# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:46:39 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-{3-[(R)-[(glycylamino)methyl](hydroxy)phosphoryl]propanoyl}glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)NC[P](O)(=O)CCC(=O)NCC(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
 4SQ  4SQ  N-{3-[(R)-[(glycylamino)methyl](hydroxy)phosphoryl]propanoyl}glycine  ligand  34  18  .  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_4SQ
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
 4SQ  C4   C  C     0   0.521  -6.0983  -0.4995   0.2669
 4SQ  N1   N  NH2   0  -0.790   6.8598  -1.0597  -0.5654
 4SQ  N2   N  NH1   0  -0.617   3.9411   0.7403   0.6407
 4SQ  C3   C  C     0   0.582  -2.6687   0.6174  -0.5058
 4SQ  O42  O  OH1   0  -0.585  -7.3206  -0.0066   0.1684
 4SQ  O41  O  O     0  -0.434  -5.8424  -1.6137   0.6462
 4SQ  CA4  C  CH2   0  -0.372  -5.0700   0.5187  -0.1545
 4SQ  N4   N  NH1   0  -0.649  -3.7485  -0.0332  -0.0481
 4SQ  O3   O  O     0  -0.496  -2.7377   1.7238  -1.0207
 4SQ  CA3  C  CH2   0  -0.586  -1.3615  -0.1378  -0.3700
 4SQ  CN3  C  CH2   0  -0.714  -0.1956   0.8038  -0.0897
 4SQ  P    P  P     0   1.208   1.3794  -0.0724   0.0404
 4SQ  OP1  O  O     0  -0.721   1.4346  -1.1052   1.1166
 4SQ  OP2  O  OH1   0  -0.782   1.6027  -0.6226  -1.4568
 4SQ  CA2  C  CH2   0  -0.542   2.6458   1.2445   0.2531
 4SQ  C1   C  C     0   0.575   4.6627  -0.0951  -0.1117
 4SQ  O1   O  O     0  -0.527   4.2519  -0.5491  -1.1798
 4SQ  CA1  C  CH2   0  -0.406   6.0094  -0.4905   0.4555
 4SQ  H1   H  HNH2  0   0.358   7.7659  -1.2500  -0.1589
 4SQ  H2   H  HNH2  0   0.349   6.4926  -1.9562  -0.8564
 4SQ  H4   H  HNH1  0   0.420   4.3290   1.0740   1.5083
 4SQ  H5   H  HOH1  0   0.490  -7.9742  -0.6702   0.4364
 4SQ  H6   H  HCH2  0   0.292  -5.2868   0.8278  -1.1809
 4SQ  H7   H  HCH2  0   0.290  -5.1881   1.4105   0.4699
 4SQ  H8   H  HNH1  0   0.406  -3.6436  -0.9316   0.3967
 4SQ  H9   H  HCH2  0   0.270  -1.4353  -0.8981   0.4094
 4SQ  H10  H  HCH2  0   0.289  -1.2047  -0.6716  -1.3116
 4SQ  H11  H  HCH2  0   0.286  -0.1112   1.5632  -0.8690
 4SQ  H12  H  HCH2  0   0.290  -0.3499   1.3281   0.8567
 4SQ  H13  H  HOH1  0   0.485   2.5734  -0.6923  -1.6138
 4SQ  H14  H  HCH2  0   0.305   2.3021   1.9049   1.0480
 4SQ  H15  H  HCH2  0   0.291   2.7017   1.8461  -0.6584
 4SQ  H16  H  HCH2  0   0.250   5.8078  -1.1544   1.3097
 4SQ  H17  H  HCH2  0   0.263   6.4938   0.3948   0.8722

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
 4SQ  O41  C4   double  1.204  0.020  1.204
 4SQ  C4   O42  single  1.322  0.020  1.322
 4SQ  C4   CA4  single  1.507  0.020  1.507
 4SQ  CA4  N4   single  1.436  0.020  1.436
 4SQ  N4   C3   single  1.341  0.020  1.341
 4SQ  C3   CA3  single  1.516  0.020  1.516
 4SQ  C3   O3   double  1.222  0.020  1.222
 4SQ  CA3  CN3  single  1.525  0.020  1.525
 4SQ  OP1  P    double  1.493  0.020  1.493
 4SQ  CN3  P    single  1.807  0.020  1.807
 4SQ  P    CA2  single  1.839  0.020  1.839
 4SQ  P    OP2  single  1.611  0.020  1.611
 4SQ  CA2  N2   single  1.443  0.020  1.443
 4SQ  N2   C1   single  1.336  0.020  1.336
 4SQ  C1   CA1  single  1.514  0.020  1.514
 4SQ  C1   O1   double  1.231  0.020  1.231
 4SQ  CA1  N1   single  1.445  0.020  1.445
 4SQ  N1   H1   single  0.890  0.020  1.040
 4SQ  N1   H2   single  0.890  0.020  1.040
 4SQ  N2   H4   single  0.860  0.020  1.020
 4SQ  O42  H5   single  0.850  0.020  0.980
 4SQ  CA4  H6   single  0.970  0.020  1.090
 4SQ  CA4  H7   single  0.970  0.020  1.090
 4SQ  N4   H8   single  0.860  0.020  1.020
 4SQ  CA3  H9   single  0.970  0.020  1.090
 4SQ  CA3  H10  single  0.970  0.020  1.090
 4SQ  CN3  H11  single  0.970  0.020  1.090
 4SQ  CN3  H12  single  0.970  0.020  1.090
 4SQ  OP2  H13  single  0.850  0.020  0.980
 4SQ  CA2  H14  single  0.970  0.020  1.090
 4SQ  CA2  H15  single  0.970  0.020  1.090
 4SQ  CA1  H16  single  0.970  0.020  1.090
 4SQ  CA1  H17  single  0.970  0.020  1.090

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
 4SQ  CA4  C4   O41  124.61  3.000
 4SQ  CA4  C4   O42  110.99  3.000
 4SQ  O41  C4   O42  124.39  3.000
 4SQ  H2   N1   H1   105.91  3.000
 4SQ  H2   N1   CA1  109.79  3.000
 4SQ  H1   N1   CA1  108.50  3.000
 4SQ  H4   N2   C1   118.97  3.000
 4SQ  H4   N2   CA2  117.47  3.000
 4SQ  C1   N2   CA2  123.51  3.000
 4SQ  CA3  C3   O3   122.51  3.000
 4SQ  O3   C3   N4   122.50  3.000
 4SQ  CA3  C3   N4   114.97  3.000
 4SQ  H5   O42  C4   110.35  3.000
 4SQ  H7   CA4  H6   106.47  3.000
 4SQ  H7   CA4  N4   111.71  3.000
 4SQ  H6   CA4  N4   111.13  3.000
 4SQ  H7   CA4  C4   108.49  3.000
 4SQ  H6   CA4  C4   108.55  3.000
 4SQ  N4   CA4  C4   110.34  3.000
 4SQ  H8   N4   CA4  118.10  3.000
 4SQ  H8   N4   C3   119.94  3.000
 4SQ  CA4  N4   C3   121.95  3.000
 4SQ  H10  CA3  H9   106.53  3.000
 4SQ  H10  CA3  CN3  110.49  3.000
 4SQ  H9   CA3  CN3  110.53  3.000
 4SQ  H10  CA3  C3   106.84  3.000
 4SQ  H9   CA3  C3   110.66  3.000
 4SQ  CN3  CA3  C3   111.60  3.000
 4SQ  H12  CN3  H11  107.19  3.000
 4SQ  H12  CN3  P    107.06  3.000
 4SQ  H11  CN3  P    108.74  3.000
 4SQ  H12  CN3  CA3  110.34  3.000
 4SQ  H11  CN3  CA3  110.95  3.000
 4SQ  P    CN3  CA3  112.35  3.000
 4SQ  CA2  P    OP2  104.87  3.000
 4SQ  OP2  P    OP1  115.38  3.000
 4SQ  CA2  P    OP1  112.74  3.000
 4SQ  OP2  P    CN3  102.68  3.000
 4SQ  CA2  P    CN3  105.15  3.000
 4SQ  OP1  P    CN3  114.81  3.000
 4SQ  H13  OP2  P    107.98  3.000
 4SQ  H15  CA2  H14  106.91  3.000
 4SQ  H15  CA2  P    109.43  3.000
 4SQ  H14  CA2  P    107.53  3.000
 4SQ  H15  CA2  N2   111.73  3.000
 4SQ  H14  CA2  N2   107.41  3.000
 4SQ  P    CA2  N2   113.51  3.000
 4SQ  CA1  C1   O1   121.71  3.000
 4SQ  O1   C1   N2   122.62  3.000
 4SQ  CA1  C1   N2   115.65  3.000
 4SQ  H17  CA1  H16  105.92  3.000
 4SQ  H17  CA1  C1   109.02  3.000
 4SQ  H16  CA1  C1   106.58  3.000
 4SQ  H17  CA1  N1   109.14  3.000
 4SQ  H16  CA1  N1   114.74  3.000
 4SQ  C1   CA1  N1   111.19  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
 4SQ  CONST_01  CA3  C3   N4   CA4   180.00   0.0  0
 4SQ  CONST_02  O3   C3   N4   CA4     0.00   0.0  0
 4SQ  CONST_03  CA1  C1   N2   CA2   180.00   0.0  0
 4SQ  CONST_04  O1   C1   N2   CA2     0.00   0.0  0
 4SQ  CONST_05  H8   N4   C3   O3    180.00   0.0  0
 4SQ  CONST_06  H4   N2   C1   O1    180.00   0.0  0
 4SQ  CONST_07  H5   O42  C4   O41     0.00   0.0  0
 4SQ  Var_01    C3   N4   CA4  C4    172.34  30.0  3
 4SQ  Var_02    N2   C1   CA1  N1   -163.36  30.0  1
 4SQ  Var_03    OP1  P    CA2  N2     42.57  30.0  1
 4SQ  Var_04    P    CN3  CA3  C3   -178.76  30.0  3
 4SQ  Var_05    N4   CA4  C4   O42  -179.73  30.0  3
 4SQ  Var_06    CN3  CA3  C3   N4   -145.80  30.0  3
 4SQ  Var_07    C1   N2   CA2  P      61.81  30.0  3
 4SQ  Var_08    H1   N1   CA1  C1    176.19  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
 4SQ  chir_01  P  CN3  CA2  OP2  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
 4SQ  plan-1  C3   0.020
 4SQ  plan-1  CA4  0.020
 4SQ  plan-1  N4   0.020
 4SQ  plan-1  O3   0.020
 4SQ  plan-1  CA3  0.020
 4SQ  plan-1  H8   0.020
 4SQ  plan-2  N2   0.020
 4SQ  plan-2  CA2  0.020
 4SQ  plan-2  C1   0.020
 4SQ  plan-2  O1   0.020
 4SQ  plan-2  CA1  0.020
 4SQ  plan-2  H4   0.020
 4SQ  plan-3  C4   0.020
 4SQ  plan-3  O42  0.020
 4SQ  plan-3  O41  0.020
 4SQ  plan-3  CA4  0.020
 4SQ  plan-3  H5   0.020

