.00634.1820.0030.0030.0000.0000.0000.000
79B122GLY00.0480.01932.738-0.002-0.0020.0000.0000.0000.000
80B123GLU-1-0.902-0.95233.793-0.035-0.0350.0000.0000.0000.000
81B124GLY0-0.006-0.01331.7950.0030.0030.0000.0000.0000.000
82B125ASN0-0.003-0.00829.391-0.004-0.0040.0000.0000.0000.000
83B126HIS00.001-0.01130.6170.0030.0030.0000.0000.0000.000
84B127ILE00.0110.00331.503-0.004-0.0040.0000.0000.0000.000
85B128TYR0-0.032-0.01934.3020.0030.0030.0000.0000.0000.000
86B129ALA00.0130.01737.587-0.001-0.0010.0000.0000.0000.000
87B130TYR0-0.020-0.02839.3900.0000.0000.0000.0000.0000.000
88B131ASP-1-0.791-0.89143.048-0.005-0.0050.0000.0000.0000.000
89B132ALA0-0.0050.00440.7970.0010.0010.0000.0000.0000.000
90B133LYS10.8910.96836.9800.0160.0160.0000.0000.0000.000
91B134ILE00.0150.00033.5070.0030.0030.0000.0000.0000.000
92B135GLU-1-0.843-0.90231.249-0.006-0.0060.0000.0000.0000.000
93B136ILE00.0650.02826.6580.0020.0020.0000.0000.0000.000
94B137GLN0-0.057-0.04626.172-0.004-0.0040.0000.0000.0000.000
95B138THR0-0.013-0.00727.2320.0050.0050.0000.0000.0000.000
96B139LEU0-0.0090.01129.0630.0030.0030.0000.0000.0000.000
97B140THR0-0.022-0.02423.5360.0030.0030.0000.0000.0000.000
98B141GLY00.0250.00924.0740.0030.0030.0000.0000.0000.000
99B142LEU0-0.035-0.01024.5640.0070.0070.0000.0000.0000.000
100B143PHE00.014-0.01822.3680.0040.0040.0000.0000.0000.000
101B144LYS10.8580.92919.915-0.017-0.0170.0000.0000.0000.000
102B145GLY00.000-0.01618.0220.0050.0050.0000.0000.0000.000
103B146ASP-1-0.897-0.96919.0010.0610.0610.0000.0000.0000.000
104B147LYS10.9220.97621.617-0.035-0.0350.0000.0000.0000.000
105B148CYS0-0.0370.00422.472-0.003-0.0030.0000.0000.0000.000
106B149HIS00.0850.03520.022-0.012-0.0120.0000.0000.0000.000
107B150SER00.0140.00119.9020.0030.0030.0000.0000.0000.000
108B151LEU00.0220.00219.547-0.004-0.0040.0000.0000.0000.000
109B152VAL0-0.0170.01215.019-0.013-0.0130.0000.0000.0000.000
110B153GLY0-0.0210.00212.5900.0180.0180.0000.0000.0000.000
111B154LYS10.7930.91113.089-0.062-0.0620.0000.0000.0000.000
112B155PRO0-0.0030.00814.987-0.001-0.0010.0000.0000.0000.000
113B156LYS10.7910.90816.0910.0130.0130.0000.0000.0000.000
114B157ILE0-0.008-0.01218.742-0.012-0.0120.0000.0000.0000.000
115B158PHE00.0310.00820.8950.0100.0100.0000.0000.0000.000
116B159ILE0-0.017-0.01123.379-0.008-0.0080.0000.0000.0000.000
117B160ILE00.0030.00925.8600.0070.0070.0000.0000.0000.000
118B161GLN0-0.027-0.03928.526-0.002-0.0020.0000.0000.0000.000
119B162ALA00.0340.01831.3250.0030.0030.0000.0000.0000.000
120B163CYS0-0.0290.00033.5540.0000.0000.0000.0000.0000.000
121B200LEU00.0170.01620.498-0.001-0.0010.0000.0000.0000.000
122B201PRO0-0.034-0.01923.2550.0060.0060.0000.0000.0000.000
123B202ALA00.029-0.00718.669-0.009-0.0090.0000.0000.0000.000
124B203GLY00.005-0.00917.6850.0170.0170.0000.0000.0000.000
125B204ALA00.0270.02112.497-0.017-0.0170.0000.0000.0000.000
126B205ASP-1-0.809-0.88111.438-0.033-0.0330.0000.0000.0000.000
127B206PHE00.0090.01114.0010.0100.0100.0000.0000.0000.000
128B207LEU0-0.001-0.00115.624-0.022-0.0220.0000.0000.0000.000
129B208MET0-0.0300.01117.7550.0130.0130.0000.0000.0000.000
130B209CYS0-0.011-0.00420.847-0.016-0.0160.0000.0000.0000.000
131B210TYR00.0650.01922.6860.0120.0120.0000.0000.0000.000
132B211SER00.0570.01926.088-0.005-0.0050.0000.0000.0000.000
133B212VAL0-0.036-0.01628.964-0.003-0.0030.0000.0000.0000.000
134B213ALA0-0.0180.00826.9110.0070.0070.0000.0000.0000.000
135B222THR00.0320.01941.0250.0000.0000.0000.0000.0000.000
136B223VAL00.001-0.01441.9060.0000.0000.0000.0000.0000.000
137B224ASN0-0.051-0.02841.0190.0010.0010.0000.0000.0000.000
138B225GLY00.0230.02137.969-0.003-0.0030.0000.0000.0000.000
139B226SER0-0.041-0.04534.8970.0000.0000.0000.0000.0000.000
140B227TRP00.0460.00034.274-0.004-0.0040.0000.0000.0000.000
141B228TYR00.0700.03225.124-0.001-0.0010.0000.0000.0000.000
142B229ILE00.0210.03030.151-0.006-0.0060.0000.0000.0000.000
143B230GLN00.0080.01031.620-0.002-0.0020.0000.0000.0000.000
144B231ASP-1-0.763-0.86829.924-0.087-0.0870.0000.0000.0000.000
145B232LEU00.0160.01225.043-0.007-0.0070.0000.0000.0000.000
146B233CYS0-0.032-0.02027.849-0.004-0.0040.0000.0000.0000.000
147B234GLU-1-0.852-0.90530.448-0.094-0.0940.0000.0000.0000.000
148B235MET0-0.025-0.01425.616-0.007-0.0070.0000.0000.0000.000
149B236LEU00.0140.00624.377-0.007-0.0070.0000.0000.0000.000
150B237GLY0-0.033-0.02926.858-0.001-0.0010.0000.0000.0000.000
151B238LYS10.8250.90728.7300.1010.1010.0000.0000.0000.000
152B239TYR00.028-0.00723.760-0.003-0.0030.0000.0000.0000.000
153B240GLY00.0320.02423.330-0.013-0.0130.0000.0000.0000.000
154B241SER0-0.027-0.00422.553-0.008-0.0080.0000.0000.0000.000
155B242SER0-0.023-0.02821.570-0.007-0.0070.0000.0000.0000.000
156B243LEU00.0120.00019.364-0.025-0.0250.0000.0000.0000.000
157B244GLU-1-0.819-0.87113.211-0.275-0.2750.0000.0000.0000.000
158B245PHE00.0710.00516.5800.0090.0090.0000.0000.0000.000
159B246THR0-0.014-0.03614.1850.0090.0090.0000.0000.0000.000
160B247GLU-1-0.875-0.93316.667-0.234-0.2340.0000.0000.0000.000
161B248LEU0-0.051-0.02218.0960.0190.0190.0000.0000.0000.000
162B249LEU00.004-0.00618.8050.0160.0160.0000.0000.0000.000
163B250THR0-0.020-0.00518.6780.0150.0150.0000.0000.0000.000
164B251LEU0-0.034-0.02121.4220.0130.0130.0000.0000.0000.000
165B252VAL0-0.0310.00424.3250.0110.0110.0000.0000.0000.000
166B253ASN00.0220.01021.8270.0170.0170.0000.0000.0000.000
167B254ARG10.9561.00223.5710.1640.1640.0000.0000.0000.000
168B255LYS10.8220.88627.4060.1000.1000.0000.0000.0000.000
169B256VAL0-0.021-0.00729.3650.0060.0060.0000.0000.0000.000
170B257SER0-0.069-0.04828.6170.0040.0040.0000.0000.0000.000
171B258GLN0-0.066-0.01631.0550.0010.0010.0000.0000.0000.000
172B259ARG10.8720.93833.5980.0760.0760.0000.0000.0000.000
173B274GLN0-0.026-0.03531.2070.0020.0020.0000.0000.0000.000
174B275VAL00.0370.01026.845-0.004-0.0040.0000.0000.0000.000
175B276PRO0-0.0220.00526.0080.0040.0040.0000.0000.0000.000
176B277CYS0-0.036-0.00922.632-0.003-0.0030.0000.0000.0000.000
177B278PHE00.0240.00515.9830.0090.0090.0000.0000.0000.000
178B279ALA00.0000.00818.018-0.007-0.0070.0000.0000.0000.000
179B280SER00.023-0.00912.6040.0140.0140.0000.0000.0000.000
180B281MET0-0.0200.01012.5600.0070.0070.0000.0000.0000.000
181B282LEU0-0.027-0.00311.4200.0190.0190.0000.0000.0000.000
182B283THR0-0.033-0.0287.003-0.042-0.0420.0000.0000.0000.000
183B284LYS10.8020.8946.171-0.374-0.3740.0000.0000.0000.000
184B285LYS10.8560.9297.5540.7090.7090.0000.0000.0000.000
185B286LEU00.010-0.00710.8010.0490.0490.0000.0000.0000.000
186B287HIS00.0470.03614.267-0.023-0.0230.0000.0000.0000.000
187B288PHE00.009-0.00617.2430.0200.0200.0000.0000.0000.000
188B289PHE00.0020.00717.021-0.001-0.0010.0000.0000.0000.000
189B290PRO00.0210.00322.1270.0120.0120.0000.0000.0000.000
190B291LYS10.8010.88422.3770.0370.0370.0000.0000.0000.000
191B292SER00.0090.01825.2760.0020.0020.0000.0000.0000.000