# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 11:27:20 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: [4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1[N+]([O-])=O)C(=O)N2CCN(CC2)C(c3ccccc3)c4ccccc4
#
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
 3UE  3UE  '[4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone'  ligand  56  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3UE
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
 3UE  O01  O  O      0  -0.481   1.9920  -3.1792   0.3039
 3UE  C02  C  C      0   0.523   1.8995  -1.9853   0.5551
 3UE  C03  C  CR6    0  -0.046   3.1294  -1.1347   0.4395
 3UE  C04  C  CR16   0  -0.273   3.6481  -0.4583   1.5378
 3UE  C05  C  CR16   0  -0.248   4.8388   0.2298   1.4124
 3UE  C06  C  CR6    0   0.187   5.5094   0.2231   0.1970
 3UE  N07  N  N      1   0.329   6.7679   0.9523   0.1492
 3UE  O08  O  O      0  -0.375   6.8631   1.9534   0.8199
 3UE  O09  O  O     -1  -0.370   7.6569   0.5138  -0.5411
 3UE  C10  C  CR6    0   0.132   5.0225  -0.4434  -0.9300
 3UE  C11  C  CH3    0  -0.715   5.6767  -0.4570  -2.2804
 3UE  C12  C  CR16   0  -0.324   3.8176  -1.1227  -0.7653
 3UE  N13  N  NT     0  -0.449   0.7649  -1.3926   0.9659
 3UE  C14  C  CH2    0  -0.322   0.5206   0.0387   0.9929
 3UE  C15  C  CH2    0  -0.278  -0.5693   0.4091   0.0012
 3UE  C16  C  CH2    0  -0.321  -0.4498  -2.1650   1.1587
 3UE  C17  C  CH2    0  -0.285  -1.5138  -1.7579   0.1557
 3UE  N18  N  NT     0  -0.433  -1.7932  -0.3332   0.2617
 3UE  C19  C  CH1    0  -0.164  -2.8701   0.0896  -0.6203
 3UE  C20  C  CR6    0   0.117  -4.1432  -0.7049  -0.3982
 3UE  C21  C  CR16   0  -0.288  -4.6304  -0.9578   0.8826
 3UE  C22  C  CR16   0  -0.240  -5.8288  -1.6332   1.0588
 3UE  C23  C  CR16   0  -0.269  -6.5620  -2.0619  -0.0422
 3UE  C24  C  CR16   0  -0.240  -6.0824  -1.8151  -1.3201
 3UE  C25  C  CR16   0  -0.317  -4.8774  -1.1443  -1.4934
 3UE  C26  C  CR6    0   0.112  -3.2083   1.5576  -0.4386
 3UE  C27  C  CR16   0  -0.295  -3.2249   2.1522   0.8210
 3UE  C28  C  CR16   0  -0.240  -3.6099   3.4767   0.9692
 3UE  C29  C  CR16   0  -0.269  -3.9872   4.2264  -0.1388
 3UE  C30  C  CR16   0  -0.241  -3.9662   3.6427  -1.3977
 3UE  C31  C  CR16   0  -0.308  -3.5755   2.3175  -1.5435
 3UE  H1   H  HCR6   0   0.283   3.1346  -0.4675   2.4901
 3UE  H2   H  HCR6   0   0.298   5.2485   0.7527   2.2648
 3UE  H3   H  HCH3   0   0.265   6.5404  -1.1205  -2.2979
 3UE  H4   H  HCH3   0   0.254   4.9662  -0.8153  -3.0225
 3UE  H5   H  HCH3   0   0.256   6.0137   0.5306  -2.5914
 3UE  H6   H  HCR6   0   0.275   3.4043  -1.6470  -1.6180
 3UE  H7   H  HCH2   0   0.252   0.2178   0.3316   2.0016
 3UE  H8   H  HCH2   0   0.276   1.4225   0.5911   0.7433
 3UE  H9   H  HCH2   0   0.261  -0.7525   1.4793   0.0935
 3UE  H10  H  HCH2   0   0.210  -0.2007   0.2297  -1.0235
 3UE  H11  H  HCH2   0   0.271  -0.2320  -3.2249   1.0620
 3UE  H12  H  HCH2   0   0.253  -0.8163  -1.9847   2.1735
 3UE  H13  H  HCH2   0   0.211  -1.1840  -2.0307  -0.8608
 3UE  H14  H  HCH2   0   0.259  -2.4138  -2.3334   0.3690
 3UE  H16  H  HCH1   0   0.236  -2.5811  -0.0521  -1.6771
 3UE  H17  H  HCR6   0   0.253  -4.0656  -0.6375   1.7495
 3UE  H18  H  HCR6   0   0.255  -6.1930  -1.8260   2.0598
 3UE  H19  H  HCR6   0   0.255  -7.4974  -2.5881   0.0981
 3UE  H20  H  HCR6   0   0.255  -6.6415  -2.1471  -2.1856
 3UE  H21  H  HCR6   0   0.249  -4.5056  -0.9602  -2.4948
 3UE  H22  H  HCR6   0   0.254  -2.9176   1.5824   1.6889
 3UE  H23  H  HCR6   0   0.254  -3.6149   3.9261   1.9542
 3UE  H24  H  HCR6   0   0.255  -4.2877   5.2595  -0.0202
 3UE  H25  H  HCR6   0   0.255  -4.2477   4.2187  -2.2700
 3UE  H26  H  HCR6   0   0.247  -3.5543   1.8702  -2.5309

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
 3UE  C11  C10  single    1.501  0.020  1.501
 3UE  O01  C02  double    1.224  0.020  1.224
 3UE  C12  C10  aromatic  1.393  0.020  1.393
 3UE  C12  C03  aromatic  1.388  0.020  1.388
 3UE  C10  C06  aromatic  1.397  0.020  1.397
 3UE  C02  C03  single    1.500  0.020  1.500
 3UE  C02  N13  single    1.344  0.020  1.344
 3UE  C03  C04  aromatic  1.390  0.020  1.390
 3UE  C06  N07  single    1.455  0.020  1.455
 3UE  C06  C05  aromatic  1.388  0.020  1.388
 3UE  O08  N07  double    1.209  0.020  1.209
 3UE  N07  O09  single    1.208  0.020  1.208
 3UE  C04  C05  aromatic  1.381  0.020  1.381
 3UE  C14  N13  single    1.452  0.020  1.452
 3UE  C14  C15  single    1.519  0.020  1.519
 3UE  N13  C16  single    1.452  0.020  1.452
 3UE  C15  N18  single    1.455  0.020  1.455
 3UE  C16  C17  single    1.518  0.020  1.518
 3UE  C27  C28  aromatic  1.387  0.020  1.387
 3UE  C27  C26  aromatic  1.393  0.020  1.393
 3UE  C28  C29  aromatic  1.390  0.020  1.390
 3UE  C17  N18  single    1.456  0.020  1.456
 3UE  N18  C19  single    1.455  0.020  1.455
 3UE  C19  C26  single    1.517  0.020  1.517
 3UE  C19  C20  single    1.517  0.020  1.517
 3UE  C26  C31  aromatic  1.390  0.020  1.390
 3UE  C29  C30  aromatic  1.388  0.020  1.388
 3UE  C30  C31  aromatic  1.389  0.020  1.389
 3UE  C20  C25  aromatic  1.390  0.020  1.390
 3UE  C20  C21  aromatic  1.394  0.020  1.394
 3UE  C25  C24  aromatic  1.390  0.020  1.390
 3UE  C21  C22  aromatic  1.387  0.020  1.387
 3UE  C24  C23  aromatic  1.387  0.020  1.387
 3UE  C22  C23  aromatic  1.391  0.020  1.391
 3UE  C04  H1   single    0.930  0.020  1.080
 3UE  C05  H2   single    0.930  0.020  1.080
 3UE  C11  H3   single    0.970  0.020  1.090
 3UE  C11  H4   single    0.970  0.020  1.090
 3UE  C11  H5   single    0.970  0.020  1.090
 3UE  C12  H6   single    0.930  0.020  1.080
 3UE  C14  H7   single    0.970  0.020  1.090
 3UE  C14  H8   single    0.970  0.020  1.090
 3UE  C15  H9   single    0.970  0.020  1.090
 3UE  C15  H10  single    0.970  0.020  1.090
 3UE  C16  H11  single    0.970  0.020  1.090
 3UE  C16  H12  single    0.970  0.020  1.090
 3UE  C17  H13  single    0.970  0.020  1.090
 3UE  C17  H14  single    0.970  0.020  1.090
 3UE  C19  H16  single    0.970  0.020  1.090
 3UE  C21  H17  single    0.930  0.020  1.080
 3UE  C22  H18  single    0.930  0.020  1.080
 3UE  C23  H19  single    0.930  0.020  1.080
 3UE  C24  H20  single    0.930  0.020  1.080
 3UE  C25  H21  single    0.930  0.020  1.080
 3UE  C27  H22  single    0.930  0.020  1.080
 3UE  C28  H23  single    0.930  0.020  1.080
 3UE  C29  H24  single    0.930  0.020  1.080
 3UE  C30  H25  single    0.930  0.020  1.080
 3UE  C31  H26  single    0.930  0.020  1.080

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
 3UE  N13  C02  C03  117.75  3.000
 3UE  N13  C02  O01  123.83  3.000
 3UE  C03  C02  O01  118.40  3.000
 3UE  C12  C03  C04  119.78  3.000
 3UE  C04  C03  C02  121.40  3.000
 3UE  C12  C03  C02  118.59  3.000
 3UE  H1   C04  C05  119.56  3.000
 3UE  H1   C04  C03  120.94  3.000
 3UE  C05  C04  C03  119.50  3.000
 3UE  H2   C05  C06  120.65  3.000
 3UE  H2   C05  C04  119.76  3.000
 3UE  C06  C05  C04  119.58  3.000
 3UE  C10  C06  N07  120.93  3.000
 3UE  N07  C06  C05  116.37  3.000
 3UE  C10  C06  C05  122.70  3.000
 3UE  O09  N07  O08  124.04  3.000
 3UE  O09  N07  C06  118.25  3.000
 3UE  O08  N07  C06  117.70  3.000
 3UE  C12  C10  C11  118.62  3.000
 3UE  C12  C10  C06  116.03  3.000
 3UE  C11  C10  C06  125.34  3.000
 3UE  H5   C11  H4   107.81  3.000
 3UE  H5   C11  H3   107.60  3.000
 3UE  H4   C11  H3   107.84  3.000
 3UE  H5   C11  C10  112.57  3.000
 3UE  H4   C11  C10  109.39  3.000
 3UE  H3   C11  C10  111.45  3.000
 3UE  H6   C12  C10  118.23  3.000
 3UE  H6   C12  C03  119.36  3.000
 3UE  C10  C12  C03  122.40  3.000
 3UE  C16  N13  C14  112.40  3.000
 3UE  C16  N13  C02  120.80  3.000
 3UE  C14  N13  C02  125.60  3.000
 3UE  H8   C14  H7   107.80  3.000
 3UE  H8   C14  C15  108.76  3.000
 3UE  H7   C14  C15  109.77  3.000
 3UE  H8   C14  N13  110.93  3.000
 3UE  H7   C14  N13  109.13  3.000
 3UE  C15  C14  N13  110.41  3.000
 3UE  H10  C15  H9   107.13  3.000
 3UE  H10  C15  N18  111.37  3.000
 3UE  H9   C15  N18  110.15  3.000
 3UE  H10  C15  C14  109.07  3.000
 3UE  H9   C15  C14  107.74  3.000
 3UE  N18  C15  C14  111.24  3.000
 3UE  H12  C16  H11  108.09  3.000
 3UE  H12  C16  C17  109.50  3.000
 3UE  H11  C16  C17  110.08  3.000
 3UE  H12  C16  N13  108.41  3.000
 3UE  H11  C16  N13  109.84  3.000
 3UE  C17  C16  N13  110.85  3.000
 3UE  H14  C17  H13  107.27  3.000
 3UE  H14  C17  N18  110.13  3.000
 3UE  H13  C17  N18  111.51  3.000
 3UE  H14  C17  C16  107.94  3.000
 3UE  H13  C17  C16  109.46  3.000
 3UE  N18  C17  C16  110.42  3.000
 3UE  C19  N18  C17  112.48  3.000
 3UE  C19  N18  C15  111.46  3.000
 3UE  C17  N18  C15  108.95  3.000
 3UE  H16  C19  C26  107.28  3.000
 3UE  H16  C19  C20  107.00  3.000
 3UE  C26  C19  C20  107.58  3.000
 3UE  H16  C19  N18  110.43  3.000
 3UE  C20  C19  N18  112.35  3.000
 3UE  C26  C19  N18  111.93  3.000
 3UE  C25  C20  C21  118.83  3.000
 3UE  C21  C20  C19  121.54  3.000
 3UE  C25  C20  C19  119.57  3.000
 3UE  H17  C21  C22  119.54  3.000
 3UE  H17  C21  C20  119.98  3.000
 3UE  C22  C21  C20  120.48  3.000
 3UE  H18  C22  C23  119.99  3.000
 3UE  H18  C22  C21  119.66  3.000
 3UE  C23  C22  C21  120.34  3.000
 3UE  H19  C23  C24  120.31  3.000
 3UE  H19  C23  C22  120.19  3.000
 3UE  C24  C23  C22  119.49  3.000
 3UE  H20  C24  C25  119.74  3.000
 3UE  H20  C24  C23  120.23  3.000
 3UE  C25  C24  C23  120.03  3.000
 3UE  H21  C25  C24  119.64  3.000
 3UE  H21  C25  C20  119.55  3.000
 3UE  C24  C25  C20  120.82  3.000
 3UE  C31  C26  C27  118.82  3.000
 3UE  C31  C26  C19  119.50  3.000
 3UE  C27  C26  C19  121.60  3.000
 3UE  H22  C27  C28  119.71  3.000
 3UE  H22  C27  C26  119.79  3.000
 3UE  C28  C27  C26  120.49  3.000
 3UE  H23  C28  C29  120.00  3.000
 3UE  H23  C28  C27  119.65  3.000
 3UE  C29  C28  C27  120.34  3.000
 3UE  H24  C29  C30  120.33  3.000
 3UE  H24  C29  C28  120.19  3.000
 3UE  C30  C29  C28  119.48  3.000
 3UE  H25  C30  C31  119.74  3.000
 3UE  H25  C30  C29  120.22  3.000
 3UE  C31  C30  C29  120.04  3.000
 3UE  H26  C31  C30  119.65  3.000
 3UE  H26  C31  C26  119.54  3.000
 3UE  C30  C31  C26  120.82  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
 3UE  CONST_01  C06  C10  C12  C03     0.00   0.0  0
 3UE  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 3UE  CONST_03  C10  C12  C03  C04     0.00   0.0  0
 3UE  CONST_04  C10  C06  C05  C04     0.00   0.0  0
 3UE  CONST_05  C12  C10  C06  C05     0.00   0.0  0
 3UE  CONST_06  C12  C03  C04  C05     0.00   0.0  0
 3UE  CONST_07  C23  C24  C25  C20     0.00   0.0  0
 3UE  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 3UE  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 3UE  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 3UE  CONST_11  C25  C20  C21  C22     0.00   0.0  0
 3UE  CONST_12  C25  C24  C23  C22     0.00   0.0  0
 3UE  CONST_13  C29  C28  C27  C26     0.00   0.0  0
 3UE  CONST_14  C29  C30  C31  C26     0.00   0.0  0
 3UE  CONST_15  C30  C29  C28  C27     0.00   0.0  0
 3UE  CONST_16  C30  C31  C26  C27     0.00   0.0  0
 3UE  CONST_17  C31  C26  C27  C28     0.00   0.0  0
 3UE  CONST_18  C31  C30  C29  C28     0.00   0.0  0
 3UE  CONST_19  C10  C12  C03  C02   180.00   0.0  0
 3UE  CONST_20  C05  C04  C03  C02   180.00   0.0  0
 3UE  CONST_21  C11  C10  C12  C03   180.00   0.0  0
 3UE  CONST_22  N07  C06  C05  C04   180.00   0.0  0
 3UE  CONST_23  C11  C10  C06  C05   180.00   0.0  0
 3UE  CONST_24  C12  C10  C06  N07   180.00   0.0  0
 3UE  CONST_25  C28  C27  C26  C19   180.00   0.0  0
 3UE  CONST_26  C30  C31  C26  C19   180.00   0.0  0
 3UE  CONST_27  C24  C25  C20  C19   180.00   0.0  0
 3UE  CONST_28  C22  C21  C20  C19   180.00   0.0  0
 3UE  CONST_30  C16  N13  C02  C03   180.00   0.0  0
 3UE  CONST_31  H2   C05  C04  C03   180.00   0.0  0
 3UE  CONST_32  H6   C12  C03  C04   180.00   0.0  0
 3UE  CONST_33  H1   C04  C05  C06   180.00   0.0  0
 3UE  CONST_34  H20  C24  C25  C20   180.00   0.0  0
 3UE  CONST_35  H18  C22  C21  C20   180.00   0.0  0
 3UE  CONST_36  H21  C25  C20  C21   180.00   0.0  0
 3UE  CONST_37  H19  C23  C22  C21   180.00   0.0  0
 3UE  CONST_38  H17  C21  C22  C23   180.00   0.0  0
 3UE  CONST_39  H23  C28  C27  C26   180.00   0.0  0
 3UE  CONST_40  H25  C30  C31  C26   180.00   0.0  0
 3UE  CONST_41  H24  C29  C28  C27   180.00   0.0  0
 3UE  CONST_42  H26  C31  C26  C27   180.00   0.0  0
 3UE  CONST_43  H22  C27  C28  C29   180.00   0.0  0
 3UE  CONST_44  C14  N13  C02  O01   180.00   0.0  0
 3UE  CONST_45  C16  N13  C02  O01     0.00   0.0  0
 3UE  Var_01    N18  C15  C14  N13    56.33  30.0  1
 3UE  Var_02    N18  C17  C16  N13   -57.20  30.0  1
 3UE  Var_03    C17  C16  N13  C14    54.19  30.0  1
 3UE  Var_04    C17  N18  C15  C14   -59.58  30.0  1
 3UE  Var_05    C16  N13  C14  C15   -53.40  30.0  1
 3UE  Var_06    C16  C17  N18  C15    59.65  30.0  1
 3UE  Var_07    N13  C02  C03  C04    59.48  30.0  2
 3UE  Var_08    C26  C19  N18  C15   -60.80  30.0  3
 3UE  Var_09    C27  C26  C19  N18   -39.34  30.0  2
 3UE  Var_10    C25  C20  C19  N18  -137.10  30.0  2
 3UE  Var_11    H3   C11  C10  C06    75.95  30.0  2

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
 3UE  plan-1  C02  0.020
 3UE  plan-1  C03  0.020
 3UE  plan-1  C04  0.020
 3UE  plan-1  C05  0.020
 3UE  plan-1  C06  0.020
 3UE  plan-1  N07  0.020
 3UE  plan-1  C10  0.020
 3UE  plan-1  C11  0.020
 3UE  plan-1  C12  0.020
 3UE  plan-1  H1   0.020
 3UE  plan-1  H2   0.020
 3UE  plan-1  H6   0.020
 3UE  plan-2  C19  0.020
 3UE  plan-2  C20  0.020
 3UE  plan-2  C21  0.020
 3UE  plan-2  C22  0.020
 3UE  plan-2  C23  0.020
 3UE  plan-2  C24  0.020
 3UE  plan-2  C25  0.020
 3UE  plan-2  H17  0.020
 3UE  plan-2  H18  0.020
 3UE  plan-2  H19  0.020
 3UE  plan-2  H20  0.020
 3UE  plan-2  H21  0.020
 3UE  plan-3  C19  0.020
 3UE  plan-3  C26  0.020
 3UE  plan-3  C27  0.020
 3UE  plan-3  C28  0.020
 3UE  plan-3  C29  0.020
 3UE  plan-3  C30  0.020
 3UE  plan-3  C31  0.020
 3UE  plan-3  H22  0.020
 3UE  plan-3  H23  0.020
 3UE  plan-3  H24  0.020
 3UE  plan-3  H25  0.020
 3UE  plan-3  H26  0.020
 3UE  plan-4  C06  0.020
 3UE  plan-4  N07  0.020
 3UE  plan-4  O08  0.020
 3UE  plan-4  O09  0.020
 3UE  plan-5  O01  0.020
 3UE  plan-5  C02  0.020
 3UE  plan-5  C03  0.020
 3UE  plan-5  N13  0.020
 3UE  plan-5  C14  0.020
 3UE  plan-5  C16  0.020

