# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 20:07:05 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2R)-2-(4-methoxyphenyl)-2-[3-(pyrimidin-5-yl)phenyl]-3,4-dihydro-2H-pyrrol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@]2(CCC(=N2)N)c3cccc(c3)c4cncnc4
#
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
 54M  54M  (2R)-2-(4-methoxyphenyl)-2-[3-(pyrimidin-5-yl)phenyl]-3,4-dihydro-2H-pyrrol-5-amine  ligand  46  26  .  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_54M
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
 54M  C15   C  CH3   0  -0.435   4.6412   3.8333   0.9077
 54M  O14   O  O2    0  -0.473   4.3166   3.1337  -0.2760
 54M  C2    C  CR6   0   0.363   3.5355   2.0389  -0.1790
 54M  C3    C  CR16  0  -0.328   3.2248   1.3897  -1.3770
 54M  C4    C  CR16  0  -0.276   2.4294   0.2612  -1.3700
 54M  C1    C  CR16  0  -0.365   3.0313   1.5294   1.0114
 54M  C6    C  CR16  0  -0.314   2.2328   0.3876   0.9963
 54M  C5    C  CR6   0   0.157   1.9187  -0.2696  -0.1830
 54M  C7    C  CR5   0  -0.086   1.0220  -1.5102  -0.2092
 54M  C19   C  CH2   0  -0.469   1.7499  -2.7022  -0.8789
 54M  C17   C  CR5   0   0.449   1.5119  -2.9487   1.4185
 54M  N16   N  N     0  -0.430   0.7394  -1.9646   1.1459
 54M  N20   N  NH2   0  -0.830   1.5824  -3.5424   2.6268
 54M  C8    C  CR6   0   0.191  -0.2730  -1.1200  -0.9050
 54M  C13   C  CR16  0  -0.365  -1.2739  -0.4809  -0.1796
 54M  C9    C  CR16  0  -0.339  -0.4702  -1.3290  -2.2662
 54M  C10   C  CR16  0  -0.222  -1.6412  -0.9088  -2.8846
 54M  C11   C  CR16  0  -0.327  -2.6312  -0.2746  -2.1543
 54M  C12   C  CR6   0   0.115  -2.4520  -0.0538  -0.7878
 54M  C21   C  CR6   0  -0.045  -3.4919   0.6241   0.0010
 54M  C14   C  CH2   0  -0.542   2.4304  -3.3730   0.3051
 54M  C26   C  CR16  0  -0.049  -4.2407   1.6828  -0.5058
 54M  N21   N  N     0  -0.387  -5.1809   2.2978   0.1970
 54M  C24   C  CR16  0   0.048  -5.3813   1.8620   1.4311
 54M  N23   N  N     0  -0.387  -4.7322   0.8719   2.0241
 54M  C22   C  CR16  0  -0.049  -3.7988   0.2601   1.3095
 54M  H151  H  HCH3  0   0.227   3.7509   4.2123   1.4168
 54M  H152  H  HCH3  0   0.227   5.2073   3.2131   1.6078
 54M  H153  H  HCH3  0   0.258   5.2592   4.6770   0.6100
 54M  H3    H  HCR6  0   0.258   3.6098   1.7790  -2.3115
 54M  H1    H  HCR6  0   0.273   3.2436   1.9987   1.9626
 54M  H4    H  HCR6  0   0.244   2.2034  -0.2106  -2.3188
 54M  H6    H  HCR6  0   0.250   1.8506   0.0123   1.9356
 54M  H191  H  HCH2  0   0.249   1.0160  -3.3865  -1.3099
 54M  H192  H  HCH2  0   0.251   2.4388  -2.4150  -1.6720
 54M  H141  H  HCH2  0   0.266   2.5189  -4.4557   0.2086
 54M  H142  H  HCH2  0   0.270   3.4332  -2.9778   0.4918
 54M  H201  H  HNH2  0   0.386   0.8783  -3.3222   3.3118
 54M  H202  H  HNH2  0   0.395   1.9743  -4.4657   2.6896
 54M  H13   H  HCR6  0   0.249  -1.1195  -0.3010   0.8769
 54M  H9    H  HCR6  0   0.258   0.2850  -1.8266  -2.8616
 54M  H10   H  HCR6  0   0.258  -1.7847  -1.0886  -3.9421
 54M  H11   H  HCR6  0   0.257  -3.5493   0.0275  -2.6425
 54M  H26   H  HCR6  0   0.276  -4.0621   2.0546  -1.5095
 54M  H22   H  HCR6  0   0.275  -3.2786  -0.5627   1.7892
 54M  H24   H  HCR6  0   0.267  -6.1487   2.3629   2.0102

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
 54M  C15  O14   single    1.413  0.020  1.413
 54M  O14  C2    single    1.348  0.020  1.348
 54M  C2   C3    aromatic  1.398  0.020  1.398
 54M  C2   C1    aromatic  1.390  0.020  1.390
 54M  C3   C4    aromatic  1.381  0.020  1.381
 54M  C4   C5    aromatic  1.397  0.020  1.397
 54M  C1   C6    aromatic  1.393  0.020  1.393
 54M  C6   C5    aromatic  1.386  0.020  1.386
 54M  C5   C7    single    1.531  0.020  1.531
 54M  C7   C19   single    1.549  0.020  1.549
 54M  C7   N16   single    1.457  0.020  1.457
 54M  C7   C8    single    1.521  0.020  1.521
 54M  C19  C14   single    1.521  0.020  1.521
 54M  C17  N16   double    1.280  0.020  1.280
 54M  C17  N20   single    1.348  0.020  1.348
 54M  C17  C14   single    1.504  0.020  1.504
 54M  C8   C13   aromatic  1.392  0.020  1.392
 54M  C8   C9    aromatic  1.391  0.020  1.391
 54M  C13  C12   aromatic  1.393  0.020  1.393
 54M  C9   C10   aromatic  1.389  0.020  1.389
 54M  C10  C11   aromatic  1.384  0.020  1.384
 54M  C11  C12   aromatic  1.396  0.020  1.396
 54M  C12  C21   single    1.471  0.020  1.471
 54M  C21  C26   aromatic  1.392  0.020  1.392
 54M  C21  C22   aromatic  1.392  0.020  1.392
 54M  C26  N21   aromatic  1.325  0.020  1.325
 54M  N21  C24   aromatic  1.324  0.020  1.324
 54M  C24  N23   aromatic  1.324  0.020  1.324
 54M  N23  C22   aromatic  1.325  0.020  1.325
 54M  C15  H151  single    0.970  0.020  1.090
 54M  C15  H152  single    0.970  0.020  1.090
 54M  C15  H153  single    0.970  0.020  1.090
 54M  C3   H3    single    0.930  0.020  1.080
 54M  C1   H1    single    0.930  0.020  1.080
 54M  C4   H4    single    0.930  0.020  1.080
 54M  C6   H6    single    0.930  0.020  1.080
 54M  C19  H191  single    0.970  0.020  1.090
 54M  C19  H192  single    0.970  0.020  1.090
 54M  C14  H141  single    0.970  0.020  1.090
 54M  C14  H142  single    0.970  0.020  1.090
 54M  N20  H201  single    0.890  0.020  1.040
 54M  N20  H202  single    0.890  0.020  1.040
 54M  C13  H13   single    0.930  0.020  1.080
 54M  C9   H9    single    0.930  0.020  1.080
 54M  C10  H10   single    0.930  0.020  1.080
 54M  C11  H11   single    0.930  0.020  1.080
 54M  C26  H26   single    0.930  0.020  1.080
 54M  C22  H22   single    0.930  0.020  1.080
 54M  C24  H24   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
 54M  H153  C15  H152  108.73  3.000
 54M  H153  C15  H151  108.75  3.000
 54M  H152  C15  H151  108.67  3.000
 54M  H153  C15  O14   106.58  3.000
 54M  H152  C15  O14   112.00  3.000
 54M  H151  C15  O14   112.01  3.000
 54M  C2    O14  C15   118.35  3.000
 54M  C1    C2   C3    118.90  3.000
 54M  C1    C2   O14   124.72  3.000
 54M  C3    C2   O14   116.38  3.000
 54M  H3    C3   C4    120.20  3.000
 54M  H3    C3   C2    119.57  3.000
 54M  C4    C3   C2    120.23  3.000
 54M  H4    C4   C5    120.15  3.000
 54M  H4    C4   C3    118.15  3.000
 54M  C5    C4   C3    121.70  3.000
 54M  H1    C1   C6    118.53  3.000
 54M  H1    C1   C2    121.53  3.000
 54M  C6    C1   C2    119.94  3.000
 54M  H6    C6   C5    119.63  3.000
 54M  H6    C6   C1    118.52  3.000
 54M  C5    C6   C1    121.85  3.000
 54M  C7    C5   C6    122.11  3.000
 54M  C7    C5   C4    120.50  3.000
 54M  C6    C5   C4    117.38  3.000
 54M  C8    C7   N16   109.90  3.000
 54M  C8    C7   C19   113.56  3.000
 54M  N16   C7   C19   104.67  3.000
 54M  C8    C7   C5    107.37  3.000
 54M  N16   C7   C5    110.51  3.000
 54M  C19   C7   C5    110.84  3.000
 54M  H192  C19  H191  107.63  3.000
 54M  H192  C19  C14   113.58  3.000
 54M  H191  C19  C14   109.35  3.000
 54M  H192  C19  C7    114.16  3.000
 54M  H191  C19  C7    109.70  3.000
 54M  C14   C19  C7    102.30  3.000
 54M  C14   C17  N20   120.48  3.000
 54M  C14   C17  N16   115.31  3.000
 54M  N20   C17  N16   124.11  3.000
 54M  C17   N16  C7    108.70  3.000
 54M  H202  N20  H201  115.54  3.000
 54M  H202  N20  C17   118.75  3.000
 54M  H201  N20  C17   118.49  3.000
 54M  C9    C8   C13   118.50  3.000
 54M  C9    C8   C7    121.99  3.000
 54M  C13   C8   C7    119.46  3.000
 54M  H13   C13  C12   119.71  3.000
 54M  H13   C13  C8    118.84  3.000
 54M  C12   C13  C8    121.44  3.000
 54M  H9    C9   C10   118.82  3.000
 54M  H9    C9   C8    120.54  3.000
 54M  C10   C9   C8    120.63  3.000
 54M  H10   C10  C11   119.80  3.000
 54M  H10   C10  C9    119.77  3.000
 54M  C11   C10  C9    120.44  3.000
 54M  H11   C11  C12   120.41  3.000
 54M  H11   C11  C10   119.76  3.000
 54M  C12   C11  C10   119.82  3.000
 54M  C21   C12  C11   120.47  3.000
 54M  C21   C12  C13   120.34  3.000
 54M  C11   C12  C13   119.18  3.000
 54M  C22   C21  C26   114.98  3.000
 54M  C22   C21  C12   122.64  3.000
 54M  C26   C21  C12   122.38  3.000
 54M  H142  C14  H141  107.41  3.000
 54M  H142  C14  C17   109.36  3.000
 54M  H141  C14  C17   113.27  3.000
 54M  H142  C14  C19   112.55  3.000
 54M  H141  C14  C19   113.90  3.000
 54M  C17   C14  C19   100.29  3.000
 54M  H26   C26  N21   116.63  3.000
 54M  H26   C26  C21   120.58  3.000
 54M  N21   C26  C21   122.78  3.000
 54M  C24   N21  C26   116.67  3.000
 54M  H24   C24  N23   116.96  3.000
 54M  H24   C24  N21   116.93  3.000
 54M  N23   C24  N21   126.11  3.000
 54M  C22   N23  C24   116.68  3.000
 54M  H22   C22  N23   116.70  3.000
 54M  H22   C22  C21   120.53  3.000
 54M  N23   C22  C21   122.77  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
 54M  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 54M  CONST_02  C5    C6   C1   C2     0.00   0.0  0
 54M  CONST_03  C6    C1   C2   C3     0.00   0.0  0
 54M  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 54M  CONST_05  C1    C2   C3   C4     0.00   0.0  0
 54M  CONST_06  C1    C6   C5   C4     0.00   0.0  0
 54M  CONST_07  C11   C12  C13  C8     0.00   0.0  0
 54M  CONST_08  C21   C12  C13  C8   180.00   0.0  0
 54M  CONST_09  C11   C10  C9   C8     0.00   0.0  0
 54M  CONST_10  C10   C9   C8   C13    0.00   0.0  0
 54M  CONST_11  C10   C11  C12  C13    0.00   0.0  0
 54M  CONST_14  C12   C13  C8   C9     0.00   0.0  0
 54M  CONST_15  C12   C11  C10  C9     0.00   0.0  0
 54M  CONST_16  C21   C12  C11  C10  180.00   0.0  0
 54M  CONST_19  N21   C26  C21  C12  180.00   0.0  0
 54M  CONST_20  N23   C22  C21  C12  180.00   0.0  0
 54M  CONST_21  C24   N21  C26  C21    0.00   0.0  0
 54M  CONST_22  C24   N23  C22  C21    0.00   0.0  0
 54M  CONST_23  N23   C22  C21  C26    0.00   0.0  0
 54M  CONST_24  N23   C24  N21  C26    0.00   0.0  0
 54M  CONST_25  C22   C21  C26  N21    0.00   0.0  0
 54M  CONST_26  C22   N23  C24  N21    0.00   0.0  0
 54M  CONST_27  C7    C5   C4   C3   180.00   0.0  0
 54M  CONST_28  C7    C5   C6   C1   180.00   0.0  0
 54M  CONST_29  C12   C13  C8   C7   180.00   0.0  0
 54M  CONST_30  C10   C9   C8   C7   180.00   0.0  0
 54M  CONST_31  C14   C17  N16  C7     0.00   0.0  0
 54M  CONST_32  C4    C3   C2   O14  180.00   0.0  0
 54M  CONST_33  C6    C1   C2   O14  180.00   0.0  0
 54M  CONST_34  N20   C17  N16  C7   180.00   0.0  0
 54M  CONST_35  H4    C4   C3   C2   180.00   0.0  0
 54M  CONST_36  H6    C6   C1   C2   180.00   0.0  0
 54M  CONST_37  H1    C1   C2   C3   180.00   0.0  0
 54M  CONST_38  H3    C3   C2   C1   180.00   0.0  0
 54M  CONST_39  H13   C13  C8   C7     0.00   0.0  0
 54M  CONST_40  H9    C9   C8   C7     0.00   0.0  0
 54M  CONST_41  H10   C10  C9   C8   180.00   0.0  0
 54M  CONST_42  H11   C11  C12  C13  180.00   0.0  0
 54M  CONST_43  H26   C26  C21  C12    0.00   0.0  0
 54M  CONST_44  H22   C22  C21  C12    0.00   0.0  0
 54M  CONST_45  H24   C24  N21  C26  180.00   0.0  0
 54M  CONST_46  H201  N20  C17  N16    0.00   0.0  0
 54M  Var_01    C17   C14  C19  C7    26.28  30.0  1
 54M  Var_02    N16   C17  C14  C19  -16.99  30.0  1
 54M  Var_03    C3    C2   O14  C15  179.13  30.0  2
 54M  Var_04    H151  C15  O14  C2   -60.51  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
 54M  chir_01  C7  C19  N16  C8  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
 54M  plan-1  O14   0.020
 54M  plan-1  C2    0.020
 54M  plan-1  C3    0.020
 54M  plan-1  C4    0.020
 54M  plan-1  C1    0.020
 54M  plan-1  C6    0.020
 54M  plan-1  C5    0.020
 54M  plan-1  C7    0.020
 54M  plan-1  H3    0.020
 54M  plan-1  H1    0.020
 54M  plan-1  H4    0.020
 54M  plan-1  H6    0.020
 54M  plan-2  C7    0.020
 54M  plan-2  C17   0.020
 54M  plan-2  N16   0.020
 54M  plan-2  N20   0.020
 54M  plan-2  C14   0.020
 54M  plan-2  H201  0.020
 54M  plan-2  H202  0.020
 54M  plan-3  C7    0.020
 54M  plan-3  C8    0.020
 54M  plan-3  C13   0.020
 54M  plan-3  C9    0.020
 54M  plan-3  C10   0.020
 54M  plan-3  C11   0.020
 54M  plan-3  C12   0.020
 54M  plan-3  C21   0.020
 54M  plan-3  H13   0.020
 54M  plan-3  H9    0.020
 54M  plan-3  H10   0.020
 54M  plan-3  H11   0.020
 54M  plan-4  C12   0.020
 54M  plan-4  C21   0.020
 54M  plan-4  C26   0.020
 54M  plan-4  N21   0.020
 54M  plan-4  C24   0.020
 54M  plan-4  N23   0.020
 54M  plan-4  C22   0.020
 54M  plan-4  H26   0.020
 54M  plan-4  H22   0.020
 54M  plan-4  H24   0.020

