# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 04:51:38 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-(pyrimidin-2-yl)-N-[3-(5,6,7,8-tetrahydronaphthalen-2-yl)-1H-pyrazol-5-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCc1ncccn1)Nc2[nH]nc(c2)c3ccc4CCCCc4c3
#
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
 9TV  9TV  3-(pyrimidin-2-yl)-N-[3-(5,6,7,8-tetrahydronaphthalen-2-yl)-1H-pyrazol-5-yl]propanamide  ligand  47  26  .  2022-07-24  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_9TV
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
 9TV  C2   C  CR5   0   0.641   0.3626  -0.9173  -0.0665
 9TV  N4   N  NH1   0  -0.749   1.7417  -0.9641  -0.0514
 9TV  C5   C  CR6   0   0.071  -3.1347   0.0839  -0.1063
 9TV  C7   C  CR6   0   0.342   6.3735   0.5564   0.1610
 9TV  C9   C  CH2   0  -0.604   4.0332  -0.2338  -0.0078
 9TV  C10  C  CR6   0   0.098  -5.5553  -0.1077   0.0908
 9TV  C11  C  CH2   0  -0.490   4.9350   0.9731   0.2326
 9TV  C15  C  CR16  0  -0.339  -3.2824   1.4529  -0.3339
 9TV  C18  C  CR16  0  -0.027   8.2325   0.2200  -1.0912
 9TV  C20  C  CH2   0  -0.498  -6.7573  -0.9929   0.3085
 9TV  C21  C  CH2   0  -0.496  -7.0429   1.9370  -0.1431
 9TV  C22  C  CH2   0  -0.444  -8.0107  -0.2136   0.6815
 9TV  C    C  CR15  0  -0.549  -0.5527   0.1141  -0.0771
 9TV  N    N  NR15  0  -0.501  -0.3499  -2.0596  -0.0726
 9TV  O    O  O     0  -0.454   2.1459   1.2586   0.0724
 9TV  C1   C  CR5   0   0.262  -1.8067  -0.5370  -0.0918
 9TV  N3   N  N     0  -0.304  -1.6653  -1.8504  -0.0906
 9TV  C6   C  C     0   0.565   2.5644   0.1205   0.0128
 9TV  C8   C  CR16  0  -0.353  -4.2835  -0.6731   0.1037
 9TV  N12  N  N     0  -0.403   6.9388   0.1111   1.2789
 9TV  N13  N  N     0  -0.404   6.9710   0.6254  -1.0246
 9TV  C14  C  CR6   0   0.054  -5.6932   1.2638  -0.1414
 9TV  C16  C  CR16  0  -0.277  -4.5421   2.0231  -0.3494
 9TV  C17  C  CR16  0  -0.343   8.9136  -0.2580   0.0145
 9TV  C19  C  CR16  0  -0.028   8.2006  -0.2919   1.2000
 9TV  C23  C  CH2   0  -0.444  -8.2011   0.9567  -0.2722
 9TV  H1   H  HNH1  0   0.424   2.1713  -1.8769  -0.0991
 9TV  H2   H  HCH2  0   0.294   4.2619  -0.6867  -0.9779
 9TV  H3   H  HCH2  0   0.287   4.2265  -1.0069   0.7412
 9TV  H4   H  HCH2  0   0.261   4.7301   1.4002   1.2144
 9TV  H5   H  HCH2  0   0.261   4.7451   1.7380  -0.5195
 9TV  H6   H  HCR6  0   0.244  -2.4150   2.0777  -0.5062
 9TV  H7   H  HCR6  0   0.278   8.7152   0.2807  -2.0604
 9TV  H8   H  HCH2  0   0.241  -6.9470  -1.5578  -0.6108
 9TV  H9   H  HCH2  0   0.246  -6.5291  -1.7396   1.0728
 9TV  H10  H  HCH2  0   0.241  -7.1513   2.5038   0.7885
 9TV  H11  H  HCH2  0   0.246  -7.0799   2.6780  -0.9455
 9TV  H12  H  HCH2  0   0.236  -8.8768  -0.8775   0.6601
 9TV  H13  H  HCH2  0   0.221  -7.9269   0.1617   1.7065
 9TV  H14  H  HCR5  0   0.274  -0.3561   1.1696  -0.0658
 9TV  H15  H  HNR5  0   0.422   0.0043  -3.0033  -0.0734
 9TV  H16  H  HCR6  0   0.237  -4.1891  -1.7372   0.2894
 9TV  H17  H  HCR6  0   0.244  -4.6384   3.0881  -0.5290
 9TV  H18  H  HCR6  0   0.283   9.9409  -0.5855  -0.0452
 9TV  H19  H  HCR6  0   0.278   8.6568  -0.6516   2.1153
 9TV  H20  H  HCH2  0   0.235  -9.1435   1.4711  -0.0754
 9TV  H21  H  HCH2  0   0.221  -8.2582   0.5804  -1.2986

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
 9TV  C23  C21  single    1.523  0.020  1.523
 9TV  C23  C22  single    1.522  0.020  1.522
 9TV  C21  C14  single    1.508  0.020  1.508
 9TV  C14  C16  aromatic  1.395  0.020  1.395
 9TV  C14  C10  aromatic  1.398  0.020  1.398
 9TV  C16  C15  aromatic  1.383  0.020  1.383
 9TV  C22  C20  single    1.522  0.020  1.522
 9TV  C20  C10  single    1.509  0.020  1.509
 9TV  C10  C8   aromatic  1.392  0.020  1.392
 9TV  C15  C5   aromatic  1.396  0.020  1.396
 9TV  C8   C5   aromatic  1.392  0.020  1.392
 9TV  C5   C1   single    1.466  0.020  1.466
 9TV  C1   C    aromatic  1.413  0.020  1.413
 9TV  C1   N3   aromatic  1.321  0.020  1.321
 9TV  C    C2   aromatic  1.379  0.020  1.379
 9TV  O    C6   double    1.214  0.020  1.214
 9TV  N3   N    aromatic  1.332  0.020  1.332
 9TV  C2   N    aromatic  1.346  0.020  1.346
 9TV  C2   N4   single    1.380  0.020  1.380
 9TV  C6   N4   single    1.363  0.020  1.363
 9TV  C6   C9   single    1.511  0.020  1.511
 9TV  C11  C9   single    1.526  0.020  1.526
 9TV  C11  C7   single    1.499  0.020  1.499
 9TV  N12  C7   aromatic  1.329  0.020  1.329
 9TV  N12  C19  aromatic  1.327  0.020  1.327
 9TV  C7   N13  aromatic  1.329  0.020  1.329
 9TV  C19  C17  aromatic  1.384  0.020  1.384
 9TV  N13  C18  aromatic  1.327  0.020  1.327
 9TV  C17  C18  aromatic  1.384  0.020  1.384
 9TV  N4   H1   single    0.860  0.020  1.020
 9TV  C9   H2   single    0.970  0.020  1.090
 9TV  C9   H3   single    0.970  0.020  1.090
 9TV  C11  H4   single    0.970  0.020  1.090
 9TV  C11  H5   single    0.970  0.020  1.090
 9TV  C15  H6   single    0.930  0.020  1.080
 9TV  C18  H7   single    0.930  0.020  1.080
 9TV  C20  H8   single    0.970  0.020  1.090
 9TV  C20  H9   single    0.970  0.020  1.090
 9TV  C21  H10  single    0.970  0.020  1.090
 9TV  C21  H11  single    0.970  0.020  1.090
 9TV  C22  H12  single    0.970  0.020  1.090
 9TV  C22  H13  single    0.970  0.020  1.090
 9TV  C    H14  single    0.930  0.020  1.080
 9TV  N    H15  single    0.860  0.020  1.020
 9TV  C8   H16  single    0.930  0.020  1.080
 9TV  C16  H17  single    0.930  0.020  1.080
 9TV  C17  H18  single    0.930  0.020  1.080
 9TV  C19  H19  single    0.930  0.020  1.080
 9TV  C23  H20  single    0.970  0.020  1.090
 9TV  C23  H21  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
 9TV  N    C2   C    106.45  3.000
 9TV  N    C2   N4   120.01  3.000
 9TV  C    C2   N4   133.53  3.000
 9TV  H1   N4   C6   117.69  3.000
 9TV  H1   N4   C2   117.08  3.000
 9TV  C6   N4   C2   125.22  3.000
 9TV  C8   C5   C1   121.05  3.000
 9TV  C1   C5   C15  120.86  3.000
 9TV  C8   C5   C15  118.09  3.000
 9TV  N13  C7   N12  125.18  3.000
 9TV  N13  C7   C11  117.34  3.000
 9TV  N12  C7   C11  117.45  3.000
 9TV  H3   C9   H2   106.11  3.000
 9TV  H3   C9   C6   109.16  3.000
 9TV  H2   C9   C6   108.19  3.000
 9TV  H3   C9   C11  110.29  3.000
 9TV  H2   C9   C11  110.09  3.000
 9TV  C6   C9   C11  112.76  3.000
 9TV  C14  C10  C8   119.36  3.000
 9TV  C8   C10  C20  119.23  3.000
 9TV  C14  C10  C20  121.41  3.000
 9TV  H5   C11  H4   108.30  3.000
 9TV  H5   C11  C9   110.09  3.000
 9TV  H4   C11  C9   109.92  3.000
 9TV  H5   C11  C7   109.24  3.000
 9TV  H4   C11  C7   109.40  3.000
 9TV  C9   C11  C7   109.86  3.000
 9TV  H6   C15  C16  119.34  3.000
 9TV  H6   C15  C5   120.48  3.000
 9TV  C16  C15  C5   120.18  3.000
 9TV  H7   C18  C17  120.95  3.000
 9TV  H7   C18  N13  116.81  3.000
 9TV  C17  C18  N13  122.24  3.000
 9TV  H9   C20  H8   105.71  3.000
 9TV  H9   C20  C22  110.51  3.000
 9TV  H8   C20  C22  109.09  3.000
 9TV  H9   C20  C10  109.61  3.000
 9TV  H8   C20  C10  108.63  3.000
 9TV  C22  C20  C10  113.02  3.000
 9TV  H11  C21  H10  105.67  3.000
 9TV  H11  C21  C23  110.39  3.000
 9TV  H10  C21  C23  109.25  3.000
 9TV  H11  C21  C14  109.50  3.000
 9TV  H10  C21  C14  108.56  3.000
 9TV  C23  C21  C14  113.17  3.000
 9TV  H13  C22  H12  106.72  3.000
 9TV  H13  C22  C23  109.43  3.000
 9TV  H12  C22  C23  110.87  3.000
 9TV  H13  C22  C20  109.99  3.000
 9TV  H12  C22  C20  109.70  3.000
 9TV  C23  C22  C20  110.07  3.000
 9TV  H14  C    C1   127.99  3.000
 9TV  H14  C    C2   127.85  3.000
 9TV  C1   C    C2   104.15  3.000
 9TV  H15  N    N3   119.61  3.000
 9TV  H15  N    C2   127.47  3.000
 9TV  N3   N    C2   112.92  3.000
 9TV  N3   C1   C    111.29  3.000
 9TV  N3   C1   C5   121.20  3.000
 9TV  C    C1   C5   127.51  3.000
 9TV  C1   N3   N    105.18  3.000
 9TV  O    C6   C9   123.75  3.000
 9TV  C9   C6   N4   113.55  3.000
 9TV  O    C6   N4   122.70  3.000
 9TV  H16  C8   C10  118.67  3.000
 9TV  H16  C8   C5   119.20  3.000
 9TV  C10  C8   C5   122.13  3.000
 9TV  C19  N12  C7   117.13  3.000
 9TV  C18  N13  C7   117.14  3.000
 9TV  C16  C14  C21  119.70  3.000
 9TV  C16  C14  C10  118.53  3.000
 9TV  C21  C14  C10  121.76  3.000
 9TV  H17  C16  C14  119.09  3.000
 9TV  H17  C16  C15  119.20  3.000
 9TV  C14  C16  C15  121.72  3.000
 9TV  H18  C17  C19  122.01  3.000
 9TV  H18  C17  C18  121.93  3.000
 9TV  C19  C17  C18  116.06  3.000
 9TV  H19  C19  C17  120.97  3.000
 9TV  H19  C19  N12  116.79  3.000
 9TV  C17  C19  N12  122.24  3.000
 9TV  H21  C23  H20  106.62  3.000
 9TV  H21  C23  C22  109.25  3.000
 9TV  H20  C23  C22  110.95  3.000
 9TV  H21  C23  C21  109.90  3.000
 9TV  H20  C23  C21  109.76  3.000
 9TV  C22  C23  C21  110.29  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
 9TV  CONST_01  C5   C1   C    C2    180.00   0.0  0
 9TV  CONST_02  N3   C1   C    C2      0.00   0.0  0
 9TV  CONST_03  C1   N3   N    C2      0.00   0.0  0
 9TV  CONST_04  C14  C16  C15  C5      0.00   0.0  0
 9TV  CONST_05  C14  C10  C8   C5      0.00   0.0  0
 9TV  CONST_06  N    N3   C1   C5    180.00   0.0  0
 9TV  CONST_07  C17  C19  N12  C7      0.00   0.0  0
 9TV  CONST_08  C17  C18  N13  C7      0.00   0.0  0
 9TV  CONST_09  C15  C16  C14  C10     0.00   0.0  0
 9TV  CONST_10  C15  C5   C8   C10     0.00   0.0  0
 9TV  CONST_11  C1   C5   C8   C10   180.00   0.0  0
 9TV  CONST_12  C    C1   C5   C15     0.00   0.0  0
 9TV  CONST_13  N3   C1   C5   C15   180.00   0.0  0
 9TV  CONST_14  N12  C7   N13  C18     0.00   0.0  0
 9TV  CONST_15  N12  C19  C17  C18     0.00   0.0  0
 9TV  CONST_16  C8   C5   C1   C     180.00   0.0  0
 9TV  CONST_17  N    N3   C1   C       0.00   0.0  0
 9TV  CONST_18  N3   N    C2   C       0.00   0.0  0
 9TV  CONST_19  C1   C    C2   N       0.00   0.0  0
 9TV  CONST_20  C16  C15  C5   C1    180.00   0.0  0
 9TV  CONST_21  C8   C5   C1   N3      0.00   0.0  0
 9TV  CONST_22  C16  C14  C10  C8      0.00   0.0  0
 9TV  CONST_23  C16  C15  C5   C8      0.00   0.0  0
 9TV  CONST_24  C19  N12  C7   N13     0.00   0.0  0
 9TV  CONST_25  C19  C17  C18  N13     0.00   0.0  0
 9TV  CONST_26  C1   C    C2   N4    180.00   0.0  0
 9TV  CONST_27  N3   N    C2   N4    180.00   0.0  0
 9TV  CONST_28  C19  N12  C7   C11   180.00   0.0  0
 9TV  CONST_29  C18  N13  C7   C11   180.00   0.0  0
 9TV  CONST_30  H17  C16  C15  C5    180.00   0.0  0
 9TV  CONST_31  H14  C    C1   C5      0.00   0.0  0
 9TV  CONST_32  H19  C19  N12  C7    180.00   0.0  0
 9TV  CONST_33  H7   C18  N13  C7    180.00   0.0  0
 9TV  CONST_34  H16  C8   C5   C15   180.00   0.0  0
 9TV  CONST_35  H15  N    C2   C     180.00   0.0  0
 9TV  CONST_36  H6   C15  C5   C1      0.00   0.0  0
 9TV  CONST_37  H18  C17  C19  N12   180.00   0.0  0
 9TV  CONST_38  C6   N4   C2   C       0.00   0.0  0
 9TV  CONST_39  C6   N4   C2   N     180.00   0.0  0
 9TV  CONST_40  H1   N4   C2   C     180.00   0.0  0
 9TV  CONST_41  O    C6   N4   C2      0.00   0.0  0
 9TV  CONST_42  C9   C6   N4   C2    180.00   0.0  0
 9TV  Var_01    C23  C21  C14  C10   -16.48  30.0  1
 9TV  Var_02    C23  C22  C20  C10    48.20  30.0  1
 9TV  Var_03    C21  C23  C22  C20   -63.37  30.0  1
 9TV  Var_04    C14  C21  C23  C22    46.61  30.0  1
 9TV  Var_05    C14  C10  C20  C22   -18.13  30.0  1
 9TV  Var_06    N12  C7   C11  C9    -87.41  30.0  2
 9TV  Var_07    C6   C9   C11  C7   -178.44  30.0  3
 9TV  Var_08    C11  C9   C6   N4   -173.11  30.0  3

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
 9TV  plan-1  C2   0.020
 9TV  plan-1  N4   0.020
 9TV  plan-1  C5   0.020
 9TV  plan-1  C    0.020
 9TV  plan-1  N    0.020
 9TV  plan-1  C1   0.020
 9TV  plan-1  N3   0.020
 9TV  plan-1  H14  0.020
 9TV  plan-1  H15  0.020
 9TV  plan-2  C7   0.020
 9TV  plan-2  C11  0.020
 9TV  plan-2  C18  0.020
 9TV  plan-2  N12  0.020
 9TV  plan-2  N13  0.020
 9TV  plan-2  C17  0.020
 9TV  plan-2  C19  0.020
 9TV  plan-2  H7   0.020
 9TV  plan-2  H18  0.020
 9TV  plan-2  H19  0.020
 9TV  plan-3  C5   0.020
 9TV  plan-3  C10  0.020
 9TV  plan-3  C15  0.020
 9TV  plan-3  C20  0.020
 9TV  plan-3  C21  0.020
 9TV  plan-3  C1   0.020
 9TV  plan-3  C8   0.020
 9TV  plan-3  C14  0.020
 9TV  plan-3  C16  0.020
 9TV  plan-3  H6   0.020
 9TV  plan-3  H16  0.020
 9TV  plan-3  H17  0.020
 9TV  plan-4  C2   0.020
 9TV  plan-4  N4   0.020
 9TV  plan-4  C9   0.020
 9TV  plan-4  O    0.020
 9TV  plan-4  C6   0.020
 9TV  plan-4  H1   0.020

