# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:11:50 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]naphthalene-2-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@H](O)CN[S](=O)(=O)c2ccc3ccccc3c2
#
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
 C3M  C3M  N-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]naphthalene-2-sulfonamide  ligand  48  26  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C3M
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
 C3M  N1    N  NH2   0  -0.788  -2.8506   0.4987   1.4419
 C3M  C2    C  CH1   0  -0.134  -2.6999   0.5234  -0.0023
 C3M  C3    C  CH2   0  -0.513  -4.0126   0.7796  -0.7684
 C3M  C4    C  CR6   0   0.128  -5.0484  -0.2618  -0.4565
 C3M  C5    C  CR16  0  -0.321  -6.0236  -0.0461   0.5151
 C3M  C6    C  CR16  0  -0.241  -6.9531  -1.0316   0.8248
 C3M  C7    C  CR16  0  -0.273  -6.9171  -2.2545   0.1690
 C3M  C8    C  CR16  0  -0.240  -5.9478  -2.4836  -0.8001
 C3M  C9    C  CR16  0  -0.302  -5.0236  -1.4951  -1.1073
 C3M  C10   C  CH1   0   0.027  -1.6396   1.5692  -0.3700
 C3M  O11   O  OH1   0  -0.661  -1.4511   1.6737  -1.7649
 C3M  C12   C  CH2   0  -0.285  -0.3134   1.2871   0.3296
 C3M  N13   N  NC1   0  -0.738   0.6366   2.3313  -0.0349
 C3M  S14   S  S     0   1.382   2.1268   2.3362   0.6520
 C3M  O15   O  OS    0  -0.655   1.9380   2.2563   2.0910
 C3M  O16   O  OS    0  -0.657   2.8368   3.4633   0.0700
 C3M  C17   C  CR6   0  -0.209   2.9314   0.8487   0.1225
 C3M  C18   C  CR16  0  -0.244   3.5034   0.8143  -1.1688
 C3M  C19   C  CR16  0  -0.300   4.0935  -0.3360  -1.6056
 C3M  C20   C  CR66  0   0.126   4.1373  -1.4905  -0.7872
 C3M  C21   C  CR16  0  -0.306   4.7479  -2.6894  -1.2193
 C3M  C22   C  CR16  0  -0.247   4.7731  -3.7884  -0.4038
 C3M  C23   C  CR16  0  -0.254   4.1896  -3.7416   0.8797
 C3M  C24   C  CR16  0  -0.303   3.5943  -2.5936   1.3260
 C3M  C25   C  CR66  0   0.128   3.5545  -1.4431   0.5053
 C3M  C26   C  CR16  0  -0.293   2.9498  -0.2436   0.9449
 C3M  H1N1  H  HNH2  0   0.341  -3.2828   1.3614   1.7548
 C3M  H1N2  H  HNH2  0   0.357  -3.4896  -0.2411   1.7060
 C3M  H2    H  HCH1  0   0.237  -2.3199  -0.4625  -0.3019
 C3M  H3C1  H  HCH2  0   0.241  -4.3874   1.7734  -0.5018
 C3M  H3C2  H  HCH2  0   0.247  -3.8185   0.7912  -1.8423
 C3M  H5    H  HCR6  0   0.248  -6.0614   0.9074   1.0297
 C3M  H6    H  HCR6  0   0.253  -7.7063  -0.8438   1.5795
 C3M  H7    H  HCR6  0   0.253  -7.6404  -3.0233   0.4087
 C3M  H8    H  HCR6  0   0.253  -5.9142  -3.4326  -1.3201
 C3M  H9    H  HCR6  0   0.245  -4.2724  -1.6809  -1.8669
 C3M  H10   H  HCH1  0   0.240  -1.9957   2.5553  -0.0497
 C3M  H11   H  HOH1  0   0.449  -1.2025   0.8071  -2.1078
 C3M  H121  H  HCH2  0   0.271  -0.4624   1.2945   1.4060
 C3M  H122  H  HCH2  0   0.234   0.0437   0.2867   0.0463
 C3M  H13   H  HNC1  0   0.407   0.6740   2.5194  -1.0323
 C3M  H18   H  HCR6  0   0.283   3.4855   1.6891  -1.8045
 C3M  H19   H  HCR6  0   0.269   4.5425  -0.3709  -2.5902
 C3M  H21   H  HCR6  0   0.263   5.1971  -2.7267  -2.2042
 C3M  H22   H  HCR6  0   0.267   5.2435  -4.7022  -0.7421
 C3M  H23   H  HCR6  0   0.267   4.2145  -4.6196   1.5113
 C3M  H24   H  HCR6  0   0.264   3.1446  -2.5544   2.3105
 C3M  H26   H  HCR6  0   0.284   2.5143  -0.2068   1.9353

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
 C3M  N1   C2    single    1.452  0.020  1.452
 C3M  N1   H1N1  single    0.890  0.020  1.040
 C3M  N1   H1N2  single    0.890  0.020  1.040
 C3M  C2   C3    single    1.541  0.020  1.541
 C3M  C2   C10   single    1.534  0.020  1.534
 C3M  C2   H2    single    0.970  0.020  1.090
 C3M  C3   C4    single    1.502  0.020  1.502
 C3M  C3   H3C1  single    0.970  0.020  1.090
 C3M  C3   H3C2  single    0.970  0.020  1.090
 C3M  C4   C5    aromatic  1.393  0.020  1.393
 C3M  C4   C9    aromatic  1.395  0.020  1.395
 C3M  C5   C6    aromatic  1.390  0.020  1.390
 C3M  C5   H5    single    0.930  0.020  1.080
 C3M  C6   C7    aromatic  1.388  0.020  1.388
 C3M  C6   H6    single    0.930  0.020  1.080
 C3M  C7   C8    aromatic  1.390  0.020  1.390
 C3M  C7   H7    single    0.930  0.020  1.080
 C3M  C8   C9    aromatic  1.388  0.020  1.388
 C3M  C8   H8    single    0.930  0.020  1.080
 C3M  C9   H9    single    0.930  0.020  1.080
 C3M  C10  O11   single    1.412  0.020  1.412
 C3M  C10  C12   single    1.526  0.020  1.526
 C3M  C10  H10   single    0.970  0.020  1.090
 C3M  O11  H11   single    0.850  0.020  0.980
 C3M  C12  N13   single    1.458  0.020  1.458
 C3M  C12  H121  single    0.970  0.020  1.090
 C3M  C12  H122  single    0.970  0.020  1.090
 C3M  N13  S14   single    1.641  0.020  1.641
 C3M  N13  H13   single    0.890  0.020  1.040
 C3M  S14  O15   double    1.454  0.020  1.454
 C3M  S14  O16   double    1.454  0.020  1.454
 C3M  S14  C17   single    1.772  0.020  1.772
 C3M  C17  C18   aromatic  1.413  0.020  1.413
 C3M  C17  C26   aromatic  1.367  0.020  1.367
 C3M  C18  C19   aromatic  1.365  0.020  1.365
 C3M  C18  H18   single    0.930  0.020  1.080
 C3M  C19  C20   aromatic  1.416  0.020  1.416
 C3M  C19  H19   single    0.930  0.020  1.080
 C3M  C20  C21   aromatic  1.413  0.020  1.413
 C3M  C20  C25   aromatic  1.419  0.020  1.419
 C3M  C21  C22   aromatic  1.369  0.020  1.369
 C3M  C21  H21   single    0.930  0.020  1.080
 C3M  C22  C23   aromatic  1.411  0.020  1.411
 C3M  C22  H22   single    0.930  0.020  1.080
 C3M  C23  C24   aromatic  1.368  0.020  1.368
 C3M  C23  H23   single    0.930  0.020  1.080
 C3M  C24  C25   aromatic  1.414  0.020  1.414
 C3M  C24  H24   single    0.930  0.020  1.080
 C3M  C25  C26   aromatic  1.413  0.020  1.413
 C3M  C26  H26   single    0.930  0.020  1.080

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
 C3M  H1N2  N1   H1N1  105.79  3.000
 C3M  H1N2  N1   C2    109.71  3.000
 C3M  H1N1  N1   C2    109.66  3.000
 C3M  H2    C2   C10   107.91  3.000
 C3M  H2    C2   C3    107.96  3.000
 C3M  C10   C2   C3    110.87  3.000
 C3M  H2    C2   N1    106.97  3.000
 C3M  C10   C2   N1    108.76  3.000
 C3M  C3    C2   N1    114.12  3.000
 C3M  H3C2  C3   H3C1  106.91  3.000
 C3M  H3C2  C3   C4    109.54  3.000
 C3M  H3C1  C3   C4    110.04  3.000
 C3M  H3C2  C3   C2    109.84  3.000
 C3M  H3C1  C3   C2    108.75  3.000
 C3M  C4    C3   C2    111.65  3.000
 C3M  C9    C4   C5    118.34  3.000
 C3M  C9    C4   C3    120.27  3.000
 C3M  C5    C4   C3    121.35  3.000
 C3M  H5    C5   C6    119.64  3.000
 C3M  H5    C5   C4    119.44  3.000
 C3M  C6    C5   C4    120.91  3.000
 C3M  H6    C6   C7    120.02  3.000
 C3M  H6    C6   C5    119.84  3.000
 C3M  C7    C6   C5    120.14  3.000
 C3M  H7    C7   C8    120.23  3.000
 C3M  H7    C7   C6    120.25  3.000
 C3M  C8    C7   C6    119.52  3.000
 C3M  H8    C8   C9    119.83  3.000
 C3M  H8    C8   C7    120.07  3.000
 C3M  C9    C8   C7    120.10  3.000
 C3M  H9    C9   C8    119.63  3.000
 C3M  H9    C9   C4    119.39  3.000
 C3M  C8    C9   C4    120.98  3.000
 C3M  H10   C10  C12   108.34  3.000
 C3M  H10   C10  O11   105.40  3.000
 C3M  C12   C10  O11   110.53  3.000
 C3M  H10   C10  C2    108.59  3.000
 C3M  C12   C10  C2    111.40  3.000
 C3M  O11   C10  C2    112.31  3.000
 C3M  H11   O11  C10   108.62  3.000
 C3M  H122  C12  H121  107.82  3.000
 C3M  H122  C12  N13   112.07  3.000
 C3M  H121  C12  N13   109.39  3.000
 C3M  H122  C12  C10   109.42  3.000
 C3M  H121  C12  C10   109.50  3.000
 C3M  N13   C12  C10   108.62  3.000
 C3M  H13   N13  S14   112.15  3.000
 C3M  H13   N13  C12   113.71  3.000
 C3M  S14   N13  C12   119.29  3.000
 C3M  C17   S14  O16   108.03  3.000
 C3M  C17   S14  O15   107.98  3.000
 C3M  O16   S14  O15   120.16  3.000
 C3M  C17   S14  N13   106.54  3.000
 C3M  O16   S14  N13   106.15  3.000
 C3M  O15   S14  N13   107.23  3.000
 C3M  C26   C17  C18   121.66  3.000
 C3M  C26   C17  S14   119.79  3.000
 C3M  C18   C17  S14   118.52  3.000
 C3M  H18   C18  C19   120.05  3.000
 C3M  H18   C18  C17   120.72  3.000
 C3M  C19   C18  C17   119.23  3.000
 C3M  H19   C19  C20   119.11  3.000
 C3M  H19   C19  C18   119.85  3.000
 C3M  C20   C19  C18   121.04  3.000
 C3M  C25   C20  C21   118.98  3.000
 C3M  C25   C20  C19   119.12  3.000
 C3M  C21   C20  C19   121.90  3.000
 C3M  H21   C21  C22   120.43  3.000
 C3M  H21   C21  C20   119.11  3.000
 C3M  C22   C21  C20   120.46  3.000
 C3M  H22   C22  C23   119.49  3.000
 C3M  H22   C22  C21   119.99  3.000
 C3M  C23   C22  C21   120.52  3.000
 C3M  H23   C23  C24   120.03  3.000
 C3M  H23   C23  C22   119.65  3.000
 C3M  C24   C23  C22   120.31  3.000
 C3M  H24   C24  C25   119.11  3.000
 C3M  H24   C24  C23   120.51  3.000
 C3M  C25   C24  C23   120.38  3.000
 C3M  C26   C25  C24   121.47  3.000
 C3M  C26   C25  C20   119.18  3.000
 C3M  C24   C25  C20   119.35  3.000
 C3M  H26   C26  C25   119.05  3.000
 C3M  H26   C26  C17   121.17  3.000
 C3M  C25   C26  C17   119.77  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
 C3M  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 C3M  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 C3M  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 C3M  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 C3M  CONST_05  C9   C4   C5   C6     0.00   0.0  0
 C3M  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 C3M  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 C3M  CONST_08  C20  C25  C26  C17    0.00   0.0  0
 C3M  CONST_09  C24  C25  C26  C17  180.00   0.0  0
 C3M  CONST_10  C25  C26  C17  C18    0.00   0.0  0
 C3M  CONST_11  C21  C20  C19  C18  180.00   0.0  0
 C3M  CONST_12  C25  C20  C19  C18    0.00   0.0  0
 C3M  CONST_13  C26  C17  C18  C19    0.00   0.0  0
 C3M  CONST_14  C22  C21  C20  C19  180.00   0.0  0
 C3M  CONST_15  C24  C25  C20  C19  180.00   0.0  0
 C3M  CONST_16  C26  C25  C20  C19    0.00   0.0  0
 C3M  CONST_17  C23  C22  C21  C20    0.00   0.0  0
 C3M  CONST_18  C23  C24  C25  C20    0.00   0.0  0
 C3M  CONST_19  C24  C25  C20  C21    0.00   0.0  0
 C3M  CONST_20  C26  C25  C20  C21  180.00   0.0  0
 C3M  CONST_21  C24  C23  C22  C21    0.00   0.0  0
 C3M  CONST_22  C25  C20  C21  C22    0.00   0.0  0
 C3M  CONST_23  C25  C24  C23  C22    0.00   0.0  0
 C3M  CONST_24  C26  C25  C24  C23  180.00   0.0  0
 C3M  CONST_25  C6   C5   C4   C3   180.00   0.0  0
 C3M  CONST_26  C8   C9   C4   C3   180.00   0.0  0
 C3M  CONST_27  C19  C18  C17  S14  180.00   0.0  0
 C3M  CONST_28  C25  C26  C17  S14  180.00   0.0  0
 C3M  CONST_29  H6   C6   C5   C4   180.00   0.0  0
 C3M  CONST_30  H8   C8   C9   C4   180.00   0.0  0
 C3M  CONST_31  H9   C9   C4   C5   180.00   0.0  0
 C3M  CONST_32  H7   C7   C6   C5   180.00   0.0  0
 C3M  CONST_33  H5   C5   C6   C7   180.00   0.0  0
 C3M  CONST_34  H19  C19  C18  C17  180.00   0.0  0
 C3M  CONST_35  H26  C26  C17  C18  180.00   0.0  0
 C3M  CONST_36  H21  C21  C20  C19    0.00   0.0  0
 C3M  CONST_37  H18  C18  C19  C20  180.00   0.0  0
 C3M  CONST_38  H22  C22  C21  C20  180.00   0.0  0
 C3M  CONST_39  H24  C24  C25  C20  180.00   0.0  0
 C3M  CONST_40  H23  C23  C22  C21  180.00   0.0  0
 C3M  Var_01    C5   C4   C3   C2    96.02  30.0  2
 C3M  Var_02    C18  C17  S14  N13   79.68  30.0  2
 C3M  Var_03    C17  S14  N13  C12   63.74  30.0  3
 C3M  Var_04    S14  N13  C12  C10  176.09  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
 C3M  chir_01  C2   N1   C3  C10  negativ
 C3M  chir_02  C10  O11  C2  C12  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
 C3M  plan-1  C3   0.020
 C3M  plan-1  C4   0.020
 C3M  plan-1  C5   0.020
 C3M  plan-1  C6   0.020
 C3M  plan-1  C7   0.020
 C3M  plan-1  C8   0.020
 C3M  plan-1  C9   0.020
 C3M  plan-1  H5   0.020
 C3M  plan-1  H6   0.020
 C3M  plan-1  H7   0.020
 C3M  plan-1  H8   0.020
 C3M  plan-1  H9   0.020
 C3M  plan-2  S14  0.020
 C3M  plan-2  C17  0.020
 C3M  plan-2  C18  0.020
 C3M  plan-2  C19  0.020
 C3M  plan-2  C20  0.020
 C3M  plan-2  C21  0.020
 C3M  plan-2  C22  0.020
 C3M  plan-2  C23  0.020
 C3M  plan-2  C24  0.020
 C3M  plan-2  C25  0.020
 C3M  plan-2  C26  0.020
 C3M  plan-2  H18  0.020
 C3M  plan-2  H19  0.020
 C3M  plan-2  H21  0.020
 C3M  plan-2  H22  0.020
 C3M  plan-2  H23  0.020
 C3M  plan-2  H24  0.020
 C3M  plan-2  H26  0.020

