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: G61Q1

Calculation Name: 3V6M-J-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: J

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 206
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2554684.884359
FMO2-HF: Nuclear repulsion 2469863.446776
FMO2-HF: Total energy -84821.437583
FMO2-MP2: Total energy -85063.762311


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(J:31:PHE)


Summations of interaction energy for fragment #1(J: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.
1.0592.824-0.026-0.649-1.090.001
Interaction energy analysis for fragmet #1(J:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.034
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].
3J33PRO00.0220.0223.807-1.0780.687-0.026-0.649-1.0900.001
4J34ALA0-0.089-0.0515.4040.4170.4170.0000.0000.0000.000
5J35GLU-1-0.925-0.9595.2642.3762.3760.0000.0000.0000.000
6J36LYS10.9430.9657.867-0.360-0.3600.0000.0000.0000.000
7J37TYR0-0.021-0.04910.2220.1230.1230.0000.0000.0000.000
8J38LYS10.8330.89311.814-0.273-0.2730.0000.0000.0000.000
9J39MET0-0.048-0.02014.174-0.048-0.0480.0000.0000.0000.000
10J40ASP-1-0.841-0.89217.5820.2540.2540.0000.0000.0000.000
11J41HIS0-0.049-0.01616.1220.0190.0190.0000.0000.0000.000
12J42ARG10.9340.95721.210-0.086-0.0860.0000.0000.0000.000
13J43ARG10.8320.89124.134-0.061-0.0610.0000.0000.0000.000
14J44ARG10.8680.93520.900-0.040-0.0400.0000.0000.0000.000
15J45GLY00.026-0.00321.923-0.001-0.0010.0000.0000.0000.000
16J46ILE0-0.028-0.01124.123-0.002-0.0020.0000.0000.0000.000
17J47ALA0-0.0060.00025.050-0.005-0.0050.0000.0000.0000.000
18J48LEU0-0.005-0.00727.2300.0030.0030.0000.0000.0000.000
19J49ILE00.0170.01128.981-0.006-0.0060.0000.0000.0000.000
20J50PHE0-0.006-0.00429.9900.0040.0040.0000.0000.0000.000
21J51ASN00.003-0.02333.777-0.006-0.0060.0000.0000.0000.000
22J52HIS00.0060.01335.7440.0030.0030.0000.0000.0000.000
23J53GLU-1-0.870-0.93139.058-0.021-0.0210.0000.0000.0000.000
24J54ARG10.9390.97142.2450.0150.0150.0000.0000.0000.000
25J55PHE0-0.025-0.01039.557-0.001-0.0010.0000.0000.0000.000
26J56PHE00.0250.01144.9310.0010.0010.0000.0000.0000.000
27J57TRP00.0420.01347.109-0.001-0.0010.0000.0000.0000.000
28J58HIS0-0.011-0.00949.791-0.001-0.0010.0000.0000.0000.000
29J59LEU0-0.038-0.00242.623-0.001-0.0010.0000.0000.0000.000
30J60THR0-0.052-0.01646.103-0.001-0.0010.0000.0000.0000.000
31J61LEU0-0.0180.00341.428-0.002-0.0020.0000.0000.0000.000
32J62PRO0-0.0010.00543.7090.0020.0020.0000.0000.0000.000
33J63GLU-1-0.824-0.91444.084-0.020-0.0200.0000.0000.0000.000
34J64ARG10.8590.94136.1990.0350.0350.0000.0000.0000.000
35J65ARG10.7800.85242.3770.0220.0220.0000.0000.0000.000
36J66GLY00.0290.01741.828-0.002-0.0020.0000.0000.0000.000
37J67THR00.0520.03337.660-0.003-0.0030.0000.0000.0000.000
38J68CYS0-0.015-0.01138.0450.0000.0000.0000.0000.0000.000
39J69ALA00.0440.03539.3990.0010.0010.0000.0000.0000.000
40J70ASP-1-0.771-0.87334.773-0.038-0.0380.0000.0000.0000.000
41J71ARG10.8300.90634.6150.0140.0140.0000.0000.0000.000
42J72ASP-1-0.842-0.91035.036-0.011-0.0110.0000.0000.0000.000
43J73ASN0-0.047-0.03434.5980.0040.0040.0000.0000.0000.000
44J74LEU00.045-0.00529.0520.0000.0000.0000.0000.0000.000
45J75THR0-0.009-0.02031.0150.0020.0020.0000.0000.0000.000
46J76ARG10.9280.98332.7530.0190.0190.0000.0000.0000.000
47J77ARG10.9130.96529.1800.0240.0240.0000.0000.0000.000
48J78PHE00.0420.01124.2790.0010.0010.0000.0000.0000.000
49J79SER00.0010.00328.2740.0060.0060.0000.0000.0000.000
50J80ASP-1-0.907-0.93630.1230.0070.0070.0000.0000.0000.000
51J81LEU0-0.069-0.02424.2400.0040.0040.0000.0000.0000.000
52J82GLY0-0.025-0.01925.3220.0070.0070.0000.0000.0000.000
53J83PHE0-0.048-0.03522.0060.0050.0050.0000.0000.0000.000
54J84GLU-1-0.914-0.95227.4530.0250.0250.0000.0000.0000.000
55J85VAL0-0.020-0.01529.400-0.003-0.0030.0000.0000.0000.000
56J86LYS10.9190.96431.051-0.011-0.0110.0000.0000.0000.000
57J87CYS0-0.025-0.00332.696-0.004-0.0040.0000.0000.0000.000
58J88PHE00.023-0.00533.2090.0030.0030.0000.0000.0000.000
59J89ASN00.0270.02337.080-0.005-0.0050.0000.0000.0000.000
60J90ASP-1-0.777-0.89339.712-0.017-0.0170.0000.0000.0000.000
61J91LEU0-0.0570.00036.2280.0010.0010.0000.0000.0000.000
62J92LYS11.0210.99839.6290.0090.0090.0000.0000.0000.000
63J93ALA00.002-0.01237.7320.0010.0010.0000.0000.0000.000
64J94GLU-1-0.913-0.95637.229-0.010-0.0100.0000.0000.0000.000
65J95GLU-1-0.857-0.94037.828-0.008-0.0080.0000.0000.0000.000
66J96LEU0-0.037-0.01432.4110.0010.0010.0000.0000.0000.000
67J97LEU00.030-0.00232.4440.0000.0000.0000.0000.0000.000
68J98LEU00.0240.01433.0530.0010.0010.0000.0000.0000.000
69J99LYS10.8970.97533.1090.0010.0010.0000.0000.0000.000
70J100ILE0-0.021-0.01727.4600.0020.0020.0000.0000.0000.000
71J101HIS00.0420.02228.8420.0000.0000.0000.0000.0000.000
72J102GLU-1-0.882-0.93329.6690.0090.0090.0000.0000.0000.000
73J103VAL00.006-0.00926.6460.0040.0040.0000.0000.0000.000
74J104SER0-0.102-0.04525.2480.0030.0030.0000.0000.0000.000
75J105THR0-0.073-0.03525.2630.0030.0030.0000.0000.0000.000
76J106VAL00.0040.02226.8190.0050.0050.0000.0000.0000.000
77J107SER00.0040.00025.1310.0010.0010.0000.0000.0000.000
78J108HIS10.8570.90721.459-0.019-0.0190.0000.0000.0000.000
79J109ALA00.0520.02620.6090.0050.0050.0000.0000.0000.000
80J110ASP-1-0.807-0.86720.6340.0860.0860.0000.0000.0000.000
81J111ALA0-0.018-0.01521.432-0.001-0.0010.0000.0000.0000.000
82J112ASP-1-0.684-0.84218.3050.1090.1090.0000.0000.0000.000
83J113CYS0-0.065-0.01517.084-0.008-0.0080.0000.0000.0000.000
84J114PHE0-0.026-0.01218.9610.0100.0100.0000.0000.0000.000
85J115VAL00.0310.03520.929-0.013-0.0130.0000.0000.0000.000
86J116CYS0-0.028-0.00423.5120.0100.0100.0000.0000.0000.000
87J117VAL0-0.009-0.00725.833-0.008-0.0080.0000.0000.0000.000
88J118PHE0-0.008-0.00827.1930.0060.0060.0000.0000.0000.000
89J119LEU0-0.016-0.00831.021-0.005-0.0050.0000.0000.0000.000
90J120SER00.017-0.00934.0470.0040.0040.0000.0000.0000.000
91J121HIS00.001-0.01035.856-0.005-0.0050.0000.0000.0000.000
92J122GLY00.028-0.01034.1930.0010.0010.0000.0000.0000.000
93J123GLU-1-0.846-0.88535.211-0.040-0.0400.0000.0000.0000.000
94J124GLY00.008-0.00133.6310.0010.0010.0000.0000.0000.000
95J125ASN0-0.0010.00029.377-0.001-0.0010.0000.0000.0000.000
96J126HIS00.000-0.01630.7180.0030.0030.0000.0000.0000.000
97J127ILE0-0.038-0.00831.328-0.002-0.0020.0000.0000.0000.000
98J128TYR0-0.018-0.02033.6910.0030.0030.0000.0000.0000.000
99J129ALA0-0.046-0.00636.9910.0000.0000.0000.0000.0000.000
100J130TYR00.0370.00138.2060.0000.0000.0000.0000.0000.000
101J131ASP-1-0.795-0.92041.676-0.018-0.0180.0000.0000.0000.000
102J132ALA00.0170.01140.4080.0000.0000.0000.0000.0000.000
103J133LYS10.8760.95936.6000.0370.0370.0000.0000.0000.000
104J134ILE00.0190.00831.9360.0020.0020.0000.0000.0000.000
105J135GLU-1-0.906-0.94630.182-0.048-0.0480.0000.0000.0000.000
106J136ILE00.023-0.00425.8320.0020.0020.0000.0000.0000.000
107J137GLN00.0110.00722.7730.0010.0010.0000.0000.0000.000
108J138THR0-0.030-0.01625.7530.0020.0020.0000.0000.0000.000
109J139LEU00.0270.02427.6180.0040.0040.0000.0000.0000.000
110J140THR00.007-0.01621.9790.0020.0020.0000.0000.0000.000
111J141GLY0-0.015-0.00722.287-0.001-0.0010.0000.0000.0000.000
112J142LEU0-0.018-0.01122.9780.0040.0040.0000.0000.0000.000
113J143PHE00.011-0.01320.6450.0070.0070.0000.0000.0000.000
114J144LYS10.9450.97818.0900.0650.0650.0000.0000.0000.000
115J145GLY00.0300.00316.5070.0090.0090.0000.0000.0000.000
116J146DAS-1-0.885-0.93717.4070.0160.0160.0000.0000.0000.000
117J147LYS10.9220.98720.2280.0060.0060.0000.0000.0000.000
118J148CYS0-0.062-0.02420.7730.0070.0070.0000.0000.0000.000
119J149HIS00.0400.01118.8880.0050.0050.0000.0000.0000.000
120J150SER0-0.024-0.01418.1280.0060.0060.0000.0000.0000.000
121J151LEU00.023-0.00617.8000.0100.0100.0000.0000.0000.000
122J152VAL0-0.0180.00112.866-0.020-0.0200.0000.0000.0000.000
123J153GLY00.0080.01410.8430.0300.0300.0000.0000.0000.000
124J154LYS10.7610.89911.643-0.066-0.0660.0000.0000.0000.000
125J155PRO00.0080.00713.696-0.026-0.0260.0000.0000.0000.000
126J156LYS10.8430.93714.5220.0870.0870.0000.0000.0000.000
127J157ILE00.0120.00518.084-0.020-0.0200.0000.0000.0000.000
128J158PHE00.012-0.00820.1650.0150.0150.0000.0000.0000.000
129J159ILE00.0020.00723.190-0.011-0.0110.0000.0000.0000.000
130J160ILE00.003-0.00525.6260.0090.0090.0000.0000.0000.000
131J161GLN0-0.030-0.00828.248-0.008-0.0080.0000.0000.0000.000
132J162ALA00.009-0.01531.2930.0050.0050.0000.0000.0000.000
133J163CYS00.0190.03833.607-0.003-0.0030.0000.0000.0000.000
134J198TYR00.011-0.01226.520-0.001-0.0010.0000.0000.0000.000
135J199THR0-0.0110.00724.0020.0020.0020.0000.0000.0000.000
136J200LEU00.0190.01920.018-0.005-0.0050.0000.0000.0000.000
137J201PRO00.011-0.00816.8510.0140.0140.0000.0000.0000.000
138J202ALA00.0250.01318.424-0.003-0.0030.0000.0000.0000.000
139J203GLY0-0.018-0.01915.5290.0100.0100.0000.0000.0000.000
140J204ALA00.0300.00710.300-0.010-0.0100.0000.0000.0000.000
141J205ASP-1-0.816-0.8829.928-0.170-0.1700.0000.0000.0000.000
142J206PHE0-0.029-0.00412.4650.0410.0410.0000.0000.0000.000
143J207LEU0-0.018-0.01115.435-0.032-0.0320.0000.0000.0000.000
144J208MET0-0.0310.00317.5000.0250.0250.0000.0000.0000.000
145J209CYS0-0.0080.00020.836-0.015-0.0150.0000.0000.0000.000
146J210TYR00.013-0.02022.6650.0160.0160.0000.0000.0000.000
147J211SER0-0.004-0.01526.188-0.005-0.0050.0000.0000.0000.000
148J212VAL0-0.0200.01827.9590.0020.0020.0000.0000.0000.000
149J222THR00.0270.00241.7010.0010.0010.0000.0000.0000.000
150J223VAL00.0420.01042.0460.0000.0000.0000.0000.0000.000
151J224ASN0-0.015-0.00441.7990.0030.0030.0000.0000.0000.000
152J225GLY00.0140.02838.1000.0000.0000.0000.0000.0000.000
153J226SER0-0.051-0.05034.822-0.002-0.0020.0000.0000.0000.000
154J227TRP00.0360.00034.660-0.001-0.0010.0000.0000.0000.000
155J228TYR00.0730.04425.1620.0020.0020.0000.0000.0000.000
156J229ILE00.0060.01230.336-0.002-0.0020.0000.0000.0000.000
157J230GLN0-0.027-0.04231.8610.0000.0000.0000.0000.0000.000
158J231ASP-1-0.788-0.89830.606-0.057-0.0570.0000.0000.0000.000
159J232LEU0-0.024-0.01525.089-0.002-0.0020.0000.0000.0000.000
160J233CYS0-0.028-0.01428.0110.0030.0030.0000.0000.0000.000
161J234GLU-1-0.956-0.96930.464-0.040-0.0400.0000.0000.0000.000
162J235MET0-0.050-0.03226.1670.0010.0010.0000.0000.0000.000
163J236LEU00.004-0.00124.4930.0020.0020.0000.0000.0000.000
164J237GLY0-0.030-0.01126.9900.0060.0060.0000.0000.0000.000
165J238LYS10.9200.97029.1580.0460.0460.0000.0000.0000.000
166J239TYR00.020-0.01124.2230.0040.0040.0000.0000.0000.000
167J240GLY00.0140.02323.587-0.004-0.0040.0000.0000.0000.000
168J241SER0-0.007-0.01822.6380.0010.0010.0000.0000.0000.000
169J242SER0-0.040-0.02722.2170.0060.0060.0000.0000.0000.000
170J243LEU0-0.014-0.00420.0150.0040.0040.0000.0000.0000.000
171J244GLU-1-0.785-0.82613.585-0.235-0.2350.0000.0000.0000.000
172J245PHE00.031-0.00816.808-0.008-0.0080.0000.0000.0000.000
173J246THR0-0.031-0.06614.537-0.005-0.0050.0000.0000.0000.000
174J247GLU-1-0.836-0.91017.223-0.173-0.1730.0000.0000.0000.000
175J248LEU0-0.036-0.01018.7930.0150.0150.0000.0000.0000.000
176J249LEU0-0.002-0.01719.1020.0110.0110.0000.0000.0000.000
177J250THR0-0.024-0.01519.4000.0030.0030.0000.0000.0000.000
178J251LEU0-0.049-0.02922.0670.0090.0090.0000.0000.0000.000
179J252VAL0-0.0060.01324.8240.0090.0090.0000.0000.0000.000
180J253ASN00.0230.01022.8500.0150.0150.0000.0000.0000.000
181J254ARG10.9730.99825.7090.1140.1140.0000.0000.0000.000
182J255LYS10.8920.94228.3230.0650.0650.0000.0000.0000.000
183J256VAL00.014-0.00330.0740.0060.0060.0000.0000.0000.000
184J257GLU-1-0.948-0.96230.229-0.091-0.0910.0000.0000.0000.000
185J258GLN0-0.064-0.04832.1470.0000.0000.0000.0000.0000.000
186J259ARG10.8010.92634.5760.0560.0560.0000.0000.0000.000
187J260ARG10.9420.98334.4890.0720.0720.0000.0000.0000.000
188J261VAL0-0.0020.00739.2180.0020.0020.0000.0000.0000.000
189J275VAL0-0.019-0.02527.5050.0030.0030.0000.0000.0000.000
190J276PRO0-0.026-0.01226.791-0.002-0.0020.0000.0000.0000.000
191J277CYS00.0270.00423.471-0.013-0.0130.0000.0000.0000.000
192J278PHE0-0.015-0.00416.2820.0110.0110.0000.0000.0000.000
193J279ALA00.0290.01418.186-0.015-0.0150.0000.0000.0000.000
194J280SER00.011-0.00312.6680.0240.0240.0000.0000.0000.000
195J281MET0-0.0130.01412.409-0.018-0.0180.0000.0000.0000.000
196J282LEU0-0.033-0.00511.0750.0090.0090.0000.0000.0000.000
197J283THR0-0.034-0.0265.630-0.043-0.0430.0000.0000.0000.000
198J284LYS10.9210.9795.607-0.639-0.6390.0000.0000.0000.000
199J285LYS10.9480.9907.8640.4810.4810.0000.0000.0000.000
200J286LEU0-0.016-0.01310.8380.1030.1030.0000.0000.0000.000
201J287HIS00.0010.00014.155-0.034-0.0340.0000.0000.0000.000
202J288PHE00.005-0.00917.2190.0190.0190.0000.0000.0000.000
203J289PHE00.0030.00917.2770.0000.0000.0000.0000.0000.000
204J290PRO00.0360.01421.9930.0060.0060.0000.0000.0000.000
205J291LYS10.8200.91121.663-0.090-0.0900.0000.0000.0000.000
206J292SER00.0140.02024.875-0.005-0.0050.0000.0000.0000.000