# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:13:36 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-amino-4-({3-[2-(2-propoxyethoxy)ethoxy]propyl}amino)cyclobut-3-ene-1,2-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOCCOCCOCCCNC1=C(N)C(=O)C1=O
#
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
 LNQ  LNQ  3-amino-4-({3-[2-(2-propoxyethoxy)ethoxy]propyl}amino)cyclobut-3-ene-1,2-dione  ligand  45  21  .  2022-07-25  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_LNQ
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
 LNQ  C1    C  CH3   0  -0.673   3.9114  -1.1217  -6.8453
 LNQ  C2    C  CH2   0  -0.465   2.4472  -1.1953  -6.4346
 LNQ  C3    C  CH2   0  -0.119   1.9243   0.1632  -6.0120
 LNQ  O4    O  O2    0  -0.489   0.5754   0.0548  -5.6253
 LNQ  C5    C  CH2   0  -0.169   0.0219   1.2832  -5.2287
 LNQ  C6    C  CH2   0  -0.169  -1.4166   1.0914  -4.8226
 LNQ  O7    O  O2    0  -0.485  -1.4807   0.3098  -3.6571
 LNQ  C8    C  CH2   0  -0.169  -2.7936   0.1202  -3.1955
 LNQ  C9    C  CH2   0  -0.171  -2.7669  -0.6679  -1.9111
 LNQ  O10   O  O2    0  -0.487  -2.1321   0.0861  -0.9097
 LNQ  C11   C  CH2   0  -0.126  -2.0659  -0.5829   0.3242
 LNQ  C12   C  CH2   0  -0.481  -1.3559   0.3042   1.3284
 LNQ  C13   C  CH2   0  -0.294  -1.2883  -0.3614   2.6969
 LNQ  N14   N  NH1   0  -0.644  -0.6621   0.4892   3.6902
 LNQ  C15   C  C     0   0.244   0.5499   0.2912   4.1825
 LNQ  C16   C  C     0   0.219   1.5632  -0.7610   4.0390
 LNQ  C17   C  C     0   0.234   2.4301   0.0178   4.9850
 LNQ  C18   C  C     0   0.178   1.3667   1.0123   5.0665
 LNQ  O19   O  OC    0  -0.444   1.6586  -1.8013   3.4196
 LNQ  O20   O  OC    0  -0.446   3.5348  -0.1063   5.4753
 LNQ  N21   N  NH2   0  -0.820   1.2515   2.1547   5.7245
 LNQ  H11   H  HCH3  0   0.236   4.2862  -2.0985  -7.1494
 LNQ  H12   H  HCH3  0   0.222   4.0571  -0.4370  -7.6829
 LNQ  H13   H  HCH3  0   0.222   4.5362  -0.7713  -6.0216
 LNQ  H21   H  HCH2  0   0.224   1.8446  -1.5749  -7.2640
 LNQ  H22   H  HCH2  0   0.224   2.3302  -1.9013  -5.6082
 LNQ  H31   H  HCH2  0   0.191   2.5337   0.5548  -5.1836
 LNQ  H32   H  HCH2  0   0.191   2.0308   0.8769  -6.8424
 LNQ  H51   H  HCH2  0   0.203   0.5896   1.7212  -4.3948
 LNQ  H52   H  HCH2  0   0.205   0.0521   2.0123  -6.0503
 LNQ  H61   H  HCH2  0   0.206  -1.8579   2.0842  -4.6560
 LNQ  H62   H  HCH2  0   0.204  -1.9813   0.6265  -5.6445
 LNQ  H81   H  HCH2  0   0.204  -3.2985   1.0838  -3.0341
 LNQ  H82   H  HCH2  0   0.207  -3.3965  -0.4360  -3.9271
 LNQ  H91   H  HCH2  0   0.207  -3.8019  -0.9063  -1.6294
 LNQ  H92   H  HCH2  0   0.205  -2.2524  -1.6262  -2.0707
 LNQ  H111  H  HCH2  0   0.198  -3.0747  -0.8303   0.6882
 LNQ  H112  H  HCH2  0   0.200  -1.5278  -1.5365   0.2198
 LNQ  H121  H  HCH2  0   0.239  -0.3429   0.5225   0.9799
 LNQ  H122  H  HCH2  0   0.237  -1.8831   1.2590   1.4107
 LNQ  H131  H  HCH2  0   0.253  -2.2918  -0.6180   3.0436
 LNQ  H132  H  HCH2  0   0.261  -0.7271  -1.2927   2.6397
 LNQ  H141  H  HNH1  0   0.406  -1.1413   1.3451   3.9262
 LNQ  H211  H  HNH2  0   0.417   1.9975   2.4788   6.3160
 LNQ  H212  H  HNH2  0   0.416   0.4555   2.7596   5.6191

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
 LNQ  C1   C2    single    1.523  0.020  1.523
 LNQ  C1   H11   single    0.970  0.020  1.090
 LNQ  C1   H12   single    0.970  0.020  1.090
 LNQ  C1   H13   single    0.970  0.020  1.090
 LNQ  C2   C3    single    1.516  0.020  1.516
 LNQ  C2   H21   single    0.970  0.020  1.090
 LNQ  C2   H22   single    0.970  0.020  1.090
 LNQ  C3   O4    single    1.407  0.020  1.407
 LNQ  C3   H31   single    0.970  0.020  1.090
 LNQ  C3   H32   single    0.970  0.020  1.090
 LNQ  O4   C5    single    1.404  0.020  1.404
 LNQ  C5   C6    single    1.507  0.020  1.507
 LNQ  C5   H51   single    0.970  0.020  1.090
 LNQ  C5   H52   single    0.970  0.020  1.090
 LNQ  C6   O7    single    1.405  0.020  1.405
 LNQ  C6   H61   single    0.970  0.020  1.090
 LNQ  C6   H62   single    0.970  0.020  1.090
 LNQ  O7   C8    single    1.405  0.020  1.405
 LNQ  C8   C9    single    1.507  0.020  1.507
 LNQ  C8   H81   single    0.970  0.020  1.090
 LNQ  C8   H82   single    0.970  0.020  1.090
 LNQ  C9   O10   single    1.405  0.020  1.405
 LNQ  C9   H91   single    0.970  0.020  1.090
 LNQ  C9   H92   single    0.970  0.020  1.090
 LNQ  O10  C11   single    1.405  0.020  1.405
 LNQ  C11  C12   single    1.516  0.020  1.516
 LNQ  C11  H111  single    0.970  0.020  1.090
 LNQ  C11  H112  single    0.970  0.020  1.090
 LNQ  C12  C13   single    1.523  0.020  1.523
 LNQ  C12  H121  single    0.970  0.020  1.090
 LNQ  C12  H122  single    0.970  0.020  1.090
 LNQ  C13  N14   single    1.450  0.020  1.450
 LNQ  C13  H131  single    0.970  0.020  1.090
 LNQ  C13  H132  single    0.970  0.020  1.090
 LNQ  N14  C15   single    1.323  0.020  1.323
 LNQ  N14  H141  single    0.860  0.020  1.020
 LNQ  C15  C16   aromatic  1.468  0.020  1.468
 LNQ  C15  C18   aromatic  1.403  0.020  1.403
 LNQ  C16  C17   aromatic  1.501  0.020  1.501
 LNQ  C16  O19   double    1.215  0.020  1.215
 LNQ  C17  C18   aromatic  1.458  0.020  1.458
 LNQ  C17  O20   double    1.215  0.020  1.215
 LNQ  C18  N21   single    1.323  0.020  1.323
 LNQ  N21  H211  single    0.860  0.020  1.020
 LNQ  N21  H212  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
 LNQ  H13   C1   H12   107.54  3.000
 LNQ  H13   C1   H11   107.55  3.000
 LNQ  H12   C1   H11   107.60  3.000
 LNQ  H13   C1   C2    111.25  3.000
 LNQ  H12   C1   C2    111.45  3.000
 LNQ  H11   C1   C2    111.27  3.000
 LNQ  H22   C2   H21   106.87  3.000
 LNQ  H22   C2   C3    109.34  3.000
 LNQ  H21   C2   C3    109.43  3.000
 LNQ  H22   C2   C1    109.76  3.000
 LNQ  H21   C2   C1    110.01  3.000
 LNQ  C3    C2   C1    111.32  3.000
 LNQ  H32   C3   H31   106.49  3.000
 LNQ  H32   C3   O4    110.50  3.000
 LNQ  H31   C3   O4    110.57  3.000
 LNQ  H32   C3   C2    109.73  3.000
 LNQ  H31   C3   C2    109.74  3.000
 LNQ  O4    C3   C2    109.77  3.000
 LNQ  C5    O4   C3    112.83  3.000
 LNQ  H52   C5   H51   106.77  3.000
 LNQ  H52   C5   C6    108.19  3.000
 LNQ  H51   C5   C6    109.82  3.000
 LNQ  H52   C5   O4    111.00  3.000
 LNQ  H51   C5   O4    111.04  3.000
 LNQ  C6    C5   O4    109.93  3.000
 LNQ  H62   C6   H61   106.79  3.000
 LNQ  H62   C6   O7    111.18  3.000
 LNQ  H61   C6   O7    111.00  3.000
 LNQ  H62   C6   C5    110.02  3.000
 LNQ  H61   C6   C5    108.00  3.000
 LNQ  O7    C6   C5    109.75  3.000
 LNQ  C8    O7   C6    112.98  3.000
 LNQ  H82   C8   H81   106.81  3.000
 LNQ  H82   C8   C9    108.20  3.000
 LNQ  H81   C8   C9    109.95  3.000
 LNQ  H82   C8   O7    111.25  3.000
 LNQ  H81   C8   O7    111.05  3.000
 LNQ  C9    C8   O7    109.52  3.000
 LNQ  H92   C9   H91   106.79  3.000
 LNQ  H92   C9   O10   111.09  3.000
 LNQ  H91   C9   O10   111.05  3.000
 LNQ  H92   C9   C8    109.90  3.000
 LNQ  H91   C9   C8    108.38  3.000
 LNQ  O10   C9   C8    109.56  3.000
 LNQ  C11   O10  C9    113.06  3.000
 LNQ  H112  C11  H111  106.55  3.000
 LNQ  H112  C11  C12   109.94  3.000
 LNQ  H111  C11  C12   109.98  3.000
 LNQ  H112  C11  O10   110.64  3.000
 LNQ  H111  C11  O10   110.75  3.000
 LNQ  C12   C11  O10   108.97  3.000
 LNQ  H122  C12  H121  107.23  3.000
 LNQ  H122  C12  C13   109.59  3.000
 LNQ  H121  C12  C13   109.42  3.000
 LNQ  H122  C12  C11   109.56  3.000
 LNQ  H121  C12  C11   109.85  3.000
 LNQ  C13   C12  C11   111.11  3.000
 LNQ  H132  C13  H131  106.81  3.000
 LNQ  H132  C13  N14   108.37  3.000
 LNQ  H131  C13  N14   108.49  3.000
 LNQ  H132  C13  C12   110.45  3.000
 LNQ  H131  C13  C12   110.31  3.000
 LNQ  N14   C13  C12   112.23  3.000
 LNQ  H141  N14  C15   118.36  3.000
 LNQ  H141  N14  C13   116.92  3.000
 LNQ  C15   N14  C13   124.25  3.000
 LNQ  C18   C15  C16    91.61  3.000
 LNQ  C18   C15  N14   133.69  3.000
 LNQ  C16   C15  N14   134.70  3.000
 LNQ  O19   C16  C17   136.10  3.000
 LNQ  O19   C16  C15   135.89  3.000
 LNQ  C17   C16  C15    88.01  3.000
 LNQ  O20   C17  C18   135.25  3.000
 LNQ  O20   C17  C16   136.59  3.000
 LNQ  C18   C17  C16    88.16  3.000
 LNQ  N21   C18  C17   132.85  3.000
 LNQ  N21   C18  C15   134.93  3.000
 LNQ  C17   C18  C15    92.22  3.000
 LNQ  H212  N21  H211  117.06  3.000
 LNQ  H212  N21  C18   122.43  3.000
 LNQ  H211  N21  C18   120.40  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
 LNQ  CONST_01  C18   C17  C16  C15     0.00   0.0  0
 LNQ  CONST_02  C17   C16  C15  N14   180.00   0.0  0
 LNQ  CONST_03  C17   C18  C15  N14   180.00   0.0  0
 LNQ  CONST_04  O20   C17  C16  C15   180.00   0.0  0
 LNQ  CONST_05  O20   C17  C18  C15   180.00   0.0  0
 LNQ  CONST_06  N21   C18  C15  C16   180.00   0.0  0
 LNQ  CONST_07  N21   C18  C17  C16   180.00   0.0  0
 LNQ  CONST_08  O19   C16  C15  C18   180.00   0.0  0
 LNQ  CONST_09  O19   C16  C17  C18   180.00   0.0  0
 LNQ  CONST_10  C16   C15  N14  C13     0.00   0.0  0
 LNQ  CONST_11  C18   C15  N14  C13   180.00   0.0  0
 LNQ  CONST_12  H211  N21  C18  C15   180.00   0.0  0
 LNQ  CONST_13  H212  N21  C18  C15     0.00   0.0  0
 LNQ  CONST_14  H141  N14  C15  C16   180.00   0.0  0
 LNQ  Var_01    C15   N14  C13  C12  -107.29  30.0  3
 LNQ  Var_02    O4    C3   C2   C1   -179.33  30.0  3
 LNQ  Var_03    C6    C5   O4   C3   -179.70  30.0  3
 LNQ  Var_04    O7    C6   C5   O4     66.73  30.0  3
 LNQ  Var_05    C9    C8   O7   C6   -177.26  30.0  3
 LNQ  Var_06    O10   C9   C8   O7     65.21  30.0  3
 LNQ  Var_07    C12   C11  O10  C9    179.48  30.0  3
 LNQ  Var_08    C13   C12  C11  O10   178.56  30.0  3
 LNQ  Var_09    N14   C13  C12  C11  -177.65  30.0  3
 LNQ  Var_10    H11   C1   C2   C3   -179.97  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
 LNQ  plan-1  C13   0.020
 LNQ  plan-1  N14   0.020
 LNQ  plan-1  C15   0.020
 LNQ  plan-1  H141  0.020
 LNQ  plan-2  C18   0.020
 LNQ  plan-2  N21   0.020
 LNQ  plan-2  H211  0.020
 LNQ  plan-2  H212  0.020
 LNQ  plan-3  C15   0.020
 LNQ  plan-3  C16   0.020
 LNQ  plan-3  C17   0.020
 LNQ  plan-3  O19   0.020
 LNQ  plan-4  C16   0.020
 LNQ  plan-4  C17   0.020
 LNQ  plan-4  C18   0.020
 LNQ  plan-4  O20   0.020

