# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:31:21 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-(3-cyclopropyl-1H-pyrazol-5-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1[nH]nc(c1)C2CC2)c3ccccc3
#
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
 N5B  N5B  N-(3-cyclopropyl-1H-pyrazol-5-yl)benzamide  ligand  30  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N5B
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
 N5B  C1    C  CR5   0   0.306  -0.1414  -0.0091   3.0877
 N5B  C2    C  CH1   0  -0.362  -0.8306   0.1343   4.3828
 N5B  C3    C  CR15  0  -0.523  -0.7337   0.1005   1.8126
 N5B  N4    N  N     0  -0.316   1.1494  -0.2653   3.0009
 N5B  C5    C  CH2   0  -0.471  -0.3965  -0.6775   5.5723
 N5B  C6    C  CH2   0  -0.470  -0.1385   0.7915   5.5460
 N5B  C7    C  CR5   0   0.636   0.3120  -0.1104   0.9360
 N5B  N8    N  NR15  0  -0.514   1.4054  -0.3224   1.6895
 N5B  N9    N  NH1   0  -0.753   0.4126  -0.1316  -0.4416
 N5B  C10   C  C     0   0.535  -0.6240   0.0604  -1.3012
 N5B  C11   C  CR6   0  -0.044  -0.2660   0.0425  -2.7483
 N5B  O12   O  O     0  -0.450  -1.7684   0.2257  -0.9224
 N5B  C13   C  CR16  0  -0.263  -1.2591  -0.3104  -3.6606
 N5B  C14   C  CR16  0  -0.294   0.9971   0.4002  -3.2177
 N5B  C15   C  CR16  0  -0.241  -0.9857  -0.3306  -5.0187
 N5B  C16   C  CR16  0  -0.239   1.2650   0.3912  -4.5787
 N5B  C17   C  CR16  0  -0.248   0.2767   0.0210  -5.4808
 N5B  H2    H  HCH1  0   0.263  -1.8940   0.3205   4.2908
 N5B  H3    H  HCR5  0   0.268  -1.7645   0.2990   1.5862
 N5B  H5C1  H  HCH2  0   0.254  -1.1675  -1.0536   6.2324
 N5B  H5C2  H  HCH2  0   0.249   0.4450  -1.3445   5.4347
 N5B  H6C1  H  HCH2  0   0.249   0.8784   1.1286   5.3887
 N5B  H6C2  H  HCH2  0   0.253  -0.7318   1.4311   6.1866
 N5B  H8    H  HNR5  0   0.419   2.3440  -0.5031   1.3699
 N5B  H9    H  HNH1  0   0.427   1.3148  -0.3715  -0.8240
 N5B  H13   H  HCR6  0   0.264  -2.2448  -0.5809  -3.3064
 N5B  H14   H  HCR6  0   0.264   1.7782   0.7177  -2.5379
 N5B  H15   H  HCR6  0   0.266  -1.7596  -0.6179  -5.7181
 N5B  H16   H  HCR6  0   0.268   2.2447   0.6822  -4.9326
 N5B  H17   H  HCR6  0   0.267   0.4884   0.0116  -6.5419

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
 N5B  C1   C2    single    1.474  0.020  1.474
 N5B  C1   C3    aromatic  1.410  0.020  1.410
 N5B  C1   N4    aromatic  1.319  0.020  1.319
 N5B  C2   C5    single    1.504  0.020  1.504
 N5B  C2   C6    single    1.505  0.020  1.505
 N5B  C2   H2    single    0.970  0.020  1.090
 N5B  C3   C7    aromatic  1.381  0.020  1.381
 N5B  C3   H3    single    0.930  0.020  1.080
 N5B  N4   N8    aromatic  1.337  0.020  1.337
 N5B  C5   C6    single    1.492  0.020  1.492
 N5B  C5   H5C1  single    0.970  0.020  1.090
 N5B  C5   H5C2  single    0.970  0.020  1.090
 N5B  C6   H6C1  single    0.970  0.020  1.090
 N5B  C6   H6C2  single    0.970  0.020  1.090
 N5B  C7   N8    aromatic  1.345  0.020  1.345
 N5B  C7   N9    single    1.381  0.020  1.381
 N5B  N8   H8    single    0.860  0.020  1.020
 N5B  N9   C10   single    1.360  0.020  1.360
 N5B  N9   H9    single    0.860  0.020  1.020
 N5B  C10  C11   single    1.491  0.020  1.491
 N5B  C10  O12   double    1.217  0.020  1.217
 N5B  C11  C13   aromatic  1.394  0.020  1.394
 N5B  C11  C14   aromatic  1.394  0.020  1.394
 N5B  C13  C15   aromatic  1.385  0.020  1.385
 N5B  C13  H13   single    0.930  0.020  1.080
 N5B  C14  C16   aromatic  1.387  0.020  1.387
 N5B  C14  H14   single    0.930  0.020  1.080
 N5B  C15  C17   aromatic  1.389  0.020  1.389
 N5B  C15  H15   single    0.930  0.020  1.080
 N5B  C16  C17   aromatic  1.388  0.020  1.388
 N5B  C16  H16   single    0.930  0.020  1.080
 N5B  C17  H17   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
 N5B  N4    C1   C3    111.51  3.000
 N5B  N4    C1   C2    122.30  3.000
 N5B  C3    C1   C2    126.19  3.000
 N5B  H2    C2   C6    116.23  3.000
 N5B  H2    C2   C5    116.30  3.000
 N5B  C6    C2   C5     59.44  3.000
 N5B  H2    C2   C1    113.65  3.000
 N5B  C6    C2   C1    120.44  3.000
 N5B  C5    C2   C1    120.49  3.000
 N5B  H3    C3   C7    128.41  3.000
 N5B  H3    C3   C1    127.46  3.000
 N5B  C7    C3   C1    104.13  3.000
 N5B  N8    N4   C1    105.08  3.000
 N5B  H5C2  C5   H5C1  114.65  3.000
 N5B  H5C2  C5   C6    118.04  3.000
 N5B  H5C1  C5   C6    118.43  3.000
 N5B  H5C2  C5   C2    117.15  3.000
 N5B  H5C1  C5   C2    117.66  3.000
 N5B  C6    C5   C2     60.30  3.000
 N5B  H6C2  C6   H6C1  114.63  3.000
 N5B  H6C2  C6   C5    118.47  3.000
 N5B  H6C1  C6   C5    118.14  3.000
 N5B  H6C2  C6   C2    117.62  3.000
 N5B  H6C1  C6   C2    117.10  3.000
 N5B  C5    C6   C2     60.26  3.000
 N5B  N9    C7   N8    119.82  3.000
 N5B  N9    C7   C3    133.68  3.000
 N5B  N8    C7   C3    106.51  3.000
 N5B  H8    N8   C7    127.43  3.000
 N5B  H8    N8   N4    119.79  3.000
 N5B  C7    N8   N4    112.78  3.000
 N5B  H9    N9   C10   118.39  3.000
 N5B  H9    N9   C7    116.54  3.000
 N5B  C10   N9   C7    124.93  3.000
 N5B  O12   C10  C11   121.98  3.000
 N5B  O12   C10  N9    122.63  3.000
 N5B  C11   C10  N9    115.39  3.000
 N5B  C14   C11  C13   119.34  3.000
 N5B  C14   C11  C10   122.77  3.000
 N5B  C13   C11  C10   117.86  3.000
 N5B  H13   C13  C15   119.81  3.000
 N5B  H13   C13  C11   119.88  3.000
 N5B  C15   C13  C11   120.31  3.000
 N5B  H14   C14  C16   118.58  3.000
 N5B  H14   C14  C11   121.15  3.000
 N5B  C16   C14  C11   120.24  3.000
 N5B  H15   C15  C17   120.14  3.000
 N5B  H15   C15  C13   119.76  3.000
 N5B  C17   C15  C13   120.10  3.000
 N5B  H16   C16  C17   120.26  3.000
 N5B  H16   C16  C14   119.62  3.000
 N5B  C17   C16  C14   120.12  3.000
 N5B  H17   C17  C16   120.01  3.000
 N5B  H17   C17  C15   120.11  3.000
 N5B  C16   C17  C15   119.88  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
 N5B  CONST_01  N8   C7   C3   C1     0.00   0.0  0
 N5B  CONST_02  C7   N8   N4   C1     0.00   0.0  0
 N5B  CONST_03  N8   N4   C1   C3     0.00   0.0  0
 N5B  CONST_04  N4   N8   C7   C3     0.00   0.0  0
 N5B  CONST_05  C7   C3   C1   N4     0.00   0.0  0
 N5B  CONST_06  C17  C15  C13  C11    0.00   0.0  0
 N5B  CONST_07  C17  C16  C14  C11    0.00   0.0  0
 N5B  CONST_08  C16  C14  C11  C13    0.00   0.0  0
 N5B  CONST_09  C16  C17  C15  C13    0.00   0.0  0
 N5B  CONST_10  C15  C13  C11  C14    0.00   0.0  0
 N5B  CONST_11  C15  C17  C16  C14    0.00   0.0  0
 N5B  CONST_12  C7   C3   C1   C2   180.00   0.0  0
 N5B  CONST_13  N8   N4   C1   C2   180.00   0.0  0
 N5B  CONST_14  N9   C7   C3   C1   180.00   0.0  0
 N5B  CONST_15  N9   C7   N8   N4   180.00   0.0  0
 N5B  CONST_16  C15  C13  C11  C10  180.00   0.0  0
 N5B  CONST_17  C16  C14  C11  C10  180.00   0.0  0
 N5B  CONST_18  H8   N8   N4   C1   180.00   0.0  0
 N5B  CONST_19  H3   C3   C1   C2     0.00   0.0  0
 N5B  CONST_20  H15  C15  C13  C11  180.00   0.0  0
 N5B  CONST_21  H16  C16  C14  C11  180.00   0.0  0
 N5B  CONST_22  H14  C14  C11  C13  180.00   0.0  0
 N5B  CONST_23  H17  C17  C15  C13  180.00   0.0  0
 N5B  CONST_24  H13  C13  C11  C14  180.00   0.0  0
 N5B  CONST_25  C11  C10  N9   C7   180.00   0.0  0
 N5B  CONST_26  C10  N9   C7   C3     0.00   0.0  0
 N5B  CONST_27  C10  N9   C7   N8   180.00   0.0  0
 N5B  CONST_28  H9   N9   C7   C3   180.00   0.0  0
 N5B  CONST_29  O12  C10  N9   C7     0.00   0.0  0
 N5B  Var_01    C6   C5   C2   C1   109.58  30.0  1
 N5B  Var_02    C5   C2   C1   C3   146.31  30.0  2
 N5B  Var_03    C13  C11  C10  N9   154.42  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
 N5B  chir_01  C2  C1  C5  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
 N5B  plan-1  C1   0.020
 N5B  plan-1  C2   0.020
 N5B  plan-1  C3   0.020
 N5B  plan-1  N4   0.020
 N5B  plan-1  C7   0.020
 N5B  plan-1  N8   0.020
 N5B  plan-1  N9   0.020
 N5B  plan-1  H3   0.020
 N5B  plan-1  H8   0.020
 N5B  plan-2  C10  0.020
 N5B  plan-2  C11  0.020
 N5B  plan-2  C13  0.020
 N5B  plan-2  C14  0.020
 N5B  plan-2  C15  0.020
 N5B  plan-2  C16  0.020
 N5B  plan-2  C17  0.020
 N5B  plan-2  H13  0.020
 N5B  plan-2  H14  0.020
 N5B  plan-2  H15  0.020
 N5B  plan-2  H16  0.020
 N5B  plan-2  H17  0.020
 N5B  plan-3  C7   0.020
 N5B  plan-3  N9   0.020
 N5B  plan-3  C10  0.020
 N5B  plan-3  C11  0.020
 N5B  plan-3  O12  0.020
 N5B  plan-3  H9   0.020

