# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 02:09:35 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S,3S,5S)-2,5-diamino-1,6-diphenylhexan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C[C@H](O)[C@@H](N)Cc1ccccc1)Cc2ccccc2
#
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
 015  015  (2S,3S,5S)-2,5-diamino-1,6-diphenylhexan-3-ol  peptide  45  21  .  2022-03-07  2022-03-07
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_015
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
 015  N11   N  NH2   0  -0.783  -2.2645  -1.1731  -1.0792
 015  C12   C  CH1   0  -0.096  -1.9624  -0.1142  -0.1328
 015  C13   C  CH1   0   0.071  -0.5538  -0.1803   0.4794
 015  C14   C  CH2   0  -0.471   0.5354  -0.0624  -0.5875
 015  C15   C  CH1   0  -0.084   1.9517  -0.0606  -0.0136
 015  C26   C  CH2   0  -0.515  -3.0249  -0.0897   0.9740
 015  C28   C  CR6   0   0.165  -4.4062   0.1728   0.4485
 015  C31   C  CR16  0  -0.307  -5.2634  -0.8751   0.1206
 015  C32   C  CR16  0  -0.246  -6.5337  -0.6296  -0.3831
 015  C33   C  CR16  0  -0.277  -6.9680   0.6761  -0.5757
 015  C34   C  CR16  0  -0.242  -6.1227   1.7305  -0.2557
 015  C35   C  CR16  0  -0.317  -4.8552   1.4776   0.2532
 015  O41   O  OH1   0  -0.715  -0.4374  -1.3733   1.2218
 015  C44   C  CH2   0  -0.519   2.9827   0.2899  -1.0987
 015  C45   C  CR6   0   0.138   4.3855   0.3288  -0.5645
 015  C48   C  CR16  0  -0.323   5.2444  -0.7584  -0.7091
 015  C49   C  CR16  0  -0.239   6.5267  -0.7314  -0.1744
 015  C50   C  CR16  0  -0.273   6.9687   0.3865   0.5196
 015  C51   C  CR16  0  -0.240   6.1209   1.4770   0.6729
 015  C52   C  CR16  0  -0.305   4.8421   1.4453   0.1354
 015  N58   N  NH2   0  -0.813   2.2031  -1.3437   0.6439
 015  H11   H  HNH2  0   0.346  -1.6530  -1.1083  -1.8836
 015  H12   H  HCH1  0   0.227  -2.0247   0.8377  -0.6743
 015  H13   H  HCH1  0   0.173  -0.4500   0.6964   1.1435
 015  H141  H  HCH2  0   0.217   0.4494  -0.8859  -1.3066
 015  H142  H  HCH2  0   0.234   0.3765   0.8619  -1.1503
 015  H15   H  HCH1  0   0.241   2.0098   0.7078   0.7659
 015  H261  H  HCH2  0   0.240  -3.0078  -1.0404   1.5137
 015  H262  H  HCH2  0   0.237  -2.7572   0.6849   1.6980
 015  H31   H  HCR6  0   0.237  -4.9329  -1.8961   0.2666
 015  H32   H  HCR6  0   0.248  -7.1856  -1.4593  -0.6268
 015  H33   H  HCR6  0   0.250  -7.9584   0.8712  -0.9667
 015  H34   H  HCR6  0   0.249  -6.4521   2.7521  -0.3975
 015  H35   H  HCR6  0   0.240  -4.2056   2.3086   0.5060
 015  HO4   H  HOH1  0   0.452   0.5217  -1.5918   1.2305
 015  H441  H  HCH2  0   0.242   2.9092  -0.4431  -1.9084
 015  H442  H  HCH2  0   0.247   2.7188   1.2609  -1.5257
 015  H48   H  HCR6  0   0.246   4.9096  -1.6355  -1.2516
 015  H49   H  HCR6  0   0.253   7.1814  -1.5842  -0.3010
 015  H50   H  HCR6  0   0.253   7.9672   0.4092   0.9370
 015  H51   H  HCR6  0   0.253   6.4576   2.3542   1.2106
 015  H52   H  HCR6  0   0.246   4.1867   2.3005   0.2586
 015  H58   H  HNH2  0   0.357   2.3696  -2.0659  -0.0493
 015  H2    H  HNH2  0   0.332  -2.0705  -2.0701  -0.6494
 015  H1    H  HNH2  0   0.370   3.0341  -1.2992   1.2204

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
 015  N11  C12   single    1.452  0.020  1.452
 015  N11  H11   single    0.890  0.020  1.040
 015  C12  C13   single    1.537  0.020  1.537
 015  C12  C26   single    1.534  0.020  1.534
 015  C12  H12   single    0.970  0.020  1.090
 015  C13  C14   single    1.529  0.020  1.529
 015  C13  O41   single    1.410  0.020  1.410
 015  C13  H13   single    0.970  0.020  1.090
 015  C14  C15   single    1.528  0.020  1.528
 015  C14  H141  single    0.970  0.020  1.090
 015  C14  H142  single    0.970  0.020  1.090
 015  C15  C44   single    1.537  0.020  1.537
 015  C15  N58   single    1.464  0.020  1.464
 015  C15  H15   single    0.970  0.020  1.090
 015  C26  C28   single    1.501  0.020  1.501
 015  C26  H261  single    0.970  0.020  1.090
 015  C26  H262  single    0.970  0.020  1.090
 015  C28  C31   aromatic  1.393  0.020  1.393
 015  C28  C35   aromatic  1.394  0.020  1.394
 015  C31  C32   aromatic  1.388  0.020  1.388
 015  C31  H31   single    0.930  0.020  1.080
 015  C32  C33   aromatic  1.389  0.020  1.389
 015  C32  H32   single    0.930  0.020  1.080
 015  C33  C34   aromatic  1.389  0.020  1.389
 015  C33  H33   single    0.930  0.020  1.080
 015  C34  C35   aromatic  1.389  0.020  1.389
 015  C34  H34   single    0.930  0.020  1.080
 015  C35  H35   single    0.930  0.020  1.080
 015  O41  HO4   single    0.850  0.020  0.980
 015  C44  C45   single    1.502  0.020  1.502
 015  C44  H441  single    0.970  0.020  1.090
 015  C44  H442  single    0.970  0.020  1.090
 015  C45  C48   aromatic  1.393  0.020  1.393
 015  C45  C52   aromatic  1.395  0.020  1.395
 015  C48  C49   aromatic  1.390  0.020  1.390
 015  C48  H48   single    0.930  0.020  1.080
 015  C49  C50   aromatic  1.388  0.020  1.388
 015  C49  H49   single    0.930  0.020  1.080
 015  C50  C51   aromatic  1.390  0.020  1.390
 015  C50  H50   single    0.930  0.020  1.080
 015  C51  C52   aromatic  1.388  0.020  1.388
 015  C51  H51   single    0.930  0.020  1.080
 015  C52  H52   single    0.930  0.020  1.080
 015  N58  H58   single    0.890  0.020  1.040
 015  N11  H2    single    0.890  0.020  1.040
 015  N58  H1    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
 015  H2    N11  H11   106.14  3.000
 015  H2    N11  C12   109.22  3.000
 015  H11   N11  C12   110.21  3.000
 015  H12   C12  C26   107.63  3.000
 015  H12   C12  C13   106.61  3.000
 015  C26   C12  C13   110.36  3.000
 015  H12   C12  N11   107.41  3.000
 015  C26   C12  N11   109.74  3.000
 015  C13   C12  N11   114.77  3.000
 015  H13   C13  O41   110.31  3.000
 015  H13   C13  C14   106.94  3.000
 015  O41   C13  C14   111.95  3.000
 015  H13   C13  C12   106.94  3.000
 015  O41   C13  C12   108.76  3.000
 015  C14   C13  C12   111.81  3.000
 015  H142  C14  H141  106.61  3.000
 015  H142  C14  C15   109.08  3.000
 015  H141  C14  C15   108.65  3.000
 015  H142  C14  C13   108.70  3.000
 015  H141  C14  C13   110.11  3.000
 015  C15   C14  C13   113.46  3.000
 015  H15   C15  N58   106.62  3.000
 015  H15   C15  C44   107.86  3.000
 015  N58   C15  C44   113.69  3.000
 015  H15   C15  C14   108.49  3.000
 015  N58   C15  C14   109.08  3.000
 015  C44   C15  C14   110.90  3.000
 015  H262  C26  H261  106.58  3.000
 015  H262  C26  C28   109.46  3.000
 015  H261  C26  C28   109.83  3.000
 015  H262  C26  C12   108.62  3.000
 015  H261  C26  C12   109.35  3.000
 015  C28   C26  C12   112.80  3.000
 015  C35   C28  C31   118.24  3.000
 015  C35   C28  C26   120.61  3.000
 015  C31   C28  C26   121.14  3.000
 015  H31   C31  C32   119.66  3.000
 015  H31   C31  C28   119.32  3.000
 015  C32   C31  C28   121.03  3.000
 015  H32   C32  C33   120.05  3.000
 015  H32   C32  C31   119.80  3.000
 015  C33   C32  C31   120.16  3.000
 015  H33   C33  C34   120.21  3.000
 015  H33   C33  C32   120.35  3.000
 015  C34   C33  C32   119.43  3.000
 015  H34   C34  C35   119.83  3.000
 015  H34   C34  C33   120.07  3.000
 015  C35   C34  C33   120.10  3.000
 015  H35   C35  C34   119.49  3.000
 015  H35   C35  C28   119.46  3.000
 015  C34   C35  C28   121.05  3.000
 015  HO4   O41  C13   105.85  3.000
 015  H442  C44  H441  106.84  3.000
 015  H442  C44  C45   109.97  3.000
 015  H441  C44  C45   110.07  3.000
 015  H442  C44  C15   108.44  3.000
 015  H441  C44  C15   108.93  3.000
 015  C45   C44  C15   112.41  3.000
 015  C52   C45  C48   118.36  3.000
 015  C52   C45  C44   120.34  3.000
 015  C48   C45  C44   121.26  3.000
 015  H48   C48  C49   119.55  3.000
 015  H48   C48  C45   119.53  3.000
 015  C49   C48  C45   120.92  3.000
 015  H49   C49  C50   120.02  3.000
 015  H49   C49  C48   119.85  3.000
 015  C50   C49  C48   120.13  3.000
 015  H50   C50  C51   120.24  3.000
 015  H50   C50  C49   120.23  3.000
 015  C51   C50  C49   119.53  3.000
 015  H51   C51  C52   119.84  3.000
 015  H51   C51  C50   120.06  3.000
 015  C52   C51  C50   120.10  3.000
 015  H52   C52  C51   119.67  3.000
 015  H52   C52  C45   119.37  3.000
 015  C51   C52  C45   120.96  3.000
 015  H1    N58  H58   106.59  3.000
 015  H1    N58  C15   110.99  3.000
 015  H58   N58  C15   110.20  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
 015  CONST_01  C33  C32  C31  C28    0.00   0.0  0
 015  CONST_02  C33  C34  C35  C28    0.00   0.0  0
 015  CONST_03  C34  C35  C28  C31    0.00   0.0  0
 015  CONST_04  C34  C33  C32  C31    0.00   0.0  0
 015  CONST_05  C35  C28  C31  C32    0.00   0.0  0
 015  CONST_06  C35  C34  C33  C32    0.00   0.0  0
 015  CONST_07  C50  C49  C48  C45    0.00   0.0  0
 015  CONST_08  C50  C51  C52  C45    0.00   0.0  0
 015  CONST_09  C51  C52  C45  C48    0.00   0.0  0
 015  CONST_10  C51  C50  C49  C48    0.00   0.0  0
 015  CONST_11  C52  C45  C48  C49    0.00   0.0  0
 015  CONST_12  C52  C51  C50  C49    0.00   0.0  0
 015  CONST_13  C32  C31  C28  C26  180.00   0.0  0
 015  CONST_14  C34  C35  C28  C26  180.00   0.0  0
 015  CONST_15  C49  C48  C45  C44  180.00   0.0  0
 015  CONST_16  C51  C52  C45  C44  180.00   0.0  0
 015  CONST_17  H32  C32  C31  C28  180.00   0.0  0
 015  CONST_18  H34  C34  C35  C28  180.00   0.0  0
 015  CONST_19  H35  C35  C28  C31  180.00   0.0  0
 015  CONST_20  H33  C33  C32  C31  180.00   0.0  0
 015  CONST_21  H31  C31  C32  C33  180.00   0.0  0
 015  CONST_22  H49  C49  C48  C45  180.00   0.0  0
 015  CONST_23  H51  C51  C52  C45  180.00   0.0  0
 015  CONST_24  H52  C52  C45  C48  180.00   0.0  0
 015  CONST_25  H50  C50  C49  C48  180.00   0.0  0
 015  CONST_26  H48  C48  C49  C50  180.00   0.0  0
 015  Var_01    C31  C28  C26  C12   93.19  30.0  2
 015  Var_02    C48  C45  C44  C15   98.08  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
 015  chir_01  C12  N11  C13  C26  positiv
 015  chir_02  C13  O41  C12  C14  positiv
 015  chir_03  C15  N58  C44  C14  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
 015  plan-1  C26  0.020
 015  plan-1  C28  0.020
 015  plan-1  C31  0.020
 015  plan-1  C32  0.020
 015  plan-1  C33  0.020
 015  plan-1  C34  0.020
 015  plan-1  C35  0.020
 015  plan-1  H31  0.020
 015  plan-1  H32  0.020
 015  plan-1  H33  0.020
 015  plan-1  H34  0.020
 015  plan-1  H35  0.020
 015  plan-2  C44  0.020
 015  plan-2  C45  0.020
 015  plan-2  C48  0.020
 015  plan-2  C49  0.020
 015  plan-2  C50  0.020
 015  plan-2  C51  0.020
 015  plan-2  C52  0.020
 015  plan-2  H48  0.020
 015  plan-2  H49  0.020
 015  plan-2  H50  0.020
 015  plan-2  H51  0.020
 015  plan-2  H52  0.020

