# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:24:26 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@@H]1CCCO1)NC2CCCC2
#
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
 REG  REG  1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea  ligand  35  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_REG
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
 REG  C4   C  CH2   0  -0.435  31.1032  14.8903  48.1330
 REG  C5   C  C     0   0.734  31.7935  14.2449  45.0787
 REG  C6   C  CH2   0  -0.313  33.3875  13.3512  43.4223
 REG  N1   N  NH1   0  -0.676  32.7731  14.4282  44.1523
 REG  C7   C  CR15  0   0.066  34.7933  13.0193  43.9013
 REG  C8   C  CH2   0  -0.495  34.9127  12.6127  45.3672
 REG  C9   C  CH2   0  -0.495  36.3058  13.1137  45.7280
 REG  C10  C  CH2   0  -0.153  36.3725  14.4045  44.9274
 REG  O    O  O     0  -0.552  31.2812  13.1508  45.3000
 REG  N    N  NH1   0  -0.678  31.3943  15.3769  45.7145
 REG  C3   C  CH1   0  -0.099  30.4588  15.3517  46.8229
 REG  C2   C  CH2   0  -0.466  30.0415  16.7811  47.1654
 REG  C1   C  CH2   0  -0.464  31.2072  17.3406  47.9989
 REG  C    C  CH2   0  -0.450  31.9155  16.1051  48.6042
 REG  O1   O  O     0  -0.513  35.6287  14.1647  43.7421
 REG  H1   H  HCH2  0   0.225  30.3090  14.6623  48.8491
 REG  H2   H  HCH2  0   0.237  31.7037  13.9874  48.0180
 REG  H3   H  HCH2  0   0.246  33.4247  13.6112  42.3611
 REG  H4   H  HCH2  0   0.247  32.7618  12.4639  43.5042
 REG  H5   H  HNH1  0   0.386  33.1795  15.3425  44.0413
 REG  H6   H  HCR5  0   0.214  35.1752  12.2100  43.2633
 REG  H7   H  HCH2  0   0.236  34.1605  13.1178  45.9781
 REG  H8   H  HCH2  0   0.250  34.7847  11.5390  45.5017
 REG  H9   H  HCH2  0   0.235  37.0691  12.4085  45.3915
 REG  H10  H  HCH2  0   0.247  36.4468  13.2764  46.7964
 REG  H11  H  HCH2  0   0.222  37.3920  14.6929  44.6614
 REG  H12  H  HCH2  0   0.198  35.9278  15.2326  45.4932
 REG  H13  H  HNH1  0   0.388  31.9186  16.2249  45.5671
 REG  H14  H  HCH1  0   0.246  29.6035  14.7344  46.5448
 REG  H15  H  HCH2  0   0.242  29.8104  17.3797  46.2824
 REG  H16  H  HCH2  0   0.243  29.1330  16.7360  47.7693
 REG  H17  H  HCH2  0   0.231  31.8955  17.9107  47.3721
 REG  H18  H  HCH2  0   0.237  30.8506  18.0279  48.7663
 REG  H19  H  HCH2  0   0.227  32.9429  16.0392  48.2427
 REG  H20  H  HCH2  0   0.233  31.9732  16.1540  49.6918

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
 REG  O1   C7   single  1.427  0.020  1.427
 REG  O1   C10  single  1.420  0.020  1.420
 REG  C6   C7   single  1.522  0.020  1.522
 REG  C6   N1   single  1.439  0.020  1.439
 REG  C7   C8   single  1.526  0.020  1.526
 REG  C10  C9   single  1.520  0.020  1.520
 REG  N1   C5   single  1.361  0.020  1.361
 REG  C9   C8   single  1.524  0.020  1.524
 REG  C5   O    double  1.228  0.020  1.228
 REG  C5   N    single  1.358  0.020  1.358
 REG  N    C3   single  1.451  0.020  1.451
 REG  C3   C2   single  1.528  0.020  1.528
 REG  C3   C4   single  1.531  0.020  1.531
 REG  C2   C1   single  1.538  0.020  1.538
 REG  C1   C    single  1.547  0.020  1.547
 REG  C4   C    single  1.535  0.020  1.535
 REG  C4   H1   single  0.970  0.020  1.090
 REG  C4   H2   single  0.970  0.020  1.090
 REG  C6   H3   single  0.970  0.020  1.090
 REG  C6   H4   single  0.970  0.020  1.090
 REG  N1   H5   single  0.860  0.020  1.020
 REG  C7   H6   single  0.970  0.020  1.090
 REG  C8   H7   single  0.970  0.020  1.090
 REG  C8   H8   single  0.970  0.020  1.090
 REG  C9   H9   single  0.970  0.020  1.090
 REG  C9   H10  single  0.970  0.020  1.090
 REG  C10  H11  single  0.970  0.020  1.090
 REG  C10  H12  single  0.970  0.020  1.090
 REG  N    H13  single  0.860  0.020  1.020
 REG  C3   H14  single  0.970  0.020  1.090
 REG  C2   H15  single  0.970  0.020  1.090
 REG  C2   H16  single  0.970  0.020  1.090
 REG  C1   H17  single  0.970  0.020  1.090
 REG  C1   H18  single  0.970  0.020  1.090
 REG  C    H19  single  0.970  0.020  1.090
 REG  C    H20  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
 REG  H2   C4   H1   107.24  3.000
 REG  H2   C4   C    113.34  3.000
 REG  H1   C4   C    110.38  3.000
 REG  H2   C4   C3   113.02  3.000
 REG  H1   C4   C3   108.51  3.000
 REG  C    C4   C3   104.29  3.000
 REG  N    C5   O    122.38  3.000
 REG  N    C5   N1   114.71  3.000
 REG  O    C5   N1   122.89  3.000
 REG  H4   C6   H3   106.64  3.000
 REG  H4   C6   C7   109.24  3.000
 REG  H3   C6   C7   109.03  3.000
 REG  H4   C6   N1   109.05  3.000
 REG  H3   C6   N1   109.21  3.000
 REG  C7   C6   N1   113.45  3.000
 REG  H5   N1   C6   116.84  3.000
 REG  H5   N1   C5   119.21  3.000
 REG  C6   N1   C5   123.50  3.000
 REG  H6   C7   O1   108.84  3.000
 REG  H6   C7   C8   109.53  3.000
 REG  O1   C7   C8   105.98  3.000
 REG  H6   C7   C6   107.39  3.000
 REG  C8   C7   C6   115.64  3.000
 REG  O1   C7   C6   109.31  3.000
 REG  H8   C8   H7   107.80  3.000
 REG  H8   C8   C9   113.71  3.000
 REG  H7   C8   C9   110.18  3.000
 REG  H8   C8   C7   111.84  3.000
 REG  H7   C8   C7   111.11  3.000
 REG  C9   C8   C7   102.21  3.000
 REG  H10  C9   H9   107.94  3.000
 REG  H10  C9   C10  112.57  3.000
 REG  H9   C9   C10  110.81  3.000
 REG  H10  C9   C8   113.55  3.000
 REG  H9   C9   C8   110.71  3.000
 REG  C10  C9   C8   101.22  3.000
 REG  H12  C10  H11  107.73  3.000
 REG  H12  C10  O1   110.22  3.000
 REG  H11  C10  O1   109.29  3.000
 REG  H12  C10  C9   110.57  3.000
 REG  H11  C10  C9   113.16  3.000
 REG  O1   C10  C9   105.86  3.000
 REG  H13  N    C3   117.51  3.000
 REG  H13  N    C5   118.67  3.000
 REG  C3   N    C5   122.19  3.000
 REG  H14  C3   C2   111.87  3.000
 REG  H14  C3   N    108.70  3.000
 REG  C2   C3   N    109.34  3.000
 REG  H14  C3   C4   112.18  3.000
 REG  C2   C3   C4   101.83  3.000
 REG  N    C3   C4   112.80  3.000
 REG  H16  C2   H15  107.09  3.000
 REG  H16  C2   C1   110.23  3.000
 REG  H15  C2   C1   113.54  3.000
 REG  H16  C2   C3   108.22  3.000
 REG  H15  C2   C3   112.92  3.000
 REG  C1   C2   C3   104.76  3.000
 REG  H18  C1   H17  106.33  3.000
 REG  H18  C1   C    112.20  3.000
 REG  H17  C1   C    110.67  3.000
 REG  H18  C1   C2   111.27  3.000
 REG  H17  C1   C2   110.89  3.000
 REG  C    C1   C2   105.57  3.000
 REG  H20  C    H19  106.46  3.000
 REG  H20  C    C1   112.25  3.000
 REG  H19  C    C1   110.46  3.000
 REG  H20  C    C4   111.70  3.000
 REG  H19  C    C4   110.41  3.000
 REG  C1   C    C4   105.63  3.000
 REG  C10  O1   C7   110.44  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
 REG  CONST_01  C3   N    C5  O      0.00   0.0  0
 REG  CONST_02  C3   N    C5  N1   180.00   0.0  0
 REG  CONST_03  O    C5   N1  C6     0.00   0.0  0
 REG  CONST_04  N    C5   N1  C6   180.00   0.0  0
 REG  CONST_05  H5   N1   C5  O    180.00   0.0  0
 REG  CONST_06  H13  N    C5  O    180.00   0.0  0
 REG  Var_01    C2   C1   C   C4    -1.79  30.0  1
 REG  Var_02    C9   C10  O1  C7    17.10  30.0  1
 REG  Var_03    O1   C10  C9  C8   -33.66  30.0  1
 REG  Var_04    C    C1   C2  C3   -23.75  30.0  1
 REG  Var_05    C1   C    C4  C3    26.60  30.0  1
 REG  Var_06    C7   C6   N1  C5  -105.29  30.0  1

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
 REG  chir_01  C7  O1  C6  C8  positiv
 REG  chir_02  C3  N   C2  C4  positiv

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
 REG  plan-1  C5   0.020
 REG  plan-1  C6   0.020
 REG  plan-1  N1   0.020
 REG  plan-1  O    0.020
 REG  plan-1  N    0.020
 REG  plan-1  C3   0.020
 REG  plan-1  H5   0.020
 REG  plan-1  H13  0.020

