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: VQLZ1

Calculation Name: 3QPA-A-Xray372

Preferred Name: Cutinase 1

Target Type: SINGLE PROTEIN

Ligand Name: monoethylphosphorylserine

ligand 3-letter code: MIR

PDB ID: 3QPA

Chain ID: A

ChEMBL ID: CHEMBL2176862

UniProt ID: P00590

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge MIR=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2086139.688984
FMO2-HF: Nuclear repulsion 2013702.708112
FMO2-HF: Total energy -72436.980872
FMO2-MP2: Total energy -72647.95455


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:16:GLY)


Summations of interaction energy for fragment #1(A:16:GLY)
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.
7.859-2.6858.4335.035-2.925-0.009
Interaction energy analysis for fragmet #1(A:16:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.026
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].
3A18THR00.0530.0222.2569.868-1.2868.0405.220-2.106-0.007
4A19THR0-0.0050.0073.337-0.711-0.8210.0770.114-0.0820.000
5A20ARG10.6570.8076.1950.8410.8410.0000.0000.0000.000
6A21ASP-1-0.800-0.9028.6540.3310.3310.0000.0000.0000.000
7A22ASP-1-0.774-0.87112.033-0.581-0.5810.0000.0000.0000.000
8A23LEU0-0.0040.01513.9760.0030.0030.0000.0000.0000.000
9A24ILE0-0.070-0.03415.5970.0110.0110.0000.0000.0000.000
10A25ASN0-0.074-0.04114.6400.0280.0280.0000.0000.0000.000
11A26GLY00.0200.03217.719-0.032-0.0320.0000.0000.0000.000
12A27ASN00.000-0.00919.3030.0390.0390.0000.0000.0000.000
13A28SER00.040-0.00122.515-0.012-0.0120.0000.0000.0000.000
14A29ALA0-0.034-0.01125.0930.0030.0030.0000.0000.0000.000
15A30SER0-0.051-0.03023.157-0.001-0.0010.0000.0000.0000.000
16A31CYS0-0.054-0.02022.526-0.026-0.0260.0000.0000.0000.000
17A32ALA00.0010.02818.692-0.010-0.0100.0000.0000.0000.000
18A33ASP-1-0.883-0.94120.747-0.224-0.2240.0000.0000.0000.000
19A34VAL0-0.044-0.02117.8210.0240.0240.0000.0000.0000.000
20A35ILE00.000-0.00417.032-0.031-0.0310.0000.0000.0000.000
21A36PHE00.004-0.00810.7780.0280.0280.0000.0000.0000.000
22A37ILE0-0.0040.00113.915-0.002-0.0020.0000.0000.0000.000
23A38TYR0-0.012-0.0019.8250.0240.0240.0000.0000.0000.000
24A39ALA00.0190.00912.2960.0810.0810.0000.0000.0000.000
25A40ARG10.8430.93810.125-0.841-0.8410.0000.0000.0000.000
26A41GLY00.0440.02811.823-0.109-0.1090.0000.0000.0000.000
27A42SER00.014-0.04213.6430.0770.0770.0000.0000.0000.000
28A43THR0-0.072-0.03114.9780.0170.0170.0000.0000.0000.000
29A44GLU-1-0.773-0.8589.6521.2111.2110.0000.0000.0000.000
30A45THR00.004-0.0097.2210.0100.0100.0000.0000.0000.000
31A46GLY0-0.006-0.0046.9910.1820.1820.0000.0000.0000.000
32A47ASN00.026-0.0047.700-0.163-0.1630.0000.0000.0000.000
33A48LEU0-0.0100.0065.212-0.268-0.2680.0000.0000.0000.000
34A49GLY0-0.027-0.0076.918-0.232-0.2320.0000.0000.0000.000
35A50THR0-0.053-0.0495.4080.6050.6050.0000.0000.0000.000
36A51LEU0-0.005-0.0026.501-0.321-0.3210.0000.0000.0000.000
37A52GLY00.0490.0267.629-0.373-0.3730.0000.0000.0000.000
38A53PRO0-0.009-0.0142.810-1.179-0.4860.317-0.295-0.716-0.002
39A54SER0-0.009-0.0035.094-0.426-0.399-0.001-0.004-0.0210.000
40A55ILE00.0170.0206.8660.1290.1290.0000.0000.0000.000
41A56ALA00.003-0.0037.3220.0410.0410.0000.0000.0000.000
42A57SER0-0.0030.0097.2560.2690.2690.0000.0000.0000.000
43A58ASN0-0.002-0.0149.0970.2890.2890.0000.0000.0000.000
44A59LEU0-0.0070.00112.0590.1470.1470.0000.0000.0000.000
45A60GLU-1-0.813-0.9129.843-1.641-1.6410.0000.0000.0000.000
46A61SER0-0.051-0.02012.9130.1060.1060.0000.0000.0000.000
47A62ALA0-0.068-0.01815.2340.0860.0860.0000.0000.0000.000
48A63PHE0-0.010-0.02217.0300.0680.0680.0000.0000.0000.000
49A64GLY00.0690.05317.5080.0520.0520.0000.0000.0000.000
50A65LYS10.9060.93611.0080.8020.8020.0000.0000.0000.000
51A66ASP-1-0.906-0.96615.425-0.423-0.4230.0000.0000.0000.000
52A67GLY00.0280.03618.2660.0510.0510.0000.0000.0000.000
53A68VAL0-0.067-0.03714.0230.0260.0260.0000.0000.0000.000
54A69TRP0-0.0040.00714.484-0.020-0.0200.0000.0000.0000.000
55A70ILE0-0.031-0.0278.5040.0150.0150.0000.0000.0000.000
56A71GLN0-0.023-0.02211.483-0.013-0.0130.0000.0000.0000.000
57A72GLY00.0320.01410.2560.0060.0060.0000.0000.0000.000
58A73VAL0-0.018-0.01111.130-0.003-0.0030.0000.0000.0000.000
59A74GLY00.009-0.01213.5710.1030.1030.0000.0000.0000.000
60A75GLY00.0430.03014.101-0.032-0.0320.0000.0000.0000.000
61A76ALA0-0.047-0.03817.4290.0440.0440.0000.0000.0000.000
62A77TYR0-0.046-0.03014.440-0.012-0.0120.0000.0000.0000.000
63A78ARG10.9040.93815.880-0.318-0.3180.0000.0000.0000.000
64A79ALA0-0.0060.03314.7720.0500.0500.0000.0000.0000.000
65A80THR00.0510.02316.7690.0620.0620.0000.0000.0000.000
66A81LEU00.0650.02919.805-0.036-0.0360.0000.0000.0000.000
67A82GLY00.0250.01121.019-0.027-0.0270.0000.0000.0000.000
68A83ASP-1-0.845-0.93922.1380.2390.2390.0000.0000.0000.000
69A84ASN0-0.079-0.05220.294-0.030-0.0300.0000.0000.0000.000
70A85ALA0-0.023-0.01523.905-0.020-0.0200.0000.0000.0000.000
71A86LEU0-0.0220.01225.713-0.019-0.0190.0000.0000.0000.000
72A87PRO00.0060.00228.143-0.001-0.0010.0000.0000.0000.000
73A88ARG10.7670.83826.875-0.084-0.0840.0000.0000.0000.000
74A89GLY0-0.044-0.01224.663-0.002-0.0020.0000.0000.0000.000
75A90THR00.027-0.00520.7870.0220.0220.0000.0000.0000.000
76A91SER00.0130.02322.447-0.027-0.0270.0000.0000.0000.000
77A92SER00.0490.00224.162-0.004-0.0040.0000.0000.0000.000
78A93ALA0-0.022-0.00423.737-0.010-0.0100.0000.0000.0000.000
79A94ALA00.0130.00319.7920.0010.0010.0000.0000.0000.000
80A95ILE00.0560.02320.861-0.006-0.0060.0000.0000.0000.000
81A96ARG10.9450.98123.244-0.128-0.1280.0000.0000.0000.000
82A97GLU-1-0.878-0.93217.9340.1860.1860.0000.0000.0000.000
83A98MET00.0040.00916.658-0.008-0.0080.0000.0000.0000.000
84A99LEU0-0.0040.00019.876-0.028-0.0280.0000.0000.0000.000
85A100GLY00.0140.01322.855-0.018-0.0180.0000.0000.0000.000
86A101LEU0-0.021-0.01216.005-0.018-0.0180.0000.0000.0000.000
87A102PHE00.0590.01120.045-0.026-0.0260.0000.0000.0000.000
88A103GLN0-0.0020.00022.022-0.013-0.0130.0000.0000.0000.000
89A104GLN00.020-0.00320.305-0.027-0.0270.0000.0000.0000.000
90A105ALA00.0150.00820.396-0.014-0.0140.0000.0000.0000.000
91A106ASN0-0.0060.00422.200-0.018-0.0180.0000.0000.0000.000
92A107THR0-0.022-0.01125.799-0.002-0.0020.0000.0000.0000.000
93A108LYS10.8580.93820.5710.0420.0420.0000.0000.0000.000
94A110PRO00.0060.00725.224-0.006-0.0060.0000.0000.0000.000
95A111ASP-1-0.882-0.93627.684-0.099-0.0990.0000.0000.0000.000
96A112ALA0-0.038-0.00722.118-0.014-0.0140.0000.0000.0000.000
97A113THR0-0.049-0.01522.8960.0150.0150.0000.0000.0000.000
98A114LEU0-0.005-0.00120.447-0.024-0.0240.0000.0000.0000.000
99A115ILE0-0.002-0.00216.288-0.002-0.0020.0000.0000.0000.000
100A116ALA00.0090.00716.6960.0020.0020.0000.0000.0000.000
101A117GLY00.030-0.00315.215-0.033-0.0330.0000.0000.0000.000
102A118GLY00.0130.00814.2360.0340.0340.0000.0000.0000.000
103A119TYR0-0.070-0.03512.367-0.052-0.0520.0000.0000.0000.000
104A120MIR-1-0.790-0.83814.9870.4810.4810.0000.0000.0000.000
105A121GLN00.027-0.00117.657-0.056-0.0560.0000.0000.0000.000
106A122GLY00.0410.02215.495-0.030-0.0300.0000.0000.0000.000
107A123ALA0-0.049-0.02416.561-0.050-0.0500.0000.0000.0000.000
108A124ALA0-0.008-0.00118.737-0.029-0.0290.0000.0000.0000.000
109A125LEU0-0.032-0.00717.176-0.021-0.0210.0000.0000.0000.000
110A126ALA00.0450.00818.069-0.022-0.0220.0000.0000.0000.000
111A127ALA0-0.020-0.00920.021-0.021-0.0210.0000.0000.0000.000
112A128ALA00.0110.00323.447-0.011-0.0110.0000.0000.0000.000
113A129SER00.004-0.02021.721-0.005-0.0050.0000.0000.0000.000
114A130ILE0-0.009-0.00521.059-0.011-0.0110.0000.0000.0000.000
115A131GLU-1-0.914-0.94124.8580.0420.0420.0000.0000.0000.000
116A132ASP-1-0.780-0.88227.3750.0600.0600.0000.0000.0000.000
117A133LEU0-0.114-0.02824.313-0.002-0.0020.0000.0000.0000.000
118A134ASP-1-0.837-0.92127.961-0.014-0.0140.0000.0000.0000.000
119A135SER00.042-0.00229.629-0.004-0.0040.0000.0000.0000.000
120A136ALA00.0400.03630.822-0.007-0.0070.0000.0000.0000.000
121A137ILE0-0.037-0.01925.292-0.009-0.0090.0000.0000.0000.000
122A138ARG10.8610.92026.126-0.007-0.0070.0000.0000.0000.000
123A139ASP-1-0.901-0.95226.723-0.052-0.0520.0000.0000.0000.000
124A140LYS10.8280.91625.9470.0670.0670.0000.0000.0000.000
125A141ILE0-0.056-0.01021.215-0.020-0.0200.0000.0000.0000.000
126A142ALA00.0090.01023.1250.0130.0130.0000.0000.0000.000
127A143GLY00.0110.00021.9180.0020.0020.0000.0000.0000.000
128A144THR0-0.010-0.01419.290-0.007-0.0070.0000.0000.0000.000
129A145VAL0-0.035-0.00415.3910.0070.0070.0000.0000.0000.000
130A146LEU0-0.024-0.00417.2650.0270.0270.0000.0000.0000.000
131A147PHE00.0440.02213.507-0.011-0.0110.0000.0000.0000.000
132A148GLY00.0220.00817.2750.0490.0490.0000.0000.0000.000
133A149TYR0-0.013-0.03719.3100.0330.0330.0000.0000.0000.000
134A150THR00.0750.03020.985-0.022-0.0220.0000.0000.0000.000
135A151LYS10.9410.98423.384-0.131-0.1310.0000.0000.0000.000
136A152ASN00.0050.00824.853-0.024-0.0240.0000.0000.0000.000
137A153LEU00.0250.02026.631-0.012-0.0120.0000.0000.0000.000
138A154GLN0-0.014-0.02028.798-0.012-0.0120.0000.0000.0000.000
139A155ASN00.0340.02026.996-0.005-0.0050.0000.0000.0000.000
140A156ARG10.8590.91930.267-0.050-0.0500.0000.0000.0000.000
141A157GLY00.0200.01627.402-0.009-0.0090.0000.0000.0000.000
142A158ARG10.8440.93227.2590.0010.0010.0000.0000.0000.000
143A159ILE00.0350.03622.5830.0150.0150.0000.0000.0000.000
144A160PRO00.0250.00826.886-0.011-0.0110.0000.0000.0000.000
145A161ASN0-0.022-0.00629.175-0.003-0.0030.0000.0000.0000.000
146A162TYR00.013-0.00423.905-0.005-0.0050.0000.0000.0000.000
147A163PRO00.0190.02128.5290.0060.0060.0000.0000.0000.000
148A164ALA00.019-0.00828.200-0.004-0.0040.0000.0000.0000.000
149A165ASP-1-0.831-0.90127.821-0.091-0.0910.0000.0000.0000.000
150A166ARG10.8990.96825.3390.0760.0760.0000.0000.0000.000
151A167THR0-0.031-0.02323.660-0.002-0.0020.0000.0000.0000.000
152A168LYS10.9370.98720.5250.1260.1260.0000.0000.0000.000
153A169VAL0-0.025-0.01420.6790.0020.0020.0000.0000.0000.000
154A170PHE0-0.0110.00317.935-0.016-0.0160.0000.0000.0000.000
155A171CYS0-0.065-0.03219.7550.0290.0290.0000.0000.0000.000
156A172ASN00.0020.00718.257-0.039-0.0390.0000.0000.0000.000
157A173THR00.0370.00122.3090.0130.0130.0000.0000.0000.000
158A174GLY00.0210.00724.6850.0050.0050.0000.0000.0000.000
159A175ASP-1-0.756-0.84520.4800.2070.2070.0000.0000.0000.000
160A176LEU00.033-0.00323.500-0.013-0.0130.0000.0000.0000.000
161A177VAL0-0.0040.00421.307-0.007-0.0070.0000.0000.0000.000
162A179THR0-0.058-0.03825.434-0.015-0.0150.0000.0000.0000.000
163A180GLY00.0310.01328.274-0.004-0.0040.0000.0000.0000.000
164A181SER0-0.0220.01227.9440.0070.0070.0000.0000.0000.000
165A182LEU00.0390.00124.1820.0050.0050.0000.0000.0000.000
166A183ILE0-0.038-0.01224.7330.0240.0240.0000.0000.0000.000
167A184VAL00.0240.01519.564-0.009-0.0090.0000.0000.0000.000
168A185ALA00.0270.01422.509-0.002-0.0020.0000.0000.0000.000
169A186ALA00.0480.00820.3390.0140.0140.0000.0000.0000.000
170A187PRO00.0390.01819.2620.0180.0180.0000.0000.0000.000
171A188HIS10.7820.86817.980-0.313-0.3130.0000.0000.0000.000
172A189LEU00.0000.00715.1820.0290.0290.0000.0000.0000.000
173A190ALA0-0.034-0.00714.5010.0220.0220.0000.0000.0000.000
174A191TYR00.025-0.00313.792-0.057-0.0570.0000.0000.0000.000
175A192GLY00.0060.00810.689-0.053-0.0530.0000.0000.0000.000
176A193PRO0-0.019-0.03411.562-0.134-0.1340.0000.0000.0000.000
177A194ASP-1-0.780-0.90414.024-0.146-0.1460.0000.0000.0000.000
178A195ALA0-0.046-0.0299.973-0.044-0.0440.0000.0000.0000.000
179A196ARG10.9310.9589.2860.2620.2620.0000.0000.0000.000
180A197GLY00.0390.03411.474-0.062-0.0620.0000.0000.0000.000
181A198PRO00.0320.02015.184-0.009-0.0090.0000.0000.0000.000
182A199ALA0-0.010-0.00614.2010.0240.0240.0000.0000.0000.000
183A200PRO00.004-0.00312.5080.0210.0210.0000.0000.0000.000
184A201GLU-1-0.945-0.95615.153-0.255-0.2550.0000.0000.0000.000
185A202PHE00.0090.00118.4000.0220.0220.0000.0000.0000.000
186A203LEU0-0.024-0.01415.1810.0170.0170.0000.0000.0000.000
187A204ILE0-0.007-0.00515.9440.0160.0160.0000.0000.0000.000
188A205GLU-1-0.951-0.96719.788-0.153-0.1530.0000.0000.0000.000
189A206LYS10.8370.90122.5500.1450.1450.0000.0000.0000.000
190A207VAL00.0020.00220.1830.0190.0190.0000.0000.0000.000
191A208ARG10.9250.96220.9830.3560.3560.0000.0000.0000.000
192A209ALA0-0.054-0.00925.3590.0140.0140.0000.0000.0000.000
193A210VAL0-0.046-0.02526.3370.0130.0130.0000.0000.0000.000
194A211ARG10.8870.94224.0100.2070.2070.0000.0000.0000.000
195A212GLY0-0.021-0.00126.874-0.006-0.0060.0000.0000.0000.000