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: V53L1

Calculation Name: 3K7E-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3K7E

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2544977.365424
FMO2-HF: Nuclear repulsion 2460227.793671
FMO2-HF: Total energy -84749.571753
FMO2-MP2: Total energy -84991.595311


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:32:ASP)


Summations of interaction energy for fragment #1(B:32:ASP)
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.
-94.115-91.0280.15-1.356-1.8790.005
Interaction energy analysis for fragmet #1(B:32:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.881 / q_NPA : -0.950
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].
3B34ALA0-0.069-0.0403.751-12.653-10.673-0.010-0.877-1.0930.004
4B35GLU-1-0.806-0.8852.78130.51131.5340.160-0.461-0.7210.001
5B36LYS10.9190.9584.480-30.627-30.5430.000-0.018-0.0650.000
6B37TYR0-0.005-0.0368.1700.7640.7640.0000.0000.0000.000
7B38LYS10.8220.9087.335-28.485-28.4850.0000.0000.0000.000
8B39MET0-0.045-0.02912.500-1.089-1.0890.0000.0000.0000.000
9B40ASP-1-0.888-0.92914.42917.27417.2740.0000.0000.0000.000
10B41HIS0-0.043-0.00916.163-0.285-0.2850.0000.0000.0000.000
11B42ARG10.8320.90120.023-10.862-10.8620.0000.0000.0000.000
12B43ARG10.7830.84223.451-11.195-11.1950.0000.0000.0000.000
13B44ARG10.8620.93619.079-13.709-13.7090.0000.0000.0000.000
14B45GLY00.0510.00821.8140.5130.5130.0000.0000.0000.000
15B46ILE0-0.046-0.01524.404-0.349-0.3490.0000.0000.0000.000
16B47ALA00.0140.02826.2980.3450.3450.0000.0000.0000.000
17B48LEU0-0.026-0.01327.913-0.438-0.4380.0000.0000.0000.000
18B49ILE00.013-0.00330.1370.1680.1680.0000.0000.0000.000
19B50PHE0-0.008-0.00232.775-0.304-0.3040.0000.0000.0000.000
20B51ASN0-0.045-0.05034.6680.1390.1390.0000.0000.0000.000
21B52HIS10.7990.89237.701-8.000-8.0000.0000.0000.0000.000
22B53GLU-1-0.828-0.89939.3767.3857.3850.0000.0000.0000.000
23B54ARG10.8140.87740.934-7.677-7.6770.0000.0000.0000.000
24B55PHE0-0.004-0.01544.0650.1010.1010.0000.0000.0000.000
25B56PHE00.0140.03544.427-0.006-0.0060.0000.0000.0000.000
26B57TRP00.019-0.00446.951-0.061-0.0610.0000.0000.0000.000
27B58HIS00.0230.01749.9570.0650.0650.0000.0000.0000.000
28B59LEU00.0490.04345.6470.0750.0750.0000.0000.0000.000
29B60THR00.0660.02649.145-0.067-0.0670.0000.0000.0000.000
30B61LEU00.033-0.00349.0210.1070.1070.0000.0000.0000.000
31B62PRO00.0260.00547.0480.0840.0840.0000.0000.0000.000
32B63GLU-1-0.703-0.83044.1477.2977.2970.0000.0000.0000.000
33B64ARG10.9210.98144.136-6.169-6.1690.0000.0000.0000.000
34B65ARG10.9400.95442.515-7.030-7.0300.0000.0000.0000.000
35B66GLY00.0740.04542.7110.1130.1130.0000.0000.0000.000
36B67THR0-0.006-0.01939.6700.2500.2500.0000.0000.0000.000
37B68CYS0-0.092-0.03639.5590.1380.1380.0000.0000.0000.000
38B69ALA0-0.0220.00639.8990.1050.1050.0000.0000.0000.000
39B70ASP-1-0.723-0.86035.9918.7348.7340.0000.0000.0000.000
40B71ARG10.8870.92435.278-7.500-7.5000.0000.0000.0000.000
41B72ASP-1-0.847-0.91235.6427.8797.8790.0000.0000.0000.000
42B73ASN0-0.052-0.03034.3760.2140.2140.0000.0000.0000.000
43B74LEU00.0610.00930.1640.2310.2310.0000.0000.0000.000
44B75THR0-0.022-0.02031.0230.3150.3150.0000.0000.0000.000
45B76ARG10.9400.98932.157-8.253-8.2530.0000.0000.0000.000
46B77ARG10.9190.97128.725-9.537-9.5370.0000.0000.0000.000
47B78PHE00.0260.00324.2300.3290.3290.0000.0000.0000.000
48B79SER0-0.001-0.01527.3240.2360.2360.0000.0000.0000.000
49B80ASP-1-0.950-0.95728.6109.8299.8290.0000.0000.0000.000
50B81LEU0-0.052-0.02223.0100.3050.3050.0000.0000.0000.000
51B82GLY0-0.013-0.01323.7770.5030.5030.0000.0000.0000.000
52B83PHE0-0.033-0.03021.6180.1180.1180.0000.0000.0000.000
53B84GLU-1-0.823-0.88926.9279.5779.5770.0000.0000.0000.000
54B85VAL0-0.026-0.02429.9500.0620.0620.0000.0000.0000.000
55B86LYS10.8430.92231.447-9.668-9.6680.0000.0000.0000.000
56B87CYS0-0.0170.01133.6740.1390.1390.0000.0000.0000.000
57B88PHE0-0.004-0.01534.440-0.233-0.2330.0000.0000.0000.000
58B89ASN00.0530.01937.8940.1160.1160.0000.0000.0000.000
59B90ASP-1-0.690-0.79139.8937.5947.5940.0000.0000.0000.000
60B91LEU0-0.025-0.00841.548-0.126-0.1260.0000.0000.0000.000
61B92LYS10.8320.91943.203-7.099-7.0990.0000.0000.0000.000
62B93ALA00.0290.01243.4310.1580.1580.0000.0000.0000.000
63B94GLU-1-0.882-0.93444.0496.7886.7880.0000.0000.0000.000
64B95GLU-1-0.784-0.89442.3077.2427.2420.0000.0000.0000.000
65B96LEU0-0.029-0.00937.5920.1870.1870.0000.0000.0000.000
66B97LEU00.0250.01838.7100.2610.2610.0000.0000.0000.000
67B98LEU00.0800.03338.7150.2280.2280.0000.0000.0000.000
68B99LYS10.8940.94437.156-7.497-7.4970.0000.0000.0000.000
69B100ILE0-0.046-0.02033.6810.2770.2770.0000.0000.0000.000
70B101HIS00.0170.00333.7780.3630.3630.0000.0000.0000.000
71B102GLU-1-0.939-0.96034.4808.7718.7710.0000.0000.0000.000
72B103VAL0-0.050-0.03229.6050.2890.2890.0000.0000.0000.000
73B104SER0-0.071-0.03929.5160.3370.3370.0000.0000.0000.000
74B105THR0-0.020-0.01529.2310.2890.2890.0000.0000.0000.000
75B106VAL00.0110.03529.1540.1750.1750.0000.0000.0000.000
76B107SER00.0200.00927.1430.5370.5370.0000.0000.0000.000
77B108HIS10.8580.89923.544-11.385-11.3850.0000.0000.0000.000
78B109ALA00.0540.02322.2870.5320.5320.0000.0000.0000.000
79B110ASP-1-0.794-0.84721.82011.58011.5800.0000.0000.0000.000
80B111ALA0-0.004-0.00822.097-0.111-0.1110.0000.0000.0000.000
81B112ASP-1-0.693-0.83117.76015.38515.3850.0000.0000.0000.000
82B113CYS0-0.076-0.03917.7840.7260.7260.0000.0000.0000.000
83B114PHE0-0.017-0.00919.831-0.771-0.7710.0000.0000.0000.000
84B115VAL00.0290.02722.1630.4350.4350.0000.0000.0000.000
85B116CYS0-0.050-0.01124.592-0.587-0.5870.0000.0000.0000.000
86B117VAL00.0220.00127.3700.2150.2150.0000.0000.0000.000
87B118PHE00.0020.00429.812-0.374-0.3740.0000.0000.0000.000
88B119LEU00.015-0.00132.3400.0690.0690.0000.0000.0000.000
89B120SER0-0.080-0.07035.319-0.228-0.2280.0000.0000.0000.000
90B121HIS10.7930.87038.208-7.407-7.4070.0000.0000.0000.000
91B122GLY00.0270.01240.7750.1100.1100.0000.0000.0000.000
92B123GLU-1-0.861-0.90642.3496.4666.4660.0000.0000.0000.000
93B124GLY0-0.014-0.01043.321-0.019-0.0190.0000.0000.0000.000
94B125ASN0-0.003-0.00444.2450.0220.0220.0000.0000.0000.000
95B126HIS00.1020.02544.7610.2510.2510.0000.0000.0000.000
96B127ILE00.0070.01244.0240.1640.1640.0000.0000.0000.000
97B128TYR0-0.019-0.01640.7610.1940.1940.0000.0000.0000.000
98B129ALA00.0590.02340.3320.2130.2130.0000.0000.0000.000
99B130TYR0-0.049-0.03039.2090.2800.2800.0000.0000.0000.000
100B131ASP-1-0.753-0.85539.3897.8267.8260.0000.0000.0000.000
101B132ALA00.0210.01536.5980.1820.1820.0000.0000.0000.000
102B133LYS10.9480.97834.719-7.901-7.9010.0000.0000.0000.000
103B134ILE00.0150.01634.3000.2620.2620.0000.0000.0000.000
104B135GLH0-0.017-0.05635.1070.1920.1920.0000.0000.0000.000
105B136ILE00.0090.01429.7780.2280.2280.0000.0000.0000.000
106B137GLN0-0.0140.00530.3400.2430.2430.0000.0000.0000.000
107B138THR0-0.012-0.00830.3630.2590.2590.0000.0000.0000.000
108B139LEU0-0.012-0.00430.0940.2230.2230.0000.0000.0000.000
109B140THR0-0.042-0.03425.9900.3210.3210.0000.0000.0000.000
110B141GLY0-0.010-0.00926.1500.4420.4420.0000.0000.0000.000
111B142LEU0-0.039-0.02027.6060.1650.1650.0000.0000.0000.000
112B143PHE00.016-0.00823.7470.0630.0630.0000.0000.0000.000
113B144LYS10.8890.95122.606-11.484-11.4840.0000.0000.0000.000
114B145GLY00.0110.00020.735-0.248-0.2480.0000.0000.0000.000
115B146ASP-1-0.839-0.90721.58710.88310.8830.0000.0000.0000.000
116B147LYS10.7930.89024.677-10.855-10.8550.0000.0000.0000.000
117B148CYS0-0.0180.00523.936-0.215-0.2150.0000.0000.0000.000
118B149HIS00.0950.03122.2730.9040.9040.0000.0000.0000.000
119B150SER0-0.046-0.01321.2420.3670.3670.0000.0000.0000.000
120B151LEU00.0270.00720.0290.2940.2940.0000.0000.0000.000
121B152VAL00.0010.01916.7670.7750.7750.0000.0000.0000.000
122B153GLY0-0.0040.00913.7450.0940.0940.0000.0000.0000.000
123B154LYS10.7990.92013.545-13.817-13.8170.0000.0000.0000.000
124B155PRO00.0230.01114.503-0.446-0.4460.0000.0000.0000.000
125B156LYS10.8150.92816.781-17.068-17.0680.0000.0000.0000.000
126B157ILE0-0.007-0.00419.1160.2500.2500.0000.0000.0000.000
127B158PHE00.015-0.00421.616-0.680-0.6800.0000.0000.0000.000
128B159ILE00.008-0.00324.6970.2190.2190.0000.0000.0000.000
129B160ILE0-0.001-0.00926.928-0.449-0.4490.0000.0000.0000.000
130B161GLN00.0190.01729.8480.0250.0250.0000.0000.0000.000
131B162ALA00.0050.01532.976-0.230-0.2300.0000.0000.0000.000
132B163CYS00.0100.02234.688-0.265-0.2650.0000.0000.0000.000
133B202ALA0-0.001-0.00620.891-0.173-0.1730.0000.0000.0000.000
134B203GLY00.0540.02219.996-0.622-0.6220.0000.0000.0000.000
135B204ALA00.0450.02414.5180.2850.2850.0000.0000.0000.000
136B205ASP-1-0.823-0.89112.53120.75720.7570.0000.0000.0000.000
137B206PHE0-0.018-0.00115.199-0.812-0.8120.0000.0000.0000.000
138B207LEU0-0.014-0.00617.4200.7190.7190.0000.0000.0000.000
139B208MET0-0.0290.00319.365-0.593-0.5930.0000.0000.0000.000
140B209CYS00.0020.00722.8340.4100.4100.0000.0000.0000.000
141B210TYR00.0270.00524.734-0.433-0.4330.0000.0000.0000.000
142B211SER00.0510.00328.1570.0620.0620.0000.0000.0000.000
143B212VAL0-0.080-0.03731.156-0.081-0.0810.0000.0000.0000.000
144B213ALA00.0200.02329.4810.1280.1280.0000.0000.0000.000
145B214GLU-1-0.834-0.89229.65310.24010.2400.0000.0000.0000.000
146B215GLY0-0.034-0.02932.906-0.117-0.1170.0000.0000.0000.000
147B216TYR0-0.150-0.09832.135-0.282-0.2820.0000.0000.0000.000
148B217TYR0-0.009-0.00237.394-0.121-0.1210.0000.0000.0000.000
149B218SER00.008-0.00337.312-0.049-0.0490.0000.0000.0000.000
150B219HIS00.0350.03139.713-0.151-0.1510.0000.0000.0000.000
151B220ARG10.6800.80142.262-6.461-6.4610.0000.0000.0000.000
152B221GLU-1-0.784-0.87539.3627.8907.8900.0000.0000.0000.000
153B222THR0-0.014-0.02141.886-0.267-0.2670.0000.0000.0000.000
154B223VAL00.000-0.00243.4050.0570.0570.0000.0000.0000.000
155B224ASN0-0.035-0.02841.453-0.124-0.1240.0000.0000.0000.000
156B225GLY00.0130.02839.0600.1830.1830.0000.0000.0000.000
157B226SER0-0.062-0.04436.208-0.028-0.0280.0000.0000.0000.000
158B227TRP00.036-0.00135.9560.2150.2150.0000.0000.0000.000
159B228TYR00.0680.04226.9620.0870.0870.0000.0000.0000.000
160B229ILE00.0110.01031.3640.3480.3480.0000.0000.0000.000
161B230GLN00.0270.01332.6380.1970.1970.0000.0000.0000.000
162B231ASP-1-0.748-0.85031.0639.4789.4780.0000.0000.0000.000
163B232LEU0-0.0030.01025.9110.2870.2870.0000.0000.0000.000
164B233CYS0-0.032-0.01728.0630.3210.3210.0000.0000.0000.000
165B234GLU-1-0.895-0.93630.0429.6349.6340.0000.0000.0000.000
166B235MET0-0.016-0.01925.7820.2390.2390.0000.0000.0000.000
167B236LEU00.0060.01024.0410.3220.3220.0000.0000.0000.000
168B237GLY0-0.025-0.01825.9930.1710.1710.0000.0000.0000.000
169B238LYS10.8850.96227.479-10.344-10.3440.0000.0000.0000.000
170B239TYR00.025-0.02122.732-0.125-0.1250.0000.0000.0000.000
171B240GLY00.0310.02521.8280.6520.6520.0000.0000.0000.000
172B241SER0-0.007-0.00220.7500.5980.5980.0000.0000.0000.000
173B242SER0-0.047-0.02719.2440.4400.4400.0000.0000.0000.000
174B243LEU0-0.007-0.00717.6710.7330.7330.0000.0000.0000.000
175B244GLU-1-0.780-0.84712.66420.88020.8800.0000.0000.0000.000
176B245PHE00.0630.00515.642-0.906-0.9060.0000.0000.0000.000
177B246THR0-0.022-0.03915.462-0.785-0.7850.0000.0000.0000.000
178B247GLU-1-0.892-0.94116.60816.85816.8580.0000.0000.0000.000
179B248LEU0-0.043-0.02018.463-0.943-0.9430.0000.0000.0000.000
180B249LEU0-0.010-0.01419.988-0.802-0.8020.0000.0000.0000.000
181B250THR0-0.004-0.00720.234-0.675-0.6750.0000.0000.0000.000
182B251LEU0-0.039-0.02422.628-0.626-0.6260.0000.0000.0000.000
183B252VAL0-0.017-0.00125.137-0.597-0.5970.0000.0000.0000.000
184B253ASN00.0290.01223.896-0.657-0.6570.0000.0000.0000.000
185B254ARG10.9430.99825.133-12.264-12.2640.0000.0000.0000.000
186B255LYS10.7980.87529.098-9.995-9.9950.0000.0000.0000.000
187B256VAL00.0250.01230.883-0.354-0.3540.0000.0000.0000.000
188B257SER0-0.096-0.05830.587-0.323-0.3230.0000.0000.0000.000
189B258GLN0-0.029-0.01032.823-0.061-0.0610.0000.0000.0000.000
190B259ARG10.7690.87635.292-9.041-9.0410.0000.0000.0000.000
191B275VAL0-0.012-0.02229.260-0.060-0.0600.0000.0000.0000.000
192B276PRO0-0.0080.01427.9120.0220.0220.0000.0000.0000.000
193B277CYS0-0.017-0.00225.4490.3980.3980.0000.0000.0000.000
194B278PHE00.001-0.01018.176-0.129-0.1290.0000.0000.0000.000
195B279ALA00.0280.02620.6710.3800.3800.0000.0000.0000.000
196B280SER00.009-0.00714.848-0.202-0.2020.0000.0000.0000.000
197B281MET0-0.001-0.00715.176-0.098-0.0980.0000.0000.0000.000
198B282LEU0-0.0250.00212.5450.3300.3300.0000.0000.0000.000
199B283THR0-0.018-0.0168.5041.1821.1820.0000.0000.0000.000
200B284LYS10.8090.9095.944-29.762-29.7620.0000.0000.0000.000
201B285LYS10.9090.9647.655-34.411-34.4110.0000.0000.0000.000
202B286LEU00.006-0.01110.339-0.162-0.1620.0000.0000.0000.000
203B287HIS00.0310.03012.1850.6090.6090.0000.0000.0000.000
204B288PHE00.013-0.00715.279-0.012-0.0120.0000.0000.0000.000
205B289PHE00.0120.01213.417-0.615-0.6150.0000.0000.0000.000
206B290PRO00.0370.02918.9530.1190.1190.0000.0000.0000.000