# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:09:19 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (1Z,2R)-1-[(1-methylethyl)imino]-3-(naphthalen-1-yloxy)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N=C[C@@H](O)COc1cccc2ccccc12
#
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
 RNP  RNP  (1Z,2R)-1-[(1-methylethyl)imino]-3-(naphthalen-1-yloxy)propan-2-ol  ligand  38  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RNP
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
 RNP  C1    C  CR6   0   0.368  -0.6181   0.1751  -1.4975
 RNP  C2    C  CR16  0  -0.408  -1.9883   0.2612  -1.4602
 RNP  C3    C  CR16  0  -0.245  -2.7319   0.2087  -2.6580
 RNP  C4    C  CR16  0  -0.344  -2.1171   0.0757  -3.8690
 RNP  C5    C  CR16  0  -0.316  -0.0349  -0.1524  -5.1751
 RNP  C6    C  CR16  0  -0.252   1.3295  -0.2400  -5.2304
 RNP  C7    C  CR16  0  -0.257   2.0884  -0.1934  -4.0446
 RNP  C8    C  CR16  0  -0.287   1.4704  -0.0609  -2.8292
 RNP  C9    C  CR66  0  -0.019   0.0618   0.0324  -2.7453
 RNP  C10   C  CR66  0   0.126  -0.7055  -0.0145  -3.9374
 RNP  O1    O  O2    0  -0.466   0.1777   0.2190  -0.4155
 RNP  C11   C  CH2   0  -0.182  -0.4147   0.3487   0.8605
 RNP  C12   C  CH1   0  -0.042   0.7027   0.3568   1.8891
 RNP  O2    O  OH1   0  -0.672   1.3953  -0.8556   1.9058
 RNP  C13   C  C1    0  -0.046   0.1165   0.6582   3.2428
 RNP  N1    N  N     0  -0.354   0.3001  -0.1649   4.1744
 RNP  C14   C  CH1   0  -0.113  -0.2447   0.0972   5.4926
 RNP  C15   C  CH3   0  -0.648  -1.1903  -1.0374   5.8634
 RNP  C16   C  CH3   0  -0.647   0.9057   0.2050   6.4848
 RNP  H2    H  HCR6  0   0.282  -2.5216   0.3727  -0.5262
 RNP  H3    H  HCR6  0   0.260  -3.8104   0.2760  -2.6000
 RNP  H4    H  HCR6  0   0.251  -2.6967   0.0376  -4.7827
 RNP  H5    H  HCR6  0   0.255  -0.6242  -0.1883  -6.0837
 RNP  H6    H  HCR6  0   0.258   1.8293  -0.3462  -6.1845
 RNP  H7    H  HCR6  0   0.258   3.1671  -0.2618  -4.0957
 RNP  H8    H  HCR6  0   0.255   2.0697  -0.0272  -1.9299
 RNP  H111  H  HCH2  0   0.236  -1.1010  -0.4833   1.0572
 RNP  H112  H  HCH2  0   0.234  -0.9871   1.2815   0.9247
 RNP  H12   H  HCH1  0   0.242   1.3835   1.1860   1.6416
 RNP  HA    H  HOH1  0   0.440   1.2885  -1.1998   2.8090
 RNP  H13   H  H     0   0.247  -0.4436   1.5917   3.3527
 RNP  H14   H  HCH1  0   0.213  -0.8061   1.0419   5.4957
 RNP  H151  H  HCH3  0   0.230  -1.6204  -0.8646   6.8502
 RNP  H152  H  HCH3  0   0.233  -2.0099  -1.1195   5.1491
 RNP  H153  H  HCH3  0   0.224  -0.6605  -1.9912   5.8874
 RNP  H161  H  HCH3  0   0.224   1.4952  -0.7132   6.4939
 RNP  H162  H  HCH3  0   0.233   1.5691   1.0341   6.2367
 RNP  H163  H  HCH3  0   0.230   0.5223   0.3716   7.4917

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
 RNP  C1   C2    aromatic  1.373  0.020  1.373
 RNP  C1   C9    aromatic  1.428  0.020  1.428
 RNP  C1   O1    single    1.344  0.020  1.344
 RNP  C2   C3    aromatic  1.411  0.020  1.411
 RNP  C2   H2    single    0.930  0.020  1.080
 RNP  C3   C4    aromatic  1.365  0.020  1.365
 RNP  C3   H3    single    0.930  0.020  1.080
 RNP  C4   C10   aromatic  1.416  0.020  1.416
 RNP  C4   H4    single    0.930  0.020  1.080
 RNP  C5   C6    aromatic  1.368  0.020  1.368
 RNP  C5   C10   aromatic  1.414  0.020  1.414
 RNP  C5   H5    single    0.930  0.020  1.080
 RNP  C6   C7    aromatic  1.409  0.020  1.409
 RNP  C6   H6    single    0.930  0.020  1.080
 RNP  C7   C8    aromatic  1.370  0.020  1.370
 RNP  C7   H7    single    0.930  0.020  1.080
 RNP  C8   C9    aromatic  1.414  0.020  1.414
 RNP  C8   H8    single    0.930  0.020  1.080
 RNP  C9   C10   aromatic  1.418  0.020  1.418
 RNP  O1   C11   single    1.413  0.020  1.413
 RNP  C11  C12   single    1.519  0.020  1.519
 RNP  C11  H111  single    0.970  0.020  1.090
 RNP  C11  H112  single    0.970  0.020  1.090
 RNP  C12  O2    single    1.396  0.020  1.396
 RNP  C12  C13   single    1.506  0.020  1.506
 RNP  C12  H12   single    0.970  0.020  1.090
 RNP  O2   HA    single    0.850  0.020  0.980
 RNP  C13  N1    double    1.257  0.020  1.257
 RNP  C13  H13   single    0.930  0.020  1.080
 RNP  N1   C14   single    1.450  0.020  1.450
 RNP  C14  C15   single    1.523  0.020  1.523
 RNP  C14  C16   single    1.523  0.020  1.523
 RNP  C14  H14   single    0.970  0.020  1.090
 RNP  C15  H151  single    0.970  0.020  1.090
 RNP  C15  H152  single    0.970  0.020  1.090
 RNP  C15  H153  single    0.970  0.020  1.090
 RNP  C16  H161  single    0.970  0.020  1.090
 RNP  C16  H162  single    0.970  0.020  1.090
 RNP  C16  H163  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
 RNP  O1    C1   C9    115.14  3.000
 RNP  O1    C1   C2    124.54  3.000
 RNP  C9    C1   C2    120.33  3.000
 RNP  H2    C2   C3    118.50  3.000
 RNP  H2    C2   C1    121.46  3.000
 RNP  C3    C2   C1    120.03  3.000
 RNP  H3    C3   C4    120.18  3.000
 RNP  H3    C3   C2    118.52  3.000
 RNP  C4    C3   C2    121.31  3.000
 RNP  H4    C4   C10   119.38  3.000
 RNP  H4    C4   C3    120.75  3.000
 RNP  C10   C4   C3    119.88  3.000
 RNP  H5    C5   C10   118.63  3.000
 RNP  H5    C5   C6    120.42  3.000
 RNP  C10   C5   C6    120.95  3.000
 RNP  H6    C6   C7    119.77  3.000
 RNP  H6    C6   C5    120.15  3.000
 RNP  C7    C6   C5    120.08  3.000
 RNP  H7    C7   C8    119.85  3.000
 RNP  H7    C7   C6    119.69  3.000
 RNP  C8    C7   C6    120.47  3.000
 RNP  H8    C8   C9    120.04  3.000
 RNP  H8    C8   C7    119.40  3.000
 RNP  C9    C8   C7    120.55  3.000
 RNP  C10   C9   C8    119.13  3.000
 RNP  C10   C9   C1    118.69  3.000
 RNP  C8    C9   C1    122.18  3.000
 RNP  C9    C10  C5    118.83  3.000
 RNP  C9    C10  C4    119.77  3.000
 RNP  C5    C10  C4    121.40  3.000
 RNP  C11   O1   C1    118.81  3.000
 RNP  H112  C11  H111  107.96  3.000
 RNP  H112  C11  C12   109.88  3.000
 RNP  H111  C11  C12   110.06  3.000
 RNP  H112  C11  O1    110.48  3.000
 RNP  H111  C11  O1    110.79  3.000
 RNP  C12   C11  O1    107.68  3.000
 RNP  H12   C12  C13   106.99  3.000
 RNP  H12   C12  O2    110.48  3.000
 RNP  C13   C12  O2    110.87  3.000
 RNP  H12   C12  C11   107.86  3.000
 RNP  C13   C12  C11   108.88  3.000
 RNP  O2    C12  C11   111.61  3.000
 RNP  HA    O2   C12   105.30  3.000
 RNP  H13   C13  N1    124.00  3.000
 RNP  H13   C13  C12   117.41  3.000
 RNP  N1    C13  C12   118.59  3.000
 RNP  C14   N1   C13   120.03  3.000
 RNP  H14   C14  C16   108.86  3.000
 RNP  H14   C14  C15   108.82  3.000
 RNP  C16   C14  C15   111.29  3.000
 RNP  H14   C14  N1    110.48  3.000
 RNP  C16   C14  N1    108.73  3.000
 RNP  C15   C14  N1    108.66  3.000
 RNP  H153  C15  H152  108.27  3.000
 RNP  H153  C15  H151  108.07  3.000
 RNP  H152  C15  H151  107.96  3.000
 RNP  H153  C15  C14   110.80  3.000
 RNP  H152  C15  C14   111.30  3.000
 RNP  H151  C15  C14   110.33  3.000
 RNP  H163  C16  H162  107.93  3.000
 RNP  H163  C16  H161  108.12  3.000
 RNP  H162  C16  H161  108.24  3.000
 RNP  H163  C16  C14   110.29  3.000
 RNP  H162  C16  C14   111.41  3.000
 RNP  H161  C16  C14   110.73  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
 RNP  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 RNP  CONST_02  C7    C8   C9   C1    180.00   0.0  0
 RNP  CONST_03  C4    C10  C9   C1      0.00   0.0  0
 RNP  CONST_04  C5    C10  C9   C1    180.00   0.0  0
 RNP  CONST_05  C8    C9   C1   C2    180.00   0.0  0
 RNP  CONST_06  C10   C9   C1   C2      0.00   0.0  0
 RNP  CONST_07  C10   C4   C3   C2      0.00   0.0  0
 RNP  CONST_08  C9    C1   C2   C3      0.00   0.0  0
 RNP  CONST_09  C5    C10  C4   C3    180.00   0.0  0
 RNP  CONST_10  C9    C10  C4   C3      0.00   0.0  0
 RNP  CONST_11  C6    C5   C10  C4    180.00   0.0  0
 RNP  CONST_12  C8    C9   C10  C4    180.00   0.0  0
 RNP  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 RNP  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 RNP  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 RNP  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 RNP  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 RNP  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 RNP  CONST_19  O1    C1   C2   C3    180.00   0.0  0
 RNP  CONST_20  O1    C1   C9   C8      0.00   0.0  0
 RNP  CONST_21  O1    C1   C9   C10   180.00   0.0  0
 RNP  CONST_22  H3    C3   C2   C1    180.00   0.0  0
 RNP  CONST_23  H8    C8   C9   C1      0.00   0.0  0
 RNP  CONST_24  H4    C4   C3   C2    180.00   0.0  0
 RNP  CONST_25  H2    C2   C3   C4    180.00   0.0  0
 RNP  CONST_26  H5    C5   C10  C4      0.00   0.0  0
 RNP  CONST_27  H7    C7   C6   C5    180.00   0.0  0
 RNP  CONST_28  H6    C6   C7   C8    180.00   0.0  0
 RNP  Var_01    C12   C11  O1   C1    179.40  30.0  3
 RNP  Var_02    C15   C14  N1   C13   120.61  30.0  3
 RNP  Var_03    H13   C13  N1   C14    -0.03   0.0  2
 RNP  Var_04    H151  C15  C14  N1   -179.71  30.0  3
 RNP  Var_05    H161  C16  C14  N1    -58.62  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
 RNP  chir_01  C12  C11  O2  C13  positiv

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
 RNP  plan-1  C1   0.020
 RNP  plan-1  C2   0.020
 RNP  plan-1  C3   0.020
 RNP  plan-1  C4   0.020
 RNP  plan-1  C5   0.020
 RNP  plan-1  C6   0.020
 RNP  plan-1  C7   0.020
 RNP  plan-1  C8   0.020
 RNP  plan-1  C9   0.020
 RNP  plan-1  C10  0.020
 RNP  plan-1  O1   0.020
 RNP  plan-1  H2   0.020
 RNP  plan-1  H3   0.020
 RNP  plan-1  H4   0.020
 RNP  plan-1  H5   0.020
 RNP  plan-1  H6   0.020
 RNP  plan-1  H7   0.020
 RNP  plan-1  H8   0.020
 RNP  plan-2  C12  0.020
 RNP  plan-2  C13  0.020
 RNP  plan-2  N1   0.020
 RNP  plan-2  C14  0.020
 RNP  plan-2  H13  0.020

