FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: KVMV3

Calculation Name: 3L77-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3L77

Chain ID: A

ChEMBL ID:

UniProt ID: C6A190

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3003416.722653
FMO2-HF: Nuclear repulsion 2912245.793316
FMO2-HF: Total energy -91170.929337
FMO2-MP2: Total energy -91440.465926


3D Structure Molmil
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:0:GLU)


Summations of interaction energy for fragment #1(A:0:GLU)
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.
7.9919.7620.014-0.764-1.0210.002
Interaction energy analysis for fragmet #1(A:0:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.038
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].
3A2LYS10.8750.9483.34514.32316.0940.014-0.764-1.0210.002
4A3VAL00.0340.0236.5881.3371.3370.0000.0000.0000.000
5A4ALA00.0030.00110.2930.1410.1410.0000.0000.0000.000
6A5VAL0-0.0090.00013.0800.3140.3140.0000.0000.0000.000
7A6ILE0-0.019-0.00315.9580.0720.0720.0000.0000.0000.000
8A7THR00.0430.02719.3410.1090.1090.0000.0000.0000.000
9A8GLY00.007-0.01023.1760.0320.0320.0000.0000.0000.000
10A9ALA00.0120.00421.2230.0410.0410.0000.0000.0000.000
11A10SER00.0010.00822.9960.0310.0310.0000.0000.0000.000
12A11ARG10.9130.93625.6830.4620.4620.0000.0000.0000.000
13A12GLY0-0.0020.00425.811-0.039-0.0390.0000.0000.0000.000
14A13ILE00.0650.02522.7040.0060.0060.0000.0000.0000.000
15A14GLY00.0680.04121.418-0.053-0.0530.0000.0000.0000.000
16A15GLU-1-0.807-0.89320.279-0.427-0.4270.0000.0000.0000.000
17A16ALA0-0.017-0.01120.154-0.003-0.0030.0000.0000.0000.000
18A17ILE00.0370.00416.4860.0090.0090.0000.0000.0000.000
19A18ALA00.0120.01215.866-0.125-0.1250.0000.0000.0000.000
20A19ARG10.7550.82315.2720.2310.2310.0000.0000.0000.000
21A20ALA0-0.057-0.02615.6050.1050.1050.0000.0000.0000.000
22A21LEU00.009-0.00211.5420.0480.0480.0000.0000.0000.000
23A22ALA00.0130.01110.461-0.216-0.2160.0000.0000.0000.000
24A23ARG10.8710.92810.6170.3390.3390.0000.0000.0000.000
25A24ASP-1-0.870-0.9187.971-0.348-0.3480.0000.0000.0000.000
26A25GLY0-0.020-0.0076.056-0.483-0.4830.0000.0000.0000.000
27A26TYR0-0.081-0.0386.409-1.491-1.4910.0000.0000.0000.000
28A27ALA00.0220.0238.4610.8270.8270.0000.0000.0000.000
29A28LEU0-0.030-0.02310.078-0.174-0.1740.0000.0000.0000.000
30A29ALA00.0430.01513.8160.1610.1610.0000.0000.0000.000
31A30LEU0-0.021-0.01016.9220.0380.0380.0000.0000.0000.000
32A31GLY00.0900.02819.9730.0650.0650.0000.0000.0000.000
33A32ALA0-0.046-0.04223.5060.0190.0190.0000.0000.0000.000
34A33ARG10.9620.99326.9610.4520.4520.0000.0000.0000.000
35A34SER0-0.049-0.01329.4200.0210.0210.0000.0000.0000.000
36A35VAL00.1050.03626.396-0.017-0.0170.0000.0000.0000.000
37A36ASP-1-0.815-0.91026.582-0.338-0.3380.0000.0000.0000.000
38A37ARG10.7420.87225.8410.3510.3510.0000.0000.0000.000
39A38LEU0-0.014-0.00322.7780.0070.0070.0000.0000.0000.000
40A39GLU-1-0.843-0.89722.187-0.311-0.3110.0000.0000.0000.000
41A40LYS10.9110.95122.8630.1780.1780.0000.0000.0000.000
42A41ILE0-0.040-0.01519.5570.0440.0440.0000.0000.0000.000
43A42ALA00.0070.00418.4440.0030.0030.0000.0000.0000.000
44A43HIS0-0.003-0.02318.1730.0290.0290.0000.0000.0000.000
45A44GLU-1-0.826-0.87019.525-0.073-0.0730.0000.0000.0000.000
46A45LEU0-0.011-0.01815.2880.0700.0700.0000.0000.0000.000
47A46MET0-0.024-0.00914.6050.0080.0080.0000.0000.0000.000
48A47GLN0-0.067-0.02115.1330.1360.1360.0000.0000.0000.000
49A48GLU-1-0.927-0.97316.3300.4600.4600.0000.0000.0000.000
50A49GLN0-0.104-0.05912.5420.0630.0630.0000.0000.0000.000
51A50GLY00.0240.03511.3630.1140.1140.0000.0000.0000.000
52A51VAL0-0.039-0.0048.9650.0200.0200.0000.0000.0000.000
53A52GLU-1-0.809-0.8979.698-1.706-1.7060.0000.0000.0000.000
54A53VAL0-0.028-0.01211.896-0.335-0.3350.0000.0000.0000.000
55A54PHE00.0010.00715.0650.1090.1090.0000.0000.0000.000
56A55TYR00.008-0.00117.717-0.058-0.0580.0000.0000.0000.000
57A56HIS0-0.008-0.00621.1110.0570.0570.0000.0000.0000.000
58A57HIS0-0.018-0.00824.217-0.003-0.0030.0000.0000.0000.000
59A58LEU0-0.0070.00024.315-0.040-0.0400.0000.0000.0000.000
60A59ASP-1-0.819-0.89127.910-0.459-0.4590.0000.0000.0000.000
61A60VAL00.0150.00527.408-0.003-0.0030.0000.0000.0000.000
62A61SER0-0.033-0.03430.299-0.001-0.0010.0000.0000.0000.000
63A62LYS10.8770.94232.8020.4610.4610.0000.0000.0000.000
64A63ALA00.0110.00631.595-0.041-0.0410.0000.0000.0000.000
65A64GLU-1-0.768-0.90530.337-0.577-0.5770.0000.0000.0000.000
66A65SER0-0.031-0.01329.139-0.016-0.0160.0000.0000.0000.000
67A66VAL0-0.012-0.01025.694-0.041-0.0410.0000.0000.0000.000
68A67GLU-1-0.904-0.94125.524-0.816-0.8160.0000.0000.0000.000
69A68GLU-1-0.809-0.89225.895-0.777-0.7770.0000.0000.0000.000
70A69PHE0-0.026-0.01421.023-0.054-0.0540.0000.0000.0000.000
71A70SER00.009-0.01321.281-0.078-0.0780.0000.0000.0000.000
72A71LYS10.8490.92120.6350.6460.6460.0000.0000.0000.000
73A72LYS10.8310.90821.1900.7320.7320.0000.0000.0000.000
74A73VAL0-0.019-0.01016.688-0.051-0.0510.0000.0000.0000.000
75A74LEU0-0.015-0.01116.307-0.187-0.1870.0000.0000.0000.000
76A75GLU-1-0.904-0.93716.694-1.019-1.0190.0000.0000.0000.000
77A76ARG10.7590.87313.0991.4921.4920.0000.0000.0000.000
78A77PHE0-0.024-0.03111.5390.0140.0140.0000.0000.0000.000
79A78GLY00.0250.03811.651-0.476-0.4760.0000.0000.0000.000
80A79ASP-1-0.791-0.84412.295-2.369-2.3690.0000.0000.0000.000
81A80VAL00.001-0.00411.417-0.486-0.4860.0000.0000.0000.000
82A81ASP-1-0.837-0.9038.275-7.353-7.3530.0000.0000.0000.000
83A82VAL0-0.016-0.00511.0360.4000.4000.0000.0000.0000.000
84A83VAL0-0.0020.00713.5920.0770.0770.0000.0000.0000.000
85A84VAL00.0120.00816.7230.1120.1120.0000.0000.0000.000
86A85ALA00.0140.00319.4000.0830.0830.0000.0000.0000.000
87A86ASN0-0.008-0.01422.6780.0920.0920.0000.0000.0000.000
88A87ALA0-0.062-0.01624.3680.0760.0760.0000.0000.0000.000
89A88GLY00.0450.00827.368-0.008-0.0080.0000.0000.0000.000
90A89LEU0-0.090-0.03030.5630.0180.0180.0000.0000.0000.000
91A90GLY00.037-0.01033.976-0.013-0.0130.0000.0000.0000.000
92A91TYR0-0.088-0.06137.0630.0190.0190.0000.0000.0000.000
93A92PHE0-0.048-0.02337.120-0.006-0.0060.0000.0000.0000.000
94A93LYS10.8970.93142.8250.2450.2450.0000.0000.0000.000
95A94ARG10.8390.89346.2650.1780.1780.0000.0000.0000.000
96A95LEU00.005-0.01245.309-0.004-0.0040.0000.0000.0000.000
97A96GLU-1-0.778-0.86448.766-0.201-0.2010.0000.0000.0000.000
98A97GLU-1-0.952-0.97050.045-0.178-0.1780.0000.0000.0000.000
99A98LEU0-0.124-0.04943.314-0.004-0.0040.0000.0000.0000.000
100A99SER00.023-0.00846.292-0.003-0.0030.0000.0000.0000.000
101A100GLU-1-0.813-0.90945.773-0.296-0.2960.0000.0000.0000.000
102A101GLU-1-0.913-0.95944.365-0.278-0.2780.0000.0000.0000.000
103A102GLU-1-0.772-0.84741.930-0.272-0.2720.0000.0000.0000.000
104A103PHE00.008-0.00140.744-0.023-0.0230.0000.0000.0000.000
105A104HIS10.8690.91640.3960.3090.3090.0000.0000.0000.000
106A105GLU-1-0.801-0.88936.662-0.400-0.4000.0000.0000.0000.000
107A106MET0-0.0400.01736.294-0.029-0.0290.0000.0000.0000.000
108A107ILE00.0110.00435.556-0.033-0.0330.0000.0000.0000.000
109A108GLU-1-0.809-0.89635.185-0.520-0.5200.0000.0000.0000.000
110A109VAL0-0.054-0.02131.095-0.040-0.0400.0000.0000.0000.000
111A110ASN0-0.052-0.04431.008-0.062-0.0620.0000.0000.0000.000
112A111LEU0-0.0030.01131.225-0.027-0.0270.0000.0000.0000.000
113A112LEU00.0090.00531.249-0.049-0.0490.0000.0000.0000.000
114A113GLY00.0440.02930.209-0.037-0.0370.0000.0000.0000.000
115A114VAL0-0.0040.01226.168-0.075-0.0750.0000.0000.0000.000
116A115TRP00.0270.00726.582-0.072-0.0720.0000.0000.0000.000
117A116ARG10.7820.87027.6770.5330.5330.0000.0000.0000.000
118A117THR0-0.025-0.03622.549-0.056-0.0560.0000.0000.0000.000
119A118LEU0-0.016-0.01222.043-0.104-0.1040.0000.0000.0000.000
120A119LYS10.9010.95823.0220.7040.7040.0000.0000.0000.000
121A120ALA0-0.037-0.00624.201-0.025-0.0250.0000.0000.0000.000
122A121PHE00.0320.00718.253-0.048-0.0480.0000.0000.0000.000
123A122LEU0-0.0120.01919.170-0.190-0.1900.0000.0000.0000.000
124A123ASP-1-0.862-0.94819.825-1.406-1.4060.0000.0000.0000.000
125A124SER0-0.097-0.06415.578-0.190-0.1900.0000.0000.0000.000
126A125LEU0-0.004-0.00415.019-0.262-0.2620.0000.0000.0000.000
127A126LYS10.8310.88815.8291.1491.1490.0000.0000.0000.000
128A127ARG10.8160.89114.8822.0592.0590.0000.0000.0000.000
129A128THR0-0.015-0.02211.018-0.120-0.1200.0000.0000.0000.000
130A129GLY0-0.0020.00611.584-0.439-0.4390.0000.0000.0000.000
131A130GLY00.012-0.00112.657-0.133-0.1330.0000.0000.0000.000
132A131LEU0-0.063-0.03313.6940.3390.3390.0000.0000.0000.000
133A132ALA00.0250.00815.423-0.061-0.0610.0000.0000.0000.000
134A133LEU0-0.0120.00018.3200.1520.1520.0000.0000.0000.000
135A134VAL00.000-0.00620.0970.0110.0110.0000.0000.0000.000
136A135THR0-0.023-0.01023.6790.0210.0210.0000.0000.0000.000
137A136THR0-0.017-0.03625.5650.0440.0440.0000.0000.0000.000
138A137SER00.026-0.00828.9530.0360.0360.0000.0000.0000.000
139A138ASP-1-0.762-0.87230.932-0.349-0.3490.0000.0000.0000.000
140A139VAL0-0.036-0.01532.5930.0060.0060.0000.0000.0000.000
141A140SER0-0.044-0.04930.9530.0180.0180.0000.0000.0000.000
142A141ALA0-0.006-0.01233.869-0.011-0.0110.0000.0000.0000.000
143A142ARG10.8230.92235.7850.3070.3070.0000.0000.0000.000
144A143LEU00.0180.01138.680-0.010-0.0100.0000.0000.0000.000
145A144ILE00.0130.00539.3070.0080.0080.0000.0000.0000.000
146A145PRO00.0170.01542.666-0.005-0.0050.0000.0000.0000.000
147A146TYR00.006-0.01244.109-0.003-0.0030.0000.0000.0000.000
148A147GLY00.0270.01241.088-0.006-0.0060.0000.0000.0000.000
149A148GLY00.0140.01340.808-0.018-0.0180.0000.0000.0000.000
150A149GLY00.0710.04141.748-0.013-0.0130.0000.0000.0000.000
151A150TYR00.0620.02232.322-0.021-0.0210.0000.0000.0000.000
152A151VAL0-0.0040.00036.789-0.027-0.0270.0000.0000.0000.000
153A152SER0-0.019-0.00537.303-0.024-0.0240.0000.0000.0000.000
154A153THR0-0.019-0.01935.520-0.024-0.0240.0000.0000.0000.000
155A154LYS10.8730.94329.6350.5250.5250.0000.0000.0000.000
156A155TRP0-0.046-0.02133.035-0.030-0.0300.0000.0000.0000.000
157A156ALA0-0.020-0.00234.642-0.020-0.0200.0000.0000.0000.000
158A157ALA00.0060.00529.981-0.029-0.0290.0000.0000.0000.000
159A158ARG10.7950.87829.9090.4830.4830.0000.0000.0000.000
160A159ALA0-0.012-0.00830.521-0.029-0.0290.0000.0000.0000.000
161A160LEU0-0.0050.01429.004-0.022-0.0220.0000.0000.0000.000
162A161VAL00.009-0.00224.699-0.043-0.0430.0000.0000.0000.000
163A162ARG10.9050.95126.4300.5550.5550.0000.0000.0000.000
164A163THR0-0.013-0.01028.6230.0020.0020.0000.0000.0000.000
165A164PHE00.0200.00224.978-0.011-0.0110.0000.0000.0000.000
166A165GLN0-0.001-0.00621.907-0.102-0.1020.0000.0000.0000.000
167A166ILE0-0.038-0.01225.221-0.021-0.0210.0000.0000.0000.000
168A167GLU-1-0.957-0.97827.764-0.756-0.7560.0000.0000.0000.000
169A168ASN0-0.052-0.01722.524-0.064-0.0640.0000.0000.0000.000
170A169PRO00.003-0.00322.360-0.083-0.0830.0000.0000.0000.000
171A170ASP-1-0.834-0.90019.168-1.438-1.4380.0000.0000.0000.000
172A171VAL0-0.033-0.00817.639-0.232-0.2320.0000.0000.0000.000
173A172ARG10.8390.92911.6692.7402.7400.0000.0000.0000.000
174A173PHE00.012-0.00618.342-0.102-0.1020.0000.0000.0000.000
175A174PHE00.0400.01518.2100.0770.0770.0000.0000.0000.000
176A175GLU-1-0.729-0.82821.616-0.604-0.6040.0000.0000.0000.000
177A176LEU0-0.0130.00021.6690.0530.0530.0000.0000.0000.000
178A177ARG10.8030.87924.4700.5040.5040.0000.0000.0000.000
179A178PRO00.0190.00226.1160.0420.0420.0000.0000.0000.000
180A179GLY00.0140.02028.7270.0080.0080.0000.0000.0000.000
181A180ALA0-0.016-0.00131.544-0.018-0.0180.0000.0000.0000.000
182A181VAL00.0510.01527.6740.0090.0090.0000.0000.0000.000
183A182ASP-1-0.801-0.87131.064-0.197-0.1970.0000.0000.0000.000
184A183THR0-0.021-0.00628.585-0.014-0.0140.0000.0000.0000.000
185A184TYR00.026-0.02130.4990.0250.0250.0000.0000.0000.000
186A185PHE00.0110.01932.1520.0010.0010.0000.0000.0000.000
187A186GLY00.0310.01333.9990.0230.0230.0000.0000.0000.000
188A187GLY00.0040.01736.9740.0160.0160.0000.0000.0000.000
189A188SER0-0.0220.00536.1290.0240.0240.0000.0000.0000.000
190A189LYS10.9510.95635.1210.1680.1680.0000.0000.0000.000
191A190PRO0-0.025-0.01731.2190.0040.0040.0000.0000.0000.000
192A191GLY00.0200.00833.4100.0160.0160.0000.0000.0000.000
193A192LYS10.7800.91234.5640.2420.2420.0000.0000.0000.000
194A193PRO00.0110.00634.808-0.007-0.0070.0000.0000.0000.000
195A194LYS10.9140.94228.8840.1220.1220.0000.0000.0000.000
196A195GLU-1-0.803-0.91835.047-0.104-0.1040.0000.0000.0000.000
197A196LYS10.8510.92738.2460.1250.1250.0000.0000.0000.000
198A197GLY00.0400.02937.454-0.008-0.0080.0000.0000.0000.000
199A198TYR0-0.063-0.03533.243-0.025-0.0250.0000.0000.0000.000
200A199LEU00.0300.02227.6500.0220.0220.0000.0000.0000.000
201A200LYS10.8080.88427.6530.1640.1640.0000.0000.0000.000
202A201PRO00.005-0.02224.906-0.023-0.0230.0000.0000.0000.000
203A202ASP-1-0.854-0.92921.892-0.278-0.2780.0000.0000.0000.000
204A203GLU-1-0.778-0.87621.501-0.217-0.2170.0000.0000.0000.000
205A204ILE0-0.010-0.00622.438-0.025-0.0250.0000.0000.0000.000
206A205ALA00.0090.00718.758-0.070-0.0700.0000.0000.0000.000
207A206GLU-1-0.735-0.82517.013-0.405-0.4050.0000.0000.0000.000
208A207ALA00.0020.00317.689-0.038-0.0380.0000.0000.0000.000
209A208VAL0-0.003-0.01416.200-0.060-0.0600.0000.0000.0000.000
210A209ARG10.7940.85811.8010.3140.3140.0000.0000.0000.000
211A210CYS0-0.093-0.04413.203-0.135-0.1350.0000.0000.0000.000
212A211LEU00.0210.00514.687-0.026-0.0260.0000.0000.0000.000
213A212LEU0-0.023-0.01911.883-0.108-0.1080.0000.0000.0000.000
214A213LYS10.8970.9596.4840.8520.8520.0000.0000.0000.000
215A214LEU0-0.055-0.00510.8730.1450.1450.0000.0000.0000.000
216A215PRO00.002-0.00311.075-0.403-0.4030.0000.0000.0000.000
217A216LYS10.8820.9439.2434.2164.2160.0000.0000.0000.000
218A217ASP-1-0.881-0.94511.673-1.483-1.4830.0000.0000.0000.000
219A218VAL0-0.028-0.00114.7710.2310.2310.0000.0000.0000.000
220A219ARG10.8620.91015.8720.8340.8340.0000.0000.0000.000
221A220VAL0-0.017-0.00218.2110.1410.1410.0000.0000.0000.000
222A221GLU-1-0.785-0.87720.376-0.891-0.8910.0000.0000.0000.000
223A222GLU-1-0.827-0.88723.232-0.533-0.5330.0000.0000.0000.000
224A223LEU00.0050.01321.8010.0220.0220.0000.0000.0000.000
225A224MET0-0.056-0.00925.0870.0030.0030.0000.0000.0000.000
226A225LEU00.0160.01224.5070.0310.0310.0000.0000.0000.000
227A226ARG10.8440.87528.5610.2850.2850.0000.0000.0000.000
228A227SER00.0190.01431.2590.0180.0180.0000.0000.0000.000
229A228VAL00.0320.01232.939-0.003-0.0030.0000.0000.0000.000
230A229TYR0-0.023-0.00235.2170.0110.0110.0000.0000.0000.000
231A230GLN0-0.022-0.00634.588-0.008-0.0080.0000.0000.0000.000
232A231ARG10.9040.94637.5160.1780.1780.0000.0000.0000.000
233A232PRO0-0.012-0.00337.835-0.017-0.0170.0000.0000.0000.000
234A233GLU-1-0.858-0.91038.855-0.212-0.2120.0000.0000.0000.000
235A234TYR-1-0.836-0.92035.387-0.300-0.3000.0000.0000.0000.000