# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 14:45:33 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNC(C)(C)C(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
 NMA  NMA  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-D-alanine  ligand  41  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NMA
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
 NMA  C4    C  CR6   0   0.037   1.0265  -0.1211  -0.3656
 NMA  C4A   C  CH2   0  -0.346  -0.2233  -0.6096  -1.0570
 NMA  P     P  P     0   1.457  -0.6018  -0.6224   4.4148
 NMA  O1P   O  O     0  -0.703  -0.4580  -2.0881   4.4789
 NMA  O2P   O  OH1   0  -0.728   0.0250   0.2412   5.5960
 NMA  O3P   O  OH1   0  -0.742  -2.1474  -0.2406   4.2819
 NMA  O4P   O  O2    0  -0.591   0.1609   0.1208   3.2230
 NMA  C5A   C  CH2   0  -0.219  -0.1118  -0.2303   1.8710
 NMA  C5    C  CR6   0  -0.073   1.1021   0.0291   1.0220
 NMA  N1    N  N     0  -0.409   3.4093   0.6265   0.8495
 NMA  C6    C  CR16  0  -0.143   2.3174   0.4026   1.5741
 NMA  C2    C  CR6   0   0.128   3.3608   0.5038  -0.4664
 NMA  C2A   C  CH3   0  -0.720   4.6063   0.7607  -1.2571
 NMA  C3    C  CR6   0   0.269   2.1758   0.1302  -1.1172
 NMA  O3    O  OH1   0  -0.648   2.1922   0.0135  -2.4519
 NMA  N     N  NH1   0  -0.673  -0.4184   0.1036  -2.3184
 NMA  C8    C  CT    0  -0.031  -1.4403  -0.4423  -3.2256
 NMA  C7    C  C     0   0.580  -1.5481   0.5195  -4.4116
 NMA  O7    O  O     0  -0.425  -1.6275   0.1788  -5.5629
 NMA  O8    O  OH1   0  -0.594  -1.5977   1.7863  -4.0237
 NMA  C9    C  CH3   0  -0.655  -1.0133  -1.8132  -3.7359
 NMA  C10   C  CH3   0  -0.666  -2.8321  -0.5246  -2.5787
 NMA  H4A1  H  HCH2  0   0.283  -0.0942  -1.6747  -1.2635
 NMA  H4A2  H  HCH2  0   0.262  -1.0955  -0.5280  -0.4036
 NMA  HOP2  H  HOH1  0   0.506  -0.1443  -0.1158   6.4782
 NMA  HOP3  H  HOH1  0   0.497  -2.3499   0.7047   4.2852
 NMA  H5A1  H  HCH2  0   0.262  -0.9585   0.3647   1.5169
 NMA  H5A2  H  HCH2  0   0.257  -0.3988  -1.2842   1.7945
 NMA  H6    H  HCR6  0   0.255   2.4269   0.5274   2.6435
 NMA  H2A1  H  HCH3  0   0.245   4.9443  -0.1372  -1.7784
 NMA  H2A2  H  HCH3  0   0.244   4.4489   1.5275  -2.0173
 NMA  H2A3  H  HCH3  0   0.244   5.4056   1.0897  -0.5962
 NMA  HO3   H  HOH1  0   0.471   1.2366   0.0368  -2.7423
 NMA  HN    H  HNH1  0   0.385  -0.6399   1.0681  -2.0959
 NMA  HO8   H  HOH1  0   0.489  -1.6967   2.3714  -4.7902
 NMA  H91   H  HCH3  0   0.244  -0.0133  -1.7846  -4.1691
 NMA  H92   H  HCH3  0   0.245  -1.0161  -2.5489  -2.9335
 NMA  H93   H  HCH3  0   0.251  -1.7033  -2.1731  -4.4961
 NMA  H101  H  HCH3  0   0.248  -3.1447   0.4363  -2.1690
 NMA  H102  H  HCH3  0   0.252  -3.5791  -0.8458  -3.3053
 NMA  H103  H  HCH3  0   0.254  -2.8316  -1.2549  -1.7691

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
 NMA  C4   C4A   single    1.510  0.020  1.510
 NMA  C4   C5    aromatic  1.398  0.020  1.398
 NMA  C4   C3    aromatic  1.396  0.020  1.396
 NMA  C4A  N     single    1.462  0.020  1.462
 NMA  C4A  H4A1  single    0.970  0.020  1.090
 NMA  C4A  H4A2  single    0.970  0.020  1.090
 NMA  P    O1P   double    1.474  0.020  1.474
 NMA  P    O2P   single    1.592  0.020  1.592
 NMA  P    O3P   single    1.598  0.020  1.598
 NMA  P    O4P   single    1.598  0.020  1.598
 NMA  O2P  HOP2  single    0.850  0.020  0.980
 NMA  O3P  HOP3  single    0.850  0.020  0.980
 NMA  O4P  C5A   single    1.423  0.020  1.423
 NMA  C5A  C5    single    1.504  0.020  1.504
 NMA  C5A  H5A1  single    0.970  0.020  1.090
 NMA  C5A  H5A2  single    0.970  0.020  1.090
 NMA  C5   C6    aromatic  1.386  0.020  1.386
 NMA  N1   C6    aromatic  1.329  0.020  1.329
 NMA  N1   C2    aromatic  1.322  0.020  1.322
 NMA  C6   H6    single    0.930  0.020  1.080
 NMA  C2   C2A   single    1.497  0.020  1.497
 NMA  C2   C3    aromatic  1.403  0.020  1.403
 NMA  C2A  H2A1  single    0.970  0.020  1.090
 NMA  C2A  H2A2  single    0.970  0.020  1.090
 NMA  C2A  H2A3  single    0.970  0.020  1.090
 NMA  C3   O3    single    1.340  0.020  1.340
 NMA  O3   HO3   single    0.850  0.020  0.980
 NMA  N    C8    single    1.472  0.020  1.472
 NMA  N    HN    single    0.890  0.020  1.040
 NMA  C8   C7    single    1.531  0.020  1.531
 NMA  C8   C9    single    1.524  0.020  1.524
 NMA  C8   C10   single    1.537  0.020  1.537
 NMA  C7   O7    double    1.203  0.020  1.203
 NMA  C7   O8    single    1.326  0.020  1.326
 NMA  O8   HO8   single    0.850  0.020  0.980
 NMA  C9   H91   single    0.970  0.020  1.090
 NMA  C9   H92   single    0.970  0.020  1.090
 NMA  C9   H93   single    0.970  0.020  1.090
 NMA  C10  H101  single    0.970  0.020  1.090
 NMA  C10  H102  single    0.970  0.020  1.090
 NMA  C10  H103  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
 NMA  C3    C4   C5    118.08  3.000
 NMA  C3    C4   C4A   119.55  3.000
 NMA  C5    C4   C4A   122.29  3.000
 NMA  H4A2  C4A  H4A1  106.26  3.000
 NMA  H4A2  C4A  N     111.89  3.000
 NMA  H4A1  C4A  N     109.16  3.000
 NMA  H4A2  C4A  C4    111.27  3.000
 NMA  H4A1  C4A  C4    107.71  3.000
 NMA  N     C4A  C4    110.35  3.000
 NMA  O4P   P    O3P   106.77  3.000
 NMA  O4P   P    O2P    96.49  3.000
 NMA  O3P   P    O2P   108.24  3.000
 NMA  O4P   P    O1P   116.63  3.000
 NMA  O3P   P    O1P   109.61  3.000
 NMA  O2P   P    O1P   117.95  3.000
 NMA  HOP2  O2P  P     114.07  3.000
 NMA  HOP3  O3P  P     115.85  3.000
 NMA  C5A   O4P  P     120.15  3.000
 NMA  H5A2  C5A  H5A1  107.34  3.000
 NMA  H5A2  C5A  C5    109.77  3.000
 NMA  H5A1  C5A  C5    110.37  3.000
 NMA  H5A2  C5A  O4P   110.73  3.000
 NMA  H5A1  C5A  O4P   108.76  3.000
 NMA  C5    C5A  O4P   109.82  3.000
 NMA  C6    C5   C5A   121.96  3.000
 NMA  C6    C5   C4    118.15  3.000
 NMA  C5A   C5   C4    119.89  3.000
 NMA  C2    N1   C6    119.78  3.000
 NMA  H6    C6   N1    115.85  3.000
 NMA  H6    C6   C5    120.89  3.000
 NMA  N1    C6   C5    123.26  3.000
 NMA  C3    C2   C2A   120.22  3.000
 NMA  C3    C2   N1    121.15  3.000
 NMA  C2A   C2   N1    118.62  3.000
 NMA  H2A3  C2A  H2A2  108.47  3.000
 NMA  H2A3  C2A  H2A1  108.14  3.000
 NMA  H2A2  C2A  H2A1  106.85  3.000
 NMA  H2A3  C2A  C2    110.01  3.000
 NMA  H2A2  C2A  C2    111.62  3.000
 NMA  H2A1  C2A  C2    111.62  3.000
 NMA  O3    C3   C2    118.36  3.000
 NMA  O3    C3   C4    122.06  3.000
 NMA  C2    C3   C4    119.58  3.000
 NMA  HO3   O3   C3    106.01  3.000
 NMA  HN    N    C8    109.65  3.000
 NMA  HN    N    C4A   107.68  3.000
 NMA  C8    N    C4A   116.33  3.000
 NMA  C10   C8   C9    110.28  3.000
 NMA  C10   C8   C7    107.22  3.000
 NMA  C9    C8   C7    109.00  3.000
 NMA  C10   C8   N     112.90  3.000
 NMA  C9    C8   N     110.22  3.000
 NMA  C7    C8   N     107.06  3.000
 NMA  O8    C7   O7    123.24  3.000
 NMA  O8    C7   C8    112.10  3.000
 NMA  O7    C7   C8    124.61  3.000
 NMA  HO8   O8   C7    110.43  3.000
 NMA  H93   C9   H92   106.85  3.000
 NMA  H93   C9   H91   108.23  3.000
 NMA  H92   C9   H91   108.24  3.000
 NMA  H93   C9   C8    110.73  3.000
 NMA  H92   C9   C8    111.12  3.000
 NMA  H91   C9   C8    111.50  3.000
 NMA  H103  C10  H102  107.32  3.000
 NMA  H103  C10  H101  108.14  3.000
 NMA  H102  C10  H101  108.28  3.000
 NMA  H103  C10  C8    110.36  3.000
 NMA  H102  C10  C8    110.83  3.000
 NMA  H101  C10  C8    111.76  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
 NMA  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 NMA  CONST_02  N1    C2   C3   C4      0.00   0.0  0
 NMA  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 NMA  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 NMA  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 NMA  CONST_06  C3    C2   N1   C6      0.00   0.0  0
 NMA  CONST_07  C2A   C2   C3   C4    180.00   0.0  0
 NMA  CONST_08  C6    C5   C4   C4A   180.00   0.0  0
 NMA  CONST_09  C2    C3   C4   C4A   180.00   0.0  0
 NMA  CONST_10  C3    C4   C5   C5A   180.00   0.0  0
 NMA  CONST_11  N1    C6   C5   C5A   180.00   0.0  0
 NMA  CONST_12  O3    C3   C4   C5    180.00   0.0  0
 NMA  CONST_13  O3    C3   C2   N1    180.00   0.0  0
 NMA  CONST_14  C2A   C2   N1   C6    180.00   0.0  0
 NMA  CONST_15  H6    C6   C5   C4    180.00   0.0  0
 NMA  CONST_16  HO8   O8   C7   C8    180.00   0.0  0
 NMA  Var_01    O4P   C5A  C5   C4   -173.86  30.0  1
 NMA  Var_02    N     C4A  C4   C5    142.10  30.0  2
 NMA  Var_03    H2A1  C2A  C2   N1    116.45  30.0  2
 NMA  Var_04    C8    N    C4A  C4    168.40  30.0  3
 NMA  Var_05    C5    C5A  O4P  P    -151.68  30.0  3
 NMA  Var_06    C7    C8   N    C4A   175.47  30.0  3
 NMA  Var_07    O7    C7   C8   N     136.86  30.0  3
 NMA  Var_08    H91   C9   C8   N     -52.75  30.0  3
 NMA  Var_09    H101  C10  C8   N      53.93  30.0  3

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
 NMA  plan-1  C4   0.020
 NMA  plan-1  C4A  0.020
 NMA  plan-1  C5A  0.020
 NMA  plan-1  C5   0.020
 NMA  plan-1  N1   0.020
 NMA  plan-1  C6   0.020
 NMA  plan-1  C2   0.020
 NMA  plan-1  C2A  0.020
 NMA  plan-1  C3   0.020
 NMA  plan-1  O3   0.020
 NMA  plan-1  H6   0.020
 NMA  plan-2  C8   0.020
 NMA  plan-2  C7   0.020
 NMA  plan-2  O7   0.020
 NMA  plan-2  O8   0.020
 NMA  plan-2  HO8  0.020

