# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:24:55 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1=CC[C@@H](N)[C@@H](O)O1
#
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
 4XR  4XR  (2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol  ligand  22  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4XR
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
 4XR  O11  O  OH1   0  -0.659  -1.6423   1.8819  -0.0890
 4XR  C11  C  CH1   0   0.295  -0.9316   0.7808  -0.5159
 4XR  O51  O  O2    0  -0.499   0.3020   0.7641   0.1906
 4XR  C21  C  CH1   0  -0.174  -1.7323  -0.4865  -0.2510
 4XR  N21  N  NH2   0  -0.801  -1.9953  -0.6161   1.1718
 4XR  C31  C  CH2   0  -0.454  -0.9046  -1.6701  -0.7466
 4XR  C41  C  C1    0  -0.390   0.5337  -1.5216  -0.3608
 4XR  C51  C  C     0   0.387   1.0363  -0.3729   0.0888
 4XR  C61  C  CH2   0  -0.378   2.4434  -0.1750   0.5575
 4XR  N61  N  NH2   0  -0.799   3.1376   0.8205  -0.2526
 4XR  H1   H  HOH1  0   0.465  -1.2700   2.6807  -0.4775
 4XR  H2   H  HCH1  0   0.206  -0.7029   0.8368  -1.5912
 4XR  H3   H  HCH1  0   0.233  -2.6455  -0.4227  -0.8603
 4XR  H4   H  HNH2  0   0.345  -2.6222   0.1183   1.4755
 4XR  H5   H  HNH2  0   0.347  -2.4928  -1.4824   1.3349
 4XR  H7   H  HCH2  0   0.245  -1.3166  -2.5980  -0.3394
 4XR  H8   H  HCH2  0   0.242  -1.0063  -1.7590  -1.8327
 4XR  H9   H  H     0   0.238   1.1913  -2.3786  -0.4309
 4XR  H10  H  HCH2  0   0.214   2.4272   0.0698   1.6299
 4XR  H11  H  HCH2  0   0.241   2.9692  -1.1262   0.4672
 4XR  H12  H  HNH2  0   0.343   2.7748   1.7409  -0.0400
 4XR  H13  H  HNH2  0   0.353   4.1103   0.8438   0.0257

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
 4XR  N61  C61  single  1.459  0.020  1.459
 4XR  O51  C51  single  1.357  0.020  1.357
 4XR  O51  C11  single  1.422  0.020  1.422
 4XR  C31  C41  single  1.497  0.020  1.497
 4XR  C31  C21  single  1.527  0.020  1.527
 4XR  C51  C41  double  1.332  0.020  1.332
 4XR  C51  C61  single  1.496  0.020  1.496
 4XR  O11  C11  single  1.378  0.020  1.378
 4XR  C11  C21  single  1.522  0.020  1.522
 4XR  N21  C21  single  1.453  0.020  1.453
 4XR  O11  H1   single  0.850  0.020  0.980
 4XR  C11  H2   single  0.970  0.020  1.090
 4XR  C21  H3   single  0.970  0.020  1.090
 4XR  N21  H4   single  0.890  0.020  1.040
 4XR  N21  H5   single  0.890  0.020  1.040
 4XR  C31  H7   single  0.970  0.020  1.090
 4XR  C31  H8   single  0.970  0.020  1.090
 4XR  C41  H9   single  0.930  0.020  1.080
 4XR  C61  H10  single  0.970  0.020  1.090
 4XR  C61  H11  single  0.970  0.020  1.090
 4XR  N61  H12  single  0.890  0.020  1.040
 4XR  N61  H13  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
 4XR  H1   O11  C11  109.78  3.000
 4XR  H2   C11  C21  108.77  3.000
 4XR  H2   C11  O51  107.80  3.000
 4XR  C21  C11  O51  111.11  3.000
 4XR  H2   C11  O11  111.65  3.000
 4XR  C21  C11  O11  109.87  3.000
 4XR  O51  C11  O11  107.63  3.000
 4XR  C51  O51  C11  116.23  3.000
 4XR  H3   C21  C31  108.37  3.000
 4XR  H3   C21  N21  113.42  3.000
 4XR  C31  C21  N21  110.29  3.000
 4XR  H3   C21  C11  106.99  3.000
 4XR  N21  C21  C11  109.88  3.000
 4XR  C31  C21  C11  107.68  3.000
 4XR  H5   N21  H4   105.56  3.000
 4XR  H5   N21  C21  108.86  3.000
 4XR  H4   N21  C21  109.95  3.000
 4XR  H8   C31  H7   105.40  3.000
 4XR  H8   C31  C41  110.68  3.000
 4XR  H7   C31  C41  110.50  3.000
 4XR  H8   C31  C21  109.56  3.000
 4XR  H7   C31  C21  109.43  3.000
 4XR  C41  C31  C21  111.12  3.000
 4XR  H9   C41  C51  118.38  3.000
 4XR  H9   C41  C31  119.25  3.000
 4XR  C51  C41  C31  122.36  3.000
 4XR  C61  C51  C41  125.08  3.000
 4XR  C61  C51  O51  112.00  3.000
 4XR  C41  C51  O51  122.92  3.000
 4XR  H11  C61  H10  106.37  3.000
 4XR  H11  C61  N61  108.64  3.000
 4XR  H10  C61  N61  113.35  3.000
 4XR  H11  C61  C51  108.19  3.000
 4XR  H10  C61  C51  108.72  3.000
 4XR  N61  C61  C51  111.33  3.000
 4XR  H13  N61  H12  105.42  3.000
 4XR  H13  N61  C61  108.68  3.000
 4XR  H12  N61  C61  109.47  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
 4XR  Var_01  C41  C51  O51  C11  -15.57  30.0  1
 4XR  Var_02  C31  C41  C51  O51   -2.33  30.0  1
 4XR  Var_03  C51  C41  C31  C21  -13.44  30.0  1
 4XR  Var_04  N61  C61  C51  O51  -61.76  30.0  3
 4XR  Var_05  H12  N61  C61  C51   71.93  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
 4XR  chir_01  C11  O51  O11  C21  positiv
 4XR  chir_02  C21  N21  C11  C31  negativ

