# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 16:43:53 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (1R)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@@H](O)c1cccc(OCC2CCCCC2)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 A3V  A3V  (1R)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol  ligand  44  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3V
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 A3V  O    O  OH1   0  -0.663   4.8248   1.0456   0.8558
 A3V  C2   C  CH1   0  -0.017   3.7132   0.2014   0.6678
 A3V  C1   C  CH2   0  -0.477   4.0254  -0.9590  -0.2770
 A3V  C    C  CH2   0  -0.272   5.1793  -1.8311   0.1975
 A3V  N    N  NH2   0  -0.800   5.3884  -2.9360  -0.7265
 A3V  C3   C  CR6   0   0.128   2.4795   0.9482   0.1989
 A3V  C15  C  CR16  0  -0.410   1.2331   0.3851   0.4313
 A3V  C7   C  CR6   0   0.411   0.0656   1.0061  -0.0117
 A3V  C6   C  CR16  0  -0.398   0.1496   2.2176  -0.6957
 A3V  C5   C  CR16  0  -0.224   1.4009   2.7776  -0.9231
 A3V  C4   C  CR16  0  -0.354   2.5616   2.1598  -0.4839
 A3V  O1   O  O2    0  -0.479  -1.0861   0.3684   0.2694
 A3V  C8   C  CH2   0  -0.156  -2.3167   0.9576  -0.1167
 A3V  C9   C  CH1   0  -0.277  -3.4497   0.0393   0.3012
 A3V  C14  C  CH2   0  -0.422  -4.7903   0.7268   0.0368
 A3V  C13  C  CH2   0  -0.430  -5.9667  -0.1633   0.4246
 A3V  C12  C  CH2   0  -0.430  -5.9030  -1.5124  -0.2834
 A3V  C11  C  CH2   0  -0.432  -4.5690  -2.2050  -0.0279
 A3V  C10  C  CH2   0  -0.413  -3.3913  -1.3136  -0.4096
 A3V  H1   H  HOH1  0   0.449   5.2354   1.2164   0.0019
 A3V  H2   H  HCH1  0   0.239   3.4917  -0.2150   1.6569
 A3V  H3   H  HCH2  0   0.238   3.1265  -1.5753  -0.3740
 A3V  H4   H  HCH2  0   0.231   4.2404  -0.5702  -1.2793
 A3V  H5   H  HCH2  0   0.217   6.0975  -1.2416   0.2352
 A3V  H6   H  HCH2  0   0.192   4.9770  -2.1538   1.2296
 A3V  H7   H  HNH2  0   0.347   6.1769  -3.4887  -0.4155
 A3V  H8   H  HNH2  0   0.338   4.5896  -3.5572  -0.6881
 A3V  H10  H  HCR6  0   0.250   1.1539  -0.5520   0.9730
 A3V  H11  H  HCR6  0   0.276  -0.7333   2.7326  -1.0490
 A3V  H12  H  HCR6  0   0.256   1.4636   3.7195  -1.4536
 A3V  H13  H  HCR6  0   0.236   3.5175   2.6314  -0.6708
 A3V  H14  H  HCH2  0   0.228  -2.4292   1.9399   0.3591
 A3V  H15  H  HCH2  0   0.214  -2.3438   1.1125  -1.2032
 A3V  H16  H  HCH1  0   0.223  -3.3673  -0.1297   1.3831
 A3V  H17  H  HCH2  0   0.229  -4.8394   1.6712   0.5860
 A3V  H18  H  HCH2  0   0.210  -4.8651   0.9797  -1.0276
 A3V  H19  H  HCH2  0   0.210  -5.9583  -0.3211   1.5084
 A3V  H20  H  HCH2  0   0.227  -6.9073   0.3416   0.1921
 A3V  H21  H  HCH2  0   0.226  -6.7289  -2.1495   0.0427
 A3V  H22  H  HCH2  0   0.208  -6.0332  -1.3617  -1.3608
 A3V  H23  H  HCH2  0   0.209  -4.4944  -2.4683   1.0330
 A3V  H24  H  HCH2  0   0.226  -4.5177  -3.1446  -0.5833
 A3V  H25  H  HCH2  0   0.205  -3.4009  -1.1425  -1.4930
 A3V  H26  H  HCH2  0   0.232  -2.4524  -1.8225  -0.1821

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 A3V  C11  C10  single    1.526  0.020  1.526
 A3V  C11  C12  single    1.525  0.020  1.525
 A3V  C10  C9   single    1.529  0.020  1.529
 A3V  C12  C13  single    1.525  0.020  1.525
 A3V  N    C    single    1.455  0.020  1.455
 A3V  C9   C8   single    1.517  0.020  1.517
 A3V  C9   C14  single    1.530  0.020  1.530
 A3V  C    C1   single    1.522  0.020  1.522
 A3V  C13  C14  single    1.525  0.020  1.525
 A3V  C8   O1   single    1.418  0.020  1.418
 A3V  C1   C2   single    1.529  0.020  1.529
 A3V  O    C2   single    1.408  0.020  1.408
 A3V  O1   C7   single    1.346  0.020  1.346
 A3V  C15  C7   aromatic  1.395  0.020  1.395
 A3V  C15  C3   aromatic  1.387  0.020  1.387
 A3V  C2   C3   single    1.516  0.020  1.516
 A3V  C7   C6   aromatic  1.394  0.020  1.394
 A3V  C3   C4   aromatic  1.393  0.020  1.393
 A3V  C6   C5   aromatic  1.390  0.020  1.390
 A3V  C4   C5   aromatic  1.386  0.020  1.386
 A3V  O    H1   single    0.850  0.020  0.980
 A3V  C2   H2   single    0.970  0.020  1.090
 A3V  C1   H3   single    0.970  0.020  1.090
 A3V  C1   H4   single    0.970  0.020  1.090
 A3V  C    H5   single    0.970  0.020  1.090
 A3V  C    H6   single    0.970  0.020  1.090
 A3V  N    H7   single    0.890  0.020  1.040
 A3V  N    H8   single    0.890  0.020  1.040
 A3V  C15  H10  single    0.930  0.020  1.080
 A3V  C6   H11  single    0.930  0.020  1.080
 A3V  C5   H12  single    0.930  0.020  1.080
 A3V  C4   H13  single    0.930  0.020  1.080
 A3V  C8   H14  single    0.970  0.020  1.090
 A3V  C8   H15  single    0.970  0.020  1.090
 A3V  C9   H16  single    0.970  0.020  1.090
 A3V  C14  H17  single    0.970  0.020  1.090
 A3V  C14  H18  single    0.970  0.020  1.090
 A3V  C13  H19  single    0.970  0.020  1.090
 A3V  C13  H20  single    0.970  0.020  1.090
 A3V  C12  H21  single    0.970  0.020  1.090
 A3V  C12  H22  single    0.970  0.020  1.090
 A3V  C11  H23  single    0.970  0.020  1.090
 A3V  C11  H24  single    0.970  0.020  1.090
 A3V  C10  H25  single    0.970  0.020  1.090
 A3V  C10  H26  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 A3V  H1   O    C2   108.94  3.000
 A3V  H2   C2   C3   107.57  3.000
 A3V  H2   C2   C1   108.10  3.000
 A3V  C3   C2   C1   110.42  3.000
 A3V  H2   C2   O    105.48  3.000
 A3V  C3   C2   O    112.84  3.000
 A3V  C1   C2   O    112.10  3.000
 A3V  H4   C1   H3   106.25  3.000
 A3V  H4   C1   C    109.84  3.000
 A3V  H3   C1   C    109.13  3.000
 A3V  H4   C1   C2   109.63  3.000
 A3V  H3   C1   C2   108.33  3.000
 A3V  C    C1   C2   113.40  3.000
 A3V  H6   C    H5   106.29  3.000
 A3V  H6   C    N    113.54  3.000
 A3V  H5   C    N    108.12  3.000
 A3V  H6   C    C1   108.73  3.000
 A3V  H5   C    C1   109.81  3.000
 A3V  N    C    C1   110.24  3.000
 A3V  H8   N    H7   105.54  3.000
 A3V  H8   N    C    109.17  3.000
 A3V  H7   N    C    109.36  3.000
 A3V  C4   C3   C15  119.21  3.000
 A3V  C4   C3   C2   122.13  3.000
 A3V  C15  C3   C2   118.63  3.000
 A3V  H10  C15  C7   118.81  3.000
 A3V  H10  C15  C3   119.98  3.000
 A3V  C7   C15  C3   121.21  3.000
 A3V  O1   C7   C6   124.46  3.000
 A3V  C6   C7   C15  119.50  3.000
 A3V  O1   C7   C15  116.04  3.000
 A3V  H11  C6   C5   119.33  3.000
 A3V  H11  C6   C7   121.66  3.000
 A3V  C5   C6   C7   119.00  3.000
 A3V  H12  C5   C4   119.62  3.000
 A3V  H12  C5   C6   118.87  3.000
 A3V  C4   C5   C6   121.50  3.000
 A3V  H13  C4   C5   119.39  3.000
 A3V  H13  C4   C3   121.04  3.000
 A3V  C5   C4   C3   119.57  3.000
 A3V  C8   O1   C7   119.27  3.000
 A3V  H15  C8   H14  107.47  3.000
 A3V  H15  C8   C9   109.85  3.000
 A3V  H14  C8   C9   110.23  3.000
 A3V  H15  C8   O1   110.46  3.000
 A3V  H14  C8   O1   110.05  3.000
 A3V  C9   C8   O1   108.77  3.000
 A3V  H16  C9   C10  108.60  3.000
 A3V  H16  C9   C14  107.78  3.000
 A3V  C10  C9   C14  110.53  3.000
 A3V  H16  C9   C8   107.96  3.000
 A3V  C14  C9   C8   109.56  3.000
 A3V  C10  C9   C8   112.26  3.000
 A3V  H18  C14  H17  106.57  3.000
 A3V  H18  C14  C13  109.19  3.000
 A3V  H17  C14  C13  109.97  3.000
 A3V  H18  C14  C9   109.34  3.000
 A3V  H17  C14  C9   109.92  3.000
 A3V  C13  C14  C9   111.70  3.000
 A3V  H20  C13  H19  106.48  3.000
 A3V  H20  C13  C12  110.24  3.000
 A3V  H19  C13  C12  109.36  3.000
 A3V  H20  C13  C14  109.90  3.000
 A3V  H19  C13  C14  109.26  3.000
 A3V  C12  C13  C14  111.47  3.000
 A3V  H22  C12  H21  106.48  3.000
 A3V  H22  C12  C11  109.34  3.000
 A3V  H21  C12  C11  110.27  3.000
 A3V  H22  C12  C13  109.26  3.000
 A3V  H21  C12  C13  110.22  3.000
 A3V  C11  C12  C13  111.14  3.000
 A3V  H24  C11  H23  106.40  3.000
 A3V  H24  C11  C10  109.82  3.000
 A3V  H23  C11  C10  109.28  3.000
 A3V  H24  C11  C12  110.27  3.000
 A3V  H23  C11  C12  109.33  3.000
 A3V  C10  C11  C12  111.60  3.000
 A3V  H26  C10  H25  106.62  3.000
 A3V  H26  C10  C11  109.84  3.000
 A3V  H25  C10  C11  109.36  3.000
 A3V  H26  C10  C9   110.39  3.000
 A3V  H25  C10  C9   108.70  3.000
 A3V  C11  C10  C9   111.78  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 A3V  CONST_01  C6   C7   C15  C3     0.00   0.0  0
 A3V  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 A3V  CONST_03  C5   C6   C7   C15    0.00   0.0  0
 A3V  CONST_04  C5   C4   C3   C15    0.00   0.0  0
 A3V  CONST_05  C4   C3   C15  C7     0.00   0.0  0
 A3V  CONST_06  C4   C5   C6   C7     0.00   0.0  0
 A3V  CONST_07  C7   C15  C3   C2   180.00   0.0  0
 A3V  CONST_08  C5   C4   C3   C2   180.00   0.0  0
 A3V  CONST_09  O1   C7   C15  C3   180.00   0.0  0
 A3V  CONST_10  O1   C7   C6   C5   180.00   0.0  0
 A3V  CONST_11  H12  C5   C4   C3   180.00   0.0  0
 A3V  CONST_12  H11  C6   C7   C15  180.00   0.0  0
 A3V  CONST_13  H13  C4   C3   C15  180.00   0.0  0
 A3V  CONST_14  H10  C15  C7   C6   180.00   0.0  0
 A3V  Var_01    C12  C11  C10  C9    55.10  30.0  1
 A3V  Var_02    C12  C13  C14  C9   -55.54  30.0  1
 A3V  Var_03    C11  C12  C13  C14   54.90  30.0  1
 A3V  Var_04    C10  C11  C12  C13  -54.69  30.0  1
 A3V  Var_05    C9   C8   O1   C7   179.44  30.0  2
 A3V  Var_06    N    C    C1   C2   178.13  30.0  2
 A3V  Var_07    H7   N    C    C1   178.13  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A3V  chir_01  C2  C1   O   C3   negativ
 A3V  chir_02  C9  C10  C8  C14  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 A3V  plan-1  C2   0.020
 A3V  plan-1  C3   0.020
 A3V  plan-1  C15  0.020
 A3V  plan-1  C7   0.020
 A3V  plan-1  C6   0.020
 A3V  plan-1  C5   0.020
 A3V  plan-1  C4   0.020
 A3V  plan-1  O1   0.020
 A3V  plan-1  H10  0.020
 A3V  plan-1  H11  0.020
 A3V  plan-1  H12  0.020
 A3V  plan-1  H13  0.020

