# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 02:17:36 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: N-methyl-1-[3-(morpholin-4-ylmethyl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cccc(CN2CCOCC2)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
 9X3  9X3  N-methyl-1-[3-(morpholin-4-ylmethyl)phenyl]methanamine  ligand  36  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9X3
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
 9X3  C10   C  CR6   0   0.124  -2.2943  -0.4091  -0.3872
 9X3  C01   C  CR16  0  -0.305  -2.7670  -1.6485   0.0463
 9X3  N01   N  NH1   0  -0.582  -3.5995   1.1714   0.9241
 9X3  C02   C  CR16  0  -0.346  -0.9609  -0.2904  -0.7531
 9X3  C03   C  CH2   0  -0.186   3.7562   1.5920  -0.6961
 9X3  C04   C  CR16  0  -0.230  -1.9173  -2.7404   0.0966
 9X3  C05   C  CH2   0  -0.302   3.2194   0.2798  -1.2362
 9X3  N     N  NT    0  -0.420   1.9499  -0.0262  -0.6052
 9X3  C06   C  CR6   0   0.103  -0.0921  -1.3810  -0.7044
 9X3  C07   C  CH2   0  -0.185   2.6721   1.2451   1.3314
 9X3  C08   C  CH3   0  -0.521  -4.5063   2.3012   0.9353
 9X3  O     O  O2    0  -0.487   3.8988   1.5573   0.7071
 9X3  C11   C  CR16  0  -0.332  -0.5822  -2.6058  -0.2730
 9X3  C     C  CH2   0  -0.298   2.1134  -0.0734   0.8354
 9X3  CAK   C  CH2   0  -0.320   1.3458  -1.2301  -1.1322
 9X3  CAJ   C  CH2   0  -0.337  -3.2140   0.7812  -0.4199
 9X3  H01   H  HCR6  0   0.244  -3.8045  -1.7546   0.3401
 9X3  H02   H  HCR6  0   0.238  -0.5788   0.6724  -1.0734
 9X3  HAJ1  H  HCH2  0   0.209  -2.7377   1.5985  -0.9833
 9X3  HAJ2  H  HCH2  0   0.233  -4.1250   0.5216  -0.9688
 9X3  H04   H  HCR6  0   0.250  -2.2895  -3.7008   0.4299
 9X3  HA    H  HNH1  0   0.343  -2.7643   1.4123   1.4439
 9X3  H081  H  HCH3  0   0.194  -4.1343   3.1859   0.3999
 9X3  H082  H  HCH3  0   0.222  -5.4556   2.0186   0.4760
 9X3  H083  H  HCH3  0   0.233  -4.7136   2.5968   1.9636
 9X3  H032  H  HCH2  0   0.199   3.0813   2.4074  -0.9938
 9X3  H051  H  HCH2  0   0.242   3.0761   0.3728  -2.3158
 9X3  H052  H  HCH2  0   0.196   3.9643  -0.5185  -1.0746
 9X3  H11   H  HCR6  0   0.246   0.0817  -3.4611  -0.2207
 9X3  HC1   H  HCH2  0   0.244   1.1467  -0.2503   1.3115
 9X3  HC2   H  HCH2  0   0.198   2.7791  -0.9001   1.1410
 9X3  HAK1  H  HCH2  0   0.252   1.3894  -1.1737  -2.2247
 9X3  HAK2  H  HCH2  0   0.212   1.9059  -2.1370  -0.8486
 9X3  H071  H  HCH2  0   0.235   2.8561   1.1979   2.4057
 9X3  H072  H  HCH2  0   0.199   1.9341   2.0387   1.1474
 9X3  H031  H  HCH2  0   0.235   4.7402   1.7996  -1.1191

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
 9X3  C10  C01   aromatic  1.395  0.020  1.395
 9X3  C10  C02   aromatic  1.388  0.020  1.388
 9X3  C10  CAJ   single    1.505  0.020  1.505
 9X3  C01  C04   aromatic  1.384  0.020  1.384
 9X3  N01  C08   single    1.449  0.020  1.449
 9X3  N01  CAJ   single    1.452  0.020  1.452
 9X3  C02  C06   aromatic  1.395  0.020  1.395
 9X3  C03  C05   single    1.517  0.020  1.517
 9X3  C03  O     single    1.411  0.020  1.411
 9X3  C04  C11   aromatic  1.392  0.020  1.392
 9X3  C05  N     single    1.450  0.020  1.450
 9X3  N    C     single    1.451  0.020  1.451
 9X3  N    CAK   single    1.446  0.020  1.446
 9X3  C06  C11   aromatic  1.388  0.020  1.388
 9X3  C06  CAK   single    1.508  0.020  1.508
 9X3  C07  O     single    1.411  0.020  1.411
 9X3  C07  C     single    1.515  0.020  1.515
 9X3  C01  H01   single    0.930  0.020  1.080
 9X3  C02  H02   single    0.930  0.020  1.080
 9X3  CAJ  HAJ1  single    0.970  0.020  1.090
 9X3  CAJ  HAJ2  single    0.970  0.020  1.090
 9X3  C04  H04   single    0.930  0.020  1.080
 9X3  N01  HA    single    0.890  0.020  1.040
 9X3  C08  H081  single    0.970  0.020  1.090
 9X3  C08  H082  single    0.970  0.020  1.090
 9X3  C08  H083  single    0.970  0.020  1.090
 9X3  C03  H031  single    0.970  0.020  1.090
 9X3  C03  H032  single    0.970  0.020  1.090
 9X3  C05  H051  single    0.970  0.020  1.090
 9X3  C05  H052  single    0.970  0.020  1.090
 9X3  C11  H11   single    0.930  0.020  1.080
 9X3  C    HC1   single    0.970  0.020  1.090
 9X3  C    HC2   single    0.970  0.020  1.090
 9X3  CAK  HAK1  single    0.970  0.020  1.090
 9X3  CAK  HAK2  single    0.970  0.020  1.090
 9X3  C07  H071  single    0.970  0.020  1.090
 9X3  C07  H072  single    0.970  0.020  1.090

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
 9X3  CAJ   C10  C02   120.93  3.000
 9X3  CAJ   C10  C01   120.15  3.000
 9X3  C02   C10  C01   118.90  3.000
 9X3  H01   C01  C04   120.04  3.000
 9X3  H01   C01  C10   119.70  3.000
 9X3  C04   C01  C10   120.26  3.000
 9X3  HA    N01  CAJ   108.67  3.000
 9X3  HA    N01  C08   109.07  3.000
 9X3  CAJ   N01  C08   112.52  3.000
 9X3  H02   C02  C06   119.01  3.000
 9X3  H02   C02  C10   119.50  3.000
 9X3  C06   C02  C10   121.49  3.000
 9X3  H032  C03  H031  107.91  3.000
 9X3  H032  C03  O     110.46  3.000
 9X3  H031  C03  O     107.41  3.000
 9X3  H032  C03  C05   109.14  3.000
 9X3  H031  C03  C05   110.22  3.000
 9X3  O     C03  C05   111.63  3.000
 9X3  H04   C04  C11   119.82  3.000
 9X3  H04   C04  C01   119.99  3.000
 9X3  C11   C04  C01   120.18  3.000
 9X3  H052  C05  H051  107.13  3.000
 9X3  H052  C05  N     111.99  3.000
 9X3  H051  C05  N     109.44  3.000
 9X3  H052  C05  C03   109.55  3.000
 9X3  H051  C05  C03   108.93  3.000
 9X3  N     C05  C03   109.71  3.000
 9X3  CAK   N    C     112.45  3.000
 9X3  CAK   N    C05   112.50  3.000
 9X3  C     N    C05   109.89  3.000
 9X3  CAK   C06  C11   120.88  3.000
 9X3  CAK   C06  C02   120.38  3.000
 9X3  C11   C06  C02   118.73  3.000
 9X3  H072  C07  H071  108.02  3.000
 9X3  H072  C07  C     109.02  3.000
 9X3  H071  C07  C     110.29  3.000
 9X3  H072  C07  O     110.48  3.000
 9X3  H071  C07  O     107.37  3.000
 9X3  C     C07  O     111.60  3.000
 9X3  H083  C08  H082  107.56  3.000
 9X3  H083  C08  H081  107.80  3.000
 9X3  H082  C08  H081  107.33  3.000
 9X3  H083  C08  N01   109.75  3.000
 9X3  H082  C08  N01   109.83  3.000
 9X3  H081  C08  N01   114.34  3.000
 9X3  C07   O    C03   110.94  3.000
 9X3  H11   C11  C06   119.66  3.000
 9X3  H11   C11  C04   119.90  3.000
 9X3  C06   C11  C04   120.44  3.000
 9X3  HC2   C    HC1   106.96  3.000
 9X3  HC2   C    C07   109.79  3.000
 9X3  HC1   C    C07   108.94  3.000
 9X3  HC2   C    N     111.53  3.000
 9X3  HC1   C    N     109.78  3.000
 9X3  C07   C    N     109.77  3.000
 9X3  HAK2  CAK  HAK1  106.19  3.000
 9X3  HAK2  CAK  C06   109.21  3.000
 9X3  HAK1  CAK  C06   109.04  3.000
 9X3  HAK2  CAK  N     112.25  3.000
 9X3  HAK1  CAK  N     107.70  3.000
 9X3  C06   CAK  N     112.23  3.000
 9X3  HAJ2  CAJ  HAJ1  106.22  3.000
 9X3  HAJ2  CAJ  N01   107.87  3.000
 9X3  HAJ1  CAJ  N01   112.90  3.000
 9X3  HAJ2  CAJ  C10   109.39  3.000
 9X3  HAJ1  CAJ  C10   109.51  3.000
 9X3  N01   CAJ  C10   110.79  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
 9X3  CONST_01  C11   C04  C01  C10     0.00   0.0  0
 9X3  CONST_02  C11   C06  C02  C10     0.00   0.0  0
 9X3  CONST_03  C06   C02  C10  C01     0.00   0.0  0
 9X3  CONST_04  C06   C11  C04  C01     0.00   0.0  0
 9X3  CONST_05  C04   C01  C10  C02     0.00   0.0  0
 9X3  CONST_06  C04   C11  C06  C02     0.00   0.0  0
 9X3  CONST_07  CAK   C06  C02  C10   180.00   0.0  0
 9X3  CONST_08  CAJ   C10  C01  C04   180.00   0.0  0
 9X3  CONST_09  CAK   C06  C11  C04   180.00   0.0  0
 9X3  CONST_10  CAJ   C10  C02  C06   180.00   0.0  0
 9X3  CONST_11  H04   C04  C01  C10   180.00   0.0  0
 9X3  CONST_12  H02   C02  C10  C01   180.00   0.0  0
 9X3  CONST_13  H11   C11  C04  C01   180.00   0.0  0
 9X3  CONST_14  H01   C01  C10  C02   180.00   0.0  0
 9X3  Var_01    C     N    C05  C03   -57.16  30.0  1
 9X3  Var_02    C     C07  O    C03    57.00  30.0  1
 9X3  Var_03    C07   C    N    C05    57.23  30.0  1
 9X3  Var_04    O     C03  C05  N      57.23  30.0  1
 9X3  Var_05    O     C07  C    N     -57.28  30.0  1
 9X3  Var_06    N     CAK  C06  C02    44.55  30.0  2
 9X3  Var_07    C06   CAK  N    C05  -167.38  30.0  3
 9X3  Var_08    N01   CAJ  C10  C01    66.91  30.0  2
 9X3  Var_09    C08   N01  CAJ  C10  -178.94  30.0  1
 9X3  Var_10    H081  C08  N01  CAJ   -55.03  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
 9X3  plan-1  C10  0.020
 9X3  plan-1  C01  0.020
 9X3  plan-1  C02  0.020
 9X3  plan-1  C04  0.020
 9X3  plan-1  C06  0.020
 9X3  plan-1  C11  0.020
 9X3  plan-1  CAK  0.020
 9X3  plan-1  CAJ  0.020
 9X3  plan-1  H01  0.020
 9X3  plan-1  H02  0.020
 9X3  plan-1  H04  0.020
 9X3  plan-1  H11  0.020

