# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:26:58 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: ~{N}-[(1~{S})-1-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)ethyl]-2-methyl-pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1cccnc1C)c2ccc3OCCCOc3c2
#
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
 6RS  6RS  ~{N}-[(1~{S})-1-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)ethyl]-2-methyl-pyridin-3-amine  ligand  41  21  .  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_6RS
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
 6RS  C17  C  CH2   0  -0.474   5.3021   0.1176  -1.4984
 6RS  C14  C  CR6   0   0.299   3.1065  -0.5294   0.6017
 6RS  C13  C  CR6   0   0.337   2.6441   0.6583   0.0234
 6RS  C20  C  CR16  0  -0.340   2.2182  -1.3152   1.3253
 6RS  C18  C  CH2   0  -0.202   4.1011   0.9811  -1.8195
 6RS  O15  O  O2    0  -0.494   4.4059  -0.9147   0.5357
 6RS  C01  C  CH3   0  -0.657  -1.4991   0.6237   2.5166
 6RS  C02  C  CH1   0  -0.199  -1.0167   0.6716   1.0672
 6RS  N03  N  NH1   0  -0.691  -1.8164  -0.1538   0.1749
 6RS  C04  C  CR6   0   0.281  -3.1137   0.1471  -0.1580
 6RS  C05  C  CR6   0   0.169  -3.9232  -0.8340  -0.7816
 6RS  C06  C  CH3   0  -0.765  -3.3822  -2.2101  -1.0292
 6RS  N07  N  N     0  -0.409  -5.1613  -0.5838  -1.1726
 6RS  C08  C  CR16  0  -0.124  -5.6869   0.6246  -0.9859
 6RS  C09  C  CR16  0  -0.315  -4.9788   1.6468  -0.3841
 6RS  C10  C  CR16  0  -0.256  -3.6810   1.4068   0.0406
 6RS  C11  C  CR6   0   0.164   0.4295   0.2523   0.9268
 6RS  C12  C  CR16  0  -0.428   1.3136   1.0256   0.1855
 6RS  C16  C  CH2   0  -0.202   4.9480  -1.1565  -0.7605
 6RS  O19  O  O2    0  -0.496   3.4629   1.5010  -0.6550
 6RS  C21  C  CR16  0  -0.318   0.8986  -0.9280   1.4958
 6RS  H1   H  HCH2  0   0.247   5.7801  -0.1606  -2.4417
 6RS  H2   H  HCH2  0   0.244   6.0372   0.6917  -0.9283
 6RS  H3   H  HCR6  0   0.267   2.5780  -2.2328   1.7739
 6RS  H4   H  HCH2  0   0.251   4.4107   1.8521  -2.3970
 6RS  H5   H  HCH2  0   0.221   3.3771   0.4209  -2.4225
 6RS  H7   H  HCH3  0   0.229  -1.4388  -0.3875   2.9202
 6RS  H8   H  HCH3  0   0.239  -0.8947   1.2775   3.1456
 6RS  H9   H  HCH1  0   0.262  -1.0891   1.7039   0.7148
 6RS  H10  H  HNH1  0   0.390  -1.5994  -1.1371   0.2231
 6RS  H11  H  HCH3  0   0.245  -3.0974  -2.7123  -0.1002
 6RS  H12  H  HCH3  0   0.262  -4.1338  -2.8240  -1.5200
 6RS  H13  H  HCH3  0   0.250  -2.4928  -2.1867  -1.6642
 6RS  H14  H  HCR6  0   0.247  -6.7042   0.7741  -1.3287
 6RS  H15  H  HCR6  0   0.261  -5.4293   2.6201  -0.2414
 6RS  H16  H  HCR6  0   0.276  -3.1254   2.2030   0.5181
 6RS  H17  H  HCR6  0   0.261   0.9767   1.9494  -0.2708
 6RS  H18  H  HCH2  0   0.221   4.2483  -1.7589  -1.3517
 6RS  H19  H  HCH2  0   0.251   5.8439  -1.7546  -0.5954
 6RS  H20  H  HCR6  0   0.255   0.2406  -1.5599   2.0793
 6RS  H6   H  HCH3  0   0.241  -2.5367   0.9492   2.5946

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
 6RS  C01  C02  single    1.528  0.020  1.528
 6RS  C02  N03  single    1.455  0.020  1.455
 6RS  C02  C11  single    1.512  0.020  1.512
 6RS  C12  C11  aromatic  1.389  0.020  1.389
 6RS  C12  C13  aromatic  1.390  0.020  1.390
 6RS  C18  O19  single    1.426  0.020  1.426
 6RS  C18  C17  single    1.514  0.020  1.514
 6RS  O19  C13  single    1.357  0.020  1.357
 6RS  N03  C04  single    1.373  0.020  1.373
 6RS  C11  C21  aromatic  1.392  0.020  1.392
 6RS  C10  C04  aromatic  1.396  0.020  1.396
 6RS  C10  C09  aromatic  1.387  0.020  1.387
 6RS  C04  C05  aromatic  1.417  0.020  1.417
 6RS  C13  C14  aromatic  1.400  0.020  1.400
 6RS  C09  C08  aromatic  1.381  0.020  1.381
 6RS  C05  C06  single    1.499  0.020  1.499
 6RS  C05  N07  aromatic  1.322  0.020  1.322
 6RS  C08  N07  aromatic  1.331  0.020  1.331
 6RS  C17  C16  single    1.514  0.020  1.514
 6RS  C21  C20  aromatic  1.386  0.020  1.386
 6RS  C14  C20  aromatic  1.389  0.020  1.389
 6RS  C14  O15  single    1.357  0.020  1.357
 6RS  C16  O15  single    1.426  0.020  1.426
 6RS  C17  H1   single    0.970  0.020  1.090
 6RS  C17  H2   single    0.970  0.020  1.090
 6RS  C20  H3   single    0.930  0.020  1.080
 6RS  C18  H4   single    0.970  0.020  1.090
 6RS  C18  H5   single    0.970  0.020  1.090
 6RS  C01  H6   single    0.970  0.020  1.090
 6RS  C01  H7   single    0.970  0.020  1.090
 6RS  C01  H8   single    0.970  0.020  1.090
 6RS  C02  H9   single    0.970  0.020  1.090
 6RS  N03  H10  single    0.890  0.020  1.040
 6RS  C06  H11  single    0.970  0.020  1.090
 6RS  C06  H12  single    0.970  0.020  1.090
 6RS  C06  H13  single    0.970  0.020  1.090
 6RS  C08  H14  single    0.930  0.020  1.080
 6RS  C09  H15  single    0.930  0.020  1.080
 6RS  C10  H16  single    0.930  0.020  1.080
 6RS  C12  H17  single    0.930  0.020  1.080
 6RS  C16  H18  single    0.970  0.020  1.090
 6RS  C16  H19  single    0.970  0.020  1.090
 6RS  C21  H20  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
 6RS  H2   C17  H1   106.83  3.000
 6RS  H2   C17  C16  110.18  3.000
 6RS  H1   C17  C16  107.97  3.000
 6RS  H2   C17  C18  110.16  3.000
 6RS  H1   C17  C18  108.00  3.000
 6RS  C16  C17  C18  113.44  3.000
 6RS  O15  C14  C20  118.49  3.000
 6RS  O15  C14  C13  122.49  3.000
 6RS  C20  C14  C13  118.95  3.000
 6RS  O19  C13  C12  118.16  3.000
 6RS  O19  C13  C14  122.30  3.000
 6RS  C12  C13  C14  119.49  3.000
 6RS  H3   C20  C21  120.15  3.000
 6RS  H3   C20  C14  118.85  3.000
 6RS  C21  C20  C14  120.99  3.000
 6RS  H5   C18  H4   107.72  3.000
 6RS  H5   C18  O19  109.87  3.000
 6RS  H4   C18  O19  105.57  3.000
 6RS  H5   C18  C17  110.44  3.000
 6RS  H4   C18  C17  110.05  3.000
 6RS  O19  C18  C17  112.95  3.000
 6RS  C16  O15  C14  117.16  3.000
 6RS  H8   C01  H7   108.18  3.000
 6RS  H8   C01  H6   107.90  3.000
 6RS  H7   C01  H6   107.64  3.000
 6RS  H8   C01  C02  110.70  3.000
 6RS  H7   C01  C02  111.26  3.000
 6RS  H6   C01  C02  111.03  3.000
 6RS  H9   C02  C11  107.17  3.000
 6RS  H9   C02  N03  107.56  3.000
 6RS  C11  C02  N03  108.14  3.000
 6RS  H9   C02  C01  108.32  3.000
 6RS  C11  C02  C01  112.40  3.000
 6RS  N03  C02  C01  112.97  3.000
 6RS  H10  N03  C04  115.39  3.000
 6RS  H10  N03  C02  113.94  3.000
 6RS  C04  N03  C02  122.95  3.000
 6RS  C10  C04  C05  117.09  3.000
 6RS  C05  C04  N03  119.67  3.000
 6RS  C10  C04  N03  123.19  3.000
 6RS  N07  C05  C06  117.57  3.000
 6RS  N07  C05  C04  122.29  3.000
 6RS  C06  C05  C04  120.15  3.000
 6RS  H13  C06  H12  108.19  3.000
 6RS  H13  C06  H11  106.94  3.000
 6RS  H12  C06  H11  107.71  3.000
 6RS  H13  C06  C05  111.70  3.000
 6RS  H12  C06  C05  110.08  3.000
 6RS  H11  C06  C05  112.03  3.000
 6RS  C08  N07  C05  120.01  3.000
 6RS  H14  C08  C09  121.12  3.000
 6RS  H14  C08  N07  116.84  3.000
 6RS  C09  C08  N07  122.04  3.000
 6RS  H15  C09  C10  120.33  3.000
 6RS  H15  C09  C08  120.65  3.000
 6RS  C10  C09  C08  119.02  3.000
 6RS  H16  C10  C09  119.24  3.000
 6RS  H16  C10  C04  121.22  3.000
 6RS  C09  C10  C04  119.54  3.000
 6RS  C21  C11  C12  118.41  3.000
 6RS  C21  C11  C02  121.30  3.000
 6RS  C12  C11  C02  120.25  3.000
 6RS  H17  C12  C11  120.08  3.000
 6RS  H17  C12  C13  118.27  3.000
 6RS  C11  C12  C13  121.64  3.000
 6RS  H19  C16  H18  107.74  3.000
 6RS  H19  C16  O15  105.54  3.000
 6RS  H18  C16  O15  109.93  3.000
 6RS  H19  C16  C17  110.08  3.000
 6RS  H18  C16  C17  110.41  3.000
 6RS  O15  C16  C17  112.91  3.000
 6RS  C18  O19  C13  116.87  3.000
 6RS  H20  C21  C11  120.69  3.000
 6RS  H20  C21  C20  118.81  3.000
 6RS  C11  C21  C20  120.51  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
 6RS  CONST_01  C11  C21  C20  C14    0.00   0.0  0
 6RS  CONST_02  C21  C11  C12  C13    0.00   0.0  0
 6RS  CONST_03  C12  C11  C21  C20    0.00   0.0  0
 6RS  CONST_04  C08  C09  C10  C04    0.00   0.0  0
 6RS  CONST_05  C08  N07  C05  C04    0.00   0.0  0
 6RS  CONST_06  C09  C10  C04  C05    0.00   0.0  0
 6RS  CONST_07  C09  C08  N07  C05    0.00   0.0  0
 6RS  CONST_08  C10  C04  C05  N07    0.00   0.0  0
 6RS  CONST_09  C10  C09  C08  N07    0.00   0.0  0
 6RS  CONST_10  C02  C11  C12  C13  180.00   0.0  0
 6RS  CONST_11  C02  C11  C21  C20  180.00   0.0  0
 6RS  CONST_12  C09  C10  C04  N03  180.00   0.0  0
 6RS  CONST_13  N07  C05  C04  N03  180.00   0.0  0
 6RS  CONST_14  C10  C04  C05  C06  180.00   0.0  0
 6RS  CONST_15  C08  N07  C05  C06  180.00   0.0  0
 6RS  CONST_16  H20  C21  C20  C14  180.00   0.0  0
 6RS  CONST_17  H15  C09  C10  C04  180.00   0.0  0
 6RS  CONST_18  H16  C10  C04  C05  180.00   0.0  0
 6RS  CONST_19  H14  C08  N07  C05  180.00   0.0  0
 6RS  CONST_20  H3   C20  C21  C11  180.00   0.0  0
 6RS  CONST_21  H17  C12  C11  C21  180.00   0.0  0
 6RS  CONST_23  C05  C04  N03  C02  180.00   0.0  0
 6RS  Var_01    H11  C06  C05  C04   60.63  30.0  2

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
 6RS  chir_01  C02  C01  N03  C11  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
 6RS  plan-1  N03  0.020
 6RS  plan-1  C04  0.020
 6RS  plan-1  C05  0.020
 6RS  plan-1  C06  0.020
 6RS  plan-1  N07  0.020
 6RS  plan-1  C08  0.020
 6RS  plan-1  C09  0.020
 6RS  plan-1  C10  0.020
 6RS  plan-1  H14  0.020
 6RS  plan-1  H15  0.020
 6RS  plan-1  H16  0.020
 6RS  plan-2  C14  0.020
 6RS  plan-2  C13  0.020
 6RS  plan-2  C20  0.020
 6RS  plan-2  O15  0.020
 6RS  plan-2  C02  0.020
 6RS  plan-2  C11  0.020
 6RS  plan-2  C12  0.020
 6RS  plan-2  O19  0.020
 6RS  plan-2  C21  0.020
 6RS  plan-2  H3   0.020
 6RS  plan-2  H17  0.020
 6RS  plan-2  H20  0.020
 6RS  plan-3  C02  0.020
 6RS  plan-3  N03  0.020
 6RS  plan-3  C04  0.020
 6RS  plan-3  H10  0.020

