# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 19:45:11 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: [(2~{S})-2-methylpiperidin-1-yl]-morpholin-4-yl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCCN1C(=O)N2CCOCC2
#
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
 T1W  T1W  "[(2~{S})-2-methylpiperidin-1-yl]-morpholin-4-yl-methanone"  ligand  35  15  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T1W
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
 T1W  C15  C  CH2   0  -0.321   0.4601  -8.0697  8.7100
 T1W  C01  C  CH3   0  -0.667   4.3559  -4.7081  6.6260
 T1W  C02  C  CH1   0  -0.099   2.9215  -4.2914  6.9452
 T1W  C03  C  CH2   0  -0.422   2.4674  -3.0778  6.1293
 T1W  C04  C  CH2   0  -0.450   2.2188  -3.4098  4.6621
 T1W  C05  C  CH2   0  -0.430   1.2493  -4.5794  4.5400
 T1W  C06  C  CH2   0  -0.321   1.7389  -5.7576  5.3642
 T1W  C08  C  C     0   0.719   1.7282  -6.2288  7.7989
 T1W  C11  C  CH2   0  -0.353  -0.6291  -6.5800  7.0848
 T1W  C12  C  CH2   0  -0.170  -1.8032  -6.8563  8.0056
 T1W  C14  C  CH2   0  -0.185  -0.7232  -8.9399  8.3367
 T1W  N07  N  NT    0  -0.498   1.9490  -5.3685  6.7543
 T1W  N10  N  NT    0  -0.495   0.6113  -7.0180  7.7146
 T1W  O09  O  O     0  -0.523   2.4719  -6.2918  8.7725
 T1W  O13  O  O2    0  -0.488  -1.9455  -8.2283  8.3117
 T1W  H1   H  HCH2  0   0.257   1.3550  -8.6932  8.7319
 T1W  H2   H  HCH2  0   0.233   0.3253  -7.6646  9.7192
 T1W  H3   H  HCH3  0   0.234   4.6522  -5.5693  7.2238
 T1W  H4   H  HCH3  0   0.223   4.5011  -4.9621  5.5758
 T1W  H5   H  HCH3  0   0.229   5.0390  -3.8900  6.8587
 T1W  H6   H  HCH1  0   0.246   2.8858  -4.0116  7.9983
 T1W  H7   H  HCH2  0   0.231   3.2160  -2.2873  6.2232
 T1W  H8   H  HCH2  0   0.225   1.5439  -2.6894  6.5693
 T1W  H9   H  HCH2  0   0.219   3.1604  -3.6667  4.1678
 T1W  H10  H  HCH2  0   0.236   1.8293  -2.5324  4.1419
 T1W  H11  H  HCH2  0   0.222   0.2557  -4.2812  4.8885
 T1W  H12  H  HCH2  0   0.233   1.1451  -4.8883  3.4978
 T1W  H13  H  HCH2  0   0.265   1.0416  -6.5879  5.3042
 T1W  H14  H  HCH2  0   0.241   2.6798  -6.1299  4.9400
 T1W  H15  H  HCH2  0   0.241  -0.7966  -7.0799  6.1247
 T1W  H16  H  HCH2  0   0.268  -0.5888  -5.5085  6.8852
 T1W  H17  H  HCH2  0   0.210  -1.6942  -6.2624  8.9224
 T1W  H18  H  HCH2  0   0.242  -2.7224  -6.5283  7.5154
 T1W  H19  H  HCH2  0   0.242  -0.8204  -9.7439  9.0689
 T1W  H20  H  HCH2  0   0.208  -0.5310  -9.4077  7.3626

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
 T1W  C05  C04  single  1.524  0.020  1.524
 T1W  C05  C06  single  1.519  0.020  1.519
 T1W  C04  C03  single  1.525  0.020  1.525
 T1W  C06  N07  single  1.459  0.020  1.459
 T1W  C01  C02  single  1.527  0.020  1.527
 T1W  C03  C02  single  1.531  0.020  1.531
 T1W  N07  C02  single  1.464  0.020  1.464
 T1W  N07  C08  single  1.371  0.020  1.371
 T1W  C11  C12  single  1.518  0.020  1.518
 T1W  C11  N10  single  1.459  0.020  1.459
 T1W  C12  O13  single  1.413  0.020  1.413
 T1W  C08  N10  single  1.370  0.020  1.370
 T1W  C08  O09  double  1.227  0.020  1.227
 T1W  N10  C15  single  1.456  0.020  1.456
 T1W  O13  C14  single  1.415  0.020  1.415
 T1W  C14  C15  single  1.516  0.020  1.516
 T1W  C15  H1   single  0.970  0.020  1.090
 T1W  C15  H2   single  0.970  0.020  1.090
 T1W  C01  H3   single  0.970  0.020  1.090
 T1W  C01  H4   single  0.970  0.020  1.090
 T1W  C01  H5   single  0.970  0.020  1.090
 T1W  C02  H6   single  0.970  0.020  1.090
 T1W  C03  H7   single  0.970  0.020  1.090
 T1W  C03  H8   single  0.970  0.020  1.090
 T1W  C04  H9   single  0.970  0.020  1.090
 T1W  C04  H10  single  0.970  0.020  1.090
 T1W  C05  H11  single  0.970  0.020  1.090
 T1W  C05  H12  single  0.970  0.020  1.090
 T1W  C06  H13  single  0.970  0.020  1.090
 T1W  C06  H14  single  0.970  0.020  1.090
 T1W  C11  H15  single  0.970  0.020  1.090
 T1W  C11  H16  single  0.970  0.020  1.090
 T1W  C12  H17  single  0.970  0.020  1.090
 T1W  C12  H18  single  0.970  0.020  1.090
 T1W  C14  H19  single  0.970  0.020  1.090
 T1W  C14  H20  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
 T1W  H2   C15  H1   107.08  3.000
 T1W  H2   C15  N10  112.05  3.000
 T1W  H1   C15  N10  109.97  3.000
 T1W  H2   C15  C14  110.06  3.000
 T1W  H1   C15  C14  108.50  3.000
 T1W  N10  C15  C14  109.11  3.000
 T1W  H5   C01  H4   107.26  3.000
 T1W  H5   C01  H3   107.79  3.000
 T1W  H4   C01  H3   107.95  3.000
 T1W  H5   C01  C02  109.81  3.000
 T1W  H4   C01  C02  112.95  3.000
 T1W  H3   C01  C02  110.88  3.000
 T1W  H6   C02  N07  107.04  3.000
 T1W  H6   C02  C03  107.55  3.000
 T1W  N07  C02  C03  108.47  3.000
 T1W  H6   C02  C01  107.61  3.000
 T1W  N07  C02  C01  113.33  3.000
 T1W  C03  C02  C01  112.54  3.000
 T1W  H8   C03  H7   106.67  3.000
 T1W  H8   C03  C04  109.07  3.000
 T1W  H7   C03  C04  110.60  3.000
 T1W  H8   C03  C02  108.50  3.000
 T1W  H7   C03  C02  108.93  3.000
 T1W  C04  C03  C02  112.86  3.000
 T1W  H10  C04  H9   106.29  3.000
 T1W  H10  C04  C05  110.58  3.000
 T1W  H9   C04  C05  109.33  3.000
 T1W  H10  C04  C03  109.98  3.000
 T1W  H9   C04  C03  110.22  3.000
 T1W  C05  C04  C03  110.36  3.000
 T1W  H12  C05  H11  107.12  3.000
 T1W  H12  C05  C06  109.22  3.000
 T1W  H11  C05  C06  109.34  3.000
 T1W  H12  C05  C04  110.75  3.000
 T1W  H11  C05  C04  110.06  3.000
 T1W  C06  C05  C04  110.29  3.000
 T1W  H14  C06  H13  105.65  3.000
 T1W  H14  C06  N07  109.59  3.000
 T1W  H13  C06  N07  110.43  3.000
 T1W  H14  C06  C05  109.26  3.000
 T1W  H13  C06  C05  110.87  3.000
 T1W  N07  C06  C05  110.89  3.000
 T1W  O09  C08  N10  120.89  3.000
 T1W  O09  C08  N07  122.63  3.000
 T1W  N10  C08  N07  116.47  3.000
 T1W  H16  C11  H15  107.07  3.000
 T1W  H16  C11  N10  110.03  3.000
 T1W  H15  C11  N10  111.81  3.000
 T1W  H16  C11  C12  108.57  3.000
 T1W  H15  C11  C12  109.30  3.000
 T1W  N10  C11  C12  109.96  3.000
 T1W  H18  C12  H17  107.21  3.000
 T1W  H18  C12  O13  107.71  3.000
 T1W  H17  C12  O13  110.76  3.000
 T1W  H18  C12  C11  108.91  3.000
 T1W  H17  C12  C11  109.35  3.000
 T1W  O13  C12  C11  112.71  3.000
 T1W  H20  C14  H19  107.27  3.000
 T1W  H20  C14  O13  110.49  3.000
 T1W  H19  C14  O13  107.78  3.000
 T1W  H20  C14  C15  109.06  3.000
 T1W  H19  C14  C15  109.10  3.000
 T1W  O13  C14  C15  112.97  3.000
 T1W  C08  N07  C06  122.38  3.000
 T1W  C08  N07  C02  117.99  3.000
 T1W  C06  N07  C02  114.60  3.000
 T1W  C11  N10  C08  123.15  3.000
 T1W  C08  N10  C15  117.30  3.000
 T1W  C11  N10  C15  115.08  3.000
 T1W  C14  O13  C12  113.91  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
 T1W  CONST_01  N07  C08  N10  C15   180.00   0.0  0
 T1W  CONST_02  N10  C08  N07  C02   180.00   0.0  0
 T1W  CONST_05  O09  C08  N10  C15     0.00   0.0  0
 T1W  CONST_06  O09  C08  N07  C02     0.00   0.0  0
 T1W  Var_01    C12  C11  N10  C15    25.03  30.0  1
 T1W  Var_02    C12  O13  C14  C15    28.32  30.0  1
 T1W  Var_03    C05  C04  C03  C02    53.65  30.0  1
 T1W  Var_04    C05  C06  N07  C02   -59.25  30.0  1
 T1W  Var_05    C06  C05  C04  C03   -53.23  30.0  1
 T1W  Var_06    N07  C06  C05  C04    55.50  30.0  1
 T1W  Var_07    C14  O13  C12  C11    31.01  30.0  1
 T1W  Var_08    C14  C15  N10  C11    30.58  30.0  1
 T1W  Var_09    O13  C12  C11  N10   -60.17  30.0  1
 T1W  Var_10    O13  C14  C15  N10   -61.62  30.0  1
 T1W  Var_11    C08  N07  C06  C05   146.40  30.0  1
 T1W  Var_12    C12  C11  N10  C08  -130.55  30.0  1
 T1W  Var_13    C14  C15  N10  C08  -172.35  30.0  1
 T1W  Var_14    H15  C11  N10  C15   -96.58  30.0  1
 T1W  Var_15    H16  C11  N10  C15   144.57  30.0  1
 T1W  Var_16    H9   C04  C03  C02   -67.21  30.0  1
 T1W  Var_17    H10  C04  C03  C02   175.92  30.0  1
 T1W  Var_18    H13  C06  N07  C02   177.45  30.0  1
 T1W  Var_19    H14  C06  N07  C02    61.46  30.0  1
 T1W  Var_20    H11  C05  C04  C03    67.50  30.0  1
 T1W  Var_21    H12  C05  C04  C03  -174.25  30.0  1
 T1W  Var_22    H13  C06  C05  C04   178.55  30.0  1
 T1W  Var_23    H14  C06  C05  C04   -65.40  30.0  1
 T1W  Var_24    H7   C03  C04  C05   175.97  30.0  1
 T1W  Var_25    H8   C03  C04  C05   -67.02  30.0  1
 T1W  Var_26    H9   C04  C05  C06    68.16  30.0  1
 T1W  Var_27    H10  C04  C05  C06  -175.14  30.0  1
 T1W  Var_28    H1   C15  N10  C11   149.47  30.0  1
 T1W  Var_29    H2   C15  N10  C11   -91.56  30.0  1
 T1W  Var_30    H19  C14  O13  C12   148.92  30.0  1
 T1W  Var_31    H20  C14  O13  C12   -94.17  30.0  1
 T1W  Var_32    H17  C12  O13  C14   -91.86  30.0  1
 T1W  Var_33    H18  C12  O13  C14   151.18  30.0  1
 T1W  Var_34    H11  C05  C06  N07   -65.65  30.0  1
 T1W  Var_35    H12  C05  C06  N07   177.43  30.0  1
 T1W  Var_36    H17  C12  C11  N10    63.50  30.0  1
 T1W  Var_37    H18  C12  C11  N10  -179.64  30.0  1
 T1W  Var_38    H19  C14  C15  N10   178.53  30.0  1
 T1W  Var_39    H20  C14  C15  N10    61.65  30.0  1
 T1W  Var_40    H15  C11  C12  O13    62.92  30.0  1
 T1W  Var_41    H16  C11  C12  O13   179.40  30.0  1
 T1W  Var_42    H1   C15  C14  O13   178.58  30.0  1
 T1W  Var_43    H2   C15  C14  O13    61.72  30.0  1
 T1W  Var_44    H13  C06  N07  C08    23.10  30.0  1
 T1W  Var_45    H14  C06  N07  C08   -92.89  30.0  1
 T1W  Var_46    H15  C11  N10  C08   107.85  30.0  1
 T1W  Var_47    H16  C11  N10  C08   -11.00  30.0  1
 T1W  Var_48    H1   C15  N10  C08   -53.46  30.0  1
 T1W  Var_49    H2   C15  N10  C08    65.51  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
 T1W  chir_01  C02  C01  C03  N07  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
 T1W  plan-1  C15  0.020
 T1W  plan-1  C02  0.020
 T1W  plan-1  C06  0.020
 T1W  plan-1  C08  0.020
 T1W  plan-1  C11  0.020
 T1W  plan-1  N07  0.020
 T1W  plan-1  N10  0.020
 T1W  plan-1  O09  0.020

