# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 05:04:35 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (1S,3R,4S)-3-formyl-4-[({2-methyl-3-oxido-5-[(phosphonooxy)methyl]pyridin-1-ium-4-yl}methyl)azaniumyl]cyclopentane-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH+]cc(CO[P](O)(O)=O)c(C[NH2+][C@H]2C[C@H](C[C@H]2C=O)C([O-])=O)c1[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
 I1T  I1T  "(1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid"  ligand  45  26  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I1T
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
 I1T  C01  C  CH2    0  -0.442  -16.0077  -34.6788  60.1511
 I1T  C06  C  CH1    0  -0.077  -15.4669  -35.8434  60.9830
 I1T  C11  C  CR6    0   0.269  -18.1182  -34.5337  64.6173
 I1T  C15  C  CR6    0   0.005  -17.2447  -36.8077  65.0429
 I1T  C16  C  CR6    0  -0.053  -17.5439  -35.7648  64.1630
 I1T  C20  C  C1     0   0.192  -12.9669  -35.9667  61.8060
 I1T  C03  C  C      0   0.421  -15.0258  -33.1575  58.2765
 I1T  C08  C  CH1    0  -0.367  -13.9491  -35.9313  60.6750
 I1T  C12  C  CR6    0   0.202  -18.4315  -34.4882  66.0217
 I1T  C14  C  CR16   0  -0.096  -17.5357  -36.6556  66.3817
 I1T  O21  O  O      0  -0.413  -13.0792  -35.3436  62.8374
 I1T  C02  C  CH1    0  -0.378  -14.9844  -34.4957  59.0381
 I1T  C09  C  CH2    0  -0.384  -17.2666  -35.8812  62.6966
 I1T  C10  C  CH2    0  -0.427  -13.6604  -34.7163  59.7709
 I1T  N07  N  NT2    1  -0.697  -15.8123  -35.7015  62.4223
 I1T  N13  N  NR16   1  -0.558  -18.1216  -35.5195  66.7952
 I1T  O04  O  O      0  -0.613  -14.1746  -33.0343  57.3724
 I1T  O05  O  OC    -1  -0.592  -15.8790  -32.3189  58.6247
 I1T  O22  O  O2     0  -0.668  -15.4300  -37.9102  63.9102
 I1T  O24  O  O      0  -0.854  -16.1119  -38.9847  61.6672
 I1T  O25  O  OP    -1  -0.832  -13.6463  -38.5249  62.2727
 I1T  O26  O  OP    -1  -0.856  -14.9532  -40.4126  63.4563
 I1T  P23  P  P      0   1.282  -14.9929  -39.0992  62.6975
 I1T  H1   H  HCH2   0   0.232  -16.0469  -33.7668  60.7543
 I1T  H2   H  HCH2   0   0.248  -17.0159  -34.8674  59.7816
 I1T  H3   H  HCH1   0   0.296  -15.9188  -36.7925  60.7025
 I1T  H4   H  HCH2   0   0.209  -17.3779  -38.6199  63.9479
 I1T  H5   H  HCH2   0   0.218  -16.4976  -38.7571  65.4634
 I1T  H6   H  HCH3   0   0.264  -20.0263  -33.0836  66.0948
 I1T  H7   H  HCH3   0   0.256  -19.3091  -33.4329  67.6721
 I1T  H8   H  HCH3   0   0.264  -18.4614  -32.4129  66.5040
 I1T  H9   H  H      0   0.195  -12.0368  -36.5082  61.5733
 I1T  H10  H  HCH1   0   0.273  -13.7946  -36.8371  60.0889
 I1T  H11  H  HCR6   0   0.309  -17.3320  -37.3976  67.1374
 I1T  H12  H  HCH1   0   0.231  -15.1045  -35.3065  58.3083
 I1T  H13  H  HCH2   0   0.301  -17.8209  -35.1288  62.1421
 I1T  H14  H  HCH2   0   0.292  -17.5172  -36.8661  62.3053
 I1T  H15  H  HCH2   0   0.247  -12.8189  -34.8897  59.1014
 I1T  H16  H  HCH2   0   0.230  -13.4277  -33.8340  60.3766
 I1T  H17  H  HNT2   0   0.477  -15.3662  -36.4574  62.9851
 I1T  H23  H  HNR6   0   0.441  -18.3406  -35.4457  67.7825
 I1T  H18  H  HNT2   0   0.437  -15.4892  -34.8076  62.7912
 I1T  C17  C  CH2    0  -0.220  -16.6419  -38.1147  64.5867
 I1T  C19  C  CH3    0  -0.723  -19.0910  -33.2972  66.6139
 I1T  O18  O  OC    -1  -0.539  -18.3639  -33.5528  63.8826

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
 I1T  O04  C03  deloc     1.248  0.020  1.248
 I1T  O05  C03  deloc     1.246  0.020  1.246
 I1T  C03  C02  single    1.540  0.020  1.540
 I1T  C02  C10  single    1.529  0.020  1.529
 I1T  C02  C01  single    1.523  0.020  1.523
 I1T  C10  C08  single    1.542  0.020  1.542
 I1T  C01  C06  single    1.530  0.020  1.530
 I1T  C08  C20  single    1.498  0.020  1.498
 I1T  C08  C06  single    1.551  0.020  1.551
 I1T  O24  P23  deloc     1.525  0.020  1.525
 I1T  C20  O21  double    1.210  0.020  1.210
 I1T  C06  N07  single    1.487  0.020  1.487
 I1T  O26  P23  deloc     1.517  0.020  1.517
 I1T  P23  O25  deloc     1.524  0.020  1.524
 I1T  P23  O22  single    1.754  0.020  1.754
 I1T  N07  C09  single    1.491  0.020  1.491
 I1T  C09  C16  single    1.497  0.020  1.497
 I1T  C17  O22  single    1.403  0.020  1.403
 I1T  C17  C15  single    1.510  0.020  1.510
 I1T  C16  C15  aromatic  1.397  0.020  1.397
 I1T  C16  C11  aromatic  1.432  0.020  1.432
 I1T  C15  C14  aromatic  1.378  0.020  1.378
 I1T  O18  C11  single    1.250  0.020  1.250
 I1T  C11  C12  aromatic  1.440  0.020  1.440
 I1T  C14  N13  aromatic  1.343  0.020  1.343
 I1T  C12  N13  aromatic  1.326  0.020  1.326
 I1T  C12  C19  single    1.485  0.020  1.485
 I1T  C01  H1   single    0.970  0.020  1.090
 I1T  C01  H2   single    0.970  0.020  1.090
 I1T  C06  H3   single    0.970  0.020  1.090
 I1T  C17  H4   single    0.970  0.020  1.090
 I1T  C17  H5   single    0.970  0.020  1.090
 I1T  C19  H6   single    0.970  0.020  1.090
 I1T  C19  H7   single    0.970  0.020  1.090
 I1T  C19  H8   single    0.970  0.020  1.090
 I1T  C20  H9   single    0.930  0.020  1.080
 I1T  C08  H10  single    0.970  0.020  1.090
 I1T  C14  H11  single    0.930  0.020  1.080
 I1T  C02  H12  single    0.970  0.020  1.090
 I1T  C09  H13  single    0.970  0.020  1.090
 I1T  C09  H14  single    0.970  0.020  1.090
 I1T  C10  H15  single    0.970  0.020  1.090
 I1T  C10  H16  single    0.970  0.020  1.090
 I1T  N07  H17  single    0.890  0.020  1.040
 I1T  N13  H23  single    0.860  0.020  1.020
 I1T  N07  H18  single    0.890  0.020  1.040

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
 I1T  H2   C01  H1   107.33  3.000
 I1T  H2   C01  C02  113.23  3.000
 I1T  H1   C01  C02  109.07  3.000
 I1T  H2   C01  C06  112.30  3.000
 I1T  H1   C01  C06  110.33  3.000
 I1T  C02  C01  C06  104.56  3.000
 I1T  H3   C06  N07  103.67  3.000
 I1T  H3   C06  C08  107.81  3.000
 I1T  N07  C06  C08  115.14  3.000
 I1T  H3   C06  C01  112.15  3.000
 I1T  N07  C06  C01  111.81  3.000
 I1T  C08  C06  C01  106.32  3.000
 I1T  O18  C11  C12  120.39  3.000
 I1T  C12  C11  C16  115.07  3.000
 I1T  O18  C11  C16  124.53  3.000
 I1T  C14  C15  C17  118.25  3.000
 I1T  C14  C15  C16  118.96  3.000
 I1T  C17  C15  C16  122.78  3.000
 I1T  C09  C16  C15  121.29  3.000
 I1T  C15  C16  C11  121.86  3.000
 I1T  C09  C16  C11  116.85  3.000
 I1T  H9   C20  O21  120.77  3.000
 I1T  H9   C20  C08  113.95  3.000
 I1T  O21  C20  C08  124.77  3.000
 I1T  O05  C03  O04  127.10  3.000
 I1T  O05  C03  C02  117.70  3.000
 I1T  O04  C03  C02  115.20  3.000
 I1T  H10  C08  C10  108.24  3.000
 I1T  H10  C08  C20  107.06  3.000
 I1T  C10  C08  C20  109.78  3.000
 I1T  H10  C08  C06  107.01  3.000
 I1T  C20  C08  C06  119.53  3.000
 I1T  C10  C08  C06  104.77  3.000
 I1T  N13  C12  C19  119.68  3.000
 I1T  C19  C12  C11  120.74  3.000
 I1T  N13  C12  C11  119.58  3.000
 I1T  H11  C14  N13  116.65  3.000
 I1T  H11  C14  C15  124.38  3.000
 I1T  N13  C14  C15  118.97  3.000
 I1T  H12  C02  C10  107.86  3.000
 I1T  H12  C02  C03  108.06  3.000
 I1T  C10  C02  C03  112.68  3.000
 I1T  H12  C02  C01  108.89  3.000
 I1T  C10  C02  C01  102.37  3.000
 I1T  C03  C02  C01  116.60  3.000
 I1T  H14  C09  H13  108.99  3.000
 I1T  H14  C09  N07  105.50  3.000
 I1T  H13  C09  N07  108.68  3.000
 I1T  H14  C09  C16  112.32  3.000
 I1T  H13  C09  C16  110.59  3.000
 I1T  N07  C09  C16  110.58  3.000
 I1T  H16  C10  H15  107.70  3.000
 I1T  H16  C10  C02  109.43  3.000
 I1T  H15  C10  C02  113.41  3.000
 I1T  H16  C10  C08  110.51  3.000
 I1T  H15  C10  C08  112.31  3.000
 I1T  C02  C10  C08  103.45  3.000
 I1T  H18  N07  H17  107.74  3.000
 I1T  H18  N07  C09  110.38  3.000
 I1T  H17  N07  C09  103.34  3.000
 I1T  H18  N07  C06  111.12  3.000
 I1T  H17  N07  C06  110.73  3.000
 I1T  C09  N07  C06  113.15  3.000
 I1T  H23  N13  C14  117.09  3.000
 I1T  H23  N13  C12  117.45  3.000
 I1T  C14  N13  C12  125.46  3.000
 I1T  P23  O22  C17  116.73  3.000
 I1T  O26  P23  O25  116.25  3.000
 I1T  O25  P23  O24  115.57  3.000
 I1T  O26  P23  O24  114.96  3.000
 I1T  O25  P23  O22   99.06  3.000
 I1T  O26  P23  O22  104.33  3.000
 I1T  O24  P23  O22  103.49  3.000
 I1T  H5   C17  H4   106.49  3.000
 I1T  H5   C17  O22  110.93  3.000
 I1T  H4   C17  O22  111.46  3.000
 I1T  H5   C17  C15  108.55  3.000
 I1T  H4   C17  C15  107.85  3.000
 I1T  O22  C17  C15  111.37  3.000
 I1T  H8   C19  H7   108.33  3.000
 I1T  H8   C19  H6   106.75  3.000
 I1T  H7   C19  H6   108.37  3.000
 I1T  H8   C19  C12  110.71  3.000
 I1T  H7   C19  C12  112.13  3.000
 I1T  H6   C19  C12  110.37  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
 I1T  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 I1T  CONST_02  C14  N13  C12  C11     0.00   0.0  0
 I1T  CONST_03  C12  C11  C16  C15     0.00   0.0  0
 I1T  CONST_04  C12  N13  C14  C15     0.00   0.0  0
 I1T  CONST_05  N13  C14  C15  C16     0.00   0.0  0
 I1T  CONST_06  N13  C12  C11  C16     0.00   0.0  0
 I1T  CONST_07  C17  C15  C16  C11   180.00   0.0  0
 I1T  CONST_08  O18  C11  C16  C15   180.00   0.0  0
 I1T  CONST_09  C19  C12  C11  C16   180.00   0.0  0
 I1T  CONST_10  N13  C14  C15  C17   180.00   0.0  0
 I1T  CONST_11  C14  N13  C12  C19   180.00   0.0  0
 I1T  CONST_12  C09  C16  C11  C12   180.00   0.0  0
 I1T  CONST_13  C09  C16  C15  C14   180.00   0.0  0
 I1T  CONST_14  O18  C11  C12  N13   180.00   0.0  0
 I1T  CONST_15  H23  N13  C12  C11   180.00   0.0  0
 I1T  CONST_16  H23  N13  C14  C15   180.00   0.0  0
 I1T  CONST_17  H11  C14  C15  C16   180.00   0.0  0
 I1T  CONST_18  H11  C14  N13  C12   180.00   0.0  0
 I1T  Var_01    C16  C09  N07  C06   178.42  30.0  3
 I1T  Var_02    N07  C09  C16  C11   102.94  30.0  1
 I1T  Var_03    N07  C09  C16  C15   -76.58  30.0  1
 I1T  Var_04    O22  C17  C15  C16    57.14  30.0  1
 I1T  Var_05    O22  C17  C15  C14  -124.28  30.0  1
 I1T  Var_06    H13  C09  C16  C11   -17.49  30.0  1
 I1T  Var_07    H14  C09  C16  C11  -139.49  30.0  1
 I1T  Var_08    H6   C19  C12  C11    56.09  30.0  2
 I1T  Var_09    H7   C19  C12  C11   177.02  30.0  2
 I1T  Var_10    H8   C19  C12  C11   -61.88  30.0  2
 I1T  Var_11    H13  C09  C16  C15   162.99  30.0  1
 I1T  Var_12    H14  C09  C16  C15    40.98  30.0  1
 I1T  Var_13    H4   C17  C15  C16   -65.45  30.0  1
 I1T  Var_14    H5   C17  C15  C16   179.55  30.0  1
 I1T  Var_15    H4   C17  C15  C14   113.12  30.0  1
 I1T  Var_16    H5   C17  C15  C14    -1.87  30.0  1
 I1T  Var_17    H6   C19  C12  N13  -124.21  30.0  2
 I1T  Var_18    H7   C19  C12  N13    -3.29  30.0  2
 I1T  Var_19    H8   C19  C12  N13   117.82  30.0  2
 I1T  Var_20    P23  O22  C17  C15  -151.58  30.0  3
 I1T  Var_21    H13  C09  N07  C06   -60.01  30.0  3
 I1T  Var_22    H14  C09  N07  C06    56.75  30.0  3
 I1T  Var_23    H17  N07  C09  C16    58.62  30.0  1
 I1T  Var_24    H18  N07  C09  C16   -56.34  30.0  1
 I1T  Var_25    O24  P23  O22  C17    62.42  30.0  3
 I1T  Var_26    O26  P23  O22  C17   -58.19  30.0  3
 I1T  Var_27    O25  P23  O22  C17  -178.39  30.0  3
 I1T  Var_28    H4   C17  O22  P23   -31.08  30.0  2
 I1T  Var_29    H5   C17  O22  P23    87.40  30.0  2

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
 I1T  chir_01  C06  C01  C08  N07  negativ
 I1T  chir_02  C08  C06  C20  C10  positiv
 I1T  chir_03  C02  C01  C10  C03  positiv

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
 I1T  plan-1  C11  0.020
 I1T  plan-1  C15  0.020
 I1T  plan-1  C16  0.020
 I1T  plan-1  C12  0.020
 I1T  plan-1  C14  0.020
 I1T  plan-1  C09  0.020
 I1T  plan-1  N13  0.020
 I1T  plan-1  H11  0.020
 I1T  plan-1  H23  0.020
 I1T  plan-1  C17  0.020
 I1T  plan-1  C19  0.020
 I1T  plan-1  O18  0.020
 I1T  plan-2  C03  0.020
 I1T  plan-2  C02  0.020
 I1T  plan-2  O04  0.020
 I1T  plan-2  O05  0.020
 I1T  plan-3  C20  0.020
 I1T  plan-3  C08  0.020
 I1T  plan-3  O21  0.020
 I1T  plan-3  H9   0.020

