# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:46:56 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 7-chloranyl-5-[3-[(3~{S})-piperidin-3-yl]propyl]pyrido[3,4-b][1,4]benzoxazin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc2Oc3cnccc3N(CCC[C@@H]4CCCNC4)c2cc1Cl
#
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
 E2X  E2X  7-chloranyl-5-[3-[(3~{S})-piperidin-3-yl]propyl]pyrido[3,4-b][1,4]benzoxazin-8-amine  ligand  48  25  .  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_E2X
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
 E2X  C4   C   CR16  0  -0.434  38.0751  -2.9615   0.4036
 E2X  C5   C   CR16  0  -0.076  37.0207  -3.0071   1.3046
 E2X  C7   C   CR16  0  -0.171  38.4057  -2.8504   3.0872
 E2X  C8   C   CR66  0   0.227  39.5186  -2.8161   2.2784
 E2X  C10  C   CR66  0   0.361  41.8122  -2.4399   2.0863
 E2X  C13  C   CR6   0  -0.132  44.0360  -1.8106   0.6162
 E2X  C15  C   CR16  0  -0.462  42.9832  -2.1037   2.7244
 E2X  C17  C   CH2   0  -0.460  40.1212  -1.6335  -2.0556
 E2X  C20  C   CH2   0  -0.434  42.4677  -1.1145  -4.0611
 E2X  C21  C   CH1   0  -0.248  41.3750  -2.1669  -4.2529
 E2X  C22  C   CH2   0  -0.261  41.1423  -2.3814  -5.7465
 E2X  C24  C   CH2   0  -0.291  43.3763  -1.7020  -6.3218
 E2X  C18  C   CH2   0  -0.425  40.0599  -1.7845  -3.5732
 E2X  N2   N   NR6   0  -0.620  40.5001  -2.8383   0.0953
 E2X  N23  N   NH1   0  -0.598  42.3762  -2.7507  -6.4151
 E2X  C11  C   CR66  0   0.323  41.7149  -2.4728   0.6916
 E2X  C3   C   CR66  0   0.441  39.3807  -2.8675   0.8839
 E2X  C12  C   CR16  0  -0.312  42.8502  -2.1406  -0.0280
 E2X  C19  C   CH2   0  -0.426  43.7208  -1.4545  -4.8618
 E2X  CL1  CL  CL    0  -0.126  45.4189  -1.4114  -0.3554
 E2X  C14  C   CR6   0   0.366  44.1435  -1.7840   2.0043
 E2X  N6   N   N     0  -0.419  37.1613  -2.9514   2.6189
 E2X  N25  N   NH2   0  -0.855  45.2938  -1.4086   2.6551
 E2X  O9   O   O     0  -0.499  40.7474  -2.7703   2.8700
 E2X  H1   H   HCR6  0   0.280  37.8607  -2.9978  -0.6544
 E2X  H2   H   HCR6  0   0.263  36.0084  -3.0868   0.9244
 E2X  H3   H   HCR6  0   0.273  38.5336  -2.8094   4.1642
 E2X  H4   H   HCR6  0   0.284  43.0079  -2.0984   3.8076
 E2X  H5   H   HCH2  0   0.238  40.8702  -0.8879  -1.7774
 E2X  H6   H   HCH2  0   0.249  39.1656  -1.2366  -1.7032
 E2X  H8   H   HCH2  0   0.213  42.0800  -0.1409  -4.3868
 E2X  H9   H   HCH1  0   0.218  41.7364  -3.1206  -3.8472
 E2X  H10  H   HCH2  0   0.178  40.6952  -1.4614  -6.1645
 E2X  H11  H   HCH2  0   0.227  40.4112  -3.1806  -5.8935
 E2X  H12  H   HCH2  0   0.228  44.2665  -2.0129  -6.8732
 E2X  H13  H   HCH2  0   0.182  43.0360  -0.7542  -6.7736
 E2X  H14  H   HCH2  0   0.228  39.7060  -0.8414  -4.0020
 E2X  H15  H   HCH2  0   0.225  39.2989  -2.5333  -3.8210
 E2X  H18  H   HNH1  0   0.349  42.1830  -2.9483  -7.3881
 E2X  H20  H   HCR6  0   0.279  42.8413  -2.1365  -1.1084
 E2X  H21  H   HCH2  0   0.213  44.1905  -2.3516  -4.4470
 E2X  H22  H   HCH2  0   0.227  44.4512  -0.6464  -4.7832
 E2X  H23  H   HNH2  0   0.388  45.3538  -1.6947   3.6192
 E2X  H24  H   HNH2  0   0.380  46.1585  -1.5691   2.1633
 E2X  C1   C   CH2   0  -0.359  40.4030  -2.9552  -1.3460
 E2X  H7   H   HCH2  0   0.222  42.7262  -1.0002  -3.0049
 E2X  H16  H   HCH2  0   0.275  39.6220  -3.6801  -1.5807
 E2X  H17  H   HCH2  0   0.271  41.3265  -3.4145  -1.7021

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
 E2X  N23  C24  single    1.452  0.020  1.452
 E2X  N23  C22  single    1.451  0.020  1.451
 E2X  C24  C19  single    1.520  0.020  1.520
 E2X  C22  C21  single    1.527  0.020  1.527
 E2X  C19  C20  single    1.525  0.020  1.525
 E2X  C21  C20  single    1.529  0.020  1.529
 E2X  C21  C18  single    1.529  0.020  1.529
 E2X  C18  C17  single    1.526  0.020  1.526
 E2X  C17  C1   single    1.526  0.020  1.526
 E2X  C1   N2   single    1.449  0.020  1.449
 E2X  CL1  C13  single    1.737  0.020  1.737
 E2X  N2   C11  single    1.402  0.020  1.402
 E2X  N2   C3   single    1.370  0.020  1.370
 E2X  C12  C11  aromatic  1.385  0.020  1.385
 E2X  C12  C13  aromatic  1.389  0.020  1.389
 E2X  C4   C3   aromatic  1.394  0.020  1.394
 E2X  C4   C5   aromatic  1.388  0.020  1.388
 E2X  C11  C10  aromatic  1.398  0.020  1.398
 E2X  C13  C14  aromatic  1.393  0.020  1.393
 E2X  C3   C8   aromatic  1.402  0.020  1.402
 E2X  C5   N6   aromatic  1.323  0.020  1.323
 E2X  C10  O9   single    1.363  0.020  1.363
 E2X  C10  C15  aromatic  1.375  0.020  1.375
 E2X  C8   O9   single    1.365  0.020  1.365
 E2X  C8   C7   aromatic  1.376  0.020  1.376
 E2X  C14  C15  aromatic  1.402  0.020  1.402
 E2X  C14  N25  single    1.374  0.020  1.374
 E2X  N6   C7   aromatic  1.333  0.020  1.333
 E2X  C4   H1   single    0.930  0.020  1.080
 E2X  C5   H2   single    0.930  0.020  1.080
 E2X  C7   H3   single    0.930  0.020  1.080
 E2X  C15  H4   single    0.930  0.020  1.080
 E2X  C17  H5   single    0.970  0.020  1.090
 E2X  C17  H6   single    0.970  0.020  1.090
 E2X  C20  H7   single    0.970  0.020  1.090
 E2X  C20  H8   single    0.970  0.020  1.090
 E2X  C21  H9   single    0.970  0.020  1.090
 E2X  C22  H10  single    0.970  0.020  1.090
 E2X  C22  H11  single    0.970  0.020  1.090
 E2X  C24  H12  single    0.970  0.020  1.090
 E2X  C24  H13  single    0.970  0.020  1.090
 E2X  C18  H14  single    0.970  0.020  1.090
 E2X  C18  H15  single    0.970  0.020  1.090
 E2X  C1   H16  single    0.970  0.020  1.090
 E2X  C1   H17  single    0.970  0.020  1.090
 E2X  N23  H18  single    0.890  0.020  1.040
 E2X  C12  H20  single    0.930  0.020  1.080
 E2X  C19  H21  single    0.970  0.020  1.090
 E2X  C19  H22  single    0.970  0.020  1.090
 E2X  N25  H23  single    0.890  0.020  1.040
 E2X  N25  H24  single    0.890  0.020  1.040

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
 E2X  H1   C4   C3   121.70  3.000
 E2X  H1   C4   C5   118.95  3.000
 E2X  C3   C4   C5   119.34  3.000
 E2X  H2   C5   N6   116.79  3.000
 E2X  H2   C5   C4   118.96  3.000
 E2X  N6   C5   C4   124.26  3.000
 E2X  H3   C7   N6   117.47  3.000
 E2X  H3   C7   C8   119.14  3.000
 E2X  N6   C7   C8   123.38  3.000
 E2X  O9   C8   C3   121.40  3.000
 E2X  O9   C8   C7   118.31  3.000
 E2X  C3   C8   C7   120.27  3.000
 E2X  O9   C10  C11  120.90  3.000
 E2X  O9   C10  C15  117.24  3.000
 E2X  C11  C10  C15  121.85  3.000
 E2X  C14  C13  CL1  119.47  3.000
 E2X  C14  C13  C12  122.19  3.000
 E2X  CL1  C13  C12  118.35  3.000
 E2X  H4   C15  C14  119.56  3.000
 E2X  H4   C15  C10  118.97  3.000
 E2X  C14  C15  C10  121.47  3.000
 E2X  H6   C17  H5   105.63  3.000
 E2X  H6   C17  C1   109.02  3.000
 E2X  H5   C17  C1   110.23  3.000
 E2X  H6   C17  C18  108.74  3.000
 E2X  H5   C17  C18  110.37  3.000
 E2X  C1   C17  C18  112.58  3.000
 E2X  H8   C20  H7   106.11  3.000
 E2X  H8   C20  C19  109.41  3.000
 E2X  H7   C20  C19  109.64  3.000
 E2X  H8   C20  C21  108.72  3.000
 E2X  H7   C20  C21  111.22  3.000
 E2X  C19  C20  C21  111.58  3.000
 E2X  H9   C21  C18  109.65  3.000
 E2X  H9   C21  C22  106.84  3.000
 E2X  C18  C21  C22  109.81  3.000
 E2X  H9   C21  C20  108.45  3.000
 E2X  C18  C21  C20  112.75  3.000
 E2X  C22  C21  C20  109.16  3.000
 E2X  H11  C22  H10  106.69  3.000
 E2X  H11  C22  N23  108.70  3.000
 E2X  H10  C22  N23  112.44  3.000
 E2X  H11  C22  C21  109.65  3.000
 E2X  H10  C22  C21  108.35  3.000
 E2X  N23  C22  C21  110.91  3.000
 E2X  H13  C24  H12  106.80  3.000
 E2X  H13  C24  C19  108.85  3.000
 E2X  H12  C24  C19  110.27  3.000
 E2X  H13  C24  N23  112.43  3.000
 E2X  H12  C24  N23  108.86  3.000
 E2X  C19  C24  N23  109.59  3.000
 E2X  H15  C18  H14  106.00  3.000
 E2X  H15  C18  C21  109.02  3.000
 E2X  H14  C18  C21  108.63  3.000
 E2X  H15  C18  C17  108.68  3.000
 E2X  H14  C18  C17  108.49  3.000
 E2X  C21  C18  C17  115.60  3.000
 E2X  C3   N2   C11  117.97  3.000
 E2X  C3   N2   C1   121.07  3.000
 E2X  C11  N2   C1   120.14  3.000
 E2X  H18  N23  C24  109.54  3.000
 E2X  H18  N23  C22  109.30  3.000
 E2X  C24  N23  C22  111.85  3.000
 E2X  C12  C11  N2   123.51  3.000
 E2X  C12  C11  C10  117.11  3.000
 E2X  N2   C11  C10  119.38  3.000
 E2X  N2   C3   C8   119.43  3.000
 E2X  C8   C3   C4   115.92  3.000
 E2X  N2   C3   C4   124.64  3.000
 E2X  H20  C12  C11  120.92  3.000
 E2X  H20  C12  C13  118.02  3.000
 E2X  C11  C12  C13  121.05  3.000
 E2X  H22  C19  H21  106.99  3.000
 E2X  H22  C19  C24  109.94  3.000
 E2X  H21  C19  C24  109.13  3.000
 E2X  H22  C19  C20  110.29  3.000
 E2X  H21  C19  C20  109.66  3.000
 E2X  C24  C19  C20  110.75  3.000
 E2X  N25  C14  C15  120.78  3.000
 E2X  N25  C14  C13  122.82  3.000
 E2X  C15  C14  C13  116.33  3.000
 E2X  C7   N6   C5   116.82  3.000
 E2X  H24  N25  H23  111.76  3.000
 E2X  H24  N25  C14  116.35  3.000
 E2X  H23  N25  C14  115.19  3.000
 E2X  C10  O9   C8   117.54  3.000
 E2X  H17  C1   H16  104.83  3.000
 E2X  H17  C1   N2   107.57  3.000
 E2X  H16  C1   N2   108.39  3.000
 E2X  H17  C1   C17  111.65  3.000
 E2X  H16  C1   C17  110.07  3.000
 E2X  N2   C1   C17  113.88  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
 E2X  CONST_01  C7   C8   C3   C4     0.00   0.0  0
 E2X  CONST_02  C7   N6   C5   C4     0.00   0.0  0
 E2X  CONST_03  C8   C3   C4   C5     0.00   0.0  0
 E2X  CONST_04  C8   C7   N6   C5     0.00   0.0  0
 E2X  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 E2X  CONST_06  C13  C14  C15  C10    0.00   0.0  0
 E2X  CONST_07  C12  C11  C10  C15    0.00   0.0  0
 E2X  CONST_08  C12  C13  C14  C15    0.00   0.0  0
 E2X  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 E2X  CONST_10  C14  C15  C10  C11    0.00   0.0  0
 E2X  CONST_11  N6   C5   C4   C3     0.00   0.0  0
 E2X  CONST_12  N6   C7   C8   C3     0.00   0.0  0
 E2X  CONST_13  N25  C14  C15  C10  180.00   0.0  0
 E2X  CONST_14  CL1  C13  C14  C15  180.00   0.0  0
 E2X  CONST_15  CL1  C13  C12  C11  180.00   0.0  0
 E2X  CONST_16  N25  C14  C13  C12  180.00   0.0  0
 E2X  CONST_17  H3   C7   N6   C5   180.00   0.0  0
 E2X  CONST_18  H2   C5   N6   C7   180.00   0.0  0
 E2X  CONST_19  H1   C4   C3   C8   180.00   0.0  0
 E2X  CONST_20  H20  C12  C11  C10  180.00   0.0  0
 E2X  CONST_21  H4   C15  C14  C13  180.00   0.0  0
 E2X  Var_01    C11  N2   C3   C4   167.36  30.0  1
 E2X  Var_02    C11  C10  O9   C8   -15.49  30.0  1
 E2X  Var_03    C3   N2   C11  C10   13.92  30.0  1
 E2X  Var_04    C3   C8   O9   C10   16.13  30.0  1
 E2X  Var_05    N23  C24  C19  C20  -56.22  30.0  1
 E2X  Var_06    C24  N23  C22  C21  -62.37  30.0  1
 E2X  Var_07    C24  C19  C20  C21   52.90  30.0  1
 E2X  Var_08    C19  C24  N23  C22   61.59  30.0  1
 E2X  Var_09    C1   C17  C18  C21  -66.30  30.0  3
 E2X  Var_10    N2   C1   C17  C18  178.55  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
 E2X  chir_01  C21  C22  C20  C18  negativ

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
 E2X  plan-1  C4   0.020
 E2X  plan-1  C5   0.020
 E2X  plan-1  C7   0.020
 E2X  plan-1  C8   0.020
 E2X  plan-1  N2   0.020
 E2X  plan-1  C3   0.020
 E2X  plan-1  N6   0.020
 E2X  plan-1  O9   0.020
 E2X  plan-1  H1   0.020
 E2X  plan-1  H2   0.020
 E2X  plan-1  H3   0.020
 E2X  plan-2  C10  0.020
 E2X  plan-2  C13  0.020
 E2X  plan-2  C15  0.020
 E2X  plan-2  N2   0.020
 E2X  plan-2  C11  0.020
 E2X  plan-2  C12  0.020
 E2X  plan-2  CL1  0.020
 E2X  plan-2  C14  0.020
 E2X  plan-2  N25  0.020
 E2X  plan-2  O9   0.020
 E2X  plan-2  H4   0.020
 E2X  plan-2  H20  0.020
 E2X  plan-3  C14  0.020
 E2X  plan-3  N25  0.020
 E2X  plan-3  H23  0.020
 E2X  plan-3  H24  0.020

