# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:34:42 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: N-[(1R)-1-methylhexyl]formamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@@H](C)NC=O
#
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
 NMH  NMH  N-[(1R)-1-methylhexyl]formamide  ligand  27  10  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NMH
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
 NMH  C7    C  CH3   0  -0.663   0.3167   0.0819   4.8636
 NMH  C6    C  CH2   0  -0.418   0.7338  -0.2015   3.4273
 NMH  C5    C  CH2   0  -0.407  -0.3826   0.0579   2.4227
 NMH  C4    C  CH2   0  -0.410   0.0364  -0.2119   0.9832
 NMH  C3    C  CH2   0  -0.434  -1.0850   0.0367  -0.0180
 NMH  C2    C  CH1   0  -0.086  -0.6878  -0.2199  -1.4685
 NMH  C1    C  CH3   0  -0.644  -1.8785  -0.1148  -2.4150
 NMH  N     N  NH1   0  -0.579   0.3675   0.7031  -1.8565
 NMH  C     C  C1    0   0.251   1.3438   0.4234  -2.7231
 NMH  O     O  O     0  -0.504   1.5163  -0.6482  -3.2825
 NMH  HC71  H  HCH3  0   0.226   1.1286  -0.1180   5.5638
 NMH  HC72  H  HCH3  0   0.216   0.0199   1.1248   4.9905
 NMH  HC73  H  HCH3  0   0.216  -0.5320  -0.5384   5.1581
 NMH  HC61  H  HCH2  0   0.210   1.6009   0.4137   3.1676
 NMH  HC62  H  HCH2  0   0.211   1.0636  -1.2411   3.3397
 NMH  HC51  H  HCH2  0   0.208  -1.2488  -0.5628   2.6774
 NMH  HC52  H  HCH2  0   0.208  -0.7173   1.0970   2.5156
 NMH  HC41  H  HCH2  0   0.214   0.8994   0.4140   0.7358
 NMH  HC42  H  HCH2  0   0.212   0.3764  -1.2491   0.8907
 NMH  HC31  H  HCH2  0   0.232  -1.9337  -0.6105   0.2205
 NMH  HC32  H  HCH2  0   0.219  -1.4527   1.0652   0.0804
 NMH  HC2   H  HCH1  0   0.241  -0.2729  -1.2285  -1.5393
 NMH  HC11  H  HCH3  0   0.221  -2.3199   0.8829  -2.3787
 NMH  HC12  H  HCH3  0   0.235  -1.5790  -0.3177  -3.4434
 NMH  HC13  H  HCH3  0   0.228  -2.6512  -0.8341  -2.1409
 NMH  HN'   H  HNH1  0   0.400   0.3164   1.6491  -1.5100
 NMH  HC'   H  H     0   0.199   2.0086   1.2860  -2.8845

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
 NMH  C7  C6    single  1.522  0.020  1.522
 NMH  C7  HC71  single  0.970  0.020  1.090
 NMH  C7  HC72  single  0.970  0.020  1.090
 NMH  C7  HC73  single  0.970  0.020  1.090
 NMH  C6  C5    single  1.524  0.020  1.524
 NMH  C6  HC61  single  0.970  0.020  1.090
 NMH  C6  HC62  single  0.970  0.020  1.090
 NMH  C5  C4    single  1.523  0.020  1.523
 NMH  C5  HC51  single  0.970  0.020  1.090
 NMH  C5  HC52  single  0.970  0.020  1.090
 NMH  C4  C3    single  1.524  0.020  1.524
 NMH  C4  HC41  single  0.970  0.020  1.090
 NMH  C4  HC42  single  0.970  0.020  1.090
 NMH  C3  C2    single  1.526  0.020  1.526
 NMH  C3  HC31  single  0.970  0.020  1.090
 NMH  C3  HC32  single  0.970  0.020  1.090
 NMH  C2  C1    single  1.525  0.020  1.525
 NMH  C2  N     single  1.455  0.020  1.455
 NMH  C2  HC2   single  0.970  0.020  1.090
 NMH  C1  HC11  single  0.970  0.020  1.090
 NMH  C1  HC12  single  0.970  0.020  1.090
 NMH  C1  HC13  single  0.970  0.020  1.090
 NMH  N   C     single  1.335  0.020  1.335
 NMH  N   HN'   single  0.860  0.020  1.020
 NMH  C   O     double  1.221  0.020  1.221
 NMH  C   HC'   single  0.930  0.020  1.080

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
 NMH  HC73  C7  HC72  107.46  3.000
 NMH  HC73  C7  HC71  107.54  3.000
 NMH  HC72  C7  HC71  107.63  3.000
 NMH  HC73  C7  C6    111.21  3.000
 NMH  HC72  C7  C6    111.23  3.000
 NMH  HC71  C7  C6    111.57  3.000
 NMH  HC62  C6  HC61  106.04  3.000
 NMH  HC62  C6  C5    109.25  3.000
 NMH  HC61  C6  C5    109.16  3.000
 NMH  HC62  C6  C7    109.58  3.000
 NMH  HC61  C6  C7    109.65  3.000
 NMH  C5    C6  C7    112.93  3.000
 NMH  HC52  C5  HC51  106.02  3.000
 NMH  HC52  C5  C4    109.40  3.000
 NMH  HC51  C5  C4    109.68  3.000
 NMH  HC52  C5  C6    109.23  3.000
 NMH  HC51  C5  C6    109.23  3.000
 NMH  C4    C5  C6    113.03  3.000
 NMH  HC42  C4  HC41  106.12  3.000
 NMH  HC42  C4  C3    109.11  3.000
 NMH  HC41  C4  C3    109.79  3.000
 NMH  HC42  C4  C5    109.44  3.000
 NMH  HC41  C4  C5    109.22  3.000
 NMH  C3    C4  C5    112.93  3.000
 NMH  HC32  C3  HC31  105.98  3.000
 NMH  HC32  C3  C2    109.29  3.000
 NMH  HC31  C3  C2    108.05  3.000
 NMH  HC32  C3  C4    109.92  3.000
 NMH  HC31  C3  C4    109.35  3.000
 NMH  C2    C3  C4    113.93  3.000
 NMH  HC2   C2  N     107.03  3.000
 NMH  HC2   C2  C1    108.66  3.000
 NMH  N     C2  C1    110.93  3.000
 NMH  HC2   C2  C3    108.40  3.000
 NMH  N     C2  C3    109.61  3.000
 NMH  C1    C2  C3    112.04  3.000
 NMH  HC13  C1  HC12  108.00  3.000
 NMH  HC13  C1  HC11  107.94  3.000
 NMH  HC12  C1  HC11  108.21  3.000
 NMH  HC13  C1  C2    110.59  3.000
 NMH  HC12  C1  C2    110.99  3.000
 NMH  HC11  C1  C2    110.99  3.000
 NMH  HN'   N   C     117.15  3.000
 NMH  HN'   N   C2    117.82  3.000
 NMH  C     N   C2    124.80  3.000
 NMH  HC'   C   O     122.35  3.000
 NMH  HC'   C   N     111.89  3.000
 NMH  O     C   N     125.77  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
 NMH  CONST_01  O     C   N   C2    0.00   0.0  0
 NMH  CONST_02  HN'   N   C   O   180.00   0.0  0
 NMH  Var_01    C4    C5  C6  C7  179.44  30.0  3
 NMH  Var_02    C3    C4  C5  C6  179.51  30.0  3
 NMH  Var_03    C2    C3  C4  C5  179.71  30.0  3
 NMH  Var_04    HC71  C7  C6  C5  179.57  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
 NMH  chir_01  C2  C3  C1  N  negativ

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
 NMH  plan-1  C2   0.020
 NMH  plan-1  N    0.020
 NMH  plan-1  C    0.020
 NMH  plan-1  O    0.020
 NMH  plan-1  HN'  0.020
 NMH  plan-1  HC'  0.020

