# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 03:15:13 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=C2CC(=C[C@H]2C(O)=O)C(O)=O)c1O
#
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
 RMT  RMT  '(3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid'  ligand  44  27  .  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_RMT
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
 RMT  N    N  N     0  -0.406   2.2583  -3.4070  -1.0977
 RMT  C    C  CR6   0   0.252   0.1867  -2.9834  -0.0210
 RMT  O    O  O2    0  -0.593   3.7402   0.2085  -0.0180
 RMT  C1   C  CR6   0   0.140   1.0450  -3.8084  -0.7668
 RMT  C10  C  CR5   0  -0.037  -4.3625   0.5318   0.2427
 RMT  C11  C  CR15  0  -0.185  -4.0193   1.4003  -0.7074
 RMT  C12  C  CR15  0  -0.511  -2.5305   1.5141  -0.8456
 RMT  C13  C  C     0   0.504  -5.7680   0.2463   0.5866
 RMT  C15  C  C     0   0.581  -2.0932   2.9162  -0.4643
 RMT  C2   C  CR16  0  -0.139   2.6829  -2.2037  -0.7208
 RMT  C3   C  CR6   0  -0.067   1.9077  -1.3254   0.0140
 RMT  C4   C  CR6   0   0.084   0.6169  -1.7253   0.3829
 RMT  C5   C  CH2   0  -0.456  -0.2903  -0.7747   1.1261
 RMT  C6   C  CH2   0  -0.200   2.3976   0.0343   0.4205
 RMT  C7   C  CH3   0  -0.720   0.5949  -5.1656  -1.2128
 RMT  C8   C  CR5   0   0.300  -2.0130   0.4742   0.1321
 RMT  C9   C  CH2   0  -0.566  -3.1796  -0.1175   0.8978
 RMT  N1   N  N     0  -0.342  -0.7853   0.2130   0.1948
 RMT  O1   O  OH1   0  -0.621  -1.0338  -3.4884   0.2443
 RMT  O14  O  O     0  -0.434  -6.7184   0.7595   0.0470
 RMT  O2   O  OH1   0  -0.729   5.8997   1.1607  -0.3330
 RMT  O3   O  OH1   0  -0.741   3.8451   2.6657  -0.7504
 RMT  O4   O  O     0  -0.709   4.4308   2.1149   1.6293
 RMT  O5   O  OH1   0  -0.590  -5.8635  -0.6427   1.5651
 RMT  O6   O  O     0  -0.418  -1.7127   3.2329   0.6308
 RMT  O7   O  OH1   0  -0.585  -2.2357   3.7541  -1.4785
 RMT  P    P  P     0   1.466   4.4841   1.5974   0.2501
 RMT  H2   H  HCR5  0   0.292  -4.7093   1.9719  -1.3126
 RMT  H4   H  HCR5  0   0.336  -2.2036   1.2983  -1.8679
 RMT  H5   H  HCR6  0   0.258   3.6871  -1.9403  -1.0256
 RMT  H6   H  HCH2  0   0.246  -1.0732  -1.3005   1.6849
 RMT  H7   H  HCH2  0   0.291   0.2816  -0.2514   1.8973
 RMT  H8   H  HCH2  0   0.259   2.3484   0.1417   1.5088
 RMT  H9   H  HCH2  0   0.260   1.7474   0.8004  -0.0138
 RMT  H10  H  HCH3  0   0.247   0.2909  -5.7879  -0.3693
 RMT  H11  H  HCH3  0   0.248  -0.2616  -5.1037  -1.8868
 RMT  H12  H  HCH3  0   0.248   1.4041  -5.6693  -1.7369
 RMT  H13  H  HCH2  0   0.300  -3.1144   0.1067   1.9665
 RMT  H14  H  HCH2  0   0.284  -3.2122  -1.2074   0.8090
 RMT  H15  H  HOH1  0   0.473  -1.5120  -2.9529   0.8853
 RMT  H16  H  HOH1  0   0.505   6.6058   1.8019  -0.1754
 RMT  H17  H  HOH1  0   0.497   3.8857   2.4408  -1.6897
 RMT  H18  H  HOH1  0   0.489  -6.7944  -0.8116   1.7766
 RMT  H19  H  HOH1  0   0.487  -2.0074   4.6562  -1.2054

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
 RMT  O4   P    double    1.474  0.020  1.474
 RMT  O3   P    single    1.597  0.020  1.597
 RMT  P    O2   single    1.592  0.020  1.592
 RMT  P    O    single    1.598  0.020  1.598
 RMT  O    C6   single    1.423  0.020  1.423
 RMT  C6   C3   single    1.501  0.020  1.501
 RMT  O14  C13  double    1.207  0.020  1.207
 RMT  C9   C8   single    1.516  0.020  1.516
 RMT  C9   C10  single    1.500  0.020  1.500
 RMT  C5   N1   single    1.445  0.020  1.445
 RMT  C5   C4   single    1.510  0.020  1.510
 RMT  C3   C4   aromatic  1.401  0.020  1.401
 RMT  C3   C2   aromatic  1.383  0.020  1.383
 RMT  C13  C10  single    1.475  0.020  1.475
 RMT  C13  O5   single    1.325  0.020  1.325
 RMT  C8   N1   double    1.257  0.020  1.257
 RMT  C8   C12  single    1.518  0.020  1.518
 RMT  C10  C11  double    1.332  0.020  1.332
 RMT  C4   C    aromatic  1.390  0.020  1.390
 RMT  C2   N    aromatic  1.331  0.020  1.331
 RMT  C12  C11  single    1.500  0.020  1.500
 RMT  C12  C15  single    1.517  0.020  1.517
 RMT  C    O1   single    1.347  0.020  1.347
 RMT  C    C1   aromatic  1.405  0.020  1.405
 RMT  N    C1   aromatic  1.320  0.020  1.320
 RMT  O6   C15  double    1.202  0.020  1.202
 RMT  C1   C7   single    1.498  0.020  1.498
 RMT  C15  O7   single    1.323  0.020  1.323
 RMT  C11  H2   single    0.930  0.020  1.080
 RMT  C12  H4   single    0.970  0.020  1.090
 RMT  C2   H5   single    0.930  0.020  1.080
 RMT  C5   H6   single    0.970  0.020  1.090
 RMT  C5   H7   single    0.970  0.020  1.090
 RMT  C6   H8   single    0.970  0.020  1.090
 RMT  C6   H9   single    0.970  0.020  1.090
 RMT  C7   H10  single    0.970  0.020  1.090
 RMT  C7   H11  single    0.970  0.020  1.090
 RMT  C7   H12  single    0.970  0.020  1.090
 RMT  C9   H13  single    0.970  0.020  1.090
 RMT  C9   H14  single    0.970  0.020  1.090
 RMT  O1   H15  single    0.850  0.020  0.980
 RMT  O2   H16  single    0.850  0.020  0.980
 RMT  O3   H17  single    0.850  0.020  0.980
 RMT  O5   H18  single    0.850  0.020  0.980
 RMT  O7   H19  single    0.850  0.020  0.980

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
 RMT  C2   N    C1   119.83  3.000
 RMT  O1   C    C4   124.24  3.000
 RMT  O1   C    C1   115.97  3.000
 RMT  C4   C    C1   119.79  3.000
 RMT  P    O    C6   119.59  3.000
 RMT  C7   C1   C    120.44  3.000
 RMT  C7   C1   N    118.50  3.000
 RMT  C    C1   N    121.06  3.000
 RMT  C9   C10  C13  124.47  3.000
 RMT  C13  C10  C11  122.55  3.000
 RMT  C9   C10  C11  112.99  3.000
 RMT  H2   C11  C12  122.82  3.000
 RMT  H2   C11  C10  125.41  3.000
 RMT  C12  C11  C10  111.77  3.000
 RMT  H4   C12  C8   111.38  3.000
 RMT  H4   C12  C15  109.31  3.000
 RMT  C8   C12  C15  111.89  3.000
 RMT  H4   C12  C11  111.56  3.000
 RMT  C15  C12  C11  109.46  3.000
 RMT  C8   C12  C11  103.13  3.000
 RMT  O5   C13  O14  123.94  3.000
 RMT  O5   C13  C10  111.76  3.000
 RMT  O14  C13  C10  124.31  3.000
 RMT  O7   C15  O6   124.45  3.000
 RMT  O7   C15  C12  111.19  3.000
 RMT  O6   C15  C12  124.31  3.000
 RMT  H5   C2   C3   121.02  3.000
 RMT  H5   C2   N    115.89  3.000
 RMT  C3   C2   N    123.09  3.000
 RMT  C6   C3   C4   119.21  3.000
 RMT  C4   C3   C2   118.37  3.000
 RMT  C6   C3   C2   122.42  3.000
 RMT  C5   C4   C3   120.24  3.000
 RMT  C3   C4   C    117.85  3.000
 RMT  C5   C4   C    121.81  3.000
 RMT  H7   C5   H6   104.10  3.000
 RMT  H7   C5   N1   107.86  3.000
 RMT  H6   C5   N1   114.31  3.000
 RMT  H7   C5   C4   109.53  3.000
 RMT  H6   C5   C4   112.22  3.000
 RMT  N1   C5   C4   108.60  3.000
 RMT  H9   C6   H8   107.40  3.000
 RMT  H9   C6   C3   109.43  3.000
 RMT  H8   C6   C3   110.08  3.000
 RMT  H9   C6   O    110.64  3.000
 RMT  H8   C6   O    109.68  3.000
 RMT  C3   C6   O    109.59  3.000
 RMT  H12  C7   H11  108.20  3.000
 RMT  H12  C7   H10  108.39  3.000
 RMT  H11  C7   H10  106.92  3.000
 RMT  H12  C7   C1   109.85  3.000
 RMT  H11  C7   C1   111.61  3.000
 RMT  H10  C7   C1   111.73  3.000
 RMT  N1   C8   C9   130.21  3.000
 RMT  N1   C8   C12  120.49  3.000
 RMT  C9   C8   C12  109.29  3.000
 RMT  H14  C9   H13  106.57  3.000
 RMT  H14  C9   C8   111.77  3.000
 RMT  H13  C9   C8   111.57  3.000
 RMT  H14  C9   C10  111.86  3.000
 RMT  H13  C9   C10  112.64  3.000
 RMT  C8   C9   C10  102.56  3.000
 RMT  C8   N1   C5   120.59  3.000
 RMT  H15  O1   C    111.88  3.000
 RMT  H16  O2   P    114.07  3.000
 RMT  H17  O3   P    115.87  3.000
 RMT  H18  O5   C13  110.32  3.000
 RMT  H19  O7   C15  110.35  3.000
 RMT  O4   P    O3   109.69  3.000
 RMT  O3   P    O2   108.05  3.000
 RMT  O4   P    O2   118.10  3.000
 RMT  O2   P    O     96.55  3.000
 RMT  O3   P    O    106.86  3.000
 RMT  O4   P    O    116.44  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
 RMT  CONST_01  C4   C3   C2   N       0.00   0.0  0
 RMT  CONST_02  C4   C    C1   N       0.00   0.0  0
 RMT  CONST_03  C2   C3   C4   C       0.00   0.0  0
 RMT  CONST_04  C2   N    C1   C       0.00   0.0  0
 RMT  CONST_05  C3   C4   C    C1      0.00   0.0  0
 RMT  CONST_06  C3   C2   N    C1      0.00   0.0  0
 RMT  CONST_07  C6   C3   C2   N     180.00   0.0  0
 RMT  CONST_08  O1   C    C1   N     180.00   0.0  0
 RMT  CONST_09  C6   C3   C4   C     180.00   0.0  0
 RMT  CONST_10  C5   C4   C    C1    180.00   0.0  0
 RMT  CONST_11  C5   C4   C3   C2    180.00   0.0  0
 RMT  CONST_12  C7   C1   N    C2    180.00   0.0  0
 RMT  CONST_13  O1   C    C4   C3    180.00   0.0  0
 RMT  CONST_14  C7   C1   C    C4    180.00   0.0  0
 RMT  CONST_15  H5   C2   N    C1    180.00   0.0  0
 RMT  CONST_16  H18  O5   C13  C10   180.00   0.0  0
 RMT  CONST_17  H19  O7   C15  C12   180.00   0.0  0
 RMT  Var_01    C12  C8   C9   C10     4.60  30.0  1
 RMT  Var_02    C8   C9   C10  C11    -2.17  30.0  1
 RMT  Var_03    C9   C10  C11  C12    -1.17  30.0  1
 RMT  Var_04    N1   C5   C4   C    -101.26  30.0  1
 RMT  Var_05    C4   C3   C6   O     178.02  30.0  2
 RMT  Var_06    O14  C13  C10  C11     0.25  30.0  3
 RMT  Var_07    C9   C8   N1   C5     -1.28  30.0  2
 RMT  Var_08    H10  C7   C1   N     123.15  30.0  2
 RMT  Var_09    O4   P    O    C6     50.12  30.0  1

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
 RMT  chir_01  C12  C8  C11  C15  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
 RMT  plan-1  N    0.020
 RMT  plan-1  C    0.020
 RMT  plan-1  C1   0.020
 RMT  plan-1  C2   0.020
 RMT  plan-1  C3   0.020
 RMT  plan-1  C4   0.020
 RMT  plan-1  C5   0.020
 RMT  plan-1  C6   0.020
 RMT  plan-1  C7   0.020
 RMT  plan-1  O1   0.020
 RMT  plan-1  H5   0.020
 RMT  plan-2  C12  0.020
 RMT  plan-2  C15  0.020
 RMT  plan-2  O6   0.020
 RMT  plan-2  O7   0.020
 RMT  plan-2  H19  0.020
 RMT  plan-3  C10  0.020
 RMT  plan-3  C13  0.020
 RMT  plan-3  O14  0.020
 RMT  plan-3  O5   0.020
 RMT  plan-3  H18  0.020

