# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 01:01:28 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3R)-3-amino-4-(4-chlorophenyl)-1-[(3R,4S)-3-(4-chlorophenyl)-4-(hydroxymethyl)pyrrolidin-1-yl]butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1C[C@@H](CO)[C@@H](C1)c2ccc(Cl)cc2)Cc3ccc(Cl)cc3
#
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
 A6M  A6M  (3R)-3-amino-4-(4-chlorophenyl)-1-[(3R,4S)-3-(4-chlorophenyl)-4-(hydroxymethyl)pyrrolidin-1-yl]butan-1-one  ligand  51  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A6M
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
 A6M  CL1   CL  CL    0  -0.140  -9.3222  -0.4824   0.7204
 A6M  C18   C   CR6   0  -0.060  -7.7084   0.0227   0.3252
 A6M  C17   C   CR16  0  -0.198  -6.9905   0.7858   1.2317
 A6M  C16   C   CR16  0  -0.319  -5.7038   1.1869   0.9009
 A6M  C19   C   CR16  0  -0.201  -7.1596  -0.3398  -0.8946
 A6M  C20   C   CR16  0  -0.314  -5.8696   0.0680  -1.2020
 A6M  C15   C   CR6   0   0.176  -5.1223   0.8381  -0.3153
 A6M  C14   C   CH2   0  -0.519  -3.7184   1.2610  -0.6319
 A6M  C     C   CH1   0  -0.080  -2.6693   0.2913  -0.0737
 A6M  N     N   NH2   0  -0.781  -2.8432  -1.0115  -0.6907
 A6M  C1    C   CH2   0  -0.601  -1.2751   0.8978  -0.2552
 A6M  C2    C   C     0   0.576  -0.1787   0.1252   0.4489
 A6M  O     O   O     0  -0.512  -0.4102  -0.8544   1.1520
 A6M  N1    N   NT    0  -0.486   1.0745   0.5775   0.2807
 A6M  C3    C   CH2   0  -0.247   1.4753   1.7246  -0.5226
 A6M  C4    C   CH1   0  -0.292   2.9840   1.5505  -0.6588
 A6M  C6    C   CH1   0  -0.412   3.3712   0.8817   0.6672
 A6M  C5    C   CH2   0  -0.130   3.7339   2.8390  -0.9059
 A6M  O1    O   OH1   0  -0.671   3.2662   3.4101  -2.1066
 A6M  C7    C   CH2   0  -0.218   2.2024  -0.0693   0.9341
 A6M  C8    C   CR6   0   0.209   4.7191   0.2174   0.6662
 A6M  C13   C   CR16  0  -0.336   5.7151   0.6324   1.5436
 A6M  C12   C   CR16  0  -0.192   6.9711   0.0403   1.5458
 A6M  C11   C   CR6   0  -0.060   7.2327  -0.9838   0.6522
 A6M  CL    CL  CL    0  -0.132   8.7977  -1.7315   0.6406
 A6M  C10   C   CR16  0  -0.193   6.2604  -1.4213  -0.2351
 A6M  C9    C   CR16  0  -0.325   5.0133  -0.8180  -0.2200
 A6M  H17   H   HCR6  0   0.275  -7.4249   1.0694   2.1810
 A6M  H19   H   HCR6  0   0.275  -7.7268  -0.9345  -1.5979
 A6M  H16   H   HCR6  0   0.255  -5.1452   1.7872   1.6097
 A6M  H20   H   HCR6  0   0.251  -5.4446  -0.2165  -2.1562
 A6M  H141  H   HCH2  0   0.243  -3.5843   1.3445  -1.7152
 A6M  H142  H   HCH2  0   0.249  -3.5352   2.2562  -0.2199
 A6M  H     H   HCH1  0   0.234  -2.8582   0.1743   0.9978
 A6M  HN1   H   HNH2  0   0.332  -2.6227  -0.9489  -1.6784
 A6M  HN2   H   HNH2  0   0.347  -2.1783  -1.6612  -0.2919
 A6M  H11C  H   HCH2  0   0.264  -1.0504   0.9651  -1.3259
 A6M  H12C  H   HCH2  0   0.268  -1.2572   1.9303   0.1117
 A6M  H71C  H   HCH2  0   0.256   2.0266  -0.2014   2.0021
 A6M  H72C  H   HCH2  0   0.240   2.3811  -1.0605   0.5066
 A6M  H31C  H   HCH2  0   0.260   0.9739   1.7306  -1.4895
 A6M  H32C  H   HCH2  0   0.239   1.2319   2.6655  -0.0154
 A6M  H6    H   HCH1  0   0.271   3.3676   1.6524   1.4469
 A6M  H4    H   HCH1  0   0.257   3.1826   0.8524  -1.4799
 A6M  H51C  H   HCH2  0   0.193   3.5773   3.5107  -0.0501
 A6M  H52C  H   HCH2  0   0.210   4.8102   2.6274  -0.9515
 A6M  H1    H   HOH1  0   0.456   3.7437   4.2312  -2.2550
 A6M  H13   H   HCR6  0   0.264   5.5152   1.4337   2.2444
 A6M  H9    H   HCR6  0   0.259   4.2624  -1.1691  -0.9178
 A6M  H12   H   HCR6  0   0.279   7.7314   0.3782   2.2367
 A6M  H10   H   HCR6  0   0.279   6.4684  -2.2222  -0.9316

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
 A6M  CL1  C18   single    1.737  0.020  1.737
 A6M  C18  C17   aromatic  1.385  0.020  1.385
 A6M  C18  C19   aromatic  1.386  0.020  1.386
 A6M  C17  C16   aromatic  1.388  0.020  1.388
 A6M  C16  C15   aromatic  1.392  0.020  1.392
 A6M  C19  C20   aromatic  1.387  0.020  1.387
 A6M  C20  C15   aromatic  1.392  0.020  1.392
 A6M  C15  C14   single    1.500  0.020  1.500
 A6M  C14  C     single    1.534  0.020  1.534
 A6M  C    N     single    1.452  0.020  1.452
 A6M  C    C1    single    1.531  0.020  1.531
 A6M  C1   C2    single    1.515  0.020  1.515
 A6M  C2   O     double    1.228  0.020  1.228
 A6M  C2   N1    single    1.343  0.020  1.343
 A6M  N1   C7    single    1.455  0.020  1.455
 A6M  N1   C3    single    1.457  0.020  1.457
 A6M  C7   C6    single    1.530  0.020  1.530
 A6M  C6   C4    single    1.535  0.020  1.535
 A6M  C6   C8    single    1.503  0.020  1.503
 A6M  C4   C5    single    1.511  0.020  1.511
 A6M  C4   C3    single    1.525  0.020  1.525
 A6M  C5   O1    single    1.409  0.020  1.409
 A6M  C8   C13   aromatic  1.391  0.020  1.391
 A6M  C8   C9    aromatic  1.394  0.020  1.394
 A6M  C13  C12   aromatic  1.389  0.020  1.389
 A6M  C12  C11   aromatic  1.384  0.020  1.384
 A6M  C11  CL    single    1.734  0.020  1.734
 A6M  C11  C10   aromatic  1.387  0.020  1.387
 A6M  C10  C9    aromatic  1.385  0.020  1.385
 A6M  C17  H17   single    0.930  0.020  1.080
 A6M  C19  H19   single    0.930  0.020  1.080
 A6M  C16  H16   single    0.930  0.020  1.080
 A6M  C20  H20   single    0.930  0.020  1.080
 A6M  C14  H141  single    0.970  0.020  1.090
 A6M  C14  H142  single    0.970  0.020  1.090
 A6M  C    H     single    0.970  0.020  1.090
 A6M  N    HN1   single    0.890  0.020  1.040
 A6M  N    HN2   single    0.890  0.020  1.040
 A6M  C1   H11C  single    0.970  0.020  1.090
 A6M  C1   H12C  single    0.970  0.020  1.090
 A6M  C7   H71C  single    0.970  0.020  1.090
 A6M  C7   H72C  single    0.970  0.020  1.090
 A6M  C3   H31C  single    0.970  0.020  1.090
 A6M  C3   H32C  single    0.970  0.020  1.090
 A6M  C6   H6    single    0.970  0.020  1.090
 A6M  C4   H4    single    0.970  0.020  1.090
 A6M  C5   H51C  single    0.970  0.020  1.090
 A6M  C5   H52C  single    0.970  0.020  1.090
 A6M  O1   H1    single    0.850  0.020  0.980
 A6M  C13  H13   single    0.930  0.020  1.080
 A6M  C9   H9    single    0.930  0.020  1.080
 A6M  C12  H12   single    0.930  0.020  1.080
 A6M  C10  H10   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
 A6M  C19   C18  C17   120.98  3.000
 A6M  C19   C18  CL1   119.49  3.000
 A6M  C17   C18  CL1   119.53  3.000
 A6M  H17   C17  C16   120.38  3.000
 A6M  H17   C17  C18   120.69  3.000
 A6M  C16   C17  C18   118.93  3.000
 A6M  H16   C16  C15   119.65  3.000
 A6M  H16   C16  C17   118.81  3.000
 A6M  C15   C16  C17   121.53  3.000
 A6M  H19   C19  C20   120.34  3.000
 A6M  H19   C19  C18   120.56  3.000
 A6M  C20   C19  C18   119.10  3.000
 A6M  H20   C20  C15   119.73  3.000
 A6M  H20   C20  C19   118.89  3.000
 A6M  C15   C20  C19   121.38  3.000
 A6M  C14   C15  C20   121.60  3.000
 A6M  C14   C15  C16   120.30  3.000
 A6M  C20   C15  C16   118.08  3.000
 A6M  H142  C14  H141  106.45  3.000
 A6M  H142  C14  C     108.90  3.000
 A6M  H141  C14  C     108.94  3.000
 A6M  H142  C14  C15   109.52  3.000
 A6M  H141  C14  C15   110.18  3.000
 A6M  C     C14  C15   112.65  3.000
 A6M  H     C    C1    108.40  3.000
 A6M  H     C    N     107.43  3.000
 A6M  C1    C    N     114.46  3.000
 A6M  H     C    C14   107.80  3.000
 A6M  C1    C    C14   109.22  3.000
 A6M  N     C    C14   109.31  3.000
 A6M  HN2   N    HN1   106.30  3.000
 A6M  HN2   N    C     109.27  3.000
 A6M  HN1   N    C     109.42  3.000
 A6M  H12C  C1   H11C  105.42  3.000
 A6M  H12C  C1   C2    108.24  3.000
 A6M  H11C  C1   C2    109.69  3.000
 A6M  H12C  C1   C     110.39  3.000
 A6M  H11C  C1   C     109.07  3.000
 A6M  C2    C1   C     113.70  3.000
 A6M  N1    C2   O     121.08  3.000
 A6M  N1    C2   C1    116.46  3.000
 A6M  O     C2   C1    122.46  3.000
 A6M  C7    N1   C3    112.60  3.000
 A6M  C3    N1   C2    126.23  3.000
 A6M  C7    N1   C2    121.17  3.000
 A6M  H32C  C3   H31C  107.69  3.000
 A6M  H32C  C3   C4    111.04  3.000
 A6M  H31C  C3   C4    112.14  3.000
 A6M  H32C  C3   N1    111.08  3.000
 A6M  H31C  C3   N1    111.54  3.000
 A6M  C4    C3   N1    103.39  3.000
 A6M  H4    C4   C5    109.31  3.000
 A6M  H4    C4   C6    108.91  3.000
 A6M  C5    C4   C6    112.81  3.000
 A6M  H4    C4   C3    108.61  3.000
 A6M  C5    C4   C3    114.09  3.000
 A6M  C6    C4   C3    102.84  3.000
 A6M  H6    C6   C8    108.31  3.000
 A6M  H6    C6   C7    108.08  3.000
 A6M  C8    C6   C7    114.24  3.000
 A6M  H6    C6   C4    107.90  3.000
 A6M  C8    C6   C4    114.73  3.000
 A6M  C7    C6   C4    103.23  3.000
 A6M  H52C  C5   H51C  106.84  3.000
 A6M  H52C  C5   O1    111.60  3.000
 A6M  H51C  C5   O1    111.62  3.000
 A6M  H52C  C5   C4    109.21  3.000
 A6M  H51C  C5   C4    108.84  3.000
 A6M  O1    C5   C4    108.67  3.000
 A6M  H1    O1   C5    108.23  3.000
 A6M  H72C  C7   H71C  107.41  3.000
 A6M  H72C  C7   C6    111.73  3.000
 A6M  H71C  C7   C6    111.67  3.000
 A6M  H72C  C7   N1    110.72  3.000
 A6M  H71C  C7   N1    111.63  3.000
 A6M  C6    C7   N1    103.74  3.000
 A6M  C9    C8   C13   118.13  3.000
 A6M  C9    C8   C6    121.19  3.000
 A6M  C13   C8   C6    120.67  3.000
 A6M  H13   C13  C12   118.77  3.000
 A6M  H13   C13  C8    119.79  3.000
 A6M  C12   C13  C8    121.44  3.000
 A6M  H12   C12  C11   120.71  3.000
 A6M  H12   C12  C13   120.25  3.000
 A6M  C11   C12  C13   119.04  3.000
 A6M  C10   C11  CL    119.49  3.000
 A6M  C10   C11  C12   120.92  3.000
 A6M  CL    C11  C12   119.59  3.000
 A6M  H10   C10  C9    120.17  3.000
 A6M  H10   C10  C11   120.71  3.000
 A6M  C9    C10  C11   119.12  3.000
 A6M  H9    C9   C10   118.41  3.000
 A6M  H9    C9   C8    120.25  3.000
 A6M  C10   C9   C8    121.35  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
 A6M  CONST_01  C15  C16  C17  C18    0.00   0.0  0
 A6M  CONST_02  C15  C20  C19  C18    0.00   0.0  0
 A6M  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 A6M  CONST_04  C20  C15  C16  C17    0.00   0.0  0
 A6M  CONST_05  C19  C18  C17  C16    0.00   0.0  0
 A6M  CONST_06  C19  C20  C15  C16    0.00   0.0  0
 A6M  CONST_07  C11  C12  C13  C8     0.00   0.0  0
 A6M  CONST_08  C11  C10  C9   C8     0.00   0.0  0
 A6M  CONST_09  C10  C9   C8   C13    0.00   0.0  0
 A6M  CONST_10  C10  C11  C12  C13    0.00   0.0  0
 A6M  CONST_11  C9   C8   C13  C12    0.00   0.0  0
 A6M  CONST_12  C9   C10  C11  C12    0.00   0.0  0
 A6M  CONST_13  C12  C13  C8   C6   180.00   0.0  0
 A6M  CONST_14  C10  C9   C8   C6   180.00   0.0  0
 A6M  CONST_15  C16  C17  C18  CL1  180.00   0.0  0
 A6M  CONST_16  C20  C19  C18  CL1  180.00   0.0  0
 A6M  CONST_17  C14  C15  C16  C17  180.00   0.0  0
 A6M  CONST_18  C14  C15  C20  C19  180.00   0.0  0
 A6M  CONST_19  CL   C11  C12  C13  180.00   0.0  0
 A6M  CONST_20  C9   C10  C11  CL   180.00   0.0  0
 A6M  CONST_21  H16  C16  C17  C18  180.00   0.0  0
 A6M  CONST_22  H20  C20  C19  C18  180.00   0.0  0
 A6M  CONST_23  H19  C19  C18  C17  180.00   0.0  0
 A6M  CONST_24  H17  C17  C18  C19  180.00   0.0  0
 A6M  CONST_25  H13  C13  C8   C6     0.00   0.0  0
 A6M  CONST_26  H9   C9   C8   C6     0.00   0.0  0
 A6M  CONST_27  H12  C12  C13  C8   180.00   0.0  0
 A6M  CONST_28  H10  C10  C9   C8   180.00   0.0  0
 A6M  CONST_29  C7   N1   C2   C1   180.00   0.0  0
 A6M  CONST_30  C3   N1   C2   C1     0.00   0.0  0
 A6M  CONST_31  C7   N1   C2   O      0.00   0.0  0
 A6M  CONST_32  C3   N1   C2   O    180.00   0.0  0
 A6M  Var_01    C6   C7   N1   C3     8.45  30.0  1
 A6M  Var_02    C7   N1   C3   C4    15.22  30.0  1
 A6M  Var_03    C    C14  C15  C16   85.10  30.0  2
 A6M  Var_04    N1   C2   C1   C    177.34  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
 A6M  chir_01  C   C14  N   C1  negativ
 A6M  chir_02  C4  C6   C5  C3  positiv
 A6M  chir_03  C6  C8   C4  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
 A6M  plan-1  CL1  0.020
 A6M  plan-1  C18  0.020
 A6M  plan-1  C17  0.020
 A6M  plan-1  C16  0.020
 A6M  plan-1  C19  0.020
 A6M  plan-1  C20  0.020
 A6M  plan-1  C15  0.020
 A6M  plan-1  C14  0.020
 A6M  plan-1  H17  0.020
 A6M  plan-1  H19  0.020
 A6M  plan-1  H16  0.020
 A6M  plan-1  H20  0.020
 A6M  plan-2  C6   0.020
 A6M  plan-2  C8   0.020
 A6M  plan-2  C13  0.020
 A6M  plan-2  C12  0.020
 A6M  plan-2  C11  0.020
 A6M  plan-2  CL   0.020
 A6M  plan-2  C10  0.020
 A6M  plan-2  C9   0.020
 A6M  plan-2  H13  0.020
 A6M  plan-2  H9   0.020
 A6M  plan-2  H12  0.020
 A6M  plan-2  H10  0.020
 A6M  plan-3  C1   0.020
 A6M  plan-3  C2   0.020
 A6M  plan-3  O    0.020
 A6M  plan-3  N1   0.020
 A6M  plan-3  C3   0.020
 A6M  plan-3  C7   0.020

