# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:40:46 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: (4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CCC(O)=O)COc2ccccc2)c1O
#
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
 QL4  QL4  '(4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid'  ligand  53  30  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QL4
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
 QL4  N1   N  N     0  -0.408  15.0340  47.1753  -29.1128
 QL4  C2   C  CH2   0  -0.145  15.6909  45.0691  -30.0833
 QL4  C3   C  CR6   0   0.268  15.8445  49.6130  -27.9066
 QL4  C4   C  CR6   0   0.422  17.4995  43.9758  -28.9937
 QL4  C5   C  CR16  0  -0.325  18.0193  43.5178  -30.2017
 QL4  C6   C  CR16  0  -0.284  19.2095  42.7978  -30.2081
 QL4  C1   C  CH1   0  -0.182  14.5228  45.9747  -29.7326
 QL4  O1   O  O2    0  -0.562  16.3464  44.6828  -28.8870
 QL4  C7   C  CR16  0  -0.198  19.8859  42.5246  -29.0305
 QL4  C8   C  CR16  0  -0.299  19.3580  42.9841  -27.8287
 QL4  C9   C  CR16  0  -0.356  18.1765  43.7049  -27.8048
 QL4  C16  C  CH2   0  -0.411  13.7466  46.3238  -30.9984
 QL4  C17  C  CH2   0  -0.593  12.5490  47.2095  -30.6990
 QL4  C18  C  C     0   0.554  11.6900  47.4655  -31.9061
 QL4  O19  O  O     0  -0.417  11.9045  47.0443  -33.0153
 QL4  O21  O  OH1   0  -0.622  10.6421  48.2279  -31.6101
 QL4  O3P  O  OH1   0  -0.715  14.6536  44.5215  -26.1087
 QL4  P    P  P     0   1.436  15.4779  44.9622  -24.8117
 QL4  O1P  O  OH1   0  -0.707  14.2961  44.7701  -23.7634
 QL4  O2P  O  O     0  -0.754  16.7531  44.2600  -24.5751
 QL4  O4P  O  O2    0  -0.555  15.7516  46.5325  -24.9363
 QL4  C51  C  CR6   0  -0.118  15.1940  48.6698  -25.7887
 QL4  C61  C  CR16  0  -0.092  15.6171  49.8475  -25.2102
 QL4  N11  N  N     0  -0.424  16.1050  50.8732  -25.9072
 QL4  C41  C  CR6   0  -0.069  15.2902  48.5520  -27.1843
 QL4  C4A  C  C1    0   0.025  14.8054  47.3651  -27.8788
 QL4  C21  C  CR6   0   0.185  16.2310  50.7807  -27.2167
 QL4  C2A  C  CH3   0  -0.717  16.8053  51.9391  -27.9684
 QL4  H1   H  HCH2  0   0.208  15.3186  44.1899  -30.6190
 QL4  H2   H  HCH2  0   0.220  16.3826  45.6044  -30.7425
 QL4  H3   H  HCR6  0   0.289  17.5208  43.7044  -31.1427
 QL4  H4   H  HCR6  0   0.249  19.6032  42.4507  -31.1546
 QL4  H5   H  HCH1  0   0.288  13.8532  45.4354  -29.0461
 QL4  H6   H  HCR6  0   0.262  20.8098  41.9622  -29.0450
 QL4  H7   H  HCR6  0   0.265  19.8711  42.7835  -26.8970
 QL4  H8   H  HCR6  0   0.271  17.7834  44.0570  -26.8595
 QL4  H9   H  HCH2  0   0.276  13.4130  45.3930  -31.4604
 QL4  H10  H  HCH2  0   0.277  14.4137  46.8164  -31.7099
 QL4  H11  H  HCH2  0   0.274  12.8643  48.1788  -30.3056
 QL4  H12  H  HCH2  0   0.267  11.9216  46.7605  -29.9223
 QL4  H13  H  HOH1  0   0.470  10.1070  48.3767  -32.4038
 QL4  H14  H  HOH1  0   0.508  15.1935  44.3534  -26.8958
 QL4  H15  H  HOH1  0   0.469  14.5471  44.9200  -22.8417
 QL4  H16  H  HCH2  0   0.273  14.5752  47.8805  -23.9032
 QL4  H17  H  HCH2  0   0.294  13.7686  47.1358  -25.2764
 QL4  H18  H  HCR6  0   0.278  15.5629  49.9769  -24.1346
 QL4  H19  H  H     0   0.268  14.1994  46.6575  -27.3152
 QL4  H20  H  HOH1  0   0.471  15.7419  48.6735  -29.5405
 QL4  H21  H  HCH3  0   0.247  17.0019  52.7633  -27.2864
 QL4  H22  H  HCH3  0   0.263  17.7416  51.6691  -28.4605
 QL4  H23  H  HCH3  0   0.251  16.1271  52.2902  -28.7480
 QL4  O3   O  OH1   0  -0.639  16.0164  49.5744  -29.2232
 QL4  C5A  C  CH2   0  -0.234  14.7231  47.5377  -24.9280

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
 QL4  O19  C18  double    1.206  0.020  1.206
 QL4  O21  C18  single    1.329  0.020  1.329
 QL4  C18  C17  single    1.504  0.020  1.504
 QL4  C16  C17  single    1.519  0.020  1.519
 QL4  C16  C1   single    1.525  0.020  1.525
 QL4  C6   C5   aromatic  1.391  0.020  1.391
 QL4  C6   C7   aromatic  1.385  0.020  1.385
 QL4  C5   C4   aromatic  1.393  0.020  1.393
 QL4  C2   C1   single    1.519  0.020  1.519
 QL4  C2   O1   single    1.418  0.020  1.418
 QL4  C1   N1   single    1.445  0.020  1.445
 QL4  C7   C8   aromatic  1.391  0.020  1.391
 QL4  C4   O1   single    1.357  0.020  1.357
 QL4  C4   C9   aromatic  1.395  0.020  1.395
 QL4  O3   C3   single    1.328  0.020  1.328
 QL4  N1   C4A  double    1.269  0.020  1.269
 QL4  C8   C9   aromatic  1.384  0.020  1.384
 QL4  C2A  C21  single    1.496  0.020  1.496
 QL4  C3   C21  aromatic  1.410  0.020  1.410
 QL4  C3   C41  aromatic  1.398  0.020  1.398
 QL4  C4A  C41  single    1.458  0.020  1.458
 QL4  C21  N11  aromatic  1.319  0.020  1.319
 QL4  C41  C51  aromatic  1.404  0.020  1.404
 QL4  N11  C61  aromatic  1.333  0.020  1.333
 QL4  C51  C61  aromatic  1.379  0.020  1.379
 QL4  C51  C5A  single    1.498  0.020  1.498
 QL4  O4P  C5A  single    1.438  0.020  1.438
 QL4  O4P  P    single    1.599  0.020  1.599
 QL4  O2P  P    double    1.475  0.020  1.475
 QL4  P    O3P  single    1.599  0.020  1.599
 QL4  P    O1P  single    1.591  0.020  1.591
 QL4  C2   H1   single    0.970  0.020  1.090
 QL4  C2   H2   single    0.970  0.020  1.090
 QL4  C5   H3   single    0.930  0.020  1.080
 QL4  C6   H4   single    0.930  0.020  1.080
 QL4  C1   H5   single    0.970  0.020  1.090
 QL4  C7   H6   single    0.930  0.020  1.080
 QL4  C8   H7   single    0.930  0.020  1.080
 QL4  C9   H8   single    0.930  0.020  1.080
 QL4  C16  H9   single    0.970  0.020  1.090
 QL4  C16  H10  single    0.970  0.020  1.090
 QL4  C17  H11  single    0.970  0.020  1.090
 QL4  C17  H12  single    0.970  0.020  1.090
 QL4  O21  H13  single    0.850  0.020  0.980
 QL4  O3P  H14  single    0.850  0.020  0.980
 QL4  O1P  H15  single    0.850  0.020  0.980
 QL4  C5A  H16  single    0.970  0.020  1.090
 QL4  C5A  H17  single    0.970  0.020  1.090
 QL4  C61  H18  single    0.930  0.020  1.080
 QL4  C4A  H19  single    0.930  0.020  1.080
 QL4  O3   H20  single    0.850  0.020  0.980
 QL4  C2A  H21  single    0.970  0.020  1.090
 QL4  C2A  H22  single    0.970  0.020  1.090
 QL4  C2A  H23  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
 QL4  C4A  N1   C1   118.54  3.000
 QL4  H2   C2   H1   108.23  3.000
 QL4  H2   C2   O1   110.43  3.000
 QL4  H1   C2   O1   110.56  3.000
 QL4  H2   C2   C1   109.46  3.000
 QL4  H1   C2   C1   109.28  3.000
 QL4  O1   C2   C1   108.86  3.000
 QL4  C21  C3   O3   118.26  3.000
 QL4  C21  C3   C41  118.96  3.000
 QL4  O3   C3   C41  122.77  3.000
 QL4  C9   C4   O1   116.53  3.000
 QL4  C9   C4   C5   119.63  3.000
 QL4  O1   C4   C5   123.84  3.000
 QL4  H3   C5   C6   118.67  3.000
 QL4  H3   C5   C4   121.75  3.000
 QL4  C6   C5   C4   119.58  3.000
 QL4  H4   C6   C7   120.17  3.000
 QL4  H4   C6   C5   118.77  3.000
 QL4  C7   C6   C5   121.06  3.000
 QL4  H5   C1   C16  108.68  3.000
 QL4  H5   C1   C2   108.66  3.000
 QL4  C16  C1   C2   109.65  3.000
 QL4  H5   C1   N1   110.79  3.000
 QL4  C2   C1   N1   108.80  3.000
 QL4  C16  C1   N1   110.24  3.000
 QL4  C4   O1   C2   117.94  3.000
 QL4  H6   C7   C8   120.50  3.000
 QL4  H6   C7   C6   120.55  3.000
 QL4  C8   C7   C6   118.95  3.000
 QL4  H7   C8   C9   119.09  3.000
 QL4  H7   C8   C7   120.18  3.000
 QL4  C9   C8   C7   120.73  3.000
 QL4  H8   C9   C8   119.63  3.000
 QL4  H8   C9   C4   120.32  3.000
 QL4  C8   C9   C4   120.05  3.000
 QL4  H10  C16  H9   107.18  3.000
 QL4  H10  C16  C17  110.29  3.000
 QL4  H9   C16  C17  109.86  3.000
 QL4  H10  C16  C1   109.44  3.000
 QL4  H9   C16  C1   108.15  3.000
 QL4  C17  C16  C1   111.78  3.000
 QL4  H12  C17  H11  105.89  3.000
 QL4  H12  C17  C18  108.18  3.000
 QL4  H11  C17  C18  107.63  3.000
 QL4  H12  C17  C16  110.64  3.000
 QL4  H11  C17  C16  111.14  3.000
 QL4  C18  C17  C16  113.04  3.000
 QL4  O21  C18  O19  123.06  3.000
 QL4  O21  C18  C17  111.67  3.000
 QL4  O19  C18  C17  125.27  3.000
 QL4  H13  O21  C18  109.94  3.000
 QL4  H14  O3P  P    114.80  3.000
 QL4  O4P  P    O2P  109.40  3.000
 QL4  O2P  P    O1P  118.61  3.000
 QL4  O4P  P    O1P  107.28  3.000
 QL4  O1P  P    O3P   96.79  3.000
 QL4  O2P  P    O3P  116.40  3.000
 QL4  O4P  P    O3P  107.21  3.000
 QL4  H15  O1P  P    114.61  3.000
 QL4  C5A  O4P  P    124.31  3.000
 QL4  C41  C51  C61  117.89  3.000
 QL4  C61  C51  C5A  120.06  3.000
 QL4  C41  C51  C5A  121.96  3.000
 QL4  H18  C61  N11  116.43  3.000
 QL4  H18  C61  C51  120.18  3.000
 QL4  N11  C61  C51  123.39  3.000
 QL4  C21  N11  C61  120.02  3.000
 QL4  C4A  C41  C51  121.27  3.000
 QL4  C51  C41  C3   118.50  3.000
 QL4  C4A  C41  C3   120.23  3.000
 QL4  H19  C4A  C41  117.87  3.000
 QL4  H19  C4A  N1   120.41  3.000
 QL4  C41  C4A  N1   121.67  3.000
 QL4  C2A  C21  N11  118.78  3.000
 QL4  N11  C21  C3   121.18  3.000
 QL4  C2A  C21  C3   120.04  3.000
 QL4  H23  C2A  H22  106.89  3.000
 QL4  H23  C2A  H21  108.45  3.000
 QL4  H22  C2A  H21  108.36  3.000
 QL4  H23  C2A  C21  111.69  3.000
 QL4  H22  C2A  C21  111.37  3.000
 QL4  H21  C2A  C21  109.95  3.000
 QL4  H20  O3   C3   107.88  3.000
 QL4  H17  C5A  H16  107.26  3.000
 QL4  H17  C5A  C51  111.67  3.000
 QL4  H16  C5A  C51  110.18  3.000
 QL4  H17  C5A  O4P  111.45  3.000
 QL4  H16  C5A  O4P  108.79  3.000
 QL4  C51  C5A  O4P  107.46  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
 QL4  CONST_01  C61  N11  C21  C3      0.00   0.0  0
 QL4  CONST_02  C61  C51  C41  C3      0.00   0.0  0
 QL4  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 QL4  CONST_04  C7   C8   C9   C4      0.00   0.0  0
 QL4  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 QL4  CONST_06  C8   C9   C4   C5      0.00   0.0  0
 QL4  CONST_07  C9   C4   C5   C6      0.00   0.0  0
 QL4  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 QL4  CONST_09  C21  C3   C41  C51     0.00   0.0  0
 QL4  CONST_10  C21  N11  C61  C51     0.00   0.0  0
 QL4  CONST_11  C41  C3   C21  N11     0.00   0.0  0
 QL4  CONST_12  C41  C51  C61  N11     0.00   0.0  0
 QL4  CONST_13  C5A  C51  C41  C3    180.00   0.0  0
 QL4  CONST_14  O1   C4   C5   C6    180.00   0.0  0
 QL4  CONST_15  C8   C9   C4   O1    180.00   0.0  0
 QL4  CONST_16  N11  C61  C51  C5A   180.00   0.0  0
 QL4  CONST_17  O3   C3   C41  C51   180.00   0.0  0
 QL4  CONST_18  C2A  C21  N11  C61   180.00   0.0  0
 QL4  CONST_19  C4A  C41  C51  C61   180.00   0.0  0
 QL4  CONST_20  O3   C3   C21  N11   180.00   0.0  0
 QL4  CONST_21  C2A  C21  C3   C41   180.00   0.0  0
 QL4  CONST_22  C21  C3   C41  C4A   180.00   0.0  0
 QL4  CONST_23  H4   C6   C5   C4    180.00   0.0  0
 QL4  CONST_24  H7   C8   C9   C4    180.00   0.0  0
 QL4  CONST_25  H6   C7   C6   C5    180.00   0.0  0
 QL4  CONST_26  H8   C9   C4   C5    180.00   0.0  0
 QL4  CONST_27  H3   C5   C6   C7    180.00   0.0  0
 QL4  CONST_28  H18  C61  C51  C41   180.00   0.0  0
 QL4  CONST_29  H13  O21  C18  C17   180.00   0.0  0
 QL4  Var_01    C3   C41  C4A  N1      9.89  30.0  2
 QL4  Var_02    C5   C4   O1   C2     -5.29  30.0  2
 QL4  Var_03    C41  C51  C5A  O4P    70.35  30.0  1
 QL4  Var_04    H21  C2A  C21  C3    177.42  30.0  2
 QL4  Var_05    C41  C4A  N1   C1    179.93   0.0  2
 QL4  Var_06    C1   C2   O1   C4   -173.65  30.0  1
 QL4  Var_07    C51  C5A  O4P  P    -148.47  30.0  3
 QL4  Var_08    C18  C17  C16  C1   -174.60  30.0  3
 QL4  Var_09    O19  C18  C17  C16    -0.89  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
 QL4  chir_01  C1  C16  C2  N1  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
 QL4  plan-1  C3   0.020
 QL4  plan-1  C51  0.020
 QL4  plan-1  C61  0.020
 QL4  plan-1  N11  0.020
 QL4  plan-1  C41  0.020
 QL4  plan-1  C4A  0.020
 QL4  plan-1  C21  0.020
 QL4  plan-1  C2A  0.020
 QL4  plan-1  H18  0.020
 QL4  plan-1  O3   0.020
 QL4  plan-1  C5A  0.020
 QL4  plan-2  C4   0.020
 QL4  plan-2  C5   0.020
 QL4  plan-2  C6   0.020
 QL4  plan-2  O1   0.020
 QL4  plan-2  C7   0.020
 QL4  plan-2  C8   0.020
 QL4  plan-2  C9   0.020
 QL4  plan-2  H3   0.020
 QL4  plan-2  H4   0.020
 QL4  plan-2  H6   0.020
 QL4  plan-2  H7   0.020
 QL4  plan-2  H8   0.020
 QL4  plan-3  C17  0.020
 QL4  plan-3  C18  0.020
 QL4  plan-3  O19  0.020
 QL4  plan-3  O21  0.020
 QL4  plan-3  H13  0.020
 QL4  plan-4  N1   0.020
 QL4  plan-4  C1   0.020
 QL4  plan-4  C41  0.020
 QL4  plan-4  C4A  0.020
 QL4  plan-4  H19  0.020

