# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 21:52:48 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-2-amino-3-(3-chlorophenyl)-1-[4-(2,5-difluorobenzoyl)piperazin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1cccc(Cl)c1)C(=O)N2CCN(CC2)C(=O)c3cc(F)ccc3F
#
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
 0DI  0DI  (2R)-2-amino-3-(3-chlorophenyl)-1-[4-(2,5-difluorobenzoyl)piperazin-1-yl]propan-1-one  ligand  48  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0DI
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
 0DI  C1    C   CH2   0  -0.311   2.0218   0.9824   0.1749
 0DI  F1    F   F     0  -0.310   6.6074   0.3324   2.7557
 0DI  N1    N   NT    0  -0.444   1.8848  -0.4638   0.1795
 0DI  O1    O   O     0  -0.493  -0.8643   3.2515  -1.0038
 0DI  CL1   CL  CL    0  -0.131  -6.1046  -2.8343   0.3766
 0DI  C2    C   CH2   0  -0.307   1.3090   1.5683  -1.0349
 0DI  F2    F   F     0  -0.301   4.5954  -0.9968  -2.0817
 0DI  N2    N   NT    0  -0.466  -0.0781   1.1407  -1.0613
 0DI  O2    O   O     0  -0.471   2.7611  -2.5450  -0.0217
 0DI  C3    C   CH2   0  -0.328  -0.2139  -0.3047  -1.0651
 0DI  N3    N   NH2   0  -0.778  -3.3823   2.5318  -1.5677
 0DI  C4    C   CH2   0  -0.311   0.5044  -0.9102   0.1337
 0DI  C5    C   C     0   0.571  -1.0797   2.0485  -1.0289
 0DI  C6    C   CH1   0  -0.234  -2.5187   1.5411  -0.9683
 0DI  C7    C   CH2   0  -0.553  -2.8396   1.2031   0.5095
 0DI  C8    C   CR6   0   0.138  -4.2379   0.6859   0.6739
 0DI  C9    C   CR16  0  -0.265  -4.5023  -0.6695   0.4902
 0DI  C10   C   CR6   0  -0.020  -5.7995  -1.1410   0.6021
 0DI  C11   C   CR16  0  -0.230  -6.8570  -0.2933   0.8941
 0DI  C12   C   CR16  0  -0.245  -6.5910   1.0560   1.0758
 0DI  C13   C   CR16  0  -0.309  -5.2960   1.5430   0.9656
 0DI  C14   C   C     0   0.531   2.9019  -1.3393   0.1037
 0DI  C15   C   CR6   0  -0.294   4.2863  -0.7719   0.2271
 0DI  C16   C   CR6   0   0.553   5.1049  -0.6754  -0.8832
 0DI  C17   C   CR16  0  -0.390   6.4123  -0.2397  -0.7975
 0DI  C18   C   CR16  0  -0.394   6.9276   0.1020   0.4427
 0DI  C19   C   CR6   0   0.534   6.1130   0.0007   1.5546
 0DI  C20   C   CR16  0  -0.384   4.8033  -0.4276   1.4707
 0DI  H1    H   HCH2  0   0.262   1.5879   1.3873   1.0937
 0DI  H1A   H   HCH2  0   0.283   3.0692   1.2724   0.1495
 0DI  H2    H   HCH2  0   0.281   1.3625   2.6526  -1.0043
 0DI  H2A   H   HCH2  0   0.252   1.8050   1.2302  -1.9508
 0DI  H3    H   HCH2  0   0.275  -1.2558  -0.6113  -1.0418
 0DI  H3A   H   HCH2  0   0.270   0.2171  -0.7022  -1.9891
 0DI  HN3   H   HNH2  0   0.357  -4.3331   2.1863  -1.5812
 0DI  HN3A  H   HNH2  0   0.343  -3.3884   3.3799  -1.0148
 0DI  H4    H   HCH2  0   0.283   0.4662  -1.9948   0.0786
 0DI  H4A   H   HCH2  0   0.260   0.0091  -0.6011   1.0597
 0DI  H6    H   HCH1  0   0.273  -2.6270   0.6332  -1.5658
 0DI  H7    H   HCH2  0   0.260  -2.1321   0.4633   0.8921
 0DI  H7A   H   HCH2  0   0.272  -2.7010   2.1050   1.1112
 0DI  H9    H   HCR6  0   0.272  -3.6939  -1.3559   0.2693
 0DI  H11   H   HCR6  0   0.279  -7.8647  -0.6758   0.9827
 0DI  H12   H   HCR6  0   0.268  -7.4046   1.7306   1.3074
 0DI  H13   H   HCR6  0   0.259  -5.1057   2.5981   1.1192
 0DI  H17   H   HCR6  0   0.298   7.0234  -0.1646  -1.6868
 0DI  H18   H   HCR6  0   0.297   7.9489   0.4454   0.5377
 0DI  H20   H   HCR6  0   0.299   4.1889  -0.4894   2.3600

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
 0DI  C1   N1    single    1.453  0.020  1.453
 0DI  C1   C2    single    1.521  0.020  1.521
 0DI  F1   C19   single    1.341  0.020  1.341
 0DI  N1   C4    single    1.451  0.020  1.451
 0DI  N1   C14   single    1.344  0.020  1.344
 0DI  O1   C5    double    1.222  0.020  1.222
 0DI  CL1  C10   single    1.735  0.020  1.735
 0DI  C2   N2    single    1.452  0.020  1.452
 0DI  F2   C16   single    1.341  0.020  1.341
 0DI  N2   C3    single    1.452  0.020  1.452
 0DI  N2   C5    single    1.352  0.020  1.352
 0DI  O2   C14   double    1.220  0.020  1.220
 0DI  C3   C4    single    1.523  0.020  1.523
 0DI  N3   C6    single    1.445  0.020  1.445
 0DI  C5   C6    single    1.527  0.020  1.527
 0DI  C6   C7    single    1.550  0.020  1.550
 0DI  C7   C8    single    1.500  0.020  1.500
 0DI  C8   C9    aromatic  1.393  0.020  1.393
 0DI  C8   C13   aromatic  1.393  0.020  1.393
 0DI  C9   C10   aromatic  1.385  0.020  1.385
 0DI  C10  C11   aromatic  1.386  0.020  1.386
 0DI  C11  C12   aromatic  1.387  0.020  1.387
 0DI  C12  C13   aromatic  1.388  0.020  1.388
 0DI  C14  C15   single    1.501  0.020  1.501
 0DI  C15  C16   aromatic  1.383  0.020  1.383
 0DI  C15  C20   aromatic  1.390  0.020  1.390
 0DI  C16  C17   aromatic  1.381  0.020  1.381
 0DI  C17  C18   aromatic  1.386  0.020  1.386
 0DI  C18  C19   aromatic  1.382  0.020  1.382
 0DI  C19  C20   aromatic  1.380  0.020  1.380
 0DI  C1   H1    single    0.970  0.020  1.090
 0DI  C1   H1A   single    0.970  0.020  1.090
 0DI  C2   H2    single    0.970  0.020  1.090
 0DI  C2   H2A   single    0.970  0.020  1.090
 0DI  C3   H3    single    0.970  0.020  1.090
 0DI  C3   H3A   single    0.970  0.020  1.090
 0DI  N3   HN3   single    0.890  0.020  1.040
 0DI  N3   HN3A  single    0.890  0.020  1.040
 0DI  C4   H4    single    0.970  0.020  1.090
 0DI  C4   H4A   single    0.970  0.020  1.090
 0DI  C6   H6    single    0.970  0.020  1.090
 0DI  C7   H7    single    0.970  0.020  1.090
 0DI  C7   H7A   single    0.970  0.020  1.090
 0DI  C9   H9    single    0.930  0.020  1.080
 0DI  C11  H11   single    0.930  0.020  1.080
 0DI  C12  H12   single    0.930  0.020  1.080
 0DI  C13  H13   single    0.930  0.020  1.080
 0DI  C17  H17   single    0.930  0.020  1.080
 0DI  C18  H18   single    0.930  0.020  1.080
 0DI  C20  H20   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
 0DI  H1A   C1   H1   107.64  3.000
 0DI  H1A   C1   C2   109.28  3.000
 0DI  H1    C1   C2   109.85  3.000
 0DI  H1A   C1   N1   110.88  3.000
 0DI  H1    C1   N1   109.17  3.000
 0DI  C2    C1   N1   109.98  3.000
 0DI  C14   N1   C4   121.16  3.000
 0DI  C14   N1   C1   125.24  3.000
 0DI  C4    N1   C1   113.32  3.000
 0DI  H2A   C2   H2   108.03  3.000
 0DI  H2A   C2   N2   109.07  3.000
 0DI  H2    C2   N2   109.98  3.000
 0DI  H2A   C2   C1   109.51  3.000
 0DI  H2    C2   C1   109.81  3.000
 0DI  N2    C2   C1   110.40  3.000
 0DI  C5    N2   C3   126.81  3.000
 0DI  C5    N2   C2   120.63  3.000
 0DI  C3    N2   C2   112.50  3.000
 0DI  H3A   C3   H3   107.06  3.000
 0DI  H3A   C3   C4   109.54  3.000
 0DI  H3    C3   C4   108.86  3.000
 0DI  H3A   C3   N2   109.08  3.000
 0DI  H3    C3   N2   111.76  3.000
 0DI  C4    C3   N2   110.46  3.000
 0DI  HN3A  N3   HN3  106.71  3.000
 0DI  HN3A  N3   C6   110.58  3.000
 0DI  HN3   N3   C6   109.46  3.000
 0DI  H4A   C4   H4   107.99  3.000
 0DI  H4A   C4   C3   109.88  3.000
 0DI  H4    C4   C3   109.89  3.000
 0DI  H4A   C4   N1   108.47  3.000
 0DI  H4    C4   N1   110.00  3.000
 0DI  C3    C4   N1   110.55  3.000
 0DI  C6    C5   N2   118.42  3.000
 0DI  C6    C5   O1   119.49  3.000
 0DI  N2    C5   O1   122.05  3.000
 0DI  H6    C6   C7   108.65  3.000
 0DI  H6    C6   C5   110.36  3.000
 0DI  C7    C6   C5   107.79  3.000
 0DI  H6    C6   N3   106.49  3.000
 0DI  C7    C6   N3   114.93  3.000
 0DI  C5    C6   N3   108.60  3.000
 0DI  H7A   C7   H7   106.48  3.000
 0DI  H7A   C7   C8   110.02  3.000
 0DI  H7    C7   C8   109.38  3.000
 0DI  H7A   C7   C6   108.59  3.000
 0DI  H7    C7   C6   110.33  3.000
 0DI  C8    C7   C6   111.89  3.000
 0DI  C13   C8   C9   118.83  3.000
 0DI  C13   C8   C7   121.27  3.000
 0DI  C9    C8   C7   119.87  3.000
 0DI  H9    C9   C10  119.98  3.000
 0DI  H9    C9   C8   120.12  3.000
 0DI  C10   C9   C8   119.90  3.000
 0DI  C11   C10  C9   121.55  3.000
 0DI  C11   C10  CL1  119.34  3.000
 0DI  C9    C10  CL1  119.11  3.000
 0DI  H11   C11  C12  120.79  3.000
 0DI  H11   C11  C10  120.78  3.000
 0DI  C12   C11  C10  118.43  3.000
 0DI  H12   C12  C13  119.99  3.000
 0DI  H12   C12  C11  119.36  3.000
 0DI  C13   C12  C11  120.65  3.000
 0DI  H13   C13  C12  119.64  3.000
 0DI  H13   C13  C8   119.72  3.000
 0DI  C12   C13  C8   120.64  3.000
 0DI  C15   C14  O2   119.23  3.000
 0DI  C15   C14  N1   116.55  3.000
 0DI  O2    C14  N1   124.19  3.000
 0DI  C20   C15  C16  118.74  3.000
 0DI  C20   C15  C14  120.67  3.000
 0DI  C16   C15  C14  120.42  3.000
 0DI  C17   C16  C15  122.19  3.000
 0DI  C17   C16  F2   119.39  3.000
 0DI  C15   C16  F2   118.42  3.000
 0DI  H17   C17  C18  120.57  3.000
 0DI  H17   C17  C16  120.39  3.000
 0DI  C18   C17  C16  119.04  3.000
 0DI  H18   C18  C19  120.60  3.000
 0DI  H18   C18  C17  120.53  3.000
 0DI  C19   C18  C17  118.86  3.000
 0DI  C20   C19  C18  122.21  3.000
 0DI  C20   C19  F1   118.76  3.000
 0DI  C18   C19  F1   119.03  3.000
 0DI  H20   C20  C19  120.41  3.000
 0DI  H20   C20  C15  120.64  3.000
 0DI  C19   C20  C15  118.95  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
 0DI  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 0DI  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 0DI  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 0DI  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 0DI  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 0DI  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 0DI  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 0DI  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 0DI  CONST_09  C19  C20  C15  C16     0.00   0.0  0
 0DI  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 0DI  CONST_11  C20  C15  C16  C17     0.00   0.0  0
 0DI  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 0DI  CONST_13  C17  C18  C19  F1    180.00   0.0  0
 0DI  CONST_14  C15  C20  C19  F1    180.00   0.0  0
 0DI  CONST_15  C8   C9   C10  CL1   180.00   0.0  0
 0DI  CONST_16  C12  C11  C10  CL1   180.00   0.0  0
 0DI  CONST_17  C20  C15  C16  F2    180.00   0.0  0
 0DI  CONST_18  C18  C17  C16  F2    180.00   0.0  0
 0DI  CONST_19  C10  C9   C8   C7    180.00   0.0  0
 0DI  CONST_20  C12  C13  C8   C7    180.00   0.0  0
 0DI  CONST_21  C17  C16  C15  C14   180.00   0.0  0
 0DI  CONST_22  C19  C20  C15  C14   180.00   0.0  0
 0DI  CONST_23  C15  C14  N1   C1      0.00   0.0  0
 0DI  CONST_24  C15  C14  N1   C4    180.00   0.0  0
 0DI  CONST_25  H12  C12  C13  C8    180.00   0.0  0
 0DI  CONST_26  H13  C13  C8   C9    180.00   0.0  0
 0DI  CONST_27  H11  C11  C10  C9    180.00   0.0  0
 0DI  CONST_28  H9   C9   C10  C11   180.00   0.0  0
 0DI  CONST_29  H17  C17  C16  C15   180.00   0.0  0
 0DI  CONST_30  H20  C20  C15  C16   180.00   0.0  0
 0DI  CONST_31  H18  C18  C17  C16   180.00   0.0  0
 0DI  CONST_32  O2   C14  N1   C1    180.00   0.0  0
 0DI  CONST_33  C2   N2   C5   O1      0.00   0.0  0
 0DI  CONST_34  C3   N2   C5   O1    180.00   0.0  0
 0DI  CONST_35  C6   C5   N2   C2    180.00   0.0  0
 0DI  CONST_36  C4   N1   C14  O2      0.00   0.0  0
 0DI  CONST_37  C6   C5   N2   C3      0.00   0.0  0
 0DI  Var_01    C3   C4   N1   C1     55.04  30.0  1
 0DI  Var_02    C3   N2   C2   C1    -57.06  30.0  1
 0DI  Var_03    N2   C2   C1   N1     55.23  30.0  1
 0DI  Var_04    N2   C3   C4   N1    -53.81  30.0  1
 0DI  Var_05    C4   N1   C1   C2    -55.62  30.0  1
 0DI  Var_06    C4   C3   N2   C2     56.19  30.0  1
 0DI  Var_07    C16  C15  C14  N1   -106.68  30.0  2
 0DI  Var_08    C9   C8   C7   C6     85.73  30.0  2

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
 0DI  chir_01  C6  N3  C5  C7  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
 0DI  plan-1  CL1  0.020
 0DI  plan-1  C7   0.020
 0DI  plan-1  C8   0.020
 0DI  plan-1  C9   0.020
 0DI  plan-1  C10  0.020
 0DI  plan-1  C11  0.020
 0DI  plan-1  C12  0.020
 0DI  plan-1  C13  0.020
 0DI  plan-1  H9   0.020
 0DI  plan-1  H11  0.020
 0DI  plan-1  H12  0.020
 0DI  plan-1  H13  0.020
 0DI  plan-2  F1   0.020
 0DI  plan-2  F2   0.020
 0DI  plan-2  C14  0.020
 0DI  plan-2  C15  0.020
 0DI  plan-2  C16  0.020
 0DI  plan-2  C17  0.020
 0DI  plan-2  C18  0.020
 0DI  plan-2  C19  0.020
 0DI  plan-2  C20  0.020
 0DI  plan-2  H17  0.020
 0DI  plan-2  H18  0.020
 0DI  plan-2  H20  0.020
 0DI  plan-3  C1   0.020
 0DI  plan-3  N1   0.020
 0DI  plan-3  O2   0.020
 0DI  plan-3  C4   0.020
 0DI  plan-3  C14  0.020
 0DI  plan-3  C15  0.020
 0DI  plan-4  O1   0.020
 0DI  plan-4  C2   0.020
 0DI  plan-4  N2   0.020
 0DI  plan-4  C3   0.020
 0DI  plan-4  C5   0.020
 0DI  plan-4  C6   0.020

