# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 09:40:01 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCCN)C(O)=O)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
 ORX  ORX  N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-ornithine  ligand  46  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ORX
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
 ORX  OXT   O  OH1   0  -0.589  -3.2056   0.3258  -1.0378
 ORX  CA    C  C     0   0.528  -2.9963  -0.7206  -1.8240
 ORX  OA    O  O     0  -0.434  -3.7923  -1.6115  -1.9810
 ORX  CAA   C  CH1   0  -0.178  -1.6619  -0.6425  -2.5556
 ORX  NA    N  NH1   0  -0.659  -0.5759  -0.0652  -1.7880
 ORX  C4A   C  CH2   0  -0.344  -0.2542  -0.7673  -0.5481
 ORX  C4    C  CR6   0   0.040   1.0679  -0.3020   0.0102
 ORX  C5    C  CR6   0  -0.075   1.2833  -0.1208   1.3790
 ORX  C6    C  CR16  0  -0.144   2.5530   0.2470   1.7966
 ORX  N1    N  N     0  -0.408   3.5696   0.4350   0.9608
 ORX  C2    C  CR6   0   0.130   3.3894   0.2790  -0.3398
 ORX  C3    C  CR6   0   0.257   2.1395  -0.0891  -0.8580
 ORX  O3    O  OH1   0  -0.650   2.0172  -0.2419  -2.1841
 ORX  C2A   C  CH3   0  -0.720   4.5538   0.4935  -1.2564
 ORX  C5A   C  CH2   0  -0.210   0.1585  -0.3485   2.3509
 ORX  OP4   O  O2    0  -0.592   0.5962  -0.0300   3.6664
 ORX  P     P  P     0   1.464  -0.4513  -0.0391   4.8741
 ORX  OP1   O  O     0  -0.708  -1.2659  -1.2576   5.0300
 ORX  OP2   O  OH1   0  -0.729   0.5943   0.3161   6.0206
 ORX  OP3   O  OH1   0  -0.741  -1.4069   1.2231   4.6642
 ORX  CBA   C  CH2   0  -0.453  -1.8809   0.1350  -3.8583
 ORX  CGA   C  CH2   0  -0.435  -0.6608   0.1519  -4.7704
 ORX  CDA   C  CH2   0  -0.270  -0.9807   0.7690  -6.1239
 ORX  NE    N  NH2   0  -0.800   0.2007   0.7930  -6.9737
 ORX  HOA   H  HOH1  0   0.487  -4.0742   0.2619  -0.6117
 ORX  HAA   H  HCH1  0   0.284  -1.3858  -1.6706  -2.8060
 ORX  HNA   H  HNH1  0   0.380  -0.7468   0.9174  -1.6000
 ORX  H4A1  H  HCH2  0   0.282  -0.1758  -1.8343  -0.7819
 ORX  H4A2  H  HCH2  0   0.254  -1.0492  -0.6762   0.1964
 ORX  H6    H  HCR6  0   0.255   2.7703   0.4003   2.8455
 ORX  HO3   H  HOH1  0   0.492   1.0408  -0.2108  -2.3768
 ORX  H2A1  H  HCH3  0   0.245   4.8155  -0.4198  -1.7946
 ORX  H2A2  H  HCH3  0   0.245   4.3397   1.2541  -2.0093
 ORX  H2A3  H  HCH3  0   0.245   5.4233   0.8113  -0.6848
 ORX  H5A1  H  HCH2  0   0.252  -0.6990   0.2758   2.0780
 ORX  H5A2  H  HCH2  0   0.264  -0.1697  -1.3913   2.3139
 ORX  HP2   H  HOH1  0   0.506   0.2355   0.2544   6.9162
 ORX  HP3   H  HOH1  0   0.497  -0.9653   2.0817   4.6141
 ORX  HBA1  H  HCH2  0   0.243  -2.1863   1.1599  -3.6250
 ORX  HBA2  H  HCH2  0   0.250  -2.7196  -0.3240  -4.3889
 ORX  HGA1  H  HCH2  0   0.225  -0.2916  -0.8672  -4.9197
 ORX  HGA2  H  HCH2  0   0.222   0.1494   0.7189  -4.3041
 ORX  HDA1  H  HCH2  0   0.191  -1.4289   1.7613  -5.9672
 ORX  HDA2  H  HCH2  0   0.216  -1.7452   0.1634  -6.6185
 ORX  HNE1  H  HNH2  0   0.347  -0.0445   1.1727  -7.8791
 ORX  HNE2  H  HNH2  0   0.338   0.8786   1.4373  -6.5848

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
 ORX  OXT  CA    single    1.325  0.020  1.325
 ORX  OXT  HOA   single    0.850  0.020  0.980
 ORX  CA   OA    double    1.205  0.020  1.205
 ORX  CA   CAA   single    1.524  0.020  1.524
 ORX  CAA  NA    single    1.450  0.020  1.450
 ORX  CAA  CBA   single    1.533  0.020  1.533
 ORX  CAA  HAA   single    0.970  0.020  1.090
 ORX  NA   C4A   single    1.461  0.020  1.461
 ORX  NA   HNA   single    0.890  0.020  1.040
 ORX  C4A  C4    single    1.509  0.020  1.509
 ORX  C4A  H4A1  single    0.970  0.020  1.090
 ORX  C4A  H4A2  single    0.970  0.020  1.090
 ORX  C4   C5    aromatic  1.397  0.020  1.397
 ORX  C4   C3    aromatic  1.395  0.020  1.395
 ORX  C5   C6    aromatic  1.386  0.020  1.386
 ORX  C5   C5A   single    1.504  0.020  1.504
 ORX  C6   N1    aromatic  1.329  0.020  1.329
 ORX  C6   H6    single    0.930  0.020  1.080
 ORX  N1   C2    aromatic  1.322  0.020  1.322
 ORX  C2   C3    aromatic  1.402  0.020  1.402
 ORX  C2   C2A   single    1.497  0.020  1.497
 ORX  C3   O3    single    1.341  0.020  1.341
 ORX  O3   HO3   single    0.850  0.020  0.980
 ORX  C2A  H2A1  single    0.970  0.020  1.090
 ORX  C2A  H2A2  single    0.970  0.020  1.090
 ORX  C2A  H2A3  single    0.970  0.020  1.090
 ORX  C5A  OP4   single    1.422  0.020  1.422
 ORX  C5A  H5A1  single    0.970  0.020  1.090
 ORX  C5A  H5A2  single    0.970  0.020  1.090
 ORX  OP4  P     single    1.599  0.020  1.599
 ORX  P    OP1   double    1.474  0.020  1.474
 ORX  P    OP2   single    1.592  0.020  1.592
 ORX  P    OP3   single    1.597  0.020  1.597
 ORX  OP2  HP2   single    0.850  0.020  0.980
 ORX  OP3  HP3   single    0.850  0.020  0.980
 ORX  CBA  CGA   single    1.523  0.020  1.523
 ORX  CBA  HBA1  single    0.970  0.020  1.090
 ORX  CBA  HBA2  single    0.970  0.020  1.090
 ORX  CGA  CDA   single    1.522  0.020  1.522
 ORX  CGA  HGA1  single    0.970  0.020  1.090
 ORX  CGA  HGA2  single    0.970  0.020  1.090
 ORX  CDA  NE    single    1.455  0.020  1.455
 ORX  CDA  HDA1  single    0.970  0.020  1.090
 ORX  CDA  HDA2  single    0.970  0.020  1.090
 ORX  NE   HNE1  single    0.890  0.020  1.040
 ORX  NE   HNE2  single    0.890  0.020  1.040

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
 ORX  HOA   OXT  CA    110.50  3.000
 ORX  CAA   CA   OA    123.63  3.000
 ORX  CAA   CA   OXT   112.49  3.000
 ORX  OA    CA   OXT   123.82  3.000
 ORX  HAA   CAA  CBA   108.56  3.000
 ORX  HAA   CAA  NA    107.84  3.000
 ORX  CBA   CAA  NA    110.80  3.000
 ORX  HAA   CAA  CA    106.43  3.000
 ORX  CBA   CAA  CA    107.99  3.000
 ORX  NA    CAA  CA    114.98  3.000
 ORX  HNA   NA   C4A   110.19  3.000
 ORX  HNA   NA   CAA   110.94  3.000
 ORX  C4A   NA   CAA   115.02  3.000
 ORX  H4A2  C4A  H4A1  106.18  3.000
 ORX  H4A2  C4A  C4    111.08  3.000
 ORX  H4A1  C4A  C4    108.46  3.000
 ORX  H4A2  C4A  NA    112.21  3.000
 ORX  H4A1  C4A  NA    107.63  3.000
 ORX  C4    C4A  NA    111.03  3.000
 ORX  C3    C4   C5    118.12  3.000
 ORX  C3    C4   C4A   119.32  3.000
 ORX  C5    C4   C4A   122.52  3.000
 ORX  C5A   C5   C6    122.04  3.000
 ORX  C5A   C5   C4    119.88  3.000
 ORX  C6    C5   C4    118.07  3.000
 ORX  H6    C6   N1    115.83  3.000
 ORX  H6    C6   C5    120.90  3.000
 ORX  N1    C6   C5    123.27  3.000
 ORX  C2    N1   C6    119.83  3.000
 ORX  C2A   C2   C3    120.30  3.000
 ORX  C2A   C2   N1    118.64  3.000
 ORX  C3    C2   N1    121.06  3.000
 ORX  O3    C3   C2    118.47  3.000
 ORX  O3    C3   C4    121.88  3.000
 ORX  C2    C3   C4    119.65  3.000
 ORX  HO3   O3   C3    106.10  3.000
 ORX  H2A3  C2A  H2A2  108.40  3.000
 ORX  H2A3  C2A  H2A1  108.16  3.000
 ORX  H2A2  C2A  H2A1  106.85  3.000
 ORX  H2A3  C2A  C2    109.98  3.000
 ORX  H2A2  C2A  C2    111.69  3.000
 ORX  H2A1  C2A  C2    111.61  3.000
 ORX  H5A2  C5A  H5A1  107.46  3.000
 ORX  H5A2  C5A  OP4   109.70  3.000
 ORX  H5A1  C5A  OP4   110.10  3.000
 ORX  H5A2  C5A  C5    110.30  3.000
 ORX  H5A1  C5A  C5    109.77  3.000
 ORX  OP4   C5A  C5    109.49  3.000
 ORX  P     OP4  C5A   119.72  3.000
 ORX  OP3   P    OP2   108.14  3.000
 ORX  OP3   P    OP1   109.67  3.000
 ORX  OP2   P    OP1   118.12  3.000
 ORX  OP3   P    OP4   106.75  3.000
 ORX  OP2   P    OP4    96.46  3.000
 ORX  OP1   P    OP4   116.53  3.000
 ORX  HP2   OP2  P     114.15  3.000
 ORX  HP3   OP3  P     115.81  3.000
 ORX  HBA2  CBA  HBA1  106.41  3.000
 ORX  HBA2  CBA  CGA   109.18  3.000
 ORX  HBA1  CBA  CGA   109.92  3.000
 ORX  HBA2  CBA  CAA   108.00  3.000
 ORX  HBA1  CBA  CAA   109.49  3.000
 ORX  CGA   CBA  CAA   113.58  3.000
 ORX  HGA2  CGA  HGA1  106.93  3.000
 ORX  HGA2  CGA  CDA   108.95  3.000
 ORX  HGA1  CGA  CDA   109.11  3.000
 ORX  HGA2  CGA  CBA   110.11  3.000
 ORX  HGA1  CGA  CBA   109.97  3.000
 ORX  CDA   CGA  CBA   111.64  3.000
 ORX  HDA2  CDA  HDA1  106.20  3.000
 ORX  HDA2  CDA  NE    108.21  3.000
 ORX  HDA1  CDA  NE    113.52  3.000
 ORX  HDA2  CDA  CGA   108.95  3.000
 ORX  HDA1  CDA  CGA   108.95  3.000
 ORX  NE    CDA  CGA   110.82  3.000
 ORX  HNE2  NE   HNE1  105.49  3.000
 ORX  HNE2  NE   CDA   109.24  3.000
 ORX  HNE1  NE   CDA   109.39  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
 ORX  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 ORX  CONST_02  N1    C2   C3   C4      0.00   0.0  0
 ORX  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 ORX  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 ORX  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 ORX  CONST_06  C3    C2   N1   C6      0.00   0.0  0
 ORX  CONST_07  C6    C5   C4   C4A   180.00   0.0  0
 ORX  CONST_08  C2    C3   C4   C4A   180.00   0.0  0
 ORX  CONST_09  C2A   C2   C3   C4    180.00   0.0  0
 ORX  CONST_10  O3    C3   C4   C5    180.00   0.0  0
 ORX  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 ORX  CONST_12  C5A   C5   C6   N1    180.00   0.0  0
 ORX  CONST_13  O3    C3   C2   N1    180.00   0.0  0
 ORX  CONST_14  C5A   C5   C4   C3    180.00   0.0  0
 ORX  CONST_15  H6    C6   C5   C4    180.00   0.0  0
 ORX  CONST_16  HOA   OXT  CA   OA      0.00   0.0  0
 ORX  Var_01    C5    C4   C4A  NA    140.82  30.0  2
 ORX  Var_02    OP4   C5A  C5   C4   -176.72  30.0  2
 ORX  Var_03    H2A1  C2A  C2   N1    117.30  30.0  2
 ORX  Var_04    C4    C4A  NA   CAA   166.79  30.0  3
 ORX  Var_05    CDA   CGA  CBA  CAA   172.32  30.0  3
 ORX  Var_06    OP1   P    OP4  C5A    51.96  30.0  3
 ORX  Var_07    NE    CDA  CGA  CBA   179.21  30.0  3
 ORX  Var_08    HNE1  NE   CDA  CGA   177.76  30.0  3

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
 ORX  chir_01  CAA  CA  NA  CBA  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
 ORX  plan-1  C4A  0.020
 ORX  plan-1  C4   0.020
 ORX  plan-1  C5   0.020
 ORX  plan-1  C6   0.020
 ORX  plan-1  N1   0.020
 ORX  plan-1  C2   0.020
 ORX  plan-1  C3   0.020
 ORX  plan-1  O3   0.020
 ORX  plan-1  C2A  0.020
 ORX  plan-1  C5A  0.020
 ORX  plan-1  H6   0.020
 ORX  plan-2  OXT  0.020
 ORX  plan-2  CA   0.020
 ORX  plan-2  OA   0.020
 ORX  plan-2  CAA  0.020
 ORX  plan-2  HOA  0.020

