# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:49:07 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-chloro-6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCc2cncn2[C@H]1c3ccc(cc3c4ccccc4Cl)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
 6M3  6M3  2'-chloro-6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile  ligand  44  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6M3
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
 6M3  C1   C   CR5   0   0.294   3.4420  -0.6986  -0.1636
 6M3  C3   C   CR15  0   0.098   2.3030  -0.8923   1.7062
 6M3  C11  C   CR16  0  -0.263  -1.8159   1.9078   0.1630
 6M3  C12  C   CR6   0   0.035  -1.2227   0.6591   0.0210
 6M3  C13  C   CR6   0   0.128  -2.1434  -0.5057   0.0028
 6M3  C14  C   CSP   0   0.052  -1.6744   4.3323   0.3817
 6M3  C16  C   CR6   0  -0.117  -2.3004  -1.3434   1.1018
 6M3  C17  C   CR16  0  -0.202  -3.2036  -2.3972   1.0982
 6M3  C18  C   CR16  0  -0.271  -3.9893  -2.6105  -0.0224
 6M3  C19  C   CR16  0  -0.241  -3.8743  -1.7698  -1.1220
 6M3  C20  C   CR16  0  -0.258  -2.9581  -0.7326  -1.1039
 6M3  C21  C   CH2   0  -0.524   3.8135  -0.5897  -1.6046
 6M3  C22  C   CH2   0  -0.464   2.9655   0.3985  -2.4008
 6M3  C23  C   CH2   0  -0.494   1.5545  -0.1071  -2.7208
 6M3  C24  C   CH1   0   0.069   0.9879  -1.1649  -1.7791
 6M3  N2   N   NR5   0  -0.477   2.1697  -0.8075   0.3584
 6M3  N4   N   N     0  -0.443   3.5490  -0.8515   2.0839
 6M3  C5   C   CR15  0  -0.271   4.2654  -0.7275   0.9280
 6M3  C6   C   CH1   0  -0.199   0.8700  -0.7648  -0.2957
 6M3  C7   C   CR6   0   0.128   0.1742   0.5645  -0.0701
 6M3  C8   C   CR16  0  -0.275   0.9310   1.7285   0.0456
 6M3  C9   C   CR16  0  -0.229   0.3449   2.9706   0.1920
 6M3  C10  C   CR6   0   0.016  -1.0423   3.0615   0.2366
 6M3  N15  N   NS    0  -0.247  -2.1836   5.3592   0.4977
 6M3  O25  O   OH1   0  -0.647  -0.3093  -1.5325  -2.1717
 6M3  CL1  CL  CL    0  -0.117  -1.3799  -1.0552   2.5457
 6M3  H1   H   HCR5  0   0.266   1.4461  -0.9796   2.3570
 6M3  H2   H   HCR6  0   0.281  -2.8934   1.9796   0.2317
 6M3  H3   H   HCR6  0   0.280  -3.2998  -3.0331   1.9677
 6M3  H4   H   HCR6  0   0.270  -4.6978  -3.4277  -0.0285
 6M3  H5   H   HCR6  0   0.263  -4.4951  -1.9259  -1.9940
 6M3  H6   H   HCR6  0   0.258  -2.8618  -0.0815  -1.9622
 6M3  H7   H   HCH2  0   0.269   4.8572  -0.2732  -1.6325
 6M3  H8   H   HCH2  0   0.254   3.7910  -1.5725  -2.0865
 6M3  H9   H   HCH2  0   0.236   2.9240   1.3448  -1.8585
 6M3  H10  H   HCH2  0   0.258   3.4762   0.6198  -3.3387
 6M3  H11  H   HCH2  0   0.246   0.8571   0.7319  -2.7817
 6M3  H12  H   HCH2  0   0.249   1.5668  -0.5663  -3.7143
 6M3  H13  H   HCH1  0   0.228   1.6471  -2.0445  -1.7986
 6M3  H14  H   HCR5  0   0.252   5.3438  -0.6682   0.9251
 6M3  H15  H   HCH1  0   0.296   0.2730  -1.5550   0.1657
 6M3  H16  H   HCR6  0   0.272   2.0109   1.6759   0.0323
 6M3  H17  H   HCR6  0   0.285   0.9593   3.8564   0.2727
 6M3  H18  H   HOH1  0   0.455  -0.3243  -1.6242  -3.1298

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
 6M3  N15  C14  triple    1.152  0.020  1.152
 6M3  C14  C10  single    1.427  0.020  1.427
 6M3  C10  C11  aromatic  1.391  0.020  1.391
 6M3  C10  C9   aromatic  1.391  0.020  1.391
 6M3  C11  C12  aromatic  1.390  0.020  1.390
 6M3  C9   C8   aromatic  1.381  0.020  1.381
 6M3  C12  C13  single    1.485  0.020  1.485
 6M3  C12  C7   aromatic  1.403  0.020  1.403
 6M3  C8   C7   aromatic  1.393  0.020  1.393
 6M3  C20  C13  aromatic  1.393  0.020  1.393
 6M3  C20  C19  aromatic  1.384  0.020  1.384
 6M3  C13  C16  aromatic  1.391  0.020  1.391
 6M3  C19  C18  aromatic  1.389  0.020  1.389
 6M3  C7   C6   single    1.517  0.020  1.517
 6M3  C16  CL1  single    1.736  0.020  1.736
 6M3  C16  C17  aromatic  1.388  0.020  1.388
 6M3  C18  C17  aromatic  1.385  0.020  1.385
 6M3  C6   C24  single    1.541  0.020  1.541
 6M3  C6   N2   single    1.456  0.020  1.456
 6M3  C3   N2   aromatic  1.357  0.020  1.357
 6M3  C3   N4   aromatic  1.303  0.020  1.303
 6M3  C24  O25  single    1.404  0.020  1.404
 6M3  C24  C23  single    1.525  0.020  1.525
 6M3  N2   C1   aromatic  1.379  0.020  1.379
 6M3  N4   C5   aromatic  1.366  0.020  1.366
 6M3  C23  C22  single    1.533  0.020  1.533
 6M3  C1   C5   aromatic  1.368  0.020  1.368
 6M3  C1   C21  single    1.492  0.020  1.492
 6M3  C21  C22  single    1.526  0.020  1.526
 6M3  C3   H1   single    0.930  0.020  1.080
 6M3  C11  H2   single    0.930  0.020  1.080
 6M3  C17  H3   single    0.930  0.020  1.080
 6M3  C18  H4   single    0.930  0.020  1.080
 6M3  C19  H5   single    0.930  0.020  1.080
 6M3  C20  H6   single    0.930  0.020  1.080
 6M3  C21  H7   single    0.970  0.020  1.090
 6M3  C21  H8   single    0.970  0.020  1.090
 6M3  C22  H9   single    0.970  0.020  1.090
 6M3  C22  H10  single    0.970  0.020  1.090
 6M3  C23  H11  single    0.970  0.020  1.090
 6M3  C23  H12  single    0.970  0.020  1.090
 6M3  C24  H13  single    0.970  0.020  1.090
 6M3  C5   H14  single    0.930  0.020  1.080
 6M3  C6   H15  single    0.970  0.020  1.090
 6M3  C8   H16  single    0.930  0.020  1.080
 6M3  C9   H17  single    0.930  0.020  1.080
 6M3  O25  H18  single    0.850  0.020  0.980

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
 6M3  C5   C1   N2   104.57  3.000
 6M3  C5   C1   C21  128.49  3.000
 6M3  N2   C1   C21  126.93  3.000
 6M3  H1   C3   N4   125.94  3.000
 6M3  H1   C3   N2   121.73  3.000
 6M3  N4   C3   N2   112.33  3.000
 6M3  H2   C11  C10  119.70  3.000
 6M3  H2   C11  C12  119.41  3.000
 6M3  C10  C11  C12  120.88  3.000
 6M3  C7   C12  C13  124.31  3.000
 6M3  C7   C12  C11  119.48  3.000
 6M3  C13  C12  C11  116.20  3.000
 6M3  C20  C13  C16  117.63  3.000
 6M3  C16  C13  C12  122.20  3.000
 6M3  C20  C13  C12  120.01  3.000
 6M3  N15  C14  C10  180.00  3.000
 6M3  CL1  C16  C17  118.24  3.000
 6M3  C17  C16  C13  121.92  3.000
 6M3  CL1  C16  C13  119.82  3.000
 6M3  H3   C17  C18  120.62  3.000
 6M3  H3   C17  C16  120.15  3.000
 6M3  C18  C17  C16  119.22  3.000
 6M3  H4   C18  C19  120.47  3.000
 6M3  H4   C18  C17  119.50  3.000
 6M3  C19  C18  C17  120.02  3.000
 6M3  H5   C19  C20  119.91  3.000
 6M3  H5   C19  C18  120.22  3.000
 6M3  C20  C19  C18  119.87  3.000
 6M3  H6   C20  C19  119.98  3.000
 6M3  H6   C20  C13  118.71  3.000
 6M3  C19  C20  C13  121.31  3.000
 6M3  H8   C21  H7   105.60  3.000
 6M3  H8   C21  C22  109.89  3.000
 6M3  H7   C21  C22  109.29  3.000
 6M3  H8   C21  C1   110.76  3.000
 6M3  H7   C21  C1   106.50  3.000
 6M3  C22  C21  C1   114.37  3.000
 6M3  H10  C22  H9   105.61  3.000
 6M3  H10  C22  C23  108.57  3.000
 6M3  H9   C22  C23  110.78  3.000
 6M3  H10  C22  C21  108.65  3.000
 6M3  H9   C22  C21  108.87  3.000
 6M3  C23  C22  C21  114.01  3.000
 6M3  H12  C23  H11  106.18  3.000
 6M3  H12  C23  C24  105.88  3.000
 6M3  H11  C23  C24  109.26  3.000
 6M3  H12  C23  C22  108.52  3.000
 6M3  H11  C23  C22  110.24  3.000
 6M3  C24  C23  C22  116.22  3.000
 6M3  H13  C24  O25  109.85  3.000
 6M3  H13  C24  C6   105.70  3.000
 6M3  O25  C24  C6   105.45  3.000
 6M3  H13  C24  C23  108.73  3.000
 6M3  O25  C24  C23  110.61  3.000
 6M3  C6   C24  C23  116.27  3.000
 6M3  C6   N2   C3   122.40  3.000
 6M3  C3   N2   C1   106.87  3.000
 6M3  C6   N2   C1   130.63  3.000
 6M3  C5   N4   C3   105.02  3.000
 6M3  H14  C5   N4   122.08  3.000
 6M3  H14  C5   C1   126.71  3.000
 6M3  N4   C5   C1   111.20  3.000
 6M3  H15  C6   C7   108.68  3.000
 6M3  H15  C6   N2   106.08  3.000
 6M3  C7   C6   N2   111.62  3.000
 6M3  H15  C6   C24  105.10  3.000
 6M3  N2   C6   C24  110.90  3.000
 6M3  C7   C6   C24  113.93  3.000
 6M3  C8   C7   C6   119.68  3.000
 6M3  C6   C7   C12  121.69  3.000
 6M3  C8   C7   C12  118.63  3.000
 6M3  H16  C8   C9   117.96  3.000
 6M3  H16  C8   C7   120.06  3.000
 6M3  C9   C8   C7   121.98  3.000
 6M3  H17  C9   C10  120.72  3.000
 6M3  H17  C9   C8   120.24  3.000
 6M3  C10  C9   C8   119.04  3.000
 6M3  C9   C10  C14  120.22  3.000
 6M3  C9   C10  C11  119.92  3.000
 6M3  C14  C10  C11  119.85  3.000
 6M3  H18  O25  C24  108.52  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
 6M3  CONST_01  C3   N4   C5   C1     0.00  0.0  0
 6M3  CONST_02  C8   C9   C10  C11    0.00  0.0  0
 6M3  CONST_05  C8   C7   C12  C11    0.00  0.0  0
 6M3  CONST_06  C9   C10  C11  C12    0.00  0.0  0
 6M3  CONST_07  C19  C20  C13  C12  180.00  0.0  0
 6M3  CONST_08  C17  C16  C13  C12  180.00  0.0  0
 6M3  CONST_09  C9   C8   C7   C12    0.00  0.0  0
 6M3  CONST_10  C10  C11  C12  C13  180.00  0.0  0
 6M3  CONST_11  C8   C7   C12  C13  180.00  0.0  0
 6M3  CONST_12  C18  C19  C20  C13    0.00  0.0  0
 6M3  CONST_13  C18  C17  C16  C13    0.00  0.0  0
 6M3  CONST_15  C19  C20  C13  C16    0.00  0.0  0
 6M3  CONST_16  C19  C18  C17  C16    0.00  0.0  0
 6M3  CONST_17  C20  C13  C16  C17    0.00  0.0  0
 6M3  CONST_18  C20  C19  C18  C17    0.00  0.0  0
 6M3  CONST_20  C5   N4   C3   N2     0.00  0.0  0
 6M3  CONST_21  C10  C11  C12  C7     0.00  0.0  0
 6M3  CONST_22  C10  C9   C8   C7     0.00  0.0  0
 6M3  CONST_23  C6   C7   C12  C11  180.00  0.0  0
 6M3  CONST_24  C6   C7   C12  C13    0.00  0.0  0
 6M3  CONST_25  C9   C8   C7   C6   180.00  0.0  0
 6M3  CONST_26  C14  C10  C11  C12  180.00  0.0  0
 6M3  CONST_27  CL1  C16  C13  C12    0.00  0.0  0
 6M3  CONST_28  C8   C9   C10  C14  180.00  0.0  0
 6M3  CONST_29  CL1  C16  C17  C18  180.00  0.0  0
 6M3  CONST_30  CL1  C16  C13  C20  180.00  0.0  0
 6M3  CONST_31  H14  C5   N4   C3   180.00  0.0  0
 6M3  CONST_32  H17  C9   C10  C11  180.00  0.0  0
 6M3  CONST_33  H6   C20  C13  C12    0.00  0.0  0
 6M3  CONST_34  H16  C8   C7   C12  180.00  0.0  0
 6M3  CONST_35  H2   C11  C12  C13    0.00  0.0  0
 6M3  CONST_36  H5   C19  C20  C13  180.00  0.0  0
 6M3  CONST_37  H3   C17  C16  C13  180.00  0.0  0
 6M3  CONST_38  H4   C18  C17  C16  180.00  0.0  0
 6M3  CONST_39  H1   C3   N4   C5   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
 6M3  chir_01  C24  C6  O25  C23  negativ
 6M3  chir_02  C6   N2  C24  C7   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
 6M3  plan-1  C12  0.020
 6M3  plan-1  C13  0.020
 6M3  plan-1  C16  0.020
 6M3  plan-1  C17  0.020
 6M3  plan-1  C18  0.020
 6M3  plan-1  C19  0.020
 6M3  plan-1  C20  0.020
 6M3  plan-1  CL1  0.020
 6M3  plan-1  H3   0.020
 6M3  plan-1  H4   0.020
 6M3  plan-1  H5   0.020
 6M3  plan-1  H6   0.020
 6M3  plan-2  C11  0.020
 6M3  plan-2  C12  0.020
 6M3  plan-2  C13  0.020
 6M3  plan-2  C14  0.020
 6M3  plan-2  C6   0.020
 6M3  plan-2  C7   0.020
 6M3  plan-2  C8   0.020
 6M3  plan-2  C9   0.020
 6M3  plan-2  C10  0.020
 6M3  plan-2  N15  0.020
 6M3  plan-2  H2   0.020
 6M3  plan-2  H16  0.020
 6M3  plan-2  H17  0.020
 6M3  plan-3  C1   0.020
 6M3  plan-3  C3   0.020
 6M3  plan-3  C21  0.020
 6M3  plan-3  N2   0.020
 6M3  plan-3  N4   0.020
 6M3  plan-3  C5   0.020
 6M3  plan-3  C6   0.020
 6M3  plan-3  H1   0.020
 6M3  plan-3  H14  0.020

