# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:55:55 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-[5-chloro-3-(propan-2-yl)-1H-pyrazol-4-yl]-N-[5-(piperazin-1-yl)pyridin-2-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1n[nH]c(Cl)c1c2ccnc(Nc3ccc(cn3)N4CCNCC4)n2
#
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
 3NV  3NV  4-[5-chloro-3-(propan-2-yl)-1H-pyrazol-4-yl]-N-[5-(piperazin-1-yl)pyridin-2-yl]pyrimidin-2-amine  ligand  51  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3NV
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
 3NV  C1    C   CH2   0  -0.316   6.2713  -1.0855   0.3566
 3NV  N1    N   NT    0  -0.513   5.6764   0.1248  -0.1800
 3NV  CL1   CL  CL    0  -0.077  -5.9566  -2.5024  -0.5090
 3NV  C2    C   CH2   0  -0.321   7.7555  -1.1394   0.0152
 3NV  N2    N   NH1   0  -0.578   8.4962   0.0366   0.4349
 3NV  C3    C   CH2   0  -0.323   7.8574   1.2385  -0.0717
 3NV  N3    N   N     0  -0.413   2.1244  -0.6971   0.4119
 3NV  C4    C   CH2   0  -0.310   6.3766   1.3257   0.2675
 3NV  N4    N   NH1   0  -0.752   0.1389   0.3587  -0.2771
 3NV  C5    C   CR16  0  -0.158   3.4563  -0.7319   0.4403
 3NV  N5    N   NR15  0  -0.447  -6.5787   0.0339  -0.1039
 3NV  C6    C   CR6   0   0.265   4.2820   0.1979  -0.1856
 3NV  N6    N   N     0  -0.279  -6.1150   1.2470   0.1843
 3NV  C7    C   CR16  0  -0.208   3.6222   1.2283  -0.8740
 3NV  N7    N   N     0  -0.425  -0.5256  -1.7820   0.4021
 3NV  C8    C   CR16  0  -0.388   2.2503   1.2722  -0.9076
 3NV  N8    N   N     0  -0.488  -2.0684  -0.0377  -0.0401
 3NV  C9    C   CR6   0   0.485   1.5240   0.2713  -0.2449
 3NV  C10   C   CR5   0  -0.118  -4.4223  -0.2442   0.1668
 3NV  C11   C   CR5   0   0.270  -5.6132  -0.8859  -0.1190
 3NV  C12   C   CR5   0   0.325  -4.8144   1.1136   0.3434
 3NV  C13   C   CH1   0  -0.316  -3.9592   2.3060   0.6576
 3NV  C14   C   CH3   0  -0.650  -3.4666   2.9581  -0.6359
 3NV  C15   C   CH3   0  -0.648  -4.6954   3.3172   1.5327
 3NV  C16   C   CR6   0   0.244  -3.0887  -0.8247   0.2714
 3NV  C17   C   CR16  0  -0.393  -2.8688  -2.1391   0.6923
 3NV  C18   C   CR16  0  -0.020  -1.5541  -2.5575   0.7208
 3NV  C19   C   CR6   0   0.575  -0.8347  -0.5394   0.0544
 3NV  H1    H   HCH2  0   0.207   6.1495  -1.1518   1.4505
 3NV  H1A   H   HCH2  0   0.247   5.7736  -1.9556  -0.0768
 3NV  H2    H   HCH2  0   0.242   8.1944  -2.0263   0.4756
 3NV  H2A   H   HCH2  0   0.224   7.8686  -1.2494  -1.0677
 3NV  HN2   H   HNH1  0   0.341   8.5061   0.0732   1.4486
 3NV  H3    H   HCH2  0   0.241   8.3682   2.1161   0.3286
 3NV  H3A   H   HCH2  0   0.224   7.9785   1.2630  -1.1591
 3NV  H4    H   HCH2  0   0.250   5.9514   2.2080  -0.2106
 3NV  H4A   H   HCH2  0   0.211   6.2576   1.4593   1.3548
 3NV  HN4   H   HNH1  0   0.410  -0.2328   1.2295  -0.6243
 3NV  H5    H   HCR6  0   0.263   3.8771  -1.5569   1.0026
 3NV  H7    H   HCR6  0   0.276   4.1853   1.9864  -1.4027
 3NV  H8    H   HCR6  0   0.275   1.7429   2.0614  -1.4479
 3NV  H13   H   HCH1  0   0.243  -3.0831   1.9502   1.2033
 3NV  H14   H   HCH3  0   0.217  -4.3029   3.3584  -1.2122
 3NV  H14A  H   HCH3  0   0.226  -2.7875   3.7826  -0.4128
 3NV  H14B  H   HCH3  0   0.237  -2.9317   2.2409  -1.2567
 3NV  H15   H   HCH3  0   0.221  -5.5808   3.7095   1.0324
 3NV  H15A  H   HCH3  0   0.229  -5.0119   2.8753   2.4781
 3NV  H15B  H   HCH3  0   0.228  -4.0410   4.1598   1.7595
 3NV  H17   H   HCR6  0   0.262  -3.6647  -2.8002   0.9969
 3NV  H18   H   HCR6  0   0.270  -1.3130  -3.5719   1.0198
 3NV  HN5   H   HNR5  0   0.431  -7.5620  -0.1101  -0.2775

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
 3NV  C1   N1    single    1.451  0.020  1.451
 3NV  C1   C2    single    1.524  0.020  1.524
 3NV  C1   H1    single    0.970  0.020  1.090
 3NV  C1   H1A   single    0.970  0.020  1.090
 3NV  C6   N1    single    1.396  0.020  1.396
 3NV  N1   C4    single    1.460  0.020  1.460
 3NV  CL1  C11   single    1.698  0.020  1.698
 3NV  C2   N2    single    1.452  0.020  1.452
 3NV  C2   H2    single    0.970  0.020  1.090
 3NV  C2   H2A   single    0.970  0.020  1.090
 3NV  N2   C3    single    1.452  0.020  1.452
 3NV  N2   HN2   single    0.890  0.020  1.040
 3NV  C4   C3    single    1.522  0.020  1.522
 3NV  C3   H3    single    0.970  0.020  1.090
 3NV  C3   H3A   single    0.970  0.020  1.090
 3NV  C9   N3    aromatic  1.315  0.020  1.315
 3NV  N3   C5    aromatic  1.333  0.020  1.333
 3NV  C4   H4    single    0.970  0.020  1.090
 3NV  C4   H4A   single    0.970  0.020  1.090
 3NV  C19  N4    single    1.365  0.020  1.365
 3NV  N4   C9    single    1.388  0.020  1.388
 3NV  N4   HN4   single    0.860  0.020  1.020
 3NV  C6   C5    aromatic  1.392  0.020  1.392
 3NV  C5   H5    single    0.930  0.020  1.080
 3NV  N5   N6    aromatic  1.330  0.020  1.330
 3NV  N5   C11   aromatic  1.334  0.020  1.334
 3NV  C7   C6    aromatic  1.404  0.020  1.404
 3NV  N6   C12   aromatic  1.317  0.020  1.317
 3NV  C8   C7    aromatic  1.373  0.020  1.373
 3NV  C7   H7    single    0.930  0.020  1.080
 3NV  C18  N7    aromatic  1.327  0.020  1.327
 3NV  N7   C19   aromatic  1.327  0.020  1.327
 3NV  C8   C9    aromatic  1.403  0.020  1.403
 3NV  C8   H8    single    0.930  0.020  1.080
 3NV  C16  N8    aromatic  1.326  0.020  1.326
 3NV  N8   C19   aromatic  1.335  0.020  1.335
 3NV  C11  C10   aromatic  1.383  0.020  1.383
 3NV  C12  C10   aromatic  1.424  0.020  1.424
 3NV  C10  C16   single    1.458  0.020  1.458
 3NV  C12  C13   single    1.501  0.020  1.501
 3NV  C14  C13   single    1.530  0.020  1.530
 3NV  C13  C15   single    1.526  0.020  1.526
 3NV  C13  H13   single    0.970  0.020  1.090
 3NV  C14  H14   single    0.970  0.020  1.090
 3NV  C14  H14A  single    0.970  0.020  1.090
 3NV  C14  H14B  single    0.970  0.020  1.090
 3NV  C15  H15   single    0.970  0.020  1.090
 3NV  C15  H15A  single    0.970  0.020  1.090
 3NV  C15  H15B  single    0.970  0.020  1.090
 3NV  C17  C16   aromatic  1.398  0.020  1.398
 3NV  C17  C18   aromatic  1.380  0.020  1.380
 3NV  C17  H17   single    0.930  0.020  1.080
 3NV  C18  H18   single    0.930  0.020  1.080
 3NV  N5   HN5   single    0.860  0.020  1.020

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
 3NV  H1A   C1   H1    107.19  3.000
 3NV  H1A   C1   C2    109.08  3.000
 3NV  H1    C1   C2    109.13  3.000
 3NV  H1A   C1   N1    109.32  3.000
 3NV  H1    C1   N1    111.81  3.000
 3NV  C2    C1   N1    110.23  3.000
 3NV  C6    N1   C4    115.91  3.000
 3NV  C4    N1   C1    112.08  3.000
 3NV  C6    N1   C1    117.03  3.000
 3NV  H2A   C2   H2    107.11  3.000
 3NV  H2A   C2   N2    108.35  3.000
 3NV  H2    C2   N2    109.34  3.000
 3NV  H2A   C2   C1    109.02  3.000
 3NV  H2    C2   C1    109.01  3.000
 3NV  N2    C2   C1    113.80  3.000
 3NV  HN2   N2   C3    108.84  3.000
 3NV  HN2   N2   C2    108.85  3.000
 3NV  C3    N2   C2    110.19  3.000
 3NV  H3A   C3   H3    107.14  3.000
 3NV  H3A   C3   C4    109.14  3.000
 3NV  H3    C3   C4    109.12  3.000
 3NV  H3A   C3   N2    108.45  3.000
 3NV  H3    C3   N2    109.37  3.000
 3NV  C4    C3   N2    113.44  3.000
 3NV  C9    N3   C5    119.09  3.000
 3NV  H4A   C4   H4    107.02  3.000
 3NV  H4A   C4   C3    109.39  3.000
 3NV  H4    C4   C3    109.17  3.000
 3NV  H4A   C4   N1    110.50  3.000
 3NV  H4    C4   N1    110.13  3.000
 3NV  C3    C4   N1    110.56  3.000
 3NV  HN4   N4   C19   112.88  3.000
 3NV  HN4   N4   C9    115.47  3.000
 3NV  C19   N4   C9    131.63  3.000
 3NV  H5    C5   C6    120.76  3.000
 3NV  H5    C5   N3    114.78  3.000
 3NV  C6    C5   N3    124.45  3.000
 3NV  HN5   N5   C11   127.25  3.000
 3NV  HN5   N5   N6    120.48  3.000
 3NV  C11   N5   N6    112.27  3.000
 3NV  C7    C6   C5    115.59  3.000
 3NV  C7    C6   N1    120.64  3.000
 3NV  C5    C6   N1    123.75  3.000
 3NV  C12   N6   N5    106.14  3.000
 3NV  H7    C7   C8    119.04  3.000
 3NV  H7    C7   C6    120.61  3.000
 3NV  C8    C7   C6    120.34  3.000
 3NV  C19   N7   C18   115.45  3.000
 3NV  H8    C8   C9    120.87  3.000
 3NV  H8    C8   C7    120.25  3.000
 3NV  C9    C8   C7    118.87  3.000
 3NV  C19   N8   C16   118.13  3.000
 3NV  C8    C9   N4    117.42  3.000
 3NV  C8    C9   N3    121.66  3.000
 3NV  N4    C9   N3    120.89  3.000
 3NV  C16   C10  C12   128.49  3.000
 3NV  C16   C10  C11   128.16  3.000
 3NV  C12   C10  C11   103.35  3.000
 3NV  C10   C11  N5    107.53  3.000
 3NV  C10   C11  CL1   131.57  3.000
 3NV  N5    C11  CL1   120.85  3.000
 3NV  C13   C12  C10   128.80  3.000
 3NV  C13   C12  N6    120.50  3.000
 3NV  C10   C12  N6    110.70  3.000
 3NV  H13   C13  C15   108.44  3.000
 3NV  H13   C13  C14   107.64  3.000
 3NV  C15   C13  C14   110.95  3.000
 3NV  H13   C13  C12   107.64  3.000
 3NV  C15   C13  C12   111.81  3.000
 3NV  C14   C13  C12   110.19  3.000
 3NV  H14B  C14  H14A  107.97  3.000
 3NV  H14B  C14  H14   108.47  3.000
 3NV  H14A  C14  H14   107.92  3.000
 3NV  H14B  C14  C13   111.07  3.000
 3NV  H14A  C14  C13   110.45  3.000
 3NV  H14   C14  C13   110.85  3.000
 3NV  H15B  C15  H15A  107.87  3.000
 3NV  H15B  C15  H15   107.74  3.000
 3NV  H15A  C15  H15   107.94  3.000
 3NV  H15B  C15  C13   109.98  3.000
 3NV  H15A  C15  C13   111.63  3.000
 3NV  H15   C15  C13   111.53  3.000
 3NV  C17   C16  C10   122.67  3.000
 3NV  C17   C16  N8    120.53  3.000
 3NV  C10   C16  N8    116.79  3.000
 3NV  H17   C17  C18   120.75  3.000
 3NV  H17   C17  C16   123.06  3.000
 3NV  C18   C17  C16   116.18  3.000
 3NV  H18   C18  C17   120.07  3.000
 3NV  H18   C18  N7    116.14  3.000
 3NV  C17   C18  N7    123.80  3.000
 3NV  N8    C19  N7    125.85  3.000
 3NV  N8    C19  N4    113.23  3.000
 3NV  N7    C19  N4    120.90  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
 3NV  CONST_01  C7   C8   C9   N3     0.00   0.0  0
 3NV  CONST_02  C7   C6   C5   N3     0.00   0.0  0
 3NV  CONST_03  C8   C9   N3   C5     0.00   0.0  0
 3NV  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 3NV  CONST_05  C10  C12  N6   N5     0.00   0.0  0
 3NV  CONST_06  C12  C10  C11  N5     0.00   0.0  0
 3NV  CONST_07  C16  C10  C11  N5   180.00   0.0  0
 3NV  CONST_08  C9   N3   C5   C6     0.00   0.0  0
 3NV  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 3NV  CONST_10  C10  C11  N5   N6     0.00   0.0  0
 3NV  CONST_11  C11  C10  C12  N6     0.00   0.0  0
 3NV  CONST_12  C16  C10  C12  N6   180.00   0.0  0
 3NV  CONST_13  C16  C17  C18  N7     0.00   0.0  0
 3NV  CONST_14  C16  N8   C19  N7     0.00   0.0  0
 3NV  CONST_17  C18  C17  C16  N8     0.00   0.0  0
 3NV  CONST_18  C18  N7   C19  N8     0.00   0.0  0
 3NV  CONST_19  C19  N8   C16  C10  180.00   0.0  0
 3NV  CONST_20  C18  C17  C16  C10  180.00   0.0  0
 3NV  CONST_21  C12  N6   N5   C11    0.00   0.0  0
 3NV  CONST_24  C19  N8   C16  C17    0.00   0.0  0
 3NV  CONST_25  C19  N7   C18  C17    0.00   0.0  0
 3NV  CONST_26  N3   C5   C6   N1   180.00   0.0  0
 3NV  CONST_27  C8   C7   C6   N1   180.00   0.0  0
 3NV  CONST_28  N6   N5   C11  CL1  180.00   0.0  0
 3NV  CONST_29  C12  C10  C11  CL1  180.00   0.0  0
 3NV  CONST_30  C16  C10  C11  CL1    0.00   0.0  0
 3NV  CONST_31  C18  N7   C19  N4   180.00   0.0  0
 3NV  CONST_32  C16  N8   C19  N4   180.00   0.0  0
 3NV  CONST_33  C5   N3   C9   N4   180.00   0.0  0
 3NV  CONST_34  C7   C8   C9   N4   180.00   0.0  0
 3NV  CONST_35  C13  C12  N6   N5   180.00   0.0  0
 3NV  CONST_36  C13  C12  C10  C11  180.00   0.0  0
 3NV  CONST_37  C16  C10  C12  C13    0.00   0.0  0
 3NV  CONST_38  H5   C5   C6   N1     0.00   0.0  0
 3NV  CONST_39  H7   C7   C6   N1     0.00   0.0  0
 3NV  CONST_40  H8   C8   C9   N3   180.00   0.0  0
 3NV  CONST_41  H17  C17  C18  N7   180.00   0.0  0
 3NV  CONST_42  HN5  N5   C11  C10  180.00   0.0  0
 3NV  CONST_43  H18  C18  C17  C16  180.00   0.0  0
 3NV  Var_01    C5   C6   N1   C1     8.51  30.0  2
 3NV  Var_02    C3   C4   N1   C1    55.12  30.0  1
 3NV  Var_03    C3   N2   C2   C1   -52.84  30.0  1
 3NV  Var_04    N2   C2   C1   N1    54.47  30.0  1
 3NV  Var_05    N2   C3   C4   N1   -54.21  30.0  1
 3NV  Var_06    C6   N1   C1   C2   167.63  30.0  1
 3NV  Var_07    C4   C3   N2   C2    52.62  30.0  1
 3NV  Var_08    C19  N4   C9   N3   -14.43  30.0  2
 3NV  Var_09    C9   N4   C19  N7    -5.23  30.0  2
 3NV  Var_10    C14  C13  C12  N6   -89.82  30.0  2
 3NV  Var_11    H14  C14  C13  C12   64.43  30.0  3
 3NV  Var_12    H15  C15  C13  C12  -61.70  30.0  3

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
 3NV  plan-1  CL1  0.020
 3NV  plan-1  N5   0.020
 3NV  plan-1  N6   0.020
 3NV  plan-1  C10  0.020
 3NV  plan-1  C11  0.020
 3NV  plan-1  C12  0.020
 3NV  plan-1  C13  0.020
 3NV  plan-1  C16  0.020
 3NV  plan-1  HN5  0.020
 3NV  plan-2  N1   0.020
 3NV  plan-2  N3   0.020
 3NV  plan-2  N4   0.020
 3NV  plan-2  C5   0.020
 3NV  plan-2  C6   0.020
 3NV  plan-2  C7   0.020
 3NV  plan-2  C8   0.020
 3NV  plan-2  C9   0.020
 3NV  plan-2  H5   0.020
 3NV  plan-2  H7   0.020
 3NV  plan-2  H8   0.020
 3NV  plan-3  N4   0.020
 3NV  plan-3  N7   0.020
 3NV  plan-3  N8   0.020
 3NV  plan-3  C10  0.020
 3NV  plan-3  C16  0.020
 3NV  plan-3  C17  0.020
 3NV  plan-3  C18  0.020
 3NV  plan-3  C19  0.020
 3NV  plan-3  H17  0.020
 3NV  plan-3  H18  0.020

