# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:54:03 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S)-2-[3-(aminomethyl)phenyl]-3-[(R)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-methylpropyl](hydroxy)phosphoryl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)OCc1ccccc1)[P@@](O)(=O)C[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
 864  864  '(2S)-2-[3-(aminomethyl)phenyl]-3-[(R)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-methylpropyl](hydroxy)phosphoryl]propanoic acid'  ligand  60  31  .  2022-03-29  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_864
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
 864  C1    C  CH1   0  -0.445  37.1310  11.3404  60.0798
 864  C2    C  C     0   0.573  36.9873  10.3252  61.1983
 864  C3    C  CR6   0   0.163  38.5694  11.2863  59.5940
 864  C4    C  CR16  0  -0.309  39.5966  11.9320  60.2779
 864  C5    C  CR16  0  -0.225  40.8972  11.8521  59.8043
 864  C6    C  CR16  0  -0.318  41.1834  11.1276  58.6554
 864  C7    C  CR6   0   0.102  40.1700  10.4773  57.9587
 864  C8    C  CR16  0  -0.349  38.8683  10.5616  58.4457
 864  C9    C  CH2   0  -0.335  40.4779   9.7308  56.6841
 864  N10   N  NH2   0  -0.794  39.5892   8.6017  56.4793
 864  O13   O  OH1   0  -0.582  37.4594  10.7690  62.3537
 864  O14   O  O     0  -0.440  36.5592   9.2107  61.0370
 864  C15   C  CH2   0  -0.747  36.7149  12.7651  60.4653
 864  P24   P  P     0   1.289  34.9137  12.9616  60.6117
 864  C25   C  CH1   0  -0.358  34.5583  14.5728  61.4456
 864  C26   C  CH1   0  -0.248  34.4771  15.7756  60.4953
 864  C27   C  CH3   0  -0.685  35.7593  16.0317  59.7080
 864  C28   C  CH3   0  -0.649  34.0492  17.0209  61.2669
 864  N29   N  NH1   0  -0.663  35.4939  14.7719  62.5229
 864  C30   C  C     0   0.763  35.2693  14.3516  63.7870
 864  O31   O  O     0  -0.504  34.2227  13.9048  64.2022
 864  O32   O  O2    0  -0.481  36.3731  14.5065  64.5222
 864  C33   C  CH2   0  -0.234  36.3549  14.0312  65.8699
 864  O34   O  O     0  -0.708  34.1632  12.7747  59.3355
 864  O35   O  OH1   0  -0.747  34.6269  11.8565  61.7572
 864  C36   C  CR6   0   0.079  37.7772  13.7974  66.2845
 864  C37   C  CR16  0  -0.305  38.2963  14.4193  67.4134
 864  C38   C  CR16  0  -0.240  39.6063  14.1809  67.8132
 864  C39   C  CR16  0  -0.264  40.4109  13.3235  67.0776
 864  C40   C  CR16  0  -0.241  39.8995  12.7010  65.9437
 864  C41   C  CR16  0  -0.284  38.5911  12.9349  65.5510
 864  H1    H  HCH1  0   0.302  36.4960  10.9919  59.2624
 864  H4    H  HCR6  0   0.247  39.3947  12.5005  61.1766
 864  H5    H  HCR6  0   0.256  41.6943  12.3536  60.3380
 864  H6    H  HCR6  0   0.249  42.2053  11.0677  58.2993
 864  H8    H  HCR6  0   0.248  38.0752  10.0489  57.9147
 864  H91   H  HCH2  0   0.243  40.3444  10.4181  55.8433
 864  H92   H  HCH2  0   0.216  41.5436   9.4653  56.6839
 864  H101  H  HNH2  0   0.355  39.7419   8.2187  55.5558
 864  H102  H  HNH2  0   0.345  39.8228   7.8641  57.1322
 864  HO13  H  HOH1  0   0.484  37.3870  10.0790  63.0299
 864  H151  H  HCH2  0   0.287  37.2052  13.0886  61.3825
 864  H152  H  HCH2  0   0.308  37.0459  13.4417  59.6758
 864  H25   H  HCH1  0   0.308  33.5634  14.4439  61.8835
 864  H26   H  HCH1  0   0.255  33.6872  15.5375  59.7780
 864  H271  H  HCH3  0   0.237  35.9649  15.2394  58.9873
 864  H272  H  HCH3  0   0.254  35.6705  16.9575  59.1392
 864  H273  H  HCH3  0   0.221  36.6349  16.1397  60.3527
 864  H281  H  HCH3  0   0.224  34.8117  17.3347  61.9812
 864  H282  H  HCH3  0   0.237  33.8809  17.8498  60.5786
 864  H283  H  HCH3  0   0.232  33.1227  16.8503  61.8175
 864  HN29  H  HNH1  0   0.405  36.4154  15.1143  62.2990
 864  H331  H  HCH2  0   0.253  35.8759  14.7679  66.5187
 864  H332  H  HCH2  0   0.255  35.7792  13.1059  65.9342
 864  HO35  H  HOH1  0   0.489  33.7035  11.8020  62.0380
 864  H37   H  HCR6  0   0.257  37.6743  15.0973  67.9856
 864  H38   H  HCR6  0   0.258  39.9974  14.6715  68.6949
 864  H39   H  HCR6  0   0.259  41.4328  13.1399  67.3829
 864  H40   H  HCR6  0   0.258  40.5227  12.0292  65.3678
 864  H41   H  HCR6  0   0.242  38.2025  12.4411  64.6679

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
 864  C1   C3    single    1.519  0.020  1.519
 864  C1   C15   single    1.533  0.020  1.533
 864  C1   C2    single    1.517  0.020  1.517
 864  C1   H1    single    0.970  0.020  1.090
 864  C2   O14   double    1.205  0.020  1.205
 864  C2   O13   single    1.325  0.020  1.325
 864  C3   C8    aromatic  1.390  0.020  1.390
 864  C3   C4    aromatic  1.393  0.020  1.393
 864  C4   C5    aromatic  1.386  0.020  1.386
 864  C4   H4    single    0.930  0.020  1.080
 864  C5   C6    aromatic  1.388  0.020  1.388
 864  C5   H5    single    0.930  0.020  1.080
 864  C6   C7    aromatic  1.391  0.020  1.391
 864  C6   H6    single    0.930  0.020  1.080
 864  C7   C9    single    1.509  0.020  1.509
 864  C7   C8    aromatic  1.392  0.020  1.392
 864  C8   H8    single    0.930  0.020  1.080
 864  C9   N10   single    1.451  0.020  1.451
 864  C9   H91   single    0.970  0.020  1.090
 864  C9   H92   single    0.970  0.020  1.090
 864  N10  H101  single    0.890  0.020  1.040
 864  N10  H102  single    0.890  0.020  1.040
 864  O13  HO13  single    0.850  0.020  0.980
 864  C15  P24   single    1.818  0.020  1.818
 864  C15  H151  single    0.970  0.020  1.090
 864  C15  H152  single    0.970  0.020  1.090
 864  P24  O34   double    1.492  0.020  1.492
 864  P24  C25   single    1.849  0.020  1.849
 864  P24  O35   single    1.617  0.020  1.617
 864  C25  C26   single    1.535  0.020  1.535
 864  C25  N29   single    1.441  0.020  1.441
 864  C25  H25   single    0.970  0.020  1.090
 864  C26  C27   single    1.526  0.020  1.526
 864  C26  C28   single    1.526  0.020  1.526
 864  C26  H26   single    0.970  0.020  1.090
 864  C27  H271  single    0.970  0.020  1.090
 864  C27  H272  single    0.970  0.020  1.090
 864  C27  H273  single    0.970  0.020  1.090
 864  C28  H281  single    0.970  0.020  1.090
 864  C28  H282  single    0.970  0.020  1.090
 864  C28  H283  single    0.970  0.020  1.090
 864  N29  C30   single    1.351  0.020  1.351
 864  N29  HN29  single    0.860  0.020  1.020
 864  C30  O31   double    1.211  0.020  1.211
 864  C30  O32   single    1.335  0.020  1.335
 864  O32  C33   single    1.429  0.020  1.429
 864  C33  C36   single    1.500  0.020  1.500
 864  C33  H331  single    0.970  0.020  1.090
 864  C33  H332  single    0.970  0.020  1.090
 864  O35  HO35  single    0.850  0.020  0.980
 864  C36  C41   aromatic  1.394  0.020  1.394
 864  C36  C37   aromatic  1.389  0.020  1.389
 864  C37  C38   aromatic  1.390  0.020  1.390
 864  C37  H37   single    0.930  0.020  1.080
 864  C38  C39   aromatic  1.387  0.020  1.387
 864  C38  H38   single    0.930  0.020  1.080
 864  C39  C40   aromatic  1.391  0.020  1.391
 864  C39  H39   single    0.930  0.020  1.080
 864  C40  C41   aromatic  1.386  0.020  1.386
 864  C40  H40   single    0.930  0.020  1.080
 864  C41  H41   single    0.930  0.020  1.080

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
 864  H1    C1   C15   109.07  3.000
 864  H1    C1   C3    107.45  3.000
 864  C15   C1   C3    111.74  3.000
 864  H1    C1   C2    106.45  3.000
 864  C15   C1   C2    114.24  3.000
 864  C3    C1   C2    107.56  3.000
 864  O14   C2   O13   123.60  3.000
 864  O13   C2   C1    112.65  3.000
 864  O14   C2   C1    123.63  3.000
 864  C8    C3   C4    119.25  3.000
 864  C4    C3   C1    121.65  3.000
 864  C8    C3   C1    119.09  3.000
 864  H4    C4   C5    119.26  3.000
 864  H4    C4   C3    120.91  3.000
 864  C5    C4   C3    119.83  3.000
 864  H5    C5   C6    119.87  3.000
 864  H5    C5   C4    119.72  3.000
 864  C6    C5   C4    120.41  3.000
 864  H6    C6   C7    119.77  3.000
 864  H6    C6   C5    119.68  3.000
 864  C7    C6   C5    120.56  3.000
 864  C9    C7   C8    121.07  3.000
 864  C8    C7   C6    118.53  3.000
 864  C9    C7   C6    120.38  3.000
 864  H8    C8   C7    118.97  3.000
 864  H8    C8   C3    119.61  3.000
 864  C7    C8   C3    121.42  3.000
 864  H92   C9   H91   105.67  3.000
 864  H92   C9   N10   113.96  3.000
 864  H91   C9   N10   107.79  3.000
 864  H92   C9   C7    108.53  3.000
 864  H91   C9   C7    108.27  3.000
 864  N10   C9   C7    112.28  3.000
 864  H102  N10  H101  106.15  3.000
 864  H102  N10  C9    109.54  3.000
 864  H101  N10  C9    109.33  3.000
 864  HO13  O13  C2    110.09  3.000
 864  H152  C15  H151  106.77  3.000
 864  H152  C15  P24   106.96  3.000
 864  H151  C15  P24   110.25  3.000
 864  H152  C15  C1    108.18  3.000
 864  H151  C15  C1    111.44  3.000
 864  P24   C15  C1    112.93  3.000
 864  O35   P24  O34   115.53  3.000
 864  O35   P24  C25   104.00  3.000
 864  O34   P24  C25   113.47  3.000
 864  O35   P24  C15    99.14  3.000
 864  C25   P24  C15   108.73  3.000
 864  O34   P24  C15   114.58  3.000
 864  H25   C25  N29   107.90  3.000
 864  H25   C25  C26   106.97  3.000
 864  N29   C25  C26   112.89  3.000
 864  H25   C25  P24   104.63  3.000
 864  N29   C25  P24   109.44  3.000
 864  C26   C25  P24   114.44  3.000
 864  H26   C26  C28   107.87  3.000
 864  H26   C26  C27   107.77  3.000
 864  C28   C26  C27   111.07  3.000
 864  H26   C26  C25   105.88  3.000
 864  C28   C26  C25   109.95  3.000
 864  C27   C26  C25   113.97  3.000
 864  H273  C27  H272  106.81  3.000
 864  H273  C27  H271  108.10  3.000
 864  H272  C27  H271  106.71  3.000
 864  H273  C27  C26   112.67  3.000
 864  H272  C27  C26   110.07  3.000
 864  H271  C27  C26   112.17  3.000
 864  H283  C28  H282  107.84  3.000
 864  H283  C28  H281  107.94  3.000
 864  H282  C28  H281  107.61  3.000
 864  H283  C28  C26   111.44  3.000
 864  H282  C28  C26   110.14  3.000
 864  H281  C28  C26   111.70  3.000
 864  HN29  N29  C30   117.73  3.000
 864  HN29  N29  C25   118.33  3.000
 864  C30   N29  C25   123.28  3.000
 864  O32   C30  O31   124.63  3.000
 864  O32   C30  N29   109.98  3.000
 864  O31   C30  N29   125.39  3.000
 864  C33   O32  C30   118.04  3.000
 864  H332  C33  H331  107.79  3.000
 864  H332  C33  C36   110.59  3.000
 864  H331  C33  C36   110.91  3.000
 864  H332  C33  O32   110.13  3.000
 864  H331  C33  O32   109.96  3.000
 864  C36   C33  O32   107.48  3.000
 864  HO35  O35  P24   114.44  3.000
 864  C41   C36  C37   119.09  3.000
 864  C37   C36  C33   120.60  3.000
 864  C41   C36  C33   120.30  3.000
 864  H37   C37  C38   119.76  3.000
 864  H37   C37  C36   119.65  3.000
 864  C38   C37  C36   120.59  3.000
 864  H38   C38  C39   120.19  3.000
 864  H38   C38  C37   119.81  3.000
 864  C39   C38  C37   120.01  3.000
 864  H39   C39  C40   120.08  3.000
 864  H39   C39  C38   120.20  3.000
 864  C40   C39  C38   119.72  3.000
 864  H40   C40  C41   119.84  3.000
 864  H40   C40  C39   119.99  3.000
 864  C41   C40  C39   120.17  3.000
 864  H41   C41  C40   119.50  3.000
 864  H41   C41  C36   120.08  3.000
 864  C40   C41  C36   120.42  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
 864  CONST_01  C6    C7   C8   C3     0.00   0.0  0
 864  CONST_02  C6    C5   C4   C3     0.00   0.0  0
 864  CONST_03  C7    C8   C3   C4     0.00   0.0  0
 864  CONST_04  C7    C6   C5   C4     0.00   0.0  0
 864  CONST_05  C8    C3   C4   C5     0.00   0.0  0
 864  CONST_06  C8    C7   C6   C5     0.00   0.0  0
 864  CONST_07  C39   C40  C41  C36    0.00   0.0  0
 864  CONST_08  C39   C38  C37  C36    0.00   0.0  0
 864  CONST_09  C40   C41  C36  C37    0.00   0.0  0
 864  CONST_10  C40   C39  C38  C37    0.00   0.0  0
 864  CONST_11  C41   C36  C37  C38    0.00   0.0  0
 864  CONST_12  C41   C40  C39  C38    0.00   0.0  0
 864  CONST_13  C7    C8   C3   C1   180.00   0.0  0
 864  CONST_14  C5    C4   C3   C1   180.00   0.0  0
 864  CONST_15  C9    C7   C8   C3   180.00   0.0  0
 864  CONST_16  C9    C7   C6   C5   180.00   0.0  0
 864  CONST_17  C40   C41  C36  C33  180.00   0.0  0
 864  CONST_18  C38   C37  C36  C33  180.00   0.0  0
 864  CONST_19  H5    C5   C4   C3   180.00   0.0  0
 864  CONST_20  H8    C8   C3   C4   180.00   0.0  0
 864  CONST_21  H6    C6   C5   C4   180.00   0.0  0
 864  CONST_22  H4    C4   C5   C6   180.00   0.0  0
 864  CONST_23  H40   C40  C41  C36  180.00   0.0  0
 864  CONST_24  H38   C38  C37  C36  180.00   0.0  0
 864  CONST_25  H41   C41  C36  C37  180.00   0.0  0
 864  CONST_26  H39   C39  C38  C37  180.00   0.0  0
 864  CONST_27  H37   C37  C38  C39  180.00   0.0  0
 864  CONST_28  HO13  O13  C2   C1   180.00   0.0  0
 864  Var_01    N10   C9   C7   C6   149.61  30.0  2
 864  Var_02    C41   C36  C33  O32  -56.93  30.0  2
 864  Var_03    C36   C33  O32  C30  157.33  30.0  3
 864  Var_04    H101  N10  C9   C7   171.70  30.0  3
 864  Var_05    O34   P24  C15  C1   -64.78  30.0  3
 864  Var_06    O31   C30  N29  C25   -8.78  30.0  2
 864  Var_07    H271  C27  C26  C25   67.53  30.0  3
 864  Var_08    H281  C28  C26  C25   66.87  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
 864  chir_01  C1   C3   C15  C2   positiv
 864  chir_03  C25  P24  C26  N29  positiv
 864  chir_04  P24  O34  C25  O35  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
 864  plan-1  C1    0.020
 864  plan-1  C3    0.020
 864  plan-1  C4    0.020
 864  plan-1  C5    0.020
 864  plan-1  C6    0.020
 864  plan-1  C7    0.020
 864  plan-1  C8    0.020
 864  plan-1  C9    0.020
 864  plan-1  H4    0.020
 864  plan-1  H5    0.020
 864  plan-1  H6    0.020
 864  plan-1  H8    0.020
 864  plan-2  C33   0.020
 864  plan-2  C36   0.020
 864  plan-2  C37   0.020
 864  plan-2  C38   0.020
 864  plan-2  C39   0.020
 864  plan-2  C40   0.020
 864  plan-2  C41   0.020
 864  plan-2  H37   0.020
 864  plan-2  H38   0.020
 864  plan-2  H39   0.020
 864  plan-2  H40   0.020
 864  plan-2  H41   0.020
 864  plan-3  C1    0.020
 864  plan-3  C2    0.020
 864  plan-3  O13   0.020
 864  plan-3  O14   0.020
 864  plan-3  HO13  0.020
 864  plan-4  N29   0.020
 864  plan-4  C30   0.020
 864  plan-4  O31   0.020
 864  plan-4  O32   0.020

