# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 08:15:06 2022
#   Inital geometry file: a 150 line input string
#   Ligand name: (2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccccc1c2ccc(cc2)c3nc4CN=CCc4c(N[C@H](C)C(O)=O)c3C#N
#
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
 OYZ  OYZ  '(2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid'  ligand  56  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYZ
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
 OYZ  C4   C  CR66   0  -0.035   8.3195   -4.9299  48.4105
 OYZ  C5   C  C      0  -0.610   8.9508   -3.7371  49.0555
 OYZ  C6   C  CR16   0  -0.037   8.2892   -2.4497  48.6827
 OYZ  C8   C  C      0  -0.352   6.7411   -3.4065  47.2117
 OYZ  C13  C  C      0   0.439  11.4649   -7.1048  51.1605
 OYZ  C20  C  CR16   0  -0.272   5.9553   -7.9878  45.1723
 OYZ  C21  C  CR16   0  -0.289   5.2366   -8.9878  44.5378
 OYZ  C22  C  CR6    0   0.092   4.7956  -10.1119  45.2365
 OYZ  C24  C  CR6    0   0.364   4.3331  -12.5037  44.5909
 OYZ  C26  C  CR16   0  -0.245   2.4290  -13.0319  43.2074
 OYZ  C28  C  CR16   0  -0.280   2.8712  -10.7613  43.8083
 OYZ  C31  C  CH3    0  -0.679   7.1164  -14.2224  46.1961
 OYZ  C30  C  CH2    0  -0.189   5.8612  -14.1719  45.3577
 OYZ  O29  O  O2     0  -0.462   5.4430  -12.8171  45.2804
 OYZ  C25  C  CR16   0  -0.382   3.5473  -13.4406  43.9235
 OYZ  C27  C  CR16   0  -0.271   2.0860  -11.6921  43.1415
 OYZ  C23  C  CR6    0  -0.055   3.9886  -11.1408  44.5448
 OYZ  C32  C  CR16   0  -0.275   5.0937  -10.2012  46.5967
 OYZ  C33  C  CR16   0  -0.268   5.8215   -9.2082  47.2301
 OYZ  C19  C  CR6    0   0.015   6.2723   -8.0945  46.5239
 OYZ  C1   C  CR6    0   0.215   7.0275   -7.0120  47.1927
 OYZ  C2   C  CR6    0  -0.146   8.1364   -7.2991  48.0148
 OYZ  N18  N  NS     0  -0.261   9.1010   -9.6820  47.9265
 OYZ  N10  N  N      0  -0.470   6.6106   -5.7865  46.9630
 OYZ  C9   C  CR66   0   0.130   7.2667   -4.7727  47.5485
 OYZ  N7   N  N      0  -0.339   7.3282   -2.2776  47.8852
 OYZ  C3   C  CR6    0   0.523   8.7869   -6.2409  48.7015
 OYZ  N11  N  NH1    0  -0.699   9.8007   -6.3875  49.5548
 OYZ  C12  C  CH1    0  -0.242  10.2485   -7.5489  50.2986
 OYZ  C16  C  CH3    0  -0.665   9.1501   -8.1088  51.2011
 OYZ  H1   H  H      0   0.280   8.9326   -3.8218  50.1493
 OYZ  H2   H  H      0   0.282  10.0136   -3.6528  48.7940
 OYZ  H3   H  HCR6   0   0.253   8.6979   -1.5626  49.1652
 OYZ  H4   H  H      0   0.264   6.8411   -3.2480  46.1325
 OYZ  H5   H  H      0   0.261   5.6624   -3.3903  47.3957
 OYZ  H6   H  HCR6   0   0.252   6.2889   -7.1261  44.6085
 OYZ  H7   H  HCR6   0   0.254   5.0218   -8.8967  43.4802
 OYZ  H8   H  HCR6   0   0.258   1.8296  -13.7755  42.6983
 OYZ  H9   H  HCR6   0   0.253   2.6039   -9.7120  43.7720
 OYZ  H10  H  HCH3   0   0.236   7.4627  -15.2530  46.2672
 OYZ  H11  H  HCH3   0   0.235   7.9162  -13.6297  45.7520
 OYZ  H12  H  HCH3   0   0.235   6.9351  -13.8594  47.2078
 OYZ  H13  H  HCH2   0   0.224   5.0755  -14.7876  45.8084
 OYZ  H14  H  HCH2   0   0.223   6.0549  -14.5660  44.3542
 OYZ  H15  H  HCR6   0   0.278   3.7974  -14.4924  43.9459
 OYZ  H16  H  HCR6   0   0.251   1.2163  -11.3712  42.5842
 OYZ  H17  H  HCR6   0   0.251   4.7330  -11.0394  47.1777
 OYZ  H18  H  HCR6   0   0.261   6.0157   -9.2941  48.2921
 OYZ  H19  H  HNH1   0   0.410  10.2535   -5.5559  49.9234
 OYZ  H20  H  HCH1   0   0.253  10.6017   -8.3311  49.6248
 OYZ  H21  H  HCH3   0   0.237   9.5102   -8.9927  51.7246
 OYZ  H22  H  HCH3   0   0.226   8.8481   -7.3680  51.9431
 OYZ  H23  H  HCH3   0   0.233   8.2601   -8.4007  50.6427
 OYZ  O15  O  O      0  -0.587  11.7176   -5.8827  51.1842
 OYZ  C17  C  CSP    0   0.009   8.6639   -8.6153  47.9983
 OYZ  O14  O  OC    -1  -0.585  12.0551   -8.0188  51.7544

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
 OYZ  C27  C26  aromatic  1.385  0.020  1.385
 OYZ  C27  C28  aromatic  1.388  0.020  1.388
 OYZ  C26  C25  aromatic  1.389  0.020  1.389
 OYZ  C28  C23  aromatic  1.391  0.020  1.391
 OYZ  C25  C24  aromatic  1.393  0.020  1.393
 OYZ  C23  C24  aromatic  1.407  0.020  1.407
 OYZ  C23  C22  single    1.479  0.020  1.479
 OYZ  C21  C22  aromatic  1.395  0.020  1.395
 OYZ  C21  C20  aromatic  1.385  0.020  1.385
 OYZ  C24  O29  single    1.344  0.020  1.344
 OYZ  C22  C32  aromatic  1.395  0.020  1.395
 OYZ  C20  C19  aromatic  1.392  0.020  1.392
 OYZ  O29  C30  single    1.420  0.020  1.420
 OYZ  C30  C31  single    1.510  0.020  1.510
 OYZ  C32  C33  aromatic  1.384  0.020  1.384
 OYZ  C19  C33  aromatic  1.394  0.020  1.394
 OYZ  C19  C1   single    1.480  0.020  1.480
 OYZ  N10  C1   aromatic  1.315  0.020  1.315
 OYZ  N10  C9   aromatic  1.342  0.020  1.342
 OYZ  C1   C2   aromatic  1.410  0.020  1.410
 OYZ  C8   C9   single    1.502  0.020  1.502
 OYZ  C8   N7   single    1.440  0.020  1.440
 OYZ  C9   C4   aromatic  1.370  0.020  1.370
 OYZ  N18  C17  triple    1.155  0.020  1.155
 OYZ  C17  C2   single    1.418  0.020  1.418
 OYZ  C2   C3   aromatic  1.419  0.020  1.419
 OYZ  N7   C6   double    1.261  0.020  1.261
 OYZ  C4   C3   aromatic  1.422  0.020  1.422
 OYZ  C4   C5   single    1.496  0.020  1.496
 OYZ  C3   N11  single    1.333  0.020  1.333
 OYZ  C6   C5   single    1.495  0.020  1.495
 OYZ  N11  C12  single    1.450  0.020  1.450
 OYZ  C12  C16  single    1.528  0.020  1.528
 OYZ  C12  C13  single    1.556  0.020  1.556
 OYZ  C13  O15  deloc     1.248  0.020  1.248
 OYZ  C13  O14  deloc     1.240  0.020  1.240
 OYZ  C5   H1   single    0.970  0.020  1.090
 OYZ  C5   H2   single    0.970  0.020  1.090
 OYZ  C6   H3   single    0.930  0.020  1.080
 OYZ  C8   H4   single    0.970  0.020  1.090
 OYZ  C8   H5   single    0.970  0.020  1.090
 OYZ  C20  H6   single    0.930  0.020  1.080
 OYZ  C21  H7   single    0.930  0.020  1.080
 OYZ  C26  H8   single    0.930  0.020  1.080
 OYZ  C28  H9   single    0.930  0.020  1.080
 OYZ  C31  H10  single    0.970  0.020  1.090
 OYZ  C31  H11  single    0.970  0.020  1.090
 OYZ  C31  H12  single    0.970  0.020  1.090
 OYZ  C30  H13  single    0.970  0.020  1.090
 OYZ  C30  H14  single    0.970  0.020  1.090
 OYZ  C25  H15  single    0.930  0.020  1.080
 OYZ  C27  H16  single    0.930  0.020  1.080
 OYZ  C32  H17  single    0.930  0.020  1.080
 OYZ  C33  H18  single    0.930  0.020  1.080
 OYZ  N11  H19  single    0.860  0.020  1.020
 OYZ  C12  H20  single    0.970  0.020  1.090
 OYZ  C16  H21  single    0.970  0.020  1.090
 OYZ  C16  H22  single    0.970  0.020  1.090
 OYZ  C16  H23  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
 OYZ  C3   C4   C9   119.16  3.000
 OYZ  C3   C4   C5   120.55  3.000
 OYZ  C9   C4   C5   120.28  3.000
 OYZ  H2   C5   H1   105.04  3.000
 OYZ  H2   C5   C6   107.64  3.000
 OYZ  H1   C5   C6   107.92  3.000
 OYZ  H2   C5   C4   111.54  3.000
 OYZ  H1   C5   C4   111.18  3.000
 OYZ  C6   C5   C4   113.11  3.000
 OYZ  H3   C6   N7   117.06  3.000
 OYZ  H3   C6   C5   115.14  3.000
 OYZ  N7   C6   C5   127.79  3.000
 OYZ  H5   C8   H4   104.68  3.000
 OYZ  H5   C8   N7   108.16  3.000
 OYZ  H4   C8   N7   108.08  3.000
 OYZ  H5   C8   C9   108.70  3.000
 OYZ  H4   C8   C9   108.70  3.000
 OYZ  N7   C8   C9   117.75  3.000
 OYZ  O14  C13  O15  128.06  3.000
 OYZ  O14  C13  C12  115.30  3.000
 OYZ  O15  C13  C12  116.63  3.000
 OYZ  H6   C20  C19  119.76  3.000
 OYZ  H6   C20  C21  119.74  3.000
 OYZ  C19  C20  C21  120.49  3.000
 OYZ  H7   C21  C22  119.61  3.000
 OYZ  H7   C21  C20  119.30  3.000
 OYZ  C22  C21  C20  121.09  3.000
 OYZ  C32  C22  C23  121.86  3.000
 OYZ  C32  C22  C21  118.18  3.000
 OYZ  C23  C22  C21  119.92  3.000
 OYZ  C23  C24  C25  119.86  3.000
 OYZ  C23  C24  O29  116.43  3.000
 OYZ  C25  C24  O29  123.71  3.000
 OYZ  H8   C26  C27  120.34  3.000
 OYZ  H8   C26  C25  119.08  3.000
 OYZ  C27  C26  C25  120.57  3.000
 OYZ  H9   C28  C23  118.70  3.000
 OYZ  H9   C28  C27  119.58  3.000
 OYZ  C23  C28  C27  121.71  3.000
 OYZ  H12  C31  H11  108.61  3.000
 OYZ  H12  C31  H10  107.89  3.000
 OYZ  H11  C31  H10  107.92  3.000
 OYZ  H12  C31  C30  111.46  3.000
 OYZ  H11  C31  C30  111.44  3.000
 OYZ  H10  C31  C30  109.39  3.000
 OYZ  H14  C30  H13  107.55  3.000
 OYZ  H14  C30  O29  110.21  3.000
 OYZ  H13  C30  O29  110.33  3.000
 OYZ  H14  C30  C31  110.46  3.000
 OYZ  H13  C30  C31  110.43  3.000
 OYZ  O29  C30  C31  107.87  3.000
 OYZ  C30  O29  C24  119.58  3.000
 OYZ  H15  C25  C26  118.88  3.000
 OYZ  H15  C25  C24  120.91  3.000
 OYZ  C26  C25  C24  120.20  3.000
 OYZ  H16  C27  C28  120.22  3.000
 OYZ  H16  C27  C26  120.72  3.000
 OYZ  C28  C27  C26  119.06  3.000
 OYZ  C28  C23  C24  118.59  3.000
 OYZ  C24  C23  C22  121.67  3.000
 OYZ  C28  C23  C22  119.74  3.000
 OYZ  H17  C32  C33  119.04  3.000
 OYZ  H17  C32  C22  120.12  3.000
 OYZ  C33  C32  C22  120.82  3.000
 OYZ  H18  C33  C19  120.15  3.000
 OYZ  H18  C33  C32  119.08  3.000
 OYZ  C19  C33  C32  120.76  3.000
 OYZ  C1   C19  C33  121.38  3.000
 OYZ  C1   C19  C20  119.93  3.000
 OYZ  C33  C19  C20  118.65  3.000
 OYZ  N10  C1   C2   122.76  3.000
 OYZ  C2   C1   C19  121.06  3.000
 OYZ  N10  C1   C19  116.18  3.000
 OYZ  C3   C2   C1   119.39  3.000
 OYZ  C3   C2   C17  121.81  3.000
 OYZ  C1   C2   C17  118.35  3.000
 OYZ  C9   N10  C1   118.23  3.000
 OYZ  N10  C9   C8   114.72  3.000
 OYZ  C8   C9   C4   120.96  3.000
 OYZ  N10  C9   C4   124.30  3.000
 OYZ  C8   N7   C6   119.98  3.000
 OYZ  N11  C3   C2   125.18  3.000
 OYZ  N11  C3   C4   118.84  3.000
 OYZ  C2   C3   C4   115.96  3.000
 OYZ  H19  N11  C12  109.38  3.000
 OYZ  H19  N11  C3   118.76  3.000
 OYZ  C12  N11  C3   130.63  3.000
 OYZ  H20  C12  C16  109.56  3.000
 OYZ  H20  C12  N11  110.94  3.000
 OYZ  C16  C12  N11  111.99  3.000
 OYZ  H20  C12  C13  107.08  3.000
 OYZ  C16  C12  C13  109.84  3.000
 OYZ  N11  C12  C13  107.28  3.000
 OYZ  H23  C16  H22  107.71  3.000
 OYZ  H23  C16  H21  107.39  3.000
 OYZ  H22  C16  H21  108.40  3.000
 OYZ  H23  C16  C12  112.48  3.000
 OYZ  H22  C16  C12  110.60  3.000
 OYZ  H21  C16  C12  110.11  3.000
 OYZ  N18  C17  C2   180.00  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
 OYZ  CONST_01  C1   N10  C9   C4      0.00   0.0  0
 OYZ  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 OYZ  CONST_03  C23  C22  C21  C20   180.00   0.0  0
 OYZ  CONST_04  C32  C22  C21  C20     0.00   0.0  0
 OYZ  CONST_05  C32  C33  C19  C20     0.00   0.0  0
 OYZ  CONST_10  C33  C32  C22  C21     0.00   0.0  0
 OYZ  CONST_11  C33  C19  C20  C21     0.00   0.0  0
 OYZ  CONST_12  C1   C19  C20  C21   180.00   0.0  0
 OYZ  CONST_13  C27  C28  C23  C22   180.00   0.0  0
 OYZ  CONST_14  C25  C24  C23  C22   180.00   0.0  0
 OYZ  CONST_15  C19  C20  C21  C22     0.00   0.0  0
 OYZ  CONST_16  C19  C33  C32  C22     0.00   0.0  0
 OYZ  CONST_17  C27  C26  C25  C24     0.00   0.0  0
 OYZ  CONST_18  C27  C28  C23  C24     0.00   0.0  0
 OYZ  CONST_20  C23  C28  C27  C26     0.00   0.0  0
 OYZ  CONST_21  C23  C24  C25  C26     0.00   0.0  0
 OYZ  CONST_22  C25  C26  C27  C28     0.00   0.0  0
 OYZ  CONST_23  C25  C24  C23  C28     0.00   0.0  0
 OYZ  CONST_25  C33  C32  C22  C23   180.00   0.0  0
 OYZ  CONST_26  C1   C19  C33  C32   180.00   0.0  0
 OYZ  CONST_29  C9   N10  C1   C19   180.00   0.0  0
 OYZ  CONST_30  C3   C2   C1   C19   180.00   0.0  0
 OYZ  CONST_31  C9   N10  C1   C2      0.00   0.0  0
 OYZ  CONST_32  C9   C4   C3   C2      0.00   0.0  0
 OYZ  CONST_33  C3   C2   C1   N10     0.00   0.0  0
 OYZ  CONST_34  C3   C4   C9   N10     0.00   0.0  0
 OYZ  CONST_35  C17  C2   C3   C4    180.00   0.0  0
 OYZ  CONST_36  N11  C3   C4   C5      0.00   0.0  0
 OYZ  CONST_37  C19  C1   C2   C17     0.00   0.0  0
 OYZ  CONST_38  N10  C1   C2   C17   180.00   0.0  0
 OYZ  CONST_39  O29  C24  C23  C22     0.00   0.0  0
 OYZ  CONST_40  O29  C24  C25  C26   180.00   0.0  0
 OYZ  CONST_41  O29  C24  C23  C28   180.00   0.0  0
 OYZ  CONST_42  N11  C3   C2   C1    180.00   0.0  0
 OYZ  CONST_43  N11  C3   C4   C9    180.00   0.0  0
 OYZ  CONST_44  H18  C33  C19  C20   180.00   0.0  0
 OYZ  CONST_45  H17  C32  C22  C21   180.00   0.0  0
 OYZ  CONST_46  H9   C28  C23  C22     0.00   0.0  0
 OYZ  CONST_47  H6   C20  C21  C22   180.00   0.0  0
 OYZ  CONST_48  H8   C26  C25  C24   180.00   0.0  0
 OYZ  CONST_49  H16  C27  C26  C25   180.00   0.0  0
 OYZ  CONST_50  H15  C25  C26  C27   180.00   0.0  0
 OYZ  CONST_51  H7   C21  C22  C23     0.00   0.0  0
 OYZ  CONST_54  H19  N11  C3   C4      0.00   0.0  0
 OYZ  Var_01    N7   C8   C9   C4     -3.62  30.0  1
 OYZ  Var_02    N7   C6   C5   C4     -2.39  30.0  1
 OYZ  Var_03    C9   C8   N7   C6      3.02  30.0  1
 OYZ  Var_04    C9   C4   C5   C6      1.62  30.0  1
 OYZ  Var_05    C25  C24  O29  C30    -0.34  30.0  1
 OYZ  Var_06    C31  C30  O29  C24  -179.54  30.0  3
 OYZ  Var_07    H10  C31  C30  O29  -179.70  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
 OYZ  chir_01  C12  N11  C16  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
 OYZ  plan-1  C20  0.020
 OYZ  plan-1  C21  0.020
 OYZ  plan-1  C22  0.020
 OYZ  plan-1  C23  0.020
 OYZ  plan-1  C32  0.020
 OYZ  plan-1  C33  0.020
 OYZ  plan-1  C19  0.020
 OYZ  plan-1  C1   0.020
 OYZ  plan-1  H6   0.020
 OYZ  plan-1  H7   0.020
 OYZ  plan-1  H17  0.020
 OYZ  plan-1  H18  0.020
 OYZ  plan-2  C22  0.020
 OYZ  plan-2  C24  0.020
 OYZ  plan-2  C26  0.020
 OYZ  plan-2  C28  0.020
 OYZ  plan-2  O29  0.020
 OYZ  plan-2  C25  0.020
 OYZ  plan-2  C27  0.020
 OYZ  plan-2  C23  0.020
 OYZ  plan-2  H8   0.020
 OYZ  plan-2  H9   0.020
 OYZ  plan-2  H15  0.020
 OYZ  plan-2  H16  0.020
 OYZ  plan-3  C4   0.020
 OYZ  plan-3  C5   0.020
 OYZ  plan-3  C8   0.020
 OYZ  plan-3  C19  0.020
 OYZ  plan-3  C1   0.020
 OYZ  plan-3  C2   0.020
 OYZ  plan-3  N18  0.020
 OYZ  plan-3  N10  0.020
 OYZ  plan-3  C9   0.020
 OYZ  plan-3  C3   0.020
 OYZ  plan-3  N11  0.020
 OYZ  plan-3  C17  0.020
 OYZ  plan-4  C3   0.020
 OYZ  plan-4  N11  0.020
 OYZ  plan-4  C12  0.020
 OYZ  plan-4  H19  0.020
 OYZ  plan-5  C13  0.020
 OYZ  plan-5  C12  0.020
 OYZ  plan-5  O15  0.020
 OYZ  plan-5  O14  0.020

