# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 02:45:48 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (1~{R},2~{R})-~{N}-(1~{H}-pyrazol-4-yl)-2-pyridin-3-yl-cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1c[nH]nc1)[C@@H]2C[C@H]2c3cccnc3
#
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
 4OI  4OI  "(1~{R},2~{R})-~{N}-(1~{H}-pyrazol-4-yl)-2-pyridin-3-yl-cyclopropane-1-carboxamide"
  ligand  29  17  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4OI
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
 4OI  C02  C  C     0   0.511  65.5807  82.4504  51.7657
 4OI  C03  C  CH1   0  -0.416  64.3383  82.6427  50.9504
 4OI  C04  C  CH2   0  -0.453  63.0037  82.3312  51.5623
 4OI  C05  C  CH1   0  -0.302  63.5756  81.4416  50.5005
 4OI  C06  C  CR6   0   0.010  62.9766  81.4109  49.1397
 4OI  C07  C  CR16  0  -0.180  61.6593  81.0183  48.9316
 4OI  C08  C  CR16  0  -0.317  61.1620  80.9691  47.6391
 4OI  C09  C  CR16  0  -0.072  62.0065  81.3080  46.5922
 4OI  C11  C  CR16  0  -0.094  63.7323  81.7225  48.0133
 4OI  C13  C  CR5   0   0.049  65.1290  84.6220  52.8253
 4OI  C14  C  CR15  0   0.041  64.9717  85.7202  52.0076
 4OI  C17  C  CR15  0  -0.059  64.3743  84.9253  53.9735
 4OI  N10  N  N     0  -0.398  63.2703  81.6745  46.7701
 4OI  N12  N  NH1   0  -0.724  65.9032  83.4769  52.5912
 4OI  N15  N  NR15  0  -0.424  64.1689  86.5611  52.6732
 4OI  N16  N  N     0  -0.265  63.7992  86.1068  53.8652
 4OI  O01  O  O     0  -0.460  66.2720  81.4490  51.6943
 4OI  H1   H  HCH1  0   0.305  64.3737  83.4857  50.2676
 4OI  H2   H  HCH2  0   0.262  62.1670  82.9687  51.3055
 4OI  H3   H  HCH2  0   0.265  62.9843  81.9607  52.5796
 4OI  H4   H  HCH1  0   0.286  63.9533  80.4820  50.8414
 4OI  H5   H  HCR6  0   0.265  61.0285  80.7599  49.7737
 4OI  H6   H  HCR6  0   0.268  60.1403  80.6726  47.4423
 4OI  H7   H  HCR6  0   0.261  61.6465  81.2849  45.5695
 4OI  H8   H  HCR6  0   0.257  64.7669  82.0308  48.1312
 4OI  H9   H  HCR5  0   0.301  65.3503  85.9387  51.0223
 4OI  H10  H  HCR5  0   0.267  64.2379  84.3209  54.8573
 4OI  H11  H  HNH1  0   0.394  66.7242  83.3422  53.1650
 4OI  H12  H  HNR5  0   0.424  63.8420  87.4604  52.3563

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
 4OI  C09  N10  aromatic  1.328  0.020  1.328
 4OI  C09  C08  aromatic  1.387  0.020  1.387
 4OI  N10  C11  aromatic  1.327  0.020  1.327
 4OI  C08  C07  aromatic  1.386  0.020  1.386
 4OI  C11  C06  aromatic  1.392  0.020  1.392
 4OI  C07  C06  aromatic  1.390  0.020  1.390
 4OI  C06  C05  single    1.487  0.020  1.487
 4OI  C05  C03  single    1.492  0.020  1.492
 4OI  C05  C04  single    1.499  0.020  1.499
 4OI  C03  C04  single    1.501  0.020  1.501
 4OI  C03  C02  single    1.498  0.020  1.498
 4OI  O01  C02  double    1.219  0.020  1.219
 4OI  C02  N12  single    1.356  0.020  1.356
 4OI  C14  C13  aromatic  1.378  0.020  1.378
 4OI  C14  N15  aromatic  1.340  0.020  1.340
 4OI  N12  C13  single    1.402  0.020  1.402
 4OI  C13  C17  aromatic  1.407  0.020  1.407
 4OI  N15  N16  aromatic  1.328  0.020  1.328
 4OI  C17  N16  aromatic  1.318  0.020  1.318
 4OI  C03  H1   single    0.970  0.020  1.090
 4OI  C04  H2   single    0.970  0.020  1.090
 4OI  C04  H3   single    0.970  0.020  1.090
 4OI  C05  H4   single    0.970  0.020  1.090
 4OI  C07  H5   single    0.930  0.020  1.080
 4OI  C08  H6   single    0.930  0.020  1.080
 4OI  C09  H7   single    0.930  0.020  1.080
 4OI  C11  H8   single    0.930  0.020  1.080
 4OI  C14  H9   single    0.930  0.020  1.080
 4OI  C17  H10  single    0.930  0.020  1.080
 4OI  N12  H11  single    0.860  0.020  1.020
 4OI  N15  H12  single    0.860  0.020  1.020

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
 4OI  O01  C02  N12  121.51  3.000
 4OI  N12  C02  C03  115.55  3.000
 4OI  O01  C02  C03  122.94  3.000
 4OI  H1   C03  C05  116.88  3.000
 4OI  H1   C03  C04  116.53  3.000
 4OI  C05  C03  C04   60.09  3.000
 4OI  H1   C03  C02  114.52  3.000
 4OI  C04  C03  C02  119.26  3.000
 4OI  C05  C03  C02  118.98  3.000
 4OI  H3   C04  H2   114.23  3.000
 4OI  H3   C04  C05  117.99  3.000
 4OI  H2   C04  C05  118.45  3.000
 4OI  H3   C04  C03  118.04  3.000
 4OI  H2   C04  C03  117.91  3.000
 4OI  C05  C04  C03   59.67  3.000
 4OI  H4   C05  C06  114.14  3.000
 4OI  H4   C05  C04  115.77  3.000
 4OI  C06  C05  C04  120.46  3.000
 4OI  H4   C05  C03  116.02  3.000
 4OI  C04  C05  C03   60.24  3.000
 4OI  C06  C05  C03  119.89  3.000
 4OI  C11  C06  C07  117.17  3.000
 4OI  C07  C06  C05  121.63  3.000
 4OI  C11  C06  C05  121.15  3.000
 4OI  H5   C07  C08  120.50  3.000
 4OI  H5   C07  C06  120.18  3.000
 4OI  C08  C07  C06  119.32  3.000
 4OI  H6   C08  C09  120.30  3.000
 4OI  H6   C08  C07  121.22  3.000
 4OI  C09  C08  C07  118.47  3.000
 4OI  H7   C09  N10  116.62  3.000
 4OI  H7   C09  C08  120.30  3.000
 4OI  N10  C09  C08  123.08  3.000
 4OI  H8   C11  N10  116.34  3.000
 4OI  H8   C11  C06  119.54  3.000
 4OI  N10  C11  C06  124.12  3.000
 4OI  N12  C13  C17  127.48  3.000
 4OI  C17  C13  C14  104.55  3.000
 4OI  N12  C13  C14  127.94  3.000
 4OI  H9   C14  N15  122.50  3.000
 4OI  H9   C14  C13  131.59  3.000
 4OI  N15  C14  C13  105.89  3.000
 4OI  H10  C17  N16  120.93  3.000
 4OI  H10  C17  C13  127.97  3.000
 4OI  N16  C17  C13  111.10  3.000
 4OI  C11  N10  C09  117.83  3.000
 4OI  H11  N12  C13  117.56  3.000
 4OI  H11  N12  C02  115.97  3.000
 4OI  C13  N12  C02  126.06  3.000
 4OI  H12  N15  N16  119.81  3.000
 4OI  H12  N15  C14  126.74  3.000
 4OI  N16  N15  C14  113.45  3.000
 4OI  N15  N16  C17  105.00  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
 4OI  CONST_01  C09  N10  C11  C06     0.00   0.0  0
 4OI  CONST_02  C09  C08  C07  C06     0.00   0.0  0
 4OI  CONST_03  N10  C09  C08  C07     0.00   0.0  0
 4OI  CONST_04  N10  C11  C06  C07     0.00   0.0  0
 4OI  CONST_05  C11  N10  C09  C08     0.00   0.0  0
 4OI  CONST_06  C11  C06  C07  C08     0.00   0.0  0
 4OI  CONST_07  N16  N15  C14  C13     0.00   0.0  0
 4OI  CONST_08  N15  N16  C17  C13     0.00   0.0  0
 4OI  CONST_09  N16  C17  C13  C14     0.00   0.0  0
 4OI  CONST_10  C17  N16  N15  C14     0.00   0.0  0
 4OI  CONST_11  N15  C14  C13  C17     0.00   0.0  0
 4OI  CONST_12  N10  C11  C06  C05   180.00   0.0  0
 4OI  CONST_13  C08  C07  C06  C05   180.00   0.0  0
 4OI  CONST_14  N15  C14  C13  N12   180.00   0.0  0
 4OI  CONST_15  N16  C17  C13  N12   180.00   0.0  0
 4OI  CONST_16  H8   C11  C06  C05     0.00   0.0  0
 4OI  CONST_17  H5   C07  C06  C05     0.00   0.0  0
 4OI  CONST_18  H6   C08  C07  C06   180.00   0.0  0
 4OI  CONST_19  H7   C09  C08  C07   180.00   0.0  0
 4OI  CONST_20  H8   C11  C06  C07   180.00   0.0  0
 4OI  CONST_21  H8   C11  N10  C09   180.00   0.0  0
 4OI  CONST_22  H5   C07  C08  C09   180.00   0.0  0
 4OI  CONST_23  H7   C09  N10  C11   180.00   0.0  0
 4OI  CONST_24  H5   C07  C06  C11   180.00   0.0  0
 4OI  CONST_25  H12  N15  C14  C13   180.00   0.0  0
 4OI  CONST_26  H10  C17  C13  C14   180.00   0.0  0
 4OI  CONST_27  H9   C14  C13  C17   180.00   0.0  0
 4OI  CONST_28  H12  N15  N16  C17   180.00   0.0  0
 4OI  CONST_29  H6   C08  C09  N10   180.00   0.0  0
 4OI  CONST_30  H10  C17  N16  N15   180.00   0.0  0
 4OI  CONST_31  H9   C14  N15  N16   180.00   0.0  0
 4OI  CONST_32  C13  N12  C02  C03     0.00   0.0  0
 4OI  CONST_37  O01  C02  N12  C13   180.00   0.0  0
 4OI  CONST_38  H11  N12  C02  C03   180.00   0.0  0
 4OI  CONST_39  H11  N12  C02  O01     0.00   0.0  0
 4OI  Var_01    C11  C06  C05  C03    50.54  30.0  2
 4OI  Var_02    C07  C06  C05  C03  -132.15  30.0  2
 4OI  Var_03    C06  C05  C04  C03  -109.25  30.0  1
 4OI  Var_04    C11  C06  C05  C04   121.51  30.0  2
 4OI  Var_05    C07  C06  C05  C04   -61.18  30.0  2
 4OI  Var_06    C06  C05  C03  C02  -140.81  30.0  1
 4OI  Var_07    C04  C05  C03  C02   109.02  30.0  1
 4OI  Var_08    H2   C04  C05  C03   107.45  30.0  1
 4OI  Var_09    H3   C04  C05  C03  -107.80  30.0  1
 4OI  Var_10    H4   C05  C04  C03   106.57  30.0  1
 4OI  Var_11    H1   C03  C05  C04  -106.62  30.0  1
 4OI  Var_12    H1   C03  C05  C06     3.55  30.0  1
 4OI  Var_13    H2   C04  C05  C06    -1.80  30.0  1
 4OI  Var_14    H3   C04  C05  C06   142.95  30.0  1
 4OI  Var_15    H4   C05  C06  C07    83.54  30.0  2
 4OI  Var_16    H4   C05  C06  C11   -93.77  30.0  2
 4OI  Var_17    O01  C02  C03  C04    97.21  30.0  3
 4OI  Var_18    N12  C02  C03  C04   -83.41  30.0  3
 4OI  Var_19    O01  C02  C03  C05    27.28  30.0  3
 4OI  Var_20    N12  C02  C03  C05  -153.34  30.0  3
 4OI  Var_21    H4   C05  C03  C02     2.87  30.0  1
 4OI  Var_22    H2   C04  C03  C02   143.10  30.0  1
 4OI  Var_23    H3   C04  C03  C02    -0.84  30.0  1
 4OI  Var_24    H1   C03  C02  N12    61.50  30.0  1
 4OI  Var_25    H1   C03  C02  O01  -117.88  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
 4OI  chir_01  C03  C05  C04  C02  both
 4OI  chir_02  C05  C06  C03  C04  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
 4OI  plan-1  C13  0.020
 4OI  plan-1  C14  0.020
 4OI  plan-1  C17  0.020
 4OI  plan-1  N12  0.020
 4OI  plan-1  N15  0.020
 4OI  plan-1  N16  0.020
 4OI  plan-1  H9   0.020
 4OI  plan-1  H10  0.020
 4OI  plan-1  H12  0.020
 4OI  plan-2  C05  0.020
 4OI  plan-2  C06  0.020
 4OI  plan-2  C07  0.020
 4OI  plan-2  C08  0.020
 4OI  plan-2  C09  0.020
 4OI  plan-2  C11  0.020
 4OI  plan-2  N10  0.020
 4OI  plan-2  H5   0.020
 4OI  plan-2  H6   0.020
 4OI  plan-2  H7   0.020
 4OI  plan-2  H8   0.020
 4OI  plan-3  C02  0.020
 4OI  plan-3  C03  0.020
 4OI  plan-3  C13  0.020
 4OI  plan-3  N12  0.020
 4OI  plan-3  O01  0.020
 4OI  plan-3  H11  0.020

