# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:52:28 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: methyl [3-(aminomethyl)phenoxy]acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)COc1cccc(CN)c1
#
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
 RCV  RCV  'methyl [3-(aminomethyl)phenoxy]acetate'  ligand  27  14  .  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_RCV
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
 RCV  C4   C  CR16  0  -0.361  24.4183   7.0027  55.0281
 RCV  C5   C  CR16  0  -0.228  25.5153   7.7615  55.4043
 RCV  C6   C  CR16  0  -0.313  26.3292   7.3633  56.4550
 RCV  C7   C  CR6   0   0.122  26.0412   6.1913  57.1464
 RCV  C8   C  CR16  0  -0.433  24.9454   5.4210  56.7668
 RCV  C9   C  CH2   0  -0.353  26.9102   5.7499  58.2960
 RCV  O1   O  O     0  -0.432  24.4079   2.8734  54.6330
 RCV  C1   C  C     0   0.551  23.5794   2.8085  55.5009
 RCV  O    O  O2    0  -0.449  23.3056   1.7269  56.2077
 RCV  C    C  CH3   0  -0.424  24.0356   0.5348  55.9048
 RCV  C2   C  CH2   0  -0.334  22.6783   3.9550  55.9177
 RCV  C3   C  CR6   0   0.410  24.1311   5.8244  55.7107
 RCV  N    N  NH2   0  -0.789  28.2980   5.6117  57.8807
 RCV  H1   H  HCR6  0   0.262  23.7847   7.3187  54.2086
 RCV  H2   H  HCR6  0   0.255  25.7328   8.6779  54.8705
 RCV  H3   H  HCR6  0   0.244  27.1856   7.9605  56.7402
 RCV  H4   H  HCR6  0   0.269  24.7492   4.5090  57.3175
 RCV  H5   H  HCH2  0   0.237  26.8727   6.5118  59.0792
 RCV  H6   H  HCH2  0   0.214  26.4842   4.8387  58.7365
 RCV  H7   H  HCH3  0   0.256  23.6450  -0.2300  56.5688
 RCV  H8   H  HCH3  0   0.243  23.8844   0.2292  54.8701
 RCV  H9   H  HCH3  0   0.244  25.1009   0.6676  56.0906
 RCV  H10  H  HCH2  0   0.272  22.6474   4.0417  57.0088
 RCV  H11  H  HCH2  0   0.316  21.6609   3.7234  55.5937
 RCV  H12  H  HNH2  0   0.351  28.8585   5.3582  58.6846
 RCV  H13  H  HNH2  0   0.342  28.3790   4.8378  57.2327
 RCV  O2   O  O2    0  -0.471  23.0337   5.1503  55.2870

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
 RCV  O1  C1   double    1.202  0.020  1.202
 RCV  C4  C5   aromatic  1.386  0.020  1.386
 RCV  C4  C3   aromatic  1.392  0.020  1.392
 RCV  O2  C3   single    1.356  0.020  1.356
 RCV  O2  C2   single    1.397  0.020  1.397
 RCV  C5  C6   aromatic  1.387  0.020  1.387
 RCV  C1  C2   single    1.517  0.020  1.517
 RCV  C1  O    single    1.321  0.020  1.321
 RCV  C3  C8   aromatic  1.393  0.020  1.393
 RCV  C   O    single    1.430  0.020  1.430
 RCV  C6  C7   aromatic  1.391  0.020  1.391
 RCV  C8  C7   aromatic  1.392  0.020  1.392
 RCV  C7  C9   single    1.507  0.020  1.507
 RCV  N   C9   single    1.455  0.020  1.455
 RCV  C4  H1   single    0.930  0.020  1.080
 RCV  C5  H2   single    0.930  0.020  1.080
 RCV  C6  H3   single    0.930  0.020  1.080
 RCV  C8  H4   single    0.930  0.020  1.080
 RCV  C9  H5   single    0.970  0.020  1.090
 RCV  C9  H6   single    0.970  0.020  1.090
 RCV  C   H7   single    0.970  0.020  1.090
 RCV  C   H8   single    0.970  0.020  1.090
 RCV  C   H9   single    0.970  0.020  1.090
 RCV  C2  H10  single    0.970  0.020  1.090
 RCV  C2  H11  single    0.970  0.020  1.090
 RCV  N   H12  single    0.890  0.020  1.040
 RCV  N   H13  single    0.890  0.020  1.040

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
 RCV  H1   C4  C3   119.83  3.000
 RCV  H1   C4  C5   120.58  3.000
 RCV  C3   C4  C5   119.58  3.000
 RCV  H2   C5  C6   119.90  3.000
 RCV  H2   C5  C4   119.25  3.000
 RCV  C6   C5  C4   120.85  3.000
 RCV  H3   C6  C7   119.86  3.000
 RCV  H3   C6  C5   120.35  3.000
 RCV  C7   C6  C5   119.79  3.000
 RCV  C9   C7  C8   119.98  3.000
 RCV  C9   C7  C6   120.43  3.000
 RCV  C8   C7  C6   119.58  3.000
 RCV  H4   C8  C3   121.55  3.000
 RCV  H4   C8  C7   118.02  3.000
 RCV  C3   C8  C7   120.43  3.000
 RCV  H6   C9  H5   106.12  3.000
 RCV  H6   C9  N    113.94  3.000
 RCV  H5   C9  N    107.66  3.000
 RCV  H6   C9  C7   108.98  3.000
 RCV  H5   C9  C7   108.82  3.000
 RCV  N    C9  C7   111.10  3.000
 RCV  C2   C1  O    110.41  3.000
 RCV  O    C1  O1   125.01  3.000
 RCV  C2   C1  O1   124.56  3.000
 RCV  C    O   C1   117.60  3.000
 RCV  H9   C   H8   109.38  3.000
 RCV  H9   C   H7   109.48  3.000
 RCV  H8   C   H7   109.48  3.000
 RCV  H9   C   O    111.18  3.000
 RCV  H8   C   O    111.35  3.000
 RCV  H7   C   O    105.90  3.000
 RCV  H11  C2  H10  106.62  3.000
 RCV  H11  C2  O2   106.52  3.000
 RCV  H10  C2  O2   112.90  3.000
 RCV  H11  C2  C1   108.15  3.000
 RCV  H10  C2  C1   110.51  3.000
 RCV  O2   C2  C1   111.81  3.000
 RCV  O2   C3  C8   124.47  3.000
 RCV  C8   C3  C4   119.76  3.000
 RCV  O2   C3  C4   115.76  3.000
 RCV  H13  N   H12  105.81  3.000
 RCV  H13  N   C9   109.36  3.000
 RCV  H12  N   C9   108.98  3.000
 RCV  C3   O2  C2   119.34  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
 RCV  CONST_01  C7   C6  C5  C4     0.00   0.0  0
 RCV  CONST_02  C7   C8  C3  C4     0.00   0.0  0
 RCV  CONST_03  C8   C3  C4  C5     0.00   0.0  0
 RCV  CONST_04  C8   C7  C6  C5     0.00   0.0  0
 RCV  CONST_05  C3   C4  C5  C6     0.00   0.0  0
 RCV  CONST_06  C3   C8  C7  C6     0.00   0.0  0
 RCV  CONST_07  O2   C3  C4  C5   180.00   0.0  0
 RCV  CONST_08  C9   C7  C6  C5   180.00   0.0  0
 RCV  CONST_09  O2   C3  C8  C7   180.00   0.0  0
 RCV  CONST_10  C3   C8  C7  C9   180.00   0.0  0
 RCV  CONST_11  H3   C6  C5  C4   180.00   0.0  0
 RCV  CONST_12  H4   C8  C3  C4   180.00   0.0  0
 RCV  CONST_13  H1   C4  C5  C6   180.00   0.0  0
 RCV  CONST_14  H2   C5  C6  C7   180.00   0.0  0
 RCV  Var_01    N    C9  C7  C6   -56.70  30.0  2
 RCV  Var_02    H12  N   C9  C7   177.32  30.0  3
 RCV  Var_03    H10  C2  O2  C3    49.76  30.0  3
 RCV  Var_04    O2   C2  C1  O1    -7.36  30.0  3
 RCV  Var_05    C2   C1  O   C    177.76  30.0  2
 RCV  Var_06    H7   C   O   C1  -178.44  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
 RCV  plan-1  C4  0.020
 RCV  plan-1  C5  0.020
 RCV  plan-1  C6  0.020
 RCV  plan-1  C7  0.020
 RCV  plan-1  C8  0.020
 RCV  plan-1  C9  0.020
 RCV  plan-1  C3  0.020
 RCV  plan-1  H1  0.020
 RCV  plan-1  H2  0.020
 RCV  plan-1  H3  0.020
 RCV  plan-1  H4  0.020
 RCV  plan-1  O2  0.020
 RCV  plan-2  O1  0.020
 RCV  plan-2  C1  0.020
 RCV  plan-2  O   0.020
 RCV  plan-2  C2  0.020

