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: KG383

Calculation Name: 1EF7-A-Xray372

Preferred Name: Cathepsin Z

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1EF7

Chain ID: A

ChEMBL ID: CHEMBL4160

UniProt ID: Q9UBR2

Base Structure: X-ray

Registration Date: 2023-09-21

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3113590.900212
FMO2-HF: Nuclear repulsion 3015712.609885
FMO2-HF: Total energy -97878.290326
FMO2-MP2: Total energy -98156.129694


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(A:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-3.6522.2746.217-3.022-9.118-0.012
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.020
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].
3A3LYS10.9440.9553.5930.5252.5910.000-1.050-1.0160.004
4A4SER0-0.014-0.0056.0920.4590.4590.0000.0000.0000.000
5A5TRP00.0070.0075.576-0.188-0.1880.0000.0000.0000.000
6A6ASP-1-0.706-0.8507.548-0.192-0.1920.0000.0000.0000.000
7A7TRP00.0270.0228.669-0.015-0.0150.0000.0000.0000.000
8A8ARG10.8230.89812.6070.2390.2390.0000.0000.0000.000
9A9ASN0-0.093-0.06514.2330.0300.0300.0000.0000.0000.000
10A10VAL00.0200.02511.466-0.058-0.0580.0000.0000.0000.000
11A11ASP-1-0.919-0.95813.661-0.198-0.1980.0000.0000.0000.000
12A12GLY0-0.032-0.01715.6210.0310.0310.0000.0000.0000.000
13A13VAL0-0.055-0.01817.2000.0190.0190.0000.0000.0000.000
14A14ASN00.0300.02516.717-0.025-0.0250.0000.0000.0000.000
15A15TYR0-0.011-0.01215.1850.0360.0360.0000.0000.0000.000
16A16ALA0-0.034-0.00617.1530.0220.0220.0000.0000.0000.000
17A17SER0-0.016-0.02718.417-0.004-0.0040.0000.0000.0000.000
18A18ILE0-0.013-0.00421.673-0.011-0.0110.0000.0000.0000.000
19A19THR00.0120.00623.7330.0050.0050.0000.0000.0000.000
20A20ARG10.8090.89424.717-0.001-0.0010.0000.0000.0000.000
21A21ASN00.030-0.00926.792-0.005-0.0050.0000.0000.0000.000
22A22GLN00.0120.01927.0070.0000.0000.0000.0000.0000.000
23A23HIS0-0.0030.01229.1660.0060.0060.0000.0000.0000.000
24A24ILE00.0070.00932.882-0.002-0.0020.0000.0000.0000.000
25A25PRO00.002-0.01234.5810.0010.0010.0000.0000.0000.000
26A26GLN0-0.058-0.00737.0530.0000.0000.0000.0000.0000.000
27A27TYR00.0320.00932.293-0.001-0.0010.0000.0000.0000.000
28A28CYS0-0.0430.00032.0110.0030.0030.0000.0000.0000.000
29A29GLY00.0420.03730.502-0.003-0.0030.0000.0000.0000.000
30A30SER00.0380.00328.9900.0040.0040.0000.0000.0000.000
31A31CYS0-0.042-0.00124.3800.0040.0040.0000.0000.0000.000
32A32TRP00.0410.01923.5680.0040.0040.0000.0000.0000.000
33A33ALA00.0470.04623.8270.0090.0090.0000.0000.0000.000
34A34HIS00.0000.01824.3600.0010.0010.0000.0000.0000.000
35A35ALA00.0060.02019.282-0.001-0.0010.0000.0000.0000.000
36A36SER00.0260.00019.3710.0030.0030.0000.0000.0000.000
37A37THR00.001-0.03620.1790.0060.0060.0000.0000.0000.000
38A38SER0-0.028-0.02620.285-0.001-0.0010.0000.0000.0000.000
39A39ALA0-0.0060.00615.908-0.003-0.0030.0000.0000.0000.000
40A40MET0-0.0030.00716.9360.0140.0140.0000.0000.0000.000
41A41ALA0-0.010-0.00519.1190.0090.0090.0000.0000.0000.000
42A42ASP-1-0.759-0.87015.937-0.013-0.0130.0000.0000.0000.000
43A43ARG10.7710.87311.139-0.247-0.2470.0000.0000.0000.000
44A44ILE0-0.016-0.00116.2140.0160.0160.0000.0000.0000.000
45A45ASN0-0.0210.00218.3190.0090.0090.0000.0000.0000.000
46A46ILE00.0170.00812.134-0.005-0.0050.0000.0000.0000.000
47A47LYS10.8120.89315.865-0.218-0.2180.0000.0000.0000.000
48A48ARG10.7670.87217.573-0.044-0.0440.0000.0000.0000.000
49A49LYS10.9070.93917.797-0.141-0.1410.0000.0000.0000.000
50A50GLY00.0430.03719.129-0.015-0.0150.0000.0000.0000.000
51A51ALA0-0.044-0.00220.778-0.010-0.0100.0000.0000.0000.000
52A52TRP00.0340.03624.2260.0020.0020.0000.0000.0000.000
53A53PRO0-0.035-0.01227.0440.0060.0060.0000.0000.0000.000
54A54SER00.023-0.00123.3520.0080.0080.0000.0000.0000.000
55A55THR0-0.005-0.03022.5120.0030.0030.0000.0000.0000.000
56A56LEU00.001-0.00623.919-0.005-0.0050.0000.0000.0000.000
57A57LEU0-0.0010.01723.4310.0020.0020.0000.0000.0000.000
58A58SER00.011-0.01027.119-0.005-0.0050.0000.0000.0000.000
59A59VAL00.0100.00226.8070.0040.0040.0000.0000.0000.000
60A60GLN0-0.023-0.02229.280-0.001-0.0010.0000.0000.0000.000
61A61ASN00.0510.04031.8310.0060.0060.0000.0000.0000.000
62A62VAL0-0.011-0.00227.1730.0030.0030.0000.0000.0000.000
63A63ILE0-0.059-0.03630.3930.0020.0020.0000.0000.0000.000
64A64ASP-1-0.767-0.86832.3730.0230.0230.0000.0000.0000.000
65A65CYS0-0.113-0.08534.0990.0000.0000.0000.0000.0000.000
66A66GLY00.0570.02830.6040.0040.0040.0000.0000.0000.000
67A67ASN0-0.088-0.04030.6930.0020.0020.0000.0000.0000.000
68A68ALA00.0360.01227.5550.0040.0040.0000.0000.0000.000
69A69GLY0-0.011-0.01428.8660.0010.0010.0000.0000.0000.000
70A70SER00.004-0.01431.2780.0000.0000.0000.0000.0000.000
71A72GLU-1-0.932-0.95433.5750.0080.0080.0000.0000.0000.000
72A73GLY0-0.039-0.01330.070-0.001-0.0010.0000.0000.0000.000
73A74GLY00.005-0.00828.5620.0020.0020.0000.0000.0000.000
74A75ASN0-0.015-0.00323.1200.0050.0050.0000.0000.0000.000
75A76ASP-1-0.723-0.83619.2830.0850.0850.0000.0000.0000.000
76A77LEU0-0.033-0.01619.7480.0060.0060.0000.0000.0000.000
77A78SER00.0270.00821.9050.0050.0050.0000.0000.0000.000
78A79VAL0-0.0150.00823.295-0.002-0.0020.0000.0000.0000.000
79A80TRP0-0.012-0.00417.0500.0050.0050.0000.0000.0000.000
80A81ASP-1-0.821-0.86122.0570.1100.1100.0000.0000.0000.000
81A82TYR00.014-0.00224.7360.0000.0000.0000.0000.0000.000
82A83ALA0-0.030-0.02523.367-0.003-0.0030.0000.0000.0000.000
83A84HIS0-0.071-0.04223.332-0.005-0.0050.0000.0000.0000.000
84A85GLN0-0.040-0.02525.197-0.007-0.0070.0000.0000.0000.000
85A86HIS0-0.089-0.03528.825-0.006-0.0060.0000.0000.0000.000
86A87GLY00.0180.01027.4750.0000.0000.0000.0000.0000.000
87A88ILE0-0.028-0.01124.813-0.006-0.0060.0000.0000.0000.000
88A89PRO00.0240.02128.4790.0030.0030.0000.0000.0000.000
89A90ASP-1-0.828-0.89829.2920.0210.0210.0000.0000.0000.000
90A91GLU-1-0.722-0.86629.6420.0080.0080.0000.0000.0000.000
91A92THR0-0.113-0.08231.241-0.001-0.0010.0000.0000.0000.000
92A93CYS0-0.130-0.05833.8680.0010.0010.0000.0000.0000.000
93A94ASN0-0.043-0.03534.838-0.003-0.0030.0000.0000.0000.000
94A95ASN00.0290.03734.2320.0010.0010.0000.0000.0000.000
95A96TYR0-0.058-0.03931.6420.0020.0020.0000.0000.0000.000
96A97GLN00.0160.00434.123-0.004-0.0040.0000.0000.0000.000
97A98ALA0-0.054-0.01634.392-0.002-0.0020.0000.0000.0000.000
98A99LYS10.9120.94635.333-0.010-0.0100.0000.0000.0000.000
99A100ASP-1-0.738-0.86136.1430.0200.0200.0000.0000.0000.000
100A101GLN0-0.104-0.07138.278-0.004-0.0040.0000.0000.0000.000
101A102GLU-1-0.898-0.93239.1790.0270.0270.0000.0000.0000.000
102A104ASP-1-0.805-0.89939.6800.0250.0250.0000.0000.0000.000
103A105LYS10.8940.92339.858-0.038-0.0380.0000.0000.0000.000
104A106PHE0-0.021-0.02140.6750.0010.0010.0000.0000.0000.000
105A107ASN00.0060.01138.435-0.002-0.0020.0000.0000.0000.000
106A108GLN0-0.053-0.02035.9390.0010.0010.0000.0000.0000.000
107A110GLY00.0510.04838.1370.0010.0010.0000.0000.0000.000
108A111THR0-0.066-0.02240.452-0.002-0.0020.0000.0000.0000.000
109A112CYS00.0920.04043.0430.0000.0000.0000.0000.0000.000
110A113ASN0-0.032-0.01746.2210.0000.0000.0000.0000.0000.000
111A114GLU-1-0.885-0.95747.4490.0050.0050.0000.0000.0000.000
112A115PHE00.0020.01250.3970.0010.0010.0000.0000.0000.000
113A116LYS10.8280.90352.009-0.010-0.0100.0000.0000.0000.000
114A117GLU-1-0.918-0.93749.3200.0130.0130.0000.0000.0000.000
115A119HIS0-0.068-0.02446.4170.0020.0020.0000.0000.0000.000
116A120ALA00.0590.02142.6700.0000.0000.0000.0000.0000.000
117A121ILE0-0.036-0.01639.5120.0000.0000.0000.0000.0000.000
118A122ARG10.9470.95340.582-0.027-0.0270.0000.0000.0000.000
119A123ASN0-0.066-0.03738.6980.0050.0050.0000.0000.0000.000
120A124TYR00.0270.01234.110-0.004-0.0040.0000.0000.0000.000
121A125THR00.0040.00129.5460.0030.0030.0000.0000.0000.000
122A126LEU0-0.0120.00230.443-0.003-0.0030.0000.0000.0000.000
123A127TRP0-0.013-0.00824.6010.0080.0080.0000.0000.0000.000
124A128ARG10.9390.95425.338-0.090-0.0900.0000.0000.0000.000
125A129VAL0-0.0150.00319.6640.0050.0050.0000.0000.0000.000
126A130GLY0-0.0160.00120.575-0.008-0.0080.0000.0000.0000.000
127A131ASP-1-0.871-0.93417.2010.2610.2610.0000.0000.0000.000
128A132TYR0-0.067-0.08317.1480.0000.0000.0000.0000.0000.000
129A133GLY0-0.0100.01616.5080.0010.0010.0000.0000.0000.000
130A134SER00.013-0.00815.209-0.020-0.0200.0000.0000.0000.000
131A135LEU0-0.073-0.0278.6330.0470.0470.0000.0000.0000.000
132A136SER00.0100.00811.766-0.030-0.0300.0000.0000.0000.000
133A137GLY00.0330.01810.8190.0490.0490.0000.0000.0000.000
134A138ARG10.8110.8596.3700.6000.6000.0000.0000.0000.000
135A139GLU-1-0.842-0.9234.8840.1120.1120.0000.0000.0000.000
136A140LYS10.9330.9744.246-0.450-0.2570.000-0.020-0.1730.000
137A141MET0-0.0020.0205.7200.0500.0500.0000.0000.0000.000
138A142MET0-0.023-0.0162.143-0.798-0.3822.043-0.553-1.9050.000
139A143ALA0-0.028-0.0192.128-2.051-0.6072.518-1.918-2.043-0.001
140A144GLU-1-0.724-0.8432.8442.4160.5390.1432.015-0.280-0.001
141A145ILE0-0.014-0.0116.317-0.054-0.0540.0000.0000.0000.000
142A146TYR0-0.050-0.0332.555-2.556-0.2100.981-1.019-2.308-0.011
143A147ALA0-0.0320.0015.1520.0020.061-0.001-0.002-0.0560.000
144A148ASN0-0.058-0.0387.086-0.081-0.0810.0000.0000.0000.000
145A149GLY00.0380.0219.436-0.061-0.0610.0000.0000.0000.000
146A150PRO0-0.083-0.03810.7790.0230.0230.0000.0000.0000.000
147A151ILE00.0110.0189.5930.0340.0340.0000.0000.0000.000
148A152SER0-0.044-0.03213.157-0.047-0.0470.0000.0000.0000.000
149A153CYS0-0.025-0.00112.693-0.002-0.0020.0000.0000.0000.000
150A154GLY00.0640.04416.098-0.013-0.0130.0000.0000.0000.000
151A155ILE0-0.013-0.01817.951-0.010-0.0100.0000.0000.0000.000
152A156MET0-0.0170.02420.2640.0050.0050.0000.0000.0000.000
153A157ALA0-0.006-0.02423.491-0.011-0.0110.0000.0000.0000.000
154A158THR0-0.016-0.03525.4260.0040.0040.0000.0000.0000.000
155A159GLU-1-0.880-0.94727.819-0.039-0.0390.0000.0000.0000.000
156A160ARG10.8660.92624.9820.0920.0920.0000.0000.0000.000
157A161LEU0-0.0070.00522.191-0.006-0.0060.0000.0000.0000.000
158A162ALA00.0300.00426.117-0.004-0.0040.0000.0000.0000.000
159A163ASN0-0.066-0.04128.7260.0010.0010.0000.0000.0000.000
160A164TYR0-0.066-0.02821.252-0.003-0.0030.0000.0000.0000.000
161A165THR00.014-0.00526.9370.0050.0050.0000.0000.0000.000
162A166GLY0-0.010-0.00323.818-0.002-0.0020.0000.0000.0000.000
163A167GLY0-0.044-0.01322.2010.0050.0050.0000.0000.0000.000
164A168ILE0-0.036-0.01717.0220.0030.0030.0000.0000.0000.000
165A169TYR00.013-0.03019.7500.0080.0080.0000.0000.0000.000
166A170ALA00.018-0.00719.392-0.012-0.0120.0000.0000.0000.000
167A171GLU-1-0.815-0.85021.441-0.059-0.0590.0000.0000.0000.000
168A172TYR0-0.049-0.01523.5770.0030.0030.0000.0000.0000.000
169A173GLN00.017-0.00224.5860.0080.0080.0000.0000.0000.000
170A174ASP-1-0.982-0.97225.175-0.024-0.0240.0000.0000.0000.000
171A175THR0-0.014-0.02326.8190.0070.0070.0000.0000.0000.000
172A176THR0-0.014-0.02122.205-0.005-0.0050.0000.0000.0000.000
173A177TYR00.001-0.00924.7220.0070.0070.0000.0000.0000.000
174A178ILE0-0.0220.00219.933-0.007-0.0070.0000.0000.0000.000
175A179ASN0-0.016-0.00123.6630.0020.0020.0000.0000.0000.000
176A180HIS00.003-0.00622.9920.0050.0050.0000.0000.0000.000
177A181VAL00.0080.00619.6420.0050.0050.0000.0000.0000.000
178A182VAL0-0.026-0.00216.922-0.008-0.0080.0000.0000.0000.000
179A183SER00.002-0.00215.3810.0110.0110.0000.0000.0000.000
180A184VAL0-0.008-0.00810.456-0.029-0.0290.0000.0000.0000.000
181A185ALA00.008-0.01211.6550.0370.0370.0000.0000.0000.000
182A186GLY00.0600.0208.563-0.010-0.0100.0000.0000.0000.000
183A187TRP0-0.064-0.0262.412-1.0170.2620.533-0.475-1.337-0.003
184A188GLY00.0360.0038.987-0.111-0.1110.0000.0000.0000.000
185A189ILE0-0.019-0.0109.2630.0350.0350.0000.0000.0000.000
186A190SER0-0.071-0.03912.4040.0090.0090.0000.0000.0000.000
187A191ASP-1-0.871-0.92016.131-0.288-0.2880.0000.0000.0000.000
188A192GLY0-0.030-0.01715.4540.0250.0250.0000.0000.0000.000
189A193THR0-0.034-0.00715.4340.0070.0070.0000.0000.0000.000
190A194GLU-1-0.753-0.8128.309-0.763-0.7630.0000.0000.0000.000
191A195TYR0-0.047-0.03911.6510.0850.0850.0000.0000.0000.000
192A196TRP00.0010.0026.945-0.105-0.1050.0000.0000.0000.000
193A197ILE0-0.043-0.02011.4610.0210.0210.0000.0000.0000.000
194A198VAL0-0.024-0.03313.2730.0250.0250.0000.0000.0000.000
195A199ARG10.8450.92915.7670.0210.0210.0000.0000.0000.000
196A200ASN00.0270.00818.5760.0230.0230.0000.0000.0000.000
197A201SER0-0.024-0.02121.693-0.001-0.0010.0000.0000.0000.000
198A202TRP0-0.012-0.01524.8070.0020.0020.0000.0000.0000.000
199A203GLY00.0340.01727.1940.0010.0010.0000.0000.0000.000
200A204GLU-1-0.879-0.93327.009-0.076-0.0760.0000.0000.0000.000
201A205PRO0-0.004-0.01228.093-0.006-0.0060.0000.0000.0000.000
202A206TRP0-0.0110.02722.377-0.005-0.0050.0000.0000.0000.000
203A207GLY00.0260.02624.660-0.005-0.0050.0000.0000.0000.000
204A208GLU-1-0.747-0.83120.154-0.196-0.1960.0000.0000.0000.000
205A209ARG10.8230.89122.6360.0870.0870.0000.0000.0000.000
206A210GLY00.0310.00724.1610.0030.0030.0000.0000.0000.000
207A211TRP0-0.068-0.03615.6530.0000.0000.0000.0000.0000.000
208A212LEU00.004-0.00118.519-0.001-0.0010.0000.0000.0000.000
209A213ARG10.8140.89715.9360.2370.2370.0000.0000.0000.000
210A214ILE00.0000.00915.4300.0130.0130.0000.0000.0000.000
211A215VAL0-0.014-0.01114.691-0.029-0.0290.0000.0000.0000.000
212A216THR0-0.002-0.0129.6360.0510.0510.0000.0000.0000.000
213A217SER00.002-0.04911.428-0.009-0.0090.0000.0000.0000.000
214A218THR0-0.050-0.04210.5090.0480.0480.0000.0000.0000.000
215A219TYR0-0.0100.00413.386-0.001-0.0010.0000.0000.0000.000
216A220LYS10.9160.93716.3790.1540.1540.0000.0000.0000.000
217A221ASP-1-0.868-0.93117.764-0.128-0.1280.0000.0000.0000.000
218A222GLY00.0310.02815.6920.0250.0250.0000.0000.0000.000
219A223LYS10.8020.90416.7470.1410.1410.0000.0000.0000.000
220A224GLY00.0370.02216.2540.0090.0090.0000.0000.0000.000
221A225ALA00.0190.00516.3630.0040.0040.0000.0000.0000.000
222A226ARG10.9110.96517.5270.0510.0510.0000.0000.0000.000
223A227TYR0-0.015-0.01619.575-0.001-0.0010.0000.0000.0000.000
224A228ASN0-0.028-0.01914.0650.0160.0160.0000.0000.0000.000
225A229LEU00.0210.02017.7800.0060.0060.0000.0000.0000.000
226A230ALA00.0930.04818.2730.0070.0070.0000.0000.0000.000
227A231ILE00.0000.01213.6350.0130.0130.0000.0000.0000.000
228A232GLU-1-0.753-0.88211.211-0.069-0.0690.0000.0000.0000.000
229A233GLU-1-0.933-0.96413.5260.0710.0710.0000.0000.0000.000
230A234HIS00.010-0.00616.2410.0280.0280.0000.0000.0000.000
231A236THR0-0.018-0.03214.8070.0310.0310.0000.0000.0000.000
232A237PHE0-0.011-0.02112.934-0.006-0.0060.0000.0000.0000.000
233A238GLY00.0750.01915.019-0.005-0.0050.0000.0000.0000.000
234A239ASP-1-0.836-0.88815.8370.2670.2670.0000.0000.0000.000
235A240PRO00.0020.01716.850-0.016-0.0160.0000.0000.0000.000
236A241ILE0-0.005-0.00919.7560.0150.0150.0000.0000.0000.000
237A242VAL0-0.033-0.01520.741-0.010-0.0100.0000.0000.0000.000