# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 03:16:30 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (5-chloro-2,4-dihydroxyphenyl)[(2R)-2-(2-methylphenyl)pyrrolidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1[C@H]2CCCN2C(=O)c3cc(Cl)c(O)cc3O
#
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
 4CD  4CD  (5-chloro-2,4-dihydroxyphenyl)[(2R)-2-(2-methylphenyl)pyrrolidin-1-yl]methanone  ligand  41  23  .  2022-07-23  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_4CD
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
 4CD  N1    N   NR5   0  -0.478  -0.7880   0.4908  -0.8499
 4CD  C4    C   CR15  0  -0.128  -2.2316   0.5878  -1.0695
 4CD  C5    C   CR6   0   0.130  -3.0319   0.3188   0.1820
 4CD  C6    C   CR16  0  -0.296  -2.6155   0.8772   1.3873
 4CD  C7    C   CR16  0  -0.262  -3.3353   0.6861   2.5568
 4CD  C8    C   CR16  0  -0.258  -4.4977  -0.0710   2.5260
 4CD  C10   C   CR6   0   0.050  -4.2049  -0.4422   0.1445
 4CD  C13   C   CR16  0  -0.194   1.7399   0.1153   0.7472
 4CD  C15   C   CR6   0   0.444   3.9433  -0.7931   0.4179
 4CD  C17   C   CR6   0   0.378   2.0897  -1.5614  -0.9312
 4CD  C1    C   CH2   0  -0.469  -2.4078   2.0166  -1.6030
 4CD  C2    C   CH2   0  -0.470  -1.0721   2.3207  -2.2692
 4CD  C3    C   CH2   0  -0.271  -0.0724   1.6764  -1.3184
 4CD  C9    C   CR16  0  -0.299  -4.9222  -0.6232   1.3265
 4CD  C11   C   CH3   0  -0.756  -4.6991  -1.0683  -1.1290
 4CD  C12   C   CR6   0  -0.206   1.2254  -0.6946  -0.2571
 4CD  C14   C   CR6   0  -0.170   3.0763   0.0695   1.0900
 4CD  C16   C   CR16  0  -0.522   3.4384  -1.6000  -0.5951
 4CD  O2    O   OH1   0  -0.606   5.2289  -0.8032   0.7807
 4CD  C18   C   C     0   0.532  -0.2416  -0.6967  -0.5354
 4CD  O3    O   O     0  -0.475  -0.9072  -1.7178  -0.4330
 4CD  CL1   CL  CL    0  -0.114   3.6933   1.0736   2.3558
 4CD  H4    H   HCR5  0   0.269  -2.5111  -0.1241  -1.8505
 4CD  H6    H   HCR6  0   0.242  -1.7090   1.4721   1.4146
 4CD  H7    H   HCR6  0   0.250  -2.9907   1.1257   3.4839
 4CD  H8    H   HCR6  0   0.250  -5.0723  -0.2308   3.4295
 4CD  H13   H   HCR6  0   0.283   1.0812   0.7835   1.2874
 4CD  H1    H   HCH2  0   0.261  -3.2602   2.0871  -2.2783
 4CD  H1A   H   HCH2  0   0.244  -2.5808   2.7102  -0.7765
 4CD  H2    H   HCH2  0   0.242  -1.0146   1.8489  -3.2522
 4CD  H2A   H   HCH2  0   0.255  -0.8901   3.3872  -2.3956
 4CD  H3    H   HCH2  0   0.240   0.1581   2.3504  -0.4883
 4CD  H3A   H   HCH2  0   0.263   0.8646   1.4060  -1.8019
 4CD  H9    H   HCR6  0   0.244  -5.8300  -1.2149   1.3054
 4CD  H11   H   HCH3  0   0.247  -3.9759  -1.7818  -1.5287
 4CD  H11A  H   HCH3  0   0.252  -5.6329  -1.6036  -0.9626
 4CD  H11B  H   HCH3  0   0.244  -4.8810  -0.3244  -1.9065
 4CD  H16   H   HCR6  0   0.297   4.1096  -2.2672  -1.1265
 4CD  HO1   H   HOH1  0   0.482   2.2698  -2.8534  -2.3243
 4CD  HO2   H   HOH1  0   0.486   5.7216  -1.4578   0.2718
 4CD  O1    O   OH1   0  -0.613   1.5809  -2.3182  -1.9134

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
 4CD  N1   C4    single    1.463  0.020  1.463
 4CD  N1   C3    single    1.462  0.020  1.462
 4CD  N1   C18   single    1.344  0.020  1.344
 4CD  C4   C5    single    1.510  0.020  1.510
 4CD  C4   C1    single    1.535  0.020  1.535
 4CD  C5   C6    aromatic  1.392  0.020  1.392
 4CD  C5   C10   aromatic  1.399  0.020  1.399
 4CD  C6   C7    aromatic  1.387  0.020  1.387
 4CD  C7   C8    aromatic  1.388  0.020  1.388
 4CD  C8   C9    aromatic  1.387  0.020  1.387
 4CD  C10  C9    aromatic  1.394  0.020  1.394
 4CD  C10  C11   single    1.503  0.020  1.503
 4CD  C13  C12   aromatic  1.389  0.020  1.389
 4CD  C13  C14   aromatic  1.380  0.020  1.380
 4CD  C15  C14   aromatic  1.395  0.020  1.395
 4CD  C15  C16   aromatic  1.390  0.020  1.390
 4CD  C15  O2    single    1.336  0.020  1.336
 4CD  C17  C12   aromatic  1.397  0.020  1.397
 4CD  C17  C16   aromatic  1.390  0.020  1.390
 4CD  C17  O1    single    1.340  0.020  1.340
 4CD  C1   C2    single    1.523  0.020  1.523
 4CD  C2   C3    single    1.523  0.020  1.523
 4CD  C12  C18   single    1.493  0.020  1.493
 4CD  C14  CL1   single    1.730  0.020  1.730
 4CD  C18  O3    double    1.223  0.020  1.223
 4CD  C4   H4    single    0.970  0.020  1.090
 4CD  C6   H6    single    0.930  0.020  1.080
 4CD  C7   H7    single    0.930  0.020  1.080
 4CD  C8   H8    single    0.930  0.020  1.080
 4CD  C13  H13   single    0.930  0.020  1.080
 4CD  C1   H1    single    0.970  0.020  1.090
 4CD  C1   H1A   single    0.970  0.020  1.090
 4CD  C2   H2    single    0.970  0.020  1.090
 4CD  C2   H2A   single    0.970  0.020  1.090
 4CD  C3   H3    single    0.970  0.020  1.090
 4CD  C3   H3A   single    0.970  0.020  1.090
 4CD  C9   H9    single    0.930  0.020  1.080
 4CD  C11  H11   single    0.970  0.020  1.090
 4CD  C11  H11A  single    0.970  0.020  1.090
 4CD  C11  H11B  single    0.970  0.020  1.090
 4CD  C16  H16   single    0.930  0.020  1.080
 4CD  O1   HO1   single    0.850  0.020  0.980
 4CD  O2   HO2   single    0.850  0.020  0.980

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
 4CD  C18   N1   C3    126.32  3.000
 4CD  C18   N1   C4    119.64  3.000
 4CD  C3    N1   C4    112.40  3.000
 4CD  H4    C4   C1    109.17  3.000
 4CD  H4    C4   C5    109.92  3.000
 4CD  C1    C4   C5    113.14  3.000
 4CD  H4    C4   N1    108.44  3.000
 4CD  C1    C4   N1    103.12  3.000
 4CD  C5    C4   N1    112.75  3.000
 4CD  C10   C5   C6    119.49  3.000
 4CD  C10   C5   C4    121.28  3.000
 4CD  C6    C5   C4    119.19  3.000
 4CD  H6    C6   C7    119.23  3.000
 4CD  H6    C6   C5    119.46  3.000
 4CD  C7    C6   C5    121.31  3.000
 4CD  H7    C7   C8    120.48  3.000
 4CD  H7    C7   C6    120.08  3.000
 4CD  C8    C7   C6    119.44  3.000
 4CD  H8    C8   C9    120.04  3.000
 4CD  H8    C8   C7    120.44  3.000
 4CD  C9    C8   C7    119.52  3.000
 4CD  C11   C10  C9    119.68  3.000
 4CD  C11   C10  C5    121.68  3.000
 4CD  C9    C10  C5    118.64  3.000
 4CD  H13   C13  C14   119.05  3.000
 4CD  H13   C13  C12   119.69  3.000
 4CD  C14   C13  C12   121.25  3.000
 4CD  O2    C15  C16   122.90  3.000
 4CD  O2    C15  C14   118.15  3.000
 4CD  C16   C15  C14   118.95  3.000
 4CD  O1    C17  C16   121.98  3.000
 4CD  O1    C17  C12   117.97  3.000
 4CD  C16   C17  C12   120.04  3.000
 4CD  H1A   C1   H1    107.69  3.000
 4CD  H1A   C1   C2    110.05  3.000
 4CD  H1    C1   C2    113.70  3.000
 4CD  H1A   C1   C4    110.24  3.000
 4CD  H1    C1   C4    111.43  3.000
 4CD  C2    C1   C4    103.72  3.000
 4CD  H2A   C2   H2    108.05  3.000
 4CD  H2A   C2   C3    112.15  3.000
 4CD  H2    C2   C3    110.17  3.000
 4CD  H2A   C2   C1    113.12  3.000
 4CD  H2    C2   C1    110.71  3.000
 4CD  C3    C2   C1    102.60  3.000
 4CD  H3A   C3   H3    107.98  3.000
 4CD  H3A   C3   C2    113.14  3.000
 4CD  H3    C3   C2    110.58  3.000
 4CD  H3A   C3   N1    111.24  3.000
 4CD  H3    C3   N1    111.08  3.000
 4CD  C2    C3   N1    102.82  3.000
 4CD  H9    C9   C10   119.03  3.000
 4CD  H9    C9   C8    119.37  3.000
 4CD  C10   C9   C8    121.60  3.000
 4CD  H11B  C11  H11A  107.52  3.000
 4CD  H11B  C11  H11   107.16  3.000
 4CD  H11A  C11  H11   107.63  3.000
 4CD  H11B  C11  C10   111.99  3.000
 4CD  H11A  C11  C10   110.93  3.000
 4CD  H11   C11  C10   111.39  3.000
 4CD  C18   C12  C17   121.12  3.000
 4CD  C18   C12  C13   119.97  3.000
 4CD  C17   C12  C13   118.78  3.000
 4CD  CL1   C14  C15   119.32  3.000
 4CD  CL1   C14  C13   120.52  3.000
 4CD  C15   C14  C13   120.16  3.000
 4CD  H16   C16  C17   119.91  3.000
 4CD  H16   C16  C15   119.27  3.000
 4CD  C17   C16  C15   120.82  3.000
 4CD  HO2   O2   C15   110.70  3.000
 4CD  O3    C18  C12   121.35  3.000
 4CD  O3    C18  N1    122.39  3.000
 4CD  C12   C18  N1    116.21  3.000
 4CD  HO1   O1   C17   110.77  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
 4CD  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 4CD  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 4CD  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 4CD  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 4CD  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 4CD  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 4CD  CONST_07  C16  C17  C12  C13    0.00   0.0  0
 4CD  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 4CD  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 4CD  CONST_10  C12  C17  C16  C15    0.00   0.0  0
 4CD  CONST_11  C14  C13  C12  C17    0.00   0.0  0
 4CD  CONST_12  C14  C15  C16  C17    0.00   0.0  0
 4CD  CONST_13  C7   C6   C5   C4   180.00   0.0  0
 4CD  CONST_14  C9   C10  C5   C4   180.00   0.0  0
 4CD  CONST_15  C11  C10  C5   C4     0.00   0.0  0
 4CD  CONST_16  C11  C10  C5   C6   180.00   0.0  0
 4CD  CONST_17  C11  C10  C9   C8   180.00   0.0  0
 4CD  CONST_18  O1   C17  C12  C13  180.00   0.0  0
 4CD  CONST_19  O2   C15  C14  C13  180.00   0.0  0
 4CD  CONST_20  O1   C17  C16  C15  180.00   0.0  0
 4CD  CONST_21  O2   C15  C16  C17  180.00   0.0  0
 4CD  CONST_22  CL1  C14  C13  C12  180.00   0.0  0
 4CD  CONST_23  C18  C12  C13  C14  180.00   0.0  0
 4CD  CONST_24  CL1  C14  C15  C16  180.00   0.0  0
 4CD  CONST_25  C18  C12  C17  C16  180.00   0.0  0
 4CD  CONST_26  C12  C18  N1   C4   180.00   0.0  0
 4CD  CONST_28  H6   C6   C5   C4     0.00   0.0  0
 4CD  CONST_29  H7   C7   C6   C5   180.00   0.0  0
 4CD  CONST_30  H9   C9   C10  C5   180.00   0.0  0
 4CD  CONST_31  H8   C8   C7   C6   180.00   0.0  0
 4CD  CONST_32  H13  C13  C14  C15  180.00   0.0  0
 4CD  CONST_33  H16  C16  C17  C12  180.00   0.0  0
 4CD  CONST_34  O3   C18  N1   C4     0.00   0.0  0
 4CD  Var_01    C1   C2   C3   N1    34.98  30.0  1
 4CD  Var_02    C2   C3   N1   C4   -18.70  30.0  1
 4CD  Var_03    C3   C2   C1   C4   -38.90  30.0  1
 4CD  Var_04    C13  C12  C18  N1    57.65  30.0  2
 4CD  Var_05    H11  C11  C10  C5    61.20  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
 4CD  chir_01  C4  N1  C5  C1  negativ

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
 4CD  plan-1  C4   0.020
 4CD  plan-1  C5   0.020
 4CD  plan-1  C6   0.020
 4CD  plan-1  C7   0.020
 4CD  plan-1  C8   0.020
 4CD  plan-1  C10  0.020
 4CD  plan-1  C9   0.020
 4CD  plan-1  C11  0.020
 4CD  plan-1  H6   0.020
 4CD  plan-1  H7   0.020
 4CD  plan-1  H8   0.020
 4CD  plan-1  H9   0.020
 4CD  plan-2  C13  0.020
 4CD  plan-2  C15  0.020
 4CD  plan-2  C17  0.020
 4CD  plan-2  C12  0.020
 4CD  plan-2  C14  0.020
 4CD  plan-2  C16  0.020
 4CD  plan-2  O2   0.020
 4CD  plan-2  C18  0.020
 4CD  plan-2  CL1  0.020
 4CD  plan-2  H13  0.020
 4CD  plan-2  H16  0.020
 4CD  plan-2  O1   0.020
 4CD  plan-3  N1   0.020
 4CD  plan-3  C4   0.020
 4CD  plan-3  C3   0.020
 4CD  plan-3  C12  0.020
 4CD  plan-3  C18  0.020
 4CD  plan-3  O3   0.020

