# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 21:18:41 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-cyclohexyl-3-(3-phenylpropyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCCc1ccccc1)NC2CCCCC2
#
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
 CPU  CPU  1-cyclohexyl-3-(3-phenylpropyl)urea  ligand  43  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CPU
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
 CPU  C1    C  CR16  0  -0.311   0.8905   0.8004   5.1795
 CPU  C2    C  CR16  0  -0.240   1.4244   0.2667   6.3450
 CPU  C3    C  CR16  0  -0.274   0.8054  -0.8108   6.9661
 CPU  C4    C  CR16  0  -0.239  -0.3500  -1.3475   6.4128
 CPU  C5    C  CR16  0  -0.312  -0.8796  -0.8099   5.2468
 CPU  C6    C  CR6   0   0.137  -0.2683   0.2710   4.6146
 CPU  N1    N  NH1   0  -0.688  -0.1762  -0.0034  -0.3273
 CPU  C7    C  CH2   0  -0.513  -0.8143   0.8184   3.3258
 CPU  C8    C  CH2   0  -0.448  -0.1836   0.1418   2.1090
 CPU  C9    C  CH2   0  -0.244  -0.7435   0.6905   0.8056
 CPU  C10   C  C     0   0.729  -0.1028   0.5550  -1.5667
 CPU  O1    O  O     0  -0.552  -0.3511   1.7399  -1.7729
 CPU  N2    N  NH1   0  -0.684   0.3198  -0.2893  -2.5462
 CPU  C11   C  CH1   0  -0.053   0.3103   0.0731  -3.9488
 CPU  C12   C  CH2   0  -0.437   1.3950  -0.7075  -4.6863
 CPU  C13   C  CH2   0  -0.437   1.4100  -0.3733  -6.1746
 CPU  C14   C  CH2   0  -0.431   0.0452  -0.5997  -6.8163
 CPU  C15   C  CH2   0  -0.438  -1.0379   0.1851  -6.0842
 CPU  C16   C  CH2   0  -0.426  -1.0567  -0.1534  -4.5968
 CPU  H1    H  HCR6  0   0.245   1.3809   1.6414   4.7019
 CPU  H2    H  HCR6  0   0.252   2.3236   0.6946   6.7699
 CPU  H3    H  HCR6  0   0.253   1.2186  -1.2270   7.8758
 CPU  H4    H  HCR6  0   0.252  -0.8430  -2.1841   6.8918
 CPU  H5    H  HCR6  0   0.245  -1.7827  -1.2348   4.8231
 CPU  HN1   H  HNH1  0   0.385  -0.1222  -1.0070  -0.2512
 CPU  H72   H  HCH2  0   0.243  -0.6344   1.8957   3.2729
 CPU  H71   H  HCH2  0   0.243  -1.8984   0.6798   3.2934
 CPU  H82   H  HCH2  0   0.232  -0.3634  -0.9367   2.1660
 CPU  H81   H  HCH2  0   0.236   0.9008   0.2809   2.1286
 CPU  H92   H  HCH2  0   0.238  -0.5075   1.7510   0.7219
 CPU  H91   H  HCH2  0   0.218  -1.8377   0.6093   0.8152
 CPU  HN2   H  HNH1  0   0.380   0.3612  -1.2768  -2.3440
 CPU  H11   H  HCH1  0   0.230   0.5518   1.1374  -4.0128
 CPU  H121  H  HCH2  0   0.235   2.3690  -0.4938  -4.2394
 CPU  H122  H  HCH2  0   0.213   1.2159  -1.7820  -4.5587
 CPU  H131  H  HCH2  0   0.213   1.7019   0.6742  -6.3069
 CPU  H132  H  HCH2  0   0.231   2.1731  -0.9710  -6.6784
 CPU  H141  H  HCH2  0   0.228   0.0734  -0.3166  -7.8712
 CPU  H142  H  HCH2  0   0.210  -0.1974  -1.6677  -6.7866
 CPU  H151  H  HCH2  0   0.212  -0.8555   1.2580  -6.2100
 CPU  H152  H  HCH2  0   0.229  -2.0182  -0.0152  -6.5229
 CPU  H161  H  HCH2  0   0.208  -1.3405  -1.2038  -4.4624
 CPU  H162  H  HCH2  0   0.232  -1.8109   0.4447  -4.0795

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
 CPU  C1   C2    aromatic  1.389  0.020  1.389
 CPU  C1   C6    aromatic  1.394  0.020  1.394
 CPU  C1   H1    single    0.930  0.020  1.080
 CPU  C2   C3    aromatic  1.389  0.020  1.389
 CPU  C2   H2    single    0.930  0.020  1.080
 CPU  C3   C4    aromatic  1.389  0.020  1.389
 CPU  C3   H3    single    0.930  0.020  1.080
 CPU  C4   C5    aromatic  1.389  0.020  1.389
 CPU  C4   H4    single    0.930  0.020  1.080
 CPU  C5   C6    aromatic  1.393  0.020  1.393
 CPU  C5   H5    single    0.930  0.020  1.080
 CPU  C6   C7    single    1.503  0.020  1.503
 CPU  N1   C9    single    1.445  0.020  1.445
 CPU  N1   C10   single    1.361  0.020  1.361
 CPU  N1   HN1   single    0.890  0.020  1.040
 CPU  C7   C8    single    1.528  0.020  1.528
 CPU  C7   H72   single    0.970  0.020  1.090
 CPU  C7   H71   single    0.970  0.020  1.090
 CPU  C8   C9    single    1.521  0.020  1.521
 CPU  C8   H82   single    0.970  0.020  1.090
 CPU  C8   H81   single    0.970  0.020  1.090
 CPU  C9   H92   single    0.970  0.020  1.090
 CPU  C9   H91   single    0.970  0.020  1.090
 CPU  C10  O1    double    1.228  0.020  1.228
 CPU  C10  N2    single    1.360  0.020  1.360
 CPU  N2   C11   single    1.449  0.020  1.449
 CPU  N2   HN2   single    0.890  0.020  1.040
 CPU  C11  C12   single    1.526  0.020  1.526
 CPU  C11  C16   single    1.530  0.020  1.530
 CPU  C11  H11   single    0.970  0.020  1.090
 CPU  C12  C13   single    1.525  0.020  1.525
 CPU  C12  H121  single    0.970  0.020  1.090
 CPU  C12  H122  single    0.970  0.020  1.090
 CPU  C13  C14   single    1.525  0.020  1.525
 CPU  C13  H131  single    0.970  0.020  1.090
 CPU  C13  H132  single    0.970  0.020  1.090
 CPU  C14  C15   single    1.525  0.020  1.525
 CPU  C14  H141  single    0.970  0.020  1.090
 CPU  C14  H142  single    0.970  0.020  1.090
 CPU  C15  C16   single    1.526  0.020  1.526
 CPU  C15  H151  single    0.970  0.020  1.090
 CPU  C15  H152  single    0.970  0.020  1.090
 CPU  C16  H161  single    0.970  0.020  1.090
 CPU  C16  H162  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
 CPU  H1    C1   C6    119.48  3.000
 CPU  H1    C1   C2    119.59  3.000
 CPU  C6    C1   C2    120.92  3.000
 CPU  H2    C2   C3    120.08  3.000
 CPU  H2    C2   C1    119.79  3.000
 CPU  C3    C2   C1    120.13  3.000
 CPU  H3    C3   C4    120.25  3.000
 CPU  H3    C3   C2    120.26  3.000
 CPU  C4    C3   C2    119.49  3.000
 CPU  H4    C4   C5    119.80  3.000
 CPU  H4    C4   C3    120.07  3.000
 CPU  C5    C4   C3    120.13  3.000
 CPU  H5    C5   C6    119.48  3.000
 CPU  H5    C5   C4    119.60  3.000
 CPU  C6    C5   C4    120.93  3.000
 CPU  C7    C6   C5    120.81  3.000
 CPU  C7    C6   C1    120.75  3.000
 CPU  C5    C6   C1    118.39  3.000
 CPU  HN1   N1   C10   118.32  3.000
 CPU  HN1   N1   C9    116.11  3.000
 CPU  C10   N1   C9    122.56  3.000
 CPU  H71   C7   H72   106.66  3.000
 CPU  H71   C7   C8    109.23  3.000
 CPU  H72   C7   C8    109.25  3.000
 CPU  H71   C7   C6    109.84  3.000
 CPU  H72   C7   C6    109.91  3.000
 CPU  C8    C7   C6    111.81  3.000
 CPU  H81   C8   H82   106.69  3.000
 CPU  H81   C8   C9    109.55  3.000
 CPU  H82   C8   C9    109.85  3.000
 CPU  H81   C8   C7    109.79  3.000
 CPU  H82   C8   C7    109.07  3.000
 CPU  C9    C8   C7    111.76  3.000
 CPU  H91   C9   H92   106.78  3.000
 CPU  H91   C9   C8    109.44  3.000
 CPU  H92   C9   C8    109.71  3.000
 CPU  H91   C9   N1    111.28  3.000
 CPU  H92   C9   N1    108.79  3.000
 CPU  C8    C9   N1    110.75  3.000
 CPU  N2    C10  O1    122.73  3.000
 CPU  N2    C10  N1    114.69  3.000
 CPU  O1    C10  N1    122.53  3.000
 CPU  HN2   N2   C11   116.05  3.000
 CPU  HN2   N2   C10   118.42  3.000
 CPU  C11   N2   C10   122.67  3.000
 CPU  H11   C11  C16   108.47  3.000
 CPU  H11   C11  C12   108.21  3.000
 CPU  C16   C11  C12   110.77  3.000
 CPU  H11   C11  N2    107.38  3.000
 CPU  C16   C11  N2    112.27  3.000
 CPU  C12   C11  N2    109.58  3.000
 CPU  H122  C12  H121  106.83  3.000
 CPU  H122  C12  C13   109.25  3.000
 CPU  H121  C12  C13   110.33  3.000
 CPU  H122  C12  C11   109.20  3.000
 CPU  H121  C12  C11   109.62  3.000
 CPU  C13   C12  C11   111.49  3.000
 CPU  H132  C13  H131  106.34  3.000
 CPU  H132  C13  C14   110.48  3.000
 CPU  H131  C13  C14   109.25  3.000
 CPU  H132  C13  C12   109.69  3.000
 CPU  H131  C13  C12   109.26  3.000
 CPU  C14   C13  C12   111.67  3.000
 CPU  H142  C14  H141  106.53  3.000
 CPU  H142  C14  C15   109.36  3.000
 CPU  H141  C14  C15   110.39  3.000
 CPU  H142  C14  C13   109.36  3.000
 CPU  H141  C14  C13   110.16  3.000
 CPU  C15   C14  C13   110.93  3.000
 CPU  H152  C15  H151  106.43  3.000
 CPU  H152  C15  C16   109.86  3.000
 CPU  H151  C15  C16   109.35  3.000
 CPU  H152  C15  C14   110.50  3.000
 CPU  H151  C15  C14   109.31  3.000
 CPU  C16   C15  C14   111.26  3.000
 CPU  H162  C16  H161  106.72  3.000
 CPU  H162  C16  C15   110.40  3.000
 CPU  H161  C16  C15   109.59  3.000
 CPU  H162  C16  C11   109.58  3.000
 CPU  H161  C16  C11   108.74  3.000
 CPU  C15   C16  C11   111.66  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
 CPU  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 CPU  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 CPU  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 CPU  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 CPU  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 CPU  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 CPU  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 CPU  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 CPU  CONST_09  H3   C3   C2   C1    180.00   0.0  0
 CPU  CONST_10  H5   C5   C6   C1    180.00   0.0  0
 CPU  CONST_11  H4   C4   C3   C2    180.00   0.0  0
 CPU  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 CPU  CONST_13  H2   C2   C3   C4    180.00   0.0  0
 CPU  CONST_14  C11  N2   C10  O1      0.00   0.0  0
 CPU  CONST_15  C11  N2   C10  N1    180.00   0.0  0
 CPU  CONST_16  O1   C10  N1   C9      0.00   0.0  0
 CPU  CONST_17  N2   C10  N1   C9    180.00   0.0  0
 CPU  CONST_18  HN1  N1   C10  O1    180.00   0.0  0
 CPU  CONST_19  HN2  N2   C10  O1    180.00   0.0  0
 CPU  Var_01    C14  C13  C12  C11   -55.32  30.0  1
 CPU  Var_02    C14  C15  C16  C11    55.62  30.0  1
 CPU  Var_03    C15  C14  C13  C12    55.27  30.0  1
 CPU  Var_04    C16  C15  C14  C13   -55.28  30.0  1
 CPU  Var_05    C8   C7   C6   C1     86.97  30.0  2
 CPU  Var_06    C9   C8   C7   C6    179.63  30.0  3
 CPU  Var_07    C7   C8   C9   N1   -177.50  30.0  1
 CPU  Var_08    C10  N1   C9   C8   -155.58  30.0  2

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
 CPU  chir_01  C11  N2  C12  C16  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
 CPU  plan-1  C1   0.020
 CPU  plan-1  C2   0.020
 CPU  plan-1  C3   0.020
 CPU  plan-1  C4   0.020
 CPU  plan-1  C5   0.020
 CPU  plan-1  C6   0.020
 CPU  plan-1  C7   0.020
 CPU  plan-1  H1   0.020
 CPU  plan-1  H2   0.020
 CPU  plan-1  H3   0.020
 CPU  plan-1  H4   0.020
 CPU  plan-1  H5   0.020
 CPU  plan-2  N1   0.020
 CPU  plan-2  C9   0.020
 CPU  plan-2  C10  0.020
 CPU  plan-2  O1   0.020
 CPU  plan-2  N2   0.020
 CPU  plan-2  C11  0.020
 CPU  plan-2  HN1  0.020
 CPU  plan-2  HN2  0.020

