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: 6Y56Z

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2808281.085222
FMO2-HF: Nuclear repulsion 2720161.790984
FMO2-HF: Total energy -88119.294238
FMO2-MP2: Total energy -88373.388621


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.
-10.666-2.17912.455-6.161-14.783-0.026
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 : 0.014 / q_NPA : 0.017
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].
3A11ARG10.8000.8682.531-0.3743.3990.575-1.809-2.539-0.002
4A12CYS0-0.074-0.0105.3340.2060.263-0.001-0.005-0.0510.000
5A13ILE00.0090.0097.997-0.077-0.0770.0000.0000.0000.000
6A14VAL00.0020.00010.8630.0700.0700.0000.0000.0000.000
7A15SER0-0.004-0.00214.381-0.035-0.0350.0000.0000.0000.000
8A16PRO0-0.0350.00316.1590.0100.0100.0000.0000.0000.000
9A17ALA00.0000.00219.0820.0080.0080.0000.0000.0000.000
10A18GLY00.0210.00522.2990.0150.0150.0000.0000.0000.000
11A19ARG10.9400.97621.3450.1240.1240.0000.0000.0000.000
12A20HIS00.012-0.00213.8500.0290.0290.0000.0000.0000.000
13A21SER0-0.047-0.02819.1010.0060.0060.0000.0000.0000.000
14A22ALA00.0310.02016.7690.0070.0070.0000.0000.0000.000
15A23SER0-0.040-0.05311.4900.0250.0250.0000.0000.0000.000
16A24LEU00.0030.02212.7910.0180.0180.0000.0000.0000.000
17A25ILE0-0.0050.0066.386-0.025-0.0250.0000.0000.0000.000
18A26PHE00.0380.0078.7180.0510.0510.0000.0000.0000.000
19A27LEU0-0.046-0.0195.481-0.039-0.0390.0000.0000.0000.000
20A28HIS00.026-0.0017.0160.0130.0130.0000.0000.0000.000
21A29GLY00.0870.05010.031-0.007-0.0070.0000.0000.0000.000
22A30SER0-0.031-0.02811.2520.0060.0060.0000.0000.0000.000
23A31GLY00.0020.01211.3290.0020.0020.0000.0000.0000.000
24A32ASP-1-0.833-0.90011.308-0.098-0.0980.0000.0000.0000.000
25A33SER0-0.040-0.0258.3080.0370.0370.0000.0000.0000.000
26A34GLY00.026-0.0137.203-0.009-0.0090.0000.0000.0000.000
27A35GLN00.028-0.0018.3550.0150.0150.0000.0000.0000.000
28A36GLY0-0.0080.01711.2120.0230.0230.0000.0000.0000.000
29A37LEU00.1000.04910.5920.0080.0080.0000.0000.0000.000
30A38ARG10.7530.85712.4190.1880.1880.0000.0000.0000.000
31A39MET0-0.038-0.04014.1190.0160.0160.0000.0000.0000.000
32A40TRP00.0480.05715.9290.0100.0100.0000.0000.0000.000
33A41ILE00.002-0.02114.7020.0090.0090.0000.0000.0000.000
34A42LYS10.9370.98318.4040.0970.0970.0000.0000.0000.000
35A43GLN0-0.041-0.02620.3490.0050.0050.0000.0000.0000.000
36A44VAL0-0.025-0.01021.3370.0060.0060.0000.0000.0000.000
37A45LEU0-0.031-0.02920.9940.0030.0030.0000.0000.0000.000
38A46ASN0-0.081-0.02524.2760.0080.0080.0000.0000.0000.000
39A47GLN00.0000.00523.8710.0080.0080.0000.0000.0000.000
40A48ASP-1-0.801-0.88518.560-0.149-0.1490.0000.0000.0000.000
41A49LEU00.0100.01416.2420.0070.0070.0000.0000.0000.000
42A50THR0-0.025-0.01118.158-0.018-0.0180.0000.0000.0000.000
43A51PHE00.016-0.01717.0990.0130.0130.0000.0000.0000.000
44A52GLN00.0730.03420.996-0.001-0.0010.0000.0000.0000.000
45A53HIS0-0.044-0.04221.0210.0090.0090.0000.0000.0000.000
46A54ILE00.0060.01715.862-0.012-0.0120.0000.0000.0000.000
47A55LYS10.8680.94010.8510.5670.5670.0000.0000.0000.000
48A56ILE00.004-0.00111.687-0.028-0.0280.0000.0000.0000.000
49A57ILE0-0.016-0.0106.299-0.019-0.0190.0000.0000.0000.000
50A58TYR00.0250.0177.8040.0280.0280.0000.0000.0000.000
51A59PRO00.0310.0072.241-0.806-0.2661.377-0.609-1.3090.001
52A60THR0-0.007-0.0152.967-0.2990.4060.039-0.161-0.5830.000
53A61ALA00.0020.0212.543-2.539-0.6011.152-1.255-1.835-0.017
54A62PRO0-0.003-0.0212.132-0.238-0.9473.582-0.762-2.1110.001
55A63PRO0-0.0010.0034.901-0.304-0.259-0.001-0.009-0.0350.000
56A64ARG10.9010.9518.520-0.060-0.0600.0000.0000.0000.000
57A65SER00.0350.02510.728-0.038-0.0380.0000.0000.0000.000
58A66TYR00.0210.01213.356-0.025-0.0250.0000.0000.0000.000
59A67THR00.030-0.02715.2460.0070.0070.0000.0000.0000.000
60A68PRO0-0.062-0.02117.2250.0020.0020.0000.0000.0000.000
61A69MET0-0.058-0.02016.0710.0030.0030.0000.0000.0000.000
62A70LYS10.9430.96419.558-0.028-0.0280.0000.0000.0000.000
63A71GLY0-0.0030.00418.0850.0050.0050.0000.0000.0000.000
64A72GLY00.0060.01217.6880.0220.0220.0000.0000.0000.000
65A73ILE0-0.031-0.01812.281-0.004-0.0040.0000.0000.0000.000
66A74SER00.0370.00512.359-0.019-0.0190.0000.0000.0000.000
67A75ASN0-0.013-0.0107.5540.1410.1410.0000.0000.0000.000
68A76VAL0-0.045-0.0418.640-0.098-0.0980.0000.0000.0000.000
69A77TRP00.037-0.0103.085-0.8280.0440.118-0.177-0.8130.001
70A78PHE00.001-0.0187.595-0.031-0.0310.0000.0000.0000.000
71A79ASP-1-0.792-0.85610.3610.0600.0600.0000.0000.0000.000
72A80ARG10.9150.95513.7210.0680.0680.0000.0000.0000.000
73A81PHE00.009-0.00517.0990.0170.0170.0000.0000.0000.000
74A82LYS10.9470.96620.5620.0200.0200.0000.0000.0000.000
75A83ILE00.0180.01418.932-0.008-0.0080.0000.0000.0000.000
76A84THR00.0460.02122.0300.0020.0020.0000.0000.0000.000
77A85ASN00.0290.01022.6660.0000.0000.0000.0000.0000.000
78A86ASP-1-0.927-0.95024.232-0.047-0.0470.0000.0000.0000.000
79A87CYS0-0.035-0.01721.8760.0090.0090.0000.0000.0000.000
80A88PRO00.0460.03322.151-0.009-0.0090.0000.0000.0000.000
81A89GLU-1-0.745-0.85917.394-0.132-0.1320.0000.0000.0000.000
82A90HIS00.0300.03215.135-0.009-0.0090.0000.0000.0000.000
83A91LEU00.0520.01814.826-0.015-0.0150.0000.0000.0000.000
84A92GLU-1-0.870-0.92914.428-0.080-0.0800.0000.0000.0000.000
85A93SER0-0.063-0.05011.072-0.017-0.0170.0000.0000.0000.000
86A94ILE00.0200.0049.837-0.050-0.0500.0000.0000.0000.000
87A95ASP-1-0.777-0.88910.190-0.298-0.2980.0000.0000.0000.000
88A96VAL0-0.034-0.0137.343-0.064-0.0640.0000.0000.0000.000
89A97MET0-0.024-0.0183.789-0.921-0.3840.047-0.125-0.4590.000
90A98CYS0-0.0200.0005.736-0.311-0.3110.0000.0000.0000.000
91A99GLN0-0.038-0.0017.642-0.030-0.0300.0000.0000.0000.000
92A100VAL00.020-0.0062.158-0.507-0.9393.123-0.534-2.156-0.007
93A101LEU0-0.040-0.0292.275-1.161-1.0911.958-0.413-1.615-0.002
94A102THR00.0090.0114.1450.1250.1820.000-0.013-0.0450.000
95A103ASP-1-0.825-0.8995.593-0.817-0.8170.0000.0000.0000.000
96A104LEU0-0.061-0.0112.670-0.9320.0710.487-0.284-1.206-0.001
97A105ILE0-0.037-0.0384.8320.3340.365-0.001-0.005-0.0260.000
98A106ASP-1-0.879-0.9468.131-0.430-0.4300.0000.0000.0000.000
99A107GLU-1-0.883-0.9245.404-1.892-1.8920.0000.0000.0000.000
100A108GLU-1-0.761-0.8538.807-0.473-0.4730.0000.0000.0000.000
101A109VAL0-0.013-0.01610.8100.1060.1060.0000.0000.0000.000
102A110LYS10.8830.96112.4320.3150.3150.0000.0000.0000.000
103A111SER0-0.020-0.00912.7900.0710.0710.0000.0000.0000.000
104A112GLY0-0.054-0.01815.0600.0350.0350.0000.0000.0000.000
105A113ILE0-0.065-0.01214.0940.0350.0350.0000.0000.0000.000
106A114LYS10.9620.97515.1800.1790.1790.0000.0000.0000.000
107A115LYS10.9810.98713.1380.3800.3800.0000.0000.0000.000
108A116ASN00.000-0.00915.828-0.010-0.0100.0000.0000.0000.000
109A117ARG10.8000.88117.2180.2300.2300.0000.0000.0000.000
110A118ILE00.0560.02911.066-0.013-0.0130.0000.0000.0000.000
111A119LEU0-0.0100.02313.6690.0250.0250.0000.0000.0000.000
112A120ILE0-0.010-0.0079.227-0.050-0.0500.0000.0000.0000.000
113A121GLY00.0830.00411.0280.0470.0470.0000.0000.0000.000
114A122GLY0-0.032-0.01010.613-0.056-0.0560.0000.0000.0000.000
115A123PHE00.0230.01612.1230.0220.0220.0000.0000.0000.000
116A124SER00.0180.00413.433-0.008-0.0080.0000.0000.0000.000
117A125MET0-0.080-0.02111.138-0.012-0.0120.0000.0000.0000.000
118A126GLY00.0760.0339.862-0.023-0.0230.0000.0000.0000.000
119A127GLY00.0230.01010.710-0.040-0.0400.0000.0000.0000.000
120A128CYS0-0.016-0.00513.5700.0030.0030.0000.0000.0000.000
121A129MET0-0.0180.0187.3940.0110.0110.0000.0000.0000.000
122A130ALA00.0050.00610.627-0.037-0.0370.0000.0000.0000.000
123A131MET00.0030.00011.4720.0020.0020.0000.0000.0000.000
124A132HIS0-0.019-0.00112.1610.0000.0000.0000.0000.0000.000
125A133LEU00.0070.0107.2340.0030.0030.0000.0000.0000.000
126A134ALA0-0.017-0.01411.3220.0100.0100.0000.0000.0000.000
127A135TYR0-0.033-0.03814.2500.0140.0140.0000.0000.0000.000
128A136ARG10.8040.89014.2990.2550.2550.0000.0000.0000.000
129A137ASN0-0.026-0.01112.476-0.011-0.0110.0000.0000.0000.000
130A138HIS00.0110.00510.3280.0430.0430.0000.0000.0000.000
131A139GLN0-0.029-0.03914.8290.0060.0060.0000.0000.0000.000
132A140ASP-1-0.842-0.92316.964-0.273-0.2730.0000.0000.0000.000
133A141VAL0-0.075-0.03413.311-0.002-0.0020.0000.0000.0000.000
134A142ALA0-0.009-0.01216.4680.0270.0270.0000.0000.0000.000
135A143GLY0-0.006-0.01517.0980.0280.0280.0000.0000.0000.000
136A144VAL0-0.0090.00114.399-0.037-0.0370.0000.0000.0000.000
137A145PHE0-0.0050.00813.0990.0240.0240.0000.0000.0000.000
138A146ALA00.003-0.00315.132-0.025-0.0250.0000.0000.0000.000
139A147LEU0-0.0240.00316.3660.0160.0160.0000.0000.0000.000
140A148SER00.0710.03917.325-0.002-0.0020.0000.0000.0000.000
141A149SER0-0.028-0.02315.978-0.002-0.0020.0000.0000.0000.000
142A150PHE0-0.037-0.02518.4510.0080.0080.0000.0000.0000.000
143A151LEU0-0.008-0.00617.129-0.014-0.0140.0000.0000.0000.000
144A152ASN0-0.055-0.04319.4110.0010.0010.0000.0000.0000.000
145A153LYS10.8970.92821.7690.0550.0550.0000.0000.0000.000
146A154ALA0-0.032-0.02124.0830.0010.0010.0000.0000.0000.000
147A155SER0-0.035-0.01918.766-0.007-0.0070.0000.0000.0000.000
148A156ALA00.024-0.01618.0050.0040.0040.0000.0000.0000.000
149A157VAL0-0.007-0.00616.928-0.005-0.0050.0000.0000.0000.000
150A158TYR00.0200.00219.4060.0000.0000.0000.0000.0000.000
151A159GLN0-0.023-0.01022.8870.0050.0050.0000.0000.0000.000
152A160ALA00.0010.00319.8700.0050.0050.0000.0000.0000.000
153A161LEU00.0000.00321.1490.0020.0020.0000.0000.0000.000
154A162GLN0-0.0150.00423.5910.0060.0060.0000.0000.0000.000
155A163LYS10.8960.94523.9030.1150.1150.0000.0000.0000.000
156A164SER0-0.0110.00923.106-0.006-0.0060.0000.0000.0000.000
157A165ASN0-0.012-0.00825.5190.0020.0020.0000.0000.0000.000
158A166GLY00.0190.02025.7790.0050.0050.0000.0000.0000.000
159A167VAL0-0.030-0.02224.9360.0020.0020.0000.0000.0000.000
160A168LEU00.0200.02321.711-0.012-0.0120.0000.0000.0000.000
161A169PRO0-0.021-0.00717.7330.0100.0100.0000.0000.0000.000
162A170GLU-1-0.868-0.92520.618-0.137-0.1370.0000.0000.0000.000
163A171LEU0-0.023-0.01218.606-0.017-0.0170.0000.0000.0000.000
164A172PHE0-0.007-0.00519.8380.0170.0170.0000.0000.0000.000
165A173GLN00.0440.01619.593-0.016-0.0160.0000.0000.0000.000
166A174CYS0-0.0440.01420.9910.0110.0110.0000.0000.0000.000
167A175HIS00.001-0.02121.850-0.015-0.0150.0000.0000.0000.000
168A176GLY00.0460.03424.1510.0030.0030.0000.0000.0000.000
169A177THR0-0.030-0.05426.4640.0010.0010.0000.0000.0000.000
170A178ALA0-0.0110.00229.1780.0030.0030.0000.0000.0000.000
171A179ASP-1-0.790-0.89323.252-0.068-0.0680.0000.0000.0000.000
172A180GLU-1-0.915-0.95926.843-0.034-0.0340.0000.0000.0000.000
173A181LEU0-0.122-0.04121.4260.0050.0050.0000.0000.0000.000
174A182VAL0-0.049-0.03119.840-0.001-0.0010.0000.0000.0000.000
175A183LEU00.0640.04523.372-0.002-0.0020.0000.0000.0000.000
176A184HIS00.0380.02725.893-0.009-0.0090.0000.0000.0000.000
177A185SER00.0390.01727.305-0.006-0.0060.0000.0000.0000.000
178A186TRP00.0180.01023.160-0.004-0.0040.0000.0000.0000.000
179A187ALA00.0320.02123.178-0.008-0.0080.0000.0000.0000.000
180A188GLU-1-0.858-0.93424.172-0.073-0.0730.0000.0000.0000.000
181A189GLU-1-0.852-0.90226.776-0.072-0.0720.0000.0000.0000.000
182A190THR0-0.024-0.00520.783-0.004-0.0040.0000.0000.0000.000
183A191ASN0-0.016-0.03523.7610.0000.0000.0000.0000.0000.000
184A192SER0-0.004-0.00825.3740.0000.0000.0000.0000.0000.000
185A193MET0-0.018-0.00525.2900.0040.0040.0000.0000.0000.000
186A194LEU0-0.022-0.01120.717-0.001-0.0010.0000.0000.0000.000
187A195LYS10.9680.99524.9400.0880.0880.0000.0000.0000.000
188A196SER0-0.107-0.05928.0180.0030.0030.0000.0000.0000.000
189A197LEU0-0.030-0.01324.7740.0030.0030.0000.0000.0000.000
190A198GLY00.0240.02727.034-0.004-0.0040.0000.0000.0000.000
191A199VAL0-0.034-0.00322.201-0.004-0.0040.0000.0000.0000.000
192A200THR0-0.009-0.00625.2030.0110.0110.0000.0000.0000.000
193A201THR00.009-0.00823.615-0.008-0.0080.0000.0000.0000.000
194A202LYS10.8750.95124.5030.1230.1230.0000.0000.0000.000
195A203PHE00.0140.01524.354-0.009-0.0090.0000.0000.0000.000
196A204HIS0-0.042-0.02825.1500.0110.0110.0000.0000.0000.000
197A205SER00.0470.01726.157-0.004-0.0040.0000.0000.0000.000
198A206PHE0-0.034-0.02725.1360.0020.0020.0000.0000.0000.000
199A207PRO00.0610.01829.0570.0010.0010.0000.0000.0000.000
200A208ASN0-0.061-0.04431.5290.0010.0010.0000.0000.0000.000
201A209VAL00.0040.03625.4360.0010.0010.0000.0000.0000.000
202A210TYR0-0.035-0.03326.6700.0010.0010.0000.0000.0000.000
203A211HIS0-0.082-0.04419.127-0.010-0.0100.0000.0000.0000.000
204A212GLU-1-0.875-0.94421.102-0.057-0.0570.0000.0000.0000.000
205A213LEU00.0040.01916.811-0.009-0.0090.0000.0000.0000.000
206A214SER00.0290.00821.1880.0110.0110.0000.0000.0000.000
207A215LYS11.0391.00823.6750.0630.0630.0000.0000.0000.000
208A216THR0-0.035-0.01625.494-0.004-0.0040.0000.0000.0000.000
209A217GLU-1-0.819-0.91721.097-0.126-0.1260.0000.0000.0000.000
210A218LEU00.016-0.00618.268-0.011-0.0110.0000.0000.0000.000
211A219ASP-1-0.911-0.95321.943-0.108-0.1080.0000.0000.0000.000
212A220ILE0-0.063-0.03924.856-0.003-0.0030.0000.0000.0000.000
213A221LEU00.0360.02417.158-0.004-0.0040.0000.0000.0000.000
214A222LYS10.9400.97421.0070.1300.1300.0000.0000.0000.000
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