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: 396NL

Calculation Name: 3V6M-G-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: G

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 -2516038.636782
FMO2-HF: Nuclear repulsion 2432068.711207
FMO2-HF: Total energy -83969.925575
FMO2-MP2: Total energy -84209.655407


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(G:31:PHE)


Summations of interaction energy for fragment #1(G: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.
-0.8351.356-0.025-0.768-1.3970
Interaction energy analysis for fragmet #1(G:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.037
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].
3G33PRO00.0110.0203.836-0.9011.061-0.024-0.763-1.1750.000
4G34ALA0-0.054-0.0276.2070.0620.0620.0000.0000.0000.000
5G35GLU-1-0.944-0.9755.1710.6970.926-0.001-0.005-0.2220.000
6G36LYS10.9390.9637.889-0.341-0.3410.0000.0000.0000.000
7G37TYR0-0.014-0.03710.4700.0620.0620.0000.0000.0000.000
8G38LYS10.8330.89611.847-0.221-0.2210.0000.0000.0000.000
9G39MET0-0.049-0.02114.259-0.040-0.0400.0000.0000.0000.000
10G40ASP-1-0.841-0.89517.6020.2200.2200.0000.0000.0000.000
11G41HIS0-0.038-0.01316.4590.0140.0140.0000.0000.0000.000
12G42ARG10.9580.97321.437-0.080-0.0800.0000.0000.0000.000
13G43ARG10.8690.92324.441-0.059-0.0590.0000.0000.0000.000
14G44ARG10.8800.94820.883-0.051-0.0510.0000.0000.0000.000
15G45GLY00.0400.00622.244-0.001-0.0010.0000.0000.0000.000
16G46ILE0-0.023-0.00724.500-0.001-0.0010.0000.0000.0000.000
17G47ALA0-0.0020.00025.463-0.004-0.0040.0000.0000.0000.000
18G48LEU0-0.005-0.00927.5510.0020.0020.0000.0000.0000.000
19G49ILE00.0130.00829.299-0.005-0.0050.0000.0000.0000.000
20G50PHE0-0.012-0.00830.4400.0030.0030.0000.0000.0000.000
21G51ASN00.015-0.00934.159-0.005-0.0050.0000.0000.0000.000
22G52HIS00.0170.01336.2120.0010.0010.0000.0000.0000.000
23G53GLU-1-0.863-0.92539.082-0.012-0.0120.0000.0000.0000.000
24G54ARG10.9110.95342.1330.0080.0080.0000.0000.0000.000
25G55PHE0-0.022-0.00439.3900.0000.0000.0000.0000.0000.000
26G56PHE00.0250.00844.9000.0010.0010.0000.0000.0000.000
27G57TRP00.0380.01447.235-0.001-0.0010.0000.0000.0000.000
28G58HIS0-0.019-0.00749.729-0.001-0.0010.0000.0000.0000.000
29G59LEU0-0.035-0.00742.668-0.001-0.0010.0000.0000.0000.000
30G60THR0-0.058-0.02045.847-0.001-0.0010.0000.0000.0000.000
31G61LEU0-0.0110.00641.163-0.001-0.0010.0000.0000.0000.000
32G62PRO0-0.016-0.00243.3620.0010.0010.0000.0000.0000.000
33G63GLU-1-0.807-0.90643.838-0.013-0.0130.0000.0000.0000.000
34G64ARG10.8540.93436.0800.0230.0230.0000.0000.0000.000
35G65ARG10.7890.85342.1000.0140.0140.0000.0000.0000.000
36G66GLY00.0300.01641.774-0.001-0.0010.0000.0000.0000.000
37G67THR00.0420.01937.631-0.002-0.0020.0000.0000.0000.000
38G68CYS0-0.019-0.00537.9480.0000.0000.0000.0000.0000.000
39G69ALA00.0390.02539.4210.0010.0010.0000.0000.0000.000
40G70ASP-1-0.772-0.87434.798-0.024-0.0240.0000.0000.0000.000
41G71ARG10.8330.90934.6980.0060.0060.0000.0000.0000.000
42G72ASP-1-0.841-0.91335.144-0.002-0.0020.0000.0000.0000.000
43G73ASN0-0.062-0.04034.6720.0040.0040.0000.0000.0000.000
44G74LEU00.0560.00129.0680.0010.0010.0000.0000.0000.000
45G75THR0-0.008-0.01231.2450.0030.0030.0000.0000.0000.000
46G76ARG10.9250.97632.8710.0080.0080.0000.0000.0000.000
47G77ARG10.9210.97129.4440.0090.0090.0000.0000.0000.000
48G78PHE00.0380.01124.4550.0020.0020.0000.0000.0000.000
49G79SER0-0.002-0.00528.3260.0050.0050.0000.0000.0000.000
50G80ASP-1-0.910-0.93830.2060.0170.0170.0000.0000.0000.000
51G81LEU0-0.080-0.02724.5980.0040.0040.0000.0000.0000.000
52G82GLY0-0.018-0.02025.4180.0070.0070.0000.0000.0000.000
53G83PHE0-0.052-0.03522.0930.0040.0040.0000.0000.0000.000
54G84GLU-1-0.904-0.94927.5670.0290.0290.0000.0000.0000.000
55G85VAL0-0.018-0.00829.684-0.003-0.0030.0000.0000.0000.000
56G86LYS10.8990.95631.523-0.018-0.0180.0000.0000.0000.000
57G87CYS0-0.024-0.00633.014-0.003-0.0030.0000.0000.0000.000
58G88PHE00.0220.00033.5950.0020.0020.0000.0000.0000.000
59G89ASN00.0300.02237.404-0.004-0.0040.0000.0000.0000.000
60G90ASP-1-0.786-0.88639.941-0.009-0.0090.0000.0000.0000.000
61G91LEU0-0.0360.00736.6820.0010.0010.0000.0000.0000.000
62G92LYS10.9980.99140.1090.0030.0030.0000.0000.0000.000
63G93ALA00.010-0.01238.2920.0010.0010.0000.0000.0000.000
64G94GLU-1-0.916-0.95437.839-0.003-0.0030.0000.0000.0000.000
65G95GLU-1-0.861-0.94038.366-0.002-0.0020.0000.0000.0000.000
66G96LEU0-0.038-0.01432.8990.0010.0010.0000.0000.0000.000
67G97LEU00.0420.00032.9590.0000.0000.0000.0000.0000.000
68G98LEU00.0230.01633.6750.0010.0010.0000.0000.0000.000
69G99LYS10.8550.95333.608-0.006-0.0060.0000.0000.0000.000
70G100ILE0-0.017-0.01627.9900.0020.0020.0000.0000.0000.000
71G101HIS00.0280.01229.4180.0000.0000.0000.0000.0000.000
72G102GLU-1-0.859-0.91230.3920.0140.0140.0000.0000.0000.000
73G103VAL0-0.006-0.01127.1300.0030.0030.0000.0000.0000.000
74G104SER0-0.097-0.05425.9590.0030.0030.0000.0000.0000.000
75G105THR0-0.069-0.04626.0390.0020.0020.0000.0000.0000.000
76G106VAL0-0.0020.02527.3500.0040.0040.0000.0000.0000.000
77G107SER0-0.033-0.01825.7880.0010.0010.0000.0000.0000.000
78G108HIS00.028-0.00922.0070.0040.0040.0000.0000.0000.000
79G109ALA00.0170.00221.3140.0050.0050.0000.0000.0000.000
80G110ASP-1-0.875-0.91821.1500.0820.0820.0000.0000.0000.000
81G111ALA0-0.030-0.02121.903-0.001-0.0010.0000.0000.0000.000
82G112ASP-1-0.705-0.84318.6750.1030.1030.0000.0000.0000.000
83G113CYS0-0.075-0.02017.589-0.007-0.0070.0000.0000.0000.000
84G114PHE00.0210.01619.4100.0060.0060.0000.0000.0000.000
85G115VAL00.0200.02621.236-0.010-0.0100.0000.0000.0000.000
86G116CYS0-0.028-0.00223.8320.0070.0070.0000.0000.0000.000
87G117VAL0-0.013-0.01126.011-0.006-0.0060.0000.0000.0000.000
88G118PHE0-0.007-0.00327.4090.0040.0040.0000.0000.0000.000
89G119LEU0-0.013-0.00531.020-0.004-0.0040.0000.0000.0000.000
90G120SER00.014-0.01433.8910.0030.0030.0000.0000.0000.000
91G121HIS00.012-0.00135.484-0.004-0.0040.0000.0000.0000.000
92G122GLY00.018-0.01633.7500.0010.0010.0000.0000.0000.000
93G123GLU-1-0.894-0.92134.792-0.030-0.0300.0000.0000.0000.000
94G124GLY00.011-0.00432.8900.0010.0010.0000.0000.0000.000
95G125ASN0-0.0010.00529.132-0.001-0.0010.0000.0000.0000.000
96G126HIS0-0.015-0.02030.3520.0030.0030.0000.0000.0000.000
97G127ILE0-0.0150.00331.067-0.002-0.0020.0000.0000.0000.000
98G128TYR00.003-0.00133.6000.0020.0020.0000.0000.0000.000
99G129ALA0-0.0220.00937.0780.0000.0000.0000.0000.0000.000
100G130TYR00.007-0.01838.414-0.001-0.0010.0000.0000.0000.000
101G131ASP-1-0.791-0.92042.017-0.011-0.0110.0000.0000.0000.000
102G132ALA00.0090.00840.7140.0000.0000.0000.0000.0000.000
103G133LYS10.8910.97036.6520.0270.0270.0000.0000.0000.000
104G134ILE00.0280.01332.3480.0020.0020.0000.0000.0000.000
105G135GLU-1-0.910-0.95130.443-0.035-0.0350.0000.0000.0000.000
106G136ILE00.0190.00025.8310.0020.0020.0000.0000.0000.000
107G137GLN00.0140.00822.7100.0020.0020.0000.0000.0000.000
108G138THR0-0.029-0.01426.2380.0020.0020.0000.0000.0000.000
109G139LEU00.0210.01628.1650.0040.0040.0000.0000.0000.000
110G140THR00.004-0.01222.4870.0020.0020.0000.0000.0000.000
111G141GLY00.002-0.00722.9710.0000.0000.0000.0000.0000.000
112G142LEU0-0.025-0.00823.6820.0040.0040.0000.0000.0000.000
113G143PHE00.023-0.00821.2610.0060.0060.0000.0000.0000.000
114G144LYS10.9090.96918.9300.0490.0490.0000.0000.0000.000
115G145GLY00.032-0.00917.3200.0080.0080.0000.0000.0000.000
116G146DAS-1-0.939-0.96518.2440.0190.0190.0000.0000.0000.000
117G147LYS10.8940.97721.109-0.001-0.0010.0000.0000.0000.000
118G148CYS0-0.071-0.02321.4460.0060.0060.0000.0000.0000.000
119G149HIS00.0840.03918.780-0.005-0.0050.0000.0000.0000.000
120G150SER00.0210.00818.9390.0040.0040.0000.0000.0000.000
121G151LEU00.0410.00418.4560.0060.0060.0000.0000.0000.000
122G152VAL0-0.043-0.00813.762-0.018-0.0180.0000.0000.0000.000
123G153GLY0-0.0070.00411.5060.0240.0240.0000.0000.0000.000
124G154LYS10.7690.90412.260-0.067-0.0670.0000.0000.0000.000
125G155PRO00.001-0.00113.933-0.019-0.0190.0000.0000.0000.000
126G156LYS10.8650.95415.1620.0630.0630.0000.0000.0000.000
127G157ILE00.002-0.00518.290-0.016-0.0160.0000.0000.0000.000
128G158PHE00.021-0.00520.4230.0110.0110.0000.0000.0000.000
129G159ILE0-0.010-0.00322.993-0.008-0.0080.0000.0000.0000.000
130G160ILE00.007-0.00925.4630.0070.0070.0000.0000.0000.000
131G161GLN0-0.0270.00727.934-0.007-0.0070.0000.0000.0000.000
132G162ALA00.014-0.01230.9850.0040.0040.0000.0000.0000.000
133G163CYS00.0060.02833.180-0.002-0.0020.0000.0000.0000.000
134G198TYR00.021-0.00523.7720.0030.0030.0000.0000.0000.000
135G199THR0-0.012-0.00223.666-0.001-0.0010.0000.0000.0000.000
136G200LEU00.0280.02119.108-0.004-0.0040.0000.0000.0000.000
137G201PRO00.006-0.01216.4830.0120.0120.0000.0000.0000.000
138G202ALA00.0360.02218.361-0.003-0.0030.0000.0000.0000.000
139G203GLY0-0.026-0.02615.8890.0090.0090.0000.0000.0000.000
140G204ALA00.0380.01210.926-0.008-0.0080.0000.0000.0000.000
141G205ASP-1-0.819-0.88910.434-0.149-0.1490.0000.0000.0000.000
142G206PHE0-0.0190.00312.9600.0350.0350.0000.0000.0000.000
143G207LEU0-0.018-0.01115.167-0.026-0.0260.0000.0000.0000.000
144G208MET0-0.0310.00317.2640.0200.0200.0000.0000.0000.000
145G209CYS0-0.017-0.00520.468-0.011-0.0110.0000.0000.0000.000
146G210TYR00.005-0.01822.0670.0110.0110.0000.0000.0000.000
147G211SER0-0.017-0.03425.773-0.004-0.0040.0000.0000.0000.000
148G212VAL00.0010.01127.6940.0010.0010.0000.0000.0000.000
149G222THR00.0290.00241.5230.0000.0000.0000.0000.0000.000
150G223VAL00.0400.01041.8640.0000.0000.0000.0000.0000.000
151G224ASN0-0.019-0.00741.8620.0020.0020.0000.0000.0000.000
152G225GLY00.0120.03138.0410.0000.0000.0000.0000.0000.000
153G226SER0-0.048-0.04734.760-0.002-0.0020.0000.0000.0000.000
154G227TRP00.0390.00134.3690.0000.0000.0000.0000.0000.000
155G228TYR00.0820.04224.8840.0020.0020.0000.0000.0000.000
156G229ILE00.0070.01030.124-0.001-0.0010.0000.0000.0000.000
157G230GLN0-0.033-0.03931.8940.0000.0000.0000.0000.0000.000
158G231ASP-1-0.782-0.89230.454-0.038-0.0380.0000.0000.0000.000
159G232LEU0-0.020-0.00825.082-0.001-0.0010.0000.0000.0000.000
160G233CYS0-0.025-0.00728.1020.0030.0030.0000.0000.0000.000
161G234GLU-1-0.965-0.97730.578-0.024-0.0240.0000.0000.0000.000
162G235MET0-0.043-0.02926.2810.0020.0020.0000.0000.0000.000
163G236LEU0-0.004-0.00224.7090.0030.0030.0000.0000.0000.000
164G237GLY0-0.027-0.01327.2700.0060.0060.0000.0000.0000.000
165G238LYS10.9220.97129.4150.0270.0270.0000.0000.0000.000
166G239TYR00.031-0.00724.4840.0030.0030.0000.0000.0000.000
167G240GLY00.0220.03423.8430.0010.0010.0000.0000.0000.000
168G241SER00.004-0.00823.0740.0020.0020.0000.0000.0000.000
169G242SER0-0.055-0.03822.9040.0080.0080.0000.0000.0000.000
170G243LEU0-0.005-0.01020.4120.0060.0060.0000.0000.0000.000
171G244GLU-1-0.793-0.83013.730-0.114-0.1140.0000.0000.0000.000
172G245PHE00.034-0.00317.160-0.014-0.0140.0000.0000.0000.000
173G246THR0-0.019-0.05514.371-0.009-0.0090.0000.0000.0000.000
174G247GLU-1-0.840-0.91117.157-0.096-0.0960.0000.0000.0000.000
175G248LEU0-0.046-0.01818.7110.0050.0050.0000.0000.0000.000
176G249LEU00.007-0.01318.9600.0040.0040.0000.0000.0000.000
177G250THR0-0.023-0.01719.121-0.003-0.0030.0000.0000.0000.000
178G251LEU0-0.050-0.03121.7760.0030.0030.0000.0000.0000.000
179G252VAL0-0.0270.00224.5880.0050.0050.0000.0000.0000.000
180G253ASN00.0330.01422.2710.0100.0100.0000.0000.0000.000
181G254ARG10.9720.99725.4990.0810.0810.0000.0000.0000.000
182G255LYS10.8810.94528.0270.0430.0430.0000.0000.0000.000
183G256VAL0-0.014-0.01929.7330.0040.0040.0000.0000.0000.000
184G257GLU-1-0.984-0.98529.766-0.072-0.0720.0000.0000.0000.000
185G258GLN0-0.030-0.01731.7340.0050.0050.0000.0000.0000.000
186G259ARG10.8080.93034.2220.0390.0390.0000.0000.0000.000
187G275VAL0-0.003-0.01726.9440.0020.0020.0000.0000.0000.000
188G276PRO0-0.0330.00926.401-0.002-0.0020.0000.0000.0000.000
189G277CYS00.0150.00322.670-0.010-0.0100.0000.0000.0000.000
190G278PHE0-0.011-0.00215.8800.0090.0090.0000.0000.0000.000
191G279ALA00.0310.01817.561-0.013-0.0130.0000.0000.0000.000
192G280SER00.001-0.00812.2340.0190.0190.0000.0000.0000.000
193G281MET0-0.0050.01211.824-0.016-0.0160.0000.0000.0000.000
194G282LEU0-0.026-0.00710.929-0.001-0.0010.0000.0000.0000.000
195G283THR0-0.038-0.0266.002-0.049-0.0490.0000.0000.0000.000
196G284LYS10.9150.9775.860-0.215-0.2150.0000.0000.0000.000
197G285LYS10.9220.9788.2160.0620.0620.0000.0000.0000.000
198G286LEU0-0.003-0.01811.2790.0540.0540.0000.0000.0000.000
199G287HIS0-0.014-0.00614.532-0.018-0.0180.0000.0000.0000.000
200G288PHE0-0.005-0.00517.5720.0140.0140.0000.0000.0000.000
201G289PHE0-0.0090.00417.337-0.003-0.0030.0000.0000.0000.000
202G290PRO00.0300.00822.1680.0040.0040.0000.0000.0000.000
203G291LYS10.8030.89121.794-0.087-0.0870.0000.0000.0000.000
204G292SER00.0120.01924.982-0.008-0.0080.0000.0000.0000.000