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: R9Z18

Calculation Name: 3V6M-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

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 204
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2514942.266769
FMO2-HF: Nuclear repulsion 2430971.991836
FMO2-HF: Total energy -83970.274933
FMO2-MP2: Total energy -84210.014482


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.
0.9452.816-0.019-0.714-1.1370
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 : -0.032 / q_NPA : -0.035
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].
3B33PRO00.0240.0223.833-0.1551.716-0.019-0.714-1.1370.000
4B34ALA0-0.045-0.0245.6420.3570.3570.0000.0000.0000.000
5B35GLU-1-0.946-0.9755.209-0.289-0.2890.0000.0000.0000.000
6B36LYS10.9270.9567.9000.4530.4530.0000.0000.0000.000
7B37TYR0-0.029-0.04910.789-0.009-0.0090.0000.0000.0000.000
8B38LYS10.8430.90012.3110.2030.2030.0000.0000.0000.000
9B39MET0-0.048-0.01714.6330.0190.0190.0000.0000.0000.000
10B40ASP-1-0.843-0.89517.900-0.183-0.1830.0000.0000.0000.000
11B41HIS0-0.054-0.02016.7460.0120.0120.0000.0000.0000.000
12B42ARG10.9640.97421.7490.0880.0880.0000.0000.0000.000
13B43ARG10.8880.94124.7500.0910.0910.0000.0000.0000.000
14B44ARG10.8610.93621.4010.1340.1340.0000.0000.0000.000
15B45GLY00.0360.00322.589-0.008-0.0080.0000.0000.0000.000
16B46ILE0-0.036-0.01624.8310.0030.0030.0000.0000.0000.000
17B47ALA0-0.0010.00225.780-0.006-0.0060.0000.0000.0000.000
18B48LEU0-0.005-0.00727.8070.0060.0060.0000.0000.0000.000
19B49ILE00.0140.00829.278-0.003-0.0030.0000.0000.0000.000
20B50PHE0-0.001-0.00130.5290.0040.0040.0000.0000.0000.000
21B51ASN00.015-0.01534.027-0.002-0.0020.0000.0000.0000.000
22B52HIS0-0.0070.00536.0110.0040.0040.0000.0000.0000.000
23B53GLU-1-0.820-0.88738.951-0.038-0.0380.0000.0000.0000.000
24B54ARG10.8420.91042.0250.0360.0360.0000.0000.0000.000
25B55PHE0-0.011-0.00839.262-0.001-0.0010.0000.0000.0000.000
26B56PHE00.0160.00544.7860.0010.0010.0000.0000.0000.000
27B57TRP00.0530.00947.1070.0000.0000.0000.0000.0000.000
28B58HIS0-0.052-0.02449.6650.0010.0010.0000.0000.0000.000
29B59LEU0-0.0300.00742.5280.0000.0000.0000.0000.0000.000
30B60THR0-0.050-0.01245.7710.0000.0000.0000.0000.0000.000
31B61LEU0-0.0080.00341.081-0.001-0.0010.0000.0000.0000.000
32B62PRO0-0.0020.00543.3520.0000.0000.0000.0000.0000.000
33B63GLU-1-0.838-0.91343.735-0.033-0.0330.0000.0000.0000.000
34B64ARG10.8440.92835.8940.0480.0480.0000.0000.0000.000
35B65ARG10.8110.86442.0300.0340.0340.0000.0000.0000.000
36B66GLY00.0310.01941.642-0.001-0.0010.0000.0000.0000.000
37B67THR00.0540.02837.463-0.003-0.0030.0000.0000.0000.000
38B68CYS0-0.030-0.00837.803-0.003-0.0030.0000.0000.0000.000
39B69ALA00.0490.03139.192-0.002-0.0020.0000.0000.0000.000
40B70ASP-1-0.786-0.88734.618-0.060-0.0600.0000.0000.0000.000
41B71ARG10.8460.91734.5760.0450.0450.0000.0000.0000.000
42B72ASP-1-0.826-0.90635.026-0.053-0.0530.0000.0000.0000.000
43B73ASN0-0.054-0.03934.583-0.004-0.0040.0000.0000.0000.000
44B74LEU00.0510.00529.034-0.004-0.0040.0000.0000.0000.000
45B75THR0-0.013-0.01531.161-0.004-0.0040.0000.0000.0000.000
46B76ARG10.9300.97233.0070.0570.0570.0000.0000.0000.000
47B77ARG10.8920.95129.3020.0740.0740.0000.0000.0000.000
48B78PHE00.0410.01924.396-0.005-0.0050.0000.0000.0000.000
49B79SER00.0080.00428.625-0.003-0.0030.0000.0000.0000.000
50B80ASP-1-0.914-0.93530.609-0.079-0.0790.0000.0000.0000.000
51B81LEU0-0.076-0.02924.632-0.005-0.0050.0000.0000.0000.000
52B82GLY0-0.019-0.02125.897-0.009-0.0090.0000.0000.0000.000
53B83PHE0-0.059-0.03922.450-0.001-0.0010.0000.0000.0000.000
54B84GLU-1-0.888-0.93728.036-0.065-0.0650.0000.0000.0000.000
55B85VAL0-0.024-0.01930.068-0.002-0.0020.0000.0000.0000.000
56B86LYS10.9160.96531.7820.0660.0660.0000.0000.0000.000
57B87CYS0-0.042-0.01233.299-0.002-0.0020.0000.0000.0000.000
58B88PHE00.0330.00633.9060.0020.0020.0000.0000.0000.000
59B89ASN00.0240.01037.352-0.003-0.0030.0000.0000.0000.000
60B90ASP-1-0.765-0.88339.790-0.037-0.0370.0000.0000.0000.000
61B91LEU0-0.0250.01136.7990.0010.0010.0000.0000.0000.000
62B92LYS10.9950.98939.9700.0280.0280.0000.0000.0000.000
63B93ALA00.001-0.01338.226-0.002-0.0020.0000.0000.0000.000
64B94GLU-1-0.912-0.95537.835-0.030-0.0300.0000.0000.0000.000
65B95GLU-1-0.863-0.94138.570-0.036-0.0360.0000.0000.0000.000
66B96LEU0-0.022-0.00932.811-0.002-0.0020.0000.0000.0000.000
67B97LEU00.0330.00033.000-0.003-0.0030.0000.0000.0000.000
68B98LEU00.0110.00733.868-0.002-0.0020.0000.0000.0000.000
69B99LYS10.8310.91634.1430.0440.0440.0000.0000.0000.000
70B100ILE0-0.004-0.00427.957-0.003-0.0030.0000.0000.0000.000
71B101HIS00.0320.01429.639-0.004-0.0040.0000.0000.0000.000
72B102GLU-1-0.842-0.88530.518-0.051-0.0510.0000.0000.0000.000
73B103VAL00.014-0.00427.420-0.003-0.0030.0000.0000.0000.000
74B104SER0-0.103-0.05226.022-0.005-0.0050.0000.0000.0000.000
75B105THR0-0.045-0.03126.078-0.001-0.0010.0000.0000.0000.000
76B106VAL0-0.0040.02327.5840.0020.0020.0000.0000.0000.000
77B107SER0-0.002-0.00525.852-0.006-0.0060.0000.0000.0000.000
78B108HIS10.8670.91422.1920.0920.0920.0000.0000.0000.000
79B109ALA00.0410.01721.356-0.010-0.0100.0000.0000.0000.000
80B110ASP-1-0.867-0.91921.300-0.099-0.0990.0000.0000.0000.000
81B111ALA0-0.031-0.02522.1110.0020.0020.0000.0000.0000.000
82B112ASP-1-0.705-0.84518.968-0.163-0.1630.0000.0000.0000.000
83B113CYS0-0.041-0.00617.729-0.014-0.0140.0000.0000.0000.000
84B114PHE0-0.038-0.01519.6000.0130.0130.0000.0000.0000.000
85B115VAL00.0370.03421.478-0.007-0.0070.0000.0000.0000.000
86B116CYS0-0.036-0.00423.9550.0100.0100.0000.0000.0000.000
87B117VAL00.001-0.00425.860-0.003-0.0030.0000.0000.0000.000
88B118PHE0-0.022-0.01227.2980.0050.0050.0000.0000.0000.000
89B119LEU0-0.005-0.00330.918-0.002-0.0020.0000.0000.0000.000
90B120SER00.010-0.02133.7640.0040.0040.0000.0000.0000.000
91B121HIS00.0060.00035.301-0.003-0.0030.0000.0000.0000.000
92B122GLY00.000-0.02233.712-0.001-0.0010.0000.0000.0000.000
93B123GLU-1-0.940-0.93734.735-0.033-0.0330.0000.0000.0000.000
94B124GLY00.0370.00632.8980.0010.0010.0000.0000.0000.000
95B125ASN0-0.018-0.00528.927-0.002-0.0020.0000.0000.0000.000
96B126HIS0-0.027-0.03030.2800.0000.0000.0000.0000.0000.000
97B127ILE0-0.025-0.00131.033-0.002-0.0020.0000.0000.0000.000
98B128TYR00.0110.00333.4720.0020.0020.0000.0000.0000.000
99B129ALA0-0.0310.00636.928-0.002-0.0020.0000.0000.0000.000
100B130TYR00.039-0.00238.2950.0020.0020.0000.0000.0000.000
101B131ASP-1-0.788-0.91641.906-0.031-0.0310.0000.0000.0000.000
102B132ALA00.0150.01240.5820.0020.0020.0000.0000.0000.000
103B133LYS10.9310.99236.5290.0290.0290.0000.0000.0000.000
104B134ILE00.0190.00332.1900.0010.0010.0000.0000.0000.000
105B135GLU-1-0.888-0.93830.271-0.038-0.0380.0000.0000.0000.000
106B136ILE00.001-0.00725.736-0.002-0.0020.0000.0000.0000.000
107B137GLN00.0200.00522.651-0.007-0.0070.0000.0000.0000.000
108B138THR0-0.026-0.01126.106-0.002-0.0020.0000.0000.0000.000
109B139LEU00.0090.01327.929-0.001-0.0010.0000.0000.0000.000
110B140THR00.017-0.00722.340-0.002-0.0020.0000.0000.0000.000
111B141GLY00.000-0.00622.935-0.006-0.0060.0000.0000.0000.000
112B142LEU0-0.035-0.01023.7300.0010.0010.0000.0000.0000.000
113B143PHE00.010-0.01721.342-0.001-0.0010.0000.0000.0000.000
114B144LYS10.8860.94518.9040.0550.0550.0000.0000.0000.000
115B145GLY00.032-0.00417.2680.0030.0030.0000.0000.0000.000
116B146DAS-1-0.925-0.95018.211-0.050-0.0500.0000.0000.0000.000
117B147LYS10.8920.96620.9910.0600.0600.0000.0000.0000.000
118B148CYS0-0.069-0.02521.4360.0000.0000.0000.0000.0000.000
119B149HIS00.1090.04918.441-0.010-0.0100.0000.0000.0000.000
120B150SER0-0.015-0.00918.900-0.011-0.0110.0000.0000.0000.000
121B151LEU00.013-0.01418.585-0.007-0.0070.0000.0000.0000.000
122B152VAL0-0.0140.00513.704-0.015-0.0150.0000.0000.0000.000
123B153GLY00.0150.01811.580-0.004-0.0040.0000.0000.0000.000
124B154LYS10.7570.90012.4030.1250.1250.0000.0000.0000.000
125B155PRO00.0100.00814.3350.0090.0090.0000.0000.0000.000
126B156LYS10.8340.92915.2060.1770.1770.0000.0000.0000.000
127B157ILE00.0290.01218.308-0.003-0.0030.0000.0000.0000.000
128B158PHE0-0.001-0.01720.2490.0110.0110.0000.0000.0000.000
129B159ILE00.0030.00922.932-0.004-0.0040.0000.0000.0000.000
130B160ILE0-0.006-0.01625.3770.0060.0060.0000.0000.0000.000
131B161GLN0-0.0150.00927.862-0.001-0.0010.0000.0000.0000.000
132B162ALA00.013-0.01630.8930.0030.0030.0000.0000.0000.000
133B163CYS00.0170.03533.1540.0000.0000.0000.0000.0000.000
134B198TYR00.0540.01925.582-0.001-0.0010.0000.0000.0000.000
135B199THR0-0.012-0.01423.6690.0050.0050.0000.0000.0000.000
136B200LEU00.0030.02918.822-0.007-0.0070.0000.0000.0000.000
137B201PRO00.027-0.01016.3770.0060.0060.0000.0000.0000.000
138B202ALA00.0420.02218.2210.0040.0040.0000.0000.0000.000
139B203GLY00.004-0.00215.7020.0150.0150.0000.0000.0000.000
140B204ALA00.0510.01810.892-0.009-0.0090.0000.0000.0000.000
141B205ASP-1-0.822-0.89110.642-0.281-0.2810.0000.0000.0000.000
142B206PHE0-0.0200.00512.9210.0180.0180.0000.0000.0000.000
143B207LEU0-0.015-0.01015.081-0.015-0.0150.0000.0000.0000.000
144B208MET0-0.0350.00517.1630.0100.0100.0000.0000.0000.000
145B209CYS0-0.002-0.00120.398-0.008-0.0080.0000.0000.0000.000
146B210TYR0-0.012-0.03021.9930.0080.0080.0000.0000.0000.000
147B211SER0-0.012-0.02525.716-0.002-0.0020.0000.0000.0000.000
148B212VAL00.0000.01127.7120.0030.0030.0000.0000.0000.000
149B222THR00.0330.00541.4490.0000.0000.0000.0000.0000.000
150B223VAL00.0380.00941.830-0.001-0.0010.0000.0000.0000.000
151B224ASN0-0.018-0.00641.7760.0000.0000.0000.0000.0000.000
152B225GLY00.0180.03738.006-0.003-0.0030.0000.0000.0000.000
153B226SER0-0.058-0.04634.6310.0010.0010.0000.0000.0000.000
154B227TRP00.0490.00534.384-0.003-0.0030.0000.0000.0000.000
155B228TYR00.0700.03624.859-0.001-0.0010.0000.0000.0000.000
156B229ILE00.0030.01330.086-0.005-0.0050.0000.0000.0000.000
157B230GLN0-0.023-0.04231.734-0.003-0.0030.0000.0000.0000.000
158B231ASP-1-0.780-0.88730.488-0.070-0.0700.0000.0000.0000.000
159B232LEU0-0.022-0.01325.005-0.005-0.0050.0000.0000.0000.000
160B233CYS0-0.045-0.01428.071-0.005-0.0050.0000.0000.0000.000
161B234GLU-1-0.953-0.97330.541-0.071-0.0710.0000.0000.0000.000
162B235MET0-0.030-0.02126.296-0.002-0.0020.0000.0000.0000.000
163B236LEU0-0.002-0.00324.615-0.006-0.0060.0000.0000.0000.000
164B237GLY0-0.029-0.01427.216-0.003-0.0030.0000.0000.0000.000
165B238LYS10.9260.97329.3910.0780.0780.0000.0000.0000.000
166B239TYR00.033-0.00224.5500.0020.0020.0000.0000.0000.000
167B240GLY00.0230.02923.893-0.011-0.0110.0000.0000.0000.000
168B241SER0-0.011-0.00923.109-0.010-0.0100.0000.0000.0000.000
169B242SER0-0.034-0.03422.919-0.005-0.0050.0000.0000.0000.000
170B243LEU00.0190.00620.319-0.012-0.0120.0000.0000.0000.000
171B244GLU-1-0.819-0.86413.792-0.279-0.2790.0000.0000.0000.000
172B245PHE00.043-0.00217.0860.0150.0150.0000.0000.0000.000
173B246THR0-0.022-0.04814.3840.0140.0140.0000.0000.0000.000
174B247GLU-1-0.829-0.90617.188-0.196-0.1960.0000.0000.0000.000
175B248LEU0-0.035-0.01018.7570.0190.0190.0000.0000.0000.000
176B249LEU00.002-0.01518.9430.0140.0140.0000.0000.0000.000
177B250THR0-0.023-0.01419.1990.0110.0110.0000.0000.0000.000
178B251LEU0-0.043-0.03321.8790.0130.0130.0000.0000.0000.000
179B252VAL0-0.0300.00624.6600.0100.0100.0000.0000.0000.000
180B253ASN00.0250.00722.3060.0110.0110.0000.0000.0000.000
181B254ARG10.9730.99825.1730.1000.1000.0000.0000.0000.000
182B255LYS10.9060.95327.9290.0780.0780.0000.0000.0000.000
183B256VAL0-0.005-0.01329.7810.0050.0050.0000.0000.0000.000
184B257GLU-1-0.993-0.98829.772-0.061-0.0610.0000.0000.0000.000
185B258GLN0-0.058-0.02931.7620.0000.0000.0000.0000.0000.000
186B259ARG10.8160.93234.1260.0620.0620.0000.0000.0000.000
187B275VAL00.002-0.01327.0290.0010.0010.0000.0000.0000.000
188B276PRO0-0.0420.00226.3510.0000.0000.0000.0000.0000.000
189B277CYS00.0260.00222.684-0.006-0.0060.0000.0000.0000.000
190B278PHE0-0.0100.00015.9320.0010.0010.0000.0000.0000.000
191B279ALA00.0270.01517.541-0.003-0.0030.0000.0000.0000.000
192B280SER00.014-0.00412.2110.0030.0030.0000.0000.0000.000
193B281MET0-0.0170.01311.7510.0000.0000.0000.0000.0000.000
194B282LEU0-0.042-0.01610.827-0.008-0.0080.0000.0000.0000.000
195B283THR0-0.021-0.0146.052-0.036-0.0360.0000.0000.0000.000
196B284LYS10.9160.9745.7670.3690.3690.0000.0000.0000.000
197B285LYS10.9260.9828.2370.3950.3950.0000.0000.0000.000
198B286LEU00.000-0.00511.2510.0050.0050.0000.0000.0000.000
199B287HIS0-0.022-0.01014.582-0.019-0.0190.0000.0000.0000.000
200B288PHE0-0.004-0.01017.757-0.001-0.0010.0000.0000.0000.000
201B289PHE0-0.0040.01617.3840.0080.0080.0000.0000.0000.000
202B290PRO00.0220.00622.3650.0000.0000.0000.0000.0000.000
203B291LYS10.8150.90622.1420.1330.1330.0000.0000.0000.000
204B292SER00.0100.01625.1050.0070.0070.0000.0000.0000.000