# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:01:56 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc(CNCc2ccccc2)c1
#
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
 5V1  5V1  '2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid'  ligand  31  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V1
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
 5V1  N1   N  N      0  -0.426   1.5441   1.9455   0.2974
 5V1  C4   C  CR16   0  -0.078   2.6349   1.8821   1.0517
 5V1  C5   C  CR6    0   0.235   1.3327   0.9658  -0.5796
 5V1  C6   C  CH2    0  -0.321   0.0574   1.0484  -1.3714
 5V1  C7   C  CH2    0  -0.328  -2.3246   0.6584  -1.2514
 5V1  C8   C  CR6    0   0.099  -3.4343   0.0938  -0.4065
 5V1  C10  C  CR16   0  -0.243  -4.3884  -1.7568   0.8213
 5V1  C13  C  CR16   0  -0.316  -4.5332   0.8682  -0.0517
 5V1  O1   O  O      0  -0.584   4.0639  -2.1903  -0.9294
 5V1  C2   C  CR6    0   0.006   3.3502  -0.1746   0.0646
 5V1  C3   C  CR16   0  -0.362   3.5603   0.8536   0.9759
 5V1  N2   N  NH1    0  -0.586  -1.0507   0.5666  -0.5613
 5V1  C9   C  CR16   0  -0.286  -3.3711  -1.2248   0.0438
 5V1  C11  C  CR16   0  -0.270  -5.4855  -0.9748   1.1678
 5V1  C12  C  CR16   0  -0.240  -5.5552   0.3394   0.7298
 5V1  C14  C  CR16   0  -0.376   2.2083  -0.1038  -0.7234
 5V1  O2   O  OC    -1  -0.585   5.2980  -1.3303   0.7199
 5V1  H1   H  HCR6   0   0.255   2.7822   2.6956   1.7542
 5V1  H2   H  HCH2   0   0.210  -0.0855   2.0822  -1.7200
 5V1  H3   H  HCH2   0   0.236   0.1289   0.4187  -2.2617
 5V1  H4   H  HCH2   0   0.238  -2.2442   0.0801  -2.1778
 5V1  H5   H  HCH2   0   0.216  -2.5780   1.6857  -1.5535
 5V1  H6   H  HCR6   0   0.253  -4.3268  -2.7836   1.1589
 5V1  H7   H  HCR6   0   0.249  -4.5940   1.8966  -0.3887
 5V1  H8   H  HCR6   0   0.255   4.4311   0.8562   1.6165
 5V1  H9   H  HNH1   0   0.344  -1.0969   1.1236   0.2851
 5V1  H11  H  HCR6   0   0.246  -2.5183  -1.8382  -0.2210
 5V1  H12  H  HCR6   0   0.253  -6.2794  -1.3900   1.7752
 5V1  H13  H  HCR6   0   0.253  -6.4018   0.9580   0.9992
 5V1  H14  H  HCR6   0   0.251   1.9991  -0.8787  -1.4489
 5V1  C1   C  C      0   0.403   4.3301  -1.3406  -0.0610

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
 5V1  O1   C1   deloc     1.244  0.020  1.244
 5V1  C1   O2   deloc     1.244  0.020  1.244
 5V1  C1   C2   single    1.528  0.020  1.528
 5V1  C10  C9   aromatic  1.386  0.020  1.386
 5V1  C10  C11  aromatic  1.391  0.020  1.391
 5V1  C3   C2   aromatic  1.390  0.020  1.390
 5V1  C3   C4   aromatic  1.386  0.020  1.386
 5V1  C2   C14  aromatic  1.389  0.020  1.389
 5V1  C9   C8   aromatic  1.395  0.020  1.395
 5V1  C11  C12  aromatic  1.387  0.020  1.387
 5V1  C4   N1   aromatic  1.328  0.020  1.328
 5V1  C14  C5   aromatic  1.390  0.020  1.390
 5V1  C8   C7   single    1.505  0.020  1.505
 5V1  C8   C13  aromatic  1.390  0.020  1.390
 5V1  C12  C13  aromatic  1.391  0.020  1.391
 5V1  C7   N2   single    1.452  0.020  1.452
 5V1  N1   C5   aromatic  1.332  0.020  1.332
 5V1  C5   C6   single    1.503  0.020  1.503
 5V1  C6   N2   single    1.455  0.020  1.455
 5V1  C4   H1   single    0.930  0.020  1.080
 5V1  C6   H2   single    0.970  0.020  1.090
 5V1  C6   H3   single    0.970  0.020  1.090
 5V1  C7   H4   single    0.970  0.020  1.090
 5V1  C7   H5   single    0.970  0.020  1.090
 5V1  C10  H6   single    0.930  0.020  1.080
 5V1  C13  H7   single    0.930  0.020  1.080
 5V1  C3   H8   single    0.930  0.020  1.080
 5V1  N2   H9   single    0.890  0.020  1.040
 5V1  C9   H11  single    0.930  0.020  1.080
 5V1  C11  H12  single    0.930  0.020  1.080
 5V1  C12  H13  single    0.930  0.020  1.080
 5V1  C14  H14  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
 5V1  C5   N1   C4   117.99  3.000
 5V1  H1   C4   C3   120.08  3.000
 5V1  H1   C4   N1   116.34  3.000
 5V1  C3   C4   N1   123.58  3.000
 5V1  C14  C5   C6   121.48  3.000
 5V1  C6   C5   N1   116.17  3.000
 5V1  C14  C5   N1   122.30  3.000
 5V1  H3   C6   H2   106.96  3.000
 5V1  H3   C6   N2   108.22  3.000
 5V1  H2   C6   N2   112.87  3.000
 5V1  H3   C6   C5   109.99  3.000
 5V1  H2   C6   C5   109.18  3.000
 5V1  N2   C6   C5   109.55  3.000
 5V1  H5   C7   H4   106.13  3.000
 5V1  H5   C7   N2   113.05  3.000
 5V1  H4   C7   N2   107.72  3.000
 5V1  H5   C7   C8   109.55  3.000
 5V1  H4   C7   C8   109.33  3.000
 5V1  N2   C7   C8   110.88  3.000
 5V1  C9   C8   C13  118.68  3.000
 5V1  C13  C8   C7   121.14  3.000
 5V1  C9   C8   C7   120.17  3.000
 5V1  H6   C10  C11  120.02  3.000
 5V1  H6   C10  C9   119.80  3.000
 5V1  C11  C10  C9   120.17  3.000
 5V1  H7   C13  C12  119.61  3.000
 5V1  H7   C13  C8   119.57  3.000
 5V1  C12  C13  C8   120.82  3.000
 5V1  C14  C2   C3   117.29  3.000
 5V1  C14  C2   C1   121.28  3.000
 5V1  C3   C2   C1   121.43  3.000
 5V1  H8   C3   C2   120.80  3.000
 5V1  H8   C3   C4   120.25  3.000
 5V1  C2   C3   C4   118.95  3.000
 5V1  H9   N2   C7   108.78  3.000
 5V1  H9   N2   C6   108.51  3.000
 5V1  C7   N2   C6   112.50  3.000
 5V1  H11  C9   C10  119.83  3.000
 5V1  H11  C9   C8   119.47  3.000
 5V1  C10  C9   C8   120.70  3.000
 5V1  H12  C11  C12  120.25  3.000
 5V1  H12  C11  C10  120.17  3.000
 5V1  C12  C11  C10  119.58  3.000
 5V1  H13  C12  C11  120.14  3.000
 5V1  H13  C12  C13  119.81  3.000
 5V1  C11  C12  C13  120.05  3.000
 5V1  H14  C14  C2   120.19  3.000
 5V1  H14  C14  C5   119.92  3.000
 5V1  C2   C14  C5   119.89  3.000
 5V1  O2   C1   C2   116.17  3.000
 5V1  C2   C1   O1   116.19  3.000
 5V1  O2   C1   O1   127.64  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
 5V1  CONST_01  C2   C3   C4   N1      0.00   0.0  0
 5V1  CONST_02  C2   C14  C5   N1      0.00   0.0  0
 5V1  CONST_03  C14  C2   C3   C4      0.00   0.0  0
 5V1  CONST_04  C14  C5   N1   C4      0.00   0.0  0
 5V1  CONST_05  C3   C2   C14  C5      0.00   0.0  0
 5V1  CONST_06  C3   C4   N1   C5      0.00   0.0  0
 5V1  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 5V1  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 5V1  CONST_09  C13  C8   C9   C10     0.00   0.0  0
 5V1  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 5V1  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 5V1  CONST_12  C12  C13  C8   C9      0.00   0.0  0
 5V1  CONST_13  C1   C2   C3   C4    180.00   0.0  0
 5V1  CONST_14  C6   C5   N1   C4    180.00   0.0  0
 5V1  CONST_15  C1   C2   C14  C5    180.00   0.0  0
 5V1  CONST_16  C2   C14  C5   C6    180.00   0.0  0
 5V1  CONST_17  C10  C9   C8   C7    180.00   0.0  0
 5V1  CONST_18  C12  C13  C8   C7    180.00   0.0  0
 5V1  CONST_19  H8   C3   C4   N1    180.00   0.0  0
 5V1  CONST_20  H14  C14  C5   N1    180.00   0.0  0
 5V1  CONST_21  H1   C4   N1   C5    180.00   0.0  0
 5V1  CONST_22  H6   C10  C9   C8    180.00   0.0  0
 5V1  CONST_23  H13  C12  C13  C8    180.00   0.0  0
 5V1  CONST_24  H11  C9   C8   C13   180.00   0.0  0
 5V1  CONST_25  H12  C11  C12  C13   180.00   0.0  0
 5V1  CONST_26  H7   C13  C8   C9    180.00   0.0  0
 5V1  Var_01    N2   C6   C5   N1    -79.80  30.0  2
 5V1  Var_02    N2   C7   C8   C13   121.94  30.0  2
 5V1  Var_03    C3   C2   C1   O1   -178.36  30.0  2
 5V1  Var_04    C7   N2   C6   C5    178.16  30.0  3
 5V1  Var_05    C8   C7   N2   C6    177.42  30.0  1

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
 5V1  plan-1  C7   0.020
 5V1  plan-1  C8   0.020
 5V1  plan-1  C10  0.020
 5V1  plan-1  C13  0.020
 5V1  plan-1  C9   0.020
 5V1  plan-1  C11  0.020
 5V1  plan-1  C12  0.020
 5V1  plan-1  H6   0.020
 5V1  plan-1  H7   0.020
 5V1  plan-1  H11  0.020
 5V1  plan-1  H12  0.020
 5V1  plan-1  H13  0.020
 5V1  plan-2  N1   0.020
 5V1  plan-2  C4   0.020
 5V1  plan-2  C5   0.020
 5V1  plan-2  C6   0.020
 5V1  plan-2  C2   0.020
 5V1  plan-2  C3   0.020
 5V1  plan-2  C14  0.020
 5V1  plan-2  H1   0.020
 5V1  plan-2  H8   0.020
 5V1  plan-2  H14  0.020
 5V1  plan-2  C1   0.020
 5V1  plan-3  O1   0.020
 5V1  plan-3  C2   0.020
 5V1  plan-3  O2   0.020
 5V1  plan-3  C1   0.020

