# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 06:13:28 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tridecanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC(=O)N[C@@H](CO)C[C@@H](O)c1ccccc1
#
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
 H13  H13  N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tridecanamide  ligand  66  27  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_H13
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
 H13  O21   O  O     0  -0.503    1.7914  -1.3436   1.8387
 H13  C21   C  C     0   0.565    1.7739  -0.9311   0.6866
 H13  N2    N  NH1   0  -0.635    2.7928  -1.1034  -0.1756
 H13  C2    C  CH1   0  -0.121    4.0157  -1.8197   0.1217
 H13  C1    C  CH2   0  -0.148    4.0355  -3.1727  -0.5738
 H13  O1    O  OH1   0  -0.673    4.0091  -2.9729  -1.9683
 H13  C3    C  CH2   0  -0.481    5.2360  -0.9719  -0.2385
 H13  C4    C  CH1   0  -0.013    5.3714   0.2968   0.6035
 H13  C5    C  CR6   0   0.117    6.5344   1.1300   0.1031
 H13  C6    C  CR16  0  -0.303    6.3629   1.9417  -1.0163
 H13  C7    C  CR16  0  -0.240    7.4160   2.6893  -1.5228
 H13  C8    C  CR16  0  -0.272    8.6633   2.6370  -0.9127
 H13  C9    C  CR16  0  -0.237    8.8433   1.8327   0.2038
 H13  C10   C  CR16  0  -0.327    7.7856   1.0862   0.7094
 H13  O4    O  OH1   0  -0.660    5.4559   0.0107   1.9793
 H13  C22   C  CH2   0  -0.580    0.5976  -0.1576   0.1295
 H13  C23   C  CH2   0  -0.414   -0.7452  -0.6604   0.6435
 H13  C24   C  CH2   0  -0.415   -1.9148   0.0995   0.0319
 H13  C25   C  CH2   0  -0.413   -3.2681  -0.3821   0.5386
 H13  C26   C  CH2   0  -0.412   -4.4418   0.3453  -0.1042
 H13  C27   C  CH2   0  -0.412   -5.7982  -0.1337   0.3976
 H13  C28   C  CH2   0  -0.412   -6.9693   0.5820  -0.2630
 H13  C29   C  CH2   0  -0.412   -8.3285   0.1041   0.2321
 H13  C30   C  CH2   0  -0.412   -9.4963   0.8158  -0.4389
 H13  C31   C  CH2   0  -0.406  -10.8576   0.3384   0.0505
 H13  C32   C  CH2   0  -0.420  -12.0242   1.0483  -0.6251
 H13  C33   C  CH3   0  -0.661  -13.3803   0.5630  -0.1320
 H13  HN2   H  HNH1  0   0.392    2.6635  -0.7948  -1.1263
 H13  H2    H  HCH1  0   0.261    4.0208  -2.0179   1.1938
 H13  H1    H  HCH2  0   0.201    4.9353  -3.7154  -0.2553
 H13  H1A   H  HCH2  0   0.213    3.1698  -3.7535  -0.2324
 H13  HO1   H  HOH1  0   0.459    3.9151  -3.8289  -2.3949
 H13  H3    H  HCH2  0   0.244    6.1392  -1.5808  -0.1141
 H13  H3A   H  HCH2  0   0.252    5.2040  -0.6966  -1.2956
 H13  H4    H  HCH1  0   0.244    4.4599   0.8916   0.4833
 H13  H6    H  HCR6  0   0.246    5.3908   1.9968  -1.4944
 H13  H7    H  HCR6  0   0.254    7.2624   3.3182  -2.3904
 H13  H8    H  HCR6  0   0.254    9.4855   3.2239  -1.3012
 H13  H9    H  HCR6  0   0.254    9.8101   1.7868   0.6887
 H13  H10   H  HCR6  0   0.239    7.9498   0.4756   1.5884
 H13  HO4   H  HOH1  0   0.449    6.0594  -0.7280   2.1113
 H13  H22   H  HCH2  0   0.266    0.7290   0.8929   0.4109
 H13  H22A  H  HCH2  0   0.245    0.6115  -0.1796  -0.9633
 H13  H23   H  HCH2  0   0.221   -0.8497  -1.7259   0.4165
 H13  H23A  H  HCH2  0   0.222   -0.7799  -0.5725   1.7319
 H13  H24   H  HCH2  0   0.211   -1.8070   1.1694   0.2417
 H13  H24A  H  HCH2  0   0.210   -1.8801   0.0011  -1.0588
 H13  H25   H  HCH2  0   0.208   -3.3628  -1.4577   0.3528
 H13  H25A  H  HCH2  0   0.208   -3.3145  -0.2588   1.6263
 H13  H26   H  HCH2  0   0.207   -4.3469   1.4215   0.0779
 H13  H26A  H  HCH2  0   0.207   -4.3924   0.2188  -1.1915
 H13  H27   H  HCH2  0   0.206   -5.8882  -1.2120   0.2253
 H13  H27A  H  HCH2  0   0.207   -5.8540   0.0033   1.4833
 H13  H28   H  HCH2  0   0.206   -6.8795   1.6605  -0.0913
 H13  H28A  H  HCH2  0   0.206   -6.9103   0.4446  -1.3486
 H13  H29   H  HCH2  0   0.206   -8.4167  -0.9751   0.0645
 H13  H29A  H  HCH2  0   0.206   -8.3913   0.2464   1.3168
 H13  H30   H  HCH2  0   0.206   -9.4084   1.8950  -0.2709
 H13  H30A  H  HCH2  0   0.206   -9.4309   0.6741  -1.5236
 H13  H31   H  HCH2  0   0.205  -10.9451  -0.7412  -0.1157
 H13  H31A  H  HCH2  0   0.206  -10.9254   0.4820   1.1349
 H13  H32   H  HCH2  0   0.210  -11.9369   2.1263  -0.4571
 H13  H32A  H  HCH2  0   0.210  -11.9549   0.9055  -1.7081
 H13  H33   H  HCH3  0   0.215  -13.5073  -0.5053  -0.3169
 H13  H33A  H  HCH3  0   0.215  -13.4897   0.7241   0.9422
 H13  H33B  H  HCH3  0   0.225  -14.1992   1.0842  -0.6290

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
 H13  O21  C21   double    1.224  0.020  1.224
 H13  C21  N2    single    1.346  0.020  1.346
 H13  C21  C22   single    1.514  0.020  1.514
 H13  N2   C2    single    1.448  0.020  1.448
 H13  C2   C1    single    1.521  0.020  1.521
 H13  C2   C3    single    1.529  0.020  1.529
 H13  C1   O1    single    1.409  0.020  1.409
 H13  C3   C4    single    1.529  0.020  1.529
 H13  C4   C5    single    1.516  0.020  1.516
 H13  C4   O4    single    1.408  0.020  1.408
 H13  C5   C6    aromatic  1.393  0.020  1.393
 H13  C5   C10   aromatic  1.391  0.020  1.391
 H13  C6   C7    aromatic  1.387  0.020  1.387
 H13  C7   C8    aromatic  1.390  0.020  1.390
 H13  C8   C9    aromatic  1.388  0.020  1.388
 H13  C9   C10   aromatic  1.390  0.020  1.390
 H13  C22  C23   single    1.523  0.020  1.523
 H13  C23  C24   single    1.523  0.020  1.523
 H13  C24  C25   single    1.523  0.020  1.523
 H13  C25  C26   single    1.523  0.020  1.523
 H13  C26  C27   single    1.523  0.020  1.523
 H13  C27  C28   single    1.523  0.020  1.523
 H13  C28  C29   single    1.523  0.020  1.523
 H13  C29  C30   single    1.523  0.020  1.523
 H13  C30  C31   single    1.523  0.020  1.523
 H13  C31  C32   single    1.524  0.020  1.524
 H13  C32  C33   single    1.522  0.020  1.522
 H13  N2   HN2   single    0.860  0.020  1.020
 H13  C2   H2    single    0.970  0.020  1.090
 H13  C1   H1    single    0.970  0.020  1.090
 H13  C1   H1A   single    0.970  0.020  1.090
 H13  O1   HO1   single    0.850  0.020  0.980
 H13  C3   H3    single    0.970  0.020  1.090
 H13  C3   H3A   single    0.970  0.020  1.090
 H13  C4   H4    single    0.970  0.020  1.090
 H13  C6   H6    single    0.930  0.020  1.080
 H13  C7   H7    single    0.930  0.020  1.080
 H13  C8   H8    single    0.930  0.020  1.080
 H13  C9   H9    single    0.930  0.020  1.080
 H13  C10  H10   single    0.930  0.020  1.080
 H13  O4   HO4   single    0.850  0.020  0.980
 H13  C22  H22   single    0.970  0.020  1.090
 H13  C22  H22A  single    0.970  0.020  1.090
 H13  C23  H23   single    0.970  0.020  1.090
 H13  C23  H23A  single    0.970  0.020  1.090
 H13  C24  H24   single    0.970  0.020  1.090
 H13  C24  H24A  single    0.970  0.020  1.090
 H13  C25  H25   single    0.970  0.020  1.090
 H13  C25  H25A  single    0.970  0.020  1.090
 H13  C26  H26   single    0.970  0.020  1.090
 H13  C26  H26A  single    0.970  0.020  1.090
 H13  C27  H27   single    0.970  0.020  1.090
 H13  C27  H27A  single    0.970  0.020  1.090
 H13  C28  H28   single    0.970  0.020  1.090
 H13  C28  H28A  single    0.970  0.020  1.090
 H13  C29  H29   single    0.970  0.020  1.090
 H13  C29  H29A  single    0.970  0.020  1.090
 H13  C30  H30   single    0.970  0.020  1.090
 H13  C30  H30A  single    0.970  0.020  1.090
 H13  C31  H31   single    0.970  0.020  1.090
 H13  C31  H31A  single    0.970  0.020  1.090
 H13  C32  H32   single    0.970  0.020  1.090
 H13  C32  H32A  single    0.970  0.020  1.090
 H13  C33  H33   single    0.970  0.020  1.090
 H13  C33  H33A  single    0.970  0.020  1.090
 H13  C33  H33B  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
 H13  C22   C21  N2    114.70  3.000
 H13  C22   C21  O21   121.99  3.000
 H13  N2    C21  O21   123.30  3.000
 H13  HN2   N2   C2    116.96  3.000
 H13  HN2   N2   C21   117.90  3.000
 H13  C2    N2   C21   124.83  3.000
 H13  H2    C2   C3    109.20  3.000
 H13  H2    C2   C1    106.72  3.000
 H13  C3    C2   C1    112.03  3.000
 H13  H2    C2   N2    107.20  3.000
 H13  C3    C2   N2    110.57  3.000
 H13  C1    C2   N2    110.92  3.000
 H13  H1A   C1   H1    107.14  3.000
 H13  H1A   C1   O1    111.61  3.000
 H13  H1    C1   O1    111.88  3.000
 H13  H1A   C1   C2    108.56  3.000
 H13  H1    C1   C2    108.52  3.000
 H13  O1    C1   C2    109.03  3.000
 H13  HO1   O1   C1    108.35  3.000
 H13  H3A   C3   H3    105.89  3.000
 H13  H3A   C3   C4    109.04  3.000
 H13  H3    C3   C4    108.99  3.000
 H13  H3A   C3   C2    110.13  3.000
 H13  H3    C3   C2    108.83  3.000
 H13  C4    C3   C2    113.65  3.000
 H13  H4    C4   O4    105.52  3.000
 H13  H4    C4   C5    107.69  3.000
 H13  O4    C4   C5    112.85  3.000
 H13  H4    C4   C3    108.45  3.000
 H13  O4    C4   C3    112.02  3.000
 H13  C5    C4   C3    110.03  3.000
 H13  C10   C5   C6    118.64  3.000
 H13  C10   C5   C4    121.94  3.000
 H13  C6    C5   C4    119.41  3.000
 H13  H6    C6   C7    119.47  3.000
 H13  H6    C6   C5    119.61  3.000
 H13  C7    C6   C5    120.92  3.000
 H13  H7    C7   C8    120.08  3.000
 H13  H7    C7   C6    119.87  3.000
 H13  C8    C7   C6    120.05  3.000
 H13  H8    C8   C9    120.30  3.000
 H13  H8    C8   C7    120.25  3.000
 H13  C9    C8   C7    119.44  3.000
 H13  H9    C9   C10   119.60  3.000
 H13  H9    C9   C8    120.05  3.000
 H13  C10   C9   C8    120.35  3.000
 H13  H10   C10  C9    118.87  3.000
 H13  H10   C10  C5    120.53  3.000
 H13  C9    C10  C5    120.60  3.000
 H13  HO4   O4   C4    109.12  3.000
 H13  H22A  C22  H22   105.94  3.000
 H13  H22A  C22  C23   109.99  3.000
 H13  H22   C22  C23   109.61  3.000
 H13  H22A  C22  C21   110.35  3.000
 H13  H22   C22  C21   107.59  3.000
 H13  C23   C22  C21   113.08  3.000
 H13  H23A  C23  H23   106.38  3.000
 H13  H23A  C23  C24   109.61  3.000
 H13  H23   C23  C24   109.21  3.000
 H13  H23A  C23  C22   109.73  3.000
 H13  H23   C23  C22   109.61  3.000
 H13  C24   C23  C22   112.13  3.000
 H13  H24A  C24  H24   105.98  3.000
 H13  H24A  C24  C25   109.32  3.000
 H13  H24   C24  C25   109.42  3.000
 H13  H24A  C24  C23   109.31  3.000
 H13  H24   C24  C23   109.56  3.000
 H13  C25   C24  C23   113.01  3.000
 H13  H25A  C25  H25   105.97  3.000
 H13  H25A  C25  C26   109.42  3.000
 H13  H25   C25  C26   109.31  3.000
 H13  H25A  C25  C24   109.41  3.000
 H13  H25   C25  C24   109.32  3.000
 H13  C26   C25  C24   113.16  3.000
 H13  H26A  C26  H26   105.93  3.000
 H13  H26A  C26  C27   109.31  3.000
 H13  H26   C26  C27   109.34  3.000
 H13  H26A  C26  C25   109.20  3.000
 H13  H26   C26  C25   109.41  3.000
 H13  C27   C26  C25   113.39  3.000
 H13  H27A  C27  H27   105.94  3.000
 H13  H27A  C27  C28   109.38  3.000
 H13  H27   C27  C28   109.33  3.000
 H13  H27A  C27  C26   109.41  3.000
 H13  H27   C27  C26   109.32  3.000
 H13  C28   C27  C26   113.20  3.000
 H13  H28A  C28  H28   105.92  3.000
 H13  H28A  C28  C29   109.31  3.000
 H13  H28   C28  C29   109.33  3.000
 H13  H28A  C28  C27   109.23  3.000
 H13  H28   C28  C27   109.35  3.000
 H13  C29   C28  C27   113.43  3.000
 H13  H29A  C29  H29   105.94  3.000
 H13  H29A  C29  C30   109.36  3.000
 H13  H29   C29  C30   109.33  3.000
 H13  H29A  C29  C28   109.40  3.000
 H13  H29   C29  C28   109.33  3.000
 H13  C30   C29  C28   113.22  3.000
 H13  H30A  C30  H30   105.92  3.000
 H13  H30A  C30  C31   109.32  3.000
 H13  H30   C30  C31   109.33  3.000
 H13  H30A  C30  C29   109.26  3.000
 H13  H30   C30  C29   109.34  3.000
 H13  C31   C30  C29   113.40  3.000
 H13  H31A  C31  H31   105.92  3.000
 H13  H31A  C31  C32   109.29  3.000
 H13  H31   C31  C32   109.30  3.000
 H13  H31A  C31  C30   109.40  3.000
 H13  H31   C31  C30   109.35  3.000
 H13  C32   C31  C30   113.31  3.000
 H13  H32A  C32  H32   105.98  3.000
 H13  H32A  C32  C33   109.59  3.000
 H13  H32   C32  C33   109.59  3.000
 H13  H32A  C32  C31   109.24  3.000
 H13  H32   C32  C31   109.25  3.000
 H13  C33   C32  C31   112.95  3.000
 H13  H33B  C33  H33A  107.62  3.000
 H13  H33B  C33  H33   107.64  3.000
 H13  H33A  C33  H33   107.43  3.000
 H13  H33B  C33  C32   111.65  3.000
 H13  H33A  C33  C32   111.16  3.000
 H13  H33   C33  C32   111.15  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
 H13  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 H13  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 H13  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 H13  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 H13  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 H13  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 H13  CONST_07  C7   C6   C5   C4    180.00   0.0  0
 H13  CONST_08  C9   C10  C5   C4    180.00   0.0  0
 H13  CONST_09  H7   C7   C6   C5    180.00   0.0  0
 H13  CONST_10  H9   C9   C10  C5    180.00   0.0  0
 H13  CONST_11  H10  C10  C5   C6    180.00   0.0  0
 H13  CONST_12  H8   C8   C7   C6    180.00   0.0  0
 H13  CONST_13  H6   C6   C7   C8    180.00   0.0  0
 H13  CONST_14  C2   N2   C21  O21     0.00   0.0  0
 H13  CONST_15  C22  C21  N2   C2    180.00   0.0  0
 H13  CONST_16  HN2  N2   C21  O21   180.00   0.0  0
 H13  Var_01    C23  C22  C21  O21   -36.89  30.0  3
 H13  Var_02    C24  C23  C22  C21  -177.96  30.0  3
 H13  Var_03    C25  C24  C23  C22  -179.67  30.0  3
 H13  Var_04    C26  C25  C24  C23  -178.16  30.0  3
 H13  Var_05    C27  C26  C25  C24   179.92  30.0  3
 H13  Var_06    C28  C27  C26  C25  -179.14  30.0  3
 H13  Var_07    C29  C28  C27  C26   179.83  30.0  3
 H13  Var_08    C30  C29  C28  C27  -179.58  30.0  3
 H13  Var_09    C31  C30  C29  C28   179.85  30.0  3
 H13  Var_10    C32  C31  C30  C29  -179.81  30.0  3
 H13  Var_11    C33  C32  C31  C30   179.88  30.0  3
 H13  Var_12    H33  C33  C32  C31   -59.77  30.0  3

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
 H13  chir_01  C2  N2  C1  C3  negativ
 H13  chir_02  C4  O4  C3  C5  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
 H13  plan-1  C4   0.020
 H13  plan-1  C5   0.020
 H13  plan-1  C6   0.020
 H13  plan-1  C7   0.020
 H13  plan-1  C8   0.020
 H13  plan-1  C9   0.020
 H13  plan-1  C10  0.020
 H13  plan-1  H6   0.020
 H13  plan-1  H7   0.020
 H13  plan-1  H8   0.020
 H13  plan-1  H9   0.020
 H13  plan-1  H10  0.020
 H13  plan-2  O21  0.020
 H13  plan-2  C21  0.020
 H13  plan-2  N2   0.020
 H13  plan-2  C2   0.020
 H13  plan-2  C22  0.020
 H13  plan-2  HN2  0.020

