# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:23:37 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: ethyl (S)-N,N-dimethylphosphonamidoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P@H](=O)N(C)C
#
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
 NTJ  NTJ  'ethyl (S)-N,N-dimethylphosphonamidoate'  ligand  20  8  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NTJ
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
 NTJ  O1    O  O     0  -0.714   1.2178   2.8691  -1.1313
 NTJ  P1    P  P     0   1.088   1.9756   1.6929  -1.6362
 NTJ  N1    N  NT    0  -0.584   1.2495   0.1960  -1.6427
 NTJ  C2    C  CH3   0  -0.523   0.7855  -0.3422  -0.3745
 NTJ  C1    C  CH3   0  -0.512   0.4364  -0.1810  -2.7849
 NTJ  O2    O  O2    0  -0.592   3.3045   1.5060  -0.7498
 NTJ  C3    C  CH2   0  -0.170   4.2678   0.4929  -1.0699
 NTJ  C4    C  CH3   0  -0.684   5.4204   0.6057  -0.1018
 NTJ  H2C1  H  HCH3  0   0.234  -0.2150   0.0129  -0.1109
 NTJ  H2C2  H  HCH3  0   0.247   1.4679  -0.0755   0.4319
 NTJ  H2C3  H  HCH3  0   0.248   0.7559  -1.4306  -0.4339
 NTJ  H1C1  H  HCH3  0   0.245   0.8389   0.2463  -3.7030
 NTJ  H1C2  H  HCH3  0   0.228  -0.6048   0.1400  -2.6855
 NTJ  H1C3  H  HCH3  0   0.246   0.4486  -1.2661  -2.8959
 NTJ  H3C1  H  HCH2  0   0.231   3.8044  -0.4940  -1.0026
 NTJ  H3C2  H  HCH2  0   0.228   4.6177   0.6242  -2.0986
 NTJ  H4C1  H  HCH3  0   0.237   6.1584  -0.1636  -0.3278
 NTJ  H4C2  H  HCH3  0   0.235   5.9132   1.5751  -0.1757
 NTJ  H4C3  H  HCH3  0   0.235   5.0889   0.4611   0.9266
 NTJ  HP1   H  H     0   0.078   2.4092   1.7890  -2.9705

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
 NTJ  O1   P1    double  1.487  0.020  1.487
 NTJ  P1   N1    single  1.664  0.020  1.664
 NTJ  P1   O2    single  1.608  0.020  1.608
 NTJ  N1   C2    single  1.454  0.020  1.454
 NTJ  N1   C1    single  1.452  0.020  1.452
 NTJ  C2   H2C1  single  0.939  0.020  1.096
 NTJ  C2   H2C2  single  0.939  0.020  1.096
 NTJ  C2   H2C3  single  0.939  0.020  1.096
 NTJ  C1   H1C1  single  0.939  0.020  1.096
 NTJ  C1   H1C2  single  0.939  0.020  1.096
 NTJ  C1   H1C3  single  0.939  0.020  1.096
 NTJ  O2   C3    single  1.434  0.020  1.434
 NTJ  C3   C4    single  1.509  0.020  1.509
 NTJ  C3   H3C1  single  0.939  0.020  1.096
 NTJ  C3   H3C2  single  0.939  0.020  1.096
 NTJ  C4   H4C1  single  0.939  0.020  1.096
 NTJ  C4   H4C2  single  0.939  0.020  1.096
 NTJ  C4   H4C3  single  0.939  0.020  1.096
 NTJ  HP1  P1    single  1.209  0.020  1.412

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
 NTJ  HP1   P1  O2    106.03  3.000
 NTJ  HP1   P1  N1    101.08  3.000
 NTJ  O2    P1  N1    104.96  3.000
 NTJ  HP1   P1  O1    115.16  3.000
 NTJ  O2    P1  O1    109.01  3.000
 NTJ  N1    P1  O1    119.37  3.000
 NTJ  C1    N1  C2    114.30  3.000
 NTJ  C1    N1  P1    118.76  3.000
 NTJ  C2    N1  P1    117.96  3.000
 NTJ  H2C3  C2  H2C2  107.55  3.000
 NTJ  H2C3  C2  H2C1  108.20  3.000
 NTJ  H2C2  C2  H2C1  108.37  3.000
 NTJ  H2C3  C2  N1    109.31  3.000
 NTJ  H2C2  C2  N1    110.80  3.000
 NTJ  H2C1  C2  N1    112.45  3.000
 NTJ  H1C3  C1  H1C2  108.16  3.000
 NTJ  H1C3  C1  H1C1  107.47  3.000
 NTJ  H1C2  C1  H1C1  108.24  3.000
 NTJ  H1C3  C1  N1    109.40  3.000
 NTJ  H1C2  C1  N1    112.66  3.000
 NTJ  H1C1  C1  N1    110.74  3.000
 NTJ  C3    O2  P1    120.94  3.000
 NTJ  H3C2  C3  H3C1  107.57  3.000
 NTJ  H3C2  C3  C4    110.47  3.000
 NTJ  H3C1  C3  C4    110.61  3.000
 NTJ  H3C2  C3  O2    109.86  3.000
 NTJ  H3C1  C3  O2    109.85  3.000
 NTJ  C4    C3  O2    108.48  3.000
 NTJ  H4C3  C4  H4C2  108.63  3.000
 NTJ  H4C3  C4  H4C1  107.93  3.000
 NTJ  H4C2  C4  H4C1  107.91  3.000
 NTJ  H4C3  C4  C3    111.28  3.000
 NTJ  H4C2  C4  C3    111.61  3.000
 NTJ  H4C1  C4  C3    109.35  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
 NTJ  Var_01  C2    N1  P1  O1  -59.04  30.0  3
 NTJ  Var_02  C4    C3  O2  P1  177.59  30.0  3
 NTJ  Var_03  H2C1  C2  N1  P1   84.87  30.0  3
 NTJ  Var_04  H1C1  C1  N1  P1   33.82  30.0  3
 NTJ  Var_05  H4C1  C4  C3  O2  179.57  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
 NTJ  chir_01  P1  O1  N1  O2  both

