# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 03:35:58 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)NC2CCN(CC2)c3ncccn3
#
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
 9WE  9WE  1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea  ligand  43  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9WE
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
 9WE  C10  C  CR16  0  -0.110  -6.0840  -0.7344  -0.6933
 9WE  C13  C  CH2   0  -0.432   1.6079   1.1601  -0.9538
 9WE  C17  C  CH2   0  -0.469   1.6386   0.7621   1.5167
 9WE  C20  C  CR16  0  -0.009   6.3037  -0.3638  -1.2247
 9WE  C21  C  CR16  0  -0.403   7.0772  -0.5278  -0.0868
 9WE  C22  C  CR16  0  -0.009   6.3650  -0.6942   1.0901
 9WE  O01  O  O     0  -0.548  -1.5582   1.9180  -1.0249
 9WE  C02  C  C     0   0.751  -1.5160   0.8466  -0.4271
 9WE  N03  N  NH1   0  -0.682  -2.5667  -0.0203  -0.3887
 9WE  C04  C  CH2   0  -0.341  -3.7816   0.1822  -1.1328
 9WE  C05  C  CR6   0   0.012  -5.0098   0.0406  -0.2740
 9WE  C06  C  CR16  0  -0.176  -5.1289   0.6844   0.9531
 9WE  C07  C  CR16  0  -0.318  -6.2959   0.5360   1.6828
 9WE  C08  C  CR16  0  -0.071  -7.3094  -0.2570   1.1609
 9WE  N09  N  N     0  -0.400  -7.2095  -0.8840  -0.0037
 9WE  N11  N  NH1   0  -0.689  -0.4197   0.4364   0.2581
 9WE  C12  C  CH1   0  -0.088   0.7886   1.2377   0.3388
 9WE  C14  C  CH2   0  -0.320   2.2257  -0.2199  -1.1396
 9WE  N15  N  NT    0  -0.483   3.0365  -0.5710   0.0129
 9WE  C16  C  CH2   0  -0.324   2.2903  -0.5944   1.2560
 9WE  C18  C  CR6   0   0.635   4.3892  -0.5360  -0.0169
 9WE  N19  N  N     0  -0.472   4.9831  -0.3630  -1.2068
 9WE  N23  N  N     0  -0.473   5.0452  -0.6996   1.1412
 9WE  H30  H  HCR6  0   0.258  -6.0247  -1.2661  -1.6390
 9WE  H34  H  HCH2  0   0.245   0.9803   1.4062  -1.8115
 9WE  H33  H  HCH2  0   0.231   2.4049   1.9085  -0.9139
 9WE  H40  H  HCH2  0   0.249   2.4234   1.5015   1.6933
 9WE  H39  H  HCH2  0   0.252   1.0356   0.7154   2.4269
 9WE  H41  H  HCR6  0   0.266   6.7694  -0.2265  -2.1953
 9WE  H42  H  HCR6  0   0.269   8.1560  -0.5228  -0.1147
 9WE  H43  H  HCR6  0   0.267   6.8815  -0.8286   2.0352
 9WE  H24  H  HNH1  0   0.393  -2.4346  -0.9297   0.0240
 9WE  H25  H  HCH2  0   0.270  -3.7493   1.1828  -1.5642
 9WE  H26  H  HCH2  0   0.253  -3.8454  -0.5159  -1.9732
 9WE  H27  H  HCR6  0   0.267  -4.3182   1.2931   1.3347
 9WE  H28  H  HCR6  0   0.271  -6.4244   1.0240   2.6392
 9WE  H29  H  HCR6  0   0.263  -8.2352  -0.3922   1.7094
 9WE  H31  H  HNH1  0   0.390  -0.4773  -0.4047   0.8092
 9WE  H32  H  HCH1  0   0.255   0.5049   2.2780   0.5152
 9WE  H35  H  HCH2  0   0.238   1.4385  -0.9735  -1.2480
 9WE  H36  H  HCH2  0   0.270   2.8338  -0.2558  -2.0383
 9WE  H38  H  HCH2  0   0.276   2.9500  -0.8604   2.0758
 9WE  H37  H  HCH2  0   0.238   1.5355  -1.3848   1.1866

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
 9WE  O01  C02  double    1.228  0.020  1.228
 9WE  C16  N15  single    1.450  0.020  1.450
 9WE  C16  C17  single    1.527  0.020  1.527
 9WE  C14  N15  single    1.452  0.020  1.452
 9WE  C14  C13  single    1.523  0.020  1.523
 9WE  N15  C18  single    1.354  0.020  1.354
 9WE  C12  C17  single    1.528  0.020  1.528
 9WE  C12  C13  single    1.532  0.020  1.532
 9WE  C12  N11  single    1.452  0.020  1.452
 9WE  C02  N11  single    1.356  0.020  1.356
 9WE  C02  N03  single    1.363  0.020  1.363
 9WE  C18  N23  aromatic  1.341  0.020  1.341
 9WE  C18  N19  aromatic  1.341  0.020  1.341
 9WE  N23  C22  aromatic  1.321  0.020  1.321
 9WE  C04  N03  single    1.439  0.020  1.439
 9WE  C04  C05  single    1.505  0.020  1.505
 9WE  N19  C20  aromatic  1.321  0.020  1.321
 9WE  C22  C21  aromatic  1.386  0.020  1.386
 9WE  C20  C21  aromatic  1.386  0.020  1.386
 9WE  C05  C06  aromatic  1.391  0.020  1.391
 9WE  C05  C10  aromatic  1.389  0.020  1.389
 9WE  C06  C07  aromatic  1.384  0.020  1.384
 9WE  C07  C08  aromatic  1.389  0.020  1.389
 9WE  C10  N09  aromatic  1.328  0.020  1.328
 9WE  C08  N09  aromatic  1.326  0.020  1.326
 9WE  C10  H30  single    0.930  0.020  1.080
 9WE  C13  H34  single    0.970  0.020  1.090
 9WE  C13  H33  single    0.970  0.020  1.090
 9WE  C17  H40  single    0.970  0.020  1.090
 9WE  C17  H39  single    0.970  0.020  1.090
 9WE  C20  H41  single    0.930  0.020  1.080
 9WE  C21  H42  single    0.930  0.020  1.080
 9WE  C22  H43  single    0.930  0.020  1.080
 9WE  N03  H24  single    0.860  0.020  1.020
 9WE  C04  H25  single    0.970  0.020  1.090
 9WE  C04  H26  single    0.970  0.020  1.090
 9WE  C06  H27  single    0.930  0.020  1.080
 9WE  C07  H28  single    0.930  0.020  1.080
 9WE  C08  H29  single    0.930  0.020  1.080
 9WE  N11  H31  single    0.860  0.020  1.020
 9WE  C12  H32  single    0.970  0.020  1.090
 9WE  C14  H35  single    0.970  0.020  1.090
 9WE  C14  H36  single    0.970  0.020  1.090
 9WE  C16  H38  single    0.970  0.020  1.090
 9WE  C16  H37  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
 9WE  H30  C10  N09  116.30  3.000
 9WE  H30  C10  C05  119.56  3.000
 9WE  N09  C10  C05  124.14  3.000
 9WE  H33  C13  H34  107.06  3.000
 9WE  H33  C13  C14  109.20  3.000
 9WE  H34  C13  C14  109.99  3.000
 9WE  H33  C13  C12  108.90  3.000
 9WE  H34  C13  C12  110.13  3.000
 9WE  C14  C13  C12  111.45  3.000
 9WE  H39  C17  H40  106.89  3.000
 9WE  H39  C17  C16  109.85  3.000
 9WE  H40  C17  C16  108.79  3.000
 9WE  H39  C17  C12  110.39  3.000
 9WE  H40  C17  C12  108.27  3.000
 9WE  C16  C17  C12  112.47  3.000
 9WE  H41  C20  N19  116.17  3.000
 9WE  H41  C20  C21  120.66  3.000
 9WE  N19  C20  C21  123.17  3.000
 9WE  H42  C21  C22  122.44  3.000
 9WE  H42  C21  C20  122.43  3.000
 9WE  C22  C21  C20  115.14  3.000
 9WE  H43  C22  N23  116.19  3.000
 9WE  H43  C22  C21  120.65  3.000
 9WE  N23  C22  C21  123.16  3.000
 9WE  N11  C02  N03  114.62  3.000
 9WE  N03  C02  O01  122.85  3.000
 9WE  N11  C02  O01  122.53  3.000
 9WE  H24  N03  C04  116.72  3.000
 9WE  H24  N03  C02  119.00  3.000
 9WE  C04  N03  C02  123.15  3.000
 9WE  H26  C04  H25  106.46  3.000
 9WE  H26  C04  C05  109.31  3.000
 9WE  H25  C04  C05  109.65  3.000
 9WE  H26  C04  N03  110.88  3.000
 9WE  H25  C04  N03  107.98  3.000
 9WE  C05  C04  N03  112.37  3.000
 9WE  C06  C05  C04  121.98  3.000
 9WE  C06  C05  C10  117.27  3.000
 9WE  C04  C05  C10  120.74  3.000
 9WE  H27  C06  C07  120.37  3.000
 9WE  H27  C06  C05  120.45  3.000
 9WE  C07  C06  C05  119.18  3.000
 9WE  H28  C07  C08  120.23  3.000
 9WE  H28  C07  C06  121.19  3.000
 9WE  C08  C07  C06  118.58  3.000
 9WE  H29  C08  N09  116.69  3.000
 9WE  H29  C08  C07  120.28  3.000
 9WE  N09  C08  C07  123.02  3.000
 9WE  C08  N09  C10  117.80  3.000
 9WE  H31  N11  C12  118.56  3.000
 9WE  H31  N11  C02  118.86  3.000
 9WE  C12  N11  C02  122.26  3.000
 9WE  H32  C12  N11  108.56  3.000
 9WE  H32  C12  C17  108.43  3.000
 9WE  N11  C12  C17  109.50  3.000
 9WE  H32  C12  C13  108.87  3.000
 9WE  N11  C12  C13  111.72  3.000
 9WE  C17  C12  C13  109.70  3.000
 9WE  H36  C14  H35  107.34  3.000
 9WE  H36  C14  N15  109.65  3.000
 9WE  H35  C14  N15  108.27  3.000
 9WE  H36  C14  C13  110.98  3.000
 9WE  H35  C14  C13  110.12  3.000
 9WE  N15  C14  C13  110.40  3.000
 9WE  C18  N15  C16  122.25  3.000
 9WE  C18  N15  C14  122.29  3.000
 9WE  C16  N15  C14  113.39  3.000
 9WE  H37  C16  H38  106.86  3.000
 9WE  H37  C16  N15  108.18  3.000
 9WE  H38  C16  N15  109.80  3.000
 9WE  H37  C16  C17  110.96  3.000
 9WE  H38  C16  C17  110.37  3.000
 9WE  N15  C16  C17  110.58  3.000
 9WE  N23  C18  N19  124.43  3.000
 9WE  N19  C18  N15  117.74  3.000
 9WE  N23  C18  N15  117.82  3.000
 9WE  C18  N19  C20  117.04  3.000
 9WE  C18  N23  C22  117.06  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
 9WE  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 9WE  CONST_02  C07  C08  N09  C10     0.00   0.0  0
 9WE  CONST_03  N23  C18  N19  C20     0.00   0.0  0
 9WE  CONST_04  N23  C22  C21  C20     0.00   0.0  0
 9WE  CONST_05  C18  N23  C22  C21     0.00   0.0  0
 9WE  CONST_06  C18  N19  C20  C21     0.00   0.0  0
 9WE  CONST_07  N19  C18  N23  C22     0.00   0.0  0
 9WE  CONST_08  N19  C20  C21  C22     0.00   0.0  0
 9WE  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 9WE  CONST_10  C08  N09  C10  C05     0.00   0.0  0
 9WE  CONST_11  N09  C10  C05  C06     0.00   0.0  0
 9WE  CONST_12  N09  C08  C07  C06     0.00   0.0  0
 9WE  CONST_13  N15  C18  N19  C20   180.00   0.0  0
 9WE  CONST_14  N15  C18  N23  C22   180.00   0.0  0
 9WE  CONST_15  C07  C06  C05  C04   180.00   0.0  0
 9WE  CONST_16  N09  C10  C05  C04   180.00   0.0  0
 9WE  CONST_17  H27  C06  C05  C10   180.00   0.0  0
 9WE  CONST_18  H29  C08  N09  C10   180.00   0.0  0
 9WE  CONST_19  H43  C22  C21  C20   180.00   0.0  0
 9WE  CONST_20  H41  C20  C21  C22   180.00   0.0  0
 9WE  CONST_21  H28  C07  C06  C05   180.00   0.0  0
 9WE  CONST_22  H30  C10  C05  C06   180.00   0.0  0
 9WE  CONST_23  H42  C21  C20  N19   180.00   0.0  0
 9WE  CONST_24  C12  N11  C02  O01     0.00   0.0  0
 9WE  CONST_25  C12  N11  C02  N03   180.00   0.0  0
 9WE  CONST_26  C04  N03  C02  O01     0.00   0.0  0
 9WE  CONST_27  N11  C02  N03  C04   180.00   0.0  0
 9WE  CONST_28  H31  N11  C02  O01   180.00   0.0  0
 9WE  CONST_29  H24  N03  C02  O01   180.00   0.0  0
 9WE  Var_01    C16  N15  C14  C13    59.47  30.0  1
 9WE  Var_02    C14  N15  C16  C17   -57.86  30.0  1
 9WE  Var_03    N15  C16  C17  C12    53.56  30.0  1
 9WE  Var_04    N15  C14  C13  C12   -56.13  30.0  1
 9WE  Var_05    N23  C18  N15  C14   171.12  30.0  2
 9WE  Var_06    N03  C04  C05  C10  -132.39  30.0  2
 9WE  Var_07    C05  C04  N03  C02  -129.92  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
 9WE  chir_01  C12  C17  C13  N11  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
 9WE  plan-1  C10  0.020
 9WE  plan-1  C04  0.020
 9WE  plan-1  C05  0.020
 9WE  plan-1  C06  0.020
 9WE  plan-1  C07  0.020
 9WE  plan-1  C08  0.020
 9WE  plan-1  N09  0.020
 9WE  plan-1  H30  0.020
 9WE  plan-1  H27  0.020
 9WE  plan-1  H28  0.020
 9WE  plan-1  H29  0.020
 9WE  plan-2  C20  0.020
 9WE  plan-2  C21  0.020
 9WE  plan-2  C22  0.020
 9WE  plan-2  N15  0.020
 9WE  plan-2  C18  0.020
 9WE  plan-2  N19  0.020
 9WE  plan-2  N23  0.020
 9WE  plan-2  H41  0.020
 9WE  plan-2  H42  0.020
 9WE  plan-2  H43  0.020
 9WE  plan-3  O01  0.020
 9WE  plan-3  C02  0.020
 9WE  plan-3  N03  0.020
 9WE  plan-3  C04  0.020
 9WE  plan-3  N11  0.020
 9WE  plan-3  C12  0.020
 9WE  plan-3  H24  0.020
 9WE  plan-3  H31  0.020

