# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:37:01 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-({[2-({(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}oxy)ethyl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@H]2CNC[C@H]2OCCNCc3ccccc3O)c1
#
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
 CXW  CXW  2-({[2-({(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}oxy)ethyl]amino}methyl)phenol  ligand  54  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CXW
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
 CXW  O22  O  OH1   0  -0.657  -3.9787   0.1700   1.2536
 CXW  C22  C  CR6   0   0.322  -4.2790  -0.6390   0.2236
 CXW  C23  C  CR16  0  -0.344  -4.7892  -1.9096   0.4857
 CXW  C24  C  CR16  0  -0.257  -5.1130  -2.7632  -0.5587
 CXW  C25  C  CR16  0  -0.276  -4.9178  -2.3697  -1.8760
 CXW  C26  C  CR16  0  -0.303  -4.4057  -1.1046  -2.1335
 CXW  C21  C  CR6   0  -0.046  -4.0940  -0.2236  -1.1059
 CXW  C13  C  CH2   0  -0.315  -3.6162   1.1740  -1.3997
 CXW  N12  N  NH1   0  -0.651  -2.5632   1.5734  -0.4718
 CXW  C11  C  CH2   0  -0.291  -2.1869   2.9741  -0.5855
 CXW  C10  C  CH2   0  -0.160  -1.0790   3.3126   0.3857
 CXW  O09  O  O2    0  -0.501   0.0486   2.5378   0.0585
 CXW  C4'  C  CH1   0   0.021   1.0598   2.5096   1.0416
 CXW  C5'  C  CH2   0  -0.307   1.9653   3.7599   0.9826
 CXW  N1'  N  NH1   0  -0.601   3.2080   3.3779   0.2984
 CXW  C2'  C  CH2   0  -0.292   2.9989   2.0395  -0.2432
 CXW  C3'  C  CH1   0  -0.277   2.0214   1.3646   0.7201
 CXW  C08  C  CH2   0  -0.495   1.3567   0.0805   0.2263
 CXW  C06  C  CR6   0   0.269   2.3323  -1.0619   0.1858
 CXW  C05  C  CR16  0  -0.430   2.4231  -1.9487   1.2458
 CXW  C04  C  CR6   0   0.204   3.3671  -2.9790   1.1936
 CXW  C07  C  CH3   0  -0.726   3.5067  -3.9451   2.3304
 CXW  N01  N  N     0  -0.477   3.1108  -1.1490  -0.8943
 CXW  C02  C  CR6   0   0.443   4.0154  -2.1221  -0.9531
 CXW  N02  N  NH2   0  -0.840   4.8280  -2.1480  -2.0509
 CXW  C03  C  CR16  0  -0.447   4.1732  -3.0651   0.0761
 CXW  H1   H  HOH1  0   0.463  -3.3880   0.8851   0.8845
 CXW  H2   H  HCR6  0   0.254  -4.9297  -2.2217   1.5136
 CXW  H3   H  HCR6  0   0.252  -5.5114  -3.7451  -0.3365
 CXW  H4   H  HCR6  0   0.247  -5.1597  -3.0375  -2.6922
 CXW  H5   H  HCR6  0   0.250  -4.2509  -0.7853  -3.1580
 CXW  H6   H  HCH2  0   0.243  -3.3035   1.2535  -2.4480
 CXW  H7   H  HCH2  0   0.255  -4.4461   1.8774  -1.2726
 CXW  H8   H  HNH1  0   0.369  -1.7427   0.9995  -0.6339
 CXW  H10  H  HCH2  0   0.220  -1.8814   3.2327  -1.6085
 CXW  H11  H  HCH2  0   0.243  -3.0562   3.5908  -0.3474
 CXW  H12  H  HCH2  0   0.212  -0.8657   4.3881   0.3282
 CXW  H13  H  HCH2  0   0.205  -1.4117   3.1008   1.4114
 CXW  H14  H  HCH1  0   0.229   0.6040   2.3861   2.0327
 CXW  H15  H  HCH2  0   0.224   1.4525   4.5636   0.4454
 CXW  H16  H  HCH2  0   0.233   2.1827   4.1391   1.9821
 CXW  H17  H  HNH1  0   0.348   3.9514   3.3293   0.9813
 CXW  H19  H  HCH2  0   0.210   2.5584   2.0959  -1.2451
 CXW  H20  H  HCH2  0   0.239   3.9473   1.5127  -0.3407
 CXW  H21  H  HCH1  0   0.248   2.5635   1.1395   1.6465
 CXW  H22  H  HCH2  0   0.243   0.5264  -0.1789   0.8878
 CXW  H23  H  HCH2  0   0.239   0.9407   0.2328  -0.7717
 CXW  H24  H  HCR6  0   0.241   1.7632  -1.8490   2.0990
 CXW  H25  H  HCH3  0   0.254   4.0156  -3.4720   3.1722
 CXW  H26  H  HCH3  0   0.248   2.5322  -4.2752   2.6905
 CXW  H27  H  HCH3  0   0.246   4.0840  -4.8234   2.0459
 CXW  H28  H  HNH2  0   0.378   4.5035  -1.6352  -2.8543
 CXW  H29  H  HNH2  0   0.387   5.2809  -3.0185  -2.2736
 CXW  H30  H  HCR6  0   0.254   4.9188  -3.8459  -0.0137

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
 CXW  C07  C04  single    1.498  0.020  1.498
 CXW  C04  C03  aromatic  1.381  0.020  1.381
 CXW  C04  C05  aromatic  1.398  0.020  1.398
 CXW  C03  C02  aromatic  1.405  0.020  1.405
 CXW  C05  C06  aromatic  1.385  0.020  1.385
 CXW  C02  N02  single    1.366  0.020  1.366
 CXW  C02  N01  aromatic  1.330  0.020  1.330
 CXW  C06  N01  aromatic  1.334  0.020  1.334
 CXW  C06  C08  single    1.503  0.020  1.503
 CXW  C3'  C2'  single    1.529  0.020  1.529
 CXW  C3'  C4'  single    1.529  0.020  1.529
 CXW  C3'  C08  single    1.528  0.020  1.528
 CXW  C2'  N1'  single    1.459  0.020  1.459
 CXW  C4'  O09  single    1.411  0.020  1.411
 CXW  C4'  C5'  single    1.545  0.020  1.545
 CXW  O09  C10  single    1.407  0.020  1.407
 CXW  C10  C11  single    1.512  0.020  1.512
 CXW  C11  N12  single    1.455  0.020  1.455
 CXW  N1'  C5'  single    1.469  0.020  1.469
 CXW  N12  C13  single    1.459  0.020  1.459
 CXW  C26  C25  aromatic  1.389  0.020  1.389
 CXW  C26  C21  aromatic  1.389  0.020  1.389
 CXW  C25  C24  aromatic  1.389  0.020  1.389
 CXW  C13  C21  single    1.506  0.020  1.506
 CXW  C21  C22  aromatic  1.405  0.020  1.405
 CXW  C24  C23  aromatic  1.387  0.020  1.387
 CXW  C22  C23  aromatic  1.394  0.020  1.394
 CXW  C22  O22  single    1.344  0.020  1.344
 CXW  O22  H1   single    0.850  0.020  0.980
 CXW  C23  H2   single    0.930  0.020  1.080
 CXW  C24  H3   single    0.930  0.020  1.080
 CXW  C25  H4   single    0.930  0.020  1.080
 CXW  C26  H5   single    0.930  0.020  1.080
 CXW  C13  H6   single    0.970  0.020  1.090
 CXW  C13  H7   single    0.970  0.020  1.090
 CXW  N12  H8   single    0.890  0.020  1.040
 CXW  C11  H10  single    0.970  0.020  1.090
 CXW  C11  H11  single    0.970  0.020  1.090
 CXW  C10  H12  single    0.970  0.020  1.090
 CXW  C10  H13  single    0.970  0.020  1.090
 CXW  C4'  H14  single    0.970  0.020  1.090
 CXW  C5'  H15  single    0.970  0.020  1.090
 CXW  C5'  H16  single    0.970  0.020  1.090
 CXW  N1'  H17  single    0.890  0.020  1.040
 CXW  C2'  H19  single    0.970  0.020  1.090
 CXW  C2'  H20  single    0.970  0.020  1.090
 CXW  C3'  H21  single    0.970  0.020  1.090
 CXW  C08  H22  single    0.970  0.020  1.090
 CXW  C08  H23  single    0.970  0.020  1.090
 CXW  C05  H24  single    0.930  0.020  1.080
 CXW  C07  H25  single    0.970  0.020  1.090
 CXW  C07  H26  single    0.970  0.020  1.090
 CXW  C07  H27  single    0.970  0.020  1.090
 CXW  N02  H28  single    0.890  0.020  1.040
 CXW  N02  H29  single    0.890  0.020  1.040
 CXW  C03  H30  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
 CXW  H1   O22  C22  106.26  3.000
 CXW  C21  C22  C23  119.70  3.000
 CXW  C23  C22  O22  119.10  3.000
 CXW  C21  C22  O22  121.19  3.000
 CXW  H2   C23  C24  120.45  3.000
 CXW  H2   C23  C22  119.24  3.000
 CXW  C24  C23  C22  120.31  3.000
 CXW  H3   C24  C25  120.23  3.000
 CXW  H3   C24  C23  119.30  3.000
 CXW  C25  C24  C23  120.47  3.000
 CXW  H4   C25  C26  120.32  3.000
 CXW  H4   C25  C24  120.62  3.000
 CXW  C26  C25  C24  119.07  3.000
 CXW  H5   C26  C21  118.70  3.000
 CXW  H5   C26  C25  119.75  3.000
 CXW  C21  C26  C25  121.56  3.000
 CXW  C13  C21  C26  121.03  3.000
 CXW  C13  C21  C22  120.05  3.000
 CXW  C26  C21  C22  118.88  3.000
 CXW  H7   C13  H6   106.28  3.000
 CXW  H7   C13  N12  107.29  3.000
 CXW  H6   C13  N12  112.47  3.000
 CXW  H7   C13  C21  109.45  3.000
 CXW  H6   C13  C21  110.13  3.000
 CXW  N12  C13  C21  111.03  3.000
 CXW  H8   N12  C11  108.84  3.000
 CXW  H8   N12  C13  109.11  3.000
 CXW  C11  N12  C13  113.61  3.000
 CXW  H11  C11  H10  106.95  3.000
 CXW  H11  C11  C10  108.47  3.000
 CXW  H10  C11  C10  109.98  3.000
 CXW  H11  C11  N12  108.71  3.000
 CXW  H10  C11  N12  111.80  3.000
 CXW  C10  C11  N12  110.79  3.000
 CXW  H13  C10  H12  107.24  3.000
 CXW  H13  C10  O09  110.71  3.000
 CXW  H12  C10  O09  111.81  3.000
 CXW  H13  C10  C11  109.55  3.000
 CXW  H12  C10  C11  109.16  3.000
 CXW  O09  C10  C11  108.34  3.000
 CXW  C4'  O09  C10  115.06  3.000
 CXW  H14  C4'  C3'  111.51  3.000
 CXW  H14  C4'  C5'  111.65  3.000
 CXW  C3'  C4'  C5'  103.26  3.000
 CXW  H14  C4'  O09  109.50  3.000
 CXW  C5'  C4'  O09  112.17  3.000
 CXW  C3'  C4'  O09  108.61  3.000
 CXW  H16  C5'  H15  106.73  3.000
 CXW  H16  C5'  N1'  110.39  3.000
 CXW  H15  C5'  N1'  111.02  3.000
 CXW  H16  C5'  C4'  111.29  3.000
 CXW  H15  C5'  C4'  109.79  3.000
 CXW  N1'  C5'  C4'  107.65  3.000
 CXW  H17  N1'  C2'  108.19  3.000
 CXW  H17  N1'  C5'  108.66  3.000
 CXW  C2'  N1'  C5'  106.86  3.000
 CXW  H20  C2'  H19  107.03  3.000
 CXW  H20  C2'  C3'  113.55  3.000
 CXW  H19  C2'  C3'  109.97  3.000
 CXW  H20  C2'  N1'  110.61  3.000
 CXW  H19  C2'  N1'  110.48  3.000
 CXW  C3'  C2'  N1'  105.23  3.000
 CXW  H21  C3'  C08  108.39  3.000
 CXW  H21  C3'  C2'  107.86  3.000
 CXW  C08  C3'  C2'  116.45  3.000
 CXW  H21  C3'  C4'  106.67  3.000
 CXW  C08  C3'  C4'  115.07  3.000
 CXW  C2'  C3'  C4'  101.77  3.000
 CXW  H23  C08  H22  107.27  3.000
 CXW  H23  C08  C06  109.19  3.000
 CXW  H22  C08  C06  109.21  3.000
 CXW  H23  C08  C3'  110.12  3.000
 CXW  H22  C08  C3'  109.54  3.000
 CXW  C06  C08  C3'  111.42  3.000
 CXW  N01  C06  C05  122.65  3.000
 CXW  N01  C06  C08  116.76  3.000
 CXW  C05  C06  C08  120.58  3.000
 CXW  H24  C05  C04  120.56  3.000
 CXW  H24  C05  C06  120.26  3.000
 CXW  C04  C05  C06  119.17  3.000
 CXW  C03  C04  C07  121.30  3.000
 CXW  C03  C04  C05  118.06  3.000
 CXW  C07  C04  C05  120.64  3.000
 CXW  H27  C07  H26  108.43  3.000
 CXW  H27  C07  H25  107.69  3.000
 CXW  H26  C07  H25  107.06  3.000
 CXW  H27  C07  C04  111.79  3.000
 CXW  H26  C07  C04  111.26  3.000
 CXW  H25  C07  C04  110.43  3.000
 CXW  C02  N01  C06  118.72  3.000
 CXW  C03  C02  N02  120.61  3.000
 CXW  N02  C02  N01  117.00  3.000
 CXW  C03  C02  N01  122.35  3.000
 CXW  H29  N02  H28  114.15  3.000
 CXW  H29  N02  C02  117.52  3.000
 CXW  H28  N02  C02  116.09  3.000
 CXW  H30  C03  C02  120.02  3.000
 CXW  H30  C03  C04  120.93  3.000
 CXW  C02  C03  C04  119.05  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
 CXW  CONST_01  C25  C26  C21  C22     0.00   0.0  0
 CXW  CONST_02  C25  C24  C23  C22     0.00   0.0  0
 CXW  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 CXW  CONST_04  C26  C21  C22  C23     0.00   0.0  0
 CXW  CONST_05  C21  C26  C25  C24     0.00   0.0  0
 CXW  CONST_06  C21  C22  C23  C24     0.00   0.0  0
 CXW  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 CXW  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 CXW  CONST_09  C02  C03  C04  C05     0.00   0.0  0
 CXW  CONST_10  C02  N01  C06  C05     0.00   0.0  0
 CXW  CONST_11  N01  C02  C03  C04     0.00   0.0  0
 CXW  CONST_12  N01  C06  C05  C04     0.00   0.0  0
 CXW  CONST_13  C26  C21  C22  O22   180.00   0.0  0
 CXW  CONST_14  C24  C23  C22  O22   180.00   0.0  0
 CXW  CONST_15  C13  C21  C22  C23   180.00   0.0  0
 CXW  CONST_16  C13  C21  C26  C25   180.00   0.0  0
 CXW  CONST_17  C04  C05  C06  C08   180.00   0.0  0
 CXW  CONST_18  C02  N01  C06  C08   180.00   0.0  0
 CXW  CONST_19  C07  C04  C05  C06   180.00   0.0  0
 CXW  CONST_20  N02  C02  N01  C06   180.00   0.0  0
 CXW  CONST_21  N02  C02  C03  C04   180.00   0.0  0
 CXW  CONST_22  C02  C03  C04  C07   180.00   0.0  0
 CXW  CONST_23  H5   C26  C21  C22   180.00   0.0  0
 CXW  CONST_24  H3   C24  C23  C22   180.00   0.0  0
 CXW  CONST_25  H4   C25  C24  C23   180.00   0.0  0
 CXW  CONST_26  H2   C23  C24  C25   180.00   0.0  0
 CXW  CONST_27  H30  C03  C04  C05   180.00   0.0  0
 CXW  CONST_28  H24  C05  C06  N01   180.00   0.0  0
 CXW  Var_01    C2'  N1'  C5'  C4'     9.17  30.0  1
 CXW  Var_02    C3'  C2'  N1'  C5'   -30.52  30.0  1
 CXW  Var_03    C05  C06  C08  C3'    95.47  30.0  1
 CXW  Var_04    N12  C13  C21  C22    41.46  30.0  3
 CXW  Var_05    H25  C07  C04  C05   -74.81  30.0  2
 CXW  Var_06    C11  N12  C13  C21  -172.08  30.0  1
 CXW  Var_07    H12  C10  O09  C4'    73.37  30.0  3
 CXW  Var_08    C10  C11  N12  C13  -179.06  30.0  2
 CXW  Var_09    O09  C10  C11  N12    62.01  30.0  1

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
 CXW  chir_01  C4'  C3'  O09  C5'  positiv
 CXW  chir_02  C3'  C08  C4'  C2'  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
 CXW  plan-1  O22  0.020
 CXW  plan-1  C22  0.020
 CXW  plan-1  C23  0.020
 CXW  plan-1  C24  0.020
 CXW  plan-1  C25  0.020
 CXW  plan-1  C26  0.020
 CXW  plan-1  C21  0.020
 CXW  plan-1  C13  0.020
 CXW  plan-1  H2   0.020
 CXW  plan-1  H3   0.020
 CXW  plan-1  H4   0.020
 CXW  plan-1  H5   0.020
 CXW  plan-2  C08  0.020
 CXW  plan-2  C06  0.020
 CXW  plan-2  C05  0.020
 CXW  plan-2  C04  0.020
 CXW  plan-2  C07  0.020
 CXW  plan-2  N01  0.020
 CXW  plan-2  C02  0.020
 CXW  plan-2  N02  0.020
 CXW  plan-2  C03  0.020
 CXW  plan-2  H24  0.020
 CXW  plan-2  H30  0.020
 CXW  plan-3  C02  0.020
 CXW  plan-3  N02  0.020
 CXW  plan-3  H28  0.020
 CXW  plan-3  H29  0.020

