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: R8458

Calculation Name: 3U0V-A-Xray372

Preferred Name: Lysophospholipase-like protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3U0V

Chain ID: A

ChEMBL ID: CHEMBL2189133

UniProt ID: Q5VWZ2

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 OptAll
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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2816613.34623
FMO2-HF: Nuclear repulsion 2728491.181268
FMO2-HF: Total energy -88122.164962
FMO2-MP2: Total energy -88375.615657


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:9:LEU)


Summations of interaction energy for fragment #1(A:9: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.
-12.561-2.6829.148-5.213-13.809-0.017
Interaction energy analysis for fragmet #1(A:9:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.011
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].
3A11ARG10.7660.8422.549-0.9402.2380.213-1.495-1.8960.001
4A12CYS0-0.085-0.0315.3620.2790.337-0.001-0.004-0.0520.000
5A13ILE00.0200.0048.025-0.105-0.1050.0000.0000.0000.000
6A14VAL0-0.019-0.00211.1220.0670.0670.0000.0000.0000.000
7A15SER00.015-0.00214.570-0.031-0.0310.0000.0000.0000.000
8A16PRO0-0.0280.01116.2220.0080.0080.0000.0000.0000.000
9A17ALA0-0.006-0.00819.1310.0120.0120.0000.0000.0000.000
10A18GLY00.0300.00421.8710.0150.0150.0000.0000.0000.000
11A19ARG10.9220.96921.5040.1000.1000.0000.0000.0000.000
12A20HIS00.0060.00014.0430.0250.0250.0000.0000.0000.000
13A21SER0-0.032-0.01819.3290.0060.0060.0000.0000.0000.000
14A22ALA00.0430.02516.9740.0050.0050.0000.0000.0000.000
15A23SER0-0.029-0.03111.6960.0320.0320.0000.0000.0000.000
16A24LEU00.0110.01712.5240.0130.0130.0000.0000.0000.000
17A25ILE00.0300.0246.250-0.007-0.0070.0000.0000.0000.000
18A26PHE0-0.012-0.0158.6550.0520.0520.0000.0000.0000.000
19A27LEU00.0070.0015.068-0.023-0.0230.0000.0000.0000.000
20A28HIS00.0080.0127.124-0.024-0.0240.0000.0000.0000.000
21A29GLY00.0760.0469.924-0.020-0.0200.0000.0000.0000.000
22A30SER00.001-0.01311.237-0.008-0.0080.0000.0000.0000.000
23A31GLY0-0.022-0.00911.1210.0190.0190.0000.0000.0000.000
24A32ASP-1-0.825-0.89711.646-0.158-0.1580.0000.0000.0000.000
25A33SER0-0.034-0.0378.5710.0170.0170.0000.0000.0000.000
26A34GLY00.0380.0227.6240.0070.0070.0000.0000.0000.000
27A35GLN00.029-0.0028.4900.0150.0150.0000.0000.0000.000
28A36GLY00.0160.02111.4340.0280.0280.0000.0000.0000.000
29A37LEU00.0760.04010.5370.0140.0140.0000.0000.0000.000
30A38ARG10.7890.87912.5150.1760.1760.0000.0000.0000.000
31A39MET0-0.038-0.03514.2010.0210.0210.0000.0000.0000.000
32A40TRP00.0210.03316.0610.0110.0110.0000.0000.0000.000
33A41ILE00.0270.00314.6280.0110.0110.0000.0000.0000.000
34A42LYS10.8120.89718.3640.1020.1020.0000.0000.0000.000
35A43GLN0-0.023-0.01120.2840.0050.0050.0000.0000.0000.000
36A44VAL0-0.0010.01121.6420.0080.0080.0000.0000.0000.000
37A45LEU0-0.026-0.03020.7240.0060.0060.0000.0000.0000.000
38A46ASN0-0.078-0.02724.1120.0110.0110.0000.0000.0000.000
39A47GLN0-0.0100.00323.7990.0070.0070.0000.0000.0000.000
40A48ASP-1-0.744-0.83618.281-0.135-0.1350.0000.0000.0000.000
41A49LEU00.0200.02716.2220.0070.0070.0000.0000.0000.000
42A50THR0-0.008-0.01418.045-0.014-0.0140.0000.0000.0000.000
43A51PHE00.029-0.00217.5520.0100.0100.0000.0000.0000.000
44A52GLN00.0410.02421.214-0.001-0.0010.0000.0000.0000.000
45A53HIS0-0.044-0.03421.2520.0110.0110.0000.0000.0000.000
46A54ILE00.0170.00815.963-0.010-0.0100.0000.0000.0000.000
47A55LYS10.8360.90810.9620.4440.4440.0000.0000.0000.000
48A56ILE00.0020.00211.782-0.039-0.0390.0000.0000.0000.000
49A57ILE0-0.017-0.0136.3510.0060.0060.0000.0000.0000.000
50A58TYR00.0480.0307.9460.0000.0000.0000.0000.0000.000
51A59PRO00.0080.0022.327-0.867-0.1930.959-0.464-1.1690.001
52A60THR0-0.016-0.0263.146-0.1170.4340.017-0.113-0.4540.000
53A61ALA00.0030.0102.663-2.464-0.7430.610-0.933-1.397-0.013
54A62PRO00.012-0.0102.401-0.648-0.2141.607-0.389-1.6510.002
55A63PRO00.0000.0145.002-0.242-0.208-0.001-0.007-0.0260.000
56A64ARG10.8390.9068.2070.1210.1210.0000.0000.0000.000
57A65SER00.0410.03310.752-0.034-0.0340.0000.0000.0000.000
58A66TYR00.0270.01513.119-0.034-0.0340.0000.0000.0000.000
59A67THR00.021-0.00915.0180.0150.0150.0000.0000.0000.000
60A68PRO0-0.046-0.01616.8940.0090.0090.0000.0000.0000.000
61A69MET0-0.059-0.00915.8430.0080.0080.0000.0000.0000.000
62A70LYS10.9370.95919.3140.0130.0130.0000.0000.0000.000
63A71GLY00.0270.02218.0180.0070.0070.0000.0000.0000.000
64A72GLY0-0.023-0.01117.3700.0190.0190.0000.0000.0000.000
65A73ILE0-0.016-0.02012.556-0.013-0.0130.0000.0000.0000.000
66A74SER00.0250.00012.259-0.011-0.0110.0000.0000.0000.000
67A75ASN0-0.0100.0037.7690.1080.1080.0000.0000.0000.000
68A76VAL0-0.034-0.0288.335-0.072-0.0720.0000.0000.0000.000
69A77TRP00.039-0.0152.558-0.897-0.0970.420-0.190-1.0300.001
70A78PHE0-0.002-0.0097.346-0.043-0.0430.0000.0000.0000.000
71A79ASP-1-0.770-0.86610.276-0.023-0.0230.0000.0000.0000.000
72A80ARG10.8230.88613.7330.1470.1470.0000.0000.0000.000
73A81PHE00.0360.01717.2250.0170.0170.0000.0000.0000.000
74A82LYS10.9310.95520.5990.0590.0590.0000.0000.0000.000
75A83ILE00.0240.01318.886-0.012-0.0120.0000.0000.0000.000
76A84THR00.0560.02421.8570.0040.0040.0000.0000.0000.000
77A85ASN0-0.009-0.01622.245-0.002-0.0020.0000.0000.0000.000
78A86ASP-1-0.887-0.93723.483-0.075-0.0750.0000.0000.0000.000
79A87CYS0-0.095-0.03922.6030.0070.0070.0000.0000.0000.000
80A88PRO00.0590.03421.924-0.010-0.0100.0000.0000.0000.000
81A89GLU-1-0.737-0.83816.789-0.199-0.1990.0000.0000.0000.000
82A90HIS00.0240.03214.709-0.012-0.0120.0000.0000.0000.000
83A91LEU00.0590.01414.332-0.024-0.0240.0000.0000.0000.000
84A92GLU-1-0.891-0.93214.136-0.151-0.1510.0000.0000.0000.000
85A93SER0-0.054-0.05910.474-0.013-0.0130.0000.0000.0000.000
86A94ILE00.008-0.0019.569-0.085-0.0850.0000.0000.0000.000
87A95ASP-1-0.742-0.8499.647-0.396-0.3960.0000.0000.0000.000
88A96VAL0-0.015-0.0057.450-0.062-0.0620.0000.0000.0000.000
89A97MET0-0.0140.0013.862-1.126-0.5070.062-0.140-0.5410.000
90A98CYS0-0.038-0.0195.467-0.318-0.3180.0000.0000.0000.000
91A99GLN0-0.043-0.0017.8290.0220.0220.0000.0000.0000.000
92A100VAL00.0200.0042.253-0.816-0.7822.483-0.447-2.070-0.005
93A101LEU0-0.038-0.0332.462-1.979-1.2761.784-0.630-1.856-0.004
94A102THR0-0.008-0.0074.2950.2080.2520.000-0.010-0.0350.000
95A103ASP-1-0.843-0.9115.209-0.955-0.9550.0000.0000.0000.000
96A104LEU0-0.060-0.0262.365-0.9660.0250.997-0.384-1.6030.000
97A105ILE0-0.031-0.0134.8260.3290.368-0.001-0.005-0.0330.000
98A106ASP-1-0.837-0.9348.063-0.378-0.3780.0000.0000.0000.000
99A107GLU-1-0.851-0.8864.992-1.400-1.401-0.001-0.0020.0040.000
100A108GLU-1-0.757-0.8328.825-0.386-0.3860.0000.0000.0000.000
101A109VAL0-0.011-0.00511.1930.0980.0980.0000.0000.0000.000
102A110LYS10.8910.95012.1220.2570.2570.0000.0000.0000.000
103A111SER0-0.055-0.03312.0960.0670.0670.0000.0000.0000.000
104A112GLY0-0.019-0.00114.7740.0290.0290.0000.0000.0000.000
105A113ILE0-0.091-0.04014.0510.0270.0270.0000.0000.0000.000
106A114LYS10.9590.96914.9670.1490.1490.0000.0000.0000.000
107A115LYS10.9280.94312.7030.3850.3850.0000.0000.0000.000
108A116ASN00.0440.02515.736-0.015-0.0150.0000.0000.0000.000
109A117ARG10.7670.86917.2050.2150.2150.0000.0000.0000.000
110A118ILE00.0270.01210.895-0.009-0.0090.0000.0000.0000.000
111A119LEU0-0.0220.01313.9730.0210.0210.0000.0000.0000.000
112A120ILE00.0110.0019.061-0.054-0.0540.0000.0000.0000.000
113A121GLY00.069-0.00410.7730.0530.0530.0000.0000.0000.000
114A122GLY0-0.011-0.00510.288-0.063-0.0630.0000.0000.0000.000
115A123PHE00.0010.01011.9400.0270.0270.0000.0000.0000.000
116A124SER00.0180.00813.092-0.023-0.0230.0000.0000.0000.000
117A125MET0-0.081-0.01610.944-0.025-0.0250.0000.0000.0000.000
118A126GLY00.0560.0229.487-0.039-0.0390.0000.0000.0000.000
119A127GLY00.0320.01810.403-0.042-0.0420.0000.0000.0000.000
120A128CYS0-0.072-0.03413.340-0.002-0.0020.0000.0000.0000.000
121A129MET0-0.0070.0007.059-0.010-0.0100.0000.0000.0000.000
122A130ALA0-0.0110.01110.232-0.043-0.0430.0000.0000.0000.000
123A131MET0-0.023-0.01011.1140.0120.0120.0000.0000.0000.000
124A132HIS00.0210.00111.957-0.003-0.0030.0000.0000.0000.000
125A133LEU0-0.0090.0057.1910.0240.0240.0000.0000.0000.000
126A134ALA00.004-0.00210.9250.0140.0140.0000.0000.0000.000
127A135TYR0-0.028-0.05413.8130.0170.0170.0000.0000.0000.000
128A136ARG10.7850.87113.9640.3240.3240.0000.0000.0000.000
129A137ASN0-0.064-0.02912.097-0.001-0.0010.0000.0000.0000.000
130A138HIS00.0280.02210.2780.0510.0510.0000.0000.0000.000
131A139GLN0-0.032-0.03314.5080.0120.0120.0000.0000.0000.000
132A140ASP-1-0.818-0.89716.298-0.295-0.2950.0000.0000.0000.000
133A141VAL0-0.030-0.01513.0550.0000.0000.0000.0000.0000.000
134A142ALA0-0.040-0.01916.1360.0290.0290.0000.0000.0000.000
135A143GLY0-0.033-0.03017.0580.0300.0300.0000.0000.0000.000
136A144VAL00.0020.00014.499-0.034-0.0340.0000.0000.0000.000
137A145PHE0-0.029-0.00912.9360.0310.0310.0000.0000.0000.000
138A146ALA0-0.011-0.00514.685-0.032-0.0320.0000.0000.0000.000
139A147LEU00.0320.01816.0740.0200.0200.0000.0000.0000.000
140A148SER00.0590.03617.137-0.011-0.0110.0000.0000.0000.000
141A149SER0-0.042-0.03616.215-0.013-0.0130.0000.0000.0000.000
142A150PHE0-0.026-0.01918.0930.0110.0110.0000.0000.0000.000
143A151LEU00.0260.01216.047-0.022-0.0220.0000.0000.0000.000
144A152ASN0-0.004-0.00519.2650.0020.0020.0000.0000.0000.000
145A153LYS10.8680.92221.2190.0830.0830.0000.0000.0000.000
146A154ALA0-0.028-0.01923.615-0.001-0.0010.0000.0000.0000.000
147A155SER0-0.022-0.01118.136-0.006-0.0060.0000.0000.0000.000
148A156ALA00.036-0.00217.4820.0060.0060.0000.0000.0000.000
149A157VAL00.0050.01116.385-0.003-0.0030.0000.0000.0000.000
150A158TYR00.016-0.00318.8700.0040.0040.0000.0000.0000.000
151A159GLN0-0.053-0.02921.9000.0080.0080.0000.0000.0000.000
152A160ALA0-0.010-0.00419.4680.0080.0080.0000.0000.0000.000
153A161LEU00.0080.01420.8760.0050.0050.0000.0000.0000.000
154A162GLN0-0.0010.00523.2510.0080.0080.0000.0000.0000.000
155A163LYS10.8860.94923.7790.1380.1380.0000.0000.0000.000
156A164SER0-0.015-0.00222.903-0.007-0.0070.0000.0000.0000.000
157A165ASN0-0.022-0.01925.2510.0010.0010.0000.0000.0000.000
158A166GLY00.0250.02526.1110.0070.0070.0000.0000.0000.000
159A167VAL0-0.038-0.02824.5620.0010.0010.0000.0000.0000.000
160A168LEU00.0380.02921.652-0.012-0.0120.0000.0000.0000.000
161A169PRO0-0.0290.00017.7200.0090.0090.0000.0000.0000.000
162A170GLU-1-0.816-0.87320.361-0.142-0.1420.0000.0000.0000.000
163A171LEU00.0040.01118.266-0.019-0.0190.0000.0000.0000.000
164A172PHE00.0030.00919.6320.0200.0200.0000.0000.0000.000
165A173GLN00.013-0.00419.372-0.017-0.0170.0000.0000.0000.000
166A174CYS0-0.067-0.00820.7740.0130.0130.0000.0000.0000.000
167A175HIS00.0320.00321.439-0.018-0.0180.0000.0000.0000.000
168A176GLY00.0480.05023.7570.0070.0070.0000.0000.0000.000
169A177THR0-0.047-0.06025.8620.0000.0000.0000.0000.0000.000
170A178ALA00.0080.01328.7230.0050.0050.0000.0000.0000.000
171A179ASP-1-0.775-0.88022.815-0.103-0.1030.0000.0000.0000.000
172A180GLU-1-0.902-0.95326.354-0.058-0.0580.0000.0000.0000.000
173A181LEU0-0.119-0.05322.2940.0030.0030.0000.0000.0000.000
174A182VAL0-0.086-0.05619.468-0.005-0.0050.0000.0000.0000.000
175A183LEU00.0610.04722.948-0.002-0.0020.0000.0000.0000.000
176A184HIS00.0210.01225.598-0.009-0.0090.0000.0000.0000.000
177A185SER00.0450.02426.775-0.006-0.0060.0000.0000.0000.000
178A186TRP00.0280.00723.248-0.004-0.0040.0000.0000.0000.000
179A187ALA00.0140.03222.907-0.010-0.0100.0000.0000.0000.000
180A188GLU-1-0.807-0.89923.835-0.094-0.0940.0000.0000.0000.000
181A189GLU-1-0.799-0.86226.404-0.096-0.0960.0000.0000.0000.000
182A190THR0-0.025-0.02520.290-0.005-0.0050.0000.0000.0000.000
183A191ASN0-0.020-0.02723.5450.0040.0040.0000.0000.0000.000
184A192SER0-0.030-0.02724.9480.0020.0020.0000.0000.0000.000
185A193MET0-0.026-0.00524.9680.0050.0050.0000.0000.0000.000
186A194LEU00.0150.01020.142-0.001-0.0010.0000.0000.0000.000
187A195LYS10.9440.98024.3440.1060.1060.0000.0000.0000.000
188A196SER0-0.112-0.06127.5340.0050.0050.0000.0000.0000.000
189A197LEU0-0.032-0.01024.7450.0040.0040.0000.0000.0000.000
190A198GLY00.0330.02526.227-0.006-0.0060.0000.0000.0000.000
191A199VAL0-0.039-0.01421.812-0.003-0.0030.0000.0000.0000.000
192A200THR0-0.0020.00224.7230.0090.0090.0000.0000.0000.000
193A201THR0-0.009-0.03723.340-0.011-0.0110.0000.0000.0000.000
194A202LYS10.8360.92124.3510.1400.1400.0000.0000.0000.000
195A203PHE00.0100.01224.176-0.011-0.0110.0000.0000.0000.000
196A204HIS0-0.028-0.02524.1610.0140.0140.0000.0000.0000.000
197A205SER00.0400.01125.856-0.005-0.0050.0000.0000.0000.000
198A206PHE0-0.016-0.01624.8480.0030.0030.0000.0000.0000.000
199A207PRO00.0540.01228.6860.0010.0010.0000.0000.0000.000
200A208ASN0-0.057-0.03131.2000.0000.0000.0000.0000.0000.000
201A209VAL00.0020.03425.1990.0010.0010.0000.0000.0000.000
202A210TYR0-0.001-0.01026.1220.0000.0000.0000.0000.0000.000
203A211HIS0-0.066-0.04318.812-0.017-0.0170.0000.0000.0000.000
204A212GLU-1-0.872-0.95020.818-0.082-0.0820.0000.0000.0000.000
205A213LEU00.0020.00816.386-0.013-0.0130.0000.0000.0000.000
206A214SER00.0240.01020.9720.0120.0120.0000.0000.0000.000
207A215LYS10.9100.90723.4620.0790.0790.0000.0000.0000.000
208A216THR00.0270.01325.074-0.005-0.0050.0000.0000.0000.000
209A217GLU-1-0.818-0.91121.052-0.145-0.1450.0000.0000.0000.000
210A218LEU00.0280.00219.168-0.012-0.0120.0000.0000.0000.000
211A219ASP-1-0.872-0.91021.940-0.104-0.1040.0000.0000.0000.000
212A220ILE0-0.010-0.01424.914-0.003-0.0030.0000.0000.0000.000
213A221LEU00.0150.02217.132-0.004-0.0040.0000.0000.0000.000
214A222LYS10.8860.94621.0990.1240.1240.0000.0000.0000.000
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