# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 02:07:59 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1Nc2ccc(OCCCCC[P](O)(O)=O)cc2C(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
 7P3  7P3  '2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid'  ligand  51  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7P3
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
 7P3  C01  C  CR6   0  -0.184  -6.2163   1.2966  -0.1318
 7P3  C02  C  C     0   0.556  -6.9476   0.3975  -1.0400
 7P3  O03  O  OH1   0  -0.594  -8.0933   0.9050  -1.4771
 7P3  O04  O  O     0  -0.463  -6.5706  -0.7072  -1.3789
 7P3  C05  C  CR16  0  -0.261  -6.8450   2.4551   0.3460
 7P3  C06  C  CR16  0  -0.274  -6.2096   3.3280   1.2010
 7P3  C07  C  CR16  0  -0.236  -4.9090   3.0366   1.6068
 7P3  C08  C  CR16  0  -0.327  -4.2638   1.9053   1.1590
 7P3  C09  C  CR6   0   0.370  -4.8872   1.0091   0.2723
 7P3  N10  N  NH1   0  -0.800  -4.2419  -0.1189  -0.1566
 7P3  C11  C  CR6   0   0.308  -2.8709  -0.3557  -0.1172
 7P3  C12  C  CR16  0  -0.287  -1.9710   0.6571  -0.4446
 7P3  C13  C  CR16  0  -0.365  -0.6020   0.4606  -0.4324
 7P3  C14  C  CR6   0   0.405  -0.0818  -0.7900  -0.1064
 7P3  C15  C  CR16  0  -0.376  -0.9616  -1.8153   0.2124
 7P3  C16  C  CR6   0  -0.123  -2.3409  -1.6184   0.2163
 7P3  C17  C  C     0   0.537  -3.2272  -2.7573   0.5555
 7P3  O18  O  O     0  -0.442  -4.3909  -2.8407   0.2368
 7P3  O19  O  OH1   0  -0.590  -2.6089  -3.7003   1.2535
 7P3  O20  O  O2    0  -0.478   1.2294  -1.0932  -0.0841
 7P3  C21  C  CH2   0  -0.173   2.1779  -0.0567  -0.2898
 7P3  C22  C  CH2   0  -0.457   3.5616  -0.6531  -0.1408
 7P3  C23  C  CH2   0  -0.420   4.6483   0.4080  -0.2604
 7P3  C24  C  CH2   0  -0.433   6.0454  -0.1845  -0.1237
 7P3  C25  C  CH2   0  -0.757   7.1248   0.8939  -0.1930
 7P3  P26  P  P     0   1.373   8.7843   0.2152  -0.0396
 7P3  O29  O  O     0  -0.721   9.1596  -0.8307  -1.0224
 7P3  O28  O  OH1   0  -0.747   9.6766   1.5541  -0.0645
 7P3  O27  O  OH1   0  -0.753   8.9085  -0.3974   1.4459
 7P3  H1   H  HOH1  0   0.487  -8.5342   0.2628  -2.0525
 7P3  H2   H  HCR6  0   0.269  -7.8590   2.6714   0.0414
 7P3  H3   H  HCR6  0   0.258  -6.7162   4.2141   1.5571
 7P3  H4   H  HCR6  0   0.266  -4.3946   3.6940   2.2959
 7P3  H5   H  HCR6  0   0.283  -3.2663   1.6960   1.5189
 7P3  H6   H  HNH1  0   0.425  -4.8268  -0.8518  -0.5318
 7P3  H7   H  HCR6  0   0.290  -2.3483   1.6286  -0.7346
 7P3  H8   H  HCR6  0   0.291   0.0384   1.2899  -0.7003
 7P3  H9   H  HCR6  0   0.276  -0.5501  -2.7853   0.4573
 7P3  H10  H  HOH1  0   0.489  -3.2143  -4.4399   1.4123
 7P3  H11  H  HCH2  0   0.224   2.0590   0.3806  -1.2880
 7P3  H12  H  HCH2  0   0.222   2.0254   0.7450   0.4427
 7P3  H13  H  HCH2  0   0.232   3.6395  -1.1459   0.8326
 7P3  H14  H  HCH2  0   0.233   3.7107  -1.4226  -0.9034
 7P3  H15  H  HCH2  0   0.225   4.5658   0.9227  -1.2231
 7P3  H16  H  HCH2  0   0.225   4.5017   1.1705   0.5110
 7P3  H17  H  HCH2  0   0.234   6.1164  -0.7239   0.8248
 7P3  H18  H  HCH2  0   0.237   6.2079  -0.9213  -0.9145
 7P3  H19  H  HCH2  0   0.284   7.0705   1.4247  -1.1472
 7P3  H20  H  HCH2  0   0.282   6.9712   1.6401   0.5912
 7P3  H21  H  HOH1  0   0.492  10.6298   1.3923  -0.0859
 7P3  H22  H  HOH1  0   0.488   8.7215   0.2211   2.1641

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
 7P3  C21  C22  single    1.514  0.020  1.514
 7P3  C21  O20  single    1.420  0.020  1.420
 7P3  C22  C23  single    1.524  0.020  1.524
 7P3  C13  C12  aromatic  1.383  0.020  1.383
 7P3  C13  C14  aromatic  1.393  0.020  1.393
 7P3  O20  C14  single    1.346  0.020  1.346
 7P3  C23  C24  single    1.524  0.020  1.524
 7P3  C12  C11  aromatic  1.394  0.020  1.394
 7P3  C14  C15  aromatic  1.388  0.020  1.388
 7P3  C24  C25  single    1.527  0.020  1.527
 7P3  O29  P26  double    1.483  0.020  1.483
 7P3  C07  C08  aromatic  1.377  0.020  1.377
 7P3  C07  C06  aromatic  1.393  0.020  1.393
 7P3  C08  C09  aromatic  1.406  0.020  1.406
 7P3  C06  C05  aromatic  1.377  0.020  1.377
 7P3  C25  P26  single    1.799  0.020  1.799
 7P3  C11  N10  single    1.392  0.020  1.392
 7P3  C11  C16  aromatic  1.409  0.020  1.409
 7P3  C09  N10  single    1.368  0.020  1.368
 7P3  C09  C01  aromatic  1.419  0.020  1.419
 7P3  C15  C16  aromatic  1.393  0.020  1.393
 7P3  C05  C01  aromatic  1.402  0.020  1.402
 7P3  P26  O27  single    1.612  0.020  1.612
 7P3  P26  O28  single    1.609  0.020  1.609
 7P3  C01  C02  single    1.472  0.020  1.472
 7P3  C16  C17  single    1.482  0.020  1.482
 7P3  C02  O04  double    1.215  0.020  1.215
 7P3  C02  O03  single    1.327  0.020  1.327
 7P3  C17  O18  double    1.210  0.020  1.210
 7P3  C17  O19  single    1.326  0.020  1.326
 7P3  O03  H1   single    0.850  0.020  0.980
 7P3  C05  H2   single    0.930  0.020  1.080
 7P3  C06  H3   single    0.930  0.020  1.080
 7P3  C07  H4   single    0.930  0.020  1.080
 7P3  C08  H5   single    0.930  0.020  1.080
 7P3  N10  H6   single    0.860  0.020  1.020
 7P3  C12  H7   single    0.930  0.020  1.080
 7P3  C13  H8   single    0.930  0.020  1.080
 7P3  C15  H9   single    0.930  0.020  1.080
 7P3  O19  H10  single    0.850  0.020  0.980
 7P3  C21  H11  single    0.970  0.020  1.090
 7P3  C21  H12  single    0.970  0.020  1.090
 7P3  C22  H13  single    0.970  0.020  1.090
 7P3  C22  H14  single    0.970  0.020  1.090
 7P3  C23  H15  single    0.970  0.020  1.090
 7P3  C23  H16  single    0.970  0.020  1.090
 7P3  C24  H17  single    0.970  0.020  1.090
 7P3  C24  H18  single    0.970  0.020  1.090
 7P3  C25  H19  single    0.970  0.020  1.090
 7P3  C25  H20  single    0.970  0.020  1.090
 7P3  O28  H21  single    0.850  0.020  0.980
 7P3  O27  H22  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
 7P3  C09  C01  C05  119.38  3.000
 7P3  C05  C01  C02  119.48  3.000
 7P3  C09  C01  C02  121.15  3.000
 7P3  O04  C02  O03  121.57  3.000
 7P3  O03  C02  C01  113.47  3.000
 7P3  O04  C02  C01  124.95  3.000
 7P3  H1   O03  C02  109.58  3.000
 7P3  H2   C05  C06  118.75  3.000
 7P3  H2   C05  C01  119.35  3.000
 7P3  C06  C05  C01  121.90  3.000
 7P3  H3   C06  C07  120.86  3.000
 7P3  H3   C06  C05  120.52  3.000
 7P3  C07  C06  C05  118.61  3.000
 7P3  H4   C07  C08  118.91  3.000
 7P3  H4   C07  C06  120.13  3.000
 7P3  C08  C07  C06  120.96  3.000
 7P3  H5   C08  C09  119.71  3.000
 7P3  H5   C08  C07  118.88  3.000
 7P3  C09  C08  C07  121.39  3.000
 7P3  N10  C09  C08  120.92  3.000
 7P3  N10  C09  C01  121.31  3.000
 7P3  C08  C09  C01  117.75  3.000
 7P3  H6   N10  C11  117.23  3.000
 7P3  H6   N10  C09  116.20  3.000
 7P3  C11  N10  C09  126.57  3.000
 7P3  C16  C11  C12  117.63  3.000
 7P3  C16  C11  N10  121.97  3.000
 7P3  C12  C11  N10  120.38  3.000
 7P3  H7   C12  C13  118.37  3.000
 7P3  H7   C12  C11  119.36  3.000
 7P3  C13  C12  C11  122.26  3.000
 7P3  H8   C13  C14  121.68  3.000
 7P3  H8   C13  C12  118.36  3.000
 7P3  C14  C13  C12  119.95  3.000
 7P3  O20  C14  C15  116.57  3.000
 7P3  C15  C14  C13  118.69  3.000
 7P3  O20  C14  C13  124.74  3.000
 7P3  H9   C15  C16  120.18  3.000
 7P3  H9   C15  C14  118.24  3.000
 7P3  C16  C15  C14  121.58  3.000
 7P3  C17  C16  C15  118.94  3.000
 7P3  C17  C16  C11  121.17  3.000
 7P3  C15  C16  C11  119.88  3.000
 7P3  O19  C17  O18  122.57  3.000
 7P3  O19  C17  C16  112.83  3.000
 7P3  O18  C17  C16  124.60  3.000
 7P3  H10  O19  C17  109.75  3.000
 7P3  C21  O20  C14  118.94  3.000
 7P3  H12  C21  H11  107.55  3.000
 7P3  H12  C21  C22  110.45  3.000
 7P3  H11  C21  C22  110.24  3.000
 7P3  H12  C21  O20  110.12  3.000
 7P3  H11  C21  O20  110.53  3.000
 7P3  C22  C21  O20  107.98  3.000
 7P3  H14  C22  H13  107.09  3.000
 7P3  H14  C22  C23  109.76  3.000
 7P3  H13  C22  C23  109.44  3.000
 7P3  H14  C22  C21  109.46  3.000
 7P3  H13  C22  C21  109.28  3.000
 7P3  C23  C22  C21  111.70  3.000
 7P3  H16  C23  H15  106.39  3.000
 7P3  H16  C23  C24  109.30  3.000
 7P3  H15  C23  C24  109.32  3.000
 7P3  H16  C23  C22  109.54  3.000
 7P3  H15  C23  C22  110.04  3.000
 7P3  C24  C23  C22  112.09  3.000
 7P3  H18  C24  H17  106.59  3.000
 7P3  H18  C24  C25  109.76  3.000
 7P3  H17  C24  C25  109.98  3.000
 7P3  H18  C24  C23  109.48  3.000
 7P3  H17  C24  C23  109.22  3.000
 7P3  C25  C24  C23  111.67  3.000
 7P3  H20  C25  H19  106.72  3.000
 7P3  H20  C25  P26  109.02  3.000
 7P3  H19  C25  P26  107.66  3.000
 7P3  H20  C25  C24  110.49  3.000
 7P3  H19  C25  C24  110.32  3.000
 7P3  P26  C25  C24  112.43  3.000
 7P3  O27  P26  O28  106.73  3.000
 7P3  O28  P26  O29  115.85  3.000
 7P3  O27  P26  O29  108.86  3.000
 7P3  O28  P26  C25  101.31  3.000
 7P3  O27  P26  C25  107.04  3.000
 7P3  O29  P26  C25  116.28  3.000
 7P3  H21  O28  P26  114.06  3.000
 7P3  H22  O27  P26  115.27  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
 7P3  CONST_01  C07  C08  C09  C01     0.00   0.0  0
 7P3  CONST_02  C07  C06  C05  C01     0.00   0.0  0
 7P3  CONST_03  C08  C07  C06  C05     0.00   0.0  0
 7P3  CONST_04  C08  C09  C01  C05     0.00   0.0  0
 7P3  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 7P3  CONST_06  C09  C01  C05  C06     0.00   0.0  0
 7P3  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 7P3  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 7P3  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 7P3  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 7P3  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 7P3  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 7P3  CONST_13  C08  C09  C01  C02   180.00   0.0  0
 7P3  CONST_14  C06  C05  C01  C02   180.00   0.0  0
 7P3  CONST_15  N10  C09  C01  C05   180.00   0.0  0
 7P3  CONST_16  N10  C09  C08  C07   180.00   0.0  0
 7P3  CONST_17  C13  C12  C11  N10   180.00   0.0  0
 7P3  CONST_18  C15  C16  C11  N10   180.00   0.0  0
 7P3  CONST_19  O20  C14  C13  C12   180.00   0.0  0
 7P3  CONST_20  C17  C16  C11  C12   180.00   0.0  0
 7P3  CONST_21  C17  C16  C15  C14   180.00   0.0  0
 7P3  CONST_22  O20  C14  C15  C16   180.00   0.0  0
 7P3  CONST_23  H5   C08  C09  C01   180.00   0.0  0
 7P3  CONST_24  H3   C06  C05  C01   180.00   0.0  0
 7P3  CONST_25  H4   C07  C06  C05   180.00   0.0  0
 7P3  CONST_26  H2   C05  C06  C07   180.00   0.0  0
 7P3  CONST_27  H8   C13  C12  C11   180.00   0.0  0
 7P3  CONST_28  H9   C15  C16  C11   180.00   0.0  0
 7P3  CONST_29  H7   C12  C13  C14   180.00   0.0  0
 7P3  CONST_30  H1   O03  C02  C01   180.00   0.0  0
 7P3  CONST_31  H10  O19  C17  C16   180.00   0.0  0
 7P3  Var_01    C11  N10  C09  C01   162.89  30.0  2
 7P3  Var_02    C12  C11  N10  C09   -41.09  30.0  3
 7P3  Var_03    C09  C01  C02  O03  -170.44  30.0  2
 7P3  Var_04    O18  C17  C16  C11    21.25  30.0  2
 7P3  Var_05    C22  C21  O20  C14   177.00  30.0  1
 7P3  Var_06    C23  C22  C21  O20  -176.46  30.0  3
 7P3  Var_07    C24  C23  C22  C21  -179.51  30.0  3
 7P3  Var_08    C25  C24  C23  C22  -177.88  30.0  3
 7P3  Var_09    P26  C25  C24  C23  -179.79  30.0  3
 7P3  Var_10    O29  P26  C25  C24    56.46  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
 7P3  plan-1  C01  0.020
 7P3  plan-1  C02  0.020
 7P3  plan-1  C05  0.020
 7P3  plan-1  C06  0.020
 7P3  plan-1  C07  0.020
 7P3  plan-1  C08  0.020
 7P3  plan-1  C09  0.020
 7P3  plan-1  N10  0.020
 7P3  plan-1  H2   0.020
 7P3  plan-1  H3   0.020
 7P3  plan-1  H4   0.020
 7P3  plan-1  H5   0.020
 7P3  plan-2  N10  0.020
 7P3  plan-2  C11  0.020
 7P3  plan-2  C12  0.020
 7P3  plan-2  C13  0.020
 7P3  plan-2  C14  0.020
 7P3  plan-2  C15  0.020
 7P3  plan-2  C16  0.020
 7P3  plan-2  C17  0.020
 7P3  plan-2  O20  0.020
 7P3  plan-2  H7   0.020
 7P3  plan-2  H8   0.020
 7P3  plan-2  H9   0.020
 7P3  plan-3  C01  0.020
 7P3  plan-3  C02  0.020
 7P3  plan-3  O03  0.020
 7P3  plan-3  O04  0.020
 7P3  plan-3  H1   0.020
 7P3  plan-4  C16  0.020
 7P3  plan-4  C17  0.020
 7P3  plan-4  O18  0.020
 7P3  plan-4  O19  0.020
 7P3  plan-4  H10  0.020

