# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:20:43 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC1CC1)Nc2c[nH]nc2c3[nH]c4ccc(CN5CCOCC5)cc4n3
#
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
 35R  35R  1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea  ligand  51  28  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_35R
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
 35R  O1   O  O     0  -0.520  -5.7036   0.6992   0.0961
 35R  C2   C  C     0   0.731  -4.5450   0.9971   0.3473
 35R  N3   N  NH1   0  -0.697  -4.1787   2.2049   0.8463
 35R  C4   C  CH1   0  -0.077  -5.1537   3.1780   1.2045
 35R  C5   C  CH2   0  -0.481  -5.8350   3.9511   0.1208
 35R  C6   C  CH2   0  -0.512  -4.8042   4.6144   0.9801
 35R  N7   N  NH1   0  -0.787  -3.5015   0.1396   0.1356
 35R  C8   C  CR5   0   0.110  -3.6381  -1.1530  -0.3317
 35R  C9   C  CR15  0  -0.023  -4.7463  -1.8752  -0.7251
 35R  N10  N  NR15  0  -0.415  -4.2802  -3.0916  -1.0843
 35R  N12  N  N     0  -0.278  -2.9817  -3.2252  -0.9621
 35R  C13  C  CR5   0   0.110  -2.5612  -2.0530  -0.5031
 35R  C14  C  CR5   0   0.506  -1.1690  -1.7928  -0.2288
 35R  N15  N  NR15  0  -0.707  -0.1929  -2.7197  -0.3914
 35R  C16  C  CR56  0   0.311   0.9902  -2.1292  -0.0347
 35R  C17  C  CR16  0  -0.301   2.3035  -2.5840  -0.0005
 35R  C18  C  CR16  0  -0.296   3.2641  -1.6850   0.4222
 35R  C19  C  CR6   0   0.078   2.9441  -0.3675   0.8029
 35R  C20  C  CH2   0  -0.328   4.0438   0.5498   1.2710
 35R  N21  N  NT    0  -0.419   5.1459   0.6097   0.3330
 35R  C23  C  CH2   0  -0.302   6.2903   1.3085   0.8865
 35R  C24  C  CH2   0  -0.189   7.4357   1.2956  -0.1079
 35R  O25  O  O2    0  -0.485   7.0590   1.8660  -1.3418
 35R  C26  C  CH2   0  -0.186   5.9450   1.1929  -1.8865
 35R  C27  C  CH2   0  -0.298   4.7650   1.2038  -0.9347
 35R  C28  C  CR16  0  -0.406   1.6322   0.0699   0.7578
 35R  C29  C  CR56  0   0.197   0.6439  -0.8216   0.3387
 35R  N30  N  N     0  -0.542  -0.7109  -0.6431   0.2056
 35R  H1   H  HNH1  0   0.397  -3.2388   2.3365   1.1848
 35R  H2   H  HCH1  0   0.260  -5.7432   2.9535   2.0891
 35R  H3   H  HCH2  0   0.253  -5.5673   3.7177  -0.9014
 35R  H4   H  HCH2  0   0.253  -6.8754   4.2098   0.2672
 35R  H5   H  HCH2  0   0.257  -5.1307   5.3300   1.7229
 35R  H6   H  HCH2  0   0.256  -3.8405   4.8350   0.5386
 35R  H7   H  HNH1  0   0.414  -2.5464   0.4190   0.3330
 35R  H8   H  HCR5  0   0.299  -5.7909  -1.6322  -0.7775
 35R  H9   H  HNR5  0   0.429  -4.8336  -3.8646  -1.4186
 35R  H10  H  HNR5  0   0.421  -0.3271  -3.6663  -0.7109
 35R  H11  H  HCR6  0   0.265   2.5662  -3.5925  -0.2915
 35R  H12  H  HCR6  0   0.246   4.3006  -1.9965   0.4541
 35R  H13  H  HCH2  0   0.212   3.6246   1.5483   1.4810
 35R  H14  H  HCH2  0   0.248   4.4395   0.1800   2.2226
 35R  H16  H  HCH2  0   0.196   6.0454   2.3514   1.1525
 35R  H17  H  HCH2  0   0.241   6.6112   0.8085   1.8040
 35R  H18  H  HCH2  0   0.236   8.2749   1.8765   0.2781
 35R  H19  H  HCH2  0   0.199   7.7795   0.2613  -0.2521
 35R  H20  H  HCH2  0   0.235   5.6814   1.6968  -2.8176
 35R  H21  H  HCH2  0   0.199   6.2058   0.1522  -2.1262
 35R  H22  H  HCH2  0   0.246   3.9499   0.6295  -1.3796
 35R  H23  H  HCH2  0   0.196   4.4003   2.2385  -0.8058
 35R  H24  H  HCR6  0   0.249   1.3727   1.0832   1.0410

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
 35R  C17  C18  aromatic  1.382  0.020  1.382
 35R  C17  C16  aromatic  1.390  0.020  1.390
 35R  C18  C19  aromatic  1.408  0.020  1.408
 35R  C27  C26  single    1.516  0.020  1.516
 35R  C27  N21  single    1.451  0.020  1.451
 35R  C26  O25  single    1.411  0.020  1.411
 35R  C16  N15  aromatic  1.370  0.020  1.370
 35R  C16  C29  aromatic  1.403  0.020  1.403
 35R  C19  C20  single    1.507  0.020  1.507
 35R  C19  C28  aromatic  1.384  0.020  1.384
 35R  C20  N21  single    1.449  0.020  1.449
 35R  N21  C23  single    1.451  0.020  1.451
 35R  N15  C14  aromatic  1.356  0.020  1.356
 35R  C29  C28  aromatic  1.395  0.020  1.395
 35R  C29  N30  aromatic  1.373  0.020  1.373
 35R  O25  C24  single    1.411  0.020  1.411
 35R  C14  N30  aromatic  1.312  0.020  1.312
 35R  C14  C13  single    1.443  0.020  1.443
 35R  N12  C13  aromatic  1.327  0.020  1.327
 35R  N12  N10  aromatic  1.311  0.020  1.311
 35R  C23  C24  single    1.517  0.020  1.517
 35R  C13  C8   aromatic  1.414  0.020  1.414
 35R  N10  C9   aromatic  1.351  0.020  1.351
 35R  C8   C9   aromatic  1.380  0.020  1.380
 35R  C8   N7   single    1.381  0.020  1.381
 35R  N7   C2   single    1.367  0.020  1.367
 35R  C5   C4   single    1.495  0.020  1.495
 35R  C5   C6   single    1.497  0.020  1.497
 35R  C4   N3   single    1.423  0.020  1.423
 35R  C4   C6   single    1.495  0.020  1.495
 35R  C2   O1   double    1.222  0.020  1.222
 35R  C2   N3   single    1.357  0.020  1.357
 35R  N3   H1   single    0.860  0.020  1.020
 35R  C4   H2   single    0.970  0.020  1.090
 35R  C5   H3   single    0.970  0.020  1.090
 35R  C5   H4   single    0.970  0.020  1.090
 35R  C6   H5   single    0.970  0.020  1.090
 35R  C6   H6   single    0.970  0.020  1.090
 35R  N7   H7   single    0.860  0.020  1.020
 35R  C9   H8   single    0.930  0.020  1.080
 35R  N10  H9   single    0.860  0.020  1.020
 35R  N15  H10  single    0.860  0.020  1.020
 35R  C17  H11  single    0.930  0.020  1.080
 35R  C18  H12  single    0.930  0.020  1.080
 35R  C20  H13  single    0.970  0.020  1.090
 35R  C20  H14  single    0.970  0.020  1.090
 35R  C23  H16  single    0.970  0.020  1.090
 35R  C23  H17  single    0.970  0.020  1.090
 35R  C24  H18  single    0.970  0.020  1.090
 35R  C24  H19  single    0.970  0.020  1.090
 35R  C26  H20  single    0.970  0.020  1.090
 35R  C26  H21  single    0.970  0.020  1.090
 35R  C27  H22  single    0.970  0.020  1.090
 35R  C27  H23  single    0.970  0.020  1.090
 35R  C28  H24  single    0.930  0.020  1.080

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
 35R  N7   C2   N3   114.15  3.000
 35R  N3   C2   O1   123.25  3.000
 35R  N7   C2   O1   122.60  3.000
 35R  H1   N3   C4   117.72  3.000
 35R  H1   N3   C2   119.44  3.000
 35R  C4   N3   C2   121.07  3.000
 35R  H2   C4   C6   116.58  3.000
 35R  H2   C4   C5   116.73  3.000
 35R  C6   C4   C5    60.07  3.000
 35R  H2   C4   N3   115.80  3.000
 35R  C6   C4   N3   117.32  3.000
 35R  C5   C4   N3   118.90  3.000
 35R  H4   C5   H3   114.66  3.000
 35R  H4   C5   C6   118.59  3.000
 35R  H3   C5   C6   117.87  3.000
 35R  H4   C5   C4   117.62  3.000
 35R  H3   C5   C4   117.41  3.000
 35R  C6   C5   C4    59.96  3.000
 35R  H6   C6   H5   114.45  3.000
 35R  H6   C6   C5   117.97  3.000
 35R  H5   C6   C5   118.65  3.000
 35R  H6   C6   C4   117.70  3.000
 35R  H5   C6   C4   117.51  3.000
 35R  C5   C6   C4    59.97  3.000
 35R  H7   N7   C8   114.62  3.000
 35R  H7   N7   C2   121.05  3.000
 35R  C8   N7   C2   124.32  3.000
 35R  C13  C8   C9   104.12  3.000
 35R  C9   C8   N7   131.73  3.000
 35R  C13  C8   N7   124.15  3.000
 35R  H8   C9   N10  121.76  3.000
 35R  H8   C9   C8   132.59  3.000
 35R  N10  C9   C8   105.65  3.000
 35R  H9   N10  N12  119.78  3.000
 35R  H9   N10  C9   126.10  3.000
 35R  N12  N10  C9   114.12  3.000
 35R  C13  N12  N10  104.83  3.000
 35R  C14  C13  N12  122.06  3.000
 35R  N12  C13  C8   111.27  3.000
 35R  C14  C13  C8   126.66  3.000
 35R  N30  C14  N15  112.80  3.000
 35R  N30  C14  C13  123.93  3.000
 35R  N15  C14  C13  123.27  3.000
 35R  H10  N15  C16  127.04  3.000
 35R  H10  N15  C14  125.74  3.000
 35R  C16  N15  C14  107.21  3.000
 35R  C29  C16  C17  122.10  3.000
 35R  C29  C16  N15  104.95  3.000
 35R  C17  C16  N15  132.96  3.000
 35R  H11  C17  C18  121.32  3.000
 35R  H11  C17  C16  121.84  3.000
 35R  C18  C17  C16  116.84  3.000
 35R  H12  C18  C19  118.60  3.000
 35R  H12  C18  C17  119.16  3.000
 35R  C19  C18  C17  122.23  3.000
 35R  C28  C19  C20  120.65  3.000
 35R  C28  C19  C18  120.16  3.000
 35R  C20  C19  C18  119.19  3.000
 35R  H14  C20  H13  106.11  3.000
 35R  H14  C20  N21  107.56  3.000
 35R  H13  C20  N21  112.03  3.000
 35R  H14  C20  C19  109.16  3.000
 35R  H13  C20  C19  109.45  3.000
 35R  N21  C20  C19  112.29  3.000
 35R  C27  N21  C23  110.07  3.000
 35R  C23  N21  C20  111.90  3.000
 35R  C27  N21  C20  112.52  3.000
 35R  H17  C23  H16  107.16  3.000
 35R  H17  C23  C24  108.95  3.000
 35R  H16  C23  C24  109.48  3.000
 35R  H17  C23  N21  109.36  3.000
 35R  H16  C23  N21  111.85  3.000
 35R  C24  C23  N21  109.97  3.000
 35R  H19  C24  H18  107.86  3.000
 35R  H19  C24  O25  110.44  3.000
 35R  H18  C24  O25  107.43  3.000
 35R  H19  C24  C23  109.27  3.000
 35R  H18  C24  C23  110.14  3.000
 35R  O25  C24  C23  111.61  3.000
 35R  C26  O25  C24  110.83  3.000
 35R  H21  C26  H20  107.97  3.000
 35R  H21  C26  C27  109.17  3.000
 35R  H20  C26  C27  110.15  3.000
 35R  H21  C26  O25  110.40  3.000
 35R  H20  C26  O25  107.45  3.000
 35R  C27  C26  O25  111.64  3.000
 35R  H23  C27  H22  107.08  3.000
 35R  H23  C27  C26  109.69  3.000
 35R  H22  C27  C26  108.75  3.000
 35R  H23  C27  N21  111.61  3.000
 35R  H22  C27  N21  109.67  3.000
 35R  C26  C27  N21  109.95  3.000
 35R  H24  C28  C29  120.42  3.000
 35R  H24  C28  C19  120.94  3.000
 35R  C29  C28  C19  118.64  3.000
 35R  N30  C29  C28  130.16  3.000
 35R  N30  C29  C16  109.80  3.000
 35R  C28  C29  C16  120.04  3.000
 35R  C29  N30  C14  105.24  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
 35R  CONST_01  N15  C14  C13  C8    180.00   0.0  0
 35R  CONST_02  N30  C14  C13  C8      0.00   0.0  0
 35R  CONST_03  N10  N12  C13  C8      0.00   0.0  0
 35R  CONST_04  N12  N10  C9   C8      0.00   0.0  0
 35R  CONST_05  C13  N12  N10  C9      0.00   0.0  0
 35R  CONST_06  C14  C13  C8   C9    180.00   0.0  0
 35R  CONST_07  N12  C13  C8   C9      0.00   0.0  0
 35R  CONST_08  C14  C13  N12  N10   180.00   0.0  0
 35R  CONST_09  C13  C8   C9   N10     0.00   0.0  0
 35R  CONST_10  N15  C14  C13  N12     0.00   0.0  0
 35R  CONST_11  N30  C14  C13  N12   180.00   0.0  0
 35R  CONST_12  C16  N15  C14  C13   180.00   0.0  0
 35R  CONST_13  C29  N30  C14  C13   180.00   0.0  0
 35R  CONST_14  C17  C16  N15  C14   180.00   0.0  0
 35R  CONST_15  C29  C16  N15  C14     0.00   0.0  0
 35R  CONST_16  C16  C29  N30  C14     0.00   0.0  0
 35R  CONST_17  C28  C29  N30  C14   180.00   0.0  0
 35R  CONST_18  C18  C17  C16  N15   180.00   0.0  0
 35R  CONST_19  C28  C29  C16  N15   180.00   0.0  0
 35R  CONST_20  N30  C29  C16  N15     0.00   0.0  0
 35R  CONST_21  C29  N30  C14  N15     0.00   0.0  0
 35R  CONST_22  C19  C18  C17  C16     0.00   0.0  0
 35R  CONST_23  N30  C14  N15  C16     0.00   0.0  0
 35R  CONST_24  C19  C28  C29  C16     0.00   0.0  0
 35R  CONST_25  C28  C19  C18  C17     0.00   0.0  0
 35R  CONST_26  C28  C29  C16  C17     0.00   0.0  0
 35R  CONST_27  N30  C29  C16  C17   180.00   0.0  0
 35R  CONST_28  C29  C16  C17  C18     0.00   0.0  0
 35R  CONST_29  C29  C28  C19  C18     0.00   0.0  0
 35R  CONST_30  N30  C29  C28  C19   180.00   0.0  0
 35R  CONST_31  C14  C13  C8   N7      0.00   0.0  0
 35R  CONST_32  N12  C13  C8   N7    180.00   0.0  0
 35R  CONST_33  N10  C9   C8   N7    180.00   0.0  0
 35R  CONST_34  C20  C19  C18  C17   180.00   0.0  0
 35R  CONST_35  C29  C28  C19  C20   180.00   0.0  0
 35R  CONST_36  H9   N10  C9   C8    180.00   0.0  0
 35R  CONST_37  H8   C9   N10  N12   180.00   0.0  0
 35R  CONST_38  H10  N15  C14  C13     0.00   0.0  0
 35R  CONST_39  H11  C17  C16  N15     0.00   0.0  0
 35R  CONST_40  H12  C18  C17  C16   180.00   0.0  0
 35R  CONST_41  H24  C28  C29  C16   180.00   0.0  0
 35R  CONST_42  C13  C8   N7   C2    180.00   0.0  0
 35R  CONST_43  C9   C8   N7   C2      0.00   0.0  0
 35R  CONST_44  H7   N7   C8   C9    180.00   0.0  0
 35R  CONST_45  C8   N7   C2   O1      0.00   0.0  0
 35R  CONST_46  C4   N3   C2   O1      0.00   0.0  0
 35R  CONST_47  C8   N7   C2   N3    180.00   0.0  0
 35R  CONST_48  N7   C2   N3   C4    180.00   0.0  0
 35R  CONST_49  H1   N3   C2   O1    180.00   0.0  0
 35R  Var_01    O25  C26  C27  N21   -57.07  30.0  1
 35R  Var_02    O25  C24  C23  N21    57.03  30.0  1
 35R  Var_03    C26  C27  N21  C23    56.44  30.0  1
 35R  Var_04    C27  C26  O25  C24    57.29  30.0  1
 35R  Var_05    C27  N21  C23  C24   -56.42  30.0  1
 35R  Var_06    C6   C5   C4   N3   -106.69  30.0  1
 35R  Var_07    N21  C20  C19  C18    52.27  30.0  2
 35R  Var_08    H5   C6   C5   C4   -106.99  30.0  1
 35R  Var_09    C5   C4   N3   C2    -76.21  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
 35R  chir_01  C4  C5  N3  C6  both

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
 35R  plan-1  N7   0.020
 35R  plan-1  C8   0.020
 35R  plan-1  C9   0.020
 35R  plan-1  N10  0.020
 35R  plan-1  N12  0.020
 35R  plan-1  C13  0.020
 35R  plan-1  C14  0.020
 35R  plan-1  H8   0.020
 35R  plan-1  H9   0.020
 35R  plan-2  C13  0.020
 35R  plan-2  C14  0.020
 35R  plan-2  N15  0.020
 35R  plan-2  C16  0.020
 35R  plan-2  C17  0.020
 35R  plan-2  C18  0.020
 35R  plan-2  C19  0.020
 35R  plan-2  C20  0.020
 35R  plan-2  C28  0.020
 35R  plan-2  C29  0.020
 35R  plan-2  N30  0.020
 35R  plan-2  H10  0.020
 35R  plan-2  H11  0.020
 35R  plan-2  H12  0.020
 35R  plan-2  H24  0.020
 35R  plan-3  O1   0.020
 35R  plan-3  C2   0.020
 35R  plan-3  N3   0.020
 35R  plan-3  C4   0.020
 35R  plan-3  N7   0.020
 35R  plan-3  C8   0.020
 35R  plan-3  H1   0.020
 35R  plan-3  H7   0.020

