# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:50:10 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2R)-2-(4-chlorophenyl)-2-[4-(1H-pyrazol-4-yl)phenyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](c1ccc(Cl)cc1)c2ccc(cc2)c3c[nH]nc3
#
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
 GVN  GVN  (2R)-2-(4-chlorophenyl)-2-[4-(1H-pyrazol-4-yl)phenyl]ethanamine  ligand  37  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GVN
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
 GVN  N1    N   NH2   0  -0.795   3.2032   0.9197   4.4138
 GVN  C2    C   CH2   0  -0.270   1.9251   0.3479   4.8016
 GVN  C3    C   CH1   0  -0.409   1.7957  -1.0755   4.2513
 GVN  C4    C   CR6   0   0.179   0.5902  -1.8260   4.7713
 GVN  C5    C   CR16  0  -0.300   0.6222  -3.2199   4.7843
 GVN  C6    C   CR16  0  -0.197  -0.4583  -3.9680   5.2212
 GVN  C7    C   CR6   0  -0.059  -1.5996  -3.3096   5.6547
 GVN  CL8   CL  CL    0  -0.135  -2.9618  -4.2316   6.2066
 GVN  C9    C   CR16  0  -0.193  -1.6638  -1.9276   5.6565
 GVN  C10   C   CR16  0  -0.338  -0.5685  -1.1957   5.2146
 GVN  C11   C   CR6   0   0.131   1.8157  -1.0778   2.7376
 GVN  C12   C   CR16  0  -0.300   2.9257  -1.5394   2.0398
 GVN  C13   C   CR16  0  -0.330   2.9625  -1.5229   0.6528
 GVN  C14   C   CR6   0   0.100   1.8840  -1.0422  -0.0889
 GVN  C15   C   CR16  0  -0.325   0.7688  -0.5778   0.6153
 GVN  C16   C   CR16  0  -0.266   0.7371  -0.5940   1.9984
 GVN  C17   C   CR5   0  -0.101   1.9164  -1.0318  -1.5495
 GVN  C18   C   CR15  0  -0.012   1.0173  -0.4414  -2.4190
 GVN  N19   N   NR15  0  -0.426   1.4563  -0.6998  -3.6578
 GVN  N20   N   N     0  -0.261   2.5734  -1.4154  -3.6801
 GVN  C21   C   CR15  0  -0.120   2.8662  -1.6238  -2.4116
 GVN  H1N1  H   HNH2  0   0.352   3.3080   1.8273   4.8487
 GVN  H1N2  H   HNH2  0   0.344   3.2087   1.0940   3.4162
 GVN  H2C1  H   HCH2  0   0.199   1.0651   0.9512   4.4802
 GVN  H2C2  H   HCH2  0   0.236   1.8858   0.3039   5.8929
 GVN  H3    H   HCH1  0   0.261   2.6853  -1.6157   4.5906
 GVN  H5    H   HCR6  0   0.259   1.5123  -3.7366   4.4447
 GVN  H10   H   HCR6  0   0.258  -0.6418  -0.1161   5.2268
 GVN  H6    H   HCR6  0   0.278  -0.4090  -5.0485   5.2258
 GVN  H9    H   HCR6  0   0.278  -2.5539  -1.4180   5.9997
 GVN  H12   H   HCR6  0   0.252   3.7790  -1.9227   2.5864
 GVN  H16   H   HCR6  0   0.252  -0.1514  -0.2330   2.5031
 GVN  H13   H   HCR6  0   0.244   3.8493  -1.8887   0.1506
 GVN  H15   H   HCR6  0   0.246  -0.0949  -0.2051   0.0786
 GVN  H18   H   HCR5  0   0.291   0.1227   0.1344  -2.2465
 GVN  H21   H   HCR5  0   0.256   3.7434  -2.1963  -2.1488
 GVN  H19   H   HNR5  0   0.423   1.0243  -0.4146  -4.5220

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
 GVN  N1   C2    single    1.453  0.020  1.453
 GVN  C2   C3    single    1.532  0.020  1.532
 GVN  C3   C4    single    1.512  0.020  1.512
 GVN  C4   C5    aromatic  1.394  0.020  1.394
 GVN  C5   C6    aromatic  1.385  0.020  1.385
 GVN  C6   C7    aromatic  1.387  0.020  1.387
 GVN  C7   CL8   single    1.735  0.020  1.735
 GVN  C7   C9    aromatic  1.384  0.020  1.384
 GVN  C4   C10   aromatic  1.391  0.020  1.391
 GVN  C9   C10   aromatic  1.389  0.020  1.389
 GVN  C3   C11   single    1.514  0.020  1.514
 GVN  C11  C12   aromatic  1.390  0.020  1.390
 GVN  C12  C13   aromatic  1.388  0.020  1.388
 GVN  C13  C14   aromatic  1.394  0.020  1.394
 GVN  C14  C15   aromatic  1.398  0.020  1.398
 GVN  C11  C16   aromatic  1.394  0.020  1.394
 GVN  C15  C16   aromatic  1.384  0.020  1.384
 GVN  C14  C17   single    1.461  0.020  1.461
 GVN  C17  C18   double    1.383  0.020  1.383
 GVN  C18  N19   single    1.339  0.020  1.339
 GVN  N19  N20   single    1.327  0.020  1.327
 GVN  C17  C21   single    1.413  0.020  1.413
 GVN  N20  C21   double    1.318  0.020  1.318
 GVN  N1   H1N1  single    0.890  0.020  1.040
 GVN  N1   H1N2  single    0.890  0.020  1.040
 GVN  C2   H2C1  single    0.970  0.020  1.090
 GVN  C2   H2C2  single    0.970  0.020  1.090
 GVN  C3   H3    single    0.970  0.020  1.090
 GVN  C5   H5    single    0.930  0.020  1.080
 GVN  C10  H10   single    0.930  0.020  1.080
 GVN  C6   H6    single    0.930  0.020  1.080
 GVN  C9   H9    single    0.930  0.020  1.080
 GVN  C12  H12   single    0.930  0.020  1.080
 GVN  C16  H16   single    0.930  0.020  1.080
 GVN  C13  H13   single    0.930  0.020  1.080
 GVN  C15  H15   single    0.930  0.020  1.080
 GVN  C18  H18   single    0.930  0.020  1.080
 GVN  C21  H21   single    0.930  0.020  1.080
 GVN  N19  H19   single    0.860  0.020  1.020

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
 GVN  H1N2  N1   H1N1  105.57  3.000
 GVN  H1N2  N1   C2    109.60  3.000
 GVN  H1N1  N1   C2    109.24  3.000
 GVN  H2C2  C2   H2C1  106.62  3.000
 GVN  H2C2  C2   C3    108.56  3.000
 GVN  H2C1  C2   C3    109.82  3.000
 GVN  H2C2  C2   N1    108.30  3.000
 GVN  H2C1  C2   N1    113.23  3.000
 GVN  C3    C2   N1    110.14  3.000
 GVN  H3    C3   C11   107.37  3.000
 GVN  H3    C3   C4    107.24  3.000
 GVN  C11   C3   C4    110.71  3.000
 GVN  H3    C3   C2    106.17  3.000
 GVN  C11   C3   C2    111.07  3.000
 GVN  C4    C3   C2    113.89  3.000
 GVN  C10   C4   C5    117.97  3.000
 GVN  C10   C4   C3    123.27  3.000
 GVN  C5    C4   C3    118.75  3.000
 GVN  H5    C5   C6    118.82  3.000
 GVN  H5    C5   C4    119.51  3.000
 GVN  C6    C5   C4    121.67  3.000
 GVN  H6    C6   C7    120.69  3.000
 GVN  H6    C6   C5    120.35  3.000
 GVN  C7    C6   C5    118.96  3.000
 GVN  C9    C7   CL8   119.61  3.000
 GVN  C9    C7   C6    120.84  3.000
 GVN  CL8   C7   C6    119.55  3.000
 GVN  H9    C9   C10   120.10  3.000
 GVN  H9    C9   C7    120.61  3.000
 GVN  C10   C9   C7    119.29  3.000
 GVN  H10   C10  C9    117.93  3.000
 GVN  H10   C10  C4    120.79  3.000
 GVN  C9    C10  C4    121.27  3.000
 GVN  C16   C11  C12   117.83  3.000
 GVN  C16   C11  C3    121.30  3.000
 GVN  C12   C11  C3    120.86  3.000
 GVN  H12   C12  C13   119.18  3.000
 GVN  H12   C12  C11   119.55  3.000
 GVN  C13   C12  C11   121.26  3.000
 GVN  H13   C13  C14   120.21  3.000
 GVN  H13   C13  C12   118.77  3.000
 GVN  C14   C13  C12   121.02  3.000
 GVN  C17   C14  C15   121.25  3.000
 GVN  C17   C14  C13   121.13  3.000
 GVN  C15   C14  C13   117.61  3.000
 GVN  H15   C15  C16   118.76  3.000
 GVN  H15   C15  C14   120.05  3.000
 GVN  C16   C15  C14   121.18  3.000
 GVN  H16   C16  C15   118.71  3.000
 GVN  H16   C16  C11   120.19  3.000
 GVN  C15   C16  C11   121.09  3.000
 GVN  C21   C17  C18   103.43  3.000
 GVN  C21   C17  C14   128.46  3.000
 GVN  C18   C17  C14   128.11  3.000
 GVN  H18   C18  N19   121.54  3.000
 GVN  H18   C18  C17   131.83  3.000
 GVN  N19   C18  C17   106.62  3.000
 GVN  H19   N19  N20   119.95  3.000
 GVN  H19   N19  C18   126.75  3.000
 GVN  N20   N19  C18   113.30  3.000
 GVN  C21   N20  N19   104.84  3.000
 GVN  H21   C21  N20   119.89  3.000
 GVN  H21   C21  C17   128.30  3.000
 GVN  N20   C21  C17   111.81  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
 GVN  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 GVN  CONST_02  C7    C9   C10  C4      0.00   0.0  0
 GVN  CONST_03  C9    C10  C4   C5      0.00   0.0  0
 GVN  CONST_04  C9    C7   C6   C5      0.00   0.0  0
 GVN  CONST_05  C10   C4   C5   C6      0.00   0.0  0
 GVN  CONST_06  C10   C9   C7   C6      0.00   0.0  0
 GVN  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 GVN  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 GVN  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 GVN  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 GVN  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 GVN  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 GVN  CONST_13  C17   C14  C13  C12   180.00   0.0  0
 GVN  CONST_14  C17   C14  C15  C16   180.00   0.0  0
 GVN  CONST_15  C6    C5   C4   C3    180.00   0.0  0
 GVN  CONST_16  C9    C10  C4   C3    180.00   0.0  0
 GVN  CONST_17  C13   C12  C11  C3    180.00   0.0  0
 GVN  CONST_18  C15   C16  C11  C3    180.00   0.0  0
 GVN  CONST_19  CL8   C7   C6   C5    180.00   0.0  0
 GVN  CONST_20  C10   C9   C7   CL8   180.00   0.0  0
 GVN  CONST_21  H6    C6   C5   C4    180.00   0.0  0
 GVN  CONST_22  H9    C9   C10  C4    180.00   0.0  0
 GVN  CONST_23  H10   C10  C4   C5    180.00   0.0  0
 GVN  CONST_24  H5    C5   C6   C7    180.00   0.0  0
 GVN  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 GVN  CONST_26  H15   C15  C16  C11   180.00   0.0  0
 GVN  CONST_27  H16   C16  C11  C12   180.00   0.0  0
 GVN  CONST_28  H12   C12  C13  C14   180.00   0.0  0
 GVN  Var_01    C18   C17  C14  C13  -171.01  30.0  2
 GVN  Var_02    H1N1  N1   C2   C3   -175.24  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
 GVN  chir_01  C3  C2  C4  C11  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
 GVN  plan-1  C14  0.020
 GVN  plan-1  C17  0.020
 GVN  plan-1  C18  0.020
 GVN  plan-1  N19  0.020
 GVN  plan-1  N20  0.020
 GVN  plan-1  C21  0.020
 GVN  plan-1  H18  0.020
 GVN  plan-1  H21  0.020
 GVN  plan-1  H19  0.020
 GVN  plan-2  C3   0.020
 GVN  plan-2  C4   0.020
 GVN  plan-2  C5   0.020
 GVN  plan-2  C6   0.020
 GVN  plan-2  C7   0.020
 GVN  plan-2  CL8  0.020
 GVN  plan-2  C9   0.020
 GVN  plan-2  C10  0.020
 GVN  plan-2  H5   0.020
 GVN  plan-2  H10  0.020
 GVN  plan-2  H6   0.020
 GVN  plan-2  H9   0.020
 GVN  plan-3  C3   0.020
 GVN  plan-3  C11  0.020
 GVN  plan-3  C12  0.020
 GVN  plan-3  C13  0.020
 GVN  plan-3  C14  0.020
 GVN  plan-3  C15  0.020
 GVN  plan-3  C16  0.020
 GVN  plan-3  C17  0.020
 GVN  plan-3  H12  0.020
 GVN  plan-3  H16  0.020
 GVN  plan-3  H13  0.020
 GVN  plan-3  H15  0.020

