# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:20:49 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5-[(trans-4-aminocyclohexyl)amino]-7-[(1-methylethyl)amino]pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Nc1cc(N[C@H]2CC[C@H](N)CC2)nc3n1ncc3C#N
#
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
 LZC  LZC  5-[(trans-4-aminocyclohexyl)amino]-7-[(1-methylethyl)amino]pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  46  23  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LZC
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
 LZC  C1    C  CH3   0  -0.667  31.5846   7.9218  67.6188
 LZC  C2    C  CH1   0  -0.108  30.9761   8.0767  66.2341
 LZC  C3    C  CH3   0  -0.650  32.0438   8.0886  65.1462
 LZC  N4    N  NH1   0  -0.672  30.0158   7.0033  66.0266
 LZC  C5    C  CR6   0   0.721  29.0177   7.0518  65.1470
 LZC  C6    C  CR16  0  -0.560  28.6320   8.1195  64.3663
 LZC  C7    C  CR6   0   0.567  27.5133   7.9874  63.5034
 LZC  N8    N  NH1   0  -0.692  27.1330   9.0436  62.7697
 LZC  C9    C  CH1   0  -0.050  26.0850   9.0250  61.7678
 LZC  C10   C  CH2   0  -0.453  25.5535  10.4401  61.5672
 LZC  C11   C  CH2   0  -0.446  24.4633  10.4677  60.5022
 LZC  C12   C  CH1   0  -0.077  24.9359   9.8878  59.1673
 LZC  N13   N  NH2   0  -0.792  23.9132   9.8743  58.1299
 LZC  C14   C  CH2   0  -0.435  25.4768   8.4779  59.3798
 LZC  C15   C  CH2   0  -0.435  26.5716   8.4438  60.4398
 LZC  N16   N  N     0  -0.525  26.8066   6.8613  63.3922
 LZC  C17   C  CR56  0   0.656  27.2032   5.8530  64.1468
 LZC  C18   C  CR5   0  -0.339  26.7224   4.5423  64.2929
 LZC  C19   C  CSP   0  -0.012  25.6332   3.9812  63.6135
 LZC  N20   N  NS    0  -0.276  24.7347   3.5208  63.0509
 LZC  C21   C  CR15  0   0.029  27.5716   3.9427  65.2478
 LZC  N22   N  N     0  -0.309  28.4965   4.7625  65.6754
 LZC  N23   N  N     0  -0.469  28.2661   5.9142  65.0045
 LZC  H1C1  H  HCH3  0   0.245  32.2987   8.7230  67.8045
 LZC  H1C2  H  HCH3  0   0.245  30.8212   7.9598  68.3960
 LZC  H1C3  H  HCH3  0   0.231  32.1198   6.9735  67.7064
 LZC  H2    H  HCH1  0   0.252  30.4260   9.0209  66.2089
 LZC  H3C1  H  HCH3  0   0.238  31.6053   8.1605  64.1507
 LZC  H3C2  H  HCH3  0   0.236  32.7100   8.9411  65.2791
 LZC  H3C3  H  HCH3  0   0.228  32.6440   7.1788  65.1888
 LZC  H4    H  HNH1  0   0.410  30.2018   6.1084  66.4562
 LZC  H6    H  HCR6  0   0.291  29.1746   9.0524  64.4045
 LZC  H8    H  HNH1  0   0.396  27.7251   9.8588  62.7948
 LZC  H9    H  HCH1  0   0.238  25.2714   8.4008  62.1479
 LZC  H101  H  HCH2  0   0.244  25.1706  10.8311  62.5127
 LZC  H102  H  HCH2  0   0.220  26.3789  11.0954  61.2632
 LZC  H151  H  HCH2  0   0.214  27.4351   9.0262  60.0990
 LZC  H152  H  HCH2  0   0.241  26.9183   7.4193  60.5903
 LZC  H111  H  HCH2  0   0.211  23.5982   9.8878  60.8465
 LZC  H112  H  HCH2  0   0.232  24.1145  11.4940  60.3588
 LZC  H12   H  HCH1  0   0.211  25.7602  10.5120  58.7998
 LZC  H131  H  HNH2  0   0.332  23.1188   9.3349  58.4583
 LZC  H132  H  HNH2  0   0.341  23.5587  10.8142  57.9964
 LZC  H141  H  HCH2  0   0.211  24.6504   7.8235  59.6855
 LZC  H142  H  HCH2  0   0.234  25.8563   8.0812  58.4353
 LZC  H21   H  HCR5  0   0.291  27.5192   2.9324  65.6237

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
 LZC  C1   C2    single    1.520  0.020  1.520
 LZC  C2   C3    single    1.524  0.020  1.524
 LZC  C2   N4    single    1.455  0.020  1.455
 LZC  N4   C5    single    1.331  0.020  1.331
 LZC  C5   C6    aromatic  1.378  0.020  1.378
 LZC  C5   N23   aromatic  1.371  0.020  1.371
 LZC  C6   C7    aromatic  1.419  0.020  1.419
 LZC  C7   N8    single    1.341  0.020  1.341
 LZC  C7   N16   aromatic  1.334  0.020  1.334
 LZC  N8   C9    single    1.450  0.020  1.450
 LZC  C9   C10   single    1.525  0.020  1.525
 LZC  C9   C15   single    1.529  0.020  1.529
 LZC  C10  C11   single    1.524  0.020  1.524
 LZC  C11  C12   single    1.530  0.020  1.530
 LZC  C12  N13   single    1.457  0.020  1.457
 LZC  C12  C14   single    1.525  0.020  1.525
 LZC  C14  C15   single    1.524  0.020  1.524
 LZC  N16  C17   aromatic  1.320  0.020  1.320
 LZC  C17  C18   aromatic  1.404  0.020  1.404
 LZC  C17  N23   aromatic  1.367  0.020  1.367
 LZC  C18  C19   single    1.401  0.020  1.401
 LZC  C18  C21   aromatic  1.412  0.020  1.412
 LZC  C19  N20   triple    1.156  0.020  1.156
 LZC  C21  N22   aromatic  1.308  0.020  1.308
 LZC  N22  N23   aromatic  1.353  0.020  1.353
 LZC  C1   H1C1  single    0.970  0.020  1.090
 LZC  C1   H1C2  single    0.970  0.020  1.090
 LZC  C1   H1C3  single    0.970  0.020  1.090
 LZC  C2   H2    single    0.970  0.020  1.090
 LZC  C3   H3C1  single    0.970  0.020  1.090
 LZC  C3   H3C2  single    0.970  0.020  1.090
 LZC  C3   H3C3  single    0.970  0.020  1.090
 LZC  N4   H4    single    0.860  0.020  1.020
 LZC  C6   H6    single    0.930  0.020  1.080
 LZC  N8   H8    single    0.860  0.020  1.020
 LZC  C9   H9    single    0.970  0.020  1.090
 LZC  C10  H101  single    0.970  0.020  1.090
 LZC  C10  H102  single    0.970  0.020  1.090
 LZC  C15  H151  single    0.970  0.020  1.090
 LZC  C15  H152  single    0.970  0.020  1.090
 LZC  C11  H111  single    0.970  0.020  1.090
 LZC  C11  H112  single    0.970  0.020  1.090
 LZC  C12  H12   single    0.970  0.020  1.090
 LZC  N13  H131  single    0.890  0.020  1.040
 LZC  N13  H132  single    0.890  0.020  1.040
 LZC  C14  H141  single    0.970  0.020  1.090
 LZC  C14  H142  single    0.970  0.020  1.090
 LZC  C21  H21   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
 LZC  H1C3  C1   H1C2  108.43  3.000
 LZC  H1C3  C1   H1C1  107.68  3.000
 LZC  H1C2  C1   H1C1  108.18  3.000
 LZC  H1C3  C1   C2    110.95  3.000
 LZC  H1C2  C1   C2    111.44  3.000
 LZC  H1C1  C1   C2    110.04  3.000
 LZC  H2    C2   N4    107.56  3.000
 LZC  H2    C2   C3    109.23  3.000
 LZC  N4    C2   C3    111.48  3.000
 LZC  H2    C2   C1    108.09  3.000
 LZC  N4    C2   C1    108.59  3.000
 LZC  C3    C2   C1    111.74  3.000
 LZC  H3C3  C3   H3C2  108.14  3.000
 LZC  H3C3  C3   H3C1  108.19  3.000
 LZC  H3C2  C3   H3C1  107.79  3.000
 LZC  H3C3  C3   C2    110.55  3.000
 LZC  H3C2  C3   C2    110.31  3.000
 LZC  H3C1  C3   C2    111.74  3.000
 LZC  H4    N4   C5    116.84  3.000
 LZC  H4    N4   C2    118.13  3.000
 LZC  C5    N4   C2    124.20  3.000
 LZC  N23   C5   C6    115.51  3.000
 LZC  N23   C5   N4    116.71  3.000
 LZC  C6    C5   N4    127.77  3.000
 LZC  H6    C6   C7    119.87  3.000
 LZC  H6    C6   C5    120.58  3.000
 LZC  C7    C6   C5    119.55  3.000
 LZC  N16   C7   N8    117.97  3.000
 LZC  N16   C7   C6    123.15  3.000
 LZC  N8    C7   C6    118.88  3.000
 LZC  H8    N8   C9    116.89  3.000
 LZC  H8    N8   C7    117.18  3.000
 LZC  C9    N8   C7    124.95  3.000
 LZC  H9    C9   C15   108.76  3.000
 LZC  H9    C9   C10   108.43  3.000
 LZC  C15   C9   C10   110.45  3.000
 LZC  H9    C9   N8    107.75  3.000
 LZC  C15   C9   N8    112.02  3.000
 LZC  C10   C9   N8    109.32  3.000
 LZC  H102  C10  H101  106.85  3.000
 LZC  H102  C10  C11   109.49  3.000
 LZC  H101  C10  C11   110.34  3.000
 LZC  H102  C10  C9    109.18  3.000
 LZC  H101  C10  C9    109.91  3.000
 LZC  C11   C10  C9    110.97  3.000
 LZC  H112  C11  H111  106.60  3.000
 LZC  H112  C11  C12   109.87  3.000
 LZC  H111  C11  C12   108.49  3.000
 LZC  H112  C11  C10   109.68  3.000
 LZC  H111  C11  C10   109.59  3.000
 LZC  C12   C11  C10   112.44  3.000
 LZC  H12   C12  C14   107.83  3.000
 LZC  H12   C12  N13   107.10  3.000
 LZC  C14   C12  N13   109.85  3.000
 LZC  H12   C12  C11   107.98  3.000
 LZC  C14   C12  C11   109.78  3.000
 LZC  N13   C12  C11   114.07  3.000
 LZC  H132  N13  H131  105.18  3.000
 LZC  H132  N13  C12   109.31  3.000
 LZC  H131  N13  C12   108.91  3.000
 LZC  H142  C14  H141  106.61  3.000
 LZC  H142  C14  C15   110.10  3.000
 LZC  H141  C14  C15   109.50  3.000
 LZC  H142  C14  C12   109.78  3.000
 LZC  H141  C14  C12   108.85  3.000
 LZC  C15   C14  C12   111.86  3.000
 LZC  H152  C15  H151  106.94  3.000
 LZC  H152  C15  C14   110.18  3.000
 LZC  H151  C15  C14   109.74  3.000
 LZC  H152  C15  C9    109.75  3.000
 LZC  H151  C15  C9    108.59  3.000
 LZC  C14   C15  C9    111.52  3.000
 LZC  C17   N16  C7    115.97  3.000
 LZC  N23   C17  C18   104.06  3.000
 LZC  N23   C17  N16   123.91  3.000
 LZC  C18   C17  N16   132.04  3.000
 LZC  C21   C18  C19   128.73  3.000
 LZC  C21   C18  C17   105.12  3.000
 LZC  C19   C18  C17   126.14  3.000
 LZC  N20   C19  C18   180.00  3.000
 LZC  H21   C21  N22   120.48  3.000
 LZC  H21   C21  C18   127.16  3.000
 LZC  N22   C21  C18   112.35  3.000
 LZC  N23   N22  C21   104.55  3.000
 LZC  N22   N23  C17   113.92  3.000
 LZC  N22   N23  C5    124.17  3.000
 LZC  C17   N23  C5    121.91  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
 LZC  CONST_01  N16   C7   C6   C5     0.00   0.0  0
 LZC  CONST_02  N16   C17  N23  C5     0.00   0.0  0
 LZC  CONST_03  C18   C17  N23  C5   180.00   0.0  0
 LZC  CONST_04  C21   N22  N23  C5   180.00   0.0  0
 LZC  CONST_05  C17   N23  C5   C6     0.00   0.0  0
 LZC  CONST_06  N22   N23  C5   C6   180.00   0.0  0
 LZC  CONST_07  C17   N16  C7   C6     0.00   0.0  0
 LZC  CONST_08  N23   C5   C6   C7     0.00   0.0  0
 LZC  CONST_09  C18   C17  N16  C7   180.00   0.0  0
 LZC  CONST_10  N23   C17  N16  C7     0.00   0.0  0
 LZC  CONST_11  C21   C18  C17  N16  180.00   0.0  0
 LZC  CONST_12  N22   N23  C17  N16  180.00   0.0  0
 LZC  CONST_13  N22   C21  C18  C17    0.00   0.0  0
 LZC  CONST_14  C21   N22  N23  C17    0.00   0.0  0
 LZC  CONST_15  N22   N23  C17  C18    0.00   0.0  0
 LZC  CONST_16  N23   N22  C21  C18    0.00   0.0  0
 LZC  CONST_17  N23   C17  C18  C21    0.00   0.0  0
 LZC  CONST_18  C7    C6   C5   N4   180.00   0.0  0
 LZC  CONST_19  C17   N23  C5   N4   180.00   0.0  0
 LZC  CONST_20  N22   N23  C5   N4     0.00   0.0  0
 LZC  CONST_21  N8    C7   C6   C5   180.00   0.0  0
 LZC  CONST_22  C17   N16  C7   N8   180.00   0.0  0
 LZC  CONST_23  C19   C18  C17  N16    0.00   0.0  0
 LZC  CONST_24  N23   C17  C18  C19  180.00   0.0  0
 LZC  CONST_25  N22   C21  C18  C19  180.00   0.0  0
 LZC  CONST_26  C9    N8   C7   C6   180.00   0.0  0
 LZC  CONST_27  N16   C7   N8   C9     0.00   0.0  0
 LZC  CONST_28  H6    C6   C7   N16  180.00   0.0  0
 LZC  CONST_29  H21   C21  C18  C17  180.00   0.0  0
 LZC  CONST_30  C6    C5   N4   C2     0.00   0.0  0
 LZC  CONST_31  N23   C5   N4   C2   180.00   0.0  0
 LZC  CONST_32  H4    N4   C5   C6   180.00   0.0  0
 LZC  CONST_33  H8    N8   C7   C6     0.00   0.0  0
 LZC  Var_01    C12   C11  C10  C9   -56.11  30.0  1
 LZC  Var_02    C12   C14  C15  C9    56.23  30.0  1
 LZC  Var_03    C5    N4   C2   C1   157.90  30.0  3
 LZC  Var_04    H3C1  C3   C2   C1   177.78  30.0  3
 LZC  Var_05    H1C1  C1   C2   C3    57.39  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
 LZC  chir_01  C9   N8   C10  C15  negativ
 LZC  chir_02  C12  N13  C11  C14  negativ

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
 LZC  plan-1  N4   0.020
 LZC  plan-1  C5   0.020
 LZC  plan-1  C6   0.020
 LZC  plan-1  C7   0.020
 LZC  plan-1  N8   0.020
 LZC  plan-1  N16  0.020
 LZC  plan-1  C17  0.020
 LZC  plan-1  C18  0.020
 LZC  plan-1  C19  0.020
 LZC  plan-1  N20  0.020
 LZC  plan-1  C21  0.020
 LZC  plan-1  N22  0.020
 LZC  plan-1  N23  0.020
 LZC  plan-1  H6   0.020
 LZC  plan-1  H21  0.020
 LZC  plan-2  C2   0.020
 LZC  plan-2  N4   0.020
 LZC  plan-2  C5   0.020
 LZC  plan-2  H4   0.020
 LZC  plan-3  C7   0.020
 LZC  plan-3  N8   0.020
 LZC  plan-3  C9   0.020
 LZC  plan-3  H8   0.020

