# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:14:50 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: {2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cn1c(cc2ccc3ccccc3c12)C(=O)NC[P](O)(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
 59Z  59Z  '{2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid'  ligand  37  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_59Z
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
 59Z  C7   C  CH2    0  -0.610   3.9953   0.1740   0.7661
 59Z  C17  C  CR66   0   0.065  -3.3518   0.1662   0.1556
 59Z  C21  C  CR16   0  -0.391  -2.2148   2.5491  -0.9737
 59Z  C24  C  CR15   0  -0.440   0.0211   1.4012  -0.3917
 59Z  C26  C  CR16   0  -0.220  -5.5610   1.1091  -0.3240
 59Z  C28  C  CR16   0  -0.243  -6.1793  -0.0146   0.1605
 59Z  P1   P  P      0   1.133   5.0099   1.6821   0.3114
 59Z  O2   O  O      0  -0.761   4.2662   2.8158   1.0360
 59Z  O3   O  OP    -1  -0.992   6.4006   1.3726   0.8700
 59Z  O5   O  OP    -1  -0.943   4.9479   1.7782  -1.2139
 59Z  N10  N  NH1    0  -0.589   2.5893   0.4846   0.6383
 59Z  C12  C  C      0   0.518   1.6236  -0.4101   0.4233
 59Z  O13  O  O      0  -0.494   1.8224  -1.6210   0.3490
 59Z  C14  C  CR5    0   0.233   0.2844   0.1930   0.2053
 59Z  N15  N  NR5    0  -0.527  -0.8980  -0.4354   0.5031
 59Z  C16  C  CR56   0   0.305  -1.9337   0.3554   0.0904
 59Z  C18  C  CR66   0  -0.074  -4.1558   1.2218  -0.3490
 59Z  C19  C  CR16   0  -0.238  -3.5620   2.4006  -0.9019
 59Z  C23  C  CR56   0   0.125  -1.3829   1.5212  -0.4692
 59Z  C30  C  CR16   0  -0.280  -5.3916  -1.0714   0.6294
 59Z  C32  C  CR16   0  -0.274  -4.0214  -0.9875   0.6255
 59Z  C34  C  CH2    0  -0.563  -1.0174  -1.7469   1.0974
 59Z  C37  C  C      0   0.357  -1.3935  -2.8599   0.0881
 59Z  O38  O  O      0  -0.400  -1.4082  -2.5586  -1.1128
 59Z  O39  O  OC    -1  -0.749  -1.6393  -3.9568   0.6215
 59Z  H1   H  HCH2   0   0.165   4.2385  -0.6772   0.1279
 59Z  H2   H  HCH2   0   0.211   4.2165  -0.1339   1.7957
 59Z  H5   H  HCR6   0   0.247  -6.1501   1.9340  -0.7079
 59Z  H6   H  HCR6   0   0.236  -7.2588  -0.0886   0.1674
 59Z  H9   H  HNH1   0   0.395   2.3591   1.4595   0.7649
 59Z  H10  H  HCR6   0   0.253  -4.2183   3.1781  -1.2743
 59Z  H11  H  HCR6   0   0.258  -5.8627  -1.9748   0.9919
 59Z  H12  H  HCR6   0   0.242  -3.4802  -1.8446   0.9889
 59Z  H13  H  HCH2   0   0.268  -0.0640  -2.0071   1.5492
 59Z  H14  H  HCH2   0   0.282  -1.7294  -1.7034   1.9222
 59Z  H3   H  HCR6   0   0.245  -1.7734   3.4397  -1.4031
 59Z  H4   H  HCR5   0   0.249   0.7512   2.1020  -0.7676

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
 59Z  O2   P1   deloc     1.537  0.020  1.537
 59Z  O38  C37  deloc     1.238  0.020  1.238
 59Z  O3   P1   deloc     1.530  0.020  1.530
 59Z  P1   O5   deloc     1.530  0.020  1.530
 59Z  P1   C7   single    1.874  0.020  1.874
 59Z  O13  C12  double    1.229  0.020  1.229
 59Z  C37  O39  deloc     1.244  0.020  1.244
 59Z  C37  C34  single    1.549  0.020  1.549
 59Z  C21  C19  aromatic  1.357  0.020  1.357
 59Z  C21  C23  aromatic  1.415  0.020  1.415
 59Z  C24  C23  aromatic  1.411  0.020  1.411
 59Z  C24  C14  aromatic  1.373  0.020  1.373
 59Z  C19  C18  aromatic  1.431  0.020  1.431
 59Z  C23  C16  aromatic  1.406  0.020  1.406
 59Z  C12  C14  single    1.485  0.020  1.485
 59Z  C12  N10  single    1.334  0.020  1.334
 59Z  C14  N15  aromatic  1.372  0.020  1.372
 59Z  C18  C17  aromatic  1.420  0.020  1.420
 59Z  C18  C26  aromatic  1.410  0.020  1.410
 59Z  C16  N15  aromatic  1.367  0.020  1.367
 59Z  C16  C17  aromatic  1.432  0.020  1.432
 59Z  N15  C34  single    1.445  0.020  1.445
 59Z  C17  C32  aromatic  1.414  0.020  1.414
 59Z  C7   N10  single    1.446  0.020  1.446
 59Z  C26  C28  aromatic  1.371  0.020  1.371
 59Z  C32  C30  aromatic  1.373  0.020  1.373
 59Z  C28  C30  aromatic  1.399  0.020  1.399
 59Z  C7   H1   single    0.970  0.020  1.090
 59Z  C7   H2   single    0.970  0.020  1.090
 59Z  C21  H3   single    0.930  0.020  1.080
 59Z  C24  H4   single    0.930  0.020  1.080
 59Z  C26  H5   single    0.930  0.020  1.080
 59Z  C28  H6   single    0.930  0.020  1.080
 59Z  N10  H9   single    0.860  0.020  1.020
 59Z  C19  H10  single    0.930  0.020  1.080
 59Z  C30  H11  single    0.930  0.020  1.080
 59Z  C32  H12  single    0.930  0.020  1.080
 59Z  C34  H13  single    0.970  0.020  1.090
 59Z  C34  H14  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
 59Z  H2   C7   H1   106.56  3.000
 59Z  H2   C7   N10  109.84  3.000
 59Z  H1   C7   N10  109.43  3.000
 59Z  H2   C7   P1   110.15  3.000
 59Z  H1   C7   P1   111.42  3.000
 59Z  N10  C7   P1   109.41  3.000
 59Z  C32  C17  C18  117.16  3.000
 59Z  C32  C17  C16  126.28  3.000
 59Z  C18  C17  C16  116.51  3.000
 59Z  H3   C21  C23  119.94  3.000
 59Z  H3   C21  C19  121.04  3.000
 59Z  C23  C21  C19  119.02  3.000
 59Z  H4   C24  C23  126.76  3.000
 59Z  H4   C24  C14  126.37  3.000
 59Z  C23  C24  C14  106.83  3.000
 59Z  H5   C26  C18  118.34  3.000
 59Z  H5   C26  C28  120.25  3.000
 59Z  C18  C26  C28  121.42  3.000
 59Z  H6   C28  C30  120.53  3.000
 59Z  H6   C28  C26  120.55  3.000
 59Z  C30  C28  C26  118.92  3.000
 59Z  O5   P1   O3   114.43  3.000
 59Z  O5   P1   O2   113.83  3.000
 59Z  O3   P1   O2   114.62  3.000
 59Z  O5   P1   C7   105.71  3.000
 59Z  O3   P1   C7   103.93  3.000
 59Z  O2   P1   C7   102.55  3.000
 59Z  H9   N10  C12  120.18  3.000
 59Z  H9   N10  C7   114.72  3.000
 59Z  C12  N10  C7   125.05  3.000
 59Z  C14  C12  O13  122.48  3.000
 59Z  C14  C12  N10  113.84  3.000
 59Z  O13  C12  N10  123.59  3.000
 59Z  N15  C14  C12  124.02  3.000
 59Z  N15  C14  C24  109.40  3.000
 59Z  C12  C14  C24  126.45  3.000
 59Z  C34  N15  C16  125.92  3.000
 59Z  C34  N15  C14  125.20  3.000
 59Z  C16  N15  C14  108.82  3.000
 59Z  C23  C16  N15  107.65  3.000
 59Z  N15  C16  C17  131.31  3.000
 59Z  C23  C16  C17  121.04  3.000
 59Z  C19  C18  C26  119.09  3.000
 59Z  C26  C18  C17  119.92  3.000
 59Z  C19  C18  C17  120.99  3.000
 59Z  H10  C19  C18  118.20  3.000
 59Z  H10  C19  C21  120.30  3.000
 59Z  C18  C19  C21  121.50  3.000
 59Z  C16  C23  C24  107.30  3.000
 59Z  C16  C23  C21  120.93  3.000
 59Z  C24  C23  C21  131.77  3.000
 59Z  H11  C30  C32  119.13  3.000
 59Z  H11  C30  C28  119.87  3.000
 59Z  C32  C30  C28  120.99  3.000
 59Z  H12  C32  C30  116.88  3.000
 59Z  H12  C32  C17  121.56  3.000
 59Z  C30  C32  C17  121.56  3.000
 59Z  H14  C34  H13  105.54  3.000
 59Z  H14  C34  C37  111.29  3.000
 59Z  H13  C34  C37  108.17  3.000
 59Z  H14  C34  N15  109.20  3.000
 59Z  H13  C34  N15  108.41  3.000
 59Z  C37  C34  N15  113.85  3.000
 59Z  O39  C37  O38  128.90  3.000
 59Z  O39  C37  C34  113.71  3.000
 59Z  O38  C37  C34  117.39  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
 59Z  CONST_01  C21  C19  C18  C17     0.00   0.0  0
 59Z  CONST_02  C28  C26  C18  C17     0.00   0.0  0
 59Z  CONST_03  C21  C23  C16  C17     0.00   0.0  0
 59Z  CONST_04  C24  C23  C16  C17   180.00   0.0  0
 59Z  CONST_05  C14  N15  C16  C17   180.00   0.0  0
 59Z  CONST_06  C28  C30  C32  C17     0.00   0.0  0
 59Z  CONST_07  C26  C18  C19  C21   180.00   0.0  0
 59Z  CONST_08  C14  C24  C23  C21   180.00   0.0  0
 59Z  CONST_09  N15  C16  C23  C21   180.00   0.0  0
 59Z  CONST_10  C19  C21  C23  C24   180.00   0.0  0
 59Z  CONST_11  N15  C16  C23  C24     0.00   0.0  0
 59Z  CONST_12  C16  N15  C14  C24     0.00   0.0  0
 59Z  CONST_13  C16  C17  C18  C26   180.00   0.0  0
 59Z  CONST_14  C32  C17  C18  C26     0.00   0.0  0
 59Z  CONST_15  C32  C30  C28  C26     0.00   0.0  0
 59Z  CONST_16  C19  C18  C26  C28   180.00   0.0  0
 59Z  CONST_17  C16  C23  C24  C14     0.00   0.0  0
 59Z  CONST_18  C23  C16  N15  C14     0.00   0.0  0
 59Z  CONST_19  C23  C24  C14  N15     0.00   0.0  0
 59Z  CONST_20  C18  C17  C16  N15   180.00   0.0  0
 59Z  CONST_21  C32  C17  C16  N15     0.00   0.0  0
 59Z  CONST_22  C19  C21  C23  C16     0.00   0.0  0
 59Z  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 59Z  CONST_24  C30  C32  C17  C16   180.00   0.0  0
 59Z  CONST_25  C23  C21  C19  C18     0.00   0.0  0
 59Z  CONST_26  C23  C16  C17  C18     0.00   0.0  0
 59Z  CONST_27  C30  C32  C17  C18     0.00   0.0  0
 59Z  CONST_28  C30  C28  C26  C18     0.00   0.0  0
 59Z  CONST_29  C32  C17  C18  C19   180.00   0.0  0
 59Z  CONST_30  C32  C17  C16  C23   180.00   0.0  0
 59Z  CONST_31  C34  N15  C16  C17     0.00   0.0  0
 59Z  CONST_32  C34  N15  C14  C24   180.00   0.0  0
 59Z  CONST_33  C23  C24  C14  C12   180.00   0.0  0
 59Z  CONST_34  C16  N15  C14  C12   180.00   0.0  0
 59Z  CONST_35  C34  N15  C16  C23   180.00   0.0  0
 59Z  CONST_36  H10  C19  C18  C17   180.00   0.0  0
 59Z  CONST_37  H5   C26  C18  C17   180.00   0.0  0
 59Z  CONST_38  H11  C30  C32  C17   180.00   0.0  0
 59Z  CONST_39  H4   C24  C23  C21     0.00   0.0  0
 59Z  CONST_40  H3   C21  C23  C24     0.00   0.0  0
 59Z  CONST_41  H12  C32  C30  C28   180.00   0.0  0
 59Z  CONST_42  H6   C28  C26  C18   180.00   0.0  0
 59Z  CONST_43  C14  C12  N10  C7    180.00   0.0  0
 59Z  CONST_44  H9   N10  C12  C14     0.00   0.0  0
 59Z  CONST_45  O13  C12  N10  C7      0.00   0.0  0
 59Z  Var_01    O13  C12  C14  C24  -144.49  30.0  2
 59Z  Var_02    C37  C34  N15  C14  -102.67  30.0  2
 59Z  Var_03    O38  C37  C34  N15     7.65  30.0  2
 59Z  Var_04    C12  N10  C7   P1    155.38  30.0  3
 59Z  Var_05    N10  C7   P1   O2     44.25  30.0  3

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
 59Z  plan-1  C17  0.020
 59Z  plan-1  C21  0.020
 59Z  plan-1  C24  0.020
 59Z  plan-1  C26  0.020
 59Z  plan-1  C28  0.020
 59Z  plan-1  C12  0.020
 59Z  plan-1  C14  0.020
 59Z  plan-1  N15  0.020
 59Z  plan-1  C16  0.020
 59Z  plan-1  C18  0.020
 59Z  plan-1  C19  0.020
 59Z  plan-1  C23  0.020
 59Z  plan-1  C30  0.020
 59Z  plan-1  C32  0.020
 59Z  plan-1  C34  0.020
 59Z  plan-1  H5   0.020
 59Z  plan-1  H6   0.020
 59Z  plan-1  H10  0.020
 59Z  plan-1  H11  0.020
 59Z  plan-1  H12  0.020
 59Z  plan-1  H3   0.020
 59Z  plan-1  H4   0.020
 59Z  plan-2  C7   0.020
 59Z  plan-2  N10  0.020
 59Z  plan-2  C12  0.020
 59Z  plan-2  O13  0.020
 59Z  plan-2  C14  0.020
 59Z  plan-2  H9   0.020
 59Z  plan-3  C34  0.020
 59Z  plan-3  C37  0.020
 59Z  plan-3  O38  0.020
 59Z  plan-3  O39  0.020

