# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 14:54:00 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (4-amino-2-methylpyrimidin-5-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(N)n1
#
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
 MP5  MP5  '(4-amino-2-methylpyrimidin-5-yl)methyl dihydrogen phosphate'  ligand  24  14  .  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_MP5
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
 MP5  C1    C  CR6   0  -0.132  -0.2922   0.0998   0.9086
 MP5  C2    C  CR6   0   0.495  -1.1885   0.1711   2.0015
 MP5  C3    C  CH2   0  -0.234  -0.8019   0.2095  -0.4938
 MP5  N1    N  NH2   0  -0.832  -2.5129   0.3180   1.8263
 MP5  N2    N  N     0  -0.389  -0.7491   0.0621   3.2535
 MP5  C4    C  CR6   0   0.263   0.5507  -0.1207   3.4524
 MP5  C5    C  CH3   0  -0.696   0.9978  -0.2536   4.8739
 MP5  N3    N  N     0  -0.421   1.4677  -0.1969   2.5000
 MP5  C6    C  CR16  0  -0.076   1.0252  -0.0857   1.2410
 MP5  O1    O  O2    0  -0.486   0.2985   0.2444  -1.3937
 MP5  P1    P  P     0   1.444   0.0586  -0.0905  -2.9402
 MP5  O2    O  OH1   0  -0.687   1.5159   0.3055  -3.4384
 MP5  O3    O  O     0  -0.759  -1.0999   0.5593  -3.5796
 MP5  O4    O  OH1   0  -0.749  -0.0904  -1.6767  -3.0447
 MP5  H31   H  HCH2  0   0.221  -1.4619  -0.6397  -0.7084
 MP5  H32   H  HCH2  0   0.239  -1.3980   1.1200  -0.6158
 MP5  HN11  H  HNH2  0   0.399  -3.0817   0.5080   2.6346
 MP5  HN12  H  HNH2  0   0.430  -2.9053   0.5964   0.9439
 MP5  H51   H  HCH3  0   0.263   0.6113   0.5647   5.4811
 MP5  H52   H  HCH3  0   0.254   0.6168  -1.1811   5.3051
 MP5  H53   H  HCH3  0   0.225   2.0825  -0.2642   4.9469
 MP5  H6    H  HCR6  0   0.227   1.7806  -0.1497   0.4670
 MP5  HO2   H  HOH1  0   0.520   1.6167   0.3238  -4.3996
 MP5  HO4   H  HOH1  0   0.482   0.6398  -2.1943  -2.6793

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
 MP5  C1  C2    aromatic  1.415  0.020  1.415
 MP5  C1  C3    single    1.496  0.020  1.496
 MP5  C1  C6    aromatic  1.371  0.020  1.371
 MP5  C2  N1    single    1.344  0.020  1.344
 MP5  C2  N2    aromatic  1.331  0.020  1.331
 MP5  C3  O1    single    1.422  0.020  1.422
 MP5  C3  H31   single    0.970  0.020  1.090
 MP5  C3  H32   single    0.970  0.020  1.090
 MP5  N1  HN11  single    0.890  0.020  1.040
 MP5  N1  HN12  single    0.890  0.020  1.040
 MP5  N2  C4    aromatic  1.328  0.020  1.328
 MP5  C4  C5    single    1.496  0.020  1.496
 MP5  C4  N3    aromatic  1.324  0.020  1.324
 MP5  C5  H51   single    0.970  0.020  1.090
 MP5  C5  H52   single    0.970  0.020  1.090
 MP5  C5  H53   single    0.970  0.020  1.090
 MP5  N3  C6    aromatic  1.339  0.020  1.339
 MP5  C6  H6    single    0.930  0.020  1.080
 MP5  O1  P1    single    1.600  0.020  1.600
 MP5  P1  O2    single    1.590  0.020  1.590
 MP5  P1  O3    double    1.474  0.020  1.474
 MP5  P1  O4    single    1.597  0.020  1.597
 MP5  O2  HO2   single    0.850  0.020  0.980
 MP5  O4  HO4   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
 MP5  C6    C1  C3    124.36  3.000
 MP5  C6    C1  C2    115.35  3.000
 MP5  C3    C1  C2    120.29  3.000
 MP5  N2    C2  N1    117.18  3.000
 MP5  N2    C2  C1    120.87  3.000
 MP5  N1    C2  C1    121.94  3.000
 MP5  H32   C3  H31   107.12  3.000
 MP5  H32   C3  O1    109.29  3.000
 MP5  H31   C3  O1    111.16  3.000
 MP5  H32   C3  C1    110.53  3.000
 MP5  H31   C3  C1    109.37  3.000
 MP5  O1    C3  C1    109.35  3.000
 MP5  HN12  N1  HN11  115.60  3.000
 MP5  HN12  N1  C2    121.97  3.000
 MP5  HN11  N1  C2    118.22  3.000
 MP5  C4    N2  C2    118.38  3.000
 MP5  N3    C4  C5    118.12  3.000
 MP5  N3    C4  N2    125.32  3.000
 MP5  C5    C4  N2    116.57  3.000
 MP5  H53   C5  H52   108.27  3.000
 MP5  H53   C5  H51   108.89  3.000
 MP5  H52   C5  H51   107.10  3.000
 MP5  H53   C5  C4    111.28  3.000
 MP5  H52   C5  C4    110.28  3.000
 MP5  H51   C5  C4    110.90  3.000
 MP5  C6    N3  C4    116.27  3.000
 MP5  H6    C6  N3    115.87  3.000
 MP5  H6    C6  C1    120.31  3.000
 MP5  N3    C6  C1    123.82  3.000
 MP5  P1    O1  C3    119.37  3.000
 MP5  O4    P1  O3    109.64  3.000
 MP5  O4    P1  O2    108.21  3.000
 MP5  O3    P1  O2    118.33  3.000
 MP5  O4    P1  O1    106.57  3.000
 MP5  O3    P1  O1    116.40  3.000
 MP5  O2    P1  O1     96.51  3.000
 MP5  HO2   O2  P1    114.32  3.000
 MP5  HO4   O4  P1    115.89  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
 MP5  CONST_01  C4    N2  C2  C1    0.00   0.0  0
 MP5  CONST_02  C4    N3  C6  C1    0.00   0.0  0
 MP5  CONST_03  N3    C6  C1  C2    0.00   0.0  0
 MP5  CONST_04  N3    C4  N2  C2    0.00   0.0  0
 MP5  CONST_05  C6    C1  C2  N2    0.00   0.0  0
 MP5  CONST_06  C6    N3  C4  N2    0.00   0.0  0
 MP5  CONST_07  C5    C4  N2  C2  180.00   0.0  0
 MP5  CONST_08  N2    C2  C1  C3  180.00   0.0  0
 MP5  CONST_09  N3    C6  C1  C3  180.00   0.0  0
 MP5  CONST_10  C6    C1  C2  N1  180.00   0.0  0
 MP5  CONST_11  C4    N2  C2  N1  180.00   0.0  0
 MP5  CONST_12  C6    N3  C4  C5  180.00   0.0  0
 MP5  CONST_13  H6    C6  C1  C2  180.00   0.0  0
 MP5  CONST_14  HN11  N1  C2  C1  180.00   0.0  0
 MP5  CONST_15  HN12  N1  C2  C1    0.00   0.0  0
 MP5  Var_01    O1    C3  C1  C2  174.16  30.0  2
 MP5  Var_02    H51   C5  C4  N2  -50.93  30.0  2
 MP5  Var_03    O2    P1  O1  C3  172.28  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
 MP5  plan-1  C1    0.020
 MP5  plan-1  C2    0.020
 MP5  plan-1  C3    0.020
 MP5  plan-1  N1    0.020
 MP5  plan-1  N2    0.020
 MP5  plan-1  C4    0.020
 MP5  plan-1  C5    0.020
 MP5  plan-1  N3    0.020
 MP5  plan-1  C6    0.020
 MP5  plan-1  H6    0.020
 MP5  plan-2  C2    0.020
 MP5  plan-2  N1    0.020
 MP5  plan-2  HN11  0.020
 MP5  plan-2  HN12  0.020

