# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:53:10 2021
#   Inital geometry file: a 110 line input string
#   Ligand name: 7-chloranyl-5-[3-[(3~{S})-piperidin-3-yl]propyl]pyrido[3,4-b][1,4]benzoxazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2Oc3cnccc3N(CCC[C@@H]4CCCNC4)c2c1
#
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
 E2O  E2O  7-chloranyl-5-[3-[(3~{S})-piperidin-3-yl]propyl]pyrido[3,4-b][1,4]benzoxazine  ligand  46  24  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E2O
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
 E2O  C4   C   CR16  0  -0.427  -39.4794  -3.5196   1.8194
 E2O  C5   C   CR16  0  -0.075  -38.3469  -4.2304   1.4451
 E2O  C7   C   CR16  0  -0.167  -38.8583  -4.0798  -0.7547
 E2O  C8   C   CR66  0   0.232  -40.0164  -3.3863  -0.4839
 E2O  C10  C   CR66  0   0.339  -41.7658  -2.0805  -1.2928
 E2O  C13  C   CR6   0  -0.045  -43.7142  -0.1808  -0.9338
 E2O  C15  C   CR16  0  -0.376  -42.3530  -1.4822  -2.3855
 E2O  C17  C   CH2   0  -0.453  -41.2938  -0.8974   3.0777
 E2O  C20  C   CH2   0  -0.437  -42.7303  -2.6438   5.7288
 E2O  C21  C   CH1   0  -0.246  -41.5010  -1.7654   5.4916
 E2O  C22  C   CH2   0  -0.302  -41.0027  -1.2346   6.8403
 E2O  C24  C   CH2   0  -0.312  -41.9036  -3.1224   8.0436
 E2O  C18  C   CH2   0  -0.435  -41.7672  -0.6202   4.5022
 E2O  N2   N   NR6   0  -0.621  -41.5202  -2.3761   1.0842
 E2O  N23  N   NH1   0  -0.579  -40.7523  -2.2567   7.8424
 E2O  C11  C   CR66  0   0.355  -42.1377  -1.7342   0.0126
 E2O  C3   C   CR66  0   0.439  -40.3599  -3.0753   0.8367
 E2O  C12  C   CR16  0  -0.312  -43.1171  -0.7622   0.1786
 E2O  C19  C   CH2   0  -0.440  -42.4465  -3.7346   6.7561
 E2O  CL1  CL  CL    0  -0.126  -44.9442   1.0140  -0.6814
 E2O  C14  C   CR16  0  -0.236  -43.3488  -0.5256  -2.2179
 E2O  N6   N   N     0  -0.414  -38.0261  -4.5101   0.1931
 E2O  O9   O   O     0  -0.496  -40.8307  -3.0467  -1.5223
 E2O  H1   H   HCR6  0   0.281  -39.6478  -3.3246   2.8684
 E2O  H2   H   HCR6  0   0.266  -37.6684  -4.5797   2.2151
 E2O  H3   H   HCR6  0   0.276  -38.6058  -4.3076  -1.7851
 E2O  H4   H   HCR6  0   0.284  -42.0434  -1.7753  -3.3803
 E2O  H5   H   HCH2  0   0.237  -40.2078  -1.0312   3.0822
 E2O  H6   H   HCH2  0   0.246  -41.4888  -0.0211   2.4541
 E2O  H8   H   HCH2  0   0.234  -43.0881  -3.0852   4.7955
 E2O  H9   H   HCH1  0   0.216  -40.6990  -2.3966   5.0817
 E2O  H10  H   HCH2  0   0.231  -40.0835  -0.6603   6.6954
 E2O  H11  H   HCH2  0   0.210  -41.7456  -0.5338   7.2429
 E2O  H12  H   HCH2  0   0.210  -42.6940  -2.5283   8.5162
 E2O  H13  H   HCH2  0   0.231  -41.6330  -3.9034   8.7576
 E2O  H14  H   HCH2  0   0.238  -41.2583   0.2862   4.8438
 E2O  H15  H   HCH2  0   0.227  -42.8343  -0.3746   4.4966
 E2O  H19  H   HNH1  0   0.336  -39.9654  -2.8216   7.5437
 E2O  H20  H   HCR6  0   0.293  -43.4270  -0.4466   1.1638
 E2O  H21  H   HCH2  0   0.225  -43.3551  -4.3045   6.9681
 E2O  H22  H   HCH2  0   0.212  -41.7170  -4.4445   6.3506
 E2O  H23  H   HCR6  0   0.283  -43.8162  -0.0685  -3.0781
 E2O  C1   C   CH2   0  -0.365  -41.9486  -2.1231   2.4474
 E2O  H7   H   HCH2  0   0.212  -43.5464  -2.0093   6.0953
 E2O  H16  H   HCH2  0   0.277  -43.0359  -2.0283   2.4526
 E2O  H17  H   HCH2  0   0.274  -41.7417  -3.0206   3.0316

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
 E2O  C15  C14  aromatic  1.391  0.020  1.391
 E2O  C15  C10  aromatic  1.377  0.020  1.377
 E2O  O9   C10  single    1.364  0.020  1.364
 E2O  O9   C8   single    1.363  0.020  1.363
 E2O  C7   N6   aromatic  1.333  0.020  1.333
 E2O  C7   C8   aromatic  1.377  0.020  1.377
 E2O  C14  C13  aromatic  1.379  0.020  1.379
 E2O  C10  C11  aromatic  1.401  0.020  1.401
 E2O  N6   C5   aromatic  1.322  0.020  1.322
 E2O  C8   C3   aromatic  1.400  0.020  1.400
 E2O  C13  C12  aromatic  1.390  0.020  1.390
 E2O  C13  CL1  single    1.733  0.020  1.733
 E2O  C11  C12  aromatic  1.390  0.020  1.390
 E2O  C11  N2   single    1.393  0.020  1.393
 E2O  C3   N2   single    1.377  0.020  1.377
 E2O  C3   C4   aromatic  1.392  0.020  1.392
 E2O  C5   C4   aromatic  1.389  0.020  1.389
 E2O  N2   C1   single    1.451  0.020  1.451
 E2O  C1   C17  single    1.526  0.020  1.526
 E2O  C17  C18  single    1.526  0.020  1.526
 E2O  C18  C21  single    1.537  0.020  1.537
 E2O  C20  C21  single    1.529  0.020  1.529
 E2O  C20  C19  single    1.525  0.020  1.525
 E2O  C21  C22  single    1.533  0.020  1.533
 E2O  C19  C24  single    1.525  0.020  1.525
 E2O  C22  N23  single    1.453  0.020  1.453
 E2O  N23  C24  single    1.454  0.020  1.454
 E2O  C4   H1   single    0.930  0.020  1.080
 E2O  C5   H2   single    0.930  0.020  1.080
 E2O  C7   H3   single    0.930  0.020  1.080
 E2O  C15  H4   single    0.930  0.020  1.080
 E2O  C17  H5   single    0.970  0.020  1.090
 E2O  C17  H6   single    0.970  0.020  1.090
 E2O  C20  H7   single    0.970  0.020  1.090
 E2O  C20  H8   single    0.970  0.020  1.090
 E2O  C21  H9   single    0.970  0.020  1.090
 E2O  C22  H10  single    0.970  0.020  1.090
 E2O  C22  H11  single    0.970  0.020  1.090
 E2O  C24  H12  single    0.970  0.020  1.090
 E2O  C24  H13  single    0.970  0.020  1.090
 E2O  C18  H14  single    0.970  0.020  1.090
 E2O  C18  H15  single    0.970  0.020  1.090
 E2O  C1   H16  single    0.970  0.020  1.090
 E2O  C1   H17  single    0.970  0.020  1.090
 E2O  N23  H19  single    0.890  0.020  1.040
 E2O  C12  H20  single    0.930  0.020  1.080
 E2O  C19  H21  single    0.970  0.020  1.090
 E2O  C19  H22  single    0.970  0.020  1.090
 E2O  C14  H23  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
 E2O  H1   C4   C3   121.96  3.000
 E2O  H1   C4   C5   118.77  3.000
 E2O  C3   C4   C5   119.27  3.000
 E2O  H2   C5   N6   116.90  3.000
 E2O  H2   C5   C4   118.94  3.000
 E2O  N6   C5   C4   124.15  3.000
 E2O  H3   C7   N6   117.54  3.000
 E2O  H3   C7   C8   119.22  3.000
 E2O  N6   C7   C8   123.23  3.000
 E2O  O9   C8   C3   121.13  3.000
 E2O  C3   C8   C7   120.26  3.000
 E2O  O9   C8   C7   118.58  3.000
 E2O  O9   C10  C11  120.92  3.000
 E2O  C11  C10  C15  121.26  3.000
 E2O  O9   C10  C15  117.81  3.000
 E2O  C14  C13  CL1  119.74  3.000
 E2O  CL1  C13  C12  118.46  3.000
 E2O  C14  C13  C12  121.80  3.000
 E2O  H4   C15  C14  120.12  3.000
 E2O  H4   C15  C10  119.32  3.000
 E2O  C14  C15  C10  120.55  3.000
 E2O  H6   C17  H5   106.11  3.000
 E2O  H6   C17  C1   109.38  3.000
 E2O  H5   C17  C1   109.23  3.000
 E2O  H6   C17  C18  109.36  3.000
 E2O  H5   C17  C18  109.03  3.000
 E2O  C1   C17  C18  113.47  3.000
 E2O  H8   C20  H7   105.99  3.000
 E2O  H8   C20  C19  110.33  3.000
 E2O  H7   C20  C19  109.10  3.000
 E2O  H8   C20  C21  111.27  3.000
 E2O  H7   C20  C21  108.52  3.000
 E2O  C19  C20  C21  111.44  3.000
 E2O  H9   C21  C18  108.30  3.000
 E2O  H9   C21  C22  106.84  3.000
 E2O  C18  C21  C22  111.39  3.000
 E2O  H9   C21  C20  108.32  3.000
 E2O  C22  C21  C20  108.89  3.000
 E2O  C18  C21  C20  112.87  3.000
 E2O  H11  C22  H10  106.39  3.000
 E2O  H11  C22  N23  108.22  3.000
 E2O  H10  C22  N23  108.42  3.000
 E2O  H11  C22  C21  108.89  3.000
 E2O  H10  C22  C21  109.79  3.000
 E2O  N23  C22  C21  114.79  3.000
 E2O  H13  C24  H12  106.53  3.000
 E2O  H13  C24  C19  110.67  3.000
 E2O  H12  C24  C19  108.96  3.000
 E2O  H13  C24  N23  108.66  3.000
 E2O  H12  C24  N23  107.93  3.000
 E2O  C19  C24  N23  113.81  3.000
 E2O  H15  C18  H14  105.61  3.000
 E2O  H15  C18  C21  109.83  3.000
 E2O  H14  C18  C21  109.62  3.000
 E2O  H15  C18  C17  109.77  3.000
 E2O  H14  C18  C17  107.31  3.000
 E2O  C21  C18  C17  114.32  3.000
 E2O  C3   N2   C11  117.98  3.000
 E2O  C3   N2   C1   120.40  3.000
 E2O  C11  N2   C1   120.75  3.000
 E2O  H19  N23  C24  108.88  3.000
 E2O  H19  N23  C22  108.81  3.000
 E2O  C24  N23  C22  112.19  3.000
 E2O  C12  C11  N2   122.86  3.000
 E2O  N2   C11  C10  119.02  3.000
 E2O  C12  C11  C10  118.12  3.000
 E2O  N2   C3   C8   119.29  3.000
 E2O  N2   C3   C4   124.62  3.000
 E2O  C8   C3   C4   116.09  3.000
 E2O  H20  C12  C11  121.04  3.000
 E2O  H20  C12  C13  118.99  3.000
 E2O  C11  C12  C13  119.97  3.000
 E2O  H22  C19  H21  106.70  3.000
 E2O  H22  C19  C24  109.60  3.000
 E2O  H21  C19  C24  109.95  3.000
 E2O  H22  C19  C20  109.75  3.000
 E2O  H21  C19  C20  110.41  3.000
 E2O  C24  C19  C20  110.35  3.000
 E2O  H23  C14  C15  120.32  3.000
 E2O  H23  C14  C13  121.40  3.000
 E2O  C15  C14  C13  118.29  3.000
 E2O  C7   N6   C5   116.97  3.000
 E2O  C10  O9   C8   117.26  3.000
 E2O  H17  C1   H16  104.94  3.000
 E2O  H17  C1   N2   107.68  3.000
 E2O  H16  C1   N2   108.28  3.000
 E2O  H17  C1   C17  111.00  3.000
 E2O  H16  C1   C17  110.84  3.000
 E2O  N2   C1   C17  113.67  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
 E2O  CONST_01  C7   C8   C3   C4     0.00   0.0  0
 E2O  CONST_02  C7   N6   C5   C4     0.00   0.0  0
 E2O  CONST_03  C8   C7   N6   C5     0.00   0.0  0
 E2O  CONST_04  C8   C3   C4   C5     0.00   0.0  0
 E2O  CONST_05  C13  C14  C15  C10    0.00   0.0  0
 E2O  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 E2O  CONST_07  C12  C13  C14  C15    0.00   0.0  0
 E2O  CONST_08  C12  C11  C10  C15    0.00   0.0  0
 E2O  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 E2O  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 E2O  CONST_11  N6   C7   C8   C3     0.00   0.0  0
 E2O  CONST_12  N6   C5   C4   C3     0.00   0.0  0
 E2O  CONST_13  CL1  C13  C14  C15  180.00   0.0  0
 E2O  CONST_14  CL1  C13  C12  C11  180.00   0.0  0
 E2O  CONST_15  H3   C7   N6   C5   180.00   0.0  0
 E2O  CONST_16  H2   C5   N6   C7   180.00   0.0  0
 E2O  CONST_17  H1   C4   C3   C8   180.00   0.0  0
 E2O  CONST_18  H23  C14  C15  C10  180.00   0.0  0
 E2O  CONST_19  H20  C12  C11  C10  180.00   0.0  0
 E2O  CONST_20  H4   C15  C14  C13  180.00   0.0  0
 E2O  Var_01    C11  N2   C3   C4   165.48  30.0  1
 E2O  Var_02    C15  C10  O9   C8   163.53  30.0  1
 E2O  Var_03    C3   C8   O9   C10   18.60  30.0  1
 E2O  Var_04    C3   N2   C11  C10   15.49  30.0  1
 E2O  Var_05    N23  C24  C19  C20  -53.35  30.0  1
 E2O  Var_06    C24  C19  C20  C21   54.02  30.0  1
 E2O  Var_07    C24  N23  C22  C21  -53.49  30.0  1
 E2O  Var_08    C19  C24  N23  C22   52.68  30.0  1
 E2O  Var_09    C1   C17  C18  C21   59.65  30.0  1
 E2O  Var_10    N2   C1   C17  C18  178.91  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
 E2O  chir_01  C21  C18  C20  C22  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
 E2O  plan-1  C4   0.020
 E2O  plan-1  C5   0.020
 E2O  plan-1  C7   0.020
 E2O  plan-1  C8   0.020
 E2O  plan-1  N2   0.020
 E2O  plan-1  C3   0.020
 E2O  plan-1  N6   0.020
 E2O  plan-1  O9   0.020
 E2O  plan-1  H1   0.020
 E2O  plan-1  H2   0.020
 E2O  plan-1  H3   0.020
 E2O  plan-2  C10  0.020
 E2O  plan-2  C13  0.020
 E2O  plan-2  C15  0.020
 E2O  plan-2  N2   0.020
 E2O  plan-2  C11  0.020
 E2O  plan-2  C12  0.020
 E2O  plan-2  CL1  0.020
 E2O  plan-2  C14  0.020
 E2O  plan-2  O9   0.020
 E2O  plan-2  H4   0.020
 E2O  plan-2  H20  0.020
 E2O  plan-2  H23  0.020

