# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:02:42 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (4-amino-2-methylpyrimidin-5-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO)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
 HMH  HMH  (4-amino-2-methylpyrimidin-5-yl)methanol  ligand  19  10  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HMH
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
 HMH  CM2   C  CH3   0  -0.737   0.4792  -0.0000   3.2961
 HMH  N1A   N  N     0  -0.466   1.4480  -0.0710   1.0818
 HMH  C2A   C  CR6   0   0.411   0.3424  -0.0188   1.8053
 HMH  N3A   N  N     0  -0.394  -0.8936   0.0321   1.3217
 HMH  C4A   C  CR6   0   0.434  -1.0518   0.0362   0.0010
 HMH  N4A   N  NH2   0  -0.865  -2.3105   0.1246  -0.4713
 HMH  C5A   C  CR6   0  -0.170   0.0628  -0.0152  -0.8688
 HMH  C6A   C  CR16  0  -0.058   1.2854  -0.0685  -0.2482
 HMH  C7A   C  CH2   0  -0.180  -0.1207  -0.0087  -2.3557
 HMH  O1    O  OH1   0  -0.674   1.1315  -0.0265  -2.9875
 HMH  HCM1  H  HCH3  0   0.236   0.2258   0.9873   3.6872
 HMH  HCM2  H  HCH3  0   0.223  -0.2034  -0.7129   3.7580
 HMH  HCM3  H  HCH3  0   0.259   1.4970  -0.2346   3.5986
 HMH  HN41  H  HNH2  0   0.382  -3.0694  -0.0113   0.1758
 HMH  HN42  H  HNH2  0   0.381  -2.5174  -0.0913  -1.4310
 HMH  HC6   H  HCR6  0   0.275   2.1944  -0.1108  -0.8367
 HMH  HC71  H  HCH2  0   0.222  -0.7294  -0.8793  -2.6464
 HMH  HC72  H  HCH2  0   0.261  -0.7035   0.8806  -2.6401
 HMH  HO1   H  HOH1  0   0.458   0.9836  -0.0437  -3.9370

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
 HMH  CM2  C2A   single    1.497  0.020  1.497
 HMH  CM2  HCM1  single    0.970  0.020  1.090
 HMH  CM2  HCM2  single    0.970  0.020  1.090
 HMH  CM2  HCM3  single    0.970  0.020  1.090
 HMH  N1A  C2A   aromatic  1.322  0.020  1.322
 HMH  N1A  C6A   aromatic  1.340  0.020  1.340
 HMH  C2A  N3A   aromatic  1.328  0.020  1.328
 HMH  N3A  C4A   aromatic  1.330  0.020  1.330
 HMH  C4A  N4A   single    1.347  0.020  1.347
 HMH  C4A  C5A   aromatic  1.415  0.020  1.415
 HMH  N4A  HN41  single    0.890  0.020  1.040
 HMH  N4A  HN42  single    0.890  0.020  1.040
 HMH  C5A  C6A   aromatic  1.372  0.020  1.372
 HMH  C5A  C7A   single    1.498  0.020  1.498
 HMH  C6A  HC6   single    0.930  0.020  1.080
 HMH  C7A  O1    single    1.403  0.020  1.403
 HMH  C7A  HC71  single    0.970  0.020  1.090
 HMH  C7A  HC72  single    0.970  0.020  1.090
 HMH  O1   HO1   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
 HMH  HCM3  CM2  HCM2  109.10  3.000
 HMH  HCM3  CM2  HCM1  108.22  3.000
 HMH  HCM2  CM2  HCM1  107.12  3.000
 HMH  HCM3  CM2  C2A   111.09  3.000
 HMH  HCM2  CM2  C2A   110.89  3.000
 HMH  HCM1  CM2  C2A   110.29  3.000
 HMH  C6A   N1A  C2A   116.20  3.000
 HMH  N3A   C2A  N1A   125.47  3.000
 HMH  N3A   C2A  CM2   116.56  3.000
 HMH  N1A   C2A  CM2   117.97  3.000
 HMH  C4A   N3A  C2A   118.18  3.000
 HMH  C5A   C4A  N4A   121.53  3.000
 HMH  C5A   C4A  N3A   121.11  3.000
 HMH  N4A   C4A  N3A   117.34  3.000
 HMH  HN42  N4A  HN41  115.44  3.000
 HMH  HN42  N4A  C4A   120.86  3.000
 HMH  HN41  N4A  C4A   118.05  3.000
 HMH  C7A   C5A  C6A   123.94  3.000
 HMH  C7A   C5A  C4A   120.90  3.000
 HMH  C6A   C5A  C4A   115.17  3.000
 HMH  HC6   C6A  C5A   120.21  3.000
 HMH  HC6   C6A  N1A   115.92  3.000
 HMH  C5A   C6A  N1A   123.87  3.000
 HMH  HC72  C7A  HC71  106.13  3.000
 HMH  HC72  C7A  O1    111.50  3.000
 HMH  HC71  C7A  O1    111.38  3.000
 HMH  HC72  C7A  C5A   108.96  3.000
 HMH  HC71  C7A  C5A   109.04  3.000
 HMH  O1    C7A  C5A   109.73  3.000
 HMH  HO1   O1   C7A   107.93  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
 HMH  CONST_01  C4A   N3A  C2A  N1A    0.00   0.0  0
 HMH  CONST_02  C4A   C5A  C6A  N1A    0.00   0.0  0
 HMH  CONST_03  C5A   C6A  N1A  C2A    0.00   0.0  0
 HMH  CONST_04  C5A   C4A  N3A  C2A    0.00   0.0  0
 HMH  CONST_05  C6A   N1A  C2A  N3A    0.00   0.0  0
 HMH  CONST_06  C6A   C5A  C4A  N3A    0.00   0.0  0
 HMH  CONST_07  C6A   N1A  C2A  CM2  180.00   0.0  0
 HMH  CONST_08  C4A   N3A  C2A  CM2  180.00   0.0  0
 HMH  CONST_09  C7A   C5A  C6A  N1A  180.00   0.0  0
 HMH  CONST_10  N4A   C4A  N3A  C2A  180.00   0.0  0
 HMH  CONST_11  C7A   C5A  C4A  N3A  180.00   0.0  0
 HMH  CONST_12  C6A   C5A  C4A  N4A  180.00   0.0  0
 HMH  CONST_13  HC6   C6A  N1A  C2A  180.00   0.0  0
 HMH  CONST_14  HN41  N4A  C4A  N3A    0.00   0.0  0
 HMH  Var_01    O1    C7A  C5A  C4A  178.28  30.0  2
 HMH  Var_02    HCM1  CM2  C2A  N1A  108.51  30.0  2

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
 HMH  plan-1  CM2   0.020
 HMH  plan-1  N1A   0.020
 HMH  plan-1  C2A   0.020
 HMH  plan-1  N3A   0.020
 HMH  plan-1  C4A   0.020
 HMH  plan-1  N4A   0.020
 HMH  plan-1  C5A   0.020
 HMH  plan-1  C6A   0.020
 HMH  plan-1  C7A   0.020
 HMH  plan-1  HC6   0.020
 HMH  plan-2  C4A   0.020
 HMH  plan-2  N4A   0.020
 HMH  plan-2  HN41  0.020
 HMH  plan-2  HN42  0.020

