# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 20:28:05 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: [2-oxidanylidene-7-[oxidanyl-[(1~{S})-1-phenylethyl]phosphoryl]oxy-chromen-4-yl]methanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](c1ccccc1)[P](O)(=O)Oc2ccc3C(=CC(=O)Oc3c2)C[S](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
 9RQ  9RQ  '[2-oxidanylidene-7-[oxidanyl-[(1~{S})-1-phenylethyl]phosphoryl]oxy-chromen-4-yl]methanesulfonic acid'  ligand  43  28  .  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_9RQ
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
 9RQ  C4   C  CR16   0  -0.314  -6.2951  -0.6078  -0.2119
 9RQ  C14  C  CH2    0  -0.762   4.5999   0.6098   1.2079
 9RQ  C5   C  CR16   0  -0.243  -7.4207  -0.1494  -0.8825
 9RQ  C6   C  CR16   0  -0.276  -7.5127   1.1842  -1.2588
 9RQ  C11  C  CR16   0  -0.311   1.6048   0.2492   1.1196
 9RQ  C7   C  CR16   0  -0.242  -6.4683   2.0491  -0.9588
 9RQ  C8   C  CR16   0  -0.299  -5.3437   1.5859  -0.2888
 9RQ  C9   C  CR6    0   0.408  -0.2816  -1.1084   0.5013
 9RQ  C10  C  CR16   0  -0.328   0.2448   0.0454   1.0966
 9RQ  C12  C  CR66   0  -0.043   2.4920  -0.6732   0.5482
 9RQ  C13  C  CR6    0   0.304   3.9292  -0.5481   0.5554
 9RQ  C3   C  CR6    0   0.146  -5.2437   0.2510   0.1028
 9RQ  P1   P  P      0   1.289  -2.7161  -0.5315  -0.4520
 9RQ  C1   C  CH1    0  -0.591  -4.0223  -0.2723   0.8139
 9RQ  C2   C  CH3    0  -0.663  -3.5624   0.6200   1.9642
 9RQ  O2   O  O2     0  -0.649  -1.6002  -1.3668   0.5260
 9RQ  S1   S  S      0   1.406   4.8184   2.0018   0.0542
 9RQ  O3   O  OS    -1  -0.755   5.4475   3.0525   0.8739
 9RQ  O4   O  OS     0  -0.748   5.6940   1.4845  -1.0100
 9RQ  O5   O  OS     0  -0.742   3.4667   2.3508  -0.4136
 9RQ  C15  C  CR16   0  -0.543   4.6719  -1.5017  -0.0501
 9RQ  C16  C  CR6    0   0.549   4.0773  -2.6505  -0.6846
 9RQ  O6   O  O      0  -0.469   2.7234  -2.7433  -0.6356
 9RQ  O7   O  O      0  -0.444   4.6703  -3.5407  -1.2460
 9RQ  C17  C  CR66   0   0.388   1.9396  -1.8063  -0.0518
 9RQ  C18  C  CR16   0  -0.433   0.5715  -2.0310  -0.0861
 9RQ  O8   O  O      0  -0.774  -2.0870   0.7686  -0.8558
 9RQ  H5   H  HCR6   0   0.244  -6.2343  -1.6494   0.0807
 9RQ  H6   H  HCR6   0   0.250  -8.2261  -0.8358  -1.1116
 9RQ  H7   H  HCR6   0   0.251  -8.3899   1.5463  -1.7794
 9RQ  H11  H  HCR6   0   0.260   1.9873   1.1497   1.5772
 9RQ  H8   H  HCR6   0   0.251  -6.5265   3.0901  -1.2509
 9RQ  H9   H  HCR6   0   0.246  -4.5378   2.2757  -0.0731
 9RQ  H10  H  HCR6   0   0.268  -0.4173   0.7670   1.5545
 9RQ  H3   H  HCH3   0   0.229  -3.2256   1.5963   1.6180
 9RQ  H4   H  HCH3   0   0.237  -4.3749   0.7770   2.6752
 9RQ  H2   H  HCH3   0   0.237  -2.7360   0.1623   2.5080
 9RQ  H15  H  HCR6   0   0.280   5.7515  -1.4469  -0.0632
 9RQ  H16  H  HCR6   0   0.283   0.1783  -2.9259  -0.5514
 9RQ  H1   H  HCH1   0   0.266  -4.2687  -1.2602   1.2162
 9RQ  H12  H  HCH2   0   0.296   4.0418   0.9768   2.0689
 9RQ  H13  H  HCH2   0   0.309   5.5973   0.3302   1.5473
 9RQ  O1   O  OP    -1  -0.765  -3.1895  -1.5166  -1.4769

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
 9RQ  C4   C5   aromatic  1.388  0.020  1.388
 9RQ  C4   C3   aromatic  1.394  0.020  1.394
 9RQ  C14  C13  single    1.489  0.020  1.489
 9RQ  C14  S1   single    1.821  0.020  1.821
 9RQ  C5   C6   aromatic  1.389  0.020  1.389
 9RQ  C6   C7   aromatic  1.389  0.020  1.389
 9RQ  C11  C10  aromatic  1.375  0.020  1.375
 9RQ  C11  C12  aromatic  1.402  0.020  1.402
 9RQ  C7   C8   aromatic  1.389  0.020  1.389
 9RQ  C8   C3   aromatic  1.395  0.020  1.395
 9RQ  C9   C10  aromatic  1.401  0.020  1.401
 9RQ  C9   O2   single    1.344  0.020  1.344
 9RQ  C9   C18  aromatic  1.387  0.020  1.387
 9RQ  C12  C13  single    1.443  0.020  1.443
 9RQ  C12  C17  aromatic  1.396  0.020  1.396
 9RQ  C13  C15  double    1.352  0.020  1.352
 9RQ  C3   C1   single    1.507  0.020  1.507
 9RQ  O1   P1   deloc     1.498  0.020  1.498
 9RQ  P1   C1   single    1.837  0.020  1.837
 9RQ  P1   O2   single    1.703  0.020  1.703
 9RQ  P1   O8   deloc     1.500  0.020  1.500
 9RQ  C1   C2   single    1.527  0.020  1.527
 9RQ  S1   O3   deloc     1.474  0.020  1.474
 9RQ  S1   O4   deloc     1.472  0.020  1.472
 9RQ  S1   O5   deloc     1.472  0.020  1.472
 9RQ  C15  C16  single    1.441  0.020  1.441
 9RQ  C16  O6   single    1.358  0.020  1.358
 9RQ  C16  O7   double    1.208  0.020  1.208
 9RQ  O6   C17  single    1.354  0.020  1.354
 9RQ  C17  C18  aromatic  1.387  0.020  1.387
 9RQ  C4   H5   single    0.930  0.020  1.080
 9RQ  C14  H12  single    0.970  0.020  1.090
 9RQ  C14  H13  single    0.970  0.020  1.090
 9RQ  C5   H6   single    0.930  0.020  1.080
 9RQ  C6   H7   single    0.930  0.020  1.080
 9RQ  C11  H11  single    0.930  0.020  1.080
 9RQ  C7   H8   single    0.930  0.020  1.080
 9RQ  C8   H9   single    0.930  0.020  1.080
 9RQ  C10  H10  single    0.930  0.020  1.080
 9RQ  C1   H1   single    0.970  0.020  1.090
 9RQ  C2   H3   single    0.970  0.020  1.090
 9RQ  C2   H4   single    0.970  0.020  1.090
 9RQ  C2   H2   single    0.970  0.020  1.090
 9RQ  C15  H15  single    0.930  0.020  1.080
 9RQ  C18  H16  single    0.930  0.020  1.080

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
 9RQ  H5   C4   C3   119.28  3.000
 9RQ  H5   C4   C5   119.56  3.000
 9RQ  C3   C4   C5   121.16  3.000
 9RQ  H13  C14  H12  108.00  3.000
 9RQ  H13  C14  S1   106.47  3.000
 9RQ  H12  C14  S1   107.73  3.000
 9RQ  H13  C14  C13  110.44  3.000
 9RQ  H12  C14  C13  112.18  3.000
 9RQ  S1   C14  C13  111.77  3.000
 9RQ  H6   C5   C6   120.14  3.000
 9RQ  H6   C5   C4   119.74  3.000
 9RQ  C6   C5   C4   120.11  3.000
 9RQ  H7   C6   C7   120.33  3.000
 9RQ  H7   C6   C5   120.35  3.000
 9RQ  C7   C6   C5   119.32  3.000
 9RQ  H11  C11  C12  119.82  3.000
 9RQ  H11  C11  C10  118.73  3.000
 9RQ  C12  C11  C10  121.44  3.000
 9RQ  H8   C7   C8   119.63  3.000
 9RQ  H8   C7   C6   120.00  3.000
 9RQ  C8   C7   C6   120.37  3.000
 9RQ  H9   C8   C3   120.04  3.000
 9RQ  H9   C8   C7   119.12  3.000
 9RQ  C3   C8   C7   120.85  3.000
 9RQ  C18  C9   O2   118.91  3.000
 9RQ  C18  C9   C10  119.78  3.000
 9RQ  O2   C9   C10  121.28  3.000
 9RQ  H10  C10  C9   119.97  3.000
 9RQ  H10  C10  C11  119.98  3.000
 9RQ  C9   C10  C11  120.04  3.000
 9RQ  C17  C12  C13  117.82  3.000
 9RQ  C17  C12  C11  117.32  3.000
 9RQ  C13  C12  C11  124.86  3.000
 9RQ  C15  C13  C12  118.94  3.000
 9RQ  C15  C13  C14  119.84  3.000
 9RQ  C12  C13  C14  121.22  3.000
 9RQ  C1   C3   C8   121.53  3.000
 9RQ  C1   C3   C4   120.26  3.000
 9RQ  C8   C3   C4   118.19  3.000
 9RQ  O8   P1   O2   107.76  3.000
 9RQ  O8   P1   C1   111.19  3.000
 9RQ  O2   P1   C1    98.01  3.000
 9RQ  O8   P1   O1   121.22  3.000
 9RQ  O2   P1   O1   106.10  3.000
 9RQ  C1   P1   O1   109.84  3.000
 9RQ  H1   C1   C2   108.56  3.000
 9RQ  H1   C1   P1   106.61  3.000
 9RQ  C2   C1   P1   112.79  3.000
 9RQ  H1   C1   C3   107.72  3.000
 9RQ  C2   C1   C3   113.37  3.000
 9RQ  P1   C1   C3   107.46  3.000
 9RQ  H2   C2   H4   107.45  3.000
 9RQ  H2   C2   H3   107.49  3.000
 9RQ  H4   C2   H3   107.96  3.000
 9RQ  H2   C2   C1   111.03  3.000
 9RQ  H4   C2   C1   110.53  3.000
 9RQ  H3   C2   C1   112.18  3.000
 9RQ  P1   O2   C9   122.56  3.000
 9RQ  O5   S1   O4   113.56  3.000
 9RQ  O5   S1   O3   113.56  3.000
 9RQ  O4   S1   O3   113.50  3.000
 9RQ  O5   S1   C14  105.80  3.000
 9RQ  O4   S1   C14  105.12  3.000
 9RQ  O3   S1   C14  104.11  3.000
 9RQ  H15  C15  C16  116.56  3.000
 9RQ  H15  C15  C13  121.22  3.000
 9RQ  C16  C15  C13  122.21  3.000
 9RQ  O7   C16  O6   117.12  3.000
 9RQ  O7   C16  C15  126.13  3.000
 9RQ  O6   C16  C15  116.75  3.000
 9RQ  C17  O6   C16  123.06  3.000
 9RQ  C18  C17  O6   116.63  3.000
 9RQ  C18  C17  C12  122.17  3.000
 9RQ  O6   C17  C12  121.20  3.000
 9RQ  H16  C18  C17  120.19  3.000
 9RQ  H16  C18  C9   120.56  3.000
 9RQ  C17  C18  C9   119.24  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
 9RQ  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 9RQ  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 9RQ  CONST_03  C8   C3   C4   C5      0.00   0.0  0
 9RQ  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 9RQ  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 9RQ  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 9RQ  CONST_07  C18  C9   C10  C11     0.00   0.0  0
 9RQ  CONST_08  C18  C17  C12  C11     0.00   0.0  0
 9RQ  CONST_09  C12  C11  C10  C9      0.00   0.0  0
 9RQ  CONST_10  C12  C17  C18  C9      0.00   0.0  0
 9RQ  CONST_11  C17  C12  C11  C10     0.00   0.0  0
 9RQ  CONST_12  C17  C18  C9   C10     0.00   0.0  0
 9RQ  CONST_13  C1   C3   C4   C5    180.00   0.0  0
 9RQ  CONST_14  O2   C9   C10  C11   180.00   0.0  0
 9RQ  CONST_15  C1   C3   C8   C7    180.00   0.0  0
 9RQ  CONST_16  C17  C18  C9   O2    180.00   0.0  0
 9RQ  CONST_17  H7   C6   C5   C4    180.00   0.0  0
 9RQ  CONST_18  H9   C8   C3   C4    180.00   0.0  0
 9RQ  CONST_19  H8   C7   C6   C5    180.00   0.0  0
 9RQ  CONST_20  H5   C4   C5   C6    180.00   0.0  0
 9RQ  CONST_21  H6   C5   C6   C7    180.00   0.0  0
 9RQ  CONST_22  H11  C11  C10  C9    180.00   0.0  0
 9RQ  CONST_23  H16  C18  C9   C10   180.00   0.0  0
 9RQ  CONST_24  H10  C10  C11  C12   180.00   0.0  0
 9RQ  Var_01    C15  C13  C12  C11  -179.05  30.0  1
 9RQ  Var_02    C16  C15  C13  C12    -1.00  30.0  1
 9RQ  Var_03    O6   C16  C15  C13    -0.69  30.0  1
 9RQ  Var_04    C18  C17  O6   C16   179.58  30.0  1
 9RQ  Var_05    S1   C14  C13  C12   -89.30  30.0  2
 9RQ  Var_06    C18  C9   O2   P1   -107.84  30.0  2
 9RQ  Var_07    O1   P1   O2   C9    109.82  30.0  1
 9RQ  Var_08    O3   S1   C14  C13   178.27  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
 9RQ  chir_02  C1  C3  P1  C2  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
 9RQ  plan-1  C4   0.020
 9RQ  plan-1  C5   0.020
 9RQ  plan-1  C6   0.020
 9RQ  plan-1  C7   0.020
 9RQ  plan-1  C8   0.020
 9RQ  plan-1  C3   0.020
 9RQ  plan-1  C1   0.020
 9RQ  plan-1  H5   0.020
 9RQ  plan-1  H6   0.020
 9RQ  plan-1  H7   0.020
 9RQ  plan-1  H8   0.020
 9RQ  plan-1  H9   0.020
 9RQ  plan-2  C11  0.020
 9RQ  plan-2  C9   0.020
 9RQ  plan-2  C10  0.020
 9RQ  plan-2  C12  0.020
 9RQ  plan-2  C13  0.020
 9RQ  plan-2  O2   0.020
 9RQ  plan-2  O6   0.020
 9RQ  plan-2  C17  0.020
 9RQ  plan-2  C18  0.020
 9RQ  plan-2  H11  0.020
 9RQ  plan-2  H10  0.020
 9RQ  plan-2  H16  0.020
 9RQ  plan-3  C15  0.020
 9RQ  plan-3  C16  0.020
 9RQ  plan-3  O6   0.020
 9RQ  plan-3  O7   0.020

