# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:10:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3-{4-[(2S)-2-(aminomethyl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}phenyl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CN(CCO1)c2ncnc3[nH]cc(c4cccc(CO)c4)c23
#
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
 YM5  YM5  (3-{4-[(2S)-2-(aminomethyl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}phenyl)methanol  ligand  46  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YM5
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
 YM5  N01   N  NH2   0  -0.796   3.5977   2.4262   0.5577
 YM5  C02   C  CH2   0  -0.304   2.2953   2.0998   1.1130
 YM5  C03   C  CH1   0   0.037   1.2207   2.1114   0.0429
 YM5  C04   C  CH2   0  -0.318  -0.0848   1.5423   0.5711
 YM5  N05   N  NT    0  -0.498  -1.1170   1.6047  -0.4561
 YM5  C06   C  CR6   0   0.439  -2.2124   0.7950  -0.3449
 YM5  N07   N  N     0  -0.478  -3.4116   1.3464  -0.5211
 YM5  C08   C  CR16  0   0.035  -4.5064   0.6165  -0.3221
 YM5  N09   N  N     0  -0.442  -4.5732  -0.6351   0.0779
 YM5  C10   C  CR56  0   0.484  -3.3733  -1.2038   0.1877
 YM5  N11   N  NR15  0  -0.659  -3.1440  -2.4952   0.5168
 YM5  C12   C  CR15  0  -0.047  -1.8041  -2.7486   0.4360
 YM5  C13   C  CR5   0  -0.034  -1.1314  -1.6157   0.0680
 YM5  C14   C  CR6   0   0.015   0.3022  -1.5709  -0.2465
 YM5  C15   C  CR16  0  -0.316   0.7416  -1.0539  -1.4669
 YM5  C16   C  CR16  0  -0.225   2.0940  -1.0310  -1.7629
 YM5  C17   C  CR16  0  -0.314   3.0291  -1.5139  -0.8544
 YM5  C18   C  CR6   0   0.064   2.6083  -2.0410   0.3611
 YM5  C19   C  CH2   0  -0.185   3.5777  -2.5370   1.3996
 YM5  O20   O  OH1   0  -0.667   4.8376  -2.7626   0.8224
 YM5  C21   C  CR16  0  -0.343   1.2462  -2.0672   0.6490
 YM5  C22   C  CR56  0  -0.078  -2.1329  -0.5895  -0.0650
 YM5  C23   C  CH2   0  -0.316  -1.2957   2.9601  -0.9485
 YM5  C24   C  CH2   0  -0.191   0.0465   3.4873  -1.4234
 YM5  O25   O  O2    0  -0.486   1.0275   3.4341  -0.4141
 YM5  H011  H  HNH2  0   0.350   4.2685   2.5135   1.3101
 YM5  H012  H  HNH2  0   0.335   3.9224   1.6504  -0.0071
 YM5  H021  H  HCH2  0   0.204   2.2630   1.1168   1.6049
 YM5  H022  H  HCH2  0   0.227   2.0450   2.8377   1.8802
 YM5  H03   H  HCH1  0   0.218   1.5469   1.4774  -0.7954
 YM5  H041  H  HCH2  0   0.275   0.0698   0.5197   0.8986
 YM5  H042  H  HCH2  0   0.238  -0.4063   2.1194   1.4511
 YM5  H231  H  HCH2  0   0.258  -1.9937   2.9645  -1.7837
 YM5  H232  H  HCH2  0   0.225  -1.7080   3.6155  -0.1703
 YM5  H15   H  HCR6  0   0.245   0.0224  -0.6712  -2.1799
 YM5  H21   H  HCR6  0   0.243   0.9106  -2.4630   1.6019
 YM5  H16   H  HCR6  0   0.255   2.4276  -0.6266  -2.7101
 YM5  H17   H  HCR6  0   0.251   4.0809  -1.4766  -1.1020
 YM5  H191  H  HCH2  0   0.221   3.6339  -1.7907   2.2035
 YM5  H192  H  HCH2  0   0.214   3.1717  -3.4489   1.8574
 YM5  H20   H  HOH1  0   0.461   5.4606  -2.9537   1.5289
 YM5  H241  H  HCH2  0   0.203   0.3667   2.9124  -2.3038
 YM5  H242  H  HCH2  0   0.241  -0.0567   4.5309  -1.7249
 YM5  H11   H  HNR5  0   0.416  -3.8568  -3.1761   0.7257
 YM5  H08   H  HCR6  0   0.248  -5.4501   1.1263  -0.4859
 YM5  H12   H  HCR5  0   0.295  -1.4192  -3.7411   0.6070

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
 YM5  N01  C02   single    1.453  0.020  1.453
 YM5  C02  C03   single    1.517  0.020  1.517
 YM5  C03  C04   single    1.519  0.020  1.519
 YM5  C03  O25   single    1.413  0.020  1.413
 YM5  C04  N05   single    1.458  0.020  1.458
 YM5  N05  C06   single    1.367  0.020  1.367
 YM5  N05  C23   single    1.453  0.020  1.453
 YM5  C06  N07   aromatic  1.332  0.020  1.332
 YM5  C06  C22   aromatic  1.415  0.020  1.415
 YM5  N07  C08   aromatic  1.331  0.020  1.331
 YM5  C08  N09   aromatic  1.316  0.020  1.316
 YM5  N09  C10   aromatic  1.332  0.020  1.332
 YM5  C10  N11   aromatic  1.352  0.020  1.352
 YM5  C10  C22   aromatic  1.407  0.020  1.407
 YM5  N11  C12   aromatic  1.366  0.020  1.366
 YM5  C12  C13   aromatic  1.368  0.020  1.368
 YM5  C13  C14   single    1.468  0.020  1.468
 YM5  C13  C22   aromatic  1.440  0.020  1.440
 YM5  C14  C15   aromatic  1.396  0.020  1.396
 YM5  C14  C21   aromatic  1.393  0.020  1.393
 YM5  C15  C16   aromatic  1.385  0.020  1.385
 YM5  C16  C17   aromatic  1.390  0.020  1.390
 YM5  C17  C18   aromatic  1.390  0.020  1.390
 YM5  C18  C19   single    1.505  0.020  1.505
 YM5  C18  C21   aromatic  1.392  0.020  1.392
 YM5  C19  O20   single    1.404  0.020  1.404
 YM5  C23  C24   single    1.518  0.020  1.518
 YM5  C24  O25   single    1.408  0.020  1.408
 YM5  N01  H011  single    0.890  0.020  1.040
 YM5  N01  H012  single    0.890  0.020  1.040
 YM5  C02  H021  single    0.970  0.020  1.090
 YM5  C02  H022  single    0.970  0.020  1.090
 YM5  C03  H03   single    0.970  0.020  1.090
 YM5  C04  H041  single    0.970  0.020  1.090
 YM5  C04  H042  single    0.970  0.020  1.090
 YM5  C23  H231  single    0.970  0.020  1.090
 YM5  C23  H232  single    0.970  0.020  1.090
 YM5  C15  H15   single    0.930  0.020  1.080
 YM5  C21  H21   single    0.930  0.020  1.080
 YM5  C16  H16   single    0.930  0.020  1.080
 YM5  C17  H17   single    0.930  0.020  1.080
 YM5  C19  H191  single    0.970  0.020  1.090
 YM5  C19  H192  single    0.970  0.020  1.090
 YM5  O20  H20   single    0.850  0.020  0.980
 YM5  C24  H241  single    0.970  0.020  1.090
 YM5  C24  H242  single    0.970  0.020  1.090
 YM5  N11  H11   single    0.860  0.020  1.020
 YM5  C08  H08   single    0.930  0.020  1.080
 YM5  C12  H12   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
 YM5  H012  N01  H011  105.55  3.000
 YM5  H012  N01  C02   109.17  3.000
 YM5  H011  N01  C02   109.24  3.000
 YM5  H022  C02  H021  106.42  3.000
 YM5  H022  C02  C03   109.13  3.000
 YM5  H021  C02  C03   107.55  3.000
 YM5  H022  C02  N01   108.77  3.000
 YM5  H021  C02  N01   113.46  3.000
 YM5  C03   C02  N01   111.33  3.000
 YM5  H03   C03  O25   109.48  3.000
 YM5  H03   C03  C04   107.69  3.000
 YM5  O25   C03  C04   110.23  3.000
 YM5  H03   C03  C02   108.85  3.000
 YM5  O25   C03  C02   109.41  3.000
 YM5  C04   C03  C02   111.15  3.000
 YM5  H042  C04  H041  107.14  3.000
 YM5  H042  C04  N05   109.53  3.000
 YM5  H041  C04  N05   110.73  3.000
 YM5  H042  C04  C03   109.43  3.000
 YM5  H041  C04  C03   109.61  3.000
 YM5  N05   C04  C03   110.34  3.000
 YM5  C23   N05  C06   118.79  3.000
 YM5  C23   N05  C04   111.46  3.000
 YM5  C06   N05  C04   119.00  3.000
 YM5  C22   C06  N07   118.82  3.000
 YM5  C22   C06  N05   123.43  3.000
 YM5  N07   C06  N05   117.75  3.000
 YM5  C08   N07  C06   119.60  3.000
 YM5  H08   C08  N09   116.66  3.000
 YM5  H08   C08  N07   115.80  3.000
 YM5  N09   C08  N07   127.52  3.000
 YM5  C10   N09  C08   112.67  3.000
 YM5  C22   C10  N11   108.13  3.000
 YM5  C22   C10  N09   126.35  3.000
 YM5  N11   C10  N09   125.48  3.000
 YM5  H11   N11  C12   125.51  3.000
 YM5  H11   N11  C10   125.16  3.000
 YM5  C12   N11  C10   109.21  3.000
 YM5  H12   C12  C13   129.01  3.000
 YM5  H12   C12  N11   120.77  3.000
 YM5  C13   C12  N11   110.16  3.000
 YM5  C22   C13  C14   129.60  3.000
 YM5  C22   C13  C12   105.85  3.000
 YM5  C14   C13  C12   124.26  3.000
 YM5  C21   C14  C15   118.73  3.000
 YM5  C21   C14  C13   120.88  3.000
 YM5  C15   C14  C13   120.38  3.000
 YM5  H15   C15  C16   120.15  3.000
 YM5  H15   C15  C14   119.83  3.000
 YM5  C16   C15  C14   120.02  3.000
 YM5  H16   C16  C17   119.62  3.000
 YM5  H16   C16  C15   119.62  3.000
 YM5  C17   C16  C15   120.76  3.000
 YM5  H17   C17  C18   120.51  3.000
 YM5  H17   C17  C16   119.52  3.000
 YM5  C18   C17  C16   119.97  3.000
 YM5  C21   C18  C19   118.77  3.000
 YM5  C21   C18  C17   118.95  3.000
 YM5  C19   C18  C17   122.24  3.000
 YM5  H192  C19  H191  106.14  3.000
 YM5  H192  C19  O20   111.70  3.000
 YM5  H191  C19  O20   111.36  3.000
 YM5  H192  C19  C18   108.86  3.000
 YM5  H191  C19  C18   108.31  3.000
 YM5  O20   C19  C18   110.32  3.000
 YM5  H20   O20  C19   108.14  3.000
 YM5  H21   C21  C18   119.40  3.000
 YM5  H21   C21  C14   119.02  3.000
 YM5  C18   C21  C14   121.56  3.000
 YM5  C13   C22  C10   106.58  3.000
 YM5  C13   C22  C06   139.00  3.000
 YM5  C10   C22  C06   114.41  3.000
 YM5  H232  C23  H231  107.50  3.000
 YM5  H232  C23  C24   110.27  3.000
 YM5  H231  C23  C24   108.99  3.000
 YM5  H232  C23  N05   111.28  3.000
 YM5  H231  C23  N05   110.04  3.000
 YM5  C24   C23  N05   108.73  3.000
 YM5  H242  C24  H241  107.85  3.000
 YM5  H242  C24  O25   107.46  3.000
 YM5  H241  C24  O25   110.56  3.000
 YM5  H242  C24  C23   109.57  3.000
 YM5  H241  C24  C23   109.05  3.000
 YM5  O25   C24  C23   112.24  3.000
 YM5  C24   O25  C03   111.25  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
 YM5  CONST_01  N09   C08  N07  C06    0.00   0.0  0
 YM5  CONST_02  N09   C10  C22  C06    0.00   0.0  0
 YM5  CONST_03  N11   C10  C22  C06  180.00   0.0  0
 YM5  CONST_04  C12   C13  C22  C06  180.00   0.0  0
 YM5  CONST_05  C14   C13  C22  C06    0.00   0.0  0
 YM5  CONST_06  C10   C22  C06  N07    0.00   0.0  0
 YM5  CONST_07  C13   C22  C06  N07  180.00   0.0  0
 YM5  CONST_08  C10   N09  C08  N07    0.00   0.0  0
 YM5  CONST_09  C22   C06  N07  C08    0.00   0.0  0
 YM5  CONST_10  N11   C10  N09  C08  180.00   0.0  0
 YM5  CONST_11  C22   C10  N09  C08    0.00   0.0  0
 YM5  CONST_12  C12   N11  C10  N09  180.00   0.0  0
 YM5  CONST_13  C13   C22  C10  N09  180.00   0.0  0
 YM5  CONST_14  C13   C12  N11  C10    0.00   0.0  0
 YM5  CONST_15  C12   C13  C22  C10    0.00   0.0  0
 YM5  CONST_16  C14   C13  C22  C10  180.00   0.0  0
 YM5  CONST_17  C13   C22  C10  N11    0.00   0.0  0
 YM5  CONST_18  C14   C13  C12  N11  180.00   0.0  0
 YM5  CONST_19  C22   C13  C12  N11    0.00   0.0  0
 YM5  CONST_20  C22   C10  N11  C12    0.00   0.0  0
 YM5  CONST_23  C16   C15  C14  C13  180.00   0.0  0
 YM5  CONST_24  C18   C21  C14  C13  180.00   0.0  0
 YM5  CONST_25  C17   C16  C15  C14    0.00   0.0  0
 YM5  CONST_26  C17   C18  C21  C14    0.00   0.0  0
 YM5  CONST_28  C18   C21  C14  C15    0.00   0.0  0
 YM5  CONST_29  C18   C17  C16  C15    0.00   0.0  0
 YM5  CONST_30  C21   C14  C15  C16    0.00   0.0  0
 YM5  CONST_31  C21   C18  C17  C16    0.00   0.0  0
 YM5  CONST_33  C08   N07  C06  N05  180.00   0.0  0
 YM5  CONST_34  C10   C22  C06  N05  180.00   0.0  0
 YM5  CONST_35  C13   C22  C06  N05    0.00   0.0  0
 YM5  CONST_36  C19   C18  C21  C14  180.00   0.0  0
 YM5  CONST_37  C19   C18  C17  C16  180.00   0.0  0
 YM5  CONST_38  H08   C08  N07  C06  180.00   0.0  0
 YM5  CONST_39  H11   N11  C10  N09    0.00   0.0  0
 YM5  CONST_40  H12   C12  N11  C10  180.00   0.0  0
 YM5  CONST_41  H15   C15  C14  C13    0.00   0.0  0
 YM5  CONST_42  H21   C21  C14  C13    0.00   0.0  0
 YM5  CONST_43  H16   C16  C15  C14  180.00   0.0  0
 YM5  CONST_44  H17   C17  C16  C15  180.00   0.0  0
 YM5  Var_01    C06   N05  C04  C03  160.00  30.0  1
 YM5  Var_02    C23   C24  O25  C03   59.13  30.0  1
 YM5  Var_03    N07   C06  N05  C04  132.51  30.0  2
 YM5  Var_04    C24   C23  N05  C04   54.78  30.0  1
 YM5  Var_05    O25   C24  C23  N05  -56.39  30.0  1
 YM5  Var_06    O20   C19  C18  C17  -17.74  30.0  2
 YM5  Var_07    H011  N01  C02  C03  173.59  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
 YM5  chir_01  C03  C02  C04  O25  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
 YM5  plan-1  C13  0.020
 YM5  plan-1  C14  0.020
 YM5  plan-1  C15  0.020
 YM5  plan-1  C16  0.020
 YM5  plan-1  C17  0.020
 YM5  plan-1  C18  0.020
 YM5  plan-1  C19  0.020
 YM5  plan-1  C21  0.020
 YM5  plan-1  H15  0.020
 YM5  plan-1  H21  0.020
 YM5  plan-1  H16  0.020
 YM5  plan-1  H17  0.020
 YM5  plan-2  N05  0.020
 YM5  plan-2  C06  0.020
 YM5  plan-2  N07  0.020
 YM5  plan-2  C08  0.020
 YM5  plan-2  N09  0.020
 YM5  plan-2  C10  0.020
 YM5  plan-2  N11  0.020
 YM5  plan-2  C12  0.020
 YM5  plan-2  C13  0.020
 YM5  plan-2  C14  0.020
 YM5  plan-2  C22  0.020
 YM5  plan-2  H11  0.020
 YM5  plan-2  H08  0.020
 YM5  plan-2  H12  0.020

