# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 23:16:03 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@]1(C[C@H]1[C@H](N)C(O)=O)C(O)=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
 M7V  M7V  '(1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid'  ligand  30  15  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M7V
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
 M7V  C10  C  CH3    0  -0.662  -4.5706  -1.9191   0.7690
 M7V  C01  C  CH1    0  -0.221   0.7155  -0.2422  -0.6737
 M7V  C02  C  CH2    0  -0.492   0.5771   0.7690  -1.7806
 M7V  C03  C  CT     0  -0.070  -0.4369   0.7053  -0.6824
 M7V  C04  C  CH2    0  -0.433  -1.7960   0.1327  -1.0471
 M7V  C05  C  C      0   0.402  -0.5261   1.8349   0.3408
 M7V  C06  C  CH1    0  -0.203   1.8482  -0.1369   0.3385
 M7V  C07  C  C      0   0.390   2.9335  -1.1836  -0.0181
 M7V  C08  C  CH2    0  -0.400  -2.5060  -0.6148   0.0756
 M7V  C09  C  CH2    0  -0.420  -3.8614  -1.1670  -0.3487
 M7V  N01  N  NH2    0  -0.801   2.3656   1.2187   0.4429
 M7V  O01  O  O      0  -0.608   4.0622  -0.7622  -0.3481
 M7V  O02  O  OC    -1  -0.623   2.5851  -2.3810   0.0397
 M7V  O03  O  OC    -1  -0.626  -0.6300   2.9979  -0.1020
 M7V  O04  O  O      0  -0.618  -0.5770   1.5027   1.5438
 M7V  H1   H  HCH3   0   0.223  -5.5506  -2.2807   0.4546
 M7V  H2   H  HCH3   0   0.214  -3.9888  -2.7851   1.0910
 M7V  H3   H  HCH3   0   0.214  -4.7178  -1.2817   1.6432
 M7V  H6   H  HCH2   0   0.211   0.2955   0.4246  -2.7709
 M7V  H7   H  HCH2   0   0.204  -2.4402   0.9450  -1.4067
 M7V  H8   H  HCH2   0   0.200  -1.6741  -0.5483  -1.8979
 M7V  H9   H  HCH1   0   0.206   1.4279  -0.4270   1.3062
 M7V  H10  H  HCH2   0   0.200  -1.8709  -1.4400   0.4170
 M7V  H11  H  HCH2   0   0.212  -2.6319   0.0443   0.9371
 M7V  H12  H  HCH2   0   0.205  -3.7318  -1.8322  -1.2085
 M7V  H13  H  HCH2   0   0.206  -4.4941  -0.3443  -0.6980
 M7V  H14  H  HNH2   0   0.331   2.5069   1.4520   1.4153
 M7V  H15  H  HNH2   0   0.324   3.2868   1.2119   0.0192
 M7V  H4   H  HCH1   0   0.212   0.4680  -1.2690  -0.9302
 M7V  H5   H  HCH2   0   0.223   1.2656   1.6042  -1.7745

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
 M7V  C10  C09  single  1.523  0.020  1.523
 M7V  C09  C08  single  1.524  0.020  1.524
 M7V  C08  C04  single  1.524  0.020  1.524
 M7V  C04  C03  single  1.519  0.020  1.519
 M7V  O04  C05  deloc   1.249  0.020  1.249
 M7V  C03  C05  single  1.527  0.020  1.527
 M7V  C03  C02  single  1.496  0.020  1.496
 M7V  C03  C01  single  1.492  0.020  1.492
 M7V  C05  O03  deloc   1.249  0.020  1.249
 M7V  C02  C01  single  1.506  0.020  1.506
 M7V  C01  C06  single  1.523  0.020  1.523
 M7V  O01  C07  deloc   1.249  0.020  1.249
 M7V  C06  C07  single  1.549  0.020  1.549
 M7V  C06  N01  single  1.455  0.020  1.455
 M7V  C07  O02  deloc   1.248  0.020  1.248
 M7V  C10  H1   single  0.970  0.020  1.090
 M7V  C10  H2   single  0.970  0.020  1.090
 M7V  C10  H3   single  0.970  0.020  1.090
 M7V  C01  H4   single  0.970  0.020  1.090
 M7V  C02  H5   single  0.970  0.020  1.090
 M7V  C02  H6   single  0.970  0.020  1.090
 M7V  C04  H7   single  0.970  0.020  1.090
 M7V  C04  H8   single  0.970  0.020  1.090
 M7V  C06  H9   single  0.970  0.020  1.090
 M7V  C08  H10  single  0.970  0.020  1.090
 M7V  C08  H11  single  0.970  0.020  1.090
 M7V  C09  H12  single  0.970  0.020  1.090
 M7V  C09  H13  single  0.970  0.020  1.090
 M7V  N01  H14  single  0.890  0.020  1.040
 M7V  N01  H15  single  0.890  0.020  1.040

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
 M7V  H3   C10  H2   107.38  3.000
 M7V  H3   C10  H1   107.65  3.000
 M7V  H2   C10  H1   107.51  3.000
 M7V  H3   C10  C09  111.24  3.000
 M7V  H2   C10  C09  111.10  3.000
 M7V  H1   C10  C09  111.75  3.000
 M7V  H4   C01  C06  113.06  3.000
 M7V  H4   C01  C03  115.00  3.000
 M7V  C06  C01  C03  122.31  3.000
 M7V  H4   C01  C02  116.10  3.000
 M7V  C06  C01  C02  120.71  3.000
 M7V  C03  C01  C02   59.88  3.000
 M7V  H6   C02  H5   114.51  3.000
 M7V  H6   C02  C03  118.70  3.000
 M7V  H5   C02  C03  117.38  3.000
 M7V  H6   C02  C01  118.78  3.000
 M7V  H5   C02  C01  117.10  3.000
 M7V  C03  C02  C01   59.61  3.000
 M7V  C05  C03  C04  112.80  3.000
 M7V  C05  C03  C02  120.00  3.000
 M7V  C04  C03  C02  116.49  3.000
 M7V  C02  C03  C01   60.51  3.000
 M7V  C05  C03  C01  120.74  3.000
 M7V  C04  C03  C01  116.94  3.000
 M7V  H8   C04  H7   105.71  3.000
 M7V  H8   C04  C08  108.58  3.000
 M7V  H7   C04  C08  109.33  3.000
 M7V  H8   C04  C03  108.72  3.000
 M7V  H7   C04  C03  108.95  3.000
 M7V  C08  C04  C03  115.13  3.000
 M7V  O04  C05  O03  125.86  3.000
 M7V  O03  C05  C03  117.15  3.000
 M7V  O04  C05  C03  116.81  3.000
 M7V  H9   C06  N01  108.68  3.000
 M7V  H9   C06  C07  107.07  3.000
 M7V  N01  C06  C07  113.38  3.000
 M7V  H9   C06  C01  106.49  3.000
 M7V  N01  C06  C01  112.13  3.000
 M7V  C07  C06  C01  108.74  3.000
 M7V  O02  C07  O01  126.01  3.000
 M7V  O02  C07  C06  116.22  3.000
 M7V  O01  C07  C06  117.77  3.000
 M7V  H11  C08  H10  105.99  3.000
 M7V  H11  C08  C09  109.62  3.000
 M7V  H10  C08  C09  109.24  3.000
 M7V  H11  C08  C04  109.80  3.000
 M7V  H10  C08  C04  109.20  3.000
 M7V  C09  C08  C04  112.77  3.000
 M7V  H13  C09  H12  105.92  3.000
 M7V  H13  C09  C08  109.30  3.000
 M7V  H12  C09  C08  109.48  3.000
 M7V  H13  C09  C10  109.64  3.000
 M7V  H12  C09  C10  109.36  3.000
 M7V  C08  C09  C10  112.89  3.000
 M7V  H15  N01  H14  106.07  3.000
 M7V  H15  N01  C06  106.68  3.000
 M7V  H14  N01  C06  109.52  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
 M7V  Var_01  C04  C03  C02  C01  -107.44  30.0  1
 M7V  Var_02  C06  C01  C03  C02   109.37  30.0  1
 M7V  Var_03  C08  C04  C03  C01    79.41  30.0  1
 M7V  Var_04  O04  C05  C03  C01   -60.86  30.0  3
 M7V  Var_05  C09  C08  C04  C03  -179.94  30.0  1
 M7V  Var_06  C04  C08  C09  C10   179.77  30.0  3
 M7V  Var_07  H1   C10  C09  C08   178.32  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
 M7V  chir_03  C06  C01  C07  N01  negativ
 M7V  chir_04  C01  C03  C02  C06  both
 M7V  chir_05  C03  C05  C02  C01  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
 M7V  plan-1  C03  0.020
 M7V  plan-1  C05  0.020
 M7V  plan-1  O03  0.020
 M7V  plan-1  O04  0.020
 M7V  plan-2  C06  0.020
 M7V  plan-2  C07  0.020
 M7V  plan-2  O01  0.020
 M7V  plan-2  O02  0.020

