# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:52:28 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-[(2~{S})-1-[[iminomethyl(methyl)amino]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-(phenylmethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)NCc1ccccc1)C(=O)N(C)N(C)C=N
#
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
 ORW  ORW  1-[(2~{S})-1-[[iminomethyl(methyl)amino]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-(phenylmethyl)urea  ligand  51  24  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ORW
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
 ORW  OAW  O  O     0  -0.529  -21.8056  12.6309  -22.5948
 ORW  CAN  C  C     0   0.750  -21.6299  11.4734  -22.9549
 ORW  N    N  NH1   0  -0.672  -20.7591  10.6422  -22.3140
 ORW  CA   C  CH1   0  -0.210  -19.8913  11.1860  -21.3090
 ORW  CB   C  CH2   0  -0.445  -19.1077  10.0665  -20.6189
 ORW  CG   C  CH1   0  -0.228  -19.9617   9.0622  -19.8421
 ORW  CD2  C  CH3   0  -0.671  -20.7876   9.7386  -18.7532
 ORW  CD1  C  CH3   0  -0.655  -19.0578   7.9890  -19.2431
 ORW  C    C  C     0   0.581  -18.9082  12.1833  -21.9274
 ORW  O    O  O     0  -0.464  -18.5499  12.0829  -23.0838
 ORW  NAE  N  NT    0  -0.356  -18.4067  13.1488  -21.1047
 ORW  CAF  C  CH3   0  -0.526  -18.8536  13.4328  -19.7520
 ORW  NAC  N  NT    0  -0.270  -17.6000  14.1056  -21.6732
 ORW  CAD  C  CH3   0  -0.514  -18.2420  15.1747  -22.4074
 ORW  CAB  C  C1    0   0.124  -16.3087  13.7465  -21.9296
 ORW  NAA  N  N     0  -0.645  -15.5572  14.4211  -22.6988
 ORW  NAO  N  NH1   0  -0.685  -22.2909  10.9246  -24.0060
 ORW  CAP  C  CH2   0  -0.335  -23.3629  11.6337  -24.6522
 ORW  CAQ  C  CR6   0   0.097  -24.6265  11.7730  -23.8325
 ORW  CAV  C  CR16  0  -0.304  -25.5043  12.8197  -24.1017
 ORW  CAU  C  CR16  0  -0.243  -26.6941  12.9504  -23.3986
 ORW  CAT  C  CR16  0  -0.272  -27.0216  12.0344  -22.4072
 ORW  CAS  C  CR16  0  -0.242  -26.1499  10.9902  -22.1288
 ORW  CAR  C  CR16  0  -0.294  -24.9620  10.8604  -22.8375
 ORW  H1   H  HNH1  0   0.391  -20.4604   9.7989  -22.7792
 ORW  H2   H  HCH1  0   0.274  -20.5164  11.7010  -20.5789
 ORW  H3   H  HCH2  0   0.252  -18.5129   9.5402  -21.3734
 ORW  H4   H  HCH2  0   0.245  -18.3846  10.5166  -19.9317
 ORW  H5   H  HCH1  0   0.226  -20.6479   8.5719  -20.5405
 ORW  H6   H  HCH3  0   0.237  -21.3306   8.9994  -18.1627
 ORW  H7   H  HCH3  0   0.217  -20.1472  10.3007  -18.0683
 ORW  H8   H  HCH3  0   0.231  -21.5273  10.4287  -19.1611
 ORW  H9   H  HCH3  0   0.230  -19.6405   7.2452  -18.6977
 ORW  H10  H  HCH3  0   0.228  -18.4905   7.4657  -20.0145
 ORW  H11  H  HCH3  0   0.216  -18.3418   8.4272  -18.5434
 ORW  H12  H  HCH3  0   0.253  -19.1228  12.5218  -19.2249
 ORW  H13  H  HCH3  0   0.268  -18.0307  13.8878  -19.2073
 ORW  H14  H  HCH3  0   0.251  -19.7085  14.1118  -19.7343
 ORW  H15  H  HCH3  0   0.247  -19.1610  15.4526  -21.8956
 ORW  H16  H  HCH3  0   0.251  -17.5864  16.0420  -22.4294
 ORW  H17  H  HCH3  0   0.236  -18.4792  14.8899  -23.4346
 ORW  H18  H  H     0   0.242  -16.0093  12.8531  -21.3791
 ORW  H19  H  H     0   0.341  -14.6294  14.0161  -22.7035
 ORW  H20  H  HNH1  0   0.398  -22.2112   9.9359  -24.1776
 ORW  H21  H  HCH2  0   0.272  -23.5917  11.0954  -25.5737
 ORW  H22  H  HCH2  0   0.254  -23.0201  12.6243  -24.9562
 ORW  H23  H  HCR6  0   0.247  -25.2543  13.5461  -24.8669
 ORW  H24  H  HCR6  0   0.253  -27.3637  13.7715  -23.6212
 ORW  H25  H  HCR6  0   0.253  -27.9469  12.1349  -21.8547
 ORW  H26  H  HCR6  0   0.253  -26.3933  10.2715  -21.3565
 ORW  H27  H  HCR6  0   0.241  -24.2913  10.0423  -22.6047

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
 ORW  CAP  CAQ  single    1.513  0.020  1.513
 ORW  CAP  NAO  single    1.439  0.020  1.439
 ORW  CAV  CAQ  aromatic  1.392  0.020  1.392
 ORW  CAV  CAU  aromatic  1.388  0.020  1.388
 ORW  CAQ  CAR  aromatic  1.391  0.020  1.391
 ORW  CAU  CAT  aromatic  1.389  0.020  1.389
 ORW  NAO  CAN  single    1.358  0.020  1.358
 ORW  O    C    double    1.215  0.020  1.215
 ORW  CAR  CAS  aromatic  1.389  0.020  1.389
 ORW  CAT  CAS  aromatic  1.388  0.020  1.388
 ORW  CAD  NAC  single    1.447  0.020  1.447
 ORW  CAN  OAW  double    1.225  0.020  1.225
 ORW  CAN  N    single    1.364  0.020  1.364
 ORW  N    CA   single    1.435  0.020  1.435
 ORW  NAA  CAB  double    1.269  0.020  1.269
 ORW  NAC  CAB  single    1.365  0.020  1.365
 ORW  NAC  NAE  single    1.375  0.020  1.375
 ORW  C    NAE  single    1.364  0.020  1.364
 ORW  C    CA   single    1.531  0.020  1.531
 ORW  NAE  CAF  single    1.453  0.020  1.453
 ORW  CA   CB   single    1.531  0.020  1.531
 ORW  CB   CG   single    1.530  0.020  1.530
 ORW  CG   CD1  single    1.526  0.020  1.526
 ORW  CG   CD2  single    1.525  0.020  1.525
 ORW  N    H1   single    0.890  0.020  1.040
 ORW  CA   H2   single    0.970  0.020  1.090
 ORW  CB   H3   single    0.970  0.020  1.090
 ORW  CB   H4   single    0.970  0.020  1.090
 ORW  CG   H5   single    0.970  0.020  1.090
 ORW  CD2  H6   single    0.970  0.020  1.090
 ORW  CD2  H7   single    0.970  0.020  1.090
 ORW  CD2  H8   single    0.970  0.020  1.090
 ORW  CD1  H9   single    0.970  0.020  1.090
 ORW  CD1  H10  single    0.970  0.020  1.090
 ORW  CD1  H11  single    0.970  0.020  1.090
 ORW  CAF  H12  single    0.970  0.020  1.090
 ORW  CAF  H13  single    0.970  0.020  1.090
 ORW  CAF  H14  single    0.970  0.020  1.090
 ORW  CAD  H15  single    0.970  0.020  1.090
 ORW  CAD  H16  single    0.970  0.020  1.090
 ORW  CAD  H17  single    0.970  0.020  1.090
 ORW  CAB  H18  single    0.930  0.020  1.080
 ORW  NAA  H19  single    0.890  0.020  1.040
 ORW  NAO  H20  single    0.860  0.020  1.020
 ORW  CAP  H21  single    0.970  0.020  1.090
 ORW  CAP  H22  single    0.970  0.020  1.090
 ORW  CAV  H23  single    0.930  0.020  1.080
 ORW  CAU  H24  single    0.930  0.020  1.080
 ORW  CAT  H25  single    0.930  0.020  1.080
 ORW  CAS  H26  single    0.930  0.020  1.080
 ORW  CAR  H27  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
 ORW  NAO  CAN  N    115.36  3.000
 ORW  N    CAN  OAW  121.97  3.000
 ORW  NAO  CAN  OAW  122.67  3.000
 ORW  H1   N    CA   117.45  3.000
 ORW  H1   N    CAN  118.82  3.000
 ORW  CA   N    CAN  118.97  3.000
 ORW  H2   CA   C    109.33  3.000
 ORW  H2   CA   CB   109.69  3.000
 ORW  C    CA   CB   109.25  3.000
 ORW  H2   CA   N    107.54  3.000
 ORW  CB   CA   N    110.38  3.000
 ORW  C    CA   N    110.63  3.000
 ORW  H4   CB   H3   105.74  3.000
 ORW  H4   CB   CG   108.66  3.000
 ORW  H3   CB   CG   109.72  3.000
 ORW  H4   CB   CA   108.69  3.000
 ORW  H3   CB   CA   108.59  3.000
 ORW  CG   CB   CA   115.03  3.000
 ORW  H5   CG   CD1  107.86  3.000
 ORW  H5   CG   CD2  108.34  3.000
 ORW  CD1  CG   CD2  110.64  3.000
 ORW  H5   CG   CB   108.65  3.000
 ORW  CD2  CG   CB   111.94  3.000
 ORW  CD1  CG   CB   109.29  3.000
 ORW  H8   CD2  H7   107.83  3.000
 ORW  H8   CD2  H6   107.07  3.000
 ORW  H7   CD2  H6   107.51  3.000
 ORW  H8   CD2  CG   112.39  3.000
 ORW  H7   CD2  CG   110.99  3.000
 ORW  H6   CD2  CG   110.83  3.000
 ORW  H11  CD1  H10  107.72  3.000
 ORW  H11  CD1  H9   107.65  3.000
 ORW  H10  CD1  H9   107.70  3.000
 ORW  H11  CD1  CG   110.95  3.000
 ORW  H10  CD1  CG   111.58  3.000
 ORW  H9   CD1  CG   111.06  3.000
 ORW  NAE  C    O    121.62  3.000
 ORW  NAE  C    CA   116.97  3.000
 ORW  O    C    CA   121.34  3.000
 ORW  NAC  NAE  CAF  115.44  3.000
 ORW  CAF  NAE  C    125.94  3.000
 ORW  NAC  NAE  C    117.33  3.000
 ORW  H14  CAF  H13  108.93  3.000
 ORW  H14  CAF  H12  108.64  3.000
 ORW  H13  CAF  H12  107.19  3.000
 ORW  H14  CAF  NAE  112.18  3.000
 ORW  H13  CAF  NAE  108.40  3.000
 ORW  H12  CAF  NAE  111.35  3.000
 ORW  CAB  NAC  CAD  121.26  3.000
 ORW  CAB  NAC  NAE  116.74  3.000
 ORW  CAD  NAC  NAE  117.62  3.000
 ORW  H17  CAD  H16  108.65  3.000
 ORW  H17  CAD  H15  109.00  3.000
 ORW  H16  CAD  H15  108.37  3.000
 ORW  H17  CAD  NAC  112.39  3.000
 ORW  H16  CAD  NAC  109.39  3.000
 ORW  H15  CAD  NAC  108.95  3.000
 ORW  H18  CAB  NAA  125.33  3.000
 ORW  H18  CAB  NAC  112.35  3.000
 ORW  NAA  CAB  NAC  122.29  3.000
 ORW  H19  NAA  CAB  109.43  3.000
 ORW  H20  NAO  CAP  117.81  3.000
 ORW  H20  NAO  CAN  119.38  3.000
 ORW  CAP  NAO  CAN  120.75  3.000
 ORW  H22  CAP  H21  106.16  3.000
 ORW  H22  CAP  CAQ  109.25  3.000
 ORW  H21  CAP  CAQ  109.13  3.000
 ORW  H22  CAP  NAO  109.78  3.000
 ORW  H21  CAP  NAO  107.00  3.000
 ORW  CAQ  CAP  NAO  115.11  3.000
 ORW  CAR  CAQ  CAV  118.65  3.000
 ORW  CAR  CAQ  CAP  121.91  3.000
 ORW  CAV  CAQ  CAP  119.41  3.000
 ORW  H23  CAV  CAU  119.47  3.000
 ORW  H23  CAV  CAQ  119.65  3.000
 ORW  CAU  CAV  CAQ  120.88  3.000
 ORW  H24  CAU  CAT  120.07  3.000
 ORW  H24  CAU  CAV  119.83  3.000
 ORW  CAT  CAU  CAV  120.10  3.000
 ORW  H25  CAT  CAS  120.28  3.000
 ORW  H25  CAT  CAU  120.31  3.000
 ORW  CAS  CAT  CAU  119.41  3.000
 ORW  H26  CAS  CAR  119.61  3.000
 ORW  H26  CAS  CAT  120.07  3.000
 ORW  CAR  CAS  CAT  120.32  3.000
 ORW  H27  CAR  CAS  119.36  3.000
 ORW  H27  CAR  CAQ  119.99  3.000
 ORW  CAS  CAR  CAQ  120.65  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
 ORW  CONST_01  CAT  CAU  CAV  CAQ     0.00   0.0  0
 ORW  CONST_02  CAT  CAS  CAR  CAQ     0.00   0.0  0
 ORW  CONST_03  CAS  CAR  CAQ  CAV     0.00   0.0  0
 ORW  CONST_04  CAS  CAT  CAU  CAV     0.00   0.0  0
 ORW  CONST_05  CAR  CAQ  CAV  CAU     0.00   0.0  0
 ORW  CONST_06  CAR  CAS  CAT  CAU     0.00   0.0  0
 ORW  CONST_07  CAU  CAV  CAQ  CAP   180.00   0.0  0
 ORW  CONST_08  CAS  CAR  CAQ  CAP   180.00   0.0  0
 ORW  CONST_09  H24  CAU  CAV  CAQ   180.00   0.0  0
 ORW  CONST_10  H26  CAS  CAR  CAQ   180.00   0.0  0
 ORW  CONST_11  H27  CAR  CAQ  CAV   180.00   0.0  0
 ORW  CONST_12  H25  CAT  CAU  CAV   180.00   0.0  0
 ORW  CONST_13  H23  CAV  CAU  CAT   180.00   0.0  0
 ORW  CONST_14  CAP  NAO  CAN  OAW     0.00   0.0  0
 ORW  CONST_15  CA   N    CAN  OAW     0.00   0.0  0
 ORW  CONST_16  NAC  NAE  C    CA    180.00   0.0  0
 ORW  CONST_17  CAF  NAE  C    CA      0.00   0.0  0
 ORW  CONST_18  NAC  NAE  C    O       0.00   0.0  0
 ORW  CONST_19  CAF  NAE  C    O     180.00   0.0  0
 ORW  CONST_20  CAP  NAO  CAN  N     180.00   0.0  0
 ORW  CONST_21  NAO  CAN  N    CA    180.00   0.0  0
 ORW  CONST_23  NAA  CAB  NAC  CAD     0.00   0.0  0
 ORW  CONST_24  H20  NAO  CAN  OAW   180.00   0.0  0
 ORW  CONST_27  H19  NAA  CAB  NAC   180.00   0.0  0
 ORW  Var_01    CAV  CAQ  CAP  NAO   155.68  30.0  2
 ORW  Var_02    CAQ  CAP  NAO  CAN   -69.93  30.0  1
 ORW  Var_03    CD1  CG   CB   CA    178.46  30.0  3
 ORW  Var_04    CAD  NAC  NAE  C      78.34  30.0  2
 ORW  Var_05    H9   CD1  CG   CB   -178.90  30.0  3
 ORW  Var_06    H6   CD2  CG   CB   -175.71  30.0  3
 ORW  Var_07    H12  CAF  NAE  C      36.55  30.0  3
 ORW  Var_08    H15  CAD  NAC  NAE    37.69  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
 ORW  chir_01  CA  N  C  CB  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
 ORW  plan-1  CAP  0.020
 ORW  plan-1  CAQ  0.020
 ORW  plan-1  CAV  0.020
 ORW  plan-1  CAU  0.020
 ORW  plan-1  CAT  0.020
 ORW  plan-1  CAS  0.020
 ORW  plan-1  CAR  0.020
 ORW  plan-1  H23  0.020
 ORW  plan-1  H24  0.020
 ORW  plan-1  H25  0.020
 ORW  plan-1  H26  0.020
 ORW  plan-1  H27  0.020
 ORW  plan-2  OAW  0.020
 ORW  plan-2  CAN  0.020
 ORW  plan-2  N    0.020
 ORW  plan-2  CA   0.020
 ORW  plan-2  NAO  0.020
 ORW  plan-2  CAP  0.020
 ORW  plan-2  H1   0.020
 ORW  plan-2  H20  0.020
 ORW  plan-3  CA   0.020
 ORW  plan-3  C    0.020
 ORW  plan-3  O    0.020
 ORW  plan-3  NAE  0.020
 ORW  plan-3  CAF  0.020
 ORW  plan-3  NAC  0.020
 ORW  plan-4  NAE  0.020
 ORW  plan-4  NAC  0.020
 ORW  plan-4  CAD  0.020
 ORW  plan-4  CAB  0.020
 ORW  plan-4  NAA  0.020
 ORW  plan-4  H18  0.020
 ORW  plan-4  H19  0.020

