# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 20:03:11 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-({4-[(3-aminopropyl)amino]butyl}amino)ethane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(O)(O)NCCCCNCCCN
#
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
 X54  X54  1-({4-[(3-aminopropyl)amino]butyl}amino)ethane-1,1-diol  ligand  37  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X54
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
 X54  C13  C  CH2   0  -0.265  29.5906  39.9091  33.0453
 X54  C01  C  CH3   0  -0.714  18.8199  40.2978  34.9448
 X54  C02  C  CT    0   0.598  20.0823  39.8056  34.2371
 X54  C06  C  CH2   0  -0.250  22.5317  40.1220  34.3383
 X54  C07  C  CH2   0  -0.443  23.6455  40.4334  35.3265
 X54  C08  C  CH2   0  -0.431  25.0278  40.3065  34.6993
 X54  C09  C  CH2   0  -0.263  26.1399  40.6058  35.6958
 X54  C11  C  CH2   0  -0.276  27.9429  39.2009  34.8592
 X54  C12  C  CH2   0  -0.457  29.3826  39.1872  34.3686
 X54  N05  N  NH1   0  -0.650  21.2309  40.2657  34.9713
 X54  N10  N  NH1   0  -0.596  27.4644  40.5503  35.1022
 X54  N14  N  NH2   0  -0.799  30.9729  39.7790  32.5994
 X54  O03  O  OH1   0  -0.658  20.1064  38.4106  34.1460
 X54  O04  O  OH1   0  -0.664  20.0690  40.1757  32.8809
 X54  H1   H  HCH2  0   0.191  29.2581  40.9498  33.1451
 X54  H2   H  HCH2  0   0.206  28.9441  39.4526  32.2897
 X54  H3   H  HCH3  0   0.233  18.7938  39.9607  35.9815
 X54  H4   H  HCH3  0   0.228  18.7674  41.3885  34.9509
 X54  H5   H  HCH3  0   0.241  17.9324  39.9207  34.4374
 X54  H6   H  HCH2  0   0.216  22.6416  39.0923  33.9916
 X54  H7   H  HCH2  0   0.194  22.6489  40.7631  33.4541
 X54  H8   H  HCH2  0   0.212  23.5142  41.4495  35.7159
 X54  H9   H  HCH2  0   0.215  23.5635  39.7605  36.1853
 X54  H10  H  HCH2  0   0.217  25.1430  39.2960  34.2953
 X54  H11  H  HCH2  0   0.212  25.1169  40.9921  33.8510
 X54  H12  H  HCH2  0   0.221  25.9930  41.6153  36.0890
 X54  H13  H  HCH2  0   0.179  26.0418  39.9196  36.5542
 X54  H14  H  HCH2  0   0.215  27.3075  38.7295  34.1039
 X54  H15  H  HCH2  0   0.194  27.8652  38.5684  35.7591
 X54  H16  H  HCH2  0   0.224  29.7055  38.1484  34.2619
 X54  H17  H  HCH2  0   0.213  30.0309  39.6315  35.1337
 X54  H18  H  HNH1  0   0.348  21.0966  41.2190  35.2854
 X54  H20  H  HNH1  0   0.340  28.1155  41.0083  35.7283
 X54  H22  H  HNH2  0   0.342  31.0851  40.2569  31.7141
 X54  H23  H  HNH2  0   0.334  31.5764  40.2714  33.2474
 X54  H25  H  HOH1  0   0.446  20.1945  38.0644  35.0401
 X54  H26  H  HOH1  0   0.447  20.0305  41.1365  32.8272

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
 X54  N14  C13  single  1.458  0.020  1.458
 X54  C13  C12  single  1.522  0.020  1.522
 X54  O04  C02  single  1.406  0.020  1.406
 X54  C02  O03  single  1.398  0.020  1.398
 X54  C02  C01  single  1.529  0.020  1.529
 X54  C02  N05  single  1.439  0.020  1.439
 X54  C12  C11  single  1.521  0.020  1.521
 X54  C06  N05  single  1.454  0.020  1.454
 X54  C06  C07  single  1.521  0.020  1.521
 X54  C08  C07  single  1.523  0.020  1.523
 X54  C08  C09  single  1.523  0.020  1.523
 X54  C11  N10  single  1.452  0.020  1.452
 X54  N10  C09  single  1.452  0.020  1.452
 X54  C13  H1   single  0.970  0.020  1.090
 X54  C13  H2   single  0.970  0.020  1.090
 X54  C01  H3   single  0.970  0.020  1.090
 X54  C01  H4   single  0.970  0.020  1.090
 X54  C01  H5   single  0.970  0.020  1.090
 X54  C06  H6   single  0.970  0.020  1.090
 X54  C06  H7   single  0.970  0.020  1.090
 X54  C07  H8   single  0.970  0.020  1.090
 X54  C07  H9   single  0.970  0.020  1.090
 X54  C08  H10  single  0.970  0.020  1.090
 X54  C08  H11  single  0.970  0.020  1.090
 X54  C09  H12  single  0.970  0.020  1.090
 X54  C09  H13  single  0.970  0.020  1.090
 X54  C11  H14  single  0.970  0.020  1.090
 X54  C11  H15  single  0.970  0.020  1.090
 X54  C12  H16  single  0.970  0.020  1.090
 X54  C12  H17  single  0.970  0.020  1.090
 X54  N05  H18  single  0.890  0.020  1.040
 X54  N10  H20  single  0.890  0.020  1.040
 X54  N14  H22  single  0.890  0.020  1.040
 X54  N14  H23  single  0.890  0.020  1.040
 X54  O03  H25  single  0.850  0.020  0.980
 X54  O04  H26  single  0.850  0.020  0.980

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
 X54  H2   C13  H1   106.23  3.000
 X54  H2   C13  N14  108.16  3.000
 X54  H1   C13  N14  113.56  3.000
 X54  H2   C13  C12  108.77  3.000
 X54  H1   C13  C12  109.24  3.000
 X54  N14  C13  C12  110.68  3.000
 X54  H5   C01  H4   108.01  3.000
 X54  H5   C01  H3   108.44  3.000
 X54  H4   C01  H3   107.59  3.000
 X54  H5   C01  C02  110.22  3.000
 X54  H4   C01  C02  111.34  3.000
 X54  H3   C01  C02  111.12  3.000
 X54  O04  C02  O03  101.53  3.000
 X54  O03  C02  N05  109.79  3.000
 X54  O04  C02  N05  114.56  3.000
 X54  N05  C02  C01  108.67  3.000
 X54  O03  C02  C01  111.45  3.000
 X54  O04  C02  C01  110.73  3.000
 X54  H7   C06  H6   106.50  3.000
 X54  H7   C06  N05  112.85  3.000
 X54  H6   C06  N05  108.75  3.000
 X54  H7   C06  C07  108.99  3.000
 X54  H6   C06  C07  109.00  3.000
 X54  N05  C06  C07  110.61  3.000
 X54  H9   C07  H8   106.40  3.000
 X54  H9   C07  C08  109.87  3.000
 X54  H8   C07  C08  109.40  3.000
 X54  H9   C07  C06  109.22  3.000
 X54  H8   C07  C06  109.45  3.000
 X54  C08  C07  C06  112.32  3.000
 X54  H11  C08  H10  106.48  3.000
 X54  H11  C08  C09  108.94  3.000
 X54  H10  C08  C09  110.26  3.000
 X54  H11  C08  C07  109.93  3.000
 X54  H10  C08  C07  108.93  3.000
 X54  C09  C08  C07  112.14  3.000
 X54  H13  C09  H12  106.41  3.000
 X54  H13  C09  N10  112.04  3.000
 X54  H12  C09  N10  107.75  3.000
 X54  H13  C09  C08  108.78  3.000
 X54  H12  C09  C08  108.59  3.000
 X54  N10  C09  C08  113.02  3.000
 X54  H15  C11  H14  105.99  3.000
 X54  H15  C11  N10  111.91  3.000
 X54  H14  C11  N10  108.94  3.000
 X54  H15  C11  C12  108.95  3.000
 X54  H14  C11  C12  108.86  3.000
 X54  N10  C11  C12  111.97  3.000
 X54  H17  C12  H16  106.17  3.000
 X54  H17  C12  C11  109.32  3.000
 X54  H16  C12  C11  108.65  3.000
 X54  H17  C12  C13  109.49  3.000
 X54  H16  C12  C13  109.00  3.000
 X54  C11  C12  C13  113.93  3.000
 X54  H18  N05  C06  110.29  3.000
 X54  H18  N05  C02  110.70  3.000
 X54  C06  N05  C02  117.42  3.000
 X54  H20  N10  C11  108.17  3.000
 X54  H20  N10  C09  108.44  3.000
 X54  C11  N10  C09  113.85  3.000
 X54  H23  N14  H22  105.30  3.000
 X54  H23  N14  C13  109.01  3.000
 X54  H22  N14  C13  109.29  3.000
 X54  H25  O03  C02  107.45  3.000
 X54  H26  O04  C02  108.47  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
 X54  Var_01  N10  C11  C12  C13   -61.69  30.0  3
 X54  Var_02  C06  N05  C02  C01  -168.80  30.0  3
 X54  Var_03  C07  C06  N05  C02  -170.47  30.0  1
 X54  Var_04  C09  C08  C07  C06  -179.44  30.0  1
 X54  Var_05  N10  C09  C08  C07  -177.35  30.0  3
 X54  Var_06  N05  C06  C07  C08  -179.50  30.0  1
 X54  Var_07  C11  N10  C09  C08   -75.58  30.0  1
 X54  Var_08  C12  C11  N10  C09  -174.30  30.0  1
 X54  Var_09  N14  C13  C12  C11  -176.33  30.0  1
 X54  Var_10  H22  N14  C13  C12   179.37  30.0  3
 X54  Var_11  H3   C01  C02  N05   -56.91  30.0  3

