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: ZV9YN

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2807726.537799
FMO2-HF: Nuclear repulsion 2719605.383223
FMO2-HF: Total energy -88121.154576
FMO2-MP2: Total energy -88374.953095


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.
-11.203-1.8869.972-5.311-13.978-0.016
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 : 0.013 / q_NPA : 0.009
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].
3A11ARG10.8060.8702.642-0.2853.1110.393-1.597-2.192-0.001
4A12CYS0-0.088-0.0275.3660.2290.279-0.001-0.004-0.0450.000
5A13ILE00.0070.0027.779-0.062-0.0620.0000.0000.0000.000
6A14VAL0-0.012-0.00210.9540.0690.0690.0000.0000.0000.000
7A15SER00.002-0.00314.463-0.029-0.0290.0000.0000.0000.000
8A16PRO0-0.0430.00116.3000.0090.0090.0000.0000.0000.000
9A17ALA0-0.002-0.00119.1570.0070.0070.0000.0000.0000.000
10A18GLY00.0220.01122.3790.0150.0150.0000.0000.0000.000
11A19ARG10.9430.97321.4210.1110.1110.0000.0000.0000.000
12A20HIS00.000-0.00714.0800.0200.0200.0000.0000.0000.000
13A21SER0-0.043-0.02919.2870.0080.0080.0000.0000.0000.000
14A22ALA00.0360.01716.9770.0080.0080.0000.0000.0000.000
15A23SER0-0.018-0.02711.6400.0210.0210.0000.0000.0000.000
16A24LEU0-0.0010.01612.7150.0180.0180.0000.0000.0000.000
17A25ILE00.0060.0136.307-0.029-0.0290.0000.0000.0000.000
18A26PHE00.0300.0028.9490.0500.0500.0000.0000.0000.000
19A27LEU0-0.038-0.0235.266-0.042-0.0420.0000.0000.0000.000
20A28HIS00.0280.0137.040-0.047-0.0470.0000.0000.0000.000
21A29GLY00.0900.0539.679-0.007-0.0070.0000.0000.0000.000
22A30SER0-0.033-0.03211.276-0.007-0.0070.0000.0000.0000.000
23A31GLY00.0000.01211.4510.0110.0110.0000.0000.0000.000
24A32ASP-1-0.813-0.88511.404-0.177-0.1770.0000.0000.0000.000
25A33SER0-0.050-0.0498.4640.0070.0070.0000.0000.0000.000
26A34GLY00.0370.0057.2320.0200.0200.0000.0000.0000.000
27A35GLN00.017-0.0168.3770.0350.0350.0000.0000.0000.000
28A36GLY0-0.0080.01511.2330.0340.0340.0000.0000.0000.000
29A37LEU00.0970.04910.6080.0170.0170.0000.0000.0000.000
30A38ARG10.7990.88612.4410.2230.2230.0000.0000.0000.000
31A39MET0-0.048-0.04114.1490.0220.0220.0000.0000.0000.000
32A40TRP00.0570.06115.7480.0120.0120.0000.0000.0000.000
33A41ILE00.008-0.01814.7670.0150.0150.0000.0000.0000.000
34A42LYS10.8340.91618.4390.1300.1300.0000.0000.0000.000
35A43GLN0-0.022-0.01420.3800.0080.0080.0000.0000.0000.000
36A44VAL0-0.037-0.01721.3500.0080.0080.0000.0000.0000.000
37A45LEU0-0.019-0.02521.1030.0060.0060.0000.0000.0000.000
38A46ASN0-0.092-0.03124.2730.0090.0090.0000.0000.0000.000
39A47GLN00.0140.01423.9170.0060.0060.0000.0000.0000.000
40A48ASP-1-0.761-0.84518.497-0.163-0.1630.0000.0000.0000.000
41A49LEU00.0280.02816.6160.0100.0100.0000.0000.0000.000
42A50THR0-0.010-0.01018.358-0.018-0.0180.0000.0000.0000.000
43A51PHE00.036-0.00417.3660.0140.0140.0000.0000.0000.000
44A52GLN00.0860.04820.992-0.003-0.0030.0000.0000.0000.000
45A53HIS0-0.036-0.03721.1490.0090.0090.0000.0000.0000.000
46A54ILE00.0040.01115.670-0.010-0.0100.0000.0000.0000.000
47A55LYS10.8340.90811.0800.5030.5030.0000.0000.0000.000
48A56ILE00.0170.00311.794-0.018-0.0180.0000.0000.0000.000
49A57ILE0-0.019-0.0086.137-0.024-0.0240.0000.0000.0000.000
50A58TYR00.0350.0187.9150.0420.0420.0000.0000.0000.000
51A59PRO00.0150.0042.257-0.887-0.3531.383-0.542-1.3750.003
52A60THR0-0.008-0.0212.986-0.2250.4920.038-0.166-0.5880.000
53A61ALA0-0.0090.0052.593-3.413-1.1980.863-1.261-1.817-0.016
54A62PRO00.006-0.0092.392-0.463-0.5272.646-0.518-2.0640.004
55A63PRO0-0.0030.0084.577-0.256-0.204-0.001-0.013-0.0380.000
56A64ARG10.8670.9208.2550.0480.0480.0000.0000.0000.000
57A65SER00.0620.04110.548-0.036-0.0360.0000.0000.0000.000
58A66TYR00.0170.01613.170-0.031-0.0310.0000.0000.0000.000
59A67THR00.026-0.00915.0930.0110.0110.0000.0000.0000.000
60A68PRO0-0.056-0.02017.1070.0050.0050.0000.0000.0000.000
61A69MET0-0.057-0.02015.7780.0040.0040.0000.0000.0000.000
62A70LYS10.9460.96719.453-0.004-0.0040.0000.0000.0000.000
63A71GLY0-0.0020.00317.8770.0070.0070.0000.0000.0000.000
64A72GLY00.0040.01317.4290.0200.0200.0000.0000.0000.000
65A73ILE0-0.035-0.02412.057-0.008-0.0080.0000.0000.0000.000
66A74SER00.0400.01212.123-0.021-0.0210.0000.0000.0000.000
67A75ASN0-0.014-0.0107.7190.1260.1260.0000.0000.0000.000
68A76VAL0-0.042-0.0368.552-0.075-0.0750.0000.0000.0000.000
69A77TRP00.033-0.0162.470-0.858-0.1210.607-0.200-1.1450.001
70A78PHE0-0.004-0.0127.646-0.023-0.0230.0000.0000.0000.000
71A79ASP-1-0.779-0.87610.3500.0160.0160.0000.0000.0000.000
72A80ARG10.8820.93313.6580.1010.1010.0000.0000.0000.000
73A81PHE00.0210.00217.0750.0160.0160.0000.0000.0000.000
74A82LYS10.9410.96020.5090.0320.0320.0000.0000.0000.000
75A83ILE00.0170.01618.985-0.009-0.0090.0000.0000.0000.000
76A84THR00.0450.01522.0680.0030.0030.0000.0000.0000.000
77A85ASN00.000-0.00522.6380.0000.0000.0000.0000.0000.000
78A86ASP-1-0.905-0.93824.000-0.052-0.0520.0000.0000.0000.000
79A87CYS0-0.071-0.02122.8130.0070.0070.0000.0000.0000.000
80A88PRO00.0770.04022.240-0.008-0.0080.0000.0000.0000.000
81A89GLU-1-0.738-0.84417.108-0.140-0.1400.0000.0000.0000.000
82A90HIS00.0330.03015.183-0.006-0.0060.0000.0000.0000.000
83A91LEU00.0400.01214.836-0.018-0.0180.0000.0000.0000.000
84A92GLU-1-0.889-0.93314.454-0.080-0.0800.0000.0000.0000.000
85A93SER0-0.040-0.04310.941-0.018-0.0180.0000.0000.0000.000
86A94ILE00.0190.0069.828-0.055-0.0550.0000.0000.0000.000
87A95ASP-1-0.744-0.85210.004-0.279-0.2790.0000.0000.0000.000
88A96VAL0-0.027-0.0107.371-0.049-0.0490.0000.0000.0000.000
89A97MET0-0.022-0.0114.004-0.879-0.3680.033-0.114-0.4300.000
90A98CYS0-0.028-0.0115.684-0.262-0.2620.0000.0000.0000.000
91A99GLN0-0.054-0.0047.820-0.014-0.0140.0000.0000.0000.000
92A100VAL00.027-0.0012.270-0.683-0.7832.551-0.433-2.018-0.006
93A101LEU0-0.053-0.0322.475-1.095-0.6791.132-0.267-1.281-0.001
94A102THR00.003-0.0074.4510.1030.143-0.001-0.009-0.0290.000
95A103ASP-1-0.818-0.8975.502-0.709-0.7090.0000.0000.0000.000
96A104LEU0-0.053-0.0132.531-0.7640.0490.329-0.187-0.9560.000
97A105ILE0-0.035-0.0365.4390.2530.2530.0000.0000.0000.000
98A106ASP-1-0.873-0.9438.558-0.332-0.3320.0000.0000.0000.000
99A107GLU-1-0.872-0.9035.282-1.573-1.5730.0000.0000.0000.000
100A108GLU-1-0.762-0.8428.928-0.449-0.4490.0000.0000.0000.000
101A109VAL00.006-0.00511.3440.0880.0880.0000.0000.0000.000
102A110LYS10.8850.96312.2590.2560.2560.0000.0000.0000.000
103A111SER0-0.062-0.03612.6280.0540.0540.0000.0000.0000.000
104A112GLY0-0.036-0.01115.3470.0280.0280.0000.0000.0000.000
105A113ILE0-0.074-0.02114.5110.0280.0280.0000.0000.0000.000
106A114LYS10.9710.98115.6300.1520.1520.0000.0000.0000.000
107A115LYS10.9650.95613.3760.3050.3050.0000.0000.0000.000
108A116ASN00.009-0.00616.145-0.011-0.0110.0000.0000.0000.000
109A117ARG10.7880.89317.4880.2060.2060.0000.0000.0000.000
110A118ILE00.0460.02511.128-0.014-0.0140.0000.0000.0000.000
111A119LEU0-0.0130.03213.6800.0230.0230.0000.0000.0000.000
112A120ILE0-0.013-0.0129.224-0.046-0.0460.0000.0000.0000.000
113A121GLY00.0870.01111.2350.0420.0420.0000.0000.0000.000
114A122GLY0-0.027-0.00810.757-0.052-0.0520.0000.0000.0000.000
115A123PHE00.0110.00712.1070.0240.0240.0000.0000.0000.000
116A124SER00.014-0.00213.130-0.016-0.0160.0000.0000.0000.000
117A125MET0-0.091-0.02110.939-0.018-0.0180.0000.0000.0000.000
118A126GLY00.0740.0309.609-0.023-0.0230.0000.0000.0000.000
119A127GLY00.0250.01110.468-0.028-0.0280.0000.0000.0000.000
120A128CYS0-0.017-0.00613.4850.0080.0080.0000.0000.0000.000
121A129MET0-0.0300.0137.140-0.005-0.0050.0000.0000.0000.000
122A130ALA00.0070.00210.503-0.025-0.0250.0000.0000.0000.000
123A131MET0-0.009-0.00111.3930.0080.0080.0000.0000.0000.000
124A132HIS0-0.016-0.00912.2150.0010.0010.0000.0000.0000.000
125A133LEU0-0.0060.0037.4860.0080.0080.0000.0000.0000.000
126A134ALA0-0.019-0.01011.3870.0120.0120.0000.0000.0000.000
127A135TYR0-0.031-0.05414.3770.0130.0130.0000.0000.0000.000
128A136ARG10.7920.87114.1260.2350.2350.0000.0000.0000.000
129A137ASN0-0.045-0.01712.664-0.003-0.0030.0000.0000.0000.000
130A138HIS00.0190.01810.6600.0400.0400.0000.0000.0000.000
131A139GLN0-0.035-0.04015.1050.0040.0040.0000.0000.0000.000
132A140ASP-1-0.831-0.89917.031-0.242-0.2420.0000.0000.0000.000
133A141VAL0-0.059-0.02613.313-0.001-0.0010.0000.0000.0000.000
134A142ALA0-0.013-0.00816.5630.0230.0230.0000.0000.0000.000
135A143GLY0-0.003-0.02417.0540.0240.0240.0000.0000.0000.000
136A144VAL0-0.0120.00214.663-0.032-0.0320.0000.0000.0000.000
137A145PHE0-0.016-0.00313.4800.0220.0220.0000.0000.0000.000
138A146ALA00.0080.00115.262-0.024-0.0240.0000.0000.0000.000
139A147LEU0-0.0040.01116.3000.0170.0170.0000.0000.0000.000
140A148SER00.0570.03917.134-0.006-0.0060.0000.0000.0000.000
141A149SER0-0.035-0.03016.430-0.009-0.0090.0000.0000.0000.000
142A150PHE0-0.007-0.00418.2120.0090.0090.0000.0000.0000.000
143A151LEU0-0.006-0.00916.588-0.014-0.0140.0000.0000.0000.000
144A152ASN0-0.050-0.03919.4130.0010.0010.0000.0000.0000.000
145A153LYS10.8750.91421.4510.0600.0600.0000.0000.0000.000
146A154ALA0-0.019-0.01323.8000.0010.0010.0000.0000.0000.000
147A155SER0-0.027-0.01918.464-0.004-0.0040.0000.0000.0000.000
148A156ALA00.033-0.01117.8860.0050.0050.0000.0000.0000.000
149A157VAL00.0030.00116.842-0.003-0.0030.0000.0000.0000.000
150A158TYR0-0.007-0.01019.3250.0010.0010.0000.0000.0000.000
151A159GLN0-0.035-0.01422.7130.0060.0060.0000.0000.0000.000
152A160ALA00.0160.00519.9510.0050.0050.0000.0000.0000.000
153A161LEU0-0.0040.00921.1860.0020.0020.0000.0000.0000.000
154A162GLN0-0.025-0.00423.6290.0070.0070.0000.0000.0000.000
155A163LYS10.8940.94524.0170.1000.1000.0000.0000.0000.000
156A164SER0-0.0090.01123.280-0.004-0.0040.0000.0000.0000.000
157A165ASN0-0.017-0.01525.6580.0020.0020.0000.0000.0000.000
158A166GLY00.0210.02326.0230.0050.0050.0000.0000.0000.000
159A167VAL0-0.049-0.03025.3580.0010.0010.0000.0000.0000.000
160A168LEU00.0430.03221.825-0.010-0.0100.0000.0000.0000.000
161A169PRO0-0.027-0.00417.8750.0080.0080.0000.0000.0000.000
162A170GLU-1-0.810-0.87620.704-0.126-0.1260.0000.0000.0000.000
163A171LEU00.0010.00218.504-0.016-0.0160.0000.0000.0000.000
164A172PHE0-0.0030.00520.0500.0150.0150.0000.0000.0000.000
165A173GLN00.0380.01519.737-0.014-0.0140.0000.0000.0000.000
166A174CYS0-0.0470.01220.9760.0110.0110.0000.0000.0000.000
167A175HIS00.019-0.00521.753-0.016-0.0160.0000.0000.0000.000
168A176GLY00.0560.04124.0020.0040.0040.0000.0000.0000.000
169A177THR0-0.049-0.05726.2440.0010.0010.0000.0000.0000.000
170A178ALA0-0.0020.00928.9060.0030.0030.0000.0000.0000.000
171A179ASP-1-0.794-0.88822.953-0.085-0.0850.0000.0000.0000.000
172A180GLU-1-0.899-0.94926.468-0.045-0.0450.0000.0000.0000.000
173A181LEU0-0.118-0.04121.7660.0040.0040.0000.0000.0000.000
174A182VAL0-0.063-0.04519.513-0.001-0.0010.0000.0000.0000.000
175A183LEU00.0640.04422.975-0.001-0.0010.0000.0000.0000.000
176A184HIS00.0330.01125.592-0.009-0.0090.0000.0000.0000.000
177A185SER00.0500.02227.094-0.005-0.0050.0000.0000.0000.000
178A186TRP00.0070.00123.145-0.003-0.0030.0000.0000.0000.000
179A187ALA00.0340.03623.070-0.007-0.0070.0000.0000.0000.000
180A188GLU-1-0.839-0.92223.997-0.076-0.0760.0000.0000.0000.000
181A189GLU-1-0.793-0.86726.564-0.073-0.0730.0000.0000.0000.000
182A190THR0-0.021-0.00620.550-0.003-0.0030.0000.0000.0000.000
183A191ASN0-0.021-0.04023.8530.0030.0030.0000.0000.0000.000
184A192SER0-0.010-0.01225.2230.0010.0010.0000.0000.0000.000
185A193MET0-0.018-0.00725.2540.0040.0040.0000.0000.0000.000
186A194LEU0-0.013-0.00520.5490.0000.0000.0000.0000.0000.000
187A195LYS10.9600.99724.8690.0860.0860.0000.0000.0000.000
188A196SER0-0.101-0.06127.9760.0040.0040.0000.0000.0000.000
189A197LEU0-0.028-0.01224.9600.0030.0030.0000.0000.0000.000
190A198GLY00.0250.02827.073-0.003-0.0030.0000.0000.0000.000
191A199VAL0-0.043-0.01122.236-0.004-0.0040.0000.0000.0000.000
192A200THR0-0.0080.00025.2470.0090.0090.0000.0000.0000.000
193A201THR0-0.005-0.02823.584-0.009-0.0090.0000.0000.0000.000
194A202LYS10.8350.91824.7150.1230.1230.0000.0000.0000.000
195A203PHE00.0020.00924.388-0.009-0.0090.0000.0000.0000.000
196A204HIS0-0.035-0.02524.8760.0110.0110.0000.0000.0000.000
197A205SER00.0470.01626.125-0.005-0.0050.0000.0000.0000.000
198A206PHE0-0.038-0.03425.3000.0030.0030.0000.0000.0000.000
199A207PRO00.0560.01428.9390.0000.0000.0000.0000.0000.000
200A208ASN0-0.064-0.04231.3410.0010.0010.0000.0000.0000.000
201A209VAL00.0140.04225.1340.0000.0000.0000.0000.0000.000
202A210TYR0-0.015-0.02626.3230.0010.0010.0000.0000.0000.000
203A211HIS0-0.075-0.04918.821-0.015-0.0150.0000.0000.0000.000
204A212GLU-1-0.880-0.94320.789-0.075-0.0750.0000.0000.0000.000
205A213LEU0-0.0070.00616.560-0.007-0.0070.0000.0000.0000.000
206A214SER00.0350.01520.9920.0110.0110.0000.0000.0000.000
207A215LYS10.9530.95123.6250.0770.0770.0000.0000.0000.000
208A216THR0-0.033-0.01425.498-0.003-0.0030.0000.0000.0000.000
209A217GLU-1-0.801-0.90721.251-0.135-0.1350.0000.0000.0000.000
210A218LEU00.008-0.01019.084-0.010-0.0100.0000.0000.0000.000
211A219ASP-1-0.843-0.90722.017-0.108-0.1080.0000.0000.0000.000
212A220ILE0-0.058-0.04425.081-0.002-0.0020.0000.0000.0000.000
213A221LEU00.0260.02317.284-0.003-0.0030.0000.0000.0000.000
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