# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:16:53 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-[(2R,5R,6S)-5-hydroxy-1,2,4,5,6,7-hexahydro-3H-2,6-methanoazocino[5,4-b]indol-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CN1C[C@H](O)[C@H]2C[C@@H]1Cc3c2[nH]c4ccccc34
#
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
 M0D  M0D  2-[(2R,5R,6S)-5-hydroxy-1,2,4,5,6,7-hexahydro-3H-2,6-methanoazocino[5,4-b]indol-3-yl]acetamide  ligand  40  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M0D
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
 M0D  N1   N  NT    0  -0.410  -32.5703  -16.6121  -18.3696
 M0D  C4   C  CH1   0  -0.417  -29.9536  -17.6366  -17.7849
 M0D  C5   C  CH2   0  -0.435  -30.8110  -16.9229  -16.7375
 M0D  C6   C  CH1   0  -0.131  -32.2840  -17.1677  -17.0505
 M0D  C7   C  CH2   0  -0.511  -32.6304  -18.6603  -16.8547
 M0D  C8   C  CR5   0  -0.015  -31.5405  -19.5498  -17.3552
 M0D  C10  C  CR56  0   0.324  -30.2236  -21.2886  -18.0299
 M0D  C13  C  CR16  0  -0.271  -32.0439  -23.3049  -17.5485
 M0D  C15  C  CR56  0   0.033  -31.5030  -20.9697  -17.5138
 M0D  N    N  NH2   0  -0.801  -35.4221  -15.7763  -20.4255
 M0D  C    C  C     0   0.497  -34.3336  -15.5099  -19.6886
 M0D  O    O  O     0  -0.484  -33.7145  -14.4613  -19.7645
 M0D  C1   C  CH2   0  -0.410  -33.9666  -16.6152  -18.7041
 M0D  C11  C  CR16  0  -0.315  -29.8452  -22.6002  -18.3061
 M0D  C12  C  CR16  0  -0.289  -30.7697  -23.5997  -18.0592
 M0D  C14  C  CR16  0  -0.377  -32.4167  -22.0020  -17.2749
 M0D  C2   C  CH2   0  -0.306  -31.7550  -17.1247  -19.4561
 M0D  C3   C  CH1   0   0.074  -30.2690  -17.0076  -19.1505
 M0D  C9   C  CR5   0   0.358  -30.3250  -19.0776  -17.7598
 M0D  N2   N  NR15  0  -0.748  -29.5345  -20.1172  -18.1695
 M0D  O1   O  OH1   0  -0.670  -29.5812  -17.6316  -20.2085
 M0D  H2   H  HCH1  0   0.266  -28.8897  -17.5019  -17.5609
 M0D  H3   H  HCH2  0   0.248  -30.5737  -17.2890  -15.7367
 M0D  H4   H  HCH2  0   0.243  -30.6060  -15.8500  -16.7498
 M0D  H5   H  HCH1  0   0.250  -32.8893  -16.5942  -16.3427
 M0D  H6   H  HCH2  0   0.242  -33.5828  -18.8951  -17.3414
 M0D  H7   H  HCH2  0   0.239  -32.8023  -18.8360  -15.7867
 M0D  H8   H  HCR6  0   0.242  -32.7412  -24.1130  -17.3677
 M0D  H9   H  HNH2  0   0.400  -35.7918  -15.0888  -21.0612
 M0D  H10  H  HNH2  0   0.406  -35.8929  -16.6632  -20.3788
 M0D  H11  H  HCH2  0   0.282  -34.5514  -16.4234  -17.7979
 M0D  H12  H  HCH2  0   0.225  -34.3203  -17.5839  -19.0920
 M0D  H13  H  HCR6  0   0.254  -28.8640  -22.8338  -18.7001
 M0D  H14  H  HCR6  0   0.246  -30.5038  -24.6290  -18.2628
 M0D  H15  H  HCR6  0   0.237  -33.4020  -21.7826  -16.8808
 M0D  H16  H  HCH2  0   0.248  -31.9678  -16.5384  -20.3537
 M0D  H17  H  HCH2  0   0.208  -31.9933  -18.1729  -19.6998
 M0D  H18  H  HCH1  0   0.217  -30.0114  -15.9406  -19.0868
 M0D  H19  H  HNR5  0   0.399  -28.5967  -20.0295  -18.5231
 M0D  H20  H  HOH1  0   0.452  -28.6411  -17.4548  -20.1045

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
 M0D  N    C    single    1.341  0.020  1.341
 M0D  O1   C3   single    1.408  0.020  1.408
 M0D  O    C    double    1.220  0.020  1.220
 M0D  C    C1   single    1.525  0.020  1.525
 M0D  C2   C3   single    1.522  0.020  1.522
 M0D  C2   N1   single    1.452  0.020  1.452
 M0D  C3   C4   single    1.536  0.020  1.536
 M0D  C1   N1   single    1.436  0.020  1.436
 M0D  N1   C6   single    1.460  0.020  1.460
 M0D  C11  C12  aromatic  1.384  0.020  1.384
 M0D  C11  C10  aromatic  1.393  0.020  1.393
 M0D  N2   C10  aromatic  1.366  0.020  1.366
 M0D  N2   C9   aromatic  1.369  0.020  1.369
 M0D  C12  C13  aromatic  1.404  0.020  1.404
 M0D  C10  C15  aromatic  1.416  0.020  1.416
 M0D  C4   C9   single    1.488  0.020  1.488
 M0D  C4   C5   single    1.530  0.020  1.530
 M0D  C9   C8   aromatic  1.365  0.020  1.365
 M0D  C15  C8   aromatic  1.429  0.020  1.429
 M0D  C15  C14  aromatic  1.399  0.020  1.399
 M0D  C13  C14  aromatic  1.383  0.020  1.383
 M0D  C8   C7   single    1.493  0.020  1.493
 M0D  C6   C7   single    1.545  0.020  1.545
 M0D  C6   C5   single    1.526  0.020  1.526
 M0D  C4   H2   single    0.970  0.020  1.090
 M0D  C5   H3   single    0.970  0.020  1.090
 M0D  C5   H4   single    0.970  0.020  1.090
 M0D  C6   H5   single    0.970  0.020  1.090
 M0D  C7   H6   single    0.970  0.020  1.090
 M0D  C7   H7   single    0.970  0.020  1.090
 M0D  C13  H8   single    0.930  0.020  1.080
 M0D  N    H9   single    0.860  0.020  1.020
 M0D  N    H10  single    0.860  0.020  1.020
 M0D  C1   H11  single    0.970  0.020  1.090
 M0D  C1   H12  single    0.970  0.020  1.090
 M0D  C11  H13  single    0.930  0.020  1.080
 M0D  C12  H14  single    0.930  0.020  1.080
 M0D  C14  H15  single    0.930  0.020  1.080
 M0D  C2   H16  single    0.970  0.020  1.090
 M0D  C2   H17  single    0.970  0.020  1.090
 M0D  C3   H18  single    0.970  0.020  1.090
 M0D  N2   H19  single    0.860  0.020  1.020
 M0D  O1   H20  single    0.850  0.020  0.980

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
 M0D  C2   N1   C1   111.77  3.000
 M0D  C1   N1   C6   113.61  3.000
 M0D  C2   N1   C6   115.58  3.000
 M0D  H2   C4   C9   110.97  3.000
 M0D  H2   C4   C3   109.32  3.000
 M0D  C9   C4   C3   111.11  3.000
 M0D  H2   C4   C5   110.30  3.000
 M0D  C9   C4   C5   107.47  3.000
 M0D  C3   C4   C5   107.61  3.000
 M0D  H4   C5   H3   107.39  3.000
 M0D  H4   C5   C6   109.66  3.000
 M0D  H3   C5   C6   110.12  3.000
 M0D  H4   C5   C4   110.20  3.000
 M0D  H3   C5   C4   110.44  3.000
 M0D  C6   C5   C4   109.01  3.000
 M0D  H5   C6   C7   107.49  3.000
 M0D  H5   C6   C5   108.50  3.000
 M0D  C7   C6   C5   110.21  3.000
 M0D  H5   C6   N1   106.06  3.000
 M0D  C5   C6   N1   108.28  3.000
 M0D  C7   C6   N1   116.00  3.000
 M0D  H7   C7   H6   105.21  3.000
 M0D  H7   C7   C8   110.22  3.000
 M0D  H6   C7   C8   110.99  3.000
 M0D  H7   C7   C6   108.28  3.000
 M0D  H6   C7   C6   110.24  3.000
 M0D  C8   C7   C6   111.68  3.000
 M0D  C9   C8   C15  106.70  3.000
 M0D  C15  C8   C7   130.40  3.000
 M0D  C9   C8   C7   122.90  3.000
 M0D  N2   C10  C11  130.56  3.000
 M0D  N2   C10  C15  107.45  3.000
 M0D  C11  C10  C15  121.99  3.000
 M0D  H8   C13  C14  119.78  3.000
 M0D  H8   C13  C12  119.25  3.000
 M0D  C14  C13  C12  120.97  3.000
 M0D  C14  C15  C10  119.09  3.000
 M0D  C14  C15  C8   134.18  3.000
 M0D  C10  C15  C8   106.73  3.000
 M0D  H10  N    H9   117.38  3.000
 M0D  H10  N    C    122.00  3.000
 M0D  H9   N    C    120.62  3.000
 M0D  C1   C    O    122.75  3.000
 M0D  C1   C    N    113.95  3.000
 M0D  O    C    N    123.26  3.000
 M0D  H12  C1   H11  105.89  3.000
 M0D  H12  C1   C    109.43  3.000
 M0D  H11  C1   C    106.18  3.000
 M0D  H12  C1   N1   113.33  3.000
 M0D  H11  C1   N1   109.03  3.000
 M0D  C    C1   N1   112.51  3.000
 M0D  H13  C11  C12  120.97  3.000
 M0D  H13  C11  C10  121.43  3.000
 M0D  C12  C11  C10  117.61  3.000
 M0D  H14  C12  C11  119.29  3.000
 M0D  H14  C12  C13  119.41  3.000
 M0D  C11  C12  C13  121.31  3.000
 M0D  H15  C14  C15  120.44  3.000
 M0D  H15  C14  C13  120.52  3.000
 M0D  C15  C14  C13  119.04  3.000
 M0D  H17  C2   H16  106.64  3.000
 M0D  H17  C2   C3   109.19  3.000
 M0D  H16  C2   C3   108.28  3.000
 M0D  H17  C2   N1   112.32  3.000
 M0D  H16  C2   N1   108.42  3.000
 M0D  C3   C2   N1   111.77  3.000
 M0D  H18  C3   O1   111.05  3.000
 M0D  H18  C3   C2   108.36  3.000
 M0D  O1   C3   C2   106.99  3.000
 M0D  H18  C3   C4   107.32  3.000
 M0D  C2   C3   C4   110.34  3.000
 M0D  O1   C3   C4   112.72  3.000
 M0D  N2   C9   C8   109.89  3.000
 M0D  C8   C9   C4   124.19  3.000
 M0D  N2   C9   C4   125.89  3.000
 M0D  H19  N2   C9   125.26  3.000
 M0D  H19  N2   C10  125.51  3.000
 M0D  C9   N2   C10  109.23  3.000
 M0D  H20  O1   C3   108.35  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
 M0D  CONST_01  C10  N2   C9   C8     0.00   0.0  0
 M0D  CONST_02  C11  C10  C15  C8   180.00   0.0  0
 M0D  CONST_03  N2   C10  C15  C8     0.00   0.0  0
 M0D  CONST_04  C13  C14  C15  C8   180.00   0.0  0
 M0D  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 M0D  CONST_06  C9   C8   C15  C10    0.00   0.0  0
 M0D  CONST_07  C13  C14  C15  C10    0.00   0.0  0
 M0D  CONST_08  C12  C11  C10  C15    0.00   0.0  0
 M0D  CONST_09  C9   N2   C10  C15    0.00   0.0  0
 M0D  CONST_10  N2   C9   C8   C15    0.00   0.0  0
 M0D  CONST_11  C12  C13  C14  C15    0.00   0.0  0
 M0D  CONST_12  C14  C13  C12  C11    0.00   0.0  0
 M0D  CONST_13  C9   N2   C10  C11  180.00   0.0  0
 M0D  CONST_14  C14  C15  C10  C11    0.00   0.0  0
 M0D  CONST_15  N2   C10  C11  C12  180.00   0.0  0
 M0D  CONST_16  N2   C10  C15  C14  180.00   0.0  0
 M0D  CONST_17  C9   C8   C15  C14  180.00   0.0  0
 M0D  CONST_18  H19  N2   C9   C4     0.00   0.0  0
 M0D  CONST_19  H15  C14  C15  C8     0.00   0.0  0
 M0D  CONST_20  H14  C12  C11  C10  180.00   0.0  0
 M0D  CONST_21  H13  C11  C12  C13  180.00   0.0  0
 M0D  CONST_22  H8   C13  C14  C15  180.00   0.0  0
 M0D  CONST_23  H9   N    C    O      0.00   0.0  0
 M0D  CONST_24  H10  N    C    O    180.00   0.0  0
 M0D  Var_01    C3   C2   N1   C6   -53.02  30.0  3
 M0D  Var_02    C9   C8   C7   C6     8.32  30.0  1
 M0D  Var_03    C    C1   N1   C6   152.84  30.0  1
 M0D  Var_04    N    C    C1   N1   154.54  30.0  1

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
 M0D  chir_01  C4  C3  C9  C5  positiv
 M0D  chir_02  C6  N1  C7  C5  negativ
 M0D  chir_03  C3  O1  C2  C4  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
 M0D  plan-1  N    0.020
 M0D  plan-1  C    0.020
 M0D  plan-1  O    0.020
 M0D  plan-1  C1   0.020
 M0D  plan-1  H9   0.020
 M0D  plan-1  H10  0.020
 M0D  plan-2  C4   0.020
 M0D  plan-2  C7   0.020
 M0D  plan-2  C8   0.020
 M0D  plan-2  C10  0.020
 M0D  plan-2  C13  0.020
 M0D  plan-2  C15  0.020
 M0D  plan-2  C11  0.020
 M0D  plan-2  C12  0.020
 M0D  plan-2  C14  0.020
 M0D  plan-2  C9   0.020
 M0D  plan-2  N2   0.020
 M0D  plan-2  H8   0.020
 M0D  plan-2  H13  0.020
 M0D  plan-2  H14  0.020
 M0D  plan-2  H15  0.020
 M0D  plan-2  H19  0.020

