# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:21:13 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (3R,4S)-1-(3,4-dimethoxyphenyl)-3-(3-methylphenyl)piperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)N2CC[C@H](N)[C@@H](C2)c3cccc(C)c3
#
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
 GVB  GVB  (3R,4S)-1-(3,4-dimethoxyphenyl)-3-(3-methylphenyl)piperidin-4-amine  ligand  50  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GVB
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
 GVB  C29   C  CH3    0  -0.407  2.5937  -8.4973  -1.5429
 GVB  O26   O  O2     0  -0.494  3.4414  -7.4742  -2.0429
 GVB  C6    C  CR6    0   0.257  3.1677  -6.2302  -1.5568
 GVB  C7    C  CR16   0  -0.325  2.3831  -5.3436  -2.2732
 GVB  C8    C  CR16   0  -0.371  2.1370  -4.0573  -1.8093
 GVB  C5    C  CR6    0   0.311  3.6935  -5.8098  -0.3312
 GVB  O25   O  O2     0  -0.495  4.4330  -6.6709   0.4218
 GVB  C28   C  CH3    0  -0.408  5.8147  -6.6884   0.0947
 GVB  C4    C  CR16   0  -0.424  3.4392  -4.5349   0.1416
 GVB  C3    C  CR6    0   0.374  2.6518  -3.6262  -0.5820
 GVB  N2    N  NT    -1  -0.523  2.3799  -2.3663  -0.0509
 GVB  C9    C  CH2    0  -0.273  3.5093  -1.5973   0.4565
 GVB  C1    C  CH2    0  -0.295  1.3913  -1.5417  -0.7179
 GVB  C22   C  CH2    0  -0.452  0.8841  -0.4608   0.2240
 GVB  C19   C  CH1    0  -0.083  2.0039   0.3941   0.8053
 GVB  N20   N  NH2    0  -0.799  2.6181   1.1860  -0.2474
 GVB  C10   C  CH1    0  -0.326  3.0433  -0.5395   1.4514
 GVB  C11   C  CR6    0   0.173  4.1772   0.2350   2.0767
 GVB  C12   C  CR16   0  -0.333  4.0589   0.6588   3.4016
 GVB  C13   C  CR16   0  -0.225  5.0608   1.4075   3.9966
 GVB  C14   C  CR16   0  -0.327  6.2030   1.7446   3.2798
 GVB  C16   C  CR6    0   0.123  6.3504   1.3325   1.9603
 GVB  C17   C  CR16   0  -0.378  5.3288   0.5820   1.3760
 GVB  C30   C  CH3    0  -0.726  7.5742   1.6838   1.1639
 GVB  H291  H  HCH3   0   0.220  2.6611  -8.5892  -0.4565
 GVB  H292  H  HCH3   0   0.236  2.9179  -9.4342  -1.9927
 GVB  H293  H  HCH3   0   0.217  1.5489  -8.3214  -1.8149
 GVB  H7    H  HCR6   0   0.261  1.9734  -5.6512  -3.2280
 GVB  H8    H  HCR6   0   0.267  1.5409  -3.3994  -2.4252
 GVB  H4    H  HCR6   0   0.266  3.8393  -4.2667   1.1115
 GVB  H281  H  HCH3   0   0.220  6.2827  -5.7184   0.2853
 GVB  H282  H  HCH3   0   0.222  5.9834  -6.9600  -0.9498
 GVB  H283  H  HCH3   0   0.238  6.2864  -7.4354   0.7303
 GVB  H9C1  H  HCH2   0   0.222  4.0534  -1.1336  -0.3764
 GVB  H9C2  H  HCH2   0   0.255  4.2097  -2.2606   0.9607
 GVB  H1C1  H  HCH2   0   0.246  0.5447  -2.1651  -1.0087
 GVB  H1C2  H  HCH2   0   0.210  1.7885  -1.0884  -1.6377
 GVB  H10   H  HCH1   0   0.245  2.5239  -1.0675   2.2591
 GVB  H221  H  HCH2   0   0.239  0.1690   0.1719  -0.3095
 GVB  H222  H  HCH2   0   0.231  0.3357  -0.9304   1.0447
 GVB  H19   H  HCH1   0   0.220  1.5728   1.0154   1.6050
 GVB  H201  H  HNH2   0   0.350  3.2614   1.8560   0.1547
 GVB  H202  H  HNH2   0   0.346  1.9064   1.7322  -0.7173
 GVB  H12   H  HCR6   0   0.244  3.1754   0.3914   3.9699
 GVB  H17   H  HCR6   0   0.242  5.4527   0.2652   0.3468
 GVB  H13   H  HCR6   0   0.250  4.9555   1.7277   5.0256
 GVB  H14   H  HCR6   0   0.245  6.9840   2.3279   3.7530
 GVB  H301  H  HCH3   0   0.243  8.2903   2.2513   1.7566
 GVB  H302  H  HCH3   0   0.245  8.0795   0.7889   0.7974
 GVB  H303  H  HCH3   0   0.245  7.3162   2.2833   0.2893

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
 GVB  C7   H7    single    0.930  0.020  1.080
 GVB  C8   H8    single    0.930  0.020  1.080
 GVB  C4   H4    single    0.930  0.020  1.080
 GVB  C28  H281  single    0.970  0.020  1.090
 GVB  C28  H282  single    0.970  0.020  1.090
 GVB  C28  H283  single    0.970  0.020  1.090
 GVB  C9   H9C1  single    0.970  0.020  1.090
 GVB  C9   H9C2  single    0.970  0.020  1.090
 GVB  C1   H1C1  single    0.970  0.020  1.090
 GVB  C1   H1C2  single    0.970  0.020  1.090
 GVB  C10  H10   single    0.970  0.020  1.090
 GVB  C22  H221  single    0.970  0.020  1.090
 GVB  C22  H222  single    0.970  0.020  1.090
 GVB  C19  H19   single    0.970  0.020  1.090
 GVB  N20  H201  single    0.890  0.020  1.040
 GVB  N20  H202  single    0.890  0.020  1.040
 GVB  C12  H12   single    0.930  0.020  1.080
 GVB  C17  H17   single    0.930  0.020  1.080
 GVB  C13  H13   single    0.930  0.020  1.080
 GVB  C14  H14   single    0.930  0.020  1.080
 GVB  C30  H301  single    0.970  0.020  1.090
 GVB  C30  H302  single    0.970  0.020  1.090
 GVB  C30  H303  single    0.970  0.020  1.090
 GVB  C29  H293  single    0.970  0.020  1.090
 GVB  C29  O26   single    1.420  0.020  1.420
 GVB  O26  C6    single    1.363  0.020  1.363
 GVB  C6   C7    aromatic  1.384  0.020  1.384
 GVB  C7   C8    aromatic  1.389  0.020  1.389
 GVB  C6   C5    aromatic  1.398  0.020  1.398
 GVB  C5   O25   single    1.362  0.020  1.362
 GVB  O25  C28   single    1.420  0.020  1.420
 GVB  C5   C4    aromatic  1.383  0.020  1.383
 GVB  C8   C3    aromatic  1.399  0.020  1.399
 GVB  C4   C3    aromatic  1.403  0.020  1.403
 GVB  C3   N2    single    1.394  0.020  1.394
 GVB  N2   C9    single    1.457  0.020  1.457
 GVB  N2   C1    single    1.450  0.020  1.450
 GVB  C1   C22   single    1.521  0.020  1.521
 GVB  C22  C19   single    1.524  0.020  1.524
 GVB  C19  N20   single    1.453  0.020  1.453
 GVB  C9   C10   single    1.525  0.020  1.525
 GVB  C19  C10   single    1.539  0.020  1.539
 GVB  C10  C11   single    1.509  0.020  1.509
 GVB  C11  C12   aromatic  1.396  0.020  1.396
 GVB  C12  C13   aromatic  1.385  0.020  1.385
 GVB  C13  C14   aromatic  1.390  0.020  1.390
 GVB  C14  C16   aromatic  1.390  0.020  1.390
 GVB  C11  C17   aromatic  1.392  0.020  1.392
 GVB  C16  C17   aromatic  1.396  0.020  1.396
 GVB  C16  C30   single    1.502  0.020  1.502
 GVB  C29  H291  single    0.970  0.020  1.090
 GVB  C29  H292  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
 GVB  H293  C29  H292  108.67  3.000
 GVB  H292  C29  H291  108.66  3.000
 GVB  H293  C29  H291  108.65  3.000
 GVB  H292  C29  O26   107.27  3.000
 GVB  H291  C29  O26   111.97  3.000
 GVB  H293  C29  O26   111.53  3.000
 GVB  C6    O26  C29   114.34  3.000
 GVB  C5    C6   C7    118.32  3.000
 GVB  C5    C6   O26   120.76  3.000
 GVB  C7    C6   O26   120.92  3.000
 GVB  H7    C7   C8    119.34  3.000
 GVB  C8    C7   C6    121.38  3.000
 GVB  H7    C7   C6    119.26  3.000
 GVB  H8    C8   C3    121.03  3.000
 GVB  C3    C8   C7    120.87  3.000
 GVB  H8    C8   C7    118.11  3.000
 GVB  C4    C5   O25   119.57  3.000
 GVB  C4    C5   C6    120.50  3.000
 GVB  O25   C5   C6    119.91  3.000
 GVB  C28   O25  C5    114.12  3.000
 GVB  H283  C28  H282  108.71  3.000
 GVB  H283  C28  H281  108.75  3.000
 GVB  H282  C28  H281  108.73  3.000
 GVB  H283  C28  O25   107.20  3.000
 GVB  H282  C28  O25   111.94  3.000
 GVB  H281  C28  O25   111.43  3.000
 GVB  H4    C4   C3    120.58  3.000
 GVB  C3    C4   C5    121.58  3.000
 GVB  H4    C4   C5    117.80  3.000
 GVB  N2    C3   C4    119.88  3.000
 GVB  N2    C3   C8    122.75  3.000
 GVB  C4    C3   C8    117.34  3.000
 GVB  C1    N2   C9    112.85  3.000
 GVB  C1    N2   C3    118.15  3.000
 GVB  C9    N2   C3    117.28  3.000
 GVB  H9C2  C9   H9C1  106.85  3.000
 GVB  H9C2  C9   C10   108.48  3.000
 GVB  H9C1  C9   C10   110.70  3.000
 GVB  C10   C9   N2    110.87  3.000
 GVB  H9C2  C9   N2    109.78  3.000
 GVB  H9C1  C9   N2    110.06  3.000
 GVB  H1C2  C1   H1C1  107.03  3.000
 GVB  H1C2  C1   C22   110.22  3.000
 GVB  H1C1  C1   C22   108.21  3.000
 GVB  C22   C1   N2    110.29  3.000
 GVB  H1C2  C1   N2    111.90  3.000
 GVB  H1C1  C1   N2    109.07  3.000
 GVB  H222  C22  H221  106.66  3.000
 GVB  H222  C22  C19   108.85  3.000
 GVB  H221  C22  C19   110.00  3.000
 GVB  C19   C22  C1    112.94  3.000
 GVB  H222  C22  C1    109.09  3.000
 GVB  H221  C22  C1    109.10  3.000
 GVB  H19   C19  C10   107.57  3.000
 GVB  C10   C19  N20   110.43  3.000
 GVB  H19   C19  N20   112.59  3.000
 GVB  C10   C19  C22   108.42  3.000
 GVB  N20   C19  C22   109.86  3.000
 GVB  H19   C19  C22   107.82  3.000
 GVB  H202  N20  H201  105.90  3.000
 GVB  H202  N20  C19   109.45  3.000
 GVB  H201  N20  C19   109.97  3.000
 GVB  H10   C10  C11   107.34  3.000
 GVB  C11   C10  C19   111.72  3.000
 GVB  H10   C10  C19   106.35  3.000
 GVB  C11   C10  C9    113.38  3.000
 GVB  C19   C10  C9    110.68  3.000
 GVB  H10   C10  C9    106.95  3.000
 GVB  C17   C11  C12   118.18  3.000
 GVB  C17   C11  C10   122.76  3.000
 GVB  C12   C11  C10   119.04  3.000
 GVB  H12   C12  C13   119.85  3.000
 GVB  C13   C12  C11   120.70  3.000
 GVB  H12   C12  C11   119.46  3.000
 GVB  H13   C13  C14   119.89  3.000
 GVB  C14   C13  C12   120.26  3.000
 GVB  H13   C13  C12   119.85  3.000
 GVB  H14   C14  C16   119.84  3.000
 GVB  C16   C14  C13   120.31  3.000
 GVB  H14   C14  C13   119.84  3.000
 GVB  C30   C16  C17   120.01  3.000
 GVB  C30   C16  C14   121.36  3.000
 GVB  C17   C16  C14   118.63  3.000
 GVB  H17   C17  C16   118.10  3.000
 GVB  C16   C17  C11   121.92  3.000
 GVB  H17   C17  C11   119.98  3.000
 GVB  H303  C30  H302  106.91  3.000
 GVB  H303  C30  H301  107.78  3.000
 GVB  H302  C30  H301  107.80  3.000
 GVB  H303  C30  C16   111.15  3.000
 GVB  H302  C30  C16   111.32  3.000
 GVB  H301  C30  C16   111.66  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
 GVB  CONST_01  C3    C8   C7   C6     0.00   0.0  0
 GVB  CONST_02  C3    C4   C5   C6     0.00   0.0  0
 GVB  CONST_03  C4    C5   C6   C7     0.00   0.0  0
 GVB  CONST_04  C4    C3   C8   C7     0.00   0.0  0
 GVB  CONST_05  C5    C6   C7   C8     0.00   0.0  0
 GVB  CONST_06  C5    C4   C3   C8     0.00   0.0  0
 GVB  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 GVB  CONST_08  C14   C16  C17  C11    0.00   0.0  0
 GVB  CONST_09  C16   C17  C11  C12    0.00   0.0  0
 GVB  CONST_10  C16   C14  C13  C12    0.00   0.0  0
 GVB  CONST_11  C17   C11  C12  C13    0.00   0.0  0
 GVB  CONST_12  C17   C16  C14  C13    0.00   0.0  0
 GVB  CONST_13  N2    C3   C8   C7   180.00   0.0  0
 GVB  CONST_14  N2    C3   C4   C5   180.00   0.0  0
 GVB  CONST_15  C13   C12  C11  C10  180.00   0.0  0
 GVB  CONST_16  C16   C17  C11  C10  180.00   0.0  0
 GVB  CONST_17  C8    C7   C6   O26  180.00   0.0  0
 GVB  CONST_18  C4    C5   C6   O26  180.00   0.0  0
 GVB  CONST_19  O25   C5   C6   C7   180.00   0.0  0
 GVB  CONST_20  C3    C4   C5   O25  180.00   0.0  0
 GVB  CONST_21  C30   C16  C17  C11  180.00   0.0  0
 GVB  CONST_22  C30   C16  C14  C13  180.00   0.0  0
 GVB  CONST_23  H8    C8   C7   C6   180.00   0.0  0
 GVB  CONST_24  H4    C4   C5   C6   180.00   0.0  0
 GVB  CONST_25  H7    C7   C6   C5   180.00   0.0  0
 GVB  CONST_26  H12   C12  C11  C10    0.00   0.0  0
 GVB  CONST_27  H17   C17  C11  C10    0.00   0.0  0
 GVB  CONST_28  H13   C13  C12  C11  180.00   0.0  0
 GVB  CONST_29  H14   C14  C13  C12  180.00   0.0  0
 GVB  Var_01    C19   C22  C1   N2    55.23  30.0  1
 GVB  Var_02    C7    C6   O26  C29  -96.89  30.0  2
 GVB  Var_03    C4    C5   O25  C28  -94.86  30.0  2
 GVB  Var_04    H301  C30  C16  C14    1.49  30.0  2
 GVB  Var_05    H293  C29  O26  C6    61.77  30.0  3
 GVB  Var_06    H281  C28  O25  C5    63.33  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
 GVB  chir_01  N2   C3   C9   C1   negativ
 GVB  chir_02  C19  N20  C22  C10  negativ
 GVB  chir_03  C10  C9   C19  C11  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
 GVB  plan-1  O26  0.020
 GVB  plan-1  C6   0.020
 GVB  plan-1  C7   0.020
 GVB  plan-1  C8   0.020
 GVB  plan-1  C5   0.020
 GVB  plan-1  O25  0.020
 GVB  plan-1  C4   0.020
 GVB  plan-1  C3   0.020
 GVB  plan-1  N2   0.020
 GVB  plan-1  H7   0.020
 GVB  plan-1  H8   0.020
 GVB  plan-1  H4   0.020
 GVB  plan-2  C10  0.020
 GVB  plan-2  C11  0.020
 GVB  plan-2  C12  0.020
 GVB  plan-2  C13  0.020
 GVB  plan-2  C14  0.020
 GVB  plan-2  C16  0.020
 GVB  plan-2  C17  0.020
 GVB  plan-2  C30  0.020
 GVB  plan-2  H12  0.020
 GVB  plan-2  H17  0.020
 GVB  plan-2  H13  0.020
 GVB  plan-2  H14  0.020

