# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:09:22 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](C[P](O)(=O)[C@@H](N)c1ccccc1)C(O)=O
#
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
 4ZN  4ZN  '(2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid'  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4ZN
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
 4ZN  N12  N  NH2    0  -0.796  -1.1992   2.2447   0.7209
 4ZN  C13  C  CR6    0   0.146  -2.9762   0.4943   0.4149
 4ZN  C15  C  CR16   0  -0.245  -4.9295   0.8479  -0.9718
 4ZN  C17  C  CR16   0  -0.250  -4.9092  -0.9536   0.6097
 4ZN  C02  C  CH3    0  -0.646   5.3732   1.8747   0.6731
 4ZN  C04  C  CH3    0  -0.661   3.6808   2.1194  -1.1623
 4ZN  C05  C  CH2    0  -0.386   3.7366   0.0239   0.2704
 4ZN  C06  C  CH1    0  -0.349   2.3734  -0.4820  -0.2194
 4ZN  P08  P  P      0   1.187  -0.4027  -0.1713  -0.2299
 4ZN  O09  O  OP    -1  -0.801  -0.8013  -1.6252  -0.1025
 4ZN  O10  O  O      0  -0.817  -0.3961   0.4736  -1.6054
 4ZN  C11  C  CH1    0  -0.406  -1.5702   0.8450   0.8240
 4ZN  C14  C  CR16   0  -0.313  -3.6452   1.2049  -0.5792
 4ZN  C16  C  CR16   0  -0.280  -5.5680  -0.2335  -0.3805
 4ZN  C18  C  CR16   0  -0.295  -3.6264  -0.5946   0.9961
 4ZN  C19  C  C      0   0.425   2.3744  -2.0223  -0.1594
 4ZN  O20  O  OC    -1  -0.631   2.4266  -2.6392  -1.2446
 4ZN  O21  O  O      0  -0.626   2.3844  -2.5410   0.9767
 4ZN  H1   H  HNH2   0   0.339  -1.0616   2.4910  -0.2512
 4ZN  H2   H  HNH2   0   0.339  -1.9399   2.8392   1.0737
 4ZN  H4   H  HCR6   0   0.245  -5.4332   1.4173  -1.7432
 4ZN  H5   H  HCR6   0   0.245  -5.3984  -1.7966   1.0818
 4ZN  H6   H  HCH3   0   0.209   6.1131   1.4452  -0.0071
 4ZN  H7   H  HCH3   0   0.220   5.5376   2.9536   0.7016
 4ZN  H8   H  HCH3   0   0.219   5.5764   1.4826   1.6714
 4ZN  H9   H  HCH1   0   0.208   3.2666   2.0124   0.9292
 4ZN  H10  H  HCH3   0   0.229   2.6412   1.9850  -1.4660
 4ZN  H11  H  HCH3   0   0.220   3.8932   3.1902  -1.1878
 4ZN  H12  H  HCH3   0   0.208   4.3083   1.6407  -1.9192
 4ZN  H13  H  HCH2   0   0.199   4.5204  -0.4509  -0.3346
 4ZN  H14  H  HCH2   0   0.204   3.8944  -0.3218   1.2972
 4ZN  H15  H  HCH1   0   0.197   2.2578  -0.1866  -1.2655
 4ZN  H16  H  HCH2   0   0.214   1.2098  -0.2755   1.5901
 4ZN  H17  H  HCH2   0   0.231   1.3326   1.2081   0.6607
 4ZN  H19  H  HCH1   0   0.234  -1.4262   0.5161   1.8602
 4ZN  H20  H  HCR6   0   0.228  -3.1684   2.0577  -1.0454
 4ZN  H21  H  HCR6   0   0.247  -6.5702  -0.5092  -0.6828
 4ZN  H22  H  HCR6   0   0.232  -3.1225  -1.1620   1.7695
 4ZN  C07  C  CH2    0  -0.687   1.2163   0.1250   0.5731
 4ZN  C03  C  CH1    0  -0.237   3.9549   1.5379   0.2210

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
 4ZN  C04  C03  single    1.525  0.020  1.525
 4ZN  C03  C02  single    1.526  0.020  1.526
 4ZN  C03  C05  single    1.530  0.020  1.530
 4ZN  C05  C06  single    1.534  0.020  1.534
 4ZN  O10  P08  deloc     1.519  0.020  1.519
 4ZN  O09  P08  deloc     1.513  0.020  1.513
 4ZN  C07  C06  single    1.528  0.020  1.528
 4ZN  C07  P08  single    1.831  0.020  1.831
 4ZN  C06  C19  single    1.542  0.020  1.542
 4ZN  P08  C11  single    1.873  0.020  1.873
 4ZN  C19  O21  deloc     1.249  0.020  1.249
 4ZN  C19  O20  deloc     1.249  0.020  1.249
 4ZN  N12  C11  single    1.452  0.020  1.452
 4ZN  C11  C13  single    1.506  0.020  1.506
 4ZN  C14  C13  aromatic  1.393  0.020  1.393
 4ZN  C14  C15  aromatic  1.390  0.020  1.390
 4ZN  C13  C18  aromatic  1.395  0.020  1.395
 4ZN  C15  C16  aromatic  1.388  0.020  1.388
 4ZN  C18  C17  aromatic  1.387  0.020  1.387
 4ZN  C16  C17  aromatic  1.390  0.020  1.390
 4ZN  N12  H1   single    0.890  0.020  1.040
 4ZN  N12  H2   single    0.890  0.020  1.040
 4ZN  C15  H4   single    0.930  0.020  1.080
 4ZN  C17  H5   single    0.930  0.020  1.080
 4ZN  C02  H6   single    0.970  0.020  1.090
 4ZN  C02  H7   single    0.970  0.020  1.090
 4ZN  C02  H8   single    0.970  0.020  1.090
 4ZN  C03  H9   single    0.970  0.020  1.090
 4ZN  C04  H10  single    0.970  0.020  1.090
 4ZN  C04  H11  single    0.970  0.020  1.090
 4ZN  C04  H12  single    0.970  0.020  1.090
 4ZN  C05  H13  single    0.970  0.020  1.090
 4ZN  C05  H14  single    0.970  0.020  1.090
 4ZN  C06  H15  single    0.970  0.020  1.090
 4ZN  C07  H16  single    0.970  0.020  1.090
 4ZN  C07  H17  single    0.970  0.020  1.090
 4ZN  C11  H19  single    0.970  0.020  1.090
 4ZN  C14  H20  single    0.930  0.020  1.080
 4ZN  C16  H21  single    0.930  0.020  1.080
 4ZN  C18  H22  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
 4ZN  H2   N12  H1   106.92  3.000
 4ZN  H2   N12  C11  110.75  3.000
 4ZN  H1   N12  C11  109.73  3.000
 4ZN  C18  C13  C14  118.14  3.000
 4ZN  C18  C13  C11  120.26  3.000
 4ZN  C14  C13  C11  121.56  3.000
 4ZN  H4   C15  C16  119.94  3.000
 4ZN  H4   C15  C14  119.73  3.000
 4ZN  C16  C15  C14  120.32  3.000
 4ZN  H5   C17  C18  119.86  3.000
 4ZN  H5   C17  C16  119.97  3.000
 4ZN  C18  C17  C16  120.17  3.000
 4ZN  H8   C02  H7   107.64  3.000
 4ZN  H8   C02  H6   107.58  3.000
 4ZN  H7   C02  H6   107.62  3.000
 4ZN  H8   C02  C03  111.38  3.000
 4ZN  H7   C02  C03  111.45  3.000
 4ZN  H6   C02  C03  110.98  3.000
 4ZN  H12  C04  H11  107.54  3.000
 4ZN  H12  C04  H10  107.46  3.000
 4ZN  H11  C04  H10  107.44  3.000
 4ZN  H12  C04  C03  110.96  3.000
 4ZN  H11  C04  C03  111.10  3.000
 4ZN  H10  C04  C03  112.12  3.000
 4ZN  H14  C05  H13  106.10  3.000
 4ZN  H14  C05  C06  108.86  3.000
 4ZN  H13  C05  C06  108.41  3.000
 4ZN  H14  C05  C03  108.79  3.000
 4ZN  H13  C05  C03  107.94  3.000
 4ZN  C06  C05  C03  116.27  3.000
 4ZN  H15  C06  C19  107.90  3.000
 4ZN  H15  C06  C07  107.99  3.000
 4ZN  C19  C06  C07  112.16  3.000
 4ZN  H15  C06  C05  108.09  3.000
 4ZN  C19  C06  C05  108.45  3.000
 4ZN  C07  C06  C05  112.10  3.000
 4ZN  C11  P08  O10  106.37  3.000
 4ZN  C11  P08  O09  108.06  3.000
 4ZN  O10  P08  O09  119.03  3.000
 4ZN  C11  P08  C07  102.51  3.000
 4ZN  O09  P08  C07  110.58  3.000
 4ZN  O10  P08  C07  108.94  3.000
 4ZN  H19  C11  P08  106.69  3.000
 4ZN  H19  C11  C13  108.02  3.000
 4ZN  P08  C11  C13  107.63  3.000
 4ZN  H19  C11  N12  108.82  3.000
 4ZN  C13  C11  N12  116.35  3.000
 4ZN  P08  C11  N12  108.91  3.000
 4ZN  H20  C14  C15  119.19  3.000
 4ZN  H20  C14  C13  119.84  3.000
 4ZN  C15  C14  C13  120.96  3.000
 4ZN  H21  C16  C17  120.38  3.000
 4ZN  H21  C16  C15  120.35  3.000
 4ZN  C17  C16  C15  119.27  3.000
 4ZN  H22  C18  C17  119.57  3.000
 4ZN  H22  C18  C13  119.29  3.000
 4ZN  C17  C18  C13  121.14  3.000
 4ZN  O21  C19  O20  125.78  3.000
 4ZN  O20  C19  C06  117.36  3.000
 4ZN  O21  C19  C06  116.77  3.000
 4ZN  H17  C07  H16  106.81  3.000
 4ZN  H17  C07  P08  106.83  3.000
 4ZN  H16  C07  P08  110.08  3.000
 4ZN  H17  C07  C06  110.77  3.000
 4ZN  H16  C07  C06  109.97  3.000
 4ZN  P08  C07  C06  112.19  3.000
 4ZN  H9   C03  C05  108.54  3.000
 4ZN  H9   C03  C04  107.95  3.000
 4ZN  C05  C03  C04  112.38  3.000
 4ZN  H9   C03  C02  107.26  3.000
 4ZN  C05  C03  C02  109.95  3.000
 4ZN  C04  C03  C02  110.58  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
 4ZN  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 4ZN  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 4ZN  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 4ZN  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 4ZN  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 4ZN  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 4ZN  CONST_07  C11  C13  C14  C15   180.00   0.0  0
 4ZN  CONST_08  C11  C13  C18  C17   180.00   0.0  0
 4ZN  CONST_09  H4   C15  C14  C13   180.00   0.0  0
 4ZN  CONST_10  H5   C17  C18  C13   180.00   0.0  0
 4ZN  CONST_11  H22  C18  C13  C14   180.00   0.0  0
 4ZN  CONST_12  H21  C16  C15  C14   180.00   0.0  0
 4ZN  CONST_13  H20  C14  C15  C16   180.00   0.0  0
 4ZN  Var_01    C06  C05  C03  C02  -177.24  30.0  3
 4ZN  Var_02    O10  P08  C07  C06   -60.83  30.0  3
 4ZN  Var_03    H10  C04  C03  C02  -173.96  30.0  3
 4ZN  Var_04    H6   C02  C03  C04   -61.38  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
 4ZN  chir_01  C06  C05  C07  C19  positiv
 4ZN  chir_03  C11  P08  N12  C13  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
 4ZN  plan-1  C13  0.020
 4ZN  plan-1  C15  0.020
 4ZN  plan-1  C17  0.020
 4ZN  plan-1  C11  0.020
 4ZN  plan-1  C14  0.020
 4ZN  plan-1  C16  0.020
 4ZN  plan-1  C18  0.020
 4ZN  plan-1  H4   0.020
 4ZN  plan-1  H5   0.020
 4ZN  plan-1  H20  0.020
 4ZN  plan-1  H21  0.020
 4ZN  plan-1  H22  0.020
 4ZN  plan-2  C06  0.020
 4ZN  plan-2  C19  0.020
 4ZN  plan-2  O20  0.020
 4ZN  plan-2  O21  0.020

