# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 15:53:49 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-(morpholin-4-ium-4-ylmethyl)naphthalen-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(C[NH+]2CCOCC2)ccc3ccccc13
#
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
 T9Z  T9Z  "2-(morpholin-4-ium-4-ylmethyl)naphthalen-1-ol"
  ligand  36  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T9Z
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
 T9Z  C10  C  CR6   0   0.305  -0.6847   -9.1019   8.3997
 T9Z  C15  C  CH2   0  -0.208  -0.7527   -4.3238   5.7379
 T9Z  C17  C  CH2   0  -0.203  -1.1913   -6.1982   4.4527
 T9Z  C01  C  CR16  0  -0.249  -1.6897  -13.1896   8.8133
 T9Z  C02  C  CR16  0  -0.249  -2.4698  -12.2105   9.4592
 T9Z  C03  C  CR16  0  -0.311  -2.1589  -10.8838   9.3367
 T9Z  C04  C  CR66  0   0.036  -1.0505  -10.4681   8.5599
 T9Z  C05  C  CR66  0   0.104  -0.2577  -11.4562   7.9162
 T9Z  C06  C  CR16  0  -0.307  -0.6101  -12.8184   8.0616
 T9Z  C07  C  CR16  0  -0.329   0.8661  -11.0706   7.1512
 T9Z  C08  C  CR16  0  -0.275   1.1904   -9.7507   7.0309
 T9Z  C09  C  CR6   0  -0.046   0.4194   -8.7479   7.6530
 T9Z  C12  C  CH2   0  -0.375   0.8045   -7.3088   7.5169
 T9Z  C14  C  CH2   0  -0.337   0.2083   -5.0827   6.6310
 T9Z  C18  C  CH2   0  -0.333  -0.2593   -7.0660   5.2749
 T9Z  N13  N  NT1   1  -0.535  -0.1584   -6.5304   6.6651
 T9Z  O11  O  OH1   0  -0.623  -1.3754   -8.0903   8.9554
 T9Z  O16  O  O2    0  -0.461  -0.7759   -4.8563   4.4379
 T9Z  H2   H  HCH2  0   0.235  -1.7568   -4.3287   6.1844
 T9Z  H3   H  HCH2  0   0.235  -2.2166   -6.2886   4.8381
 T9Z  H4   H  HCH2  0   0.276  -1.1894   -6.5653   3.4267
 T9Z  H5   H  HCR6  0   0.263  -1.9468  -14.2355   8.9178
 T9Z  H6   H  HCR6  0   0.265  -3.3191  -12.5094  10.0587
 T9Z  H7   H  HCR6  0   0.252  -2.7823  -10.1695   9.8609
 T9Z  H8   H  HCR6  0   0.261  -0.0033  -13.5662   7.5660
 T9Z  H9   H  HCR6  0   0.257   1.4642  -11.8320   6.6674
 T9Z  H10  H  HCR6  0   0.265   2.0541   -9.4548   6.4481
 T9Z  H11  H  HCH2  0   0.318   1.7814   -7.2089   7.0456
 T9Z  H12  H  HCH2  0   0.318   0.8394   -6.7961   8.4783
 T9Z  H13  H  HCH2  0   0.301   1.2323   -5.0216   6.2611
 T9Z  H14  H  HCH2  0   0.310   0.1740   -4.7048   7.6517
 T9Z  H15  H  HCH2  0   0.312  -0.6333   -8.0867   5.3257
 T9Z  H16  H  HCH2  0   0.300   0.7509   -7.0757   4.8644
 T9Z  H17  H  HNT1  0   0.463  -1.0812   -6.6043   7.1053
 T9Z  H18  H  HOH1  0   0.491  -2.2101   -8.3704   9.3459
 T9Z  H1   H  HCH2  0   0.276  -0.4225   -3.2871   5.6749

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
 T9Z  C17  O16  single    1.405  0.020  1.405
 T9Z  C17  C18  single    1.516  0.020  1.516
 T9Z  O16  C15  single    1.405  0.020  1.405
 T9Z  C18  N13  single    1.493  0.020  1.493
 T9Z  C15  C14  single    1.516  0.020  1.516
 T9Z  N13  C14  single    1.494  0.020  1.494
 T9Z  N13  C12  single    1.503  0.020  1.503
 T9Z  C12  C09  single    1.496  0.020  1.496
 T9Z  C08  C09  aromatic  1.410  0.020  1.410
 T9Z  C08  C07  aromatic  1.364  0.020  1.364
 T9Z  C09  C10  aromatic  1.379  0.020  1.379
 T9Z  C07  C05  aromatic  1.413  0.020  1.413
 T9Z  C10  O11  single    1.345  0.020  1.345
 T9Z  C10  C04  aromatic  1.423  0.020  1.423
 T9Z  C05  C04  aromatic  1.421  0.020  1.421
 T9Z  C05  C06  aromatic  1.415  0.020  1.415
 T9Z  C04  C03  aromatic  1.416  0.020  1.416
 T9Z  C06  C01  aromatic  1.367  0.020  1.367
 T9Z  C03  C02  aromatic  1.368  0.020  1.368
 T9Z  C01  C02  aromatic  1.409  0.020  1.409
 T9Z  C15  H1   single    0.970  0.020  1.090
 T9Z  C15  H2   single    0.970  0.020  1.090
 T9Z  C17  H3   single    0.970  0.020  1.090
 T9Z  C17  H4   single    0.970  0.020  1.090
 T9Z  C01  H5   single    0.930  0.020  1.080
 T9Z  C02  H6   single    0.930  0.020  1.080
 T9Z  C03  H7   single    0.930  0.020  1.080
 T9Z  C06  H8   single    0.930  0.020  1.080
 T9Z  C07  H9   single    0.930  0.020  1.080
 T9Z  C08  H10  single    0.930  0.020  1.080
 T9Z  C12  H11  single    0.970  0.020  1.090
 T9Z  C12  H12  single    0.970  0.020  1.090
 T9Z  C14  H13  single    0.970  0.020  1.090
 T9Z  C14  H14  single    0.970  0.020  1.090
 T9Z  C18  H15  single    0.970  0.020  1.090
 T9Z  C18  H16  single    0.970  0.020  1.090
 T9Z  N13  H17  single    0.890  0.020  1.040
 T9Z  O11  H18  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
 T9Z  O11  C10  C09  116.22  3.000
 T9Z  O11  C10  C04  122.91  3.000
 T9Z  C09  C10  C04  120.87  3.000
 T9Z  H2   C15  H1   107.73  3.000
 T9Z  H2   C15  O16  111.05  3.000
 T9Z  H1   C15  O16  108.18  3.000
 T9Z  H2   C15  C14  109.74  3.000
 T9Z  H1   C15  C14  108.56  3.000
 T9Z  O16  C15  C14  111.46  3.000
 T9Z  H4   C17  H3   107.71  3.000
 T9Z  H4   C17  O16  108.14  3.000
 T9Z  H3   C17  O16  110.98  3.000
 T9Z  H4   C17  C18  108.47  3.000
 T9Z  H3   C17  C18  109.65  3.000
 T9Z  O16  C17  C18  111.76  3.000
 T9Z  H5   C01  C06  120.22  3.000
 T9Z  H5   C01  C02  119.73  3.000
 T9Z  C06  C01  C02  120.05  3.000
 T9Z  H6   C02  C03  119.73  3.000
 T9Z  H6   C02  C01  119.80  3.000
 T9Z  C03  C02  C01  120.47  3.000
 T9Z  H7   C03  C04  121.49  3.000
 T9Z  H7   C03  C02  117.73  3.000
 T9Z  C04  C03  C02  120.78  3.000
 T9Z  C05  C04  C03  118.76  3.000
 T9Z  C03  C04  C10  123.01  3.000
 T9Z  C05  C04  C10  118.23  3.000
 T9Z  C07  C05  C06  121.10  3.000
 T9Z  C06  C05  C04  118.95  3.000
 T9Z  C07  C05  C04  119.95  3.000
 T9Z  H8   C06  C05  118.57  3.000
 T9Z  H8   C06  C01  120.44  3.000
 T9Z  C05  C06  C01  120.99  3.000
 T9Z  H9   C07  C08  120.65  3.000
 T9Z  H9   C07  C05  119.31  3.000
 T9Z  C08  C07  C05  120.04  3.000
 T9Z  H10  C08  C09  118.63  3.000
 T9Z  H10  C08  C07  120.08  3.000
 T9Z  C09  C08  C07  121.29  3.000
 T9Z  C12  C09  C08  120.23  3.000
 T9Z  C08  C09  C10  119.61  3.000
 T9Z  C12  C09  C10  120.15  3.000
 T9Z  H12  C12  H11  108.04  3.000
 T9Z  H12  C12  N13  106.07  3.000
 T9Z  H11  C12  N13  106.38  3.000
 T9Z  H12  C12  C09  112.36  3.000
 T9Z  H11  C12  C09  111.00  3.000
 T9Z  N13  C12  C09  112.64  3.000
 T9Z  H14  C14  H13  109.15  3.000
 T9Z  H14  C14  N13  107.89  3.000
 T9Z  H13  C14  N13  107.02  3.000
 T9Z  H14  C14  C15  111.01  3.000
 T9Z  H13  C14  C15  111.56  3.000
 T9Z  N13  C14  C15  110.06  3.000
 T9Z  H16  C18  H15  109.11  3.000
 T9Z  H16  C18  N13  106.93  3.000
 T9Z  H15  C18  N13  108.44  3.000
 T9Z  H16  C18  C17  111.75  3.000
 T9Z  H15  C18  C17  110.55  3.000
 T9Z  N13  C18  C17  109.95  3.000
 T9Z  H17  N13  C18  108.25  3.000
 T9Z  H17  N13  C14  107.50  3.000
 T9Z  C18  N13  C14  110.06  3.000
 T9Z  H17  N13  C12  107.22  3.000
 T9Z  C14  N13  C12  110.95  3.000
 T9Z  C18  N13  C12  112.66  3.000
 T9Z  H18  O11  C10  113.20  3.000
 T9Z  C17  O16  C15  110.92  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
 T9Z  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 T9Z  CONST_02  C07  C05  C04  C10     0.00   0.0  0
 T9Z  CONST_03  C06  C05  C04  C10   180.00   0.0  0
 T9Z  CONST_04  C02  C03  C04  C10   180.00   0.0  0
 T9Z  CONST_05  C07  C05  C06  C01   180.00   0.0  0
 T9Z  CONST_06  C04  C05  C06  C01     0.00   0.0  0
 T9Z  CONST_07  C04  C03  C02  C01     0.00   0.0  0
 T9Z  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 T9Z  CONST_09  C05  C06  C01  C02     0.00   0.0  0
 T9Z  CONST_10  C09  C10  C04  C03   180.00   0.0  0
 T9Z  CONST_11  C07  C05  C04  C03   180.00   0.0  0
 T9Z  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 T9Z  CONST_13  C06  C01  C02  C03     0.00   0.0  0
 T9Z  CONST_14  C08  C09  C10  C04     0.00   0.0  0
 T9Z  CONST_15  C08  C07  C05  C04     0.00   0.0  0
 T9Z  CONST_16  C09  C08  C07  C05     0.00   0.0  0
 T9Z  CONST_17  C09  C10  C04  C05     0.00   0.0  0
 T9Z  CONST_18  C08  C07  C05  C06   180.00   0.0  0
 T9Z  CONST_19  O11  C10  C04  C03     0.00   0.0  0
 T9Z  CONST_20  C12  C09  C10  C04   180.00   0.0  0
 T9Z  CONST_21  O11  C10  C04  C05   180.00   0.0  0
 T9Z  CONST_22  C12  C09  C08  C07   180.00   0.0  0
 T9Z  CONST_23  O11  C10  C09  C08   180.00   0.0  0
 T9Z  CONST_24  H10  C08  C09  C10   180.00   0.0  0
 T9Z  CONST_25  H7   C03  C04  C10     0.00   0.0  0
 T9Z  CONST_26  H7   C03  C02  C01   180.00   0.0  0
 T9Z  CONST_27  H8   C06  C01  C02   180.00   0.0  0
 T9Z  CONST_28  H5   C01  C02  C03   180.00   0.0  0
 T9Z  CONST_29  H9   C07  C05  C04   180.00   0.0  0
 T9Z  CONST_30  H8   C06  C05  C04   180.00   0.0  0
 T9Z  CONST_31  H6   C02  C03  C04   180.00   0.0  0
 T9Z  CONST_32  H10  C08  C07  C05   180.00   0.0  0
 T9Z  CONST_33  H7   C03  C04  C05   180.00   0.0  0
 T9Z  CONST_34  H5   C01  C06  C05   180.00   0.0  0
 T9Z  CONST_35  H9   C07  C05  C06     0.00   0.0  0
 T9Z  CONST_36  H6   C02  C01  C06   180.00   0.0  0
 T9Z  CONST_37  H8   C06  C05  C07     0.00   0.0  0
 T9Z  CONST_38  H9   C07  C08  C09   180.00   0.0  0
 T9Z  Var_01    C18  C17  O16  C15   -60.48  30.0  1
 T9Z  Var_02    C14  C15  O16  C17    60.53  30.0  1
 T9Z  Var_03    O16  C17  C18  N13    56.70  30.0  1
 T9Z  Var_04    O16  C15  C14  N13   -57.03  30.0  1
 T9Z  Var_05    N13  C12  C09  C10   -70.49  30.0  1
 T9Z  Var_06    N13  C12  C09  C08   110.17  30.0  1
 T9Z  Var_07    H3   C17  O16  C15    62.27  30.0  1
 T9Z  Var_08    H4   C17  O16  C15  -179.80  30.0  1
 T9Z  Var_09    H1   C15  O16  C17   179.81  30.0  1
 T9Z  Var_10    H2   C15  O16  C17   -62.17  30.0  1
 T9Z  Var_11    H3   C17  C18  N13   -66.80  30.0  1
 T9Z  Var_12    H4   C17  C18  N13   175.82  30.0  1
 T9Z  Var_13    H1   C15  C14  N13  -176.08  30.0  1
 T9Z  Var_14    H2   C15  C14  N13    66.41  30.0  1
 T9Z  Var_15    H15  C18  C17  O16   176.40  30.0  1
 T9Z  Var_16    H16  C18  C17  O16   -61.87  30.0  1
 T9Z  Var_17    H13  C14  C15  O16    61.61  30.0  1
 T9Z  Var_18    H14  C14  C15  O16  -176.41  30.0  1
 T9Z  Var_19    H11  C12  C09  C10   170.34  30.0  1
 T9Z  Var_20    H12  C12  C09  C10    49.23  30.0  1
 T9Z  Var_21    H11  C12  C09  C08    -9.00  30.0  1
 T9Z  Var_22    H12  C12  C09  C08  -130.11  30.0  1

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
 T9Z  chir_01  N13  C18  C14  C12  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
 T9Z  plan-1  C10  0.020
 T9Z  plan-1  C01  0.020
 T9Z  plan-1  C02  0.020
 T9Z  plan-1  C03  0.020
 T9Z  plan-1  C04  0.020
 T9Z  plan-1  C05  0.020
 T9Z  plan-1  C06  0.020
 T9Z  plan-1  C07  0.020
 T9Z  plan-1  C08  0.020
 T9Z  plan-1  C09  0.020
 T9Z  plan-1  C12  0.020
 T9Z  plan-1  O11  0.020
 T9Z  plan-1  H5   0.020
 T9Z  plan-1  H6   0.020
 T9Z  plan-1  H7   0.020
 T9Z  plan-1  H8   0.020
 T9Z  plan-1  H9   0.020
 T9Z  plan-1  H10  0.020

