# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:38:24 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (5E)-12-chloro-13,15-dihydroxy-4,7,8,9-tetrahydro-2-benzoxacyclotridecine-1,10(3H,11H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)OCC/C=C/CCCC(=O)Cc2c1Cl
#
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
 NP5  NP5  (5E)-12-chloro-13,15-dihydroxy-4,7,8,9-tetrahydro-2-benzoxacyclotridecine-1,10(3H,11H)-dione  ligand  39  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NP5
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
 NP5  C1    C   C     0   0.594  -0.5700   1.1513  -0.7709
 NP5  O10   O   O2    0  -0.506  -1.1599   2.1845  -0.1608
 NP5  C2    C   CR6   0  -0.252   0.8143   0.9365  -0.2889
 NP5  C3    C   CR6   0   0.382   1.6087   2.0158   0.1393
 NP5  C4    C   CR16  0  -0.499   2.9418   1.8136   0.4817
 NP5  C5    C   CR6   0   0.469   3.4900   0.5483   0.4444
 NP5  C6    C   CR6   0  -0.278   2.6875  -0.5381   0.0641
 NP5  C7    C   CR6   0   0.268   1.3673  -0.3645  -0.3122
 NP5  C8    C   CH2   0  -0.660   0.5234  -1.5504  -0.6798
 NP5  C9    C   C     0   0.413  -0.6722  -1.7437   0.2362
 NP5  C10   C   CH2   0  -0.559  -1.7143  -2.6972  -0.2780
 NP5  C11   C   CH2   0  -0.432  -2.9074  -2.9384   0.6380
 NP5  C12   C   CH2   0  -0.491  -4.0591  -1.9494   0.4402
 NP5  C13   C   C1    0  -0.191  -3.7434  -0.5249   0.7698
 NP5  C14   C   C1    0  -0.205  -3.8006   0.4787  -0.0995
 NP5  C15   C   CH2   0  -0.507  -3.5685   1.9183   0.2347
 NP5  C16   C   CH2   0  -0.199  -2.4774   2.6025  -0.5699
 NP5  O1    O   O     0  -0.428  -1.1141   0.5063  -1.6293
 NP5  O3    O   OH1   0  -0.622   1.1856   3.2808   0.2169
 NP5  O4    O   OH1   0  -0.600   4.7585   0.2989   0.7691
 NP5  CL1   CL  CL    0  -0.107   3.4430  -2.0990   0.0932
 NP5  O5    O   O     0  -0.392  -0.7269  -1.2164   1.3212
 NP5  H4    H   HCR6  0   0.293   3.5418   2.6637   0.7857
 NP5  H8C1  H   HCH2  0   0.302   1.1057  -2.4711  -0.6031
 NP5  H8C2  H   HCH2  0   0.301   0.1956  -1.5060  -1.7171
 NP5  H101  H   HCH2  0   0.277  -1.1933  -3.6389  -0.4856
 NP5  H102  H   HCH2  0   0.268  -2.0383  -2.3393  -1.2614
 NP5  H111  H   HCH2  0   0.229  -2.5851  -2.9362   1.6816
 NP5  H112  H   HCH2  0   0.238  -3.2943  -3.9406   0.4430
 NP5  H121  H   HCH2  0   0.237  -4.8930  -2.2797   1.0688
 NP5  H122  H   HCH2  0   0.228  -4.4107  -2.0164  -0.5936
 NP5  H13   H   H     0   0.222  -3.4724  -0.3170   1.8021
 NP5  H14   H   H     0   0.224  -4.0639   0.2662  -1.1332
 NP5  H151  H   HCH2  0   0.248  -3.3686   2.0426   1.3023
 NP5  H152  H   HCH2  0   0.250  -4.4818   2.4863   0.0256
 NP5  H161  H   HCH2  0   0.264  -2.4931   3.6737  -0.3769
 NP5  H162  H   HCH2  0   0.248  -2.6081   2.4470  -1.6411
 NP5  H3    H   HOH1  0   0.485   0.2216   3.3150   0.1148
 NP5  HA    H   HOH1  0   0.488   5.2114   1.1154   1.0126

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
 NP5  C1   O10   single    1.337  0.020  1.337
 NP5  C1   C2    single    1.482  0.020  1.482
 NP5  C1   O1    double    1.204  0.020  1.204
 NP5  O10  C16   single    1.442  0.020  1.442
 NP5  C2   C3    single    1.407  0.020  1.407
 NP5  C2   C7    aromatic  1.414  0.020  1.414
 NP5  C3   C4    aromatic  1.391  0.020  1.391
 NP5  C3   O3    single    1.336  0.020  1.336
 NP5  C4   C5    aromatic  1.379  0.020  1.379
 NP5  C4   H4    single    0.930  0.020  1.080
 NP5  C5   C6    aromatic  1.403  0.020  1.403
 NP5  C5   O4    single    1.333  0.020  1.333
 NP5  C6   C7    single    1.384  0.020  1.384
 NP5  C6   CL1   single    1.734  0.020  1.734
 NP5  C7   C8    single    1.501  0.020  1.501
 NP5  C8   C9    single    1.519  0.020  1.519
 NP5  C8   H8C1  single    0.970  0.020  1.090
 NP5  C8   H8C2  single    0.970  0.020  1.090
 NP5  C9   C10   single    1.503  0.020  1.503
 NP5  C9   O5    double    1.208  0.020  1.208
 NP5  C10  C11   single    1.523  0.020  1.523
 NP5  C10  H101  single    0.970  0.020  1.090
 NP5  C10  H102  single    0.970  0.020  1.090
 NP5  C11  C12   single    1.531  0.020  1.531
 NP5  C11  H111  single    0.970  0.020  1.090
 NP5  C11  H112  single    0.970  0.020  1.090
 NP5  C12  C13   single    1.496  0.020  1.496
 NP5  C12  H121  single    0.970  0.020  1.090
 NP5  C12  H122  single    0.970  0.020  1.090
 NP5  C13  C14   double    1.329  0.020  1.329
 NP5  C13  H13   single    0.930  0.020  1.080
 NP5  C14  C15   single    1.496  0.020  1.496
 NP5  C14  H14   single    0.930  0.020  1.080
 NP5  C15  C16   single    1.519  0.020  1.519
 NP5  C15  H151  single    0.970  0.020  1.090
 NP5  C15  H152  single    0.970  0.020  1.090
 NP5  C16  H161  single    0.970  0.020  1.090
 NP5  C16  H162  single    0.970  0.020  1.090
 NP5  O3   H3    single    0.850  0.020  0.980
 NP5  O4   HA    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
 NP5  O1    C1   C2    125.21  3.000
 NP5  O1    C1   O10   122.69  3.000
 NP5  C2    C1   O10   112.08  3.000
 NP5  C16   O10  C1    119.86  3.000
 NP5  C7    C2   C3    119.35  3.000
 NP5  C7    C2   C1    119.58  3.000
 NP5  C3    C2   C1    121.02  3.000
 NP5  O3    C3   C4    115.27  3.000
 NP5  O3    C3   C2    124.42  3.000
 NP5  C4    C3   C2    120.29  3.000
 NP5  H4    C4   C5    120.46  3.000
 NP5  H4    C4   C3    119.04  3.000
 NP5  C5    C4   C3    120.50  3.000
 NP5  O4    C5   C6    117.74  3.000
 NP5  O4    C5   C4    122.90  3.000
 NP5  C6    C5   C4    119.35  3.000
 NP5  CL1   C6   C7    122.21  3.000
 NP5  CL1   C6   C5    116.31  3.000
 NP5  C7    C6   C5    121.48  3.000
 NP5  C8    C7   C6    120.25  3.000
 NP5  C8    C7   C2    120.74  3.000
 NP5  C6    C7   C2    118.96  3.000
 NP5  H8C2  C8   H8C1  105.18  3.000
 NP5  H8C2  C8   C9    110.05  3.000
 NP5  H8C1  C8   C9    105.67  3.000
 NP5  H8C2  C8   C7    111.74  3.000
 NP5  H8C1  C8   C7    110.43  3.000
 NP5  C9    C8   C7    113.29  3.000
 NP5  O5    C9   C10   123.57  3.000
 NP5  O5    C9   C8    121.47  3.000
 NP5  C10   C9   C8    114.85  3.000
 NP5  H102  C10  H101  104.56  3.000
 NP5  H102  C10  C11   111.09  3.000
 NP5  H101  C10  C11   110.49  3.000
 NP5  H102  C10  C9    107.75  3.000
 NP5  H101  C10  C9    106.28  3.000
 NP5  C11   C10  C9    115.96  3.000
 NP5  H112  C11  H111  106.09  3.000
 NP5  H112  C11  C12   107.66  3.000
 NP5  H111  C11  C12   110.13  3.000
 NP5  H112  C11  C10   108.39  3.000
 NP5  H111  C11  C10   110.07  3.000
 NP5  C12   C11  C10   114.15  3.000
 NP5  H122  C12  H121  106.20  3.000
 NP5  H122  C12  C13   109.54  3.000
 NP5  H121  C12  C13   108.75  3.000
 NP5  H122  C12  C11   108.92  3.000
 NP5  H121  C12  C11   107.68  3.000
 NP5  C13   C12  C11   115.34  3.000
 NP5  H13   C13  C14   119.16  3.000
 NP5  H13   C13  C12   116.35  3.000
 NP5  C14   C13  C12   124.47  3.000
 NP5  H14   C14  C15   115.97  3.000
 NP5  H14   C14  C13   118.98  3.000
 NP5  C15   C14  C13   125.02  3.000
 NP5  H152  C15  H151  106.25  3.000
 NP5  H152  C15  C16   105.32  3.000
 NP5  H151  C15  C16   109.56  3.000
 NP5  H152  C15  C14   109.08  3.000
 NP5  H151  C15  C14   110.85  3.000
 NP5  C16   C15  C14   115.26  3.000
 NP5  H162  C16  H161  108.23  3.000
 NP5  H162  C16  C15   111.73  3.000
 NP5  H161  C16  C15   109.82  3.000
 NP5  H162  C16  O10   110.30  3.000
 NP5  H161  C16  O10   104.37  3.000
 NP5  C15   C16  O10   112.07  3.000
 NP5  H3    O3   C3    110.00  3.000
 NP5  HA    O4   C5    110.48  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
 NP5  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 NP5  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 NP5  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 NP5  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 NP5  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 NP5  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 NP5  CONST_07  O3   C3   C2   C1     0.00   0.0  0
 NP5  CONST_08  CL1  C6   C7   C2   180.00   0.0  0
 NP5  CONST_09  O4   C5   C4   C3   180.00   0.0  0
 NP5  CONST_10  CL1  C6   C5   C4   180.00   0.0  0
 NP5  CONST_11  O3   C3   C4   C5   180.00   0.0  0
 NP5  CONST_12  O3   C3   C2   C7   180.00   0.0  0
 NP5  CONST_13  O4   C5   C6   C7   180.00   0.0  0
 NP5  CONST_14  CL1  C6   C7   C8     0.00   0.0  0
 NP5  CONST_15  H4   C4   C3   C2   180.00   0.0  0
 NP5  Var_01    C15  C14  C13  C12  176.09   0.0  0
 NP5  Var_02    C15  C16  O10  C1    91.68  30.0  1
 NP5  Var_03    C3   C2   C1   O10  -31.61  30.0  1
 NP5  Var_04    C14  C15  C16  O10  -73.78  30.0  1
 NP5  Var_05    C9   C8   C7   C2   -59.32  30.0  1
 NP5  Var_06    C10  C9   C8   C7   165.91  30.0  1
 NP5  Var_07    C11  C10  C9   C8   178.43  30.0  1
 NP5  Var_08    C12  C11  C10  C9    88.38  30.0  1
 NP5  Var_09    C13  C12  C11  C10  -64.21  30.0  1
 NP5  Var_10    C14  C13  C12  C11  119.12  30.0  1
 NP5  Var_11    C16  C15  C14  C13  123.71  30.0  1
 NP5  Var_12    H13  C13  C14  C15   -2.47   0.0  0

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
 NP5  plan-1  C1   0.020
 NP5  plan-1  C2   0.020
 NP5  plan-1  C3   0.020
 NP5  plan-1  C4   0.020
 NP5  plan-1  C5   0.020
 NP5  plan-1  C6   0.020
 NP5  plan-1  C7   0.020
 NP5  plan-1  C8   0.020
 NP5  plan-1  O3   0.020
 NP5  plan-1  O4   0.020
 NP5  plan-1  CL1  0.020
 NP5  plan-1  H4   0.020
 NP5  plan-2  C8   0.020
 NP5  plan-2  C9   0.020
 NP5  plan-2  C10  0.020
 NP5  plan-2  O5   0.020
 NP5  plan-3  C1   0.020
 NP5  plan-3  O10  0.020
 NP5  plan-3  C2   0.020
 NP5  plan-3  O1   0.020
 NP5  plan-4  C12  0.020
 NP5  plan-4  C13  0.020
 NP5  plan-4  C14  0.020
 NP5  plan-4  C15  0.020
 NP5  plan-4  H13  0.020
 NP5  plan-4  H14  0.020

