# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:40:31 2021
#   Inital geometry file: a 66 line input string
#   Ligand name: (3R)-3-methyl-1,2,3,4-tetrahydro-5H-1,4-benzodiazepin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CNc2ccccc2C(=O)N1
#
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
 XLY  XLY  (3R)-3-methyl-1,2,3,4-tetrahydro-5H-1,4-benzodiazepin-5-one  ligand  25  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XLY
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
 XLY  N1   N  NH1   0  -0.625   -9.4316   -7.7309  96.8499
 XLY  C4   C  CR16  0  -0.367   -5.9436   -5.0339  96.2317
 XLY  C5   C  CR16  0  -0.240   -6.1711   -3.7364  96.6195
 XLY  C6   C  CR16  0  -0.288   -7.4491   -3.3302  97.0046
 XLY  C7   C  CR16  0  -0.269   -8.4661   -4.2569  96.9701
 XLY  C8   C  CR6   0  -0.130   -8.2687   -5.5947  96.5920
 XLY  C9   C  C     0   0.496   -9.5123   -6.4173  96.5817
 XLY  C1   C  CH1   0  -0.116   -8.2394   -8.5021  97.1329
 XLY  C    C  CH3   0  -0.691   -8.6508   -9.9229  97.4820
 XLY  C3   C  CR6   0   0.390   -6.9710   -6.0065  96.2079
 XLY  N    N  NH1   0  -0.710   -6.6087   -7.2415  95.7662
 XLY  C2   C  CH2   0  -0.241   -7.3060   -8.4925  95.9300
 XLY  H11  H  HNH1  0   0.395  -10.3061   -8.2344  96.8046
 XLY  H7   H  HCR6  0   0.260   -4.9450   -5.3349  95.9368
 XLY  H8   H  HCR6  0   0.258   -5.3468   -3.0348  96.6280
 XLY  H9   H  HCR6  0   0.248   -7.6403   -2.3136  97.3195
 XLY  H10  H  HCR6  0   0.256   -9.4645   -3.9515  97.2523
 XLY  H3   H  HCH1  0   0.260   -7.7153   -8.0681  97.9912
 XLY  H    H  HCH3  0   0.252   -9.3572   -9.9327  98.3122
 XLY  H2   H  HCH3  0   0.237   -9.1166  -10.4196  96.6289
 XLY  H1   H  HCH3  0   0.252   -7.7802  -10.5058  97.7791
 XLY  H6   H  HNH1  0   0.395   -5.6301   -7.3351  95.5550
 XLY  H4   H  HCH2  0   0.251   -6.5458   -9.2649  96.0531
 XLY  H5   H  HCH2  0   0.230   -7.8873   -8.7565  95.0393
 XLY  O    O  O     0  -0.501  -10.6030   -5.8887  96.3777

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
 XLY  C   C1   single    1.520  0.020  1.520
 XLY  C1  C2   single    1.523  0.020  1.523
 XLY  C2  N    single    1.442  0.020  1.442
 XLY  N   C3   single    1.361  0.020  1.361
 XLY  C3  C4   aromatic  1.415  0.020  1.415
 XLY  C4  C5   aromatic  1.373  0.020  1.373
 XLY  C5  C6   aromatic  1.395  0.020  1.395
 XLY  C6  C7   aromatic  1.376  0.020  1.376
 XLY  C7  C8   aromatic  1.404  0.020  1.404
 XLY  C3  C8   aromatic  1.415  0.020  1.415
 XLY  C8  C9   single    1.491  0.020  1.491
 XLY  N1  C9   single    1.343  0.020  1.343
 XLY  C1  N1   single    1.448  0.020  1.448
 XLY  C9  O    double    1.229  0.020  1.229
 XLY  N1  H11  single    0.860  0.020  1.020
 XLY  C4  H7   single    0.930  0.020  1.080
 XLY  C5  H8   single    0.930  0.020  1.080
 XLY  C6  H9   single    0.930  0.020  1.080
 XLY  C7  H10  single    0.930  0.020  1.080
 XLY  C1  H3   single    0.970  0.020  1.090
 XLY  C   H    single    0.970  0.020  1.090
 XLY  C   H2   single    0.970  0.020  1.090
 XLY  C   H1   single    0.970  0.020  1.090
 XLY  N   H6   single    0.890  0.020  1.040
 XLY  C2  H4   single    0.970  0.020  1.090
 XLY  C2  H5   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
 XLY  H11  N1  C1  117.14  3.000
 XLY  H11  N1  C9  115.25  3.000
 XLY  C1   N1  C9  127.55  3.000
 XLY  H7   C4  C3  118.26  3.000
 XLY  H7   C4  C5  119.47  3.000
 XLY  C3   C4  C5  122.28  3.000
 XLY  H8   C5  C6  120.44  3.000
 XLY  H8   C5  C4  119.24  3.000
 XLY  C6   C5  C4  120.32  3.000
 XLY  H9   C6  C7  120.64  3.000
 XLY  H9   C6  C5  121.07  3.000
 XLY  C7   C6  C5  118.28  3.000
 XLY  H10  C7  C8  117.97  3.000
 XLY  H10  C7  C6  119.04  3.000
 XLY  C8   C7  C6  122.98  3.000
 XLY  C3   C8  C9  127.06  3.000
 XLY  C9   C8  C7  114.22  3.000
 XLY  C3   C8  C7  118.65  3.000
 XLY  O    C9  C8  120.27  3.000
 XLY  O    C9  N1  120.47  3.000
 XLY  C8   C9  N1  119.21  3.000
 XLY  H3   C1  C2  108.86  3.000
 XLY  H3   C1  C   108.66  3.000
 XLY  C2   C1  C   110.69  3.000
 XLY  H3   C1  N1  109.64  3.000
 XLY  C2   C1  N1  110.31  3.000
 XLY  C    C1  N1  108.66  3.000
 XLY  H1   C   H2  108.10  3.000
 XLY  H1   C   H   107.78  3.000
 XLY  H2   C   H   108.34  3.000
 XLY  H1   C   C1  110.28  3.000
 XLY  H2   C   C1  111.19  3.000
 XLY  H    C   C1  111.03  3.000
 XLY  N    C3  C8  126.62  3.000
 XLY  C8   C3  C4  117.48  3.000
 XLY  N    C3  C4  115.85  3.000
 XLY  H6   N   C2  114.45  3.000
 XLY  H6   N   C3  114.31  3.000
 XLY  C2   N   C3  128.46  3.000
 XLY  H5   C2  H4  106.91  3.000
 XLY  H5   C2  N   111.92  3.000
 XLY  H4   C2  N   106.87  3.000
 XLY  H5   C2  C1  108.38  3.000
 XLY  H4   C2  C1  109.49  3.000
 XLY  N    C2  C1  113.06  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
 XLY  CONST_01  C7   C6  C5  C4    0.00  0.0  0
 XLY  CONST_02  C8   C7  C6  C5    0.00  0.0  0
 XLY  CONST_03  C3   C4  C5  C6    0.00  0.0  0
 XLY  CONST_04  H9   C6  C5  C4  180.00  0.0  0
 XLY  CONST_05  H10  C7  C6  C5  180.00  0.0  0
 XLY  CONST_06  H7   C4  C5  C6  180.00  0.0  0
 XLY  CONST_07  H8   C5  C6  C7  180.00  0.0  0

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
 XLY  chir_01  C1  C  C2  N1  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
 XLY  plan-1  N1   0.020
 XLY  plan-1  C8   0.020
 XLY  plan-1  C9   0.020
 XLY  plan-1  C1   0.020
 XLY  plan-1  H11  0.020
 XLY  plan-1  O    0.020
 XLY  plan-2  C4   0.020
 XLY  plan-2  C5   0.020
 XLY  plan-2  C6   0.020
 XLY  plan-2  C7   0.020
 XLY  plan-2  C8   0.020
 XLY  plan-2  C9   0.020
 XLY  plan-2  C3   0.020
 XLY  plan-2  N    0.020
 XLY  plan-2  H7   0.020
 XLY  plan-2  H8   0.020
 XLY  plan-2  H9   0.020
 XLY  plan-2  H10  0.020

