# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:06:03 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: (5R,6S,8S)-8-[3-(aminomethyl)phenyl]-6-hydroxy-5-(1-methylethyl)-3-oxo-1-phenyl-2,7-dioxa-4-aza-6-phosphanonan-9-oic acid 6-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)OCc1ccccc1)[P@@](O)(=O)O[C@H](C(O)=O)c2cccc(CN)c2
#
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
 578  578  '(5R,6S,8S)-8-[3-(aminomethyl)phenyl]-6-hydroxy-5-(1-methylethyl)-3-oxo-1-phenyl-2,7-dioxa-4-aza-6-phosphanonan-9-oic acid 6-oxide'  ligand  58  31  .  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 (reasonable std)
;

data_comp_578
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
 578  C27   C  CR16  0  -0.293  37.7560  13.6674  67.5620
 578  C28   C  CR16  0  -0.241  38.9859  13.4035  68.1475
 578  C29   C  CR16  0  -0.267  40.0763  13.0688  67.3551
 578  C30   C  CR16  0  -0.236  39.9239  13.0007  65.9773
 578  C31   C  CR16  0  -0.304  38.6908  13.2585  65.3917
 578  C26   C  CR6   0   0.041  37.5939  13.5929  66.1810
 578  C23   C  CH2   0  -0.192  36.2244  13.8191  65.6059
 578  O22   O  O2    0  -0.485  36.3586  14.2646  64.2631
 578  C20   C  C     0   0.773  35.2510  14.3218  63.5189
 578  O21   O  O     0  -0.506  34.1369  14.0939  63.9368
 578  N19   N  NH1   0  -0.653  35.5562  14.6915  62.2569
 578  C15   C  CH1   0  -0.381  34.5893  14.7073  61.1924
 578  C16   C  CH1   0  -0.250  34.6881  15.9592  60.3042
 578  C18   C  CH3   0  -0.651  34.4192  17.2039  61.1438
 578  C17   C  CH3   0  -0.672  36.0106  16.0861  59.5529
 578  P14   P  P     0   1.420  34.6561  13.1309  60.2625
 578  O24   O  O     0  -0.687  33.8769  13.1016  59.0024
 578  O25   O  OH1   0  -0.740  34.2992  11.9708  61.3154
 578  O13   O  O2    0  -0.601  36.2450  12.9097  60.1171
 578  C1    C  CH1   0  -0.113  36.8288  11.6352  59.9341
 578  C2    C  C     0   0.541  37.0069  10.8973  61.2546
 578  O12   O  O     0  -0.430  37.0509   9.6963  61.3135
 578  O11   O  OH1   0  -0.570  37.1779  11.7101  62.2797
 578  C3    C  CR6   0   0.084  38.1961  11.8033  59.3166
 578  C8    C  CR16  0  -0.335  38.6524  10.8532  58.4132
 578  C4    C  CR16  0  -0.299  39.0182  12.8647  59.6847
 578  C5    C  CR16  0  -0.243  40.2860  12.9650  59.1345
 578  C6    C  CR16  0  -0.341  40.7382  12.0108  58.2323
 578  C7    C  CR6   0   0.099  39.9259  10.9463  57.8570
 578  C9    C  CH2   0  -0.374  40.4043   9.9368  56.8443
 578  N10   N  NH2   0  -0.812  39.9541   8.5930  57.1621
 578  H27   H  HCR6  0   0.253  36.9121  13.9351  68.1875
 578  H28   H  HCR6  0   0.258  39.0932  13.4663  69.2227
 578  H29   H  HCR6  0   0.257  41.0382  12.8661  67.8079
 578  H30   H  HCR6  0   0.257  40.7687  12.7449  65.3508
 578  H31   H  HCR6  0   0.249  38.5987  13.2035  64.3151
 578  H231  H  HCH2  0   0.255  35.6491  12.8895  65.6386
 578  H232  H  HCH2  0   0.249  35.6824  14.5580  66.2018
 578  HN19  H  HNH1  0   0.403  36.5326  14.7488  62.0113
 578  H15   H  HCH1  0   0.313  33.5935  14.7117  61.6450
 578  H16   H  HCH1  0   0.253  33.8874  15.8677  59.5652
 578  H181  H  HCH3  0   0.227  35.1967  17.3550  61.8941
 578  H182  H  HCH3  0   0.237  34.3945  18.0904  60.5095
 578  H183  H  HCH3  0   0.231  33.4607  17.1407  61.6617
 578  H171  H  HCH3  0   0.242  36.0314  17.0273  59.0027
 578  H172  H  HCH3  0   0.219  36.8702  16.0941  60.2264
 578  H173  H  HCH3  0   0.242  36.1603  15.2879  58.8264
 578  HO25  H  HOH1  0   0.498  33.3724  11.6959  61.3035
 578  H1    H  HCH1  0   0.298  36.2148  11.0015  59.2870
 578  HO11  H  HOH1  0   0.483  37.3230  11.1938  63.0871
 578  H8    H  HCR6  0   0.251  38.0124  10.0271  58.1269
 578  H4    H  HCR6  0   0.257  38.6799  13.6125  60.3897
 578  H5    H  HCR6  0   0.274  40.9315  13.7859  59.4189
 578  H6    H  HCR6  0   0.286  41.7360  12.0962  57.8183
 578  H91   H  HCH2  0   0.256  39.9926  10.2055  55.8671
 578  H92   H  HCH2  0   0.250  41.4938  10.0322  56.7458
 578  H101  H  HNH2  0   0.364  40.2070   7.9705  56.4059
 578  H102  H  HNH2  0   0.356  40.4490   8.2564  57.9785

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
 578  C27  C26   aromatic  1.393  0.020  1.393
 578  C27  C28   aromatic  1.387  0.020  1.387
 578  C27  H27   single    0.930  0.020  1.080
 578  C28  C29   aromatic  1.389  0.020  1.389
 578  C28  H28   single    0.930  0.020  1.080
 578  C29  C30   aromatic  1.388  0.020  1.388
 578  C29  H29   single    0.930  0.020  1.080
 578  C30  C31   aromatic  1.389  0.020  1.389
 578  C30  H30   single    0.930  0.020  1.080
 578  C31  C26   aromatic  1.392  0.020  1.392
 578  C31  H31   single    0.930  0.020  1.080
 578  C26  C23   single    1.503  0.020  1.503
 578  C23  O22   single    1.421  0.020  1.421
 578  C23  H231  single    0.970  0.020  1.090
 578  C23  H232  single    0.970  0.020  1.090
 578  O22  C20   single    1.336  0.020  1.336
 578  C20  N19   single    1.350  0.020  1.350
 578  C20  O21   double    1.212  0.020  1.212
 578  N19  C15   single    1.438  0.020  1.438
 578  N19  HN19  single    0.860  0.020  1.020
 578  C15  C16   single    1.538  0.020  1.538
 578  C15  P14   single    1.831  0.020  1.831
 578  C15  H15   single    0.970  0.020  1.090
 578  C16  C17   single    1.526  0.020  1.526
 578  C16  C18   single    1.525  0.020  1.525
 578  C16  H16   single    0.970  0.020  1.090
 578  C18  H181  single    0.970  0.020  1.090
 578  C18  H182  single    0.970  0.020  1.090
 578  C18  H183  single    0.970  0.020  1.090
 578  C17  H171  single    0.970  0.020  1.090
 578  C17  H172  single    0.970  0.020  1.090
 578  C17  H173  single    0.970  0.020  1.090
 578  P14  O24   double    1.482  0.020  1.482
 578  P14  O13   single    1.611  0.020  1.611
 578  P14  O25   single    1.607  0.020  1.607
 578  O25  HO25  single    0.850  0.020  0.980
 578  O13  C1    single    1.414  0.020  1.414
 578  C1   C3    single    1.510  0.020  1.510
 578  C1   C2    single    1.523  0.020  1.523
 578  C1   H1    single    0.970  0.020  1.090
 578  C2   O12   double    1.203  0.020  1.203
 578  C2   O11   single    1.319  0.020  1.319
 578  O11  HO11  single    0.850  0.020  0.980
 578  C3   C8    aromatic  1.388  0.020  1.388
 578  C3   C4    aromatic  1.392  0.020  1.392
 578  C8   C7    aromatic  1.393  0.020  1.393
 578  C8   H8    single    0.930  0.020  1.080
 578  C4   C5    aromatic  1.386  0.020  1.386
 578  C4   H4    single    0.930  0.020  1.080
 578  C5   C6    aromatic  1.389  0.020  1.389
 578  C5   H5    single    0.930  0.020  1.080
 578  C6   C7    aromatic  1.391  0.020  1.391
 578  C6   H6    single    0.930  0.020  1.080
 578  C7   C9    single    1.508  0.020  1.508
 578  C9   N10   single    1.452  0.020  1.452
 578  C9   H91   single    0.970  0.020  1.090
 578  C9   H92   single    0.970  0.020  1.090
 578  N10  H101  single    0.890  0.020  1.040
 578  N10  H102  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
 578  H27   C27  C26   119.65  3.000
 578  H27   C27  C28   119.58  3.000
 578  C26   C27  C28   120.77  3.000
 578  H28   C28  C29   120.20  3.000
 578  H28   C28  C27   119.74  3.000
 578  C29   C28  C27   120.07  3.000
 578  H29   C29  C30   120.25  3.000
 578  H29   C29  C28   120.28  3.000
 578  C30   C29  C28   119.47  3.000
 578  H30   C30  C31   119.51  3.000
 578  H30   C30  C29   120.03  3.000
 578  C31   C30  C29   120.45  3.000
 578  H31   C31  C26   120.61  3.000
 578  H31   C31  C30   119.05  3.000
 578  C26   C31  C30   120.33  3.000
 578  C23   C26  C31   122.50  3.000
 578  C23   C26  C27   118.53  3.000
 578  C31   C26  C27   118.91  3.000
 578  H232  C23  H231  107.31  3.000
 578  H232  C23  O22   110.49  3.000
 578  H231  C23  O22   110.14  3.000
 578  H232  C23  C26   110.19  3.000
 578  H231  C23  C26   109.88  3.000
 578  O22   C23  C26   108.83  3.000
 578  C20   O22  C23   117.49  3.000
 578  N19   C20  O21   125.59  3.000
 578  O21   C20  O22   124.21  3.000
 578  N19   C20  O22   110.19  3.000
 578  HN19  N19  C15   118.04  3.000
 578  HN19  N19  C20   117.52  3.000
 578  C15   N19  C20   122.89  3.000
 578  H15   C15  P14   104.28  3.000
 578  H15   C15  C16   107.11  3.000
 578  P14   C15  C16   113.89  3.000
 578  H15   C15  N19   107.81  3.000
 578  P14   C15  N19   109.99  3.000
 578  C16   C15  N19   113.16  3.000
 578  H16   C16  C17   107.99  3.000
 578  H16   C16  C18   108.13  3.000
 578  C17   C16  C18   110.84  3.000
 578  H16   C16  C15   105.97  3.000
 578  C18   C16  C15   109.57  3.000
 578  C17   C16  C15   114.05  3.000
 578  H183  C18  H182  107.65  3.000
 578  H183  C18  H181  107.92  3.000
 578  H182  C18  H181  107.67  3.000
 578  H183  C18  C16   111.64  3.000
 578  H182  C18  C16   110.32  3.000
 578  H181  C18  C16   111.47  3.000
 578  H173  C17  H172  107.96  3.000
 578  H173  C17  H171  107.06  3.000
 578  H172  C17  H171  106.85  3.000
 578  H173  C17  C16   112.73  3.000
 578  H172  C17  C16   112.28  3.000
 578  H171  C17  C16   109.67  3.000
 578  O13   P14  O25   100.32  3.000
 578  O25   P14  O24   115.22  3.000
 578  O13   P14  O24   116.05  3.000
 578  O25   P14  C15   106.30  3.000
 578  O13   P14  C15   101.54  3.000
 578  O24   P14  C15   115.44  3.000
 578  HO25  O25  P14   114.21  3.000
 578  C1    O13  P14   122.88  3.000
 578  H1    C1   C3    109.32  3.000
 578  H1    C1   C2    107.33  3.000
 578  C3    C1   C2    107.61  3.000
 578  H1    C1   O13   111.53  3.000
 578  C2    C1   O13   111.89  3.000
 578  C3    C1   O13   109.06  3.000
 578  O11   C2   O12   124.90  3.000
 578  O11   C2   C1    112.97  3.000
 578  O12   C2   C1    122.02  3.000
 578  HO11  O11  C2    109.78  3.000
 578  C4    C3   C8    119.99  3.000
 578  C4    C3   C1    120.77  3.000
 578  C8    C3   C1    119.19  3.000
 578  H8    C8   C7    119.04  3.000
 578  H8    C8   C3    119.98  3.000
 578  C7    C8   C3    120.98  3.000
 578  H4    C4   C5    119.65  3.000
 578  H4    C4   C3    120.97  3.000
 578  C5    C4   C3    119.38  3.000
 578  H5    C5   C6    119.84  3.000
 578  H5    C5   C4    119.76  3.000
 578  C6    C5   C4    120.40  3.000
 578  H6    C6   C7    119.68  3.000
 578  H6    C6   C5    119.59  3.000
 578  C7    C6   C5    120.73  3.000
 578  C9    C7   C6    120.55  3.000
 578  C9    C7   C8    120.90  3.000
 578  C6    C7   C8    118.52  3.000
 578  H92   C9   H91   105.77  3.000
 578  H92   C9   N10   114.05  3.000
 578  H91   C9   N10   107.82  3.000
 578  H92   C9   C7    108.48  3.000
 578  H91   C9   C7    108.43  3.000
 578  N10   C9   C7    111.97  3.000
 578  H102  N10  H101  106.03  3.000
 578  H102  N10  C9    109.42  3.000
 578  H101  N10  C9    109.17  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
 578  CONST_01  C30   C31  C26  C27     0.00   0.0  0
 578  CONST_02  C30   C29  C28  C27     0.00   0.0  0
 578  CONST_03  C31   C26  C27  C28     0.00   0.0  0
 578  CONST_04  C31   C30  C29  C28     0.00   0.0  0
 578  CONST_05  C26   C27  C28  C29     0.00   0.0  0
 578  CONST_06  C26   C31  C30  C29     0.00   0.0  0
 578  CONST_07  C6    C7   C8   C3      0.00   0.0  0
 578  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 578  CONST_09  C5    C4   C3   C8      0.00   0.0  0
 578  CONST_10  C5    C6   C7   C8      0.00   0.0  0
 578  CONST_11  C7    C8   C3   C4      0.00   0.0  0
 578  CONST_12  C7    C6   C5   C4      0.00   0.0  0
 578  CONST_13  C23   C26  C27  C28   180.00   0.0  0
 578  CONST_14  C23   C26  C31  C30   180.00   0.0  0
 578  CONST_15  C7    C8   C3   C1    180.00   0.0  0
 578  CONST_16  C5    C4   C3   C1    180.00   0.0  0
 578  CONST_17  C9    C7   C8   C3    180.00   0.0  0
 578  CONST_18  C9    C7   C6   C5    180.00   0.0  0
 578  CONST_19  H31   C31  C26  C27   180.00   0.0  0
 578  CONST_20  H29   C29  C28  C27   180.00   0.0  0
 578  CONST_21  H30   C30  C29  C28   180.00   0.0  0
 578  CONST_22  H27   C27  C28  C29   180.00   0.0  0
 578  CONST_23  H28   C28  C29  C30   180.00   0.0  0
 578  CONST_24  H5    C5   C4   C3    180.00   0.0  0
 578  CONST_25  H4    C4   C3   C8    180.00   0.0  0
 578  CONST_26  H6    C6   C7   C8    180.00   0.0  0
 578  CONST_27  H8    C8   C3   C4    180.00   0.0  0
 578  CONST_28  HO11  O11  C2   C1    180.00   0.0  0
 578  Var_01    O22   C23  C26  C27   155.25  30.0  2
 578  Var_02    N10   C9   C7   C8    -38.26  30.0  2
 578  Var_03    H101  N10  C9   C7    173.63  30.0  3
 578  Var_04    N19   C20  O22  C23  -176.69  30.0  3
 578  Var_05    C15   N19  C20  O22   173.47  30.0  2
 578  Var_06    H171  C17  C16  C15  -176.11  30.0  3
 578  Var_07    H181  C18  C16  C15    65.67  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
 578  chir_01  C15  N19  C16  P14  negativ
 578  chir_03  C1   O13  C3   C2   negativ
 578  chir_04  P14  O24  O13  O25  both

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
 578  plan-1  C27   0.020
 578  plan-1  C28   0.020
 578  plan-1  C29   0.020
 578  plan-1  C30   0.020
 578  plan-1  C31   0.020
 578  plan-1  C26   0.020
 578  plan-1  C23   0.020
 578  plan-1  H27   0.020
 578  plan-1  H28   0.020
 578  plan-1  H29   0.020
 578  plan-1  H30   0.020
 578  plan-1  H31   0.020
 578  plan-2  C1    0.020
 578  plan-2  C3    0.020
 578  plan-2  C8    0.020
 578  plan-2  C4    0.020
 578  plan-2  C5    0.020
 578  plan-2  C6    0.020
 578  plan-2  C7    0.020
 578  plan-2  C9    0.020
 578  plan-2  H8    0.020
 578  plan-2  H4    0.020
 578  plan-2  H5    0.020
 578  plan-2  H6    0.020
 578  plan-3  C1    0.020
 578  plan-3  C2    0.020
 578  plan-3  O12   0.020
 578  plan-3  O11   0.020
 578  plan-3  HO11  0.020
 578  plan-4  O22   0.020
 578  plan-4  C20   0.020
 578  plan-4  O21   0.020
 578  plan-4  N19   0.020

