# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:37:05 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: N-(cyclopropylmethyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNCC1CC1
#
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
 NMC  NMC  N-(cyclopropylmethyl)glycine  L-peptide  19  9  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_NMC
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
 NMC  N     N  NH1    0  -0.584  17.2725  24.3956  45.7592
 NMC  CA    C  CH2    0  -0.428  18.2592  23.4056  45.3695
 NMC  C     C  C      0   0.406  18.7263  22.4152  46.4586
 NMC  O     O  O      0  -0.612  17.9708  22.2525  47.4388
 NMC  CN    C  CH2    0  -0.301  17.8280  25.6000  46.3481
 NMC  CX1   C  CH1    0  -0.239  18.6969  25.4434  47.5767
 NMC  CX2   C  CH2    0  -0.500  19.6377  26.5511  47.9427
 NMC  CX3   C  CH2    0  -0.476  20.1733  25.2416  47.4445
 NMC  OXT   O  OC    -1  -0.621  19.7946  21.8132  46.2279
 NMC  H     H  HNH1   0   0.323  16.6564  23.9561  46.4334
 NMC  HA1   H  HCH2   0   0.216  17.8427  22.7959  44.5552
 NMC  HA2   H  HCH2   0   0.210  19.1242  23.9145  44.9368
 NMC  HCN1  H  HCH2   0   0.203  18.4097  26.1211  45.5781
 NMC  HCN2  H  HCH2   0   0.219  16.9909  26.2621  46.5915
 NMC  HCX1  H  HCH1   0   0.236  18.2213  24.9307  48.4059
 NMC  HC21  H  HCH2   0   0.233  19.6945  27.4071  47.2795
 NMC  HC22  H  HCH2   0   0.240  19.7667  26.7958  48.9894
 NMC  HC31  H  HCH2   0   0.239  20.6712  24.5879  48.1494
 NMC  HC32  H  HCH2   0   0.235  20.5922  25.2148  46.4458

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
 NMC  N    CA    single  1.451  0.016  1.451
 NMC  N    CN    single  1.451  0.020  1.451
 NMC  N    H     single  0.860  0.020  0.860
 NMC  CA   C     single  1.516  0.018  1.516
 NMC  CA   HA1   single  0.970  0.020  1.090
 NMC  CA   HA2   single  0.970  0.020  1.090
 NMC  C    O     deloc   1.231  0.020  1.231
 NMC  C    OXT   deloc   1.248  0.020  1.248
 NMC  CN   CX1   single  1.513  0.020  1.513
 NMC  CN   HCN1  single  0.970  0.020  1.090
 NMC  CN   HCN2  single  0.970  0.020  1.090
 NMC  CX1  CX2   single  1.499  0.020  1.499
 NMC  CX1  CX3   single  1.496  0.020  1.496
 NMC  CX1  HCX1  single  0.970  0.020  1.090
 NMC  CX2  CX3   single  1.500  0.020  1.500
 NMC  CX2  HC21  single  0.970  0.020  1.090
 NMC  CX2  HC22  single  0.970  0.020  1.090
 NMC  CX3  HC31  single  0.970  0.020  1.090
 NMC  CX3  HC32  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
 NMC  H     N    CN    108.82  3.000
 NMC  H     N    CA    114.00  3.000
 NMC  CN    N    CA    114.52  3.000
 NMC  HA2   CA   HA1   105.36  3.000
 NMC  HA2   CA   C     109.78  3.000
 NMC  HA1   CA   C     106.34  3.000
 NMC  HA2   CA   N     109.07  3.000
 NMC  HA1   CA   N     108.65  3.000
 NMC  C     CA   N     113.30  2.900
 NMC  OXT   C    O     126.91  3.000
 NMC  OXT   C    CA    115.97  3.000
 NMC  O     C    CA    120.80  2.100
 NMC  HCN2  CN   HCN1  105.92  3.000
 NMC  HCN2  CN   CX1   108.74  3.000
 NMC  HCN1  CN   CX1   108.34  3.000
 NMC  HCN2  CN   N     107.42  3.000
 NMC  HCN1  CN   N     108.21  3.000
 NMC  CX1   CN   N     117.61  3.000
 NMC  HCX1  CX1  CX3   115.88  3.000
 NMC  HCX1  CX1  CX2   115.97  3.000
 NMC  CX3   CX1  CX2    60.11  3.000
 NMC  HCX1  CX1  CN    114.70  3.000
 NMC  CX3   CX1  CN    120.60  3.000
 NMC  CX2   CX1  CN    118.84  3.000
 NMC  HC22  CX2  HC21  114.00  3.000
 NMC  HC22  CX2  CX3   118.41  3.000
 NMC  HC21  CX2  CX3   117.86  3.000
 NMC  HC22  CX2  CX1   118.55  3.000
 NMC  HC21  CX2  CX1   117.84  3.000
 NMC  CX3   CX2  CX1    59.85  3.000
 NMC  HC32  CX3  HC31  114.05  3.000
 NMC  HC32  CX3  CX2   117.76  3.000
 NMC  HC31  CX3  CX2   118.37  3.000
 NMC  HC32  CX3  CX1   117.80  3.000
 NMC  HC31  CX3  CX1   118.54  3.000
 NMC  CX2   CX3  CX1    60.03  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
 NMC  Var_01  CX3   CX2  CX1  CN   -110.72  30.0  1
 NMC  Var_02  HC31  CX3  CX2  CX1  -108.39  30.0  1
 NMC  Var_03  CX2   CX1  CN   N     159.97  30.0  3
 NMC  Var_04  CX1   CN   N    CA    -57.31  30.0  3
 NMC  Var_05  O     C    CA   N      21.29  30.0  3
 NMC  Var_06  CN    N    CA   C      85.89  30.0  1

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
 NMC  chir_01  CX1  CN  CX2  CX3  both

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
 NMC  plan-1  CA   0.020
 NMC  plan-1  C    0.020
 NMC  plan-1  O    0.020
 NMC  plan-1  OXT  0.020

