# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:01:16 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (3S)-3-amino-1-(cyclopropylamino)heptane-2,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N)C(O)(O)CNC1CC1
#
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
 M1C  M1C  (3S)-3-amino-1-(cyclopropylamino)heptane-2,2-diol  ligand  36  14  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M1C
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
 M1C  C13   C  CH2   0  -0.503   0.1634  -0.3611  -5.0586
 M1C  C12   C  CH2   0  -0.489  -1.1139  -0.5591  -4.2961
 M1C  C11   C  CH1   0  -0.079  -0.1947   0.5662  -3.9435
 M1C  N3    N  NH2   0  -0.794  -1.6817  -0.0828   0.7385
 M1C  C2    C  CH1   0  -0.137  -0.3373   0.4285   0.9673
 M1C  C1    C  CT    0   0.473   0.4970   0.2428  -0.3129
 M1C  C9    C  CH2   0  -0.304  -0.1576   0.8984  -1.5392
 M1C  N10   N  NH1   0  -0.628   0.5468   0.4500  -2.7266
 M1C  O8    O  OH1   0  -0.678   1.7998   0.7774  -0.1407
 M1C  O14   O  OH1   0  -0.688   0.6538  -1.1106  -0.5607
 M1C  C4    C  CH2   0  -0.413   0.3498  -0.1609   2.2059
 M1C  C5    C  CH2   0  -0.418  -0.3254   0.2437   3.5119
 M1C  C6    C  CH2   0  -0.417   0.3436  -0.3672   4.7371
 M1C  C7    C  CH3   0  -0.662  -0.2919   0.0801   6.0460
 M1C  H131  H  HCH2  0   0.248   0.1056   0.0107  -6.0734
 M1C  H132  H  HCH2  0   0.247   0.9695  -1.0616  -4.8809
 M1C  H121  H  HCH2  0   0.246  -1.1634  -1.3904  -3.6035
 M1C  H122  H  HCH2  0   0.248  -2.0496  -0.3239  -4.7864
 M1C  H11   H  HCH1  0   0.234  -0.5264   1.5639  -4.2314
 M1C  HN32  H  HNH2  0   0.350  -2.2697   0.1310   1.5332
 M1C  H2    H  HCH1  0   0.218  -0.4333   1.5123   1.1189
 M1C  H91   H  HCH2  0   0.211  -0.1764   1.9909  -1.4218
 M1C  H92   H  HCH2  0   0.246  -1.1941   0.5697  -1.6097
 M1C  H10   H  HNH1  0   0.355   1.4353   0.9271  -2.8122
 M1C  HO8   H  HOH1  0   0.444   1.7260   1.7165   0.0628
 M1C  H14   H  HOH1  0   0.439   0.7739  -1.1763  -1.5257
 M1C  H41   H  HCH2  0   0.214   1.3939   0.1589   2.2472
 M1C  H42   H  HCH2  0   0.212   0.3639  -1.2529   2.1237
 M1C  H51   H  HCH2  0   0.201  -1.3816  -0.0463   3.5050
 M1C  H52   H  HCH2  0   0.209  -0.3128   1.3362   3.5997
 M1C  H61   H  HCH2  0   0.211   1.4060  -0.1044   4.7374
 M1C  H62   H  HCH2  0   0.211   0.3036  -1.4583   4.6633
 M1C  H71   H  HCH3  0   0.226   0.2013  -0.3732   6.9066
 M1C  H72   H  HCH3  0   0.216  -0.2310   1.1638   6.1630
 M1C  H73   H  HCH3  0   0.216  -1.3477  -0.1943   6.0880
 M1C  HN31  H  HNH2  0   0.336  -1.6483  -1.0938   0.6773

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
 M1C  C13  C12   single  1.501  0.020  1.501
 M1C  C13  C11   single  1.494  0.020  1.494
 M1C  C13  H131  single  0.970  0.020  1.090
 M1C  C13  H132  single  0.970  0.020  1.090
 M1C  C12  C11   single  1.495  0.020  1.495
 M1C  C12  H121  single  0.970  0.020  1.090
 M1C  C12  H122  single  0.970  0.020  1.090
 M1C  C11  N10   single  1.430  0.020  1.430
 M1C  C11  H11   single  0.970  0.020  1.090
 M1C  N3   C2    single  1.457  0.020  1.457
 M1C  N3   HN31  single  0.890  0.020  1.040
 M1C  N3   HN32  single  0.890  0.020  1.040
 M1C  C2   C1    single  1.539  0.020  1.539
 M1C  C2   C4    single  1.534  0.020  1.534
 M1C  C2   H2    single  0.970  0.020  1.090
 M1C  C1   C9    single  1.537  0.020  1.537
 M1C  C1   O8    single  1.419  0.020  1.419
 M1C  C1   O14   single  1.385  0.020  1.385
 M1C  C9   N10   single  1.452  0.020  1.452
 M1C  C9   H91   single  0.970  0.020  1.090
 M1C  C9   H92   single  0.970  0.020  1.090
 M1C  N10  H10   single  0.890  0.020  1.040
 M1C  O8   HO8   single  0.850  0.020  0.980
 M1C  O14  H14   single  0.850  0.020  0.980
 M1C  C4   C5    single  1.525  0.020  1.525
 M1C  C4   H41   single  0.970  0.020  1.090
 M1C  C4   H42   single  0.970  0.020  1.090
 M1C  C5   C6    single  1.524  0.020  1.524
 M1C  C5   H51   single  0.970  0.020  1.090
 M1C  C5   H52   single  0.970  0.020  1.090
 M1C  C6   C7    single  1.522  0.020  1.522
 M1C  C6   H61   single  0.970  0.020  1.090
 M1C  C6   H62   single  0.970  0.020  1.090
 M1C  C7   H71   single  0.970  0.020  1.090
 M1C  C7   H72   single  0.970  0.020  1.090
 M1C  C7   H73   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
 M1C  H132  C13  H131  114.58  3.000
 M1C  H132  C13  C11   117.23  3.000
 M1C  H131  C13  C11   118.28  3.000
 M1C  H132  C13  C12   117.71  3.000
 M1C  H131  C13  C12   118.44  3.000
 M1C  C11   C13  C12    59.91  3.000
 M1C  H122  C12  H121  114.64  3.000
 M1C  H122  C12  C11   118.35  3.000
 M1C  H121  C12  C11   117.07  3.000
 M1C  H122  C12  C13   118.49  3.000
 M1C  H121  C12  C13   117.71  3.000
 M1C  C11   C12  C13    59.82  3.000
 M1C  H11   C11  N10   117.19  3.000
 M1C  H11   C11  C12   116.07  3.000
 M1C  N10   C11  C12   117.28  3.000
 M1C  H11   C11  C13   116.36  3.000
 M1C  N10   C11  C13   117.42  3.000
 M1C  C12   C11  C13    60.27  3.000
 M1C  HN32  N3   HN31  106.11  3.000
 M1C  HN32  N3   C2    109.81  3.000
 M1C  HN31  N3   C2    109.22  3.000
 M1C  H2    C2   C4    107.86  3.000
 M1C  H2    C2   C1    106.33  3.000
 M1C  C4    C2   C1    112.48  3.000
 M1C  H2    C2   N3    106.70  3.000
 M1C  C4    C2   N3    113.91  3.000
 M1C  C1    C2   N3    109.10  3.000
 M1C  O14   C1   O8    106.61  3.000
 M1C  O14   C1   C9    108.81  3.000
 M1C  O8    C1   C9    109.10  3.000
 M1C  O14   C1   C2    109.15  3.000
 M1C  O8    C1   C2    110.57  3.000
 M1C  C9    C1   C2    112.42  3.000
 M1C  H92   C9   H91   106.90  3.000
 M1C  H92   C9   N10   108.39  3.000
 M1C  H91   C9   N10   113.75  3.000
 M1C  H92   C9   C1    109.15  3.000
 M1C  H91   C9   C1    110.25  3.000
 M1C  N10   C9   C1    108.31  3.000
 M1C  H10   N10  C9    110.46  3.000
 M1C  H10   N10  C11   110.18  3.000
 M1C  C9    N10  C11   114.80  3.000
 M1C  HO8   O8   C1    108.81  3.000
 M1C  H14   O14  C1    104.89  3.000
 M1C  H42   C4   H41   106.40  3.000
 M1C  H42   C4   C5    109.54  3.000
 M1C  H41   C4   C5    108.24  3.000
 M1C  H42   C4   C2    109.16  3.000
 M1C  H41   C4   C2    110.24  3.000
 M1C  C5    C4   C2    113.03  3.000
 M1C  H52   C5   H51   105.99  3.000
 M1C  H52   C5   C6    109.28  3.000
 M1C  H51   C5   C6    108.80  3.000
 M1C  H52   C5   C4    109.15  3.000
 M1C  H51   C5   C4    110.57  3.000
 M1C  C6    C5   C4    112.82  3.000
 M1C  H62   C6   H61   105.95  3.000
 M1C  H62   C6   C7    109.62  3.000
 M1C  H61   C6   C7    109.54  3.000
 M1C  H62   C6   C5    109.23  3.000
 M1C  H61   C6   C5    109.27  3.000
 M1C  C7    C6   C5    112.97  3.000
 M1C  H73   C7   H72   107.42  3.000
 M1C  H73   C7   H71   107.61  3.000
 M1C  H72   C7   H71   107.62  3.000
 M1C  H73   C7   C6    111.29  3.000
 M1C  H72   C7   C6    111.14  3.000
 M1C  H71   C7   C6    111.57  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
 M1C  Var_01  N10  C11  C12  C13  -107.60  30.0  1
 M1C  Var_02  C9   N10  C11  C13  -154.21  30.0  3
 M1C  Var_03  C1   C9   N10  C11   158.69  30.0  1
 M1C  Var_04  N10  C9   C1   C2   -168.75  30.0  3
 M1C  Var_05  C6   C5   C4   C2    178.83  30.0  3
 M1C  Var_06  C7   C6   C5   C4    177.62  30.0  3
 M1C  Var_07  H71  C7   C6   C5    179.77  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
 M1C  chir_02  C2   N3   C1   C4   positiv
 M1C  chir_03  C11  C13  C12  N10  both

