# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:03:38 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (4S)-4-amino-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNC[C@@H](N)CCC(O)=O)c1O
#
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
 EA5  EA5  '(4S)-4-amino-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid'  ligand  46  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EA5
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
 EA5  P     P  P     0   1.458  7.1406  17.4775  -29.3017
 EA5  OP1   O  OH1   0  -0.726  6.3170  18.4190  -28.3177
 EA5  OP2   O  OH1   0  -0.742  7.2331  16.0606  -28.5622
 EA5  OP3   O  O     0  -0.708  8.4353  17.9812  -29.8055
 EA5  OP4   O  O2    0  -0.582  5.9763  17.2727  -30.3728
 EA5  C5A   C  CH2   0  -0.298  6.2100  16.4508  -31.5289
 EA5  C5    C  CR6   0  -0.009  5.2868  16.8885  -32.6209
 EA5  C6    C  CR16  0  -0.154  4.2950  16.0244  -33.0525
 EA5  N1    N  N     0  -0.410  3.4300  16.3230  -34.0137
 EA5  C2    C  CR6   0   0.129  3.5037  17.5066  -34.6014
 EA5  C2A   C  CH3   0  -0.720  2.5180  17.8247  -35.6826
 EA5  C3    C  CR6   0   0.255  4.4704  18.4588  -34.2310
 EA5  O3    O  OH1   0  -0.654  4.4638  19.6355  -34.8646
 EA5  C4    C  CR6   0   0.029  5.3844  18.1490  -33.2177
 EA5  C4A   C  CH2   0  -0.314  6.3877  19.1808  -32.7608
 EA5  N4A   N  NH1   0  -0.665  6.8016  20.0329  -33.8673
 EA5  N4    N  NH2   0  -0.780  6.3542  22.3958  -35.4004
 EA5  CA    C  CH1   0  -0.120  7.6094  22.1933  -34.6937
 EA5  C     C  CH2   0  -0.246  7.3671  21.3118  -33.4735
 EA5  CB    C  CH2   0  -0.453  8.3701  23.4835  -34.3465
 EA5  CG    C  CH2   0  -0.581  7.6329  24.4677  -33.4432
 EA5  CD    C  C     0   0.538  7.7173  24.1570  -31.9730
 EA5  OE1   O  O     0  -0.446  8.6674  23.6476  -31.4306
 EA5  OE2   O  OH1   0  -0.593  6.6342  24.5503  -31.3098
 EA5  HOP1  H  HOH1  0   0.504  6.8578  18.8450  -27.6391
 EA5  HOP2  H  HOH1  0   0.499  8.1339  15.7253  -28.4688
 EA5  H5A1  H  HCH2  0   0.273  6.0171  15.4075  -31.2711
 EA5  H5A2  H  HCH2  0   0.256  7.2534  16.5266  -31.8484
 EA5  H6    H  HCR6  0   0.253  4.1976  15.0423  -32.6002
 EA5  H2A1  H  HCH3  0   0.243  1.8305  16.9919  -35.8161
 EA5  H2A2  H  HCH3  0   0.245  3.0167  18.0134  -36.6352
 EA5  H2A3  H  HCH3  0   0.244  1.9345  18.7172  -35.4507
 EA5  HO3   H  HOH1  0   0.486  5.3497  20.0748  -34.6586
 EA5  H4A1  H  HCH2  0   0.248  7.2451  18.7197  -32.2619
 EA5  H4A2  H  HCH2  0   0.268  5.9064  19.8153  -32.0099
 EA5  HN4A  H  HNH1  0   0.374  7.4612  19.5333  -34.4537
 EA5  HN42  H  HNH2  0   0.340  5.6877  22.8791  -34.8101
 EA5  HA    H  HCH1  0   0.237  8.2684  21.6351  -35.3698
 EA5  H1    H  HCH2  0   0.228  8.3027  21.1958  -32.9135
 EA5  H2    H  HCH2  0   0.225  6.6480  21.7911  -32.8009
 EA5  HB1   H  HCH2  0   0.248  8.5898  23.9922  -35.2878
 EA5  HB2   H  HCH2  0   0.237  9.3391  23.2335  -33.9087
 EA5  HG1   H  HCH2  0   0.256  6.5917  24.5920  -33.7469
 EA5  HG2   H  HCH2  0   0.300  8.0817  25.4602  -33.5600
 EA5  HOE2  H  HOH1  0   0.478  6.7478  24.3794  -30.3626
 EA5  HN41  H  HNH2  0   0.350  6.5045  22.9917  -36.2055

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
 EA5  P    OP1   single    1.592  0.020  1.592
 EA5  P    OP2   single    1.601  0.020  1.601
 EA5  P    OP3   double    1.478  0.020  1.478
 EA5  P    OP4   single    1.595  0.020  1.595
 EA5  OP1  HOP1  single    0.850  0.020  0.980
 EA5  OP2  HOP2  single    0.850  0.020  0.980
 EA5  OP4  C5A   single    1.438  0.020  1.438
 EA5  C5A  C5    single    1.495  0.020  1.495
 EA5  C5A  H5A1  single    0.970  0.020  1.090
 EA5  C5A  H5A2  single    0.970  0.020  1.090
 EA5  C5   C6    aromatic  1.384  0.020  1.384
 EA5  C5   C4    aromatic  1.398  0.020  1.398
 EA5  C6   N1    aromatic  1.327  0.020  1.327
 EA5  C6   H6    single    0.930  0.020  1.080
 EA5  N1   C2    aromatic  1.324  0.020  1.324
 EA5  C2   C2A   single    1.497  0.020  1.497
 EA5  C2   C3    aromatic  1.407  0.020  1.407
 EA5  C2A  H2A1  single    0.970  0.020  1.090
 EA5  C2A  H2A2  single    0.970  0.020  1.090
 EA5  C2A  H2A3  single    0.970  0.020  1.090
 EA5  C3   O3    single    1.337  0.020  1.337
 EA5  C3   C4    aromatic  1.399  0.020  1.399
 EA5  O3   HO3   single    0.850  0.020  0.980
 EA5  C4   C4A   single    1.510  0.020  1.510
 EA5  C4A  N4A   single    1.457  0.020  1.457
 EA5  C4A  H4A1  single    0.970  0.020  1.090
 EA5  C4A  H4A2  single    0.970  0.020  1.090
 EA5  N4A  C     single    1.453  0.020  1.453
 EA5  N4A  HN4A  single    0.890  0.020  1.040
 EA5  N4   CA    single    1.455  0.020  1.455
 EA5  N4   HN41  single    0.890  0.020  1.040
 EA5  N4   HN42  single    0.890  0.020  1.040
 EA5  CA   C     single    1.525  0.020  1.525
 EA5  CA   CB    single    1.537  0.020  1.537
 EA5  CA   HA    single    0.970  0.020  1.090
 EA5  C    H1    single    0.970  0.020  1.090
 EA5  C    H2    single    0.970  0.020  1.090
 EA5  CB   CG    single    1.526  0.020  1.526
 EA5  CB   HB1   single    0.970  0.020  1.090
 EA5  CB   HB2   single    0.970  0.020  1.090
 EA5  CG   CD    single    1.505  0.020  1.505
 EA5  CG   HG1   single    0.970  0.020  1.090
 EA5  CG   HG2   single    0.970  0.020  1.090
 EA5  CD   OE1   double    1.207  0.020  1.207
 EA5  CD   OE2   single    1.329  0.020  1.329
 EA5  OE2  HOE2  single    0.850  0.020  0.980

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
 EA5  OP4   P    OP3   117.02  3.000
 EA5  OP4   P    OP2   103.81  3.000
 EA5  OP3   P    OP2   114.11  3.000
 EA5  OP4   P    OP1    96.52  3.000
 EA5  OP3   P    OP1   117.55  3.000
 EA5  OP2   P    OP1   105.54  3.000
 EA5  HOP1  OP1  P     113.91  3.000
 EA5  HOP2  OP2  P     113.94  3.000
 EA5  C5A   OP4  P     119.65  3.000
 EA5  H5A2  C5A  H5A1  107.68  3.000
 EA5  H5A2  C5A  C5    110.81  3.000
 EA5  H5A1  C5A  C5    110.06  3.000
 EA5  H5A2  C5A  OP4   110.51  3.000
 EA5  H5A1  C5A  OP4   109.12  3.000
 EA5  C5    C5A  OP4   108.64  3.000
 EA5  C4    C5   C6    118.67  3.000
 EA5  C4    C5   C5A   122.18  3.000
 EA5  C6    C5   C5A   119.16  3.000
 EA5  H6    C6   N1    116.53  3.000
 EA5  H6    C6   C5    119.94  3.000
 EA5  N1    C6   C5    123.53  3.000
 EA5  C2    N1   C6    119.11  3.000
 EA5  C3    C2   C2A   119.92  3.000
 EA5  C3    C2   N1    121.78  3.000
 EA5  C2A   C2   N1    118.29  3.000
 EA5  H2A3  C2A  H2A2  106.76  3.000
 EA5  H2A3  C2A  H2A1  108.31  3.000
 EA5  H2A2  C2A  H2A1  108.29  3.000
 EA5  H2A3  C2A  C2    111.86  3.000
 EA5  H2A2  C2A  C2    111.47  3.000
 EA5  H2A1  C2A  C2    110.00  3.000
 EA5  C4    C3   O3    122.78  3.000
 EA5  C4    C3   C2    119.33  3.000
 EA5  O3    C3   C2    117.89  3.000
 EA5  HO3   O3   C3    106.37  3.000
 EA5  C4A   C4   C3    120.13  3.000
 EA5  C4A   C4   C5    122.23  3.000
 EA5  C3    C4   C5    117.59  3.000
 EA5  H4A2  C4A  H4A1  106.03  3.000
 EA5  H4A2  C4A  N4A   107.87  3.000
 EA5  H4A1  C4A  N4A   111.73  3.000
 EA5  H4A2  C4A  C4    108.15  3.000
 EA5  H4A1  C4A  C4    111.77  3.000
 EA5  N4A   C4A  C4    111.02  3.000
 EA5  HN4A  N4A  C     109.71  3.000
 EA5  HN4A  N4A  C4A   109.62  3.000
 EA5  C     N4A  C4A   114.81  3.000
 EA5  HN42  N4   HN41  106.27  3.000
 EA5  HN42  N4   CA    110.55  3.000
 EA5  HN41  N4   CA    109.88  3.000
 EA5  HA    CA   CB    105.60  3.000
 EA5  HA    CA   C     107.13  3.000
 EA5  CB    CA   C     112.52  3.000
 EA5  HA    CA   N4    106.85  3.000
 EA5  CB    CA   N4    114.82  3.000
 EA5  C     CA   N4    109.40  3.000
 EA5  H2    C    H1    107.03  3.000
 EA5  H2    C    CA    110.05  3.000
 EA5  H1    C    CA    109.53  3.000
 EA5  H2    C    N4A   107.23  3.000
 EA5  H1    C    N4A   112.17  3.000
 EA5  CA    C    N4A   110.72  3.000
 EA5  HB2   CB   HB1   105.87  3.000
 EA5  HB2   CB   CG    109.81  3.000
 EA5  HB1   CB   CG    107.88  3.000
 EA5  HB2   CB   CA    109.72  3.000
 EA5  HB1   CB   CA    107.20  3.000
 EA5  CG    CB   CA    115.85  3.000
 EA5  HG2   CG   HG1   104.95  3.000
 EA5  HG2   CG   CD    105.55  3.000
 EA5  HG1   CG   CD    110.41  3.000
 EA5  HG2   CG   CB    108.87  3.000
 EA5  HG1   CG   CB    111.69  3.000
 EA5  CD    CG   CB    114.71  3.000
 EA5  OE2   CD   OE1   122.82  3.000
 EA5  OE2   CD   CG    112.37  3.000
 EA5  OE1   CD   CG    124.77  3.000
 EA5  HOE2  OE2  CD    109.87  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
 EA5  CONST_01  C2    N1   C6   C5      0.00   0.0  0
 EA5  CONST_02  C2    C3   C4   C5      0.00   0.0  0
 EA5  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 EA5  CONST_04  C3    C2   N1   C6      0.00   0.0  0
 EA5  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 EA5  CONST_06  C4    C3   C2   N1      0.00   0.0  0
 EA5  CONST_07  N1    C6   C5   C5A   180.00   0.0  0
 EA5  CONST_08  C3    C4   C5   C5A   180.00   0.0  0
 EA5  CONST_09  O3    C3   C4   C5    180.00   0.0  0
 EA5  CONST_10  C4A   C4   C5   C6    180.00   0.0  0
 EA5  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 EA5  CONST_12  O3    C3   C2   N1    180.00   0.0  0
 EA5  CONST_13  C4A   C4   C3   C2    180.00   0.0  0
 EA5  CONST_14  C4    C3   C2   C2A   180.00   0.0  0
 EA5  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 EA5  CONST_16  HOE2  OE2  CD   CG    180.00   0.0  0
 EA5  Var_01    C6    C5   C5A  OP4  -113.91  30.0  2
 EA5  Var_02    N4A   C4A  C4   C5    149.48  30.0  2
 EA5  Var_03    H2A1  C2A  C2   N1      1.39  30.0  2
 EA5  Var_04    C5    C5A  OP4  P    -154.82  30.0  3
 EA5  Var_05    C     N4A  C4A  C4    159.13  30.0  3
 EA5  Var_06    CA    C    N4A  C4A  -173.10  30.0  3
 EA5  Var_07    CD    CG   CB   CA     82.47  30.0  3
 EA5  Var_08    OE1   CD   CG   CB     33.12  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
 EA5  chir_01  CA  N4  C  CB  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
 EA5  plan-1  C5A   0.020
 EA5  plan-1  C5    0.020
 EA5  plan-1  C6    0.020
 EA5  plan-1  N1    0.020
 EA5  plan-1  C2    0.020
 EA5  plan-1  C2A   0.020
 EA5  plan-1  C3    0.020
 EA5  plan-1  O3    0.020
 EA5  plan-1  C4    0.020
 EA5  plan-1  C4A   0.020
 EA5  plan-1  H6    0.020
 EA5  plan-2  CG    0.020
 EA5  plan-2  CD    0.020
 EA5  plan-2  OE1   0.020
 EA5  plan-2  OE2   0.020
 EA5  plan-2  HOE2  0.020

