# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:49:31 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(5-methyl-1~{H}-indol-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2[nH]cc(C[C@H](N)C(O)=O)c2c1
#
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
 D0Q  D0Q  '(2~{S})-2-azanyl-3-(5-methyl-1~{H}-indol-3-yl)propanoic acid'  L-peptide  29  16  .  2022-07-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_D0Q
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
 D0Q  C4    C  CR56   0   0.033   1.1212  -0.3200   0.2403
 D0Q  C5    C  CR56   0   0.334   2.1321  -1.2393  -0.1132
 D0Q  C6    C  CR16   0  -0.294   3.4507  -0.8363  -0.3187
 D0Q  C11   C  CH1    0  -0.194  -2.2585  -0.0164  -0.4961
 D0Q  C7    C  CR16   0  -0.323   3.7428   0.5038  -0.1609
 D0Q  C8    C  CR15   0  -0.087   0.2229  -2.3627   0.1051
 D0Q  C9    C  CR5    0   0.009  -0.1005  -1.0608   0.3767
 D0Q  C10   C  CH2    0  -0.545  -1.4525  -0.5280   0.7216
 D0Q  C12   C  C      0   0.398  -3.6138   0.5105   0.0222
 D0Q  N1    N  NR15   0  -0.686   1.5530  -2.4715  -0.1911
 D0Q  N2    N  NH2    0  -0.796  -1.5813   0.9806  -1.3028
 D0Q  C3    C  CR16   0  -0.433   1.4558   1.0329   0.3905
 D0Q  C2    C  CR6    0   0.090   2.7597   1.4511   0.1951
 D0Q  O1    O  O      0  -0.605  -3.7712   1.7462   0.0658
 D0Q  O2    O  OC    -1  -0.623  -4.4280  -0.3564   0.4013
 D0Q  H61   H  HCR6   0   0.254   4.2220  -1.5453  -0.5933
 D0Q  H111  H  HCH1   0   0.205  -2.4519  -0.8861  -1.1343
 D0Q  H71   H  HCR6   0   0.239   4.7607   0.8404  -0.3206
 D0Q  H81   H  HCR5   0   0.276  -0.4100  -3.2369   0.1074
 D0Q  H102  H  HCH2   0   0.222  -1.3488   0.2899   1.4440
 D0Q  H101  H  HCH2   0   0.233  -2.0372  -1.3062   1.2168
 D0Q  H1    H  HNR5   0   0.405   2.0258  -3.3308  -0.4137
 D0Q  H2    H  HNH2   0   0.325  -1.5020   1.8386  -0.7713
 D0Q  H21   H  HNH2   0   0.339  -0.6386   0.6748  -1.5110
 D0Q  H31   H  HCR6   0   0.231   0.6911   1.7556   0.6547
 D0Q  H11   H  HCH3   0   0.239   3.5985   3.0643   1.3568
 D0Q  H13   H  HCH3   0   0.236   3.8700   3.2144  -0.3693
 D0Q  H12   H  HCH3   0   0.239   2.2774   3.5500   0.3052
 D0Q  C1    C  CH3    0  -0.722   3.1438   2.8932   0.3784

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
 D0Q  O1   C12   deloc     1.246  0.020  1.246
 D0Q  C10  C9    single    1.494  0.020  1.494
 D0Q  C10  C11   single    1.547  0.020  1.547
 D0Q  C8   C9    aromatic  1.369  0.020  1.369
 D0Q  C8   N1    aromatic  1.367  0.020  1.367
 D0Q  C9   C4    aromatic  1.435  0.020  1.435
 D0Q  C12  C11   single    1.544  0.020  1.544
 D0Q  C12  O2    deloc     1.248  0.020  1.248
 D0Q  N2   C11   single    1.450  0.020  1.450
 D0Q  N1   C5    aromatic  1.364  0.020  1.364
 D0Q  C4   C5    aromatic  1.411  0.020  1.411
 D0Q  C4   C3    aromatic  1.402  0.020  1.402
 D0Q  C5   C6    aromatic  1.394  0.020  1.394
 D0Q  C3   C2    aromatic  1.383  0.020  1.383
 D0Q  C6   C7    aromatic  1.381  0.020  1.381
 D0Q  C2   C7    aromatic  1.411  0.020  1.411
 D0Q  C2   C1    single    1.504  0.020  1.504
 D0Q  C6   H61   single    0.930  0.020  1.080
 D0Q  C11  H111  single    0.970  0.020  1.090
 D0Q  C7   H71   single    0.930  0.020  1.080
 D0Q  C8   H81   single    0.930  0.020  1.080
 D0Q  C10  H102  single    0.970  0.020  1.090
 D0Q  C10  H101  single    0.970  0.020  1.090
 D0Q  N1   H1    single    0.860  0.020  1.020
 D0Q  N2   H2    single    0.890  0.020  1.040
 D0Q  N2   H21   single    0.890  0.020  1.040
 D0Q  C3   H31   single    0.930  0.020  1.080
 D0Q  C1   H11   single    0.970  0.020  1.090
 D0Q  C1   H13   single    0.970  0.020  1.090
 D0Q  C1   H12   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
 D0Q  C3    C4   C9    133.72  3.000
 D0Q  C3    C4   C5    118.98  3.000
 D0Q  C9    C4   C5    107.30  3.000
 D0Q  N1    C5   C6    130.87  3.000
 D0Q  C6    C5   C4    121.74  3.000
 D0Q  N1    C5   C4    107.38  3.000
 D0Q  H61   C6   C7    120.92  3.000
 D0Q  H61   C6   C5    121.45  3.000
 D0Q  C7    C6   C5    117.64  3.000
 D0Q  H111  C11  N2    107.70  3.000
 D0Q  H111  C11  C12   108.15  3.000
 D0Q  N2    C11  C12   111.23  3.000
 D0Q  H111  C11  C10   106.72  3.000
 D0Q  N2    C11  C10   114.95  3.000
 D0Q  C12   C11  C10   107.82  3.000
 D0Q  H71   C7   C2    118.89  3.000
 D0Q  H71   C7   C6    118.89  3.000
 D0Q  C2    C7   C6    122.22  3.000
 D0Q  H81   C8   N1    120.43  3.000
 D0Q  H81   C8   C9    129.16  3.000
 D0Q  N1    C8   C9    110.41  3.000
 D0Q  C10   C9   C8    126.80  3.000
 D0Q  C8    C9   C4    105.72  3.000
 D0Q  C10   C9   C4    127.47  3.000
 D0Q  H101  C10  H102  106.47  3.000
 D0Q  H101  C10  C9    109.59  3.000
 D0Q  H102  C10  C9    109.44  3.000
 D0Q  H101  C10  C11   108.27  3.000
 D0Q  H102  C10  C11   108.73  3.000
 D0Q  C9    C10  C11   114.06  3.000
 D0Q  O2    C12  O1    126.55  3.000
 D0Q  O2    C12  C11   115.95  3.000
 D0Q  O1    C12  C11   117.45  3.000
 D0Q  H1    N1   C8    124.99  3.000
 D0Q  H1    N1   C5    125.81  3.000
 D0Q  C8    N1   C5    109.19  3.000
 D0Q  H21   N2   H2    106.91  3.000
 D0Q  H21   N2   C11   109.97  3.000
 D0Q  H2    N2   C11   109.10  3.000
 D0Q  H31   C3   C2    119.83  3.000
 D0Q  H31   C3   C4    120.05  3.000
 D0Q  C2    C3   C4    120.11  3.000
 D0Q  C1    C2   C3    120.90  3.000
 D0Q  C1    C2   C7    119.78  3.000
 D0Q  C3    C2   C7    119.31  3.000
 D0Q  H12   C1   H13   107.81  3.000
 D0Q  H12   C1   H11   107.26  3.000
 D0Q  H13   C1   H11   106.91  3.000
 D0Q  H12   C1   C2    111.52  3.000
 D0Q  H13   C1   C2    111.65  3.000
 D0Q  H11   C1   C2    111.45  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
 D0Q  CONST_01  N1   C8   C9  C4     0.00   0.0  0
 D0Q  CONST_02  C8   N1   C5  C4     0.00   0.0  0
 D0Q  CONST_03  C7   C6   C5  C4     0.00   0.0  0
 D0Q  CONST_04  C7   C2   C3  C4     0.00   0.0  0
 D0Q  CONST_05  C9   C8   N1  C5     0.00   0.0  0
 D0Q  CONST_06  C8   C9   C4  C5     0.00   0.0  0
 D0Q  CONST_07  C2   C3   C4  C5     0.00   0.0  0
 D0Q  CONST_08  C2   C7   C6  C5     0.00   0.0  0
 D0Q  CONST_09  C8   N1   C5  C6   180.00   0.0  0
 D0Q  CONST_10  C9   C4   C5  C6   180.00   0.0  0
 D0Q  CONST_11  C3   C4   C5  C6     0.00   0.0  0
 D0Q  CONST_12  C3   C2   C7  C6     0.00   0.0  0
 D0Q  CONST_13  N1   C5   C6  C7   180.00   0.0  0
 D0Q  CONST_14  C3   C4   C9  C8   180.00   0.0  0
 D0Q  CONST_15  N1   C5   C4  C9     0.00   0.0  0
 D0Q  CONST_16  C2   C3   C4  C9   180.00   0.0  0
 D0Q  CONST_17  C3   C4   C5  N1   180.00   0.0  0
 D0Q  CONST_18  C1   C2   C3  C4   180.00   0.0  0
 D0Q  CONST_19  C10  C9   C4  C5   180.00   0.0  0
 D0Q  CONST_20  C1   C2   C7  C6   180.00   0.0  0
 D0Q  CONST_21  N1   C8   C9  C10  180.00   0.0  0
 D0Q  CONST_22  C3   C4   C9  C10    0.00   0.0  0
 D0Q  CONST_23  H81  C8   C9  C4   180.00   0.0  0
 D0Q  CONST_24  H1   N1   C5  C4   180.00   0.0  0
 D0Q  CONST_25  H61  C6   C5  C4   180.00   0.0  0
 D0Q  CONST_26  H31  C3   C4  C5   180.00   0.0  0
 D0Q  CONST_27  H71  C7   C6  C5   180.00   0.0  0
 D0Q  Var_01    C11  C10  C9  C4    86.04  30.0  3
 D0Q  Var_02    H11  C1   C2  C7   -79.98  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
 D0Q  chir_01  C11  C10  C12  N2  negativ

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
 D0Q  plan-1  C4   0.020
 D0Q  plan-1  C5   0.020
 D0Q  plan-1  C6   0.020
 D0Q  plan-1  C7   0.020
 D0Q  plan-1  C8   0.020
 D0Q  plan-1  C9   0.020
 D0Q  plan-1  C10  0.020
 D0Q  plan-1  N1   0.020
 D0Q  plan-1  C3   0.020
 D0Q  plan-1  C2   0.020
 D0Q  plan-1  H61  0.020
 D0Q  plan-1  H71  0.020
 D0Q  plan-1  H81  0.020
 D0Q  plan-1  H1   0.020
 D0Q  plan-1  H31  0.020
 D0Q  plan-1  C1   0.020
 D0Q  plan-2  C11  0.020
 D0Q  plan-2  C12  0.020
 D0Q  plan-2  O1   0.020
 D0Q  plan-2  O2   0.020

