# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:11:24 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-(4-bromophenyl)piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1(CCNCC1)c2ccc(Br)cc2
#
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
 UMK  UMK  4-(4-bromophenyl)piperidin-4-ol  ligand  28  14  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UMK
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
 UMK  BR    BR  BR    0  -0.055  -3.8876  -0.2099   0.0024
 UMK  C8    C   CR6   0  -0.128  -2.0075  -0.0238  -0.0484
 UMK  C7    C   CR16  0  -0.207  -1.4446   1.0962  -0.6354
 UMK  C6    C   CR16  0  -0.327  -0.0611   1.2236  -0.6688
 UMK  C9    C   CR16  0  -0.212  -1.2058  -1.0134   0.5019
 UMK  C10   C   CR16  0  -0.307   0.1715  -0.8648   0.4615
 UMK  C5    C   CR6   0   0.138   0.7702   0.2540  -0.1182
 UMK  C     C   CT    0   0.167   2.2866   0.3848  -0.1647
 UMK  O     O   OH1   0  -0.671   2.6707   1.6108  -0.7516
 UMK  C4    C   CH2   0  -0.439   2.8740  -0.7170  -1.0563
 UMK  C3    C   CH2   0  -0.315   4.4013  -0.7282  -1.0131
 UMK  N     N   NH1   0  -0.578   4.9522  -0.8094   0.3299
 UMK  C2    C   CH2   0  -0.310   4.4180   0.2264   1.1982
 UMK  C1    C   CH2   0  -0.471   2.8910   0.2659   1.2437
 UMK  H7    H   HCR6  0   0.276  -2.0624   1.8712  -1.0694
 UMK  H9    H   HCR6  0   0.278  -1.6373  -1.8940   0.9582
 UMK  H6    H   HCR6  0   0.257   0.3581   2.1009  -1.1410
 UMK  H10   H   HCR6  0   0.259   0.7785  -1.6505   0.8942
 UMK  H     H   HOH1  0   0.449   2.5219   2.3220  -0.1182
 UMK  H41C  H   HCH2  0   0.233   2.4958  -1.6855  -0.7169
 UMK  H42C  H   HCH2  0   0.238   2.5217  -0.5845  -2.0837
 UMK  H11C  H   HCH2  0   0.241   2.5471   1.0995   1.8657
 UMK  H12C  H   HCH2  0   0.233   2.5282  -0.6457   1.7258
 UMK  H31C  H   HCH2  0   0.236   4.7744  -1.5740  -1.5943
 UMK  H32C  H   HCH2  0   0.222   4.7935   0.1733  -1.4918
 UMK  HA    H   HNH1  0   0.338   4.7258  -1.7163   0.7229
 UMK  H21C  H   HCH2  0   0.237   4.8057   0.0718   2.2072
 UMK  H22C  H   HCH2  0   0.219   4.8076   1.1928   0.8650

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
 UMK  BR   C8    single    1.890  0.020  1.890
 UMK  C8   C7    aromatic  1.384  0.020  1.384
 UMK  C8   C9    aromatic  1.387  0.020  1.387
 UMK  C7   C6    aromatic  1.390  0.020  1.390
 UMK  C6   C5    aromatic  1.391  0.020  1.391
 UMK  C9   C10   aromatic  1.386  0.020  1.386
 UMK  C10  C5    aromatic  1.395  0.020  1.395
 UMK  C5   C     single    1.523  0.020  1.523
 UMK  C    O     single    1.413  0.020  1.413
 UMK  C    C4    single    1.534  0.020  1.534
 UMK  C    C1    single    1.537  0.020  1.537
 UMK  C4   C3    single    1.528  0.020  1.528
 UMK  C3   N     single    1.454  0.020  1.454
 UMK  N    C2    single    1.453  0.020  1.453
 UMK  C2   C1    single    1.528  0.020  1.528
 UMK  C7   H7    single    0.930  0.020  1.080
 UMK  C9   H9    single    0.930  0.020  1.080
 UMK  C6   H6    single    0.930  0.020  1.080
 UMK  C10  H10   single    0.930  0.020  1.080
 UMK  O    H     single    0.850  0.020  0.980
 UMK  C4   H41C  single    0.970  0.020  1.090
 UMK  C4   H42C  single    0.970  0.020  1.090
 UMK  C1   H11C  single    0.970  0.020  1.090
 UMK  C1   H12C  single    0.970  0.020  1.090
 UMK  C3   H31C  single    0.970  0.020  1.090
 UMK  C3   H32C  single    0.970  0.020  1.090
 UMK  N    HA    single    0.890  0.020  1.040
 UMK  C2   H21C  single    0.970  0.020  1.090
 UMK  C2   H22C  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
 UMK  C9    C8   C7    120.69  3.000
 UMK  C9    C8   BR    119.60  3.000
 UMK  C7    C8   BR    119.71  3.000
 UMK  H7    C7   C6    119.55  3.000
 UMK  H7    C7   C8    121.17  3.000
 UMK  C6    C7   C8    119.29  3.000
 UMK  H6    C6   C5    120.46  3.000
 UMK  H6    C6   C7    118.10  3.000
 UMK  C5    C6   C7    121.44  3.000
 UMK  H9    C9   C10   119.74  3.000
 UMK  H9    C9   C8    121.16  3.000
 UMK  C10   C9   C8    119.10  3.000
 UMK  H10   C10  C5    120.48  3.000
 UMK  H10   C10  C9    117.87  3.000
 UMK  C5    C10  C9    121.64  3.000
 UMK  C     C5   C10   120.59  3.000
 UMK  C     C5   C6    121.55  3.000
 UMK  C10   C5   C6    117.84  3.000
 UMK  C1    C    C4    109.05  3.000
 UMK  C1    C    O     109.93  3.000
 UMK  C4    C    O     106.13  3.000
 UMK  C1    C    C5    110.91  3.000
 UMK  C4    C    C5    109.72  3.000
 UMK  O     C    C5    110.98  3.000
 UMK  H     O    C     108.99  3.000
 UMK  H42C  C4   H41C  106.69  3.000
 UMK  H42C  C4   C3    110.45  3.000
 UMK  H41C  C4   C3    109.29  3.000
 UMK  H42C  C4   C     109.60  3.000
 UMK  H41C  C4   C     108.85  3.000
 UMK  C3    C4   C     111.82  3.000
 UMK  H32C  C3   H31C  106.44  3.000
 UMK  H32C  C3   N     108.33  3.000
 UMK  H31C  C3   N     108.60  3.000
 UMK  H32C  C3   C4    109.88  3.000
 UMK  H31C  C3   C4    109.40  3.000
 UMK  N     C3   C4    113.91  3.000
 UMK  HA    N    C2    108.89  3.000
 UMK  HA    N    C3    108.87  3.000
 UMK  C2    N    C3    111.89  3.000
 UMK  H22C  C2   H21C  106.27  3.000
 UMK  H22C  C2   C1    110.01  3.000
 UMK  H21C  C2   C1    109.33  3.000
 UMK  H22C  C2   N     108.46  3.000
 UMK  H21C  C2   N     108.70  3.000
 UMK  C1    C2   N     113.80  3.000
 UMK  H12C  C1   H11C  106.26  3.000
 UMK  H12C  C1   C2    108.85  3.000
 UMK  H11C  C1   C2    110.50  3.000
 UMK  H12C  C1   C     109.76  3.000
 UMK  H11C  C1   C     109.75  3.000
 UMK  C2    C1   C     111.57  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
 UMK  CONST_01  C5   C6   C7   C8    0.00   0.0  0
 UMK  CONST_02  C5   C10  C9   C8    0.00   0.0  0
 UMK  CONST_03  C10  C9   C8   C7    0.00   0.0  0
 UMK  CONST_04  C10  C5   C6   C7    0.00   0.0  0
 UMK  CONST_05  C9   C8   C7   C6    0.00   0.0  0
 UMK  CONST_06  C9   C10  C5   C6    0.00   0.0  0
 UMK  CONST_07  C    C5   C6   C7  180.00   0.0  0
 UMK  CONST_08  C    C5   C10  C9  180.00   0.0  0
 UMK  CONST_09  C6   C7   C8   BR  180.00   0.0  0
 UMK  CONST_10  C10  C9   C8   BR  180.00   0.0  0
 UMK  CONST_11  H6   C6   C7   C8  180.00   0.0  0
 UMK  CONST_12  H10  C10  C9   C8  180.00   0.0  0
 UMK  CONST_13  H9   C9   C8   C7  180.00   0.0  0
 UMK  CONST_14  H7   C7   C8   C9  180.00   0.0  0
 UMK  Var_01    N    C3   C4   C    53.72  30.0  1
 UMK  Var_02    N    C2   C1   C   -54.34  30.0  1
 UMK  Var_03    C2   N    C3   C4  -53.31  30.0  1
 UMK  Var_04    C1   C2   N    C3   53.67  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
 UMK  chir_01  C  C5  C4  C1  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
 UMK  plan-1  BR   0.020
 UMK  plan-1  C8   0.020
 UMK  plan-1  C7   0.020
 UMK  plan-1  C6   0.020
 UMK  plan-1  C9   0.020
 UMK  plan-1  C10  0.020
 UMK  plan-1  C5   0.020
 UMK  plan-1  C    0.020
 UMK  plan-1  H7   0.020
 UMK  plan-1  H9   0.020
 UMK  plan-1  H6   0.020
 UMK  plan-1  H10  0.020

