# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:57:55 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[(2-{4-[(cyclopropylcarbamoyl)amino]-1H-pyrazol-3-yl}-1H-benzimidazol-6-yl)methyl]morpholin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC1CC1)Nc2c[nH]nc2c3[nH]c4cc(C[NH+]5CCOCC5)ccc4n3
#
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
 L0I  L0I  4-[(2-{4-[(cyclopropylcarbamoyl)amino]-1H-pyrazol-3-yl}-1H-benzimidazol-6-yl)methyl]morpholin-4-ium  ligand  52  28  .  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_L0I
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
 L0I  O1   O  O     0  -0.519  -5.9724   0.1885  -0.5501
 L0I  C2   C  C     0   0.732  -4.9716  -0.4886  -0.3663
 L0I  N3   N  NH1   0  -0.697  -4.9961  -1.8397  -0.2481
 L0I  C4   C  CH1   0  -0.078  -6.2031  -2.5756  -0.4116
 L0I  C5   C  CH2   0  -0.511  -6.3977  -3.7729   0.4631
 L0I  C6   C  CH2   0  -0.481  -7.2233  -2.5433   0.6816
 L0I  N7   N  NH1   0  -0.788  -3.7232   0.0585  -0.2489
 L0I  C8   C  CR5   0   0.114  -3.4535   1.4104  -0.3255
 L0I  C9   C  CR15  0  -0.022  -4.2719   2.4986  -0.5515
 L0I  N10  N  NR15  0  -0.413  -3.4605   3.5787  -0.5134
 L0I  N12  N  N     0  -0.275  -2.2023   3.2969  -0.2841
 L0I  C13  C  CR5   0   0.108  -2.1670   1.9749  -0.1660
 L0I  C14  C  CR5   0   0.518  -0.9417   1.2672   0.1069
 L0I  N15  N  N     0  -0.537  -0.8577  -0.0374   0.2171
 L0I  C16  C  CR56  0   0.183   0.4601  -0.2911   0.4943
 L0I  C17  C  CR16  0  -0.328   1.1167  -1.4975   0.7260
 L0I  C18  C  CR16  0  -0.294   2.4682  -1.4542   1.0123
 L0I  C19  C  CR6   0   0.058   3.1743  -0.2405   1.0679
 L0I  C20  C  CH2   0  -0.401   4.6349  -0.2351   1.3945
 L0I  N21  N  NT1   1  -0.532   5.4991  -0.1488   0.1674
 L0I  C23  C  CH2   0  -0.337   6.9296   0.0576   0.5455
 L0I  C24  C  CH2   0  -0.210   7.8044   0.0867  -0.6909
 L0I  O25  O  O2    0  -0.465   7.6583  -1.0860  -1.4519
 L0I  C26  C  CH2   0  -0.204   6.3301  -1.2335  -1.8871
 L0I  C27  C  CH2   0  -0.340   5.3667  -1.3396  -0.7223
 L0I  C28  C  CR16  0  -0.347   2.5314   0.9689   0.8355
 L0I  C29  C  CR56  0   0.348   1.1770   0.9184   0.5490
 L0I  N30  N  NR15  0  -0.709   0.2486   1.8895   0.2923
 L0I  H11  H  HNR5  0   0.431  -3.7434   4.5380  -0.6383
 L0I  H22  H  HNT1  0   0.462   5.1923   0.6742  -0.3579
 L0I  H31  H  HNR5  0   0.426   0.4044   2.8854   0.2575
 L0I  H32  H  HNH1  0   0.398  -4.1296  -2.3538  -0.2540
 L0I  H33  H  HCH1  0   0.261  -6.5773  -2.6506  -1.4288
 L0I  H34  H  HCH2  0   0.257  -6.8670  -4.6433   0.0247
 L0I  H35  H  HCH2  0   0.256  -5.6240  -3.9955   1.1872
 L0I  H36  H  HCH2  0   0.254  -7.0012  -1.9379   1.5505
 L0I  H37  H  HCH2  0   0.253  -8.2669  -2.5615   0.3965
 L0I  H38  H  HNH1  0   0.415  -2.9160  -0.5261  -0.0613
 L0I  H39  H  HCR5  0   0.301  -5.3268   2.5903  -0.7303
 L0I  H40  H  HCR6  0   0.264   0.5828  -2.4379   0.6924
 L0I  H41  H  HCR6  0   0.265   2.9959  -2.3783   1.2133
 L0I  H42  H  HCH2  0   0.320   4.8999   0.6289   2.0026
 L0I  H43  H  HCH2  0   0.321   4.9418  -1.1353   1.9242
 L0I  H44  H  HCH2  0   0.314   6.9974   0.9957   1.0935
 L0I  H45  H  HCH2  0   0.303   7.2028  -0.7615   1.2101
 L0I  H46  H  HCH2  0   0.236   7.5744   0.9768  -1.2923
 L0I  H47  H  HCH2  0   0.280   8.8444   0.1607  -0.3743
 L0I  H48  H  HCH2  0   0.237   6.0372  -0.4021  -2.5424
 L0I  H49  H  HCH2  0   0.280   6.2640  -2.1518  -2.4697
 L0I  H50  H  HCH2  0   0.301   5.5721  -2.2179  -0.1104
 L0I  H51  H  HCH2  0   0.314   4.3407  -1.3884  -1.0812
 L0I  H52  H  HCR6  0   0.277   3.0650   1.9100   0.8928

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
 L0I  C2   O1   double    1.222  0.020  1.222
 L0I  N3   C2   single    1.356  0.020  1.356
 L0I  C2   N7   single    1.368  0.020  1.368
 L0I  C4   N3   single    1.423  0.020  1.423
 L0I  N3   H32  single    0.860  0.020  1.020
 L0I  C5   C4   single    1.495  0.020  1.495
 L0I  C6   C4   single    1.496  0.020  1.496
 L0I  H33  C4   single    0.970  0.020  1.090
 L0I  H34  C5   single    0.970  0.020  1.090
 L0I  C5   H35  single    0.970  0.020  1.090
 L0I  C5   C6   single    1.497  0.020  1.497
 L0I  H37  C6   single    0.970  0.020  1.090
 L0I  C6   H36  single    0.970  0.020  1.090
 L0I  H38  N7   single    0.860  0.020  1.020
 L0I  N7   C8   single    1.381  0.020  1.381
 L0I  C13  C8   aromatic  1.414  0.020  1.414
 L0I  C8   C9   aromatic  1.380  0.020  1.380
 L0I  C9   N10  aromatic  1.351  0.020  1.351
 L0I  C9   H39  single    0.930  0.020  1.080
 L0I  N12  N10  aromatic  1.310  0.020  1.310
 L0I  N10  H11  single    0.860  0.020  1.020
 L0I  C13  N12  aromatic  1.328  0.020  1.328
 L0I  C14  C13  single    1.441  0.020  1.441
 L0I  N15  C14  aromatic  1.312  0.020  1.312
 L0I  C14  N30  aromatic  1.356  0.020  1.356
 L0I  C16  N15  aromatic  1.370  0.020  1.370
 L0I  C17  C16  aromatic  1.393  0.020  1.393
 L0I  C16  C29  aromatic  1.407  0.020  1.407
 L0I  H40  C17  single    0.930  0.020  1.080
 L0I  C18  C17  aromatic  1.382  0.020  1.382
 L0I  H41  C18  single    0.930  0.020  1.080
 L0I  C18  C19  aromatic  1.405  0.020  1.405
 L0I  C20  C19  single    1.497  0.020  1.497
 L0I  C19  C28  aromatic  1.389  0.020  1.389
 L0I  N21  C20  single    1.503  0.020  1.503
 L0I  H43  C20  single    0.970  0.020  1.090
 L0I  C20  H42  single    0.970  0.020  1.090
 L0I  H22  N21  single    0.890  0.020  1.040
 L0I  C27  N21  single    1.492  0.020  1.492
 L0I  N21  C23  single    1.494  0.020  1.494
 L0I  C24  C23  single    1.515  0.020  1.515
 L0I  C23  H44  single    0.970  0.020  1.090
 L0I  C23  H45  single    0.970  0.020  1.090
 L0I  H46  C24  single    0.970  0.020  1.090
 L0I  O25  C24  single    1.406  0.020  1.406
 L0I  C24  H47  single    0.970  0.020  1.090
 L0I  C26  O25  single    1.405  0.020  1.405
 L0I  H48  C26  single    0.970  0.020  1.090
 L0I  H49  C26  single    0.970  0.020  1.090
 L0I  C26  C27  single    1.515  0.020  1.515
 L0I  H51  C27  single    0.970  0.020  1.090
 L0I  C27  H50  single    0.970  0.020  1.090
 L0I  C28  C29  aromatic  1.385  0.020  1.385
 L0I  C28  H52  single    0.930  0.020  1.080
 L0I  C29  N30  aromatic  1.368  0.020  1.368
 L0I  N30  H31  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
 L0I  N7   C2   N3   114.04  3.000
 L0I  N7   C2   O1   122.58  3.000
 L0I  N3   C2   O1   123.38  3.000
 L0I  H32  N3   C4   117.70  3.000
 L0I  H32  N3   C2   119.49  3.000
 L0I  C4   N3   C2   121.36  3.000
 L0I  H33  C4   C6   116.80  3.000
 L0I  H33  C4   C5   116.58  3.000
 L0I  C6   C4   C5    60.07  3.000
 L0I  H33  C4   N3   115.81  3.000
 L0I  C6   C4   N3   118.91  3.000
 L0I  C5   C4   N3   117.21  3.000
 L0I  H35  C5   H34  114.56  3.000
 L0I  H35  C5   C6   117.73  3.000
 L0I  H34  C5   C6   118.74  3.000
 L0I  C6   C5   C4    59.97  3.000
 L0I  H35  C5   C4   117.57  3.000
 L0I  H34  C5   C4   117.62  3.000
 L0I  H37  C6   H36  114.77  3.000
 L0I  H36  C6   C5   117.61  3.000
 L0I  H37  C6   C5   118.66  3.000
 L0I  H36  C6   C4   117.32  3.000
 L0I  H37  C6   C4   117.71  3.000
 L0I  C5   C6   C4    59.96  3.000
 L0I  H38  N7   C8   114.78  3.000
 L0I  C8   N7   C2   124.41  3.000
 L0I  H38  N7   C2   120.77  3.000
 L0I  C13  C8   C9   104.08  3.000
 L0I  C9   C8   N7   131.70  3.000
 L0I  C13  C8   N7   124.22  3.000
 L0I  H39  C9   N10  121.75  3.000
 L0I  H39  C9   C8   132.62  3.000
 L0I  N10  C9   C8   105.63  3.000
 L0I  H11  N10  N12  119.74  3.000
 L0I  H11  N10  C9   126.07  3.000
 L0I  N12  N10  C9   114.19  3.000
 L0I  C13  N12  N10  104.79  3.000
 L0I  C14  C13  N12  121.89  3.000
 L0I  C14  C13  C8   126.80  3.000
 L0I  N12  C13  C8   111.30  3.000
 L0I  N30  C14  N15  112.87  3.000
 L0I  N30  C14  C13  123.16  3.000
 L0I  N15  C14  C13  123.96  3.000
 L0I  C16  N15  C14  105.23  3.000
 L0I  C29  C16  C17  119.86  3.000
 L0I  C29  C16  N15  109.80  3.000
 L0I  C17  C16  N15  130.34  3.000
 L0I  H40  C17  C18  121.08  3.000
 L0I  C18  C17  C16  117.92  3.000
 L0I  H40  C17  C16  121.00  3.000
 L0I  H41  C18  C19  119.00  3.000
 L0I  C19  C18  C17  121.77  3.000
 L0I  H41  C18  C17  119.22  3.000
 L0I  C28  C19  C20  119.01  3.000
 L0I  C28  C19  C18  120.85  3.000
 L0I  C20  C19  C18  120.13  3.000
 L0I  H43  C20  H42  108.40  3.000
 L0I  H42  C20  N21  105.69  3.000
 L0I  H43  C20  N21  106.42  3.000
 L0I  H42  C20  C19  111.22  3.000
 L0I  H43  C20  C19  112.23  3.000
 L0I  N21  C20  C19  112.52  3.000
 L0I  H22  N21  C27  108.00  3.000
 L0I  C27  N21  C23  110.24  3.000
 L0I  H22  N21  C23  107.81  3.000
 L0I  C23  N21  C20  110.60  3.000
 L0I  C27  N21  C20  112.94  3.000
 L0I  H22  N21  C20  107.03  3.000
 L0I  H45  C23  H44  108.97  3.000
 L0I  H45  C23  C24  111.57  3.000
 L0I  H44  C23  C24  111.00  3.000
 L0I  H45  C23  N21  106.90  3.000
 L0I  H44  C23  N21  107.82  3.000
 L0I  C24  C23  N21  110.43  3.000
 L0I  H47  C24  H46  107.69  3.000
 L0I  H47  C24  O25  108.25  3.000
 L0I  H46  C24  O25  110.97  3.000
 L0I  H47  C24  C23  108.38  3.000
 L0I  O25  C24  C23  111.45  3.000
 L0I  H46  C24  C23  109.97  3.000
 L0I  C26  O25  C24  110.70  3.000
 L0I  H49  C26  H48  107.62  3.000
 L0I  H49  C26  C27  108.27  3.000
 L0I  H48  C26  C27  110.00  3.000
 L0I  C27  C26  O25  111.72  3.000
 L0I  H49  C26  O25  108.14  3.000
 L0I  H48  C26  O25  110.93  3.000
 L0I  H51  C27  H50  109.07  3.000
 L0I  H50  C27  C26  111.60  3.000
 L0I  H51  C27  C26  110.43  3.000
 L0I  H50  C27  N21  106.96  3.000
 L0I  H51  C27  N21  108.43  3.000
 L0I  C26  C27  N21  110.24  3.000
 L0I  H52  C28  C29  121.61  3.000
 L0I  H52  C28  C19  121.29  3.000
 L0I  C29  C28  C19  117.09  3.000
 L0I  N30  C29  C28  132.58  3.000
 L0I  N30  C29  C16  104.90  3.000
 L0I  C28  C29  C16  122.51  3.000
 L0I  H31  N30  C29  127.06  3.000
 L0I  H31  N30  C14  125.74  3.000
 L0I  C29  N30  C14  107.20  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
 L0I  CONST_01  N10  N12  C13  C8      0.00   0.0  0
 L0I  CONST_02  N15  C14  C13  C8      0.00   0.0  0
 L0I  CONST_03  N30  C14  C13  C8    180.00   0.0  0
 L0I  CONST_04  N12  N10  C9   C8      0.00   0.0  0
 L0I  CONST_05  N12  C13  C8   C9      0.00   0.0  0
 L0I  CONST_06  C14  C13  C8   C9    180.00   0.0  0
 L0I  CONST_07  C13  N12  N10  C9      0.00   0.0  0
 L0I  CONST_08  C13  C8   C9   N10     0.00   0.0  0
 L0I  CONST_09  C14  C13  N12  N10   180.00   0.0  0
 L0I  CONST_10  N15  C14  C13  N12   180.00   0.0  0
 L0I  CONST_11  N30  C14  C13  N12     0.00   0.0  0
 L0I  CONST_12  C16  N15  C14  C13   180.00   0.0  0
 L0I  CONST_13  C29  N30  C14  C13   180.00   0.0  0
 L0I  CONST_14  C17  C16  N15  C14   180.00   0.0  0
 L0I  CONST_15  C29  C16  N15  C14     0.00   0.0  0
 L0I  CONST_16  C16  C29  N30  C14     0.00   0.0  0
 L0I  CONST_17  C28  C29  N30  C14   180.00   0.0  0
 L0I  CONST_18  C29  N30  C14  N15     0.00   0.0  0
 L0I  CONST_19  C18  C17  C16  N15   180.00   0.0  0
 L0I  CONST_20  C28  C29  C16  N15   180.00   0.0  0
 L0I  CONST_21  N30  C29  C16  N15     0.00   0.0  0
 L0I  CONST_22  N30  C14  N15  C16     0.00   0.0  0
 L0I  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 L0I  CONST_24  C19  C28  C29  C16     0.00   0.0  0
 L0I  CONST_25  C28  C29  C16  C17     0.00   0.0  0
 L0I  CONST_26  N30  C29  C16  C17   180.00   0.0  0
 L0I  CONST_27  C28  C19  C18  C17     0.00   0.0  0
 L0I  CONST_28  C29  C16  C17  C18     0.00   0.0  0
 L0I  CONST_29  C29  C28  C19  C18     0.00   0.0  0
 L0I  CONST_30  N30  C29  C28  C19   180.00   0.0  0
 L0I  CONST_31  N12  C13  C8   N7    180.00   0.0  0
 L0I  CONST_32  C14  C13  C8   N7      0.00   0.0  0
 L0I  CONST_33  N10  C9   C8   N7    180.00   0.0  0
 L0I  CONST_34  C20  C19  C18  C17   180.00   0.0  0
 L0I  CONST_35  C29  C28  C19  C20   180.00   0.0  0
 L0I  CONST_36  H11  N10  C9   C8    180.00   0.0  0
 L0I  CONST_37  H39  C9   N10  N12   180.00   0.0  0
 L0I  CONST_38  H31  N30  C14  C13     0.00   0.0  0
 L0I  CONST_39  H40  C17  C16  N15     0.00   0.0  0
 L0I  CONST_40  H41  C18  C17  C16   180.00   0.0  0
 L0I  CONST_41  H52  C28  C29  C16   180.00   0.0  0
 L0I  CONST_42  C13  C8   N7   C2    180.00   0.0  0
 L0I  CONST_43  C9   C8   N7   C2      0.00   0.0  0
 L0I  CONST_44  H38  N7   C8   C9    180.00   0.0  0
 L0I  CONST_45  C4   N3   C2   O1      0.00   0.0  0
 L0I  CONST_46  C8   N7   C2   O1      0.00   0.0  0
 L0I  CONST_47  C8   N7   C2   N3    180.00   0.0  0
 L0I  CONST_48  N7   C2   N3   C4    180.00   0.0  0
 L0I  CONST_49  H32  N3   C2   O1    180.00   0.0  0
 L0I  Var_01    O25  C26  C27  N21    56.56  30.0  1
 L0I  Var_02    O25  C24  C23  N21   -56.65  30.0  1
 L0I  Var_03    C27  C26  O25  C24   -60.91  30.0  1
 L0I  Var_04    C6   C5   C4   N3    109.34  30.0  1
 L0I  Var_05    N21  C20  C19  C18    98.20  30.0  2
 L0I  Var_06    H37  C6   C5   C4    107.22  30.0  1
 L0I  Var_07    C5   C4   N3   C2   -143.80  30.0  2

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
 L0I  chir_02  N21  C20  C27  C23  positiv
 L0I  chir_03  C4   N3   C5   C6   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
 L0I  plan-1  N7   0.020
 L0I  plan-1  C8   0.020
 L0I  plan-1  C9   0.020
 L0I  plan-1  N10  0.020
 L0I  plan-1  N12  0.020
 L0I  plan-1  C13  0.020
 L0I  plan-1  C14  0.020
 L0I  plan-1  H11  0.020
 L0I  plan-1  H39  0.020
 L0I  plan-2  C13  0.020
 L0I  plan-2  C14  0.020
 L0I  plan-2  N15  0.020
 L0I  plan-2  C16  0.020
 L0I  plan-2  C17  0.020
 L0I  plan-2  C18  0.020
 L0I  plan-2  C19  0.020
 L0I  plan-2  C20  0.020
 L0I  plan-2  C28  0.020
 L0I  plan-2  C29  0.020
 L0I  plan-2  N30  0.020
 L0I  plan-2  H31  0.020
 L0I  plan-2  H40  0.020
 L0I  plan-2  H41  0.020
 L0I  plan-2  H52  0.020
 L0I  plan-3  O1   0.020
 L0I  plan-3  C2   0.020
 L0I  plan-3  N3   0.020
 L0I  plan-3  C4   0.020
 L0I  plan-3  N7   0.020
 L0I  plan-3  C8   0.020
 L0I  plan-3  H32  0.020
 L0I  plan-3  H38  0.020

