# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 12:49:10 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N~6~-[(1R)-2-{[(R)-carboxy(cyclopropyl)methyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC(=O)N[C@@H](CS)C(=O)N[C@H](C1CC1)C(O)=O)C(O)=O
#
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
 BCV  BCV  N~6~-[(1R)-2-{[(R)-carboxy(cyclopropyl)methyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine  ligand  47  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BCV
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
 BCV  N14   N  NH2   0  -0.776   6.4522   1.2515   0.2575
 BCV  C2    C  CH1   0  -0.208   6.2535  -0.1439   0.5640
 BCV  C1    C  C     0   0.521   7.4030  -1.0353   0.1118
 BCV  O19   O  O     0  -0.441   8.2554  -0.7076  -0.6757
 BCV  O20   O  OH1   0  -0.594   7.3562  -2.2377   0.6751
 BCV  C3    C  CH2   0  -0.434   4.9467  -0.6577  -0.0563
 BCV  C4    C  CH2   0  -0.408   3.7189   0.0810   0.4588
 BCV  C7    C  CH2   0  -0.590   2.4489  -0.4678  -0.1725
 BCV  C10   C  C     0   0.578   1.1871   0.2147   0.3089
 BCV  O15   O  O     0  -0.493   1.1227   0.8276   1.3630
 BCV  N11   N  NH1   0  -0.633   0.1310   0.0672  -0.5176
 BCV  C12   C  CH1   0  -0.227  -1.1772   0.5937  -0.2501
 BCV  C16   C  CH2   0  -0.534  -1.4962   1.8229  -1.1076
 BCV  S17   S  S2    0  -0.236  -0.2672   3.1260  -0.7748
 BCV  C13   C  C     0   0.573  -2.2279  -0.4778  -0.5473
 BCV  O18   O  O     0  -0.477  -2.0367  -1.3442  -1.3844
 BCV  N29   N  NH1   0  -0.632  -3.3614  -0.3482   0.1546
 BCV  C30   C  CH1   0  -0.191  -4.5321  -1.1610  -0.0865
 BCV  C31   C  C     0   0.529  -5.2853  -1.3086   1.2215
 BCV  O42   O  O     0  -0.427  -5.2623  -0.4885   2.1041
 BCV  O43   O  OH1   0  -0.579  -5.9798  -2.4304   1.2674
 BCV  C32   C  CH1   0  -0.236  -5.3840  -0.5608  -1.1948
 BCV  C37   C  CH2   0  -0.492  -6.8793  -0.6013  -1.2369
 BCV  C33   C  CH2   0  -0.489  -6.1683   0.6958  -0.9885
 BCV  H141  H  HNH2  0   0.354   7.2806   1.6016   0.7210
 BCV  H142  H  HNH2  0   0.343   6.6095   1.3711  -0.7360
 BCV  H2    H  HCH1  0   0.266   6.1724  -0.2483   1.6511
 BCV  H20   H  HOH1  0   0.480   8.0759  -2.7919   0.3383
 BCV  H3C1  H  HCH2  0   0.231   5.0085  -0.5622  -1.1463
 BCV  H3C2  H  HCH2  0   0.242   4.8396  -1.7246   0.1530
 BCV  H4C1  H  HCH2  0   0.226   3.6676  -0.0183   1.5457
 BCV  H4C2  H  HCH2  0   0.235   3.8144   1.1465   0.2459
 BCV  H7C1  H  HCH2  0   0.257   2.5080  -0.3959  -1.2623
 BCV  H7C2  H  HCH2  0   0.274   2.3503  -1.5365   0.0486
 BCV  H11   H  HNH1  0   0.400   0.2531  -0.4451  -1.3781
 BCV  H12   H  HCH1  0   0.296  -1.2255   0.8727   0.8042
 BCV  H161  H  HCH2  0   0.280  -1.4735   1.5579  -2.1654
 BCV  H162  H  HCH2  0   0.280  -2.4922   2.1945  -0.8663
 BCV  H17   H  HSH1  0   0.229  -0.7791   4.0338  -1.6130
 BCV  H29   H  HNH1  0   0.409  -3.4511   0.4161   0.8071
 BCV  H30   H  HCH1  0   0.302  -4.1997  -2.1509  -0.4035
 BCV  H43   H  HOH1  0   0.489  -6.4897  -2.4778   2.0914
 BCV  H32   H  HCH1  0   0.276  -4.8913  -0.6538  -2.1563
 BCV  H371  H  HCH2  0   0.263  -7.3404  -0.7617  -2.2029
 BCV  H372  H  HCH2  0   0.253  -7.4271  -1.0458  -0.4164
 BCV  H331  H  HCH2  0   0.252  -6.2245   1.1155   0.0086
 BCV  H332  H  HCH2  0   0.260  -6.1463   1.4379  -1.7753

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
 BCV  N14  C2    single  1.442  0.020  1.442
 BCV  N14  H141  single  0.890  0.020  1.040
 BCV  N14  H142  single  0.890  0.020  1.040
 BCV  C2   C1    single  1.523  0.020  1.523
 BCV  C2   C3    single  1.535  0.020  1.535
 BCV  C2   H2    single  0.970  0.020  1.090
 BCV  C1   O19   double  1.206  0.020  1.206
 BCV  C1   O20   single  1.329  0.020  1.329
 BCV  O20  H20   single  0.850  0.020  0.980
 BCV  C3   C4    single  1.523  0.020  1.523
 BCV  C3   H3C1  single  0.970  0.020  1.090
 BCV  C3   H3C2  single  0.970  0.020  1.090
 BCV  C4   C7    single  1.521  0.020  1.521
 BCV  C4   H4C1  single  0.970  0.020  1.090
 BCV  C4   H4C2  single  0.970  0.020  1.090
 BCV  C7   C10   single  1.513  0.020  1.513
 BCV  C7   H7C1  single  0.970  0.020  1.090
 BCV  C7   H7C2  single  0.970  0.020  1.090
 BCV  C10  O15   double  1.221  0.020  1.221
 BCV  C10  N11   single  1.349  0.020  1.349
 BCV  N11  C12   single  1.435  0.020  1.435
 BCV  N11  H11   single  0.860  0.020  1.020
 BCV  C12  C16   single  1.532  0.020  1.532
 BCV  C12  C13   single  1.530  0.020  1.530
 BCV  C12  H12   single  0.970  0.020  1.090
 BCV  C16  S17   single  1.822  0.020  1.822
 BCV  C16  H161  single  0.970  0.020  1.090
 BCV  C16  H162  single  0.970  0.020  1.090
 BCV  S17  H17   single  1.200  0.020  1.300
 BCV  C13  O18   double  1.220  0.020  1.220
 BCV  C13  N29   single  1.339  0.020  1.339
 BCV  N29  C30   single  1.445  0.020  1.445
 BCV  N29  H29   single  0.860  0.020  1.020
 BCV  C30  C31   single  1.517  0.020  1.517
 BCV  C30  C32   single  1.521  0.020  1.521
 BCV  C30  H30   single  0.970  0.020  1.090
 BCV  C31  O42   double  1.205  0.020  1.205
 BCV  C31  O43   single  1.320  0.020  1.320
 BCV  O43  H43   single  0.850  0.020  0.980
 BCV  C32  C37   single  1.497  0.020  1.497
 BCV  C32  C33   single  1.496  0.020  1.496
 BCV  C32  H32   single  0.970  0.020  1.090
 BCV  C37  C33   single  1.500  0.020  1.500
 BCV  C37  H371  single  0.970  0.020  1.090
 BCV  C37  H372  single  0.970  0.020  1.090
 BCV  C33  H331  single  0.970  0.020  1.090
 BCV  C33  H332  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
 BCV  H142  N14  H141  106.34  3.000
 BCV  H142  N14  C2    110.12  3.000
 BCV  H141  N14  C2    110.50  3.000
 BCV  H2    C2   C3    107.83  3.000
 BCV  H2    C2   C1    107.15  3.000
 BCV  C3    C2   C1    109.06  3.000
 BCV  H2    C2   N14   108.26  3.000
 BCV  C3    C2   N14   110.80  3.000
 BCV  C1    C2   N14   113.52  3.000
 BCV  O20   C1   O19   123.21  3.000
 BCV  O20   C1   C2    112.16  3.000
 BCV  O19   C1   C2    124.63  3.000
 BCV  H20   O20  C1    110.13  3.000
 BCV  H3C2  C3   H3C1  106.33  3.000
 BCV  H3C2  C3   C4    109.26  3.000
 BCV  H3C1  C3   C4    109.86  3.000
 BCV  H3C2  C3   C2    109.44  3.000
 BCV  H3C1  C3   C2    108.95  3.000
 BCV  C4    C3   C2    112.79  3.000
 BCV  H4C2  C4   H4C1  106.68  3.000
 BCV  H4C2  C4   C7    110.15  3.000
 BCV  H4C1  C4   C7    109.93  3.000
 BCV  H4C2  C4   C3    109.71  3.000
 BCV  H4C1  C4   C3    109.29  3.000
 BCV  C7    C4   C3    110.97  3.000
 BCV  H7C2  C7   H7C1  105.66  3.000
 BCV  H7C2  C7   C10   107.50  3.000
 BCV  H7C1  C7   C10   109.41  3.000
 BCV  H7C2  C7   C4    110.08  3.000
 BCV  H7C1  C7   C4    110.17  3.000
 BCV  C10   C7   C4    113.68  3.000
 BCV  N11   C10  O15   122.85  3.000
 BCV  N11   C10  C7    114.11  3.000
 BCV  O15   C10  C7    123.02  3.000
 BCV  H11   N11  C12   117.10  3.000
 BCV  H11   N11  C10   118.90  3.000
 BCV  C12   N11  C10   124.00  3.000
 BCV  H12   C12  C13   109.64  3.000
 BCV  H12   C12  C16   109.04  3.000
 BCV  C13   C12  C16   108.07  3.000
 BCV  H12   C12  N11   108.31  3.000
 BCV  C13   C12  N11   109.44  3.000
 BCV  C16   C12  N11   112.32  3.000
 BCV  H162  C16  H161  108.45  3.000
 BCV  H162  C16  S17   109.40  3.000
 BCV  H161  C16  S17   109.69  3.000
 BCV  H162  C16  C12   109.86  3.000
 BCV  H161  C16  C12   110.09  3.000
 BCV  S17   C16  C12   109.33  3.000
 BCV  H17   S17  C16    96.47  3.000
 BCV  N29   C13  O18   124.12  3.000
 BCV  N29   C13  C12   114.31  3.000
 BCV  O18   C13  C12   121.54  3.000
 BCV  H29   N29  C30   117.51  3.000
 BCV  H29   N29  C13   119.17  3.000
 BCV  C30   N29  C13   122.93  3.000
 BCV  H30   C30  C32   108.47  3.000
 BCV  H30   C30  C31   108.27  3.000
 BCV  C32   C30  C31   112.87  3.000
 BCV  H30   C30  N29   108.17  3.000
 BCV  C32   C30  N29   110.68  3.000
 BCV  C31   C30  N29   108.25  3.000
 BCV  O43   C31  O42   124.25  3.000
 BCV  O43   C31  C30   111.96  3.000
 BCV  O42   C31  C30   123.78  3.000
 BCV  H43   O43  C31   110.34  3.000
 BCV  H32   C32  C33   115.64  3.000
 BCV  H32   C32  C37   115.26  3.000
 BCV  C33   C32  C37    60.17  3.000
 BCV  H32   C32  C30   110.96  3.000
 BCV  C33   C32  C30   121.64  3.000
 BCV  C37   C32  C30   124.70  3.000
 BCV  H372  C37  H371  113.60  3.000
 BCV  H372  C37  C33   118.01  3.000
 BCV  H371  C37  C33   118.55  3.000
 BCV  H372  C37  C32   119.71  3.000
 BCV  H371  C37  C32   117.05  3.000
 BCV  C33   C37  C32    59.88  3.000
 BCV  H332  C33  H331  113.88  3.000
 BCV  H332  C33  C37   118.84  3.000
 BCV  H331  C33  C37   117.57  3.000
 BCV  H332  C33  C32   117.73  3.000
 BCV  H331  C33  C32   118.66  3.000
 BCV  C37   C33  C32    59.94  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
 BCV  CONST_01  C12   N11  C10  C7    180.00   0.0  0
 BCV  CONST_02  C12   N11  C10  O15     0.00   0.0  0
 BCV  CONST_03  C30   N29  C13  C12   180.00   0.0  0
 BCV  CONST_04  C30   N29  C13  O18     0.00   0.0  0
 BCV  CONST_05  H11   N11  C10  C7      0.00   0.0  0
 BCV  CONST_06  H29   N29  C13  C12     0.00   0.0  0
 BCV  CONST_07  H20   O20  C1   C2    180.00   0.0  0
 BCV  CONST_08  H43   O43  C31  C30   180.00   0.0  0
 BCV  Var_01    C33   C37  C32  C30   109.79  30.0  1
 BCV  Var_02    H331  C33  C37  C32  -108.85  30.0  1
 BCV  Var_03    C7    C4   C3   C2   -179.52  30.0  3
 BCV  Var_04    C10   C7   C4   C3    179.39  30.0  3
 BCV  Var_05    O15   C10  C7   C4    -21.52  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
 BCV  chir_01  C2   N14  C1   C3   positiv
 BCV  chir_02  C12  N11  C16  C13  negativ
 BCV  chir_03  C30  N29  C31  C32  negativ
 BCV  chir_04  C32  C30  C37  C33  both

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
 BCV  plan-1  C7   0.020
 BCV  plan-1  C10  0.020
 BCV  plan-1  O15  0.020
 BCV  plan-1  N11  0.020
 BCV  plan-1  C12  0.020
 BCV  plan-1  H11  0.020
 BCV  plan-2  C12  0.020
 BCV  plan-2  C13  0.020
 BCV  plan-2  O18  0.020
 BCV  plan-2  N29  0.020
 BCV  plan-2  C30  0.020
 BCV  plan-2  H29  0.020
 BCV  plan-3  C2   0.020
 BCV  plan-3  C1   0.020
 BCV  plan-3  O19  0.020
 BCV  plan-3  O20  0.020
 BCV  plan-3  H20  0.020
 BCV  plan-4  C30  0.020
 BCV  plan-4  C31  0.020
 BCV  plan-4  O42  0.020
 BCV  plan-4  O43  0.020
 BCV  plan-4  H43  0.020

