# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:00:14 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-[(cyclopropylcarbonyl)amino]-N-(4-methoxypyridin-3-yl)pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccncc1NC(=O)c2ccnc(NC(=O)C3CC3)c2
#
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
 3UO  3UO  2-[(cyclopropylcarbonyl)amino]-N-(4-methoxypyridin-3-yl)pyridine-4-carboxamide  ligand  39  23  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3UO
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
 3UO  C1   C  CR6   0   0.067  -0.0888   0.0158   0.9100
 3UO  C2   C  CR16  0  -0.435  -1.2462   0.4582   0.3008
 3UO  C3   C  CR6   0   0.552  -2.4536  -0.1781   0.6095
 3UO  N4   N  N     0  -0.417  -2.5368  -1.1721   1.4767
 3UO  C5   C  CR16  0  -0.050  -1.4179  -1.5799   2.0642
 3UO  C6   C  CR16  0  -0.388  -0.1711  -1.0340   1.8231
 3UO  C7   C  C     0   0.534   1.1933   0.7150   0.5761
 3UO  N8   N  NH1   0  -0.750  -3.5957   0.2861  -0.0270
 3UO  N9   N  NH1   0  -0.745   2.3102  -0.0351   0.7251
 3UO  O10  O  O     0  -0.448   1.2009   1.8704   0.1964
 3UO  C11  C  C     0   0.588  -4.8675  -0.2246  -0.0241
 3UO  C12  C  CH1   0  -0.445  -5.8116   0.5739  -0.8499
 3UO  O13  O  O     0  -0.451  -5.2051  -1.2210   0.5807
 3UO  C14  C  CH2   0  -0.462  -6.9379  -0.1558  -1.5349
 3UO  C15  C  CH2   0  -0.463  -7.2330   0.7033  -0.3630
 3UO  C16  C  CR6   0   0.176   3.6010   0.4270   0.4250
 3UO  C17  C  CR16  0  -0.095   4.1080   1.5918   0.9769
 3UO  N18  N  N     0  -0.415   5.3186   2.0690   0.7132
 3UO  C19  C  CR16  0  -0.070   6.0810   1.3680  -0.1146
 3UO  C20  C  CR16  0  -0.441   5.6917   0.1802  -0.7125
 3UO  C21  C  CR6   0   0.438   4.4162  -0.3079  -0.4483
 3UO  O22  O  O2    0  -0.452   3.8991  -1.4254  -0.9534
 3UO  C23  C  CH3   0  -0.441   4.7079  -2.2286  -1.8005
 3UO  H1   H  HCR6  0   0.287  -1.2186   1.2742  -0.4094
 3UO  H2   H  HCR6  0   0.273  -1.5223  -2.3887   2.7778
 3UO  H3   H  HCR6  0   0.278   0.6871  -1.4082   2.3638
 3UO  H4   H  HNH1  0   0.424  -3.4537   1.1001  -0.6050
 3UO  H5   H  HNH1  0   0.421   2.2032  -1.0266   0.8794
 3UO  H6   H  HCH1  0   0.286  -5.4006   1.4301  -1.3717
 3UO  H7   H  HCH2  0   0.267  -7.2133   0.1960  -2.5197
 3UO  H8   H  HCH2  0   0.260  -6.9817  -1.2292  -1.4053
 3UO  H9   H  HCH2  0   0.261  -7.4809   0.2238   0.5748
 3UO  H10  H  HCH2  0   0.266  -7.7130   1.6586  -0.5273
 3UO  H11  H  HCR6  0   0.275   3.5006   2.1590   1.6725
 3UO  H12  H  HCR6  0   0.269   7.0700   1.7625  -0.3185
 3UO  H13  H  HCR6  0   0.297   6.3779  -0.3284  -1.3747
 3UO  H14  H  HCH3  0   0.240   4.9888  -1.6933  -2.7094
 3UO  H15  H  HCH3  0   0.241   5.6099  -2.5676  -1.2880
 3UO  H16  H  HCH3  0   0.269   4.1055  -3.0919  -2.0682

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
 3UO  C5   N4   aromatic  1.328  0.020  1.328
 3UO  C5   C6   aromatic  1.382  0.020  1.382
 3UO  N4   C3   aromatic  1.322  0.020  1.322
 3UO  C6   C1   aromatic  1.394  0.020  1.394
 3UO  C3   N8   single    1.387  0.020  1.387
 3UO  C3   C2   aromatic  1.399  0.020  1.399
 3UO  C1   C2   aromatic  1.381  0.020  1.381
 3UO  C1   C7   single    1.498  0.020  1.498
 3UO  N8   C11  single    1.370  0.020  1.370
 3UO  O10  C7   double    1.216  0.020  1.216
 3UO  C7   N9   single    1.354  0.020  1.354
 3UO  C12  C11  single    1.487  0.020  1.487
 3UO  C12  C14  single    1.507  0.020  1.507
 3UO  C12  C15  single    1.508  0.020  1.508
 3UO  C11  O13  double    1.214  0.020  1.214
 3UO  C14  C15  single    1.483  0.020  1.483
 3UO  N9   C16  single    1.404  0.020  1.404
 3UO  C17  C16  aromatic  1.385  0.020  1.385
 3UO  C17  N18  aromatic  1.328  0.020  1.328
 3UO  C16  C21  aromatic  1.403  0.020  1.403
 3UO  N18  C19  aromatic  1.326  0.020  1.326
 3UO  C21  O22  single    1.331  0.020  1.331
 3UO  C21  C20  aromatic  1.391  0.020  1.391
 3UO  O22  C23  single    1.420  0.020  1.420
 3UO  C19  C20  aromatic  1.386  0.020  1.386
 3UO  C2   H1   single    0.930  0.020  1.080
 3UO  C5   H2   single    0.930  0.020  1.080
 3UO  C6   H3   single    0.930  0.020  1.080
 3UO  N8   H4   single    0.860  0.020  1.020
 3UO  N9   H5   single    0.860  0.020  1.020
 3UO  C12  H6   single    0.970  0.020  1.090
 3UO  C14  H7   single    0.970  0.020  1.090
 3UO  C14  H8   single    0.970  0.020  1.090
 3UO  C15  H9   single    0.970  0.020  1.090
 3UO  C15  H10  single    0.970  0.020  1.090
 3UO  C17  H11  single    0.930  0.020  1.080
 3UO  C19  H12  single    0.930  0.020  1.080
 3UO  C20  H13  single    0.930  0.020  1.080
 3UO  C23  H14  single    0.970  0.020  1.090
 3UO  C23  H15  single    0.970  0.020  1.090
 3UO  C23  H16  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
 3UO  C7   C1   C6   123.24  3.000
 3UO  C7   C1   C2   118.00  3.000
 3UO  C6   C1   C2   118.75  3.000
 3UO  H1   C2   C3   120.64  3.000
 3UO  H1   C2   C1   120.66  3.000
 3UO  C3   C2   C1   118.70  3.000
 3UO  N8   C3   N4   120.05  3.000
 3UO  N8   C3   C2   117.19  3.000
 3UO  N4   C3   C2   122.75  3.000
 3UO  C5   N4   C3   117.91  3.000
 3UO  H2   C5   C6   119.76  3.000
 3UO  H2   C5   N4   116.07  3.000
 3UO  C6   C5   N4   124.17  3.000
 3UO  H3   C6   C5   119.48  3.000
 3UO  H3   C6   C1   122.78  3.000
 3UO  C5   C6   C1   117.71  3.000
 3UO  O10  C7   N9   123.76  3.000
 3UO  N9   C7   C1   115.02  3.000
 3UO  O10  C7   C1   121.22  3.000
 3UO  H4   N8   C11  115.64  3.000
 3UO  H4   N8   C3   114.65  3.000
 3UO  C11  N8   C3   129.66  3.000
 3UO  H5   N9   C16  116.98  3.000
 3UO  H5   N9   C7   118.28  3.000
 3UO  C16  N9   C7   123.56  3.000
 3UO  O13  C11  C12  122.76  3.000
 3UO  O13  C11  N8   124.42  3.000
 3UO  C12  C11  N8   112.82  3.000
 3UO  H6   C12  C15  116.43  3.000
 3UO  H6   C12  C14  116.57  3.000
 3UO  C15  C12  C14   58.92  3.000
 3UO  H6   C12  C11  116.81  3.000
 3UO  C15  C12  C11  117.72  3.000
 3UO  C14  C12  C11  117.84  3.000
 3UO  H8   C14  H7   114.93  3.000
 3UO  H8   C14  C15  118.17  3.000
 3UO  H7   C14  C15  118.72  3.000
 3UO  H8   C14  C12  117.14  3.000
 3UO  H7   C14  C12  116.53  3.000
 3UO  C15  C14  C12   60.59  3.000
 3UO  H10  C15  H9   114.92  3.000
 3UO  H10  C15  C14  118.68  3.000
 3UO  H9   C15  C14  118.28  3.000
 3UO  H10  C15  C12  116.42  3.000
 3UO  H9   C15  C12  117.24  3.000
 3UO  C14  C15  C12   60.49  3.000
 3UO  C21  C16  C17  118.42  3.000
 3UO  C21  C16  N9   119.68  3.000
 3UO  C17  C16  N9   121.89  3.000
 3UO  H11  C17  N18  116.77  3.000
 3UO  H11  C17  C16  119.39  3.000
 3UO  N18  C17  C16  123.84  3.000
 3UO  C19  N18  C17  117.28  3.000
 3UO  H12  C19  C20  119.15  3.000
 3UO  H12  C19  N18  116.72  3.000
 3UO  C20  C19  N18  124.13  3.000
 3UO  H13  C20  C21  122.23  3.000
 3UO  H13  C20  C19  119.30  3.000
 3UO  C21  C20  C19  118.46  3.000
 3UO  O22  C21  C20  125.37  3.000
 3UO  C20  C21  C16  117.86  3.000
 3UO  O22  C21  C16  116.77  3.000
 3UO  C23  O22  C21  118.68  3.000
 3UO  H16  C23  H15  109.10  3.000
 3UO  H16  C23  H14  109.10  3.000
 3UO  H15  C23  H14  109.31  3.000
 3UO  H16  C23  O22  106.30  3.000
 3UO  H15  C23  O22  111.48  3.000
 3UO  H14  C23  O22  111.46  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
 3UO  CONST_01  N4   C5   C6   C1      0.00   0.0  0
 3UO  CONST_02  N4   C3   C2   C1      0.00   0.0  0
 3UO  CONST_03  C5   N4   C3   C2      0.00   0.0  0
 3UO  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 3UO  CONST_05  C6   C5   N4   C3      0.00   0.0  0
 3UO  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 3UO  CONST_07  C19  N18  C17  C16     0.00   0.0  0
 3UO  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 3UO  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 3UO  CONST_10  C20  C19  N18  C17     0.00   0.0  0
 3UO  CONST_11  C21  C16  C17  N18     0.00   0.0  0
 3UO  CONST_12  C21  C20  C19  N18     0.00   0.0  0
 3UO  CONST_13  N8   C3   C2   C1    180.00   0.0  0
 3UO  CONST_14  C7   C1   C2   C3    180.00   0.0  0
 3UO  CONST_15  N8   C3   N4   C5    180.00   0.0  0
 3UO  CONST_16  C7   C1   C6   C5    180.00   0.0  0
 3UO  CONST_17  N18  C17  C16  N9    180.00   0.0  0
 3UO  CONST_18  C20  C21  C16  N9    180.00   0.0  0
 3UO  CONST_19  O22  C21  C16  C17   180.00   0.0  0
 3UO  CONST_20  O22  C21  C20  C19   180.00   0.0  0
 3UO  CONST_21  H2   C5   C6   C1    180.00   0.0  0
 3UO  CONST_22  H3   C6   C1   C2    180.00   0.0  0
 3UO  CONST_23  H1   C2   C3   N4    180.00   0.0  0
 3UO  CONST_24  H13  C20  C21  C16   180.00   0.0  0
 3UO  CONST_25  H12  C19  N18  C17   180.00   0.0  0
 3UO  CONST_26  H11  C17  N18  C19   180.00   0.0  0
 3UO  CONST_27  C16  N9   C7   C1    180.00   0.0  0
 3UO  CONST_28  C12  C11  N8   C3    180.00   0.0  0
 3UO  CONST_29  C11  N8   C3   C2    180.00   0.0  0
 3UO  CONST_30  C11  N8   C3   N4      0.00   0.0  0
 3UO  CONST_33  H4   N8   C3   C2      0.00   0.0  0
 3UO  CONST_35  O13  C11  N8   C3      0.00   0.0  0
 3UO  CONST_36  C16  N9   C7   O10     0.00   0.0  0
 3UO  Var_01    C15  C14  C12  C11   107.21  30.0  1
 3UO  Var_02    H9   C15  C14  C12  -107.03  30.0  1
 3UO  Var_03    O10  C7   C1   C2     25.72  30.0  2
 3UO  Var_04    C14  C12  C11  N8    148.11  30.0  2
 3UO  Var_05    H14  C23  O22  C21   -62.94  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
 3UO  chir_01  C12  C11  C14  C15  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
 3UO  plan-1  C1   0.020
 3UO  plan-1  C2   0.020
 3UO  plan-1  C3   0.020
 3UO  plan-1  N4   0.020
 3UO  plan-1  C5   0.020
 3UO  plan-1  C6   0.020
 3UO  plan-1  C7   0.020
 3UO  plan-1  N8   0.020
 3UO  plan-1  H1   0.020
 3UO  plan-1  H2   0.020
 3UO  plan-1  H3   0.020
 3UO  plan-2  N9   0.020
 3UO  plan-2  C16  0.020
 3UO  plan-2  C17  0.020
 3UO  plan-2  N18  0.020
 3UO  plan-2  C19  0.020
 3UO  plan-2  C20  0.020
 3UO  plan-2  C21  0.020
 3UO  plan-2  O22  0.020
 3UO  plan-2  H11  0.020
 3UO  plan-2  H12  0.020
 3UO  plan-2  H13  0.020
 3UO  plan-3  C3   0.020
 3UO  plan-3  N8   0.020
 3UO  plan-3  C11  0.020
 3UO  plan-3  C12  0.020
 3UO  plan-3  O13  0.020
 3UO  plan-3  H4   0.020
 3UO  plan-4  C1   0.020
 3UO  plan-4  C7   0.020
 3UO  plan-4  N9   0.020
 3UO  plan-4  O10  0.020
 3UO  plan-4  C16  0.020
 3UO  plan-4  H5   0.020

