# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:49:14 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-(4-chlorophenyl)-7-[(6,7-dimethoxyquinolin-4-yl)oxy]-2,3-dihydro-4H-1,4-benzoxazine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2nccc(Oc3ccc4N(CCOc4c3)C(=O)Nc5ccc(Cl)cc5)c2cc1OC
#
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
 2RL  2RL  N-(4-chlorophenyl)-7-[(6,7-dimethoxyquinolin-4-yl)oxy]-2,3-dihydro-4H-1,4-benzoxazine-4-carboxamide  ligand  57  35  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2RL
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
 2RL  C1    C   CR6   0   0.329   -7.4921   0.7912   0.3277
 2RL  C2    C   CR16  0  -0.452   -7.0643  -0.0677   1.3022
 2RL  C3    C   CR66  0   0.203   -5.7163  -0.4974   1.3570
 2RL  C4    C   CR66  0  -0.009   -4.8118  -0.0246   0.3819
 2RL  C5    C   CR16  0  -0.458   -5.2624   0.8646  -0.6244
 2RL  C6    C   CR6   0   0.344   -6.5682   1.2683  -0.6594
 2RL  N7    N   N     0  -0.452   -5.3574  -1.3430   2.3495
 2RL  C8    C   CR16  0  -0.091   -4.1093  -1.7341   2.3892
 2RL  C9    C   CR16  0  -0.425   -3.1181  -1.3416   1.4771
 2RL  C10   C   CR6   0   0.435   -3.4741  -0.4769   0.4704
 2RL  O11   O   O2    0  -0.508   -2.6306  -0.0139  -0.4734
 2RL  C12   C   CR6   0   0.315   -1.2950  -0.3399  -0.3980
 2RL  C13   C   CR16  0  -0.420   -0.8218  -1.3886  -1.1577
 2RL  C14   C   CR6   0   0.346    0.5364  -1.6955  -1.1355
 2RL  C15   C   CR6   0   0.292    1.4154  -0.9525  -0.3374
 2RL  C16   C   CR16  0  -0.301    0.8951   0.0767   0.4466
 2RL  C17   C   CR16  0  -0.319   -0.4485   0.4005   0.4129
 2RL  O25   O   O2    0  -0.472    0.9261  -2.7428  -1.8864
 2RL  C26   C   CH2   0  -0.180    2.3200  -2.9866  -1.9751
 2RL  C27   C   CH2   0  -0.386    3.0090  -2.7193  -0.6542
 2RL  N28   N   NT    0  -0.605    2.7696  -1.3326  -0.2811
 2RL  O33   O   O2    0  -0.459   -7.0983   2.1048  -1.5625
 2RL  O34   O   O2    0  -0.455   -8.7398   1.2548   0.1969
 2RL  C35   C   C     0   0.703    3.7630  -0.3748  -0.2245
 2RL  O36   O   O     0  -0.482    3.5549   0.8041  -0.4357
 2RL  N37   N   NH1   0  -0.787    4.9934  -0.8736   0.1110
 2RL  C38   C   CR6   0   0.391    6.1813  -0.1429   0.1830
 2RL  C39   C   CR16  0  -0.301    6.4588   0.9640  -0.6196
 2RL  C40   C   CR16  0  -0.205    7.6783   1.6147  -0.5115
 2RL  C41   C   CR6   0  -0.059    8.6320   1.1618   0.3849
 2RL  C42   C   CR16  0  -0.203    8.3792   0.0540   1.1771
 2RL  C43   C   CR16  0  -0.348    7.1575  -0.5881   1.0748
 2RL  CL48  CL  CL    0  -0.135   10.1539   1.9832   0.5135
 2RL  C49   C   CH3   0  -0.441   -6.2485   2.6255  -2.5659
 2RL  C53   C   CH3   0  -0.440   -9.7092   0.8377   1.1404
 2RL  H2    H   HCR6  0   0.284   -7.7351  -0.4476   2.0605
 2RL  H5    H   HCR6  0   0.289   -4.5608   1.2233  -1.3638
 2RL  H8    H   HCR6  0   0.261   -3.8364  -2.4124   3.1910
 2RL  H9    H   HCR6  0   0.286   -2.1118  -1.7194   1.5890
 2RL  H13   H   HCR6  0   0.285   -1.4909  -1.9693  -1.7804
 2RL  H16   H   HCR6  0   0.278    1.5472   0.6330   1.1032
 2RL  H17   H   HCR6  0   0.277   -0.8304   1.2122   1.0177
 2RL  H26   H   HCH2  0   0.261    2.4377  -4.0296  -2.2661
 2RL  H26A  H   HCH2  0   0.243    2.7605  -2.3584  -2.7551
 2RL  H27   H   HCH2  0   0.278    2.6395  -3.3891   0.1254
 2RL  H27A  H   HCH2  0   0.285    4.0698  -2.9112  -0.7883
 2RL  HN37  H   HNH1  0   0.425    5.0196  -1.7645   0.5831
 2RL  H39   H   HCR6  0   0.280    5.7430   1.3291  -1.3388
 2RL  H40   H   HCR6  0   0.282    7.8780   2.4727  -1.1382
 2RL  H42   H   HCR6  0   0.282    9.1200  -0.3096   1.8758
 2RL  H43   H   HCR6  0   0.280    6.9646  -1.4500   1.7020
 2RL  H49   H   HCH3  0   0.232   -5.4339   3.2172  -2.1400
 2RL  H49A  H   HCH3  0   0.232   -5.8225   1.8343  -3.1882
 2RL  H49B  H   HCH3  0   0.264   -6.8643   3.2692  -3.1883
 2RL  H53   H   HCH3  0   0.233   -9.8619  -0.2441   1.1132
 2RL  H53A  H   HCH3  0   0.233   -9.4364   1.1306   2.1571
 2RL  H53B  H   HCH3  0   0.265  -10.6373   1.3323   0.8664

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
 2RL  O34   C1    single    1.337  0.020  1.337
 2RL  C2    C1    aromatic  1.368  0.020  1.368
 2RL  C1    C6    aromatic  1.434  0.020  1.434
 2RL  C2    C3    aromatic  1.416  0.020  1.416
 2RL  C2    H2    single    0.930  0.020  1.080
 2RL  N7    C3    aromatic  1.352  0.020  1.352
 2RL  C3    C4    aromatic  1.412  0.020  1.412
 2RL  C4    C5    aromatic  1.416  0.020  1.416
 2RL  C4    C10   aromatic  1.415  0.020  1.415
 2RL  C6    C5    aromatic  1.367  0.020  1.367
 2RL  C5    H5    single    0.930  0.020  1.080
 2RL  C6    O33   single    1.340  0.020  1.340
 2RL  N7    C8    aromatic  1.309  0.020  1.309
 2RL  C8    C9    aromatic  1.403  0.020  1.403
 2RL  C8    H8    single    0.930  0.020  1.080
 2RL  C9    C10   aromatic  1.374  0.020  1.374
 2RL  C9    H9    single    0.930  0.020  1.080
 2RL  C10   O11   single    1.348  0.020  1.348
 2RL  O11   C12   single    1.377  0.020  1.377
 2RL  C17   C12   aromatic  1.387  0.020  1.387
 2RL  C12   C13   aromatic  1.379  0.020  1.379
 2RL  C13   C14   aromatic  1.393  0.020  1.393
 2RL  C13   H13   single    0.930  0.020  1.080
 2RL  C15   C14   aromatic  1.401  0.020  1.401
 2RL  C14   O25   single    1.346  0.020  1.346
 2RL  C16   C15   aromatic  1.395  0.020  1.395
 2RL  C15   N28   single    1.408  0.020  1.408
 2RL  C17   C16   aromatic  1.382  0.020  1.382
 2RL  C16   H16   single    0.930  0.020  1.080
 2RL  C17   H17   single    0.930  0.020  1.080
 2RL  O25   C26   single    1.418  0.020  1.418
 2RL  C27   C26   single    1.514  0.020  1.514
 2RL  C26   H26   single    0.970  0.020  1.090
 2RL  C26   H26A  single    0.970  0.020  1.090
 2RL  N28   C27   single    1.456  0.020  1.456
 2RL  C27   H27   single    0.970  0.020  1.090
 2RL  C27   H27A  single    0.970  0.020  1.090
 2RL  C35   N28   single    1.381  0.020  1.381
 2RL  O33   C49   single    1.414  0.020  1.414
 2RL  C53   O34   single    1.416  0.020  1.416
 2RL  O36   C35   double    1.216  0.020  1.216
 2RL  C35   N37   single    1.369  0.020  1.369
 2RL  C38   N37   single    1.397  0.020  1.397
 2RL  N37   HN37  single    0.860  0.020  1.020
 2RL  C39   C38   aromatic  1.395  0.020  1.395
 2RL  C38   C43   aromatic  1.395  0.020  1.395
 2RL  C40   C39   aromatic  1.386  0.020  1.386
 2RL  C39   H39   single    0.930  0.020  1.080
 2RL  C40   C41   aromatic  1.385  0.020  1.385
 2RL  C40   H40   single    0.930  0.020  1.080
 2RL  CL48  C41   single    1.734  0.020  1.734
 2RL  C41   C42   aromatic  1.385  0.020  1.385
 2RL  C42   C43   aromatic  1.384  0.020  1.384
 2RL  C42   H42   single    0.930  0.020  1.080
 2RL  C43   H43   single    0.930  0.020  1.080
 2RL  C49   H49   single    0.970  0.020  1.090
 2RL  C49   H49A  single    0.970  0.020  1.090
 2RL  C49   H49B  single    0.970  0.020  1.090
 2RL  C53   H53   single    0.970  0.020  1.090
 2RL  C53   H53A  single    0.970  0.020  1.090
 2RL  C53   H53B  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
 2RL  O34   C1   C6    114.74  3.000
 2RL  C6    C1   C2    119.86  3.000
 2RL  O34   C1   C2    125.40  3.000
 2RL  H2    C2   C3    117.18  3.000
 2RL  H2    C2   C1    121.75  3.000
 2RL  C3    C2   C1    121.07  3.000
 2RL  N7    C3   C4    123.12  3.000
 2RL  C4    C3   C2    118.80  3.000
 2RL  N7    C3   C2    118.09  3.000
 2RL  C10   C4   C5    123.09  3.000
 2RL  C10   C4   C3    117.10  3.000
 2RL  C5    C4   C3    119.81  3.000
 2RL  H5    C5   C6    120.30  3.000
 2RL  H5    C5   C4    119.21  3.000
 2RL  C6    C5   C4    120.49  3.000
 2RL  O33   C6   C5    125.40  3.000
 2RL  O33   C6   C1    114.63  3.000
 2RL  C5    C6   C1    119.97  3.000
 2RL  C8    N7   C3    117.53  3.000
 2RL  H8    C8   C9    118.53  3.000
 2RL  H8    C8   N7    116.68  3.000
 2RL  C9    C8   N7    124.79  3.000
 2RL  H9    C9   C10   122.50  3.000
 2RL  H9    C9   C8    119.52  3.000
 2RL  C10   C9   C8    117.99  3.000
 2RL  O11   C10  C9    124.54  3.000
 2RL  O11   C10  C4    115.98  3.000
 2RL  C9    C10  C4    119.47  3.000
 2RL  C12   O11  C10   119.17  3.000
 2RL  C17   C12  C13   121.26  3.000
 2RL  C13   C12  O11   118.88  3.000
 2RL  C17   C12  O11   119.85  3.000
 2RL  H13   C13  C14   119.58  3.000
 2RL  H13   C13  C12   120.84  3.000
 2RL  C14   C13  C12   119.58  3.000
 2RL  O25   C14  C15   123.29  3.000
 2RL  O25   C14  C13   116.42  3.000
 2RL  C15   C14  C13   120.28  3.000
 2RL  N28   C15  C16   122.40  3.000
 2RL  N28   C15  C14   118.90  3.000
 2RL  C16   C15  C14   118.54  3.000
 2RL  H16   C16  C17   118.76  3.000
 2RL  H16   C16  C15   119.79  3.000
 2RL  C17   C16  C15   121.45  3.000
 2RL  H17   C17  C16   120.34  3.000
 2RL  H17   C17  C12   120.80  3.000
 2RL  C16   C17  C12   118.85  3.000
 2RL  C26   O25  C14   116.95  3.000
 2RL  H26A  C26  H26   108.41  3.000
 2RL  H26A  C26  C27   109.73  3.000
 2RL  H26   C26  C27   110.67  3.000
 2RL  H26A  C26  O25   109.98  3.000
 2RL  H26   C26  O25   106.72  3.000
 2RL  C27   C26  O25   111.26  3.000
 2RL  H27A  C27  H27   108.07  3.000
 2RL  H27A  C27  N28   111.13  3.000
 2RL  H27   C27  N28   110.22  3.000
 2RL  H27A  C27  C26   107.79  3.000
 2RL  H27   C27  C26   111.14  3.000
 2RL  N28   C27  C26   108.48  3.000
 2RL  C35   N28  C27   123.56  3.000
 2RL  C35   N28  C15   120.42  3.000
 2RL  C27   N28  C15   113.90  3.000
 2RL  C49   O33  C6    118.05  3.000
 2RL  C53   O34  C1    118.14  3.000
 2RL  N37   C35  O36   123.35  3.000
 2RL  N37   C35  N28   113.81  3.000
 2RL  O36   C35  N28   122.84  3.000
 2RL  HN37  N37  C38   114.58  3.000
 2RL  HN37  N37  C35   117.37  3.000
 2RL  C38   N37  C35   125.90  3.000
 2RL  C43   C38  C39   118.80  3.000
 2RL  C43   C38  N37   117.46  3.000
 2RL  C39   C38  N37   123.68  3.000
 2RL  H39   C39  C40   118.48  3.000
 2RL  H39   C39  C38   121.36  3.000
 2RL  C40   C39  C38   120.16  3.000
 2RL  H40   C40  C41   120.50  3.000
 2RL  H40   C40  C39   119.32  3.000
 2RL  C41   C40  C39   120.18  3.000
 2RL  CL48  C41  C42   119.77  3.000
 2RL  C42   C41  C40   120.40  3.000
 2RL  CL48  C41  C40   119.83  3.000
 2RL  H42   C42  C43   119.77  3.000
 2RL  H42   C42  C41   120.89  3.000
 2RL  C43   C42  C41   119.34  3.000
 2RL  H43   C43  C42   118.92  3.000
 2RL  H43   C43  C38   119.96  3.000
 2RL  C42   C43  C38   121.12  3.000
 2RL  H49B  C49  H49A  108.87  3.000
 2RL  H49B  C49  H49   108.95  3.000
 2RL  H49A  C49  H49   108.86  3.000
 2RL  H49B  C49  O33   106.50  3.000
 2RL  H49A  C49  O33   111.82  3.000
 2RL  H49   C49  O33   111.75  3.000
 2RL  H53B  C53  H53A  109.01  3.000
 2RL  H53B  C53  H53   108.96  3.000
 2RL  H53A  C53  H53   108.87  3.000
 2RL  H53B  C53  O34   106.42  3.000
 2RL  H53A  C53  O34   111.73  3.000
 2RL  H53   C53  O34   111.77  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
 2RL  CONST_01  N7    C3   C2   C1   180.00   0.0  0
 2RL  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 2RL  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 2RL  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 2RL  CONST_05  C8    N7   C3   C2   180.00   0.0  0
 2RL  CONST_06  C5    C4   C3   C2     0.00   0.0  0
 2RL  CONST_07  C10   C4   C3   C2   180.00   0.0  0
 2RL  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 2RL  CONST_09  C9    C8   N7   C3     0.00   0.0  0
 2RL  CONST_10  C6    C5   C4   C3     0.00   0.0  0
 2RL  CONST_11  C9    C10  C4   C3     0.00   0.0  0
 2RL  CONST_12  C8    N7   C3   C4     0.00   0.0  0
 2RL  CONST_13  C8    C9   C10  C4     0.00   0.0  0
 2RL  CONST_14  N7    C3   C4   C5   180.00   0.0  0
 2RL  CONST_15  C9    C10  C4   C5   180.00   0.0  0
 2RL  CONST_16  C10   C4   C5   C6   180.00   0.0  0
 2RL  CONST_17  C10   C4   C3   N7     0.00   0.0  0
 2RL  CONST_18  C10   C9   C8   N7     0.00   0.0  0
 2RL  CONST_19  C15   C16  C17  C12    0.00   0.0  0
 2RL  CONST_20  C15   C14  C13  C12    0.00   0.0  0
 2RL  CONST_21  C16   C17  C12  C13    0.00   0.0  0
 2RL  CONST_22  C16   C15  C14  C13    0.00   0.0  0
 2RL  CONST_23  C17   C12  C13  C14    0.00   0.0  0
 2RL  CONST_24  C17   C16  C15  C14    0.00   0.0  0
 2RL  CONST_25  C41   C40  C39  C38    0.00   0.0  0
 2RL  CONST_26  C41   C42  C43  C38    0.00   0.0  0
 2RL  CONST_27  C42   C43  C38  C39    0.00   0.0  0
 2RL  CONST_28  C42   C41  C40  C39    0.00   0.0  0
 2RL  CONST_29  C43   C38  C39  C40    0.00   0.0  0
 2RL  CONST_30  C43   C42  C41  C40    0.00   0.0  0
 2RL  CONST_31  O33   C6   C1   C2   180.00   0.0  0
 2RL  CONST_32  O34   C1   C2   C3   180.00   0.0  0
 2RL  CONST_33  O11   C10  C4   C3   180.00   0.0  0
 2RL  CONST_34  O33   C6   C5   C4   180.00   0.0  0
 2RL  CONST_35  O11   C10  C4   C5     0.00   0.0  0
 2RL  CONST_36  O34   C1   C6   C5   180.00   0.0  0
 2RL  CONST_37  O11   C10  C9   C8   180.00   0.0  0
 2RL  CONST_38  C16   C17  C12  O11  180.00   0.0  0
 2RL  CONST_39  C14   C13  C12  O11  180.00   0.0  0
 2RL  CONST_40  C40   C39  C38  N37  180.00   0.0  0
 2RL  CONST_41  C42   C43  C38  N37  180.00   0.0  0
 2RL  CONST_42  CL48  C41  C40  C39  180.00   0.0  0
 2RL  CONST_43  CL48  C41  C42  C43  180.00   0.0  0
 2RL  CONST_44  H5    C5   C6   C1   180.00   0.0  0
 2RL  CONST_45  H8    C8   N7   C3   180.00   0.0  0
 2RL  CONST_46  H2    C2   C3   C4   180.00   0.0  0
 2RL  CONST_47  H9    C9   C10  C4   180.00   0.0  0
 2RL  CONST_48  H16   C16  C17  C12  180.00   0.0  0
 2RL  CONST_49  H17   C17  C12  C13  180.00   0.0  0
 2RL  CONST_50  H13   C13  C14  C15  180.00   0.0  0
 2RL  CONST_51  H40   C40  C39  C38  180.00   0.0  0
 2RL  CONST_52  H42   C42  C43  C38  180.00   0.0  0
 2RL  CONST_53  H43   C43  C38  C39  180.00   0.0  0
 2RL  CONST_54  H39   C39  C40  C41  180.00   0.0  0
 2RL  CONST_55  O36   C35  N28  C15    0.00   0.0  0
 2RL  CONST_57  C38   N37  C35  N28  180.00   0.0  0
 2RL  CONST_60  N37   C35  N28  C15  180.00   0.0  0
 2RL  CONST_62  HN37  N37  C38  C39  180.00   0.0  0
 2RL  CONST_63  C38   N37  C35  O36    0.00   0.0  0
 2RL  Var_01    C27   N28  C15  C14  -21.65  30.0  1
 2RL  Var_02    C27   C26  O25  C14   37.77  30.0  1
 2RL  Var_03    C26   C27  N28  C15   50.33  30.0  1
 2RL  Var_04    N28   C27  C26  O25  -58.92  30.0  1
 2RL  Var_05    C17   C12  O11  C10  -83.43  30.0  2
 2RL  Var_06    H53   C53  O34  C1   -61.94  30.0  3
 2RL  Var_07    H49   C49  O33  C6   -61.30  30.0  3

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
 2RL  plan-1  N37   0.020
 2RL  plan-1  C38   0.020
 2RL  plan-1  C39   0.020
 2RL  plan-1  C40   0.020
 2RL  plan-1  C41   0.020
 2RL  plan-1  C42   0.020
 2RL  plan-1  C43   0.020
 2RL  plan-1  CL48  0.020
 2RL  plan-1  H39   0.020
 2RL  plan-1  H40   0.020
 2RL  plan-1  H42   0.020
 2RL  plan-1  H43   0.020
 2RL  plan-2  C1    0.020
 2RL  plan-2  C2    0.020
 2RL  plan-2  C3    0.020
 2RL  plan-2  C4    0.020
 2RL  plan-2  C5    0.020
 2RL  plan-2  C6    0.020
 2RL  plan-2  N7    0.020
 2RL  plan-2  C8    0.020
 2RL  plan-2  C9    0.020
 2RL  plan-2  C10   0.020
 2RL  plan-2  O11   0.020
 2RL  plan-2  O33   0.020
 2RL  plan-2  O34   0.020
 2RL  plan-2  H2    0.020
 2RL  plan-2  H5    0.020
 2RL  plan-2  H8    0.020
 2RL  plan-2  H9    0.020
 2RL  plan-3  O11   0.020
 2RL  plan-3  C12   0.020
 2RL  plan-3  C13   0.020
 2RL  plan-3  C14   0.020
 2RL  plan-3  C15   0.020
 2RL  plan-3  C16   0.020
 2RL  plan-3  C17   0.020
 2RL  plan-3  O25   0.020
 2RL  plan-3  N28   0.020
 2RL  plan-3  H13   0.020
 2RL  plan-3  H16   0.020
 2RL  plan-3  H17   0.020
 2RL  plan-4  C15   0.020
 2RL  plan-4  C27   0.020
 2RL  plan-4  N28   0.020
 2RL  plan-4  C35   0.020
 2RL  plan-4  O36   0.020
 2RL  plan-4  N37   0.020
 2RL  plan-4  C38   0.020
 2RL  plan-4  HN37  0.020

