# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:33:09 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (5Z)-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
 NP4  NP4  (5Z)-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_NP4
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
 NP4  C1    C   C     0   0.557  -0.7945   1.1993   0.2374
 NP4  C2    C   CR6   0  -0.261   0.6631   1.0541   0.0383
 NP4  O10   O   O2    0  -0.489  -1.2980   2.3022  -0.3147
 NP4  C3    C   CR6   0   0.393   1.5277   2.1477   0.1877
 NP4  C4    C   CR16  0  -0.500   2.9039   1.9456   0.2089
 NP4  C5    C   CR6   0   0.464   3.4268   0.6749   0.0569
 NP4  C6    C   CR6   0  -0.272   2.5606  -0.4079  -0.1546
 NP4  C7    C   CR6   0   0.298   1.1899  -0.2341  -0.1795
 NP4  C8    C   CH2   0  -0.719   0.2826  -1.3780  -0.5313
 NP4  C9    C   C     0   0.438  -0.2557  -2.1654   0.6401
 NP4  C10   C   CH2   0  -0.561  -1.4264  -3.0797   0.3528
 NP4  C11   C   CH2   0  -0.434  -2.7912  -2.4119   0.6116
 NP4  C12   C   CH2   0  -0.497  -3.3580  -1.6234  -0.5775
 NP4  C13   C   C1    0  -0.186  -4.4292  -0.6737  -0.1432
 NP4  C14   C   C1    0  -0.223  -4.4782   0.6436  -0.3345
 NP4  C15   C   CH2   0  -0.555  -3.5113   1.5016  -1.0962
 NP4  C16   C   CH2   0  -0.186  -2.7254   2.4942  -0.2177
 NP4  O1    O   O     0  -0.408  -1.4684   0.4108   0.8480
 NP4  O3    O   OH1   0  -0.619   1.1158   3.4092   0.3582
 NP4  O4    O   OH1   0  -0.601   4.7358   0.4239   0.0803
 NP4  CL1   CL  CL    0  -0.102   3.2784  -1.9651  -0.3908
 NP4  O5    O   O     0  -0.395   0.2509  -2.1008   1.7351
 NP4  H4    H   HCR6  0   0.295   3.5617   2.7959   0.3473
 NP4  H8C1  H   HCH2  0   0.314   0.8125  -2.0985  -1.1623
 NP4  H8C2  H   HCH2  0   0.296  -0.5459  -1.0429  -1.1552
 NP4  H101  H   HCH2  0   0.267  -1.3284  -3.9466   1.0087
 NP4  H102  H   HCH2  0   0.252  -1.3814  -3.4426  -0.6778
 NP4  H111  H   HCH2  0   0.245  -2.7219  -1.7732   1.4926
 NP4  H112  H   HCH2  0   0.243  -3.5024  -3.1994   0.8690
 NP4  H121  H   HCH2  0   0.240  -3.7716  -2.3397  -1.2953
 NP4  H122  H   HCH2  0   0.229  -2.5747  -1.0906  -1.1124
 NP4  H13   H   H     0   0.232  -5.2445  -1.1244   0.4180
 NP4  H14   H   H     0   0.237  -5.3246   1.1780   0.0881
 NP4  H151  H   HCH2  0   0.265  -4.0770   2.0806  -1.8306
 NP4  H152  H   HCH2  0   0.259  -2.8162   0.8986  -1.6820
 NP4  H161  H   HCH2  0   0.253  -3.0321   2.4372   0.8277
 NP4  H162  H   HCH2  0   0.264  -2.8684   3.5171  -0.5557
 NP4  H3    H   HOH1  0   0.482   0.1672   3.4940   0.1861
 NP4  HA    H   HOH1  0   0.488   5.2350   1.2343   0.2382

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
 NP4  C1   C2    single    1.478  0.020  1.478
 NP4  C1   O10   single    1.332  0.020  1.332
 NP4  C1   O1    double    1.204  0.020  1.204
 NP4  C2   C3    single    1.402  0.020  1.402
 NP4  C2   C7    aromatic  1.409  0.020  1.409
 NP4  O10  C16   single    1.444  0.020  1.444
 NP4  C3   C4    aromatic  1.391  0.020  1.391
 NP4  C3   O3    single    1.338  0.020  1.338
 NP4  C4   C5    aromatic  1.383  0.020  1.383
 NP4  C4   H4    single    0.930  0.020  1.080
 NP4  C5   C6    aromatic  1.403  0.020  1.403
 NP4  C5   O4    single    1.333  0.020  1.333
 NP4  C6   C7    single    1.382  0.020  1.382
 NP4  C6   CL1   single    1.731  0.020  1.731
 NP4  C7   C8    single    1.502  0.020  1.502
 NP4  C8   C9    single    1.511  0.020  1.511
 NP4  C8   H8C1  single    0.970  0.020  1.090
 NP4  C8   H8C2  single    0.970  0.020  1.090
 NP4  C9   C10   single    1.513  0.020  1.513
 NP4  C9   O5    double    1.208  0.020  1.208
 NP4  C10  C11   single    1.541  0.020  1.541
 NP4  C10  H101  single    0.970  0.020  1.090
 NP4  C10  H102  single    0.970  0.020  1.090
 NP4  C11  C12   single    1.535  0.020  1.535
 NP4  C11  H111  single    0.970  0.020  1.090
 NP4  C11  H112  single    0.970  0.020  1.090
 NP4  C12  C13   single    1.496  0.020  1.496
 NP4  C12  H121  single    0.970  0.020  1.090
 NP4  C12  H122  single    0.970  0.020  1.090
 NP4  C13  C14   double    1.332  0.020  1.332
 NP4  C13  H13   single    0.930  0.020  1.080
 NP4  C14  C15   single    1.500  0.020  1.500
 NP4  C14  H14   single    0.930  0.020  1.080
 NP4  C15  C16   single    1.541  0.020  1.541
 NP4  C15  H151  single    0.970  0.020  1.090
 NP4  C15  H152  single    0.970  0.020  1.090
 NP4  C16  H161  single    0.970  0.020  1.090
 NP4  C16  H162  single    0.970  0.020  1.090
 NP4  O3   H3    single    0.850  0.020  0.980
 NP4  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
 NP4  O1    C1   O10   122.75  3.000
 NP4  O1    C1   C2    123.79  3.000
 NP4  O10   C1   C2    113.46  3.000
 NP4  C7    C2   C3    119.94  3.000
 NP4  C7    C2   C1    118.64  3.000
 NP4  C3    C2   C1    121.14  3.000
 NP4  C16   O10  C1    117.12  3.000
 NP4  O3    C3   C4    116.08  3.000
 NP4  O3    C3   C2    124.00  3.000
 NP4  C4    C3   C2    119.89  3.000
 NP4  H4    C4   C5    120.36  3.000
 NP4  H4    C4   C3    119.24  3.000
 NP4  C5    C4   C3    120.40  3.000
 NP4  O4    C5   C6    117.63  3.000
 NP4  O4    C5   C4    122.86  3.000
 NP4  C6    C5   C4    119.51  3.000
 NP4  CL1   C6   C7    121.47  3.000
 NP4  CL1   C6   C5    117.32  3.000
 NP4  C7    C6   C5    121.21  3.000
 NP4  C8    C7   C6    120.51  3.000
 NP4  C8    C7   C2    120.45  3.000
 NP4  C6    C7   C2    118.89  3.000
 NP4  H8C2  C8   H8C1  103.91  3.000
 NP4  H8C2  C8   C9    109.46  3.000
 NP4  H8C1  C8   C9    106.05  3.000
 NP4  H8C2  C8   C7    111.05  3.000
 NP4  H8C1  C8   C7    110.12  3.000
 NP4  C9    C8   C7    115.51  3.000
 NP4  O5    C9   C10   121.93  3.000
 NP4  O5    C9   C8    121.70  3.000
 NP4  C10   C9   C8    116.33  3.000
 NP4  H102  C10  H101  107.40  3.000
 NP4  H102  C10  C11   109.79  3.000
 NP4  H101  C10  C11   108.83  3.000
 NP4  H102  C10  C9    110.35  3.000
 NP4  H101  C10  C9    107.24  3.000
 NP4  C11   C10  C9    113.04  3.000
 NP4  H112  C11  H111  105.87  3.000
 NP4  H112  C11  C12   108.21  3.000
 NP4  H111  C11  C12   110.40  3.000
 NP4  H112  C11  C10   107.68  3.000
 NP4  H111  C11  C10   109.46  3.000
 NP4  C12   C11  C10   114.80  3.000
 NP4  H122  C12  H121  105.66  3.000
 NP4  H122  C12  C13   110.32  3.000
 NP4  H121  C12  C13   109.58  3.000
 NP4  H122  C12  C11   111.50  3.000
 NP4  H121  C12  C11   108.14  3.000
 NP4  C13   C12  C11   111.44  3.000
 NP4  H13   C13  C14   117.16  3.000
 NP4  H13   C13  C12   115.05  3.000
 NP4  C14   C13  C12   127.77  3.000
 NP4  H14   C14  C15   114.73  3.000
 NP4  H14   C14  C13   117.33  3.000
 NP4  C15   C14  C13   127.93  3.000
 NP4  H152  C15  H151  105.18  3.000
 NP4  H152  C15  C16   109.71  3.000
 NP4  H151  C15  C16   107.80  3.000
 NP4  H152  C15  C14   111.54  3.000
 NP4  H151  C15  C14   108.09  3.000
 NP4  C16   C15  C14   114.05  3.000
 NP4  H162  C16  H161  108.07  3.000
 NP4  H162  C16  C15   111.22  3.000
 NP4  H161  C16  C15   111.67  3.000
 NP4  H162  C16  O10   103.55  3.000
 NP4  H161  C16  O10   109.60  3.000
 NP4  C15   C16  O10   112.35  3.000
 NP4  H3    O3   C3    111.21  3.000
 NP4  HA    O4   C5    110.65  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
 NP4  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 NP4  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 NP4  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 NP4  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 NP4  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 NP4  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 NP4  CONST_07  O3   C3   C2   C1      0.00   0.0  0
 NP4  CONST_08  CL1  C6   C7   C2    180.00   0.0  0
 NP4  CONST_09  O4   C5   C4   C3    180.00   0.0  0
 NP4  CONST_10  CL1  C6   C5   C4    180.00   0.0  0
 NP4  CONST_11  O3   C3   C4   C5    180.00   0.0  0
 NP4  CONST_12  O3   C3   C2   C7    180.00   0.0  0
 NP4  CONST_13  O4   C5   C6   C7    180.00   0.0  0
 NP4  CONST_14  CL1  C6   C7   C8      0.00   0.0  0
 NP4  CONST_15  H4   C4   C3   C2    180.00   0.0  0
 NP4  Var_01    C15  C14  C13  C12     3.58   0.0  0
 NP4  Var_02    C15  C16  O10  C1    -70.28  30.0  1
 NP4  Var_03    C9   C8   C7   C2    -90.39  30.0  1
 NP4  Var_04    C3   C2   C1   O10    42.98  30.0  1
 NP4  Var_05    C14  C15  C16  O10   121.43  30.0  1
 NP4  Var_06    C10  C9   C8   C7    164.97  30.0  1
 NP4  Var_07    C11  C10  C9   C8    -93.22  30.0  1
 NP4  Var_08    C12  C11  C10  C9     87.14  30.0  1
 NP4  Var_09    C13  C12  C11  C10  -162.20  30.0  1
 NP4  Var_10    C14  C13  C12  C11   123.75  30.0  1
 NP4  Var_11    C16  C15  C14  C13  -113.39  30.0  1
 NP4  Var_12    H13  C13  C14  C15  -178.27   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
 NP4  plan-1  C1   0.020
 NP4  plan-1  C2   0.020
 NP4  plan-1  C3   0.020
 NP4  plan-1  C4   0.020
 NP4  plan-1  C5   0.020
 NP4  plan-1  C6   0.020
 NP4  plan-1  C7   0.020
 NP4  plan-1  C8   0.020
 NP4  plan-1  O3   0.020
 NP4  plan-1  O4   0.020
 NP4  plan-1  CL1  0.020
 NP4  plan-1  H4   0.020
 NP4  plan-2  C8   0.020
 NP4  plan-2  C9   0.020
 NP4  plan-2  C10  0.020
 NP4  plan-2  O5   0.020
 NP4  plan-3  C1   0.020
 NP4  plan-3  C2   0.020
 NP4  plan-3  O10  0.020
 NP4  plan-3  O1   0.020
 NP4  plan-4  C12  0.020
 NP4  plan-4  C13  0.020
 NP4  plan-4  C14  0.020
 NP4  plan-4  C15  0.020
 NP4  plan-4  H13  0.020
 NP4  plan-4  H14  0.020

