# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 12:53:26 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2S,3S,5S)-2,5-diamino-6-phenyl-1-[4-(pyridin-3-yl)phenyl]hexan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C[C@H](O)[C@@H](N)Cc1ccc(cc1)c2cccnc2)Cc3ccccc3
#
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
 02H  02H  (2S,3S,5S)-2,5-diamino-6-phenyl-1-[4-(pyridin-3-yl)phenyl]hexan-3-ol  ligand  54  27  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_02H
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
 02H  N1    N  NH2   0  -0.793  -0.1141   1.3605   0.9587
 02H  C4    C  CH2   0  -0.450   2.5615   0.1505   0.5473
 02H  C5    C  CH2   0  -0.519  -0.7993   0.6361  -1.3541
 02H  C7    C  CH1   0  -0.087   4.0197   0.1190   0.0897
 02H  C8    C  CH2   0  -0.517   4.9297  -0.4915   1.1676
 02H  C10   C  CR16  0  -0.321   7.3014   0.3563   1.0426
 02H  C13   C  CR16  0  -0.239   8.0548  -1.7656  -0.5704
 02H  C15   C  CR6   0   0.126  -2.2386   0.4089  -1.0018
 02H  C17   C  CR16  0  -0.292  -4.0967  -1.1026  -0.6452
 02H  C20   C  CR16  0  -0.308  -3.0649   1.4600  -0.6089
 02H  C2    C  CH1   0  -0.098   0.1345   0.4441  -0.1391
 02H  C3    C  CH1   0   0.077   1.5970   0.5228  -0.5782
 02H  N6    N  NH2   0  -0.813   4.4214   1.4621  -0.3311
 02H  C9    C  CR6   0   0.134   6.3552  -0.6105   0.7101
 02H  C11   C  CR16  0  -0.240   8.6086   0.2663   0.5799
 02H  C12   C  CR16  0  -0.273   8.9893  -0.7949  -0.2297
 02H  C14   C  CR16  0  -0.305   6.7510  -1.6713  -0.1044
 02H  C16   C  CR16  0  -0.292  -2.7797  -0.8757  -1.0083
 02H  C18   C  CR6   0   0.068  -4.9239  -0.0468  -0.2581
 02H  C19   C  CR16  0  -0.295  -4.3844   1.2390  -0.2440
 02H  C44   C  CR6   0  -0.004  -6.3294  -0.2853   0.1135
 02H  C45   C  CR16  0  -0.104  -7.1016  -1.2291  -0.5665
 02H  N46   N  N     0  -0.398  -8.3677  -1.4988  -0.2828
 02H  C47   C  CR16  0  -0.074  -8.9425  -0.8261   0.7076
 02H  C48   C  CR16  0  -0.315  -8.2776   0.1406   1.4469
 02H  C49   C  CR16  0  -0.198  -6.9535   0.4119   1.1461
 02H  O51   O  OH1   0  -0.717   1.8479   1.8142  -1.0861
 02H  HN1   H  HNH2  0   0.335  -0.0345   2.3147   0.6279
 02H  H4    H  HCH2  0   0.227   2.2883  -0.8393   0.9238
 02H  H4A   H  HCH2  0   0.226   2.4493   0.8476   1.3836
 02H  H5    H  HCH2  0   0.237  -0.5012  -0.0600  -2.1438
 02H  H5A   H  HCH2  0   0.244  -0.6663   1.6455  -1.7508
 02H  H7    H  HCH1  0   0.238   4.0820  -0.5194  -0.7988
 02H  H8    H  HCH2  0   0.241   4.8772   0.1255   2.0704
 02H  H8A   H  HCH2  0   0.246   4.5407  -1.4781   1.4332
 02H  H13   H  HCR6  0   0.253   8.3431  -2.5999  -1.1975
 02H  H17   H  HCR6  0   0.252  -4.4783  -2.1164  -0.6475
 02H  H20   H  HCR6  0   0.251  -2.6767   2.4720  -0.6050
 02H  H2    H  HCH1  0   0.231  -0.0254  -0.5729   0.2372
 02H  H3    H  HCH1  0   0.178   1.7257  -0.2336  -1.3725
 02H  HN6   H  HNH2  0   0.356   4.5423   2.0586   0.4809
 02H  H11   H  HCR6  0   0.253   9.3301   1.0254   0.8544
 02H  H12   H  HCR6  0   0.253  10.0073  -0.8676  -0.5905
 02H  H14   H  HCR6  0   0.246   6.0300  -2.4352  -0.3736
 02H  H16   H  HCR6  0   0.247  -2.1600  -1.7155  -1.3012
 02H  H19   H  HCR6  0   0.253  -5.0039   2.0838   0.0320
 02H  H45   H  HCR6  0   0.260  -6.6696  -1.7821  -1.3948
 02H  H47   H  HCR6  0   0.266  -9.9778  -1.0654   0.9225
 02H  H48   H  HCR6  0   0.273  -8.7862   0.6610   2.2467
 02H  H49   H  HCR6  0   0.270  -6.4052   1.1468   1.7224
 02H  HO51  H  HOH1  0   0.451   2.8216   1.9378  -1.0208
 02H  H1    H  HNH2  0   0.348  -1.0625   1.2546   1.2961
 02H  H6    H  HNH2  0   0.369   5.3146   1.4409  -0.8080
 02H  H10   H  HCR6  0   0.246   7.0148   1.1862   1.6783

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
 02H  N1   C2    single    1.451  0.020  1.451
 02H  N1   HN1   single    0.890  0.020  1.040
 02H  C3   C4    single    1.528  0.020  1.528
 02H  C4   C7    single    1.529  0.020  1.529
 02H  C4   H4    single    0.970  0.020  1.090
 02H  C4   H4A   single    0.970  0.020  1.090
 02H  C5   C15   single    1.499  0.020  1.499
 02H  C5   C2    single    1.544  0.020  1.544
 02H  C5   H5    single    0.970  0.020  1.090
 02H  C5   H5A   single    0.970  0.020  1.090
 02H  C7   C8    single    1.537  0.020  1.537
 02H  C7   N6    single    1.464  0.020  1.464
 02H  C7   H7    single    0.970  0.020  1.090
 02H  C8   C9    single    1.502  0.020  1.502
 02H  C8   H8    single    0.970  0.020  1.090
 02H  C8   H8A   single    0.970  0.020  1.090
 02H  C9   C10   aromatic  1.393  0.020  1.393
 02H  C10  C11   aromatic  1.390  0.020  1.390
 02H  C10  H10   single    0.930  0.020  1.080
 02H  C14  C13   aromatic  1.388  0.020  1.388
 02H  C13  C12   aromatic  1.390  0.020  1.390
 02H  C13  H13   single    0.930  0.020  1.080
 02H  C16  C15   aromatic  1.394  0.020  1.394
 02H  C15  C20   aromatic  1.393  0.020  1.393
 02H  C17  C16   aromatic  1.385  0.020  1.385
 02H  C17  C18   aromatic  1.396  0.020  1.396
 02H  C17  H17   single    0.930  0.020  1.080
 02H  C19  C20   aromatic  1.387  0.020  1.387
 02H  C20  H20   single    0.930  0.020  1.080
 02H  C2   C3    single    1.529  0.020  1.529
 02H  C2   H2    single    0.970  0.020  1.090
 02H  O51  C3    single    1.410  0.020  1.410
 02H  C3   H3    single    0.970  0.020  1.090
 02H  N6   HN6   single    0.890  0.020  1.040
 02H  C9   C14   aromatic  1.395  0.020  1.395
 02H  C11  C12   aromatic  1.388  0.020  1.388
 02H  C11  H11   single    0.930  0.020  1.080
 02H  C12  H12   single    0.930  0.020  1.080
 02H  C14  H14   single    0.930  0.020  1.080
 02H  C16  H16   single    0.930  0.020  1.080
 02H  C44  C18   single    1.473  0.020  1.473
 02H  C18  C19   aromatic  1.394  0.020  1.394
 02H  C19  H19   single    0.930  0.020  1.080
 02H  C45  C44   aromatic  1.396  0.020  1.396
 02H  C44  C49   aromatic  1.394  0.020  1.394
 02H  N46  C45   aromatic  1.325  0.020  1.325
 02H  C45  H45   single    0.930  0.020  1.080
 02H  N46  C47   aromatic  1.328  0.020  1.328
 02H  C47  C48   aromatic  1.387  0.020  1.387
 02H  C47  H47   single    0.930  0.020  1.080
 02H  C48  C49   aromatic  1.385  0.020  1.385
 02H  C48  H48   single    0.930  0.020  1.080
 02H  C49  H49   single    0.930  0.020  1.080
 02H  O51  HO51  single    0.850  0.020  0.980
 02H  N1   H1    single    0.890  0.020  1.040
 02H  N6   H6    single    0.890  0.020  1.040

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
 02H  H1    N1   HN1  106.32  3.000
 02H  H1    N1   C2   110.27  3.000
 02H  HN1   N1   C2   109.52  3.000
 02H  H4A   C4   H4   106.72  3.000
 02H  H4A   C4   C3   110.05  3.000
 02H  H4    C4   C3   108.44  3.000
 02H  H4A   C4   C7   109.86  3.000
 02H  H4    C4   C7   108.83  3.000
 02H  C3    C4   C7   112.74  3.000
 02H  H5A   C5   H5   107.01  3.000
 02H  H5A   C5   C2   109.08  3.000
 02H  H5    C5   C2   108.91  3.000
 02H  H5A   C5   C15  110.00  3.000
 02H  H5    C5   C15  109.56  3.000
 02H  C2    C5   C15  112.14  3.000
 02H  H7    C7   N6   106.61  3.000
 02H  H7    C7   C8   107.66  3.000
 02H  N6    C7   C8   113.80  3.000
 02H  H7    C7   C4   108.00  3.000
 02H  N6    C7   C4   109.21  3.000
 02H  C8    C7   C4   111.29  3.000
 02H  H8A   C8   H8   106.93  3.000
 02H  H8A   C8   C9   109.89  3.000
 02H  H8    C8   C9   109.96  3.000
 02H  H8A   C8   C7   108.55  3.000
 02H  H8    C8   C7   109.03  3.000
 02H  C9    C8   C7   112.32  3.000
 02H  H10   C10  C11  119.58  3.000
 02H  H10   C10  C9   119.45  3.000
 02H  C11   C10  C9   120.97  3.000
 02H  H13   C13  C14  119.80  3.000
 02H  H13   C13  C12  120.07  3.000
 02H  C14   C13  C12  120.13  3.000
 02H  C16   C15  C20  117.79  3.000
 02H  C20   C15  C5   121.42  3.000
 02H  C16   C15  C5   120.74  3.000
 02H  H17   C17  C18  119.98  3.000
 02H  H17   C17  C16  119.19  3.000
 02H  C18   C17  C16  120.82  3.000
 02H  H20   C20  C19  119.25  3.000
 02H  H20   C20  C15  119.53  3.000
 02H  C19   C20  C15  121.21  3.000
 02H  H2    C2   C3   106.61  3.000
 02H  H2    C2   C5   107.29  3.000
 02H  C3    C2   C5   110.24  3.000
 02H  H2    C2   N1   107.53  3.000
 02H  C3    C2   N1   110.40  3.000
 02H  C5    C2   N1   114.40  3.000
 02H  H3    C3   O51  110.34  3.000
 02H  H3    C3   C2   106.43  3.000
 02H  O51   C3   C2   108.70  3.000
 02H  H3    C3   C4   106.81  3.000
 02H  O51   C3   C4   112.09  3.000
 02H  C2    C3   C4   112.31  3.000
 02H  H6    N6   HN6  106.50  3.000
 02H  H6    N6   C7   110.99  3.000
 02H  HN6   N6   C7   110.00  3.000
 02H  C14   C9   C10  118.32  3.000
 02H  C14   C9   C8   120.50  3.000
 02H  C10   C9   C8   121.13  3.000
 02H  H11   C11  C12  120.08  3.000
 02H  H11   C11  C10  119.80  3.000
 02H  C12   C11  C10  120.12  3.000
 02H  H12   C12  C11  120.24  3.000
 02H  H12   C12  C13  120.25  3.000
 02H  C11   C12  C13  119.51  3.000
 02H  H14   C14  C9   119.47  3.000
 02H  H14   C14  C13  119.57  3.000
 02H  C9    C14  C13  120.96  3.000
 02H  H16   C16  C17  119.18  3.000
 02H  H16   C16  C15  119.56  3.000
 02H  C17   C16  C15  121.26  3.000
 02H  C44   C18  C19  121.05  3.000
 02H  C19   C18  C17  118.09  3.000
 02H  C44   C18  C17  120.85  3.000
 02H  H19   C19  C18  120.03  3.000
 02H  H19   C19  C20  119.13  3.000
 02H  C18   C19  C20  120.82  3.000
 02H  C49   C44  C45  116.83  3.000
 02H  C49   C44  C18  122.22  3.000
 02H  C45   C44  C18  120.95  3.000
 02H  H45   C45  N46  116.10  3.000
 02H  H45   C45  C44  119.72  3.000
 02H  N46   C45  C44  124.17  3.000
 02H  C47   N46  C45  118.04  3.000
 02H  H47   C47  C48  120.40  3.000
 02H  H47   C47  N46  116.70  3.000
 02H  C48   C47  N46  122.90  3.000
 02H  H48   C48  C49  121.08  3.000
 02H  H48   C48  C47  120.29  3.000
 02H  C49   C48  C47  118.63  3.000
 02H  H49   C49  C48  120.10  3.000
 02H  H49   C49  C44  120.47  3.000
 02H  C48   C49  C44  119.42  3.000
 02H  HO51  O51  C3   105.50  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
 02H  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 02H  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 02H  CONST_03  C18  C17  C16  C15    0.00   0.0  0
 02H  CONST_04  C18  C19  C20  C15    0.00   0.0  0
 02H  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 02H  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 02H  CONST_09  C44  C18  C19  C20  180.00   0.0  0
 02H  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 02H  CONST_11  C12  C13  C14  C9     0.00   0.0  0
 02H  CONST_12  C14  C9   C10  C11    0.00   0.0  0
 02H  CONST_13  C14  C13  C12  C11    0.00   0.0  0
 02H  CONST_14  C19  C20  C15  C16    0.00   0.0  0
 02H  CONST_15  C44  C18  C17  C16  180.00   0.0  0
 02H  CONST_16  C19  C18  C17  C16    0.00   0.0  0
 02H  CONST_17  N46  C45  C44  C18  180.00   0.0  0
 02H  CONST_18  C48  C49  C44  C18  180.00   0.0  0
 02H  CONST_21  C47  N46  C45  C44    0.00   0.0  0
 02H  CONST_22  C47  C48  C49  C44    0.00   0.0  0
 02H  CONST_23  C48  C49  C44  C45    0.00   0.0  0
 02H  CONST_24  C48  C47  N46  C45    0.00   0.0  0
 02H  CONST_25  C49  C44  C45  N46    0.00   0.0  0
 02H  CONST_26  C49  C48  C47  N46    0.00   0.0  0
 02H  CONST_27  C17  C16  C15  C5   180.00   0.0  0
 02H  CONST_28  C19  C20  C15  C5   180.00   0.0  0
 02H  CONST_29  C11  C10  C9   C8   180.00   0.0  0
 02H  CONST_30  C13  C14  C9   C8   180.00   0.0  0
 02H  CONST_31  H14  C14  C9   C10  180.00   0.0  0
 02H  CONST_32  H12  C12  C11  C10  180.00   0.0  0
 02H  CONST_33  H11  C11  C12  C13  180.00   0.0  0
 02H  CONST_34  H17  C17  C16  C15  180.00   0.0  0
 02H  CONST_35  H19  C19  C20  C15  180.00   0.0  0
 02H  CONST_36  H16  C16  C15  C20  180.00   0.0  0
 02H  CONST_37  H13  C13  C14  C9   180.00   0.0  0
 02H  CONST_38  H10  C10  C11  C12  180.00   0.0  0
 02H  CONST_39  H20  C20  C15  C16  180.00   0.0  0
 02H  CONST_40  H45  C45  C44  C18    0.00   0.0  0
 02H  CONST_41  H49  C49  C44  C18    0.00   0.0  0
 02H  CONST_42  H48  C48  C49  C44  180.00   0.0  0
 02H  CONST_43  H47  C47  N46  C45  180.00   0.0  0
 02H  Var_01    C10  C9   C8   C7    97.07  30.0  2
 02H  Var_02    C2   C5   C15  C20   92.47  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
 02H  chir_01  C7  C4   C8  N6  positiv
 02H  chir_02  C2  N1   C3  C5  positiv
 02H  chir_03  C3  O51  C2  C4  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
 02H  plan-1  C8   0.020
 02H  plan-1  C10  0.020
 02H  plan-1  C13  0.020
 02H  plan-1  C9   0.020
 02H  plan-1  C11  0.020
 02H  plan-1  C12  0.020
 02H  plan-1  C14  0.020
 02H  plan-1  H13  0.020
 02H  plan-1  H11  0.020
 02H  plan-1  H12  0.020
 02H  plan-1  H14  0.020
 02H  plan-1  H10  0.020
 02H  plan-2  C5   0.020
 02H  plan-2  C15  0.020
 02H  plan-2  C17  0.020
 02H  plan-2  C20  0.020
 02H  plan-2  C16  0.020
 02H  plan-2  C18  0.020
 02H  plan-2  C19  0.020
 02H  plan-2  C44  0.020
 02H  plan-2  H17  0.020
 02H  plan-2  H20  0.020
 02H  plan-2  H16  0.020
 02H  plan-2  H19  0.020
 02H  plan-3  C18  0.020
 02H  plan-3  C44  0.020
 02H  plan-3  C45  0.020
 02H  plan-3  N46  0.020
 02H  plan-3  C47  0.020
 02H  plan-3  C48  0.020
 02H  plan-3  C49  0.020
 02H  plan-3  H45  0.020
 02H  plan-3  H47  0.020
 02H  plan-3  H48  0.020
 02H  plan-3  H49  0.020

