# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:49:19 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 1-(phenylmethyl)-4-pyrrol-1-yl-piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCC1n2cccc2)Cc3ccccc3
#
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
 AXG  AXG  1-(phenylmethyl)-4-pyrrol-1-yl-piperidine  ligand  38  18  .  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_AXG
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
 AXG  N1   N  NR6   0  -0.413  -0.6901   0.9209   0.0047
 AXG  C4   C  CR6   0   0.079  -3.0968   0.4146   0.1699
 AXG  C5   C  CR16  0  -0.283  -3.1359  -0.4135  -0.9509
 AXG  C6   C  CR16  0  -0.242  -4.1665  -1.3269  -1.1189
 AXG  C7   C  CH2   0  -0.315  -2.0022   1.4373   0.3349
 AXG  C8   C  C     0  -0.285   0.2898   1.9894  -0.0718
 AXG  C10  C  CR16  0  -0.090   2.1280   0.3679   0.3920
 AXG  C13  C  CR15  0  -0.060   4.5631  -0.0839   0.7110
 AXG  C15  C  CR15  0  -0.371   5.0042  -1.1619  -1.2049
 AXG  C1   C  CR16  0  -0.271  -5.1770  -1.4262  -0.1687
 AXG  C2   C  CR16  0  -0.241  -5.1444  -0.6082   0.9514
 AXG  C3   C  CR16  0  -0.314  -4.1073   0.3023   1.1186
 AXG  C9   C  C     0  -0.432   1.6374   1.4663  -0.5435
 AXG  C11  C  C     0  -0.430   1.0644  -0.7172   0.5122
 AXG  C12  C  C     0  -0.283  -0.2631  -0.1079   0.9360
 AXG  N2   N  NR5   0  -0.407   3.4154  -0.1667  -0.0177
 AXG  C14  C  CR15  0  -0.378   5.5725  -0.6919   0.0055
 AXG  C16  C  CR15  0  -0.064   3.6739  -0.8205  -1.1853
 AXG  H2   H  HCR6  0   0.244  -2.3452  -0.3458  -1.6878
 AXG  H3   H  HCR6  0   0.252  -4.1820  -1.9645  -1.9939
 AXG  H4   H  HCH2  0   0.210  -2.0388   1.8476   1.3587
 AXG  H5   H  HCH2  0   0.252  -2.2075   2.2791  -0.3346
 AXG  H6   H  H     0   0.244  -0.0718   2.7498  -0.7676
 AXG  H7   H  H     0   0.192   0.4158   2.4904   0.9049
 AXG  H8   H  HCR6  0   0.248   2.2885   0.8053   1.3820
 AXG  H9   H  HCR5  0   0.270   4.5724   0.4036   1.6729
 AXG  H10  H  HCR5  0   0.237   5.5083  -1.6897  -1.9994
 AXG  H11  H  HCR6  0   0.253  -5.9810  -2.1388  -0.3007
 AXG  H12  H  HCR6  0   0.253  -5.9213  -0.6821   1.7016
 AXG  H13  H  HCR6  0   0.247  -4.0854   0.9320   2.0006
 AXG  H14  H  H     0   0.229   1.5380   1.0736  -1.5595
 AXG  H15  H  H     0   0.247   2.3595   2.2846  -0.5766
 AXG  H16  H  H     0   0.228   0.9364  -1.2225  -0.4494
 AXG  H17  H  H     0   0.246   1.3713  -1.4701   1.2409
 AXG  H18  H  H     0   0.194  -0.1732   0.2951   1.9615
 AXG  H19  H  H     0   0.249  -1.0203  -0.8928   0.9758
 AXG  H20  H  HCR5  0   0.237   6.5989  -0.7868   0.3237
 AXG  H21  H  HCR5  0   0.269   2.9012  -0.9929  -1.9175

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
 AXG  C15  C14  aromatic  1.417  0.020  1.417
 AXG  C15  C16  aromatic  1.374  0.020  1.374
 AXG  C14  C13  aromatic  1.373  0.020  1.373
 AXG  C16  N2   aromatic  1.363  0.020  1.363
 AXG  C13  N2   aromatic  1.362  0.020  1.362
 AXG  N2   C10  single    1.453  0.020  1.453
 AXG  C10  C11  single    1.524  0.020  1.524
 AXG  C10  C9   single    1.524  0.020  1.524
 AXG  C11  C12  single    1.521  0.020  1.521
 AXG  C9   C8   single    1.521  0.020  1.521
 AXG  C12  N1   single    1.452  0.020  1.452
 AXG  C8   N1   single    1.452  0.020  1.452
 AXG  N1   C7   single    1.448  0.020  1.448
 AXG  C7   C4   single    1.507  0.020  1.507
 AXG  C4   C3   aromatic  1.391  0.020  1.391
 AXG  C4   C5   aromatic  1.394  0.020  1.394
 AXG  C3   C2   aromatic  1.390  0.020  1.390
 AXG  C5   C6   aromatic  1.387  0.020  1.387
 AXG  C2   C1   aromatic  1.387  0.020  1.387
 AXG  C6   C1   aromatic  1.391  0.020  1.391
 AXG  C5   H2   single    0.930  0.020  1.080
 AXG  C6   H3   single    0.930  0.020  1.080
 AXG  C7   H4   single    0.970  0.020  1.090
 AXG  C7   H5   single    0.970  0.020  1.090
 AXG  C8   H6   single    0.970  0.020  1.090
 AXG  C8   H7   single    0.970  0.020  1.090
 AXG  C10  H8   single    0.970  0.020  1.090
 AXG  C13  H9   single    0.930  0.020  1.080
 AXG  C15  H10  single    0.930  0.020  1.080
 AXG  C1   H11  single    0.930  0.020  1.080
 AXG  C2   H12  single    0.930  0.020  1.080
 AXG  C3   H13  single    0.930  0.020  1.080
 AXG  C9   H14  single    0.970  0.020  1.090
 AXG  C9   H15  single    0.970  0.020  1.090
 AXG  C11  H16  single    0.970  0.020  1.090
 AXG  C11  H17  single    0.970  0.020  1.090
 AXG  C12  H18  single    0.970  0.020  1.090
 AXG  C12  H19  single    0.970  0.020  1.090
 AXG  C14  H20  single    0.930  0.020  1.080
 AXG  C16  H21  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
 AXG  C12  N1   C8   110.90  3.000
 AXG  C8   N1   C7   111.17  3.000
 AXG  C12  N1   C7   111.89  3.000
 AXG  C3   C4   C7   120.52  3.000
 AXG  C3   C4   C5   118.70  3.000
 AXG  C7   C4   C5   120.76  3.000
 AXG  H2   C5   C6   120.08  3.000
 AXG  H2   C5   C4   119.30  3.000
 AXG  C6   C5   C4   120.61  3.000
 AXG  H3   C6   C1   119.98  3.000
 AXG  H3   C6   C5   119.75  3.000
 AXG  C1   C6   C5   120.27  3.000
 AXG  H5   C7   H4   105.97  3.000
 AXG  H5   C7   C4   108.58  3.000
 AXG  H4   C7   C4   109.26  3.000
 AXG  H5   C7   N1   107.73  3.000
 AXG  H4   C7   N1   111.97  3.000
 AXG  C4   C7   N1   113.02  3.000
 AXG  H7   C8   H6   106.57  3.000
 AXG  H7   C8   C9   109.21  3.000
 AXG  H6   C8   C9   109.59  3.000
 AXG  H7   C8   N1   111.36  3.000
 AXG  H6   C8   N1   108.82  3.000
 AXG  C9   C8   N1   111.18  3.000
 AXG  H8   C10  N2   105.80  3.000
 AXG  H8   C10  C11  108.40  3.000
 AXG  N2   C10  C11  112.24  3.000
 AXG  H8   C10  C9   108.33  3.000
 AXG  C11  C10  C9   109.69  3.000
 AXG  N2   C10  C9   112.17  3.000
 AXG  H9   C13  C14  130.69  3.000
 AXG  H9   C13  N2   120.79  3.000
 AXG  C14  C13  N2   108.52  3.000
 AXG  H10  C15  C16  125.78  3.000
 AXG  H10  C15  C14  127.14  3.000
 AXG  C16  C15  C14  107.08  3.000
 AXG  H11  C1   C2   120.27  3.000
 AXG  H11  C1   C6   120.23  3.000
 AXG  C2   C1   C6   119.50  3.000
 AXG  H12  C2   C3   119.79  3.000
 AXG  H12  C2   C1   120.16  3.000
 AXG  C3   C2   C1   120.05  3.000
 AXG  H13  C3   C2   119.57  3.000
 AXG  H13  C3   C4   119.57  3.000
 AXG  C2   C3   C4   120.86  3.000
 AXG  H15  C9   H14  107.52  3.000
 AXG  H15  C9   C10  110.23  3.000
 AXG  H14  C9   C10  109.92  3.000
 AXG  H15  C9   C8   109.74  3.000
 AXG  H14  C9   C8   109.34  3.000
 AXG  C10  C9   C8   110.05  3.000
 AXG  H17  C11  H16  107.53  3.000
 AXG  H17  C11  C12  109.61  3.000
 AXG  H16  C11  C12  109.14  3.000
 AXG  H17  C11  C10  110.33  3.000
 AXG  H16  C11  C10  109.95  3.000
 AXG  C12  C11  C10  110.23  3.000
 AXG  H19  C12  H18  106.54  3.000
 AXG  H19  C12  C11  109.12  3.000
 AXG  H18  C12  C11  109.48  3.000
 AXG  H19  C12  N1   109.21  3.000
 AXG  H18  C12  N1   111.14  3.000
 AXG  C11  C12  N1   111.21  3.000
 AXG  C16  N2   C13  109.13  3.000
 AXG  C13  N2   C10  124.99  3.000
 AXG  C16  N2   C10  125.88  3.000
 AXG  H20  C14  C15  127.17  3.000
 AXG  H20  C14  C13  125.92  3.000
 AXG  C15  C14  C13  106.90  3.000
 AXG  H21  C16  N2   121.50  3.000
 AXG  H21  C16  C15  130.13  3.000
 AXG  N2   C16  C15  108.37  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
 AXG  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 AXG  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 AXG  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 AXG  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 AXG  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 AXG  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 AXG  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 AXG  CONST_08  C15  C16  N2   C13    0.00   0.0  0
 AXG  CONST_09  N2   C13  C14  C15    0.00   0.0  0
 AXG  CONST_10  C14  C15  C16  N2     0.00   0.0  0
 AXG  CONST_11  C16  N2   C13  C14    0.00   0.0  0
 AXG  CONST_12  C15  C16  N2   C10  180.00   0.0  0
 AXG  CONST_13  C14  C13  N2   C10  180.00   0.0  0
 AXG  CONST_14  C7   C4   C5   C6   180.00   0.0  0
 AXG  CONST_15  C2   C3   C4   C7   180.00   0.0  0
 AXG  CONST_16  H12  C2   C3   C4   180.00   0.0  0
 AXG  CONST_17  H3   C6   C5   C4   180.00   0.0  0
 AXG  CONST_18  H13  C3   C4   C5   180.00   0.0  0
 AXG  CONST_19  H11  C1   C6   C5   180.00   0.0  0
 AXG  CONST_20  H21  C16  N2   C10    0.00   0.0  0
 AXG  CONST_21  H9   C13  N2   C10    0.00   0.0  0
 AXG  CONST_22  H10  C15  C14  C13  180.00   0.0  0
 AXG  CONST_23  H2   C5   C6   C1   180.00   0.0  0
 AXG  CONST_24  H20  C14  C13  N2   180.00   0.0  0
 AXG  Var_01    C10  C11  C12  N1    57.11  30.0  1
 AXG  Var_02    C10  C9   C8   N1   -57.60  30.0  1
 AXG  Var_03    C11  C12  N1   C8   -59.80  30.0  1
 AXG  Var_04    C12  N1   C8   C9    60.09  30.0  1
 AXG  Var_05    C3   C4   C7   N1   137.71  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
 AXG  chir_01  C10  N2  C11  C9  positiv

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
 AXG  plan-1  C10  0.020
 AXG  plan-1  C13  0.020
 AXG  plan-1  C15  0.020
 AXG  plan-1  N2   0.020
 AXG  plan-1  C14  0.020
 AXG  plan-1  C16  0.020
 AXG  plan-1  H9   0.020
 AXG  plan-1  H10  0.020
 AXG  plan-1  H20  0.020
 AXG  plan-1  H21  0.020
 AXG  plan-2  C4   0.020
 AXG  plan-2  C5   0.020
 AXG  plan-2  C6   0.020
 AXG  plan-2  C7   0.020
 AXG  plan-2  C1   0.020
 AXG  plan-2  C2   0.020
 AXG  plan-2  C3   0.020
 AXG  plan-2  H2   0.020
 AXG  plan-2  H3   0.020
 AXG  plan-2  H11  0.020
 AXG  plan-2  H12  0.020
 AXG  plan-2  H13  0.020

