# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:08:26 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N-[4-(2-{[4-(morpholin-4-yl)phenyl]amino}pyrimidin-4-yl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(cc1)c2ccnc(Nc3ccc(cc3)N4CCOCC4)n2
#
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
 3O4  3O4  N-[4-(2-{[4-(morpholin-4-yl)phenyl]amino}pyrimidin-4-yl)phenyl]acetamide  ligand  52  29  .  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_3O4
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
 3O4  O23   O  O     0  -0.462   -7.6504  -2.7468  -0.0645
 3O4  C22   C  C     0   0.508   -8.3033  -1.7285   0.0649
 3O4  N24   N  NH1   0  -0.731   -7.7539  -0.4842   0.1618
 3O4  C25   C  CR6   0   0.377   -6.4186  -0.0973   0.1115
 3O4  C26   C  CR16  0  -0.330   -6.1572   1.2766   0.1392
 3O4  C19   C  CH3   0  -0.788   -9.8099  -1.7237   0.0978
 3O4  C17   C  CR16  0  -0.266   -4.0454  -0.4835   0.0090
 3O4  C16   C  CR6   0   0.034   -3.7748   0.8843   0.0305
 3O4  C12   C  CR6   0   0.308   -2.3847   1.3727  -0.0180
 3O4  C11   C  CR16  0  -0.413   -2.0640   2.7288  -0.1447
 3O4  C10   C  CR16  0   0.004   -0.7217   3.0404  -0.1932
 3O4  N15   N  N     0  -0.470    0.2459   2.1350  -0.1248
 3O4  C14   C  CR6   0   0.596   -0.1559   0.8732   0.0020
 3O4  N13   N  N     0  -0.504   -1.4254   0.4620   0.0562
 3O4  N7    N  NH1   0  -0.770    0.7576  -0.1274   0.0931
 3O4  C1    C  CR6   0   0.336    2.1527  -0.1101   0.0845
 3O4  C2    C  CR16  0  -0.342    2.7982  -1.3055   0.4210
 3O4  C3    C  CR16  0  -0.314    4.1733  -1.4069   0.4254
 3O4  C4    C  CR6   0   0.346    4.9873  -0.3180   0.0837
 3O4  C5    C  CR16  0  -0.345    4.3366   0.8684  -0.2555
 3O4  C6    C  CR16  0  -0.301    2.9501   0.9801  -0.2499
 3O4  C90   C  CR16  0  -0.298   -5.3368  -0.9794   0.0451
 3O4  N8    N  NT    0  -0.519    6.3812  -0.4389   0.1254
 3O4  C13   C  CR16  0  -0.316   -4.8641   1.7552   0.0973
 3O4  C9    C  CH2   0  -0.322    6.9563  -1.5930  -0.5544
 3O4  C31   C  CH2   0  -0.188    8.4165  -1.7494  -0.1787
 3O4  O30   O  O2    0  -0.482    9.1550  -0.5811  -0.4532
 3O4  C29   C  CH2   0  -0.185    8.6135   0.5162   0.2449
 3O4  C28   C  CH2   0  -0.328    7.1601   0.7591  -0.1172
 3O4  H24   H  HNH1  0   0.419   -8.4094   0.2774   0.2505
 3O4  H191  H  HCH3  0   0.269  -10.1796  -2.7076   0.3739
 3O4  H192  H  HCH3  0   0.262  -10.2083  -0.9865   0.7937
 3O4  H193  H  HCH3  0   0.279  -10.1948  -1.4810  -0.8947
 3O4  H26   H  HCR6  0   0.276   -6.9793   1.9804   0.1925
 3O4  H90   H  HCR6  0   0.283   -5.4890  -2.0453   0.0236
 3O4  H13   H  HCR6  0   0.260   -4.7225   2.8271   0.1239
 3O4  H17   H  HCR6  0   0.261   -3.2240  -1.1849  -0.0392
 3O4  H11   H  HCR6  0   0.272   -2.8060   3.5082  -0.2126
 3O4  H10   H  HCR6  0   0.273   -0.4054   4.0726  -0.2960
 3O4  H2    H  HCR6  0   0.264    2.2103  -2.1730   0.6989
 3O4  H6    H  HCR6  0   0.278    2.5036   1.9228  -0.5204
 3O4  H3    H  HCR6  0   0.262    4.6140  -2.3492   0.7227
 3O4  H5    H  HCR6  0   0.266    4.9001   1.7451  -0.5442
 3O4  H281  H  HCH2  0   0.215    7.0906   1.0915  -1.1651
 3O4  H282  H  HCH2  0   0.254    6.7902   1.5739   0.5081
 3O4  H91C  H  HCH2  0   0.256    6.4387  -2.5060  -0.2640
 3O4  H92C  H  HCH2  0   0.219    6.8590  -1.4942  -1.6462
 3O4  H291  H  HCH2  0   0.204    8.6954   0.3583   1.3298
 3O4  H292  H  HCH2  0   0.241    9.2057   1.3953  -0.0130
 3O4  H311  H  HCH2  0   0.204    8.4908  -2.0090   0.8869
 3O4  H312  H  HCH2  0   0.241    8.8585  -2.5630  -0.7554
 3O4  H7    H  HNH1  0   0.405    0.3390  -1.0343   0.2337

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
 3O4  O23  C22   double    1.217  0.020  1.217
 3O4  C22  N24   single    1.364  0.020  1.364
 3O4  C22  C19   single    1.507  0.020  1.507
 3O4  N24  C25   single    1.391  0.020  1.391
 3O4  C25  C26   aromatic  1.399  0.020  1.399
 3O4  C25  C90   aromatic  1.397  0.020  1.397
 3O4  C26  C13   aromatic  1.379  0.020  1.379
 3O4  C17  C16   aromatic  1.394  0.020  1.394
 3O4  C17  C90   aromatic  1.384  0.020  1.384
 3O4  C16  C12   single    1.474  0.020  1.474
 3O4  C16  C13   aromatic  1.396  0.020  1.396
 3O4  C12  C11   aromatic  1.399  0.020  1.399
 3O4  C12  N13   aromatic  1.325  0.020  1.325
 3O4  C11  C10   aromatic  1.379  0.020  1.379
 3O4  C10  N15   aromatic  1.327  0.020  1.327
 3O4  N15  C14   aromatic  1.330  0.020  1.330
 3O4  C14  N13   aromatic  1.336  0.020  1.336
 3O4  C14  N7    single    1.358  0.020  1.358
 3O4  N7   C1    single    1.395  0.020  1.395
 3O4  C1   C2    aromatic  1.400  0.020  1.400
 3O4  C1   C6    aromatic  1.392  0.020  1.392
 3O4  C2   C3    aromatic  1.379  0.020  1.379
 3O4  C3   C4    aromatic  1.402  0.020  1.402
 3O4  C4   C5    aromatic  1.395  0.020  1.395
 3O4  C4   N8    single    1.400  0.020  1.400
 3O4  C5   C6    aromatic  1.391  0.020  1.391
 3O4  N8   C28   single    1.449  0.020  1.449
 3O4  N8   C9    single    1.458  0.020  1.458
 3O4  C28  C29   single    1.517  0.020  1.517
 3O4  C29  O30   single    1.409  0.020  1.409
 3O4  O30  C31   single    1.409  0.020  1.409
 3O4  C31  C9    single    1.516  0.020  1.516
 3O4  N24  H24   single    0.860  0.020  1.020
 3O4  C19  H191  single    0.970  0.020  1.090
 3O4  C19  H192  single    0.970  0.020  1.090
 3O4  C19  H193  single    0.970  0.020  1.090
 3O4  C26  H26   single    0.930  0.020  1.080
 3O4  C90  H90   single    0.930  0.020  1.080
 3O4  C13  H13   single    0.930  0.020  1.080
 3O4  C17  H17   single    0.930  0.020  1.080
 3O4  C11  H11   single    0.930  0.020  1.080
 3O4  C10  H10   single    0.930  0.020  1.080
 3O4  C2   H2    single    0.930  0.020  1.080
 3O4  C6   H6    single    0.930  0.020  1.080
 3O4  C3   H3    single    0.930  0.020  1.080
 3O4  C5   H5    single    0.930  0.020  1.080
 3O4  C28  H281  single    0.970  0.020  1.090
 3O4  C28  H282  single    0.970  0.020  1.090
 3O4  C9   H91C  single    0.970  0.020  1.090
 3O4  C9   H92C  single    0.970  0.020  1.090
 3O4  C29  H291  single    0.970  0.020  1.090
 3O4  C29  H292  single    0.970  0.020  1.090
 3O4  C31  H311  single    0.970  0.020  1.090
 3O4  C31  H312  single    0.970  0.020  1.090
 3O4  N7   H7    single    0.860  0.020  1.020

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
 3O4  C19   C22  N24   113.48  3.000
 3O4  C19   C22  O23   122.79  3.000
 3O4  N24   C22  O23   123.72  3.000
 3O4  H24   N24  C25   114.64  3.000
 3O4  H24   N24  C22   115.68  3.000
 3O4  C25   N24  C22   129.64  3.000
 3O4  C90   C25  C26   118.44  3.000
 3O4  C90   C25  N24   124.70  3.000
 3O4  C26   C25  N24   116.86  3.000
 3O4  H26   C26  C13   119.17  3.000
 3O4  H26   C26  C25   119.81  3.000
 3O4  C13   C26  C25   121.02  3.000
 3O4  H193  C19  H192  107.54  3.000
 3O4  H193  C19  H191  108.20  3.000
 3O4  H192  C19  H191  109.03  3.000
 3O4  H193  C19  C22   109.47  3.000
 3O4  H192  C19  C22   112.44  3.000
 3O4  H191  C19  C22   110.04  3.000
 3O4  H17   C17  C90   118.53  3.000
 3O4  H17   C17  C16   119.32  3.000
 3O4  C90   C17  C16   122.16  3.000
 3O4  C13   C16  C12   122.04  3.000
 3O4  C13   C16  C17   117.46  3.000
 3O4  C12   C16  C17   120.49  3.000
 3O4  N13   C12  C11   120.35  3.000
 3O4  N13   C12  C16   116.95  3.000
 3O4  C11   C12  C16   122.70  3.000
 3O4  H11   C11  C10   120.29  3.000
 3O4  H11   C11  C12   123.26  3.000
 3O4  C10   C11  C12   116.45  3.000
 3O4  H10   C10  N15   116.21  3.000
 3O4  H10   C10  C11   120.16  3.000
 3O4  N15   C10  C11   123.63  3.000
 3O4  C14   N15  C10   115.59  3.000
 3O4  N7    C14  N13   114.19  3.000
 3O4  N7    C14  N15   120.14  3.000
 3O4  N13   C14  N15   125.66  3.000
 3O4  C14   N13  C12   118.31  3.000
 3O4  H7    N7   C1    115.28  3.000
 3O4  H7    N7   C14   113.12  3.000
 3O4  C1    N7   C14   131.54  3.000
 3O4  C6    C1   C2    117.56  3.000
 3O4  C6    C1   N7    125.75  3.000
 3O4  C2    C1   N7    116.68  3.000
 3O4  H2    C2   C3    118.76  3.000
 3O4  H2    C2   C1    119.67  3.000
 3O4  C3    C2   C1    121.57  3.000
 3O4  H3    C3   C4    120.46  3.000
 3O4  H3    C3   C2    118.11  3.000
 3O4  C4    C3   C2    121.42  3.000
 3O4  N8    C4   C5    123.04  3.000
 3O4  N8    C4   C3    120.26  3.000
 3O4  C5    C4   C3    116.68  3.000
 3O4  H5    C5   C6    117.09  3.000
 3O4  H5    C5   C4    120.75  3.000
 3O4  C6    C5   C4    122.16  3.000
 3O4  H6    C6   C5    118.83  3.000
 3O4  H6    C6   C1    120.55  3.000
 3O4  C5    C6   C1    120.61  3.000
 3O4  H90   C90  C17   119.09  3.000
 3O4  H90   C90  C25   121.08  3.000
 3O4  C17   C90  C25   119.83  3.000
 3O4  C28   N8   C9    111.37  3.000
 3O4  C9    N8   C4    116.57  3.000
 3O4  C28   N8   C4    117.31  3.000
 3O4  H13   C13  C16   121.15  3.000
 3O4  H13   C13  C26   117.76  3.000
 3O4  C16   C13  C26   121.09  3.000
 3O4  H92C  C9   H91C  107.32  3.000
 3O4  H92C  C9   C31   109.90  3.000
 3O4  H91C  C9   C31   107.78  3.000
 3O4  H92C  C9   N8    110.89  3.000
 3O4  H91C  C9   N8    110.60  3.000
 3O4  C31   C9   N8    110.25  3.000
 3O4  H312  C31  H311  108.00  3.000
 3O4  H312  C31  O30   107.64  3.000
 3O4  H311  C31  O30   110.44  3.000
 3O4  H312  C31  C9    109.65  3.000
 3O4  H311  C31  C9    109.25  3.000
 3O4  O30   C31  C9    111.78  3.000
 3O4  C29   O30  C31   110.36  3.000
 3O4  H292  C29  H291  107.98  3.000
 3O4  H292  C29  C28   109.55  3.000
 3O4  H291  C29  C28   109.26  3.000
 3O4  H292  C29  O30   107.57  3.000
 3O4  H291  C29  O30   110.39  3.000
 3O4  C28   C29  O30   112.00  3.000
 3O4  H282  C28  H281  107.35  3.000
 3O4  H282  C28  C29   107.89  3.000
 3O4  H281  C28  C29   109.62  3.000
 3O4  H282  C28  N8    109.82  3.000
 3O4  H281  C28  N8    112.01  3.000
 3O4  C29   C28  N8    110.03  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
 3O4  CONST_01  C16   C13  C26  C25     0.00   0.0  0
 3O4  CONST_02  C16   C17  C90  C25     0.00   0.0  0
 3O4  CONST_03  C17   C90  C25  C26     0.00   0.0  0
 3O4  CONST_04  C17   C16  C13  C26     0.00   0.0  0
 3O4  CONST_05  C12   C16  C13  C26   180.00   0.0  0
 3O4  CONST_06  C11   C12  C16  C17   180.00   0.0  0
 3O4  CONST_07  N13   C12  C16  C17     0.00   0.0  0
 3O4  CONST_08  C10   C11  C12  C16   180.00   0.0  0
 3O4  CONST_09  C14   N13  C12  C16   180.00   0.0  0
 3O4  CONST_10  C90   C17  C16  C12   180.00   0.0  0
 3O4  CONST_11  N15   C10  C11  C12     0.00   0.0  0
 3O4  CONST_12  N15   C14  N13  C12     0.00   0.0  0
 3O4  CONST_13  C13   C16  C12  C11     0.00   0.0  0
 3O4  CONST_14  C14   N13  C12  C11     0.00   0.0  0
 3O4  CONST_15  C14   N15  C10  C11     0.00   0.0  0
 3O4  CONST_16  N13   C12  C11  C10     0.00   0.0  0
 3O4  CONST_17  N13   C14  N15  C10     0.00   0.0  0
 3O4  CONST_18  C13   C16  C12  N13   180.00   0.0  0
 3O4  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 3O4  CONST_20  C4    C5   C6   C1      0.00   0.0  0
 3O4  CONST_21  C5    C6   C1   C2      0.00   0.0  0
 3O4  CONST_22  C5    C4   C3   C2      0.00   0.0  0
 3O4  CONST_23  C6    C1   C2   C3      0.00   0.0  0
 3O4  CONST_24  C6    C5   C4   C3      0.00   0.0  0
 3O4  CONST_25  C13   C26  C25  C90     0.00   0.0  0
 3O4  CONST_26  C13   C16  C17  C90     0.00   0.0  0
 3O4  CONST_27  N8    C4   C3   C2    180.00   0.0  0
 3O4  CONST_28  N8    C4   C5   C6    180.00   0.0  0
 3O4  CONST_29  C13   C26  C25  N24   180.00   0.0  0
 3O4  CONST_30  C17   C90  C25  N24   180.00   0.0  0
 3O4  CONST_31  N7    C14  N13  C12   180.00   0.0  0
 3O4  CONST_32  N7    C14  N15  C10   180.00   0.0  0
 3O4  CONST_33  C3    C2   C1   N7    180.00   0.0  0
 3O4  CONST_34  C5    C6   C1   N7    180.00   0.0  0
 3O4  CONST_35  H13   C13  C26  C25   180.00   0.0  0
 3O4  CONST_36  H17   C17  C90  C25   180.00   0.0  0
 3O4  CONST_37  H90   C90  C25  C26   180.00   0.0  0
 3O4  CONST_38  H11   C11  C12  C16     0.00   0.0  0
 3O4  CONST_39  H26   C26  C13  C16   180.00   0.0  0
 3O4  CONST_40  H10   C10  C11  C12   180.00   0.0  0
 3O4  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 3O4  CONST_42  H5    C5   C6   C1    180.00   0.0  0
 3O4  CONST_43  H6    C6   C1   C2    180.00   0.0  0
 3O4  CONST_44  H2    C2   C3   C4    180.00   0.0  0
 3O4  CONST_45  C26   C25  N24  C22   180.00   0.0  0
 3O4  CONST_46  C90   C25  N24  C22     0.00   0.0  0
 3O4  CONST_47  H24   N24  C25  C26     0.00   0.0  0
 3O4  CONST_48  C25   N24  C22  O23     0.00   0.0  0
 3O4  CONST_49  C19   C22  N24  C25   180.00   0.0  0
 3O4  Var_01    C28   N8   C4   C3   -174.32  30.0  2
 3O4  Var_02    C29   C28  N8   C4    168.35  30.0  1
 3O4  Var_03    C31   C9   N8   C4   -167.99  30.0  1
 3O4  Var_04    O30   C29  C28  N8     56.36  30.0  1
 3O4  Var_05    O30   C31  C9   N8    -55.99  30.0  1
 3O4  Var_06    C28   C29  O30  C31   -58.59  30.0  1
 3O4  Var_07    C1    N7   C14  N15     0.20  30.0  2
 3O4  Var_08    C2    C1   N7   C14   169.66  30.0  2
 3O4  Var_09    H191  C19  C22  O23    21.68  30.0  3

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
 3O4  plan-1  N24  0.020
 3O4  plan-1  C25  0.020
 3O4  plan-1  C26  0.020
 3O4  plan-1  C17  0.020
 3O4  plan-1  C16  0.020
 3O4  plan-1  C12  0.020
 3O4  plan-1  C90  0.020
 3O4  plan-1  C13  0.020
 3O4  plan-1  H26  0.020
 3O4  plan-1  H90  0.020
 3O4  plan-1  H13  0.020
 3O4  plan-1  H17  0.020
 3O4  plan-2  C16  0.020
 3O4  plan-2  C12  0.020
 3O4  plan-2  C11  0.020
 3O4  plan-2  C10  0.020
 3O4  plan-2  N15  0.020
 3O4  plan-2  C14  0.020
 3O4  plan-2  N13  0.020
 3O4  plan-2  N7   0.020
 3O4  plan-2  H11  0.020
 3O4  plan-2  H10  0.020
 3O4  plan-3  N7   0.020
 3O4  plan-3  C1   0.020
 3O4  plan-3  C2   0.020
 3O4  plan-3  C3   0.020
 3O4  plan-3  C4   0.020
 3O4  plan-3  C5   0.020
 3O4  plan-3  C6   0.020
 3O4  plan-3  N8   0.020
 3O4  plan-3  H2   0.020
 3O4  plan-3  H6   0.020
 3O4  plan-3  H3   0.020
 3O4  plan-3  H5   0.020
 3O4  plan-4  O23  0.020
 3O4  plan-4  C22  0.020
 3O4  plan-4  N24  0.020
 3O4  plan-4  C25  0.020
 3O4  plan-4  C19  0.020
 3O4  plan-4  H24  0.020

