# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:21:35 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1C(=O)c2ccc(Cl)cc2Nc3ncccc13
#
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
 NJT  NJT  9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one  ligand  34  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NJT
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
 NJT  N3   N   NT    0  -0.576  6.1969  -45.5750  -45.1704
 NJT  C4   C   CR16  0  -0.181  7.4523  -44.2996  -46.8140
 NJT  C7   C   C     0   0.556  5.5702  -45.4311  -43.9745
 NJT  C8   C   CH2   0  -0.316  6.7436  -46.8917  -45.5128
 NJT  C10  C   CR6   0   0.312  3.8903  -43.6477  -44.6251
 NJT  C15  C   CR16  0  -0.267  2.9765  -42.6760  -44.2168
 NJT  C17  C   CH3   0  -0.668  6.3018  -49.1092  -46.6185
 NJT  C1   C   CR6   0   0.221  6.2541  -44.5827  -46.1727
 NJT  C2   C   CR6   0   0.377  5.1114  -43.9314  -46.6466
 NJT  N5   N   NH1   0  -0.716  3.9021  -44.0529  -45.9618
 NJT  N6   N   N     0  -0.421  5.1128  -43.1636  -47.7209
 NJT  C9   C   CR16  0  -0.337  7.4617  -43.4744  -47.9273
 NJT  C11  C   CR16  0  -0.063  6.2543  -42.9601  -48.3657
 NJT  C12  C   CR6   0  -0.108  4.7786  -44.1981  -43.6984
 NJT  O13  O   O     0  -0.464  5.6224  -46.2969  -43.1157
 NJT  C14  C   CH2   0  -0.427  5.7195  -47.7567  -46.2355
 NJT  C16  C   CR16  0  -0.292  4.7597  -43.7297  -42.3852
 NJT  C18  C   CR6   0  -0.041  2.9819  -42.2420  -42.9062
 NJT  C19  C   CR16  0  -0.221  3.8869  -42.7398  -41.9786
 NJT  CL1  CL  CL    0  -0.112  1.8471  -41.0319  -42.4190
 NJT  H1   H   HCR6  0   0.292  8.3743  -44.7445  -46.4629
 NJT  H2   H   HCH2  0   0.262  7.0879  -47.3788  -44.6032
 NJT  H3   H   HCH2  0   0.256  7.6224  -46.7540  -46.1413
 NJT  H4   H   HCR6  0   0.291  2.2789  -42.2588  -44.9313
 NJT  H5   H   HCH3  0   0.236  5.5578  -49.7276  -47.1199
 NJT  H6   H   HCH3  0   0.224  7.1501  -48.9970  -47.2956
 NJT  H7   H   HCH3  0   0.224  6.6495  -49.6561  -45.7404
 NJT  H8   H   HNH1  0   0.396  3.1429  -43.6570  -46.5005
 NJT  H9   H   HCR6  0   0.276  8.3818  -43.2525  -48.4484
 NJT  H10  H   HCR6  0   0.271  6.2019  -42.3511  -49.2602
 NJT  H11  H   HCH2  0   0.227  5.3749  -47.2348  -47.1324
 NJT  H12  H   HCH2  0   0.231  4.8448  -47.8920  -45.5953
 NJT  H13  H   HCR6  0   0.275  5.4371  -44.1600  -41.6599
 NJT  H14  H   HCR6  0   0.284  3.8927  -42.3832  -40.9586

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
 NJT  C11  C9   aromatic  1.384  0.020  1.384
 NJT  C11  N6   aromatic  1.327  0.020  1.327
 NJT  C9   C4   aromatic  1.386  0.020  1.386
 NJT  N6   C2   aromatic  1.320  0.020  1.320
 NJT  C4   C1   aromatic  1.388  0.020  1.388
 NJT  C2   C1   aromatic  1.398  0.020  1.398
 NJT  C2   N5   single    1.395  0.020  1.395
 NJT  C17  C14  single    1.522  0.020  1.522
 NJT  C1   N3   single    1.412  0.020  1.412
 NJT  C14  C8   single    1.523  0.020  1.523
 NJT  N5   C10  single    1.397  0.020  1.397
 NJT  C8   N3   single    1.466  0.020  1.466
 NJT  N3   C7   single    1.358  0.020  1.358
 NJT  C10  C15  aromatic  1.395  0.020  1.395
 NJT  C10  C12  aromatic  1.397  0.020  1.397
 NJT  C15  C18  aromatic  1.381  0.020  1.381
 NJT  C7   C12  single    1.491  0.020  1.491
 NJT  C7   O13  double    1.221  0.020  1.221
 NJT  C12  C16  aromatic  1.394  0.020  1.394
 NJT  C18  CL1  single    1.729  0.020  1.729
 NJT  C18  C19  aromatic  1.388  0.020  1.388
 NJT  C16  C19  aromatic  1.381  0.020  1.381
 NJT  C4   H1   single    0.930  0.020  1.080
 NJT  C8   H2   single    0.970  0.020  1.090
 NJT  C8   H3   single    0.970  0.020  1.090
 NJT  C15  H4   single    0.930  0.020  1.080
 NJT  C17  H5   single    0.970  0.020  1.090
 NJT  C17  H6   single    0.970  0.020  1.090
 NJT  C17  H7   single    0.970  0.020  1.090
 NJT  N5   H8   single    0.890  0.020  1.040
 NJT  C9   H9   single    0.930  0.020  1.080
 NJT  C11  H10  single    0.930  0.020  1.080
 NJT  C14  H11  single    0.970  0.020  1.090
 NJT  C14  H12  single    0.970  0.020  1.090
 NJT  C16  H13  single    0.930  0.020  1.080
 NJT  C19  H14  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
 NJT  C1   N3   C8   116.77  3.000
 NJT  C8   N3   C7   118.23  3.000
 NJT  C1   N3   C7   124.72  3.000
 NJT  H1   C4   C9   119.98  3.000
 NJT  H1   C4   C1   120.11  3.000
 NJT  C9   C4   C1   119.90  3.000
 NJT  O13  C7   C12  118.62  3.000
 NJT  O13  C7   N3   121.65  3.000
 NJT  C12  C7   N3   119.72  3.000
 NJT  H3   C8   H2   106.48  3.000
 NJT  H3   C8   C14  109.91  3.000
 NJT  H2   C8   C14  110.81  3.000
 NJT  H3   C8   N3   108.79  3.000
 NJT  H2   C8   N3   108.96  3.000
 NJT  C14  C8   N3   111.73  3.000
 NJT  C12  C10  N5   121.01  3.000
 NJT  C12  C10  C15  119.80  3.000
 NJT  N5   C10  C15  119.19  3.000
 NJT  H4   C15  C18  120.53  3.000
 NJT  H4   C15  C10  119.84  3.000
 NJT  C18  C15  C10  119.62  3.000
 NJT  H7   C17  H6   107.64  3.000
 NJT  H7   C17  H5   107.66  3.000
 NJT  H6   C17  H5   107.68  3.000
 NJT  H7   C17  C14  111.40  3.000
 NJT  H6   C17  C14  111.25  3.000
 NJT  H5   C17  C14  111.04  3.000
 NJT  C2   C1   C4   116.99  3.000
 NJT  C2   C1   N3   122.35  3.000
 NJT  C4   C1   N3   120.42  3.000
 NJT  N6   C2   N5   116.81  3.000
 NJT  N5   C2   C1   120.10  3.000
 NJT  N6   C2   C1   123.08  3.000
 NJT  H8   N5   C2   110.80  3.000
 NJT  H8   N5   C10  112.94  3.000
 NJT  C2   N5   C10  116.86  3.000
 NJT  C11  N6   C2   119.05  3.000
 NJT  H9   C9   C11  120.93  3.000
 NJT  H9   C9   C4   121.03  3.000
 NJT  C11  C9   C4   118.03  3.000
 NJT  H10  C11  C9   120.85  3.000
 NJT  H10  C11  N6   116.48  3.000
 NJT  C9   C11  N6   122.67  3.000
 NJT  C16  C12  C10  118.94  3.000
 NJT  C16  C12  C7   117.34  3.000
 NJT  C10  C12  C7   122.73  3.000
 NJT  H12  C14  H11  106.71  3.000
 NJT  H12  C14  C17  110.11  3.000
 NJT  H11  C14  C17  109.78  3.000
 NJT  H12  C14  C8   109.31  3.000
 NJT  H11  C14  C8   109.27  3.000
 NJT  C17  C14  C8   111.53  3.000
 NJT  H13  C16  C19  118.92  3.000
 NJT  H13  C16  C12  119.30  3.000
 NJT  C19  C16  C12  121.78  3.000
 NJT  CL1  C18  C19  119.37  3.000
 NJT  C19  C18  C15  121.61  3.000
 NJT  CL1  C18  C15  119.01  3.000
 NJT  H14  C19  C18  121.06  3.000
 NJT  H14  C19  C16  120.74  3.000
 NJT  C18  C19  C16  118.19  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
 NJT  CONST_01  N6   C11  C9   C4      0.00   0.0  0
 NJT  CONST_02  N6   C2   C1   C4      0.00   0.0  0
 NJT  CONST_03  C19  C18  C15  C10     0.00   0.0  0
 NJT  CONST_04  C19  C16  C12  C10     0.00   0.0  0
 NJT  CONST_05  C16  C12  C10  C15     0.00   0.0  0
 NJT  CONST_06  C16  C19  C18  C15     0.00   0.0  0
 NJT  CONST_07  C11  C9   C4   C1      0.00   0.0  0
 NJT  CONST_08  C11  N6   C2   C1      0.00   0.0  0
 NJT  CONST_09  C9   C11  N6   C2      0.00   0.0  0
 NJT  CONST_10  C9   C4   C1   C2      0.00   0.0  0
 NJT  CONST_11  C18  C15  C10  C12     0.00   0.0  0
 NJT  CONST_12  C18  C19  C16  C12     0.00   0.0  0
 NJT  CONST_13  C12  C7   N3   C1      0.00   0.0  0
 NJT  CONST_14  CL1  C18  C15  C10   180.00   0.0  0
 NJT  CONST_15  CL1  C18  C19  C16   180.00   0.0  0
 NJT  CONST_16  C12  C7   N3   C8    180.00   0.0  0
 NJT  CONST_17  O13  C7   N3   C1    180.00   0.0  0
 NJT  CONST_18  H1   C4   C1   N3      0.00   0.0  0
 NJT  CONST_19  H10  C11  C9   C4    180.00   0.0  0
 NJT  CONST_20  H13  C16  C12  C7      0.00   0.0  0
 NJT  CONST_21  H14  C19  C18  C15   180.00   0.0  0
 NJT  CONST_22  H9   C9   C4   C1    180.00   0.0  0
 NJT  CONST_23  H4   C15  C10  N5      0.00   0.0  0
 NJT  CONST_24  O13  C7   N3   C8      0.00   0.0  0
 NJT  Var_01    C10  C12  C7   N3     44.94  30.0  1
 NJT  Var_02    C7   N3   C1   C4    134.33  30.0  1
 NJT  Var_03    N6   C2   N5   C10  -120.67  30.0  1
 NJT  Var_04    C2   N5   C10  C15   123.56  30.0  1
 NJT  Var_05    C14  C8   N3   C7     89.49  30.0  3
 NJT  Var_06    C17  C14  C8   N3    178.62  30.0  1
 NJT  Var_07    H5   C17  C14  C8    179.04  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
 NJT  plan-1  N3   0.020
 NJT  plan-1  C7   0.020
 NJT  plan-1  C8   0.020
 NJT  plan-1  C1   0.020
 NJT  plan-1  C12  0.020
 NJT  plan-1  O13  0.020
 NJT  plan-2  C7   0.020
 NJT  plan-2  C10  0.020
 NJT  plan-2  C15  0.020
 NJT  plan-2  N5   0.020
 NJT  plan-2  C12  0.020
 NJT  plan-2  C16  0.020
 NJT  plan-2  C18  0.020
 NJT  plan-2  C19  0.020
 NJT  plan-2  CL1  0.020
 NJT  plan-2  H4   0.020
 NJT  plan-2  H13  0.020
 NJT  plan-2  H14  0.020
 NJT  plan-3  N3   0.020
 NJT  plan-3  C4   0.020
 NJT  plan-3  C1   0.020
 NJT  plan-3  C2   0.020
 NJT  plan-3  N5   0.020
 NJT  plan-3  N6   0.020
 NJT  plan-3  C9   0.020
 NJT  plan-3  C11  0.020
 NJT  plan-3  H1   0.020
 NJT  plan-3  H9   0.020
 NJT  plan-3  H10  0.020

