Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 632NZ

Calculation Name: 2YJ2-A-Other153

Preferred Name: Cathepsin L

Target Type: SINGLE PROTEIN

Ligand Name: (2s,4r)-1-[1-(4-bromophenyl)cyclopropyl]carbonyl-4-(2-chlorophenyl)sulfonyl-n-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide

ligand 3-letter code: YJ2

PDB ID: 2YJ2

Chain ID: A

ChEMBL ID: CHEMBL3837

UniProt ID: P07711

Base Structure: Other

Registration Date: 2020-08-21

Reference: D. Takaya, C. Watanabe, S. Nagase, K. Kamisaka, H. Moriwaki, Y. Okiyama, H. Yuki, T. Sato, K. Fukuzawa, T. Homma et al., FMODB: The world's first quantum mechanical database for biomacromolecules based on the fragment molecular orbital method,To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHL
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Water(s) essential for molecular recognition.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Manual
Number of fragment 223
LigandCharge
Software ABINIT-MP 7.2
Total energy (hartree)
FMO2-HF: Electronic energy -2756486.287666
FMO2-HF: Nuclear repulsion 2666711.894653
FMO2-HF: Total energy -89774.393013
FMO2-MP2: Total energy -90027.309359


3D Structure
Snapshot
 
Ligand structure

YJ2

ligand structure
Ligand Interaction
ligand interaction
Ligand-binding energy (frag 27,219,220 : frag 1-23,28-218)
"
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.
-373.3630-331.765865.3995-36.5544-70.4423-0.0081


Interactive mode: IFIE and PIEDA for fragment #27(A:1221:YJ2 )


Summations of interaction energy for fragment #27(A:1221:YJ2 )
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.
-170.552-262.9957.01569.193-33.771-0.273
Interaction energy analysis for fragmet #27(A:1221:YJ2 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.676 / q_NPA : 1.001
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].
1A1ALA 10.8310.91225.17710.66010.6600.0000.0000.0000.000
2A2PRO 00.1310.06625.5660.3160.3160.0000.0000.0000.000
3A3ARG 10.9700.99626.0239.7209.7200.0000.0000.0000.000
4A4SER 00.0140.00023.679-0.113-0.1130.0000.0000.0000.000
5A5VAL 0-0.064-0.02620.1650.4720.4720.0000.0000.0000.000
6A6ASP -1-0.705-0.85719.099-15.055-15.0550.0000.0000.0000.000
7A7TRP 0-0.064-0.03417.5860.7850.7850.0000.0000.0000.000
8A8ARG 10.8660.93215.93615.76715.7670.0000.0000.0000.000
9A9GLU -1-0.949-0.96519.177-11.409-11.4090.0000.0000.0000.000
10A10LYS 10.8440.92322.03111.53911.5390.0000.0000.0000.000
11A11GLY 00.0260.01721.7040.2460.2460.0000.0000.0000.000
12A12TYR 0-0.018-0.00617.810-0.099-0.0990.0000.0000.0000.000
13A13VAL 0-0.017-0.01013.649-0.719-0.7190.0000.0000.0000.000
14A14THR 0-0.030-0.01213.5790.3570.3570.0000.0000.0000.000
15A15PRO 00.0470.00714.488-0.606-0.6060.0000.0000.0000.000
16A16VAL 0-0.024-0.00310.339-1.008-1.0080.0000.0000.0000.000
17A17LYS 10.8170.9249.47922.99622.9960.0000.0000.0000.000
18A18ASN 00.021-0.0158.473-3.952-3.9520.0000.0000.0000.000
19A19GLN 00.0350.0311.793-19.772-16.5326.997-5.886-4.350-0.054
20A20GLY 00.0460.0436.6580.9540.9540.0000.0000.0000.000
21A21GLN 0-0.065-0.0436.350-4.023-4.0230.0000.0000.0000.000
22A65CYS 0-0.059-0.0205.6230.0480.0480.0000.0000.0000.000
23A23GLY 00.0100.0132.347-9.924-9.5052.377-1.337-1.459-0.003
24A24SER 00.068-0.0032.7862.4822.8560.2331.242-1.849-0.007
26A26TRP 00.058-0.0731.547130.12926.13223.61488.407-8.024-0.111
28A27ALA 00.0350.0284.3904.7375.1190.014-0.051-0.3440.000
29A28PHE 00.0080.0054.5454.1354.407-0.002-0.053-0.2170.000
30A29SER 0-0.098-0.0494.6695.5105.683-0.002-0.016-0.1550.000
31A30ALA 00.0310.0116.2143.4143.4140.0000.0000.0000.000
32A31THR 00.008-0.0299.0121.9431.9430.0000.0000.0000.000
33A32GLY 00.0140.0179.3271.9061.9060.0000.0000.0000.000
34A33ALA 0-0.017-0.01810.5521.9231.9230.0000.0000.0000.000
35A34LEU 0-0.007-0.00412.5061.4661.4660.0000.0000.0000.000
36A35GLU -1-0.760-0.87713.117-18.835-18.8350.0000.0000.0000.000
37A36GLY 00.0020.00015.0331.0701.0700.0000.0000.0000.000
38A37GLN 0-0.057-0.03816.7991.5461.5460.0000.0000.0000.000
39A38MET 00.0360.02318.4330.9760.9760.0000.0000.0000.000
40A39PHE 0-0.0070.00819.6360.8030.8030.0000.0000.0000.000
41A40ARG 10.8750.94021.11612.97912.9790.0000.0000.0000.000
42A41LYS 10.8240.91922.84111.87311.8730.0000.0000.0000.000
43A42THR 0-0.036-0.02723.7360.5740.5740.0000.0000.0000.000
44A43GLY 0-0.010-0.00525.0620.4360.4360.0000.0000.0000.000
45A44ARG 10.8650.93124.25710.41610.4160.0000.0000.0000.000
46A45LEU 0-0.0110.01017.364-0.320-0.3200.0000.0000.0000.000
47A46ILE 00.005-0.00419.4580.3230.3230.0000.0000.0000.000
48A47SER 0-0.017-0.00615.382-0.902-0.9020.0000.0000.0000.000
49A48LEU 0-0.006-0.00613.8560.8440.8440.0000.0000.0000.000
50A49SER 0-0.005-0.00713.487-1.474-1.4740.0000.0000.0000.000
51A50GLU -1-0.701-0.8158.179-24.157-24.1570.0000.0000.0000.000
52A51GLN 00.0110.00710.745-2.196-2.1960.0000.0000.0000.000
53A52ASN 00.0480.02312.8270.8980.8980.0000.0000.0000.000
54A53LEU 0-0.025-0.01410.1520.3360.3360.0000.0000.0000.000
55A54VAL 0-0.051-0.0148.522-0.311-0.3110.0000.0000.0000.000
56A55ASP -1-0.680-0.81110.774-19.292-19.2920.0000.0000.0000.000
57A98CYS 0-0.107-0.03014.0001.2741.2740.0000.0000.0000.000
58A57SER 0-0.034-0.01910.9630.3690.3690.0000.0000.0000.000
59A58GLY 00.0450.02912.191-0.501-0.5010.0000.0000.0000.000
60A59PRO 0-0.048-0.02713.2470.1010.1010.0000.0000.0000.000
61A60GLN 00.002-0.01513.111-0.229-0.2290.0000.0000.0000.000
62A61GLY 0-0.0040.01211.654-0.224-0.2240.0000.0000.0000.000
63A62ASN 0-0.013-0.0057.697-2.239-2.2390.0000.0000.0000.000
64A63GLU -1-0.914-0.9616.921-25.106-25.1060.0000.0000.0000.000
65A64GLY 00.0750.0457.687-1.304-1.3040.0000.0000.0000.000
66A66ASN 0-0.019-0.0104.592-7.079-6.937-0.002-0.021-0.1200.000
67A67GLY 00.0210.0172.512-3.321-1.9911.896-1.357-1.8690.007
68A68GLY 00.0480.0182.6600.9891.1860.4810.380-1.0580.008
69A69LEU 0-0.054-0.0293.807-3.661-3.2370.016-0.136-0.3050.000
70A70MET 00.0130.0056.538-0.270-0.137-0.002-0.011-0.1210.000
71A71ASP 0-0.043-0.0498.7091.1041.1040.0000.0000.0000.000
72A72TYR 00.0380.0299.0201.1491.1490.0000.0000.0000.000
73A73ALA 00.0040.0039.5410.9690.9690.0000.0000.0000.000
74A74PHE 0-0.030-0.02611.3450.7510.7510.0000.0000.0000.000
75A75GLN 0-0.022-0.00514.0990.7300.7300.0000.0000.0000.000
76A76TYR 00.0180.00813.9470.6030.6030.0000.0000.0000.000
77A77VAL 0-0.027-0.00715.1680.8280.8280.0000.0000.0000.000
78A78GLN 0-0.024-0.00417.5810.5260.5260.0000.0000.0000.000
79A79ASP -1-0.868-0.92818.561-13.619-13.6190.0000.0000.0000.000
80A80ASN 0-0.124-0.07119.0180.8690.8690.0000.0000.0000.000
81A81GLY 0-0.0200.00320.9860.4810.4810.0000.0000.0000.000
82A82GLY 0-0.051-0.04121.1010.5200.5200.0000.0000.0000.000
83A83LEU 0-0.0190.00114.064-0.633-0.6330.0000.0000.0000.000
84A84ASP -1-0.756-0.87918.380-13.482-13.4820.0000.0000.0000.000
85A85SER 00.000-0.01017.394-0.995-0.9950.0000.0000.0000.000
86A86GLU 0-0.071-0.08412.4830.1810.1810.0000.0000.0000.000
87A87GLU -1-1.001-1.00316.874-12.257-12.2570.0000.0000.0000.000
88A88SER 0-0.081-0.04320.3260.3440.3440.0000.0000.0000.000
89A89TYR 0-0.044-0.03116.9990.5940.5940.0000.0000.0000.000
90A90PRO 00.0040.00616.391-1.123-1.1230.0000.0000.0000.000
91A91TYR 0-0.026-0.0377.353-1.241-1.2410.0000.0000.0000.000
92A92GLU -1-0.923-0.97513.170-16.587-16.5870.0000.0000.0000.000
93A93ALA 0-0.088-0.0279.505-0.073-0.0730.0000.0000.0000.000
94A94THR 0-0.020-0.04410.492-1.372-1.3720.0000.0000.0000.000
95A95GLU -1-0.942-0.96910.349-21.666-21.6660.0000.0000.0000.000
96A96GLU -1-0.895-0.91412.072-16.178-16.1780.0000.0000.0000.000
97A97SER 0-0.043-0.03115.813-0.104-0.1040.0000.0000.0000.000
98A99LYS 10.8750.92918.89716.23316.2330.0000.0000.0000.000
99A100TYR 00.0440.02719.6220.3020.3020.0000.0000.0000.000
100A101ASN 0-0.044-0.03121.1360.9200.9200.0000.0000.0000.000
101A102PRO 00.0730.03523.876-0.057-0.0570.0000.0000.0000.000
102A103LYS 10.8480.94025.3749.9719.9710.0000.0000.0000.000
103A104TYR 0-0.041-0.03723.1810.6210.6210.0000.0000.0000.000
104A105SER 00.0800.05621.764-0.756-0.7560.0000.0000.0000.000
105A106VAL 0-0.088-0.04719.8510.5560.5560.0000.0000.0000.000
106A107ALA 0-0.050-0.02718.3090.0540.0540.0000.0000.0000.000
107A108ASN 0-0.021-0.01920.3410.3130.3130.0000.0000.0000.000
108A109ASP -1-0.807-0.92516.859-16.353-16.3530.0000.0000.0000.000
109A110THR 0-0.040-0.01820.3520.2710.2710.0000.0000.0000.000
110A111GLY 00.0490.04619.3510.5210.5210.0000.0000.0000.000
111A112PHE 0-0.007-0.00715.953-0.637-0.6370.0000.0000.0000.000
112A113VAL 0-0.054-0.01217.6510.7100.7100.0000.0000.0000.000
113A114ASP -1-0.797-0.86714.977-18.899-18.8990.0000.0000.0000.000
114A115ILE 0-0.086-0.05215.6201.1751.1750.0000.0000.0000.000
115A116PRO 0-0.020-0.02017.957-0.315-0.3150.0000.0000.0000.000
116A117LYS 10.9971.01914.67118.22718.2270.0000.0000.0000.000
117A118GLN 0-0.017-0.03018.6820.5640.5640.0000.0000.0000.000
118A119GLU -1-0.683-0.84218.011-15.655-15.6550.0000.0000.0000.000
119A120LYS 10.9110.95220.02811.83111.8310.0000.0000.0000.000
120A121ALA 0-0.013-0.00121.0760.3480.3480.0000.0000.0000.000
121A122LEU 00.1080.06114.6180.3610.3610.0000.0000.0000.000
122A123MET 0-0.0260.00918.5950.2180.2180.0000.0000.0000.000
123A124LYS 10.9040.93620.71711.35311.3530.0000.0000.0000.000
124A125ALA 00.0650.06218.5120.3940.3940.0000.0000.0000.000
125A126VAL 00.0760.04216.0930.2130.2130.0000.0000.0000.000
126A127ALA 0-0.078-0.04718.7930.3420.3420.0000.0000.0000.000
127A128THR 0-0.096-0.06822.2570.3690.3690.0000.0000.0000.000
128A129VAL 00.0240.03918.3030.4010.4010.0000.0000.0000.000
129A130GLY 00.011-0.00118.4490.3110.3110.0000.0000.0000.000
130A131PRO 0-0.049-0.03413.468-0.117-0.1170.0000.0000.0000.000
131A132ILE 0-0.0380.00512.8410.3630.3630.0000.0000.0000.000
132A133SER 00.0280.0238.723-0.349-0.3490.0000.0000.0000.000
133A134VAL 0-0.046-0.0258.2092.0772.0770.0000.0000.0000.000
134A135ALA 00.0480.0336.985-3.380-3.3800.0000.0000.0000.000
135A136ILE 0-0.064-0.0496.9504.1994.1990.0000.0000.0000.000
136A137ASP -1-0.727-0.8506.481-32.941-32.9410.0000.0000.0000.000
137A138ALA 0-0.056-0.0376.1713.2773.2770.0000.0000.0000.000
138A139GLY 00.0630.0477.834-0.037-0.0370.0000.0000.0000.000
139A140HIS 10.8210.9018.48626.36726.3670.0000.0000.0000.000
140A141GLU -1-0.870-0.94611.744-22.610-22.6100.0000.0000.0000.000
141A142SER 0-0.068-0.04513.314-0.222-0.2220.0000.0000.0000.000
142A143PHE 00.004-0.0057.5030.9280.9280.0000.0000.0000.000
143A144LEU 00.0270.0209.226-0.199-0.1990.0000.0000.0000.000
144A145PHE 0-0.057-0.03411.6090.5370.5370.0000.0000.0000.000
145A146TYR 0-0.004-0.01413.4921.5751.5750.0000.0000.0000.000
146A147LYS 10.9030.94915.18717.28217.2820.0000.0000.0000.000
147A148GLU -1-0.914-0.97217.718-13.384-13.3840.0000.0000.0000.000
148A149GLY 00.0290.02619.3170.0630.0630.0000.0000.0000.000
149A150ILE 0-0.054-0.01818.482-1.008-1.0080.0000.0000.0000.000
150A151TYR 00.006-0.02413.6660.0680.0680.0000.0000.0000.000
151A152PHE 0-0.063-0.06217.1660.0810.0810.0000.0000.0000.000
152A153GLU -1-0.784-0.86214.703-17.734-17.7340.0000.0000.0000.000
153A154PRO 0-0.058-0.05217.316-0.203-0.2030.0000.0000.0000.000
154A155ASP -1-0.908-0.95216.048-17.766-17.7660.0000.0000.0000.000
155A209CYS 0-0.077-0.00411.377-1.592-1.5920.0000.0000.0000.000
156A157SER 00.0390.02911.6561.7731.7730.0000.0000.0000.000
157A158SER 0-0.079-0.06712.470-0.980-0.9800.0000.0000.0000.000
158A159GLU -1-0.983-1.00413.230-17.172-17.1720.0000.0000.0000.000
159A160ASP -1-0.970-0.9789.088-28.143-28.1430.0000.0000.0000.000
160A161MET 0-0.066-0.0167.0010.1930.1930.0000.0000.0000.000
161A162ASP -1-0.764-0.8883.416-48.281-47.1250.011-0.474-0.693-0.003
162A163HIS 0-0.020-0.0241.800-43.499-43.58017.170-8.827-8.262-0.086
163A164GLY 00.0440.0182.5318.4978.0103.396-0.954-1.955-0.005
164A165VAL 0-0.026-0.0182.551-9.268-7.0510.856-1.519-1.554-0.021
165A166LEU 00.0150.0225.3382.4832.500-0.0020.000-0.0150.000
166A167VAL 0-0.0070.0138.8440.9260.9260.0000.0000.0000.000
167A168VAL 00.024-0.00212.2160.8580.8580.0000.0000.0000.000
168A169GLY 00.019-0.00814.7501.2061.2060.0000.0000.0000.000
169A170TYR 0-0.061-0.04716.827-0.699-0.6990.0000.0000.0000.000
170A171GLY 00.0090.00419.3970.6060.6060.0000.0000.0000.000
171A172PHE 0-0.066-0.03622.532-0.242-0.2420.0000.0000.0000.000
172A173GLU -1-0.823-0.89722.705-13.085-13.0850.0000.0000.0000.000
173A174SER 0-0.089-0.06425.9160.2830.2830.0000.0000.0000.000
174A175THR -1-0.670-0.70927.338-10.683-10.6830.0000.0000.0000.000
175A176GLU -1-0.888-0.85230.110-8.633-8.6330.0000.0000.0000.000
176A177SER 0-0.136-0.18127.718-0.102-0.1020.0000.0000.0000.000
177A178ASP -1-1.011-1.07729.839-9.719-9.7190.0000.0000.0000.000
178A179ASN 0-0.147-0.09424.755-0.174-0.1740.0000.0000.0000.000
179A180ASN 00.0350.02024.879-0.456-0.4560.0000.0000.0000.000
180A181LYS 10.8830.94422.68111.89411.8940.0000.0000.0000.000
181A182TYR 00.0230.00118.065-0.212-0.2120.0000.0000.0000.000
182A183TRP 0-0.010-0.03014.6251.0141.0140.0000.0000.0000.000
183A184LEU 0-0.030-0.01215.300-0.386-0.3860.0000.0000.0000.000
184A185VAL 00.012-0.0019.0240.1160.1160.0000.0000.0000.000
185A186LYS 10.9020.9759.62622.55422.5540.0000.0000.0000.000
186A187ASN 00.0600.0395.461-6.779-6.7790.0000.0000.0000.000
187A188SER 0-0.002-0.0013.723-0.768-0.6120.004-0.065-0.0950.000
188A189TRP 00.001-0.0103.9151.1631.415-0.001-0.028-0.2230.000
189A190GLY 00.0510.0307.8691.8651.8650.0000.0000.0000.000
190A191GLU -1-0.964-0.99311.263-17.076-17.0760.0000.0000.0000.000
191A192GLU -1-0.940-0.97714.103-20.235-20.2350.0000.0000.0000.000
192A193TRP 0-0.062-0.00510.5810.1620.1620.0000.0000.0000.000
193A194GLY 00.0020.00413.174-0.008-0.0080.0000.0000.0000.000
194A195MET 0-0.047-0.01414.6871.2381.2380.0000.0000.0000.000
195A196GLY 00.0340.01516.0300.0250.0250.0000.0000.0000.000
196A197GLY 00.0550.02612.098-0.115-0.1150.0000.0000.0000.000
197A198TYR 0-0.079-0.04910.765-1.819-1.8190.0000.0000.0000.000
198A199VAL 00.0360.02110.4010.5510.5510.0000.0000.0000.000
199A200LYS 10.8290.92313.34014.15714.1570.0000.0000.0000.000
200A201MET 00.0650.05011.3980.2630.2630.0000.0000.0000.000
201A202ALA 00.0020.00115.1650.9850.9850.0000.0000.0000.000
202A203LYS 10.7920.90317.56913.09313.0930.0000.0000.0000.000
203A204ASP -1-0.936-0.97219.572-12.313-12.3130.0000.0000.0000.000
204A205ARG 10.9460.97620.91414.12114.1210.0000.0000.0000.000
205A206ARG 10.9220.95220.46013.27613.2760.0000.0000.0000.000
206A207ASN 00.0410.02715.617-0.698-0.6980.0000.0000.0000.000
207A208HIS 00.0530.04516.111-1.128-1.1280.0000.0000.0000.000
208A210GLY 00.1140.06111.088-2.096-2.0960.0000.0000.0000.000
209A211ILE 0-0.0090.02011.324-0.312-0.3120.0000.0000.0000.000
210A212ALA 0-0.050-0.04312.8540.0730.0730.0000.0000.0000.000
211A213SER 0-0.028-0.03912.4781.6241.6240.0000.0000.0000.000
212A214ALA 0-0.056-0.03310.0150.8990.8990.0000.0000.0000.000
213A215ALA 00.0070.02511.037-1.418-1.4180.0000.0000.0000.000
214A216SER 00.000-0.01612.3930.9040.9040.0000.0000.0000.000
215A217TYR 0-0.022-0.02212.933-0.663-0.6630.0000.0000.0000.000
216A218PRO 00.0590.05413.9450.6260.6260.0000.0000.0000.000
217A219THR 0-0.041-0.05416.7710.2940.2940.0000.0000.0000.000
218A220VAL -1-0.843-0.90319.493-11.913-11.9130.0000.0000.0000.000
220A1221YJ2 00.0690.1353.7490.6481.891-0.039-0.101-1.1030.002
221A2170HOH 0-0.059-0.03913.4350.3200.3200.0000.0000.0000.000
222A2172HOH 0-0.014-0.00810.4090.5920.5920.0000.0000.0000.000
223A2182HOH 0-0.014-0.01212.4980.5290.5290.0000.0000.0000.000