# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:26:51 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCCc2cnn3c(NC4CC4)nc(Nc5cccc(N1)c5)nc23
#
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
 P04  P04  19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one  ligand  48  27  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P04
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
 P04  N01   N  N     0  -0.327  -2.7925   2.4532   0.4154
 P04  C02   C  CR15  0  -0.048  -1.7181   3.2198   0.4884
 P04  C03   C  CR5   0  -0.221  -0.5041   2.5079   0.5348
 P04  C04   C  CR56  0   0.610  -0.9125   1.1842   0.4845
 P04  N05   N  N     0  -0.444  -2.2841   1.2092   0.4114
 P04  N06   N  N     0  -0.502  -0.2577   0.0177   0.4734
 P04  C07   C  CR6   0   0.541  -0.9956  -1.0515   0.3126
 P04  N08   N  N     0  -0.514  -2.3474  -1.0985   0.2760
 P04  C09   C  CR6   0   0.774  -2.9874   0.0419   0.3362
 P04  N10   N  NH1   0  -0.669  -4.3127   0.1253   0.3176
 P04  C11   C  CH1   0  -0.089  -5.1552  -1.0253   0.2767
 P04  C12   C  CH2   0  -0.511  -6.4271  -0.9115  -0.4968
 P04  C13   C  CH2   0  -0.477  -5.3098  -1.7630  -1.0144
 P04  N17   N  NH1   0  -0.767  -0.3730  -2.2571   0.1641
 P04  C18   C  CR6   0   0.341   1.0158  -2.4174   0.1068
 P04  C19   C  CR16  0  -0.308   1.7939  -1.4969  -0.5852
 P04  C20   C  CR6   0   0.307   3.1768  -1.5336  -0.5104
 P04  C21   C  CR16  0  -0.302   3.8137  -2.5687   0.1604
 P04  C22   C  CR16  0  -0.262   3.0339  -3.5471   0.7661
 P04  C23   C  CR16  0  -0.316   1.6472  -3.4690   0.7677
 P04  N27   N  NH1   0  -0.714   3.8706  -0.4298  -1.0709
 P04  C28   C  C     0   0.495   4.3854   0.5317  -0.2437
 P04  O29   O  O     0  -0.460   4.7518   0.2834   0.8894
 P04  C30   C  CH2   0  -0.565   4.3887   1.9403  -0.7951
 P04  C31   C  CH2   0  -0.434   3.3412   2.7850  -0.0492
 P04  C32   C  CH2   0  -0.452   1.9100   2.2866  -0.2279
 P04  C33   C  CH2   0  -0.494   0.8941   3.0410   0.6359
 P04  H02   H  HCR5  0   0.269  -1.8363   4.2944   0.5020
 P04  HN10  H  HNH1  0   0.419  -4.7263   1.0372   0.4461
 P04  H11   H  HCH1  0   0.277  -5.1732  -1.6109   1.1901
 P04  H12   H  HCH2  0   0.264  -7.3039  -1.3935  -0.0863
 P04  H12A  H  HCH2  0   0.263  -6.6244   0.0254  -1.0028
 P04  H13   H  HCH2  0   0.259  -4.7506  -1.3978  -1.8661
 P04  H13A  H  HCH2  0   0.259  -5.4088  -2.8391  -0.9645
 P04  HN17  H  HNH1  0   0.406  -0.9489  -3.0764   0.2788
 P04  H19   H  HCR6  0   0.275   1.3252  -0.6962  -1.1349
 P04  H21   H  HCR6  0   0.259   4.8927  -2.6156   0.2099
 P04  H22   H  HCR6  0   0.261   3.5157  -4.3685   1.2797
 P04  H23   H  HCR6  0   0.267   1.0614  -4.2098   1.2977
 P04  HN27  H  HNH1  0   0.402   3.4882  -0.0914  -1.9420
 P04  H30   H  HCH2  0   0.272   5.3779   2.3751  -0.6407
 P04  H30A  H  HCH2  0   0.252   4.1897   1.9552  -1.8693
 P04  H31   H  HCH2  0   0.228   3.5967   2.8007   1.0139
 P04  H31A  H  HCH2  0   0.239   3.4234   3.8174  -0.3980
 P04  H32   H  HCH2  0   0.220   1.6219   2.3603  -1.2816
 P04  H32A  H  HCH2  0   0.251   1.8472   1.2294   0.0323
 P04  H33   H  HCH2  0   0.236   0.8892   4.1007   0.3662
 P04  H33A  H  HCH2  0   0.232   1.2290   3.0026   1.6783

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
 P04  C02  N01   aromatic  1.322  0.020  1.322
 P04  N01  N05   aromatic  1.344  0.020  1.344
 P04  C03  C02   single    1.408  0.020  1.408
 P04  C02  H02   single    0.930  0.020  1.080
 P04  C33  C03   single    1.500  0.020  1.500
 P04  C03  C04   aromatic  1.386  0.020  1.386
 P04  C04  N06   aromatic  1.338  0.020  1.338
 P04  C04  N05   single    1.374  0.020  1.374
 P04  N05  C09   aromatic  1.365  0.020  1.365
 P04  N06  C07   aromatic  1.309  0.020  1.309
 P04  C07  N17   single    1.365  0.020  1.365
 P04  C07  N08   single    1.353  0.020  1.353
 P04  C09  N08   aromatic  1.309  0.020  1.309
 P04  C09  N10   single    1.328  0.020  1.328
 P04  N10  C11   single    1.427  0.020  1.427
 P04  N10  HN10  single    0.860  0.020  1.020
 P04  C11  C12   single    1.493  0.020  1.493
 P04  C11  C13   single    1.495  0.020  1.495
 P04  C11  H11   single    0.970  0.020  1.090
 P04  C12  C13   single    1.497  0.020  1.497
 P04  C12  H12   single    0.970  0.020  1.090
 P04  C12  H12A  single    0.970  0.020  1.090
 P04  C13  H13   single    0.970  0.020  1.090
 P04  C13  H13A  single    0.970  0.020  1.090
 P04  C18  N17   single    1.399  0.020  1.399
 P04  N17  HN17  single    0.860  0.020  1.020
 P04  C19  C18   aromatic  1.390  0.020  1.390
 P04  C18  C23   single    1.393  0.020  1.393
 P04  C20  C19   aromatic  1.385  0.020  1.385
 P04  C19  H19   single    0.930  0.020  1.080
 P04  N27  C20   single    1.419  0.020  1.419
 P04  C20  C21   single    1.388  0.020  1.388
 P04  C21  C22   aromatic  1.390  0.020  1.390
 P04  C21  H21   single    0.930  0.020  1.080
 P04  C22  C23   aromatic  1.389  0.020  1.389
 P04  C22  H22   single    0.930  0.020  1.080
 P04  C23  H23   single    0.930  0.020  1.080
 P04  C28  N27   single    1.369  0.020  1.369
 P04  N27  HN27  single    0.890  0.020  1.040
 P04  O29  C28   double    1.216  0.020  1.216
 P04  C28  C30   single    1.513  0.020  1.513
 P04  C30  C31   single    1.539  0.020  1.539
 P04  C30  H30   single    0.970  0.020  1.090
 P04  C30  H30A  single    0.970  0.020  1.090
 P04  C31  C32   single    1.526  0.020  1.526
 P04  C31  H31   single    0.970  0.020  1.090
 P04  C31  H31A  single    0.970  0.020  1.090
 P04  C32  C33   single    1.532  0.020  1.532
 P04  C32  H32   single    0.970  0.020  1.090
 P04  C32  H32A  single    0.970  0.020  1.090
 P04  C33  H33   single    0.970  0.020  1.090
 P04  C33  H33A  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
 P04  N05   N01  C02  103.27  3.000
 P04  H02   C02  C03  126.61  3.000
 P04  H02   C02  N01  119.23  3.000
 P04  C03   C02  N01  114.16  3.000
 P04  C33   C03  C04  128.06  3.000
 P04  C04   C03  C02  103.16  3.000
 P04  C33   C03  C02  128.78  3.000
 P04  N06   C04  N05  120.27  3.000
 P04  N05   C04  C03  106.18  3.000
 P04  N06   C04  C03  133.54  3.000
 P04  C09   N05  C04  120.12  3.000
 P04  C09   N05  N01  126.65  3.000
 P04  C04   N05  N01  113.23  3.000
 P04  C07   N06  C04  115.94  3.000
 P04  N17   C07  N08  114.97  3.000
 P04  N08   C07  N06  126.50  3.000
 P04  N17   C07  N06  118.54  3.000
 P04  C09   N08  C07  117.19  3.000
 P04  N10   C09  N08  122.82  3.000
 P04  N10   C09  N05  117.47  3.000
 P04  N08   C09  N05  119.71  3.000
 P04  HN10  N10  C11  119.36  3.000
 P04  HN10  N10  C09  117.63  3.000
 P04  C11   N10  C09  122.61  3.000
 P04  H11   C11  C13  117.32  3.000
 P04  H11   C11  C12  117.59  3.000
 P04  C13   C11  C12   60.14  3.000
 P04  H11   C11  N10  114.89  3.000
 P04  C13   C11  N10  118.93  3.000
 P04  C12   C11  N10  117.16  3.000
 P04  H12A  C12  H12  114.54  3.000
 P04  H12A  C12  C13  117.81  3.000
 P04  H12   C12  C13  118.87  3.000
 P04  H12A  C12  C11  117.59  3.000
 P04  H12   C12  C11  117.39  3.000
 P04  C13   C12  C11   60.00  3.000
 P04  H13A  C13  H13  114.79  3.000
 P04  H13A  C13  C12  118.78  3.000
 P04  H13   C13  C12  117.76  3.000
 P04  H13A  C13  C11  117.41  3.000
 P04  H13   C13  C11  117.36  3.000
 P04  C12   C13  C11   59.86  3.000
 P04  HN17  N17  C18  118.60  3.000
 P04  HN17  N17  C07  116.42  3.000
 P04  C18   N17  C07  123.94  3.000
 P04  C23   C18  C19  118.84  3.000
 P04  C23   C18  N17  121.12  3.000
 P04  C19   C18  N17  120.01  3.000
 P04  H19   C19  C20  118.75  3.000
 P04  H19   C19  C18  120.15  3.000
 P04  C20   C19  C18  120.96  3.000
 P04  N27   C20  C21  123.13  3.000
 P04  C21   C20  C19  120.25  3.000
 P04  N27   C20  C19  116.49  3.000
 P04  H21   C21  C22  120.63  3.000
 P04  H21   C21  C20  120.82  3.000
 P04  C22   C21  C20  118.56  3.000
 P04  H22   C22  C23  119.12  3.000
 P04  H22   C22  C21  119.44  3.000
 P04  C23   C22  C21  121.40  3.000
 P04  H23   C23  C22  120.14  3.000
 P04  H23   C23  C18  120.22  3.000
 P04  C22   C23  C18  119.63  3.000
 P04  HN27  N27  C28  115.36  3.000
 P04  HN27  N27  C20  114.60  3.000
 P04  C28   N27  C20  119.44  3.000
 P04  C30   C28  O29  121.94  3.000
 P04  C30   C28  N27  115.76  3.000
 P04  O29   C28  N27  122.20  3.000
 P04  H30A  C30  H30  107.38  3.000
 P04  H30A  C30  C31  110.19  3.000
 P04  H30   C30  C31  109.25  3.000
 P04  H30A  C30  C28  111.76  3.000
 P04  H30   C30  C28  108.75  3.000
 P04  C31   C30  C28  109.45  3.000
 P04  H31A  C31  H31  106.21  3.000
 P04  H31A  C31  C32  109.98  3.000
 P04  H31   C31  C32  109.74  3.000
 P04  H31A  C31  C30  108.23  3.000
 P04  H31   C31  C30  108.67  3.000
 P04  C32   C31  C30  113.73  3.000
 P04  H32A  C32  H32  106.25  3.000
 P04  H32A  C32  C33  107.74  3.000
 P04  H32   C32  C33  109.57  3.000
 P04  H32A  C32  C31  110.04  3.000
 P04  H32   C32  C31  109.72  3.000
 P04  C33   C32  C31  113.27  3.000
 P04  H33A  C33  H33  105.66  3.000
 P04  H33A  C33  C32  108.45  3.000
 P04  H33   C33  C32  109.94  3.000
 P04  H33A  C33  C03  109.67  3.000
 P04  H33   C33  C03  108.89  3.000
 P04  C32   C33  C03  113.90  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
 P04  CONST_01  C04   C03  C02  N01     0.00   0.0  0
 P04  CONST_02  C03   C04  N05  N01     0.00   0.0  0
 P04  CONST_03  N06   C04  N05  N01   180.00   0.0  0
 P04  CONST_04  N08   C09  N05  N01   180.00   0.0  0
 P04  CONST_05  C04   N05  N01  C02     0.00   0.0  0
 P04  CONST_06  C09   N05  N01  C02   180.00   0.0  0
 P04  CONST_07  N06   C04  C03  C02   180.00   0.0  0
 P04  CONST_08  N05   C04  C03  C02     0.00   0.0  0
 P04  CONST_09  N05   N01  C02  C03     0.00   0.0  0
 P04  CONST_10  C07   N06  C04  C03   180.00   0.0  0
 P04  CONST_11  C09   N05  C04  C03   180.00   0.0  0
 P04  CONST_12  N08   C07  N06  C04     0.00   0.0  0
 P04  CONST_13  N08   C09  N05  C04     0.00   0.0  0
 P04  CONST_14  C07   N06  C04  N05     0.00   0.0  0
 P04  CONST_15  C07   N08  C09  N05     0.00   0.0  0
 P04  CONST_16  C09   N05  C04  N06     0.00   0.0  0
 P04  CONST_17  C09   N08  C07  N06     0.00   0.0  0
 P04  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 P04  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 P04  CONST_20  C22   C23  C18  C19     0.00   0.0  0
 P04  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 P04  CONST_22  C23   C18  C19  C20     0.00   0.0  0
 P04  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 P04  CONST_27  N10   C09  N05  N01     0.00   0.0  0
 P04  CONST_28  N10   C09  N05  C04   180.00   0.0  0
 P04  CONST_29  N10   C09  N08  C07   180.00   0.0  0
 P04  CONST_31  C11   N10  C09  N05   180.00   0.0  0
 P04  CONST_32  C11   N10  C09  N08     0.00   0.0  0
 P04  CONST_33  H02   C02  C03  C04   180.00   0.0  0
 P04  CONST_34  H19   C19  C18  N17     0.00   0.0  0
 P04  CONST_35  H23   C23  C18  N17     0.00   0.0  0
 P04  CONST_36  H22   C22  C23  C18   180.00   0.0  0
 P04  CONST_37  H21   C21  C20  C19   180.00   0.0  0
 P04  CONST_38  HN27  N27  C28  C30     0.00   0.0  0
 P04  CONST_39  HN10  N10  C09  N05     0.00   0.0  0
 P04  Var_01    C32   C33  C03  C02  -140.29  30.0  1
 P04  Var_02    C31   C32  C33  C03  -176.45  30.0  1
 P04  Var_03    C18   N17  C07  N06    -3.28  30.0  1
 P04  Var_04    C19   C18  N17  C07   -39.44  30.0  1
 P04  Var_05    C31   C30  C28  N27   109.10  30.0  1
 P04  Var_06    C32   C31  C30  C28   -62.58  30.0  1
 P04  Var_07    C33   C32  C31  C30   173.84  30.0  1
 P04  Var_08    C12   C11  N10  C09  -145.30  30.0  3
 P04  Var_09    C13   C12  C11  N10   109.42  30.0  1
 P04  Var_10    H13   C13  C12  C11  -107.16  30.0  1

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
 P04  chir_01  C11  N10  C12  C13  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
 P04  plan-1  N01   0.020
 P04  plan-1  C02   0.020
 P04  plan-1  C03   0.020
 P04  plan-1  C04   0.020
 P04  plan-1  N05   0.020
 P04  plan-1  N06   0.020
 P04  plan-1  C07   0.020
 P04  plan-1  N08   0.020
 P04  plan-1  C09   0.020
 P04  plan-1  N10   0.020
 P04  plan-1  N17   0.020
 P04  plan-1  C33   0.020
 P04  plan-1  H02   0.020
 P04  plan-2  N17   0.020
 P04  plan-2  C18   0.020
 P04  plan-2  C19   0.020
 P04  plan-2  C20   0.020
 P04  plan-2  C21   0.020
 P04  plan-2  C22   0.020
 P04  plan-2  C23   0.020
 P04  plan-2  N27   0.020
 P04  plan-2  H19   0.020
 P04  plan-2  H21   0.020
 P04  plan-2  H22   0.020
 P04  plan-2  H23   0.020
 P04  plan-3  C20   0.020
 P04  plan-3  N27   0.020
 P04  plan-3  C28   0.020
 P04  plan-3  O29   0.020
 P04  plan-3  C30   0.020
 P04  plan-3  HN27  0.020
 P04  plan-4  C09   0.020
 P04  plan-4  N10   0.020
 P04  plan-4  C11   0.020
 P04  plan-4  HN10  0.020

