# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:10:37 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: methyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CC(=O)NCCCNCc1ccc(c(Cl)c1)c2ccccc2
#
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
 551  551  'methyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate'  ligand  49  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_551
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
 551  C1   C   C     0   0.610   -8.3221   0.6604  -0.4607
 551  O2   O   O     0  -0.495   -6.6494  -1.7858  -0.0253
 551  C3   C   C     0   0.549   -6.2482  -0.7151  -0.4566
 551  C5   C   CH2   0  -0.491   -2.6010  -0.5268   0.0586
 551  C6   C   CH2   0  -0.253   -1.5190  -1.2669   0.8277
 551  C7   C   CH2   0  -0.311    0.8632  -1.5065   1.1255
 551  C8   C   CR6   0   0.064    2.2201  -1.0429   0.6671
 551  C9   C   CR16  0  -0.267    2.4897  -0.8162  -0.6801
 551  C10  C   CR16  0  -0.296    3.7473  -0.4042  -1.0835
 551  C11  C   CR6   0   0.138    4.7847  -0.1964  -0.1722
 551  C12  C   CR6   0  -0.106    4.4992  -0.4402   1.1689
 551  C14  C   CR6   0   0.062    6.1040   0.2630  -0.6576
 551  C15  C   CR16  0  -0.293    6.7881  -0.4776  -1.6196
 551  C17  C   CR16  0  -0.263    8.5584   1.1513  -1.6548
 551  C18  C   CR16  0  -0.243    7.8794   1.8994  -0.7009
 551  C19  C   CR16  0  -0.285    6.6620   1.4579  -0.2044
 551  CL   CL  CL    0  -0.130    5.7349  -0.2686   2.3763
 551  C16  C   CR16  0  -0.243    8.0092  -0.0379  -2.1136
 551  C13  C   CR16  0  -0.252    3.2417  -0.8505   1.5875
 551  N1   N   NH1   0  -0.597   -0.2005  -0.8109   0.4313
 551  C4   C   CH2   0  -0.244   -3.9915  -0.9845   0.4683
 551  N    N   NH1   0  -0.633   -5.0046  -0.2598  -0.2692
 551  C2   C   CH2   0  -0.715   -7.1507   0.1816  -1.2791
 551  O1   O   O     0  -0.442   -8.3270   0.7369   0.7410
 551  O    O   O2    0  -0.448   -9.3318   1.0291  -1.2315
 551  C    C   CH3   0  -0.425  -10.4825   1.5841  -0.5910
 551  H1   H   HCH2  0   0.233   -2.5018   0.5491   0.2394
 551  H2   H   HCH2  0   0.239   -2.4614  -0.6869  -1.0134
 551  H3   H   HCH2  0   0.196   -1.6942  -1.1567   1.9098
 551  H4   H   HCH2  0   0.225   -1.5883  -2.3382   0.6150
 551  H5   H   HCH2  0   0.246    0.7620  -2.5759   0.9110
 551  H6   H   HCH2  0   0.218    0.7995  -1.4123   2.2203
 551  H7   H   HCR6  0   0.254    1.7073  -0.9493  -1.4153
 551  H8   H   HCR6  0   0.260    3.9361  -0.2200  -2.1338
 551  H9   H   HCR6  0   0.255    6.3674  -1.4096  -1.9771
 551  H10  H   HCR6  0   0.258    9.5095   1.4950  -2.0400
 551  H11  H   HCR6  0   0.258    8.2960   2.8327  -0.3448
 551  H12  H   HCR6  0   0.254    6.1346   2.0563   0.5274
 551  H13  H   HCR6  0   0.258    8.5315  -0.6277  -2.8556
 551  H14  H   HCR6  0   0.273    3.0579  -1.0209   2.6409
 551  H15  H   HNH1  0   0.344   -0.1230   0.1809   0.6275
 551  H17  H   HCH2  0   0.241   -4.1075  -2.0505   0.2678
 551  H18  H   HCH2  0   0.235   -4.1301  -0.8449   1.5453
 551  H19  H   HNH1  0   0.404   -4.7659   0.6550  -0.6166
 551  H20  H   HCH2  0   0.309   -7.4984  -0.3742  -2.1518
 551  H21  H   HCH2  0   0.309   -6.6306   1.0644  -1.6612
 551  H22  H   HCH3  0   0.242  -10.9492   0.8637   0.0801
 551  H23  H   HCH3  0   0.241  -10.2307   2.4861  -0.0339
 551  H24  H   HCH3  0   0.254  -11.1745   1.8347  -1.3893

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
 551  C16  C15  aromatic  1.389  0.020  1.389
 551  C16  C17  aromatic  1.388  0.020  1.388
 551  C15  C14  aromatic  1.394  0.020  1.394
 551  C17  C18  aromatic  1.389  0.020  1.389
 551  C10  C9   aromatic  1.384  0.020  1.384
 551  C10  C11  aromatic  1.396  0.020  1.396
 551  C14  C11  single    1.479  0.020  1.479
 551  C14  C19  aromatic  1.394  0.020  1.394
 551  C9   C8   aromatic  1.392  0.020  1.392
 551  C11  C12  aromatic  1.393  0.020  1.393
 551  C8   C7   single    1.505  0.020  1.505
 551  C8   C13  aromatic  1.388  0.020  1.388
 551  C12  CL   single    1.736  0.020  1.736
 551  C12  C13  aromatic  1.387  0.020  1.387
 551  C7   N1   single    1.448  0.020  1.448
 551  C18  C19  aromatic  1.387  0.020  1.387
 551  C6   N1   single    1.450  0.020  1.450
 551  C6   C5   single    1.520  0.020  1.520
 551  C4   C5   single    1.520  0.020  1.520
 551  C4   N    single    1.448  0.020  1.448
 551  N    C3   single    1.337  0.020  1.337
 551  C3   O2   double    1.222  0.020  1.222
 551  C3   C2   single    1.515  0.020  1.515
 551  C    O    single    1.429  0.020  1.429
 551  O    C1   single    1.323  0.020  1.323
 551  C2   C1   single    1.507  0.020  1.507
 551  C1   O1   double    1.204  0.020  1.204
 551  C5   H1   single    0.970  0.020  1.090
 551  C5   H2   single    0.970  0.020  1.090
 551  C6   H3   single    0.970  0.020  1.090
 551  C6   H4   single    0.970  0.020  1.090
 551  C7   H5   single    0.970  0.020  1.090
 551  C7   H6   single    0.970  0.020  1.090
 551  C9   H7   single    0.930  0.020  1.080
 551  C10  H8   single    0.930  0.020  1.080
 551  C15  H9   single    0.930  0.020  1.080
 551  C17  H10  single    0.930  0.020  1.080
 551  C18  H11  single    0.930  0.020  1.080
 551  C19  H12  single    0.930  0.020  1.080
 551  C16  H13  single    0.930  0.020  1.080
 551  C13  H14  single    0.930  0.020  1.080
 551  N1   H15  single    0.890  0.020  1.040
 551  C4   H17  single    0.970  0.020  1.090
 551  C4   H18  single    0.970  0.020  1.090
 551  N    H19  single    0.860  0.020  1.020
 551  C2   H20  single    0.970  0.020  1.090
 551  C2   H21  single    0.970  0.020  1.090
 551  C    H22  single    0.970  0.020  1.090
 551  C    H23  single    0.970  0.020  1.090
 551  C    H24  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
 551  O    C1   O1   124.11  3.000
 551  O1   C1   C2   124.42  3.000
 551  O    C1   C2   111.44  3.000
 551  C2   C3   N    115.37  3.000
 551  C2   C3   O2   120.97  3.000
 551  N    C3   O2   123.65  3.000
 551  H2   C5   H1   107.11  3.000
 551  H2   C5   C4   109.70  3.000
 551  H1   C5   C4   109.51  3.000
 551  H2   C5   C6   109.52  3.000
 551  H1   C5   C6   109.28  3.000
 551  C4   C5   C6   111.60  3.000
 551  H4   C6   H3   106.18  3.000
 551  H4   C6   N1   108.19  3.000
 551  H3   C6   N1   112.43  3.000
 551  H4   C6   C5   109.47  3.000
 551  H3   C6   C5   109.58  3.000
 551  N1   C6   C5   110.84  3.000
 551  H6   C7   H5   105.84  3.000
 551  H6   C7   N1   113.15  3.000
 551  H5   C7   N1   107.89  3.000
 551  H6   C7   C8   109.19  3.000
 551  H5   C7   C8   108.92  3.000
 551  N1   C7   C8   111.60  3.000
 551  C13  C8   C9   118.44  3.000
 551  C13  C8   C7   120.27  3.000
 551  C9   C8   C7   121.28  3.000
 551  H7   C9   C10  119.73  3.000
 551  H7   C9   C8   119.83  3.000
 551  C10  C9   C8   120.43  3.000
 551  H8   C10  C11  118.57  3.000
 551  H8   C10  C9   119.46  3.000
 551  C11  C10  C9   121.96  3.000
 551  C14  C11  C12  123.59  3.000
 551  C12  C11  C10  116.75  3.000
 551  C14  C11  C10  119.65  3.000
 551  C13  C12  CL   117.68  3.000
 551  C13  C12  C11  121.88  3.000
 551  CL   C12  C11  120.43  3.000
 551  C19  C14  C15  118.91  3.000
 551  C19  C14  C11  121.09  3.000
 551  C15  C14  C11  119.96  3.000
 551  H9   C15  C16  119.78  3.000
 551  H9   C15  C14  119.63  3.000
 551  C16  C15  C14  120.59  3.000
 551  H10  C17  C16  120.15  3.000
 551  H10  C17  C18  120.19  3.000
 551  C16  C17  C18  119.66  3.000
 551  H11  C18  C19  119.64  3.000
 551  H11  C18  C17  120.13  3.000
 551  C19  C18  C17  120.22  3.000
 551  H12  C19  C18  119.58  3.000
 551  H12  C19  C14  119.90  3.000
 551  C18  C19  C14  120.51  3.000
 551  H13  C16  C17  120.17  3.000
 551  H13  C16  C15  119.71  3.000
 551  C17  C16  C15  120.11  3.000
 551  H14  C13  C12  119.60  3.000
 551  H14  C13  C8   119.88  3.000
 551  C12  C13  C8   120.52  3.000
 551  H15  N1   C7   108.72  3.000
 551  H15  N1   C6   108.91  3.000
 551  C7   N1   C6   112.69  3.000
 551  H18  C4   H17  106.97  3.000
 551  H18  C4   N    110.41  3.000
 551  H17  C4   N    108.73  3.000
 551  H18  C4   C5   110.04  3.000
 551  H17  C4   C5   109.99  3.000
 551  N    C4   C5   110.62  3.000
 551  H19  N    C4   117.67  3.000
 551  H19  N    C3   118.77  3.000
 551  C4   N    C3   123.48  3.000
 551  H21  C2   H20  106.46  3.000
 551  H21  C2   C3   112.60  3.000
 551  H20  C2   C3   108.81  3.000
 551  H21  C2   C1   107.63  3.000
 551  H20  C2   C1   110.38  3.000
 551  C3   C2   C1   110.87  3.000
 551  C    O    C1   117.50  3.000
 551  H24  C    H23  109.40  3.000
 551  H24  C    H22  109.42  3.000
 551  H23  C    H22  109.36  3.000
 551  H24  C    O    105.86  3.000
 551  H23  C    O    111.38  3.000
 551  H22  C    O    111.35  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
 551  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 551  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 551  CONST_03  C14  C11  C10  C9    180.00   0.0  0
 551  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 551  CONST_05  C12  C13  C8   C9      0.00   0.0  0
 551  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 551  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 551  CONST_10  C16  C15  C14  C11   180.00   0.0  0
 551  CONST_11  C18  C19  C14  C11   180.00   0.0  0
 551  CONST_14  C17  C16  C15  C14     0.00   0.0  0
 551  CONST_15  C13  C12  C11  C14   180.00   0.0  0
 551  CONST_16  C17  C18  C19  C14     0.00   0.0  0
 551  CONST_17  C18  C17  C16  C15     0.00   0.0  0
 551  CONST_18  C18  C19  C14  C15     0.00   0.0  0
 551  CONST_19  C16  C15  C14  C19     0.00   0.0  0
 551  CONST_20  C16  C17  C18  C19     0.00   0.0  0
 551  CONST_21  C10  C9   C8   C7    180.00   0.0  0
 551  CONST_22  C12  C13  C8   C7    180.00   0.0  0
 551  CONST_23  CL   C12  C13  C8    180.00   0.0  0
 551  CONST_24  CL   C12  C11  C10   180.00   0.0  0
 551  CONST_25  CL   C12  C11  C14     0.00   0.0  0
 551  CONST_26  H8   C10  C9   C8    180.00   0.0  0
 551  CONST_27  H14  C13  C8   C9    180.00   0.0  0
 551  CONST_28  H7   C9   C10  C11   180.00   0.0  0
 551  CONST_29  H9   C15  C14  C11     0.00   0.0  0
 551  CONST_30  H12  C19  C14  C11     0.00   0.0  0
 551  CONST_31  H13  C16  C15  C14   180.00   0.0  0
 551  CONST_32  H11  C18  C19  C14   180.00   0.0  0
 551  CONST_33  H10  C17  C16  C15   180.00   0.0  0
 551  CONST_34  C4   N    C3   O2      0.00   0.0  0
 551  CONST_35  C2   C3   N    C4    180.00   0.0  0
 551  CONST_36  H19  N    C3   O2    180.00   0.0  0
 551  Var_01    N1   C7   C8   C9    -41.96  30.0  2
 551  Var_02    C8   C7   N1   C6    178.35  30.0  1
 551  Var_03    N    C3   C2   C1   -117.20  30.0  1
 551  Var_04    C5   C4   N    C3    157.45  30.0  1
 551  Var_05    O    C1   C2   C3   -157.92  30.0  3
 551  Var_06    C7   N1   C6   C5   -179.07  30.0  3
 551  Var_07    N    C4   C5   C6    179.58  30.0  1
 551  Var_08    C4   C5   C6   N1   -179.58  30.0  3
 551  Var_09    H22  C    O    C1    -62.27  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
 551  plan-1  C7   0.020
 551  plan-1  C8   0.020
 551  plan-1  C9   0.020
 551  plan-1  C10  0.020
 551  plan-1  C11  0.020
 551  plan-1  C12  0.020
 551  plan-1  C14  0.020
 551  plan-1  CL   0.020
 551  plan-1  C13  0.020
 551  plan-1  H7   0.020
 551  plan-1  H8   0.020
 551  plan-1  H14  0.020
 551  plan-2  C11  0.020
 551  plan-2  C14  0.020
 551  plan-2  C15  0.020
 551  plan-2  C17  0.020
 551  plan-2  C18  0.020
 551  plan-2  C19  0.020
 551  plan-2  C16  0.020
 551  plan-2  H9   0.020
 551  plan-2  H10  0.020
 551  plan-2  H11  0.020
 551  plan-2  H12  0.020
 551  plan-2  H13  0.020
 551  plan-3  O2   0.020
 551  plan-3  C3   0.020
 551  plan-3  C4   0.020
 551  plan-3  N    0.020
 551  plan-3  C2   0.020
 551  plan-3  H19  0.020
 551  plan-4  C1   0.020
 551  plan-4  C2   0.020
 551  plan-4  O1   0.020
 551  plan-4  O    0.020

