# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:45:24 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[2,2-bis(hydroxymethyl)-5-oxo-pyrrolidin-1-yl]-3-[(dipropylamino)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(CCC)Cc1cc(ccc1N2C(=O)CCC2(CO)CO)C(O)=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
 3LV  3LV  '4-[2,2-bis(hydroxymethyl)-5-oxo-pyrrolidin-1-yl]-3-[(dipropylamino)methyl]benzoic acid'  ligand  57  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3LV
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
 3LV  C1    C  C     0   0.533  -3.0003   2.9274   1.0241
 3LV  O1    O  OH1   0  -0.594  -2.9220   4.2462   1.1342
 3LV  C2    C  CR6   0  -0.053  -1.6727   2.2799   0.8801
 3LV  O2    O  O     0  -0.436  -4.0459   2.3236   1.0413
 3LV  C3    C  CR16  0  -0.316  -1.6233   0.8957   0.7784
 3LV  C4    C  CR6   0   0.108  -0.4221   0.2110   0.6378
 3LV  C5    C  CR6   0   0.256   0.7625   0.9560   0.5922
 3LV  N5    N  NT    0  -0.599   2.0242   0.3242   0.4426
 3LV  C6    C  CR16  0  -0.255   0.7163   2.3422   0.7236
 3LV  C7    C  CR16  0  -0.286  -0.4866   3.0086   0.8569
 3LV  C8    C  CH2   0  -0.338  -0.4498  -1.2981   0.6028
 3LV  N8    N  NT    0  -0.422  -1.6508  -1.8188  -0.0137
 3LV  C9    C  CH2   0  -0.267  -1.6056  -1.6673  -1.4594
 3LV  C10   C  CH2   0  -0.437  -2.9711  -1.7430  -2.1279
 3LV  C11   C  CH3   0  -0.665  -2.8713  -1.5271  -3.6316
 3LV  C12   C  CH2   0  -0.268  -1.9349  -3.1781   0.4193
 3LV  C13   C  CH2   0  -0.434  -2.5475  -3.2397   1.8127
 3LV  C14   C  CH3   0  -0.666  -2.8742  -4.6672   2.2278
 3LV  C15   C  C     0   0.528   2.5256  -0.4799   1.4207
 3LV  O15   O  O     0  -0.472   2.0119  -0.6442   2.5098
 3LV  C16   C  CH2   0  -0.593   3.7814  -1.1237   0.8947
 3LV  C17   C  CH2   0  -0.466   4.1567  -0.2728  -0.3099
 3LV  C18   C  CT    0   0.059   2.8296   0.3352  -0.7954
 3LV  C19   C  CH2   0  -0.127   2.1209  -0.5651  -1.8119
 3LV  O19   O  OH1   0  -0.654   2.8381  -0.6084  -3.0154
 3LV  C20   C  CH2   0  -0.154   3.0294   1.7672  -1.2996
 3LV  O20   O  OH1   0  -0.656   4.0399   1.7914  -2.2747
 3LV  HO1   H  HOH1  0   0.488  -3.8089   4.6223   1.2353
 3LV  H3    H  HCR6  0   0.260  -2.5358   0.3150   0.7963
 3LV  H6    H  HCR6  0   0.275   1.6352   2.9111   0.7360
 3LV  H7    H  HCR6  0   0.269  -0.4826   4.0852   0.9504
 3LV  H8    H  HCH2  0   0.216   0.4568  -1.6933   0.1226
 3LV  H8A   H  HCH2  0   0.271  -0.4010  -1.6416   1.6386
 3LV  H9    H  HCH2  0   0.228  -1.1840  -0.6817  -1.6785
 3LV  H9A   H  HCH2  0   0.194  -0.9219  -2.4008  -1.9221
 3LV  H10   H  HCH2  0   0.221  -3.4407  -2.7104  -1.9347
 3LV  H10A  H  HCH2  0   0.219  -3.6226  -0.9878  -1.6811
 3LV  H11   H  HCH3  0   0.231  -3.8513  -1.5845  -4.1053
 3LV  H11A  H  HCH3  0   0.218  -2.4486  -0.5480  -3.8642
 3LV  H11B  H  HCH3  0   0.219  -2.2344  -2.2803  -4.0989
 3LV  H12   H  HCH2  0   0.230  -2.6476  -3.6229  -0.2777
 3LV  H12A  H  HCH2  0   0.194  -1.0348  -3.8148   0.3772
 3LV  H13   H  HCH2  0   0.218  -1.8712  -2.7970   2.5490
 3LV  H13A  H  HCH2  0   0.219  -3.4520  -2.6268   1.8197
 3LV  H14   H  HCH3  0   0.218  -3.5911  -5.1246   1.5435
 3LV  H14A  H  HCH3  0   0.219  -1.9798  -5.2924   2.2340
 3LV  H14B  H  HCH3  0   0.231  -3.3063  -4.7000   3.2281
 3LV  H16   H  HCH2  0   0.284   4.5531  -1.1658   1.6619
 3LV  H16A  H  HCH2  0   0.278   3.5449  -2.1556   0.6185
 3LV  H17   H  HCH2  0   0.259   4.8329   0.5251   0.0006
 3LV  H17A  H  HCH2  0   0.265   4.6557  -0.8354  -1.0956
 3LV  H19   H  HCH2  0   0.205   2.0251  -1.5683  -1.3732
 3LV  H19A  H  HCH2  0   0.207   1.0999  -0.1849  -1.9661
 3LV  HO19  H  HOH1  0   0.457   2.4069  -1.2477  -3.5895
 3LV  H20   H  HCH2  0   0.209   2.0837   2.1674  -1.6905
 3LV  H20A  H  HCH2  0   0.216   3.3115   2.3815  -0.4360
 3LV  HO20  H  HOH1  0   0.456   4.3708   2.6921  -2.3254

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
 3LV  C2   C1    single    1.484  0.020  1.484
 3LV  C1   O2    double    1.208  0.020  1.208
 3LV  C1   O1    single    1.326  0.020  1.326
 3LV  O1   HO1   single    0.850  0.020  0.980
 3LV  C3   C2    aromatic  1.389  0.020  1.389
 3LV  C7   C2    aromatic  1.392  0.020  1.392
 3LV  C4   C3    aromatic  1.390  0.020  1.390
 3LV  C3   H3    single    0.930  0.020  1.080
 3LV  C8   C4    single    1.510  0.020  1.510
 3LV  C5   C4    aromatic  1.400  0.020  1.400
 3LV  N5   C5    single    1.419  0.020  1.419
 3LV  C5   C6    aromatic  1.393  0.020  1.393
 3LV  C18  N5    single    1.477  0.020  1.477
 3LV  N5   C15   single    1.362  0.020  1.362
 3LV  C6   C7    aromatic  1.382  0.020  1.382
 3LV  C6   H6    single    0.930  0.020  1.080
 3LV  C7   H7    single    0.930  0.020  1.080
 3LV  C8   N8    single    1.447  0.020  1.447
 3LV  C8   H8    single    0.970  0.020  1.090
 3LV  C8   H8A   single    0.970  0.020  1.090
 3LV  C9   N8    single    1.454  0.020  1.454
 3LV  N8   C12   single    1.455  0.020  1.455
 3LV  C9   C10   single    1.522  0.020  1.522
 3LV  C9   H9    single    0.970  0.020  1.090
 3LV  C9   H9A   single    0.970  0.020  1.090
 3LV  C11  C10   single    1.522  0.020  1.522
 3LV  C10  H10   single    0.970  0.020  1.090
 3LV  C10  H10A  single    0.970  0.020  1.090
 3LV  C11  H11   single    0.970  0.020  1.090
 3LV  C11  H11A  single    0.970  0.020  1.090
 3LV  C11  H11B  single    0.970  0.020  1.090
 3LV  C13  C12   single    1.523  0.020  1.523
 3LV  C12  H12   single    0.970  0.020  1.090
 3LV  C12  H12A  single    0.970  0.020  1.090
 3LV  C13  C14   single    1.522  0.020  1.522
 3LV  C13  H13   single    0.970  0.020  1.090
 3LV  C13  H13A  single    0.970  0.020  1.090
 3LV  C14  H14   single    0.970  0.020  1.090
 3LV  C14  H14A  single    0.970  0.020  1.090
 3LV  C14  H14B  single    0.970  0.020  1.090
 3LV  C16  C15   single    1.506  0.020  1.506
 3LV  C15  O15   double    1.215  0.020  1.215
 3LV  C17  C16   single    1.522  0.020  1.522
 3LV  C16  H16   single    0.970  0.020  1.090
 3LV  C16  H16A  single    0.970  0.020  1.090
 3LV  C17  C18   single    1.538  0.020  1.538
 3LV  C17  H17   single    0.970  0.020  1.090
 3LV  C17  H17A  single    0.970  0.020  1.090
 3LV  C20  C18   single    1.531  0.020  1.531
 3LV  C18  C19   single    1.532  0.020  1.532
 3LV  C19  O19   single    1.402  0.020  1.402
 3LV  C19  H19   single    0.970  0.020  1.090
 3LV  C19  H19A  single    0.970  0.020  1.090
 3LV  O19  HO19  single    0.850  0.020  0.980
 3LV  O20  C20   single    1.404  0.020  1.404
 3LV  C20  H20   single    0.970  0.020  1.090
 3LV  C20  H20A  single    0.970  0.020  1.090
 3LV  O20  HO20  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
 3LV  O2    C1   C2    123.90  3.000
 3LV  O2    C1   O1    123.19  3.000
 3LV  C2    C1   O1    112.91  3.000
 3LV  HO1   O1   C1    109.93  3.000
 3LV  C7    C2   C3    119.35  3.000
 3LV  C7    C2   C1    122.37  3.000
 3LV  C3    C2   C1    118.28  3.000
 3LV  H3    C3   C4    117.79  3.000
 3LV  H3    C3   C2    120.25  3.000
 3LV  C4    C3   C2    121.95  3.000
 3LV  C8    C4   C5    123.14  3.000
 3LV  C5    C4   C3    118.19  3.000
 3LV  C8    C4   C3    118.61  3.000
 3LV  C6    C5   N5    118.85  3.000
 3LV  C6    C5   C4    119.89  3.000
 3LV  N5    C5   C4    121.25  3.000
 3LV  C18   N5   C15   113.93  3.000
 3LV  C15   N5   C5    120.97  3.000
 3LV  C18   N5   C5    124.75  3.000
 3LV  H6    C6   C7    119.03  3.000
 3LV  H6    C6   C5    119.78  3.000
 3LV  C7    C6   C5    121.19  3.000
 3LV  H7    C7   C6    119.06  3.000
 3LV  H7    C7   C2    121.54  3.000
 3LV  C6    C7   C2    119.40  3.000
 3LV  H8A   C8   H8    105.32  3.000
 3LV  H8A   C8   N8    109.14  3.000
 3LV  H8    C8   N8    111.66  3.000
 3LV  H8A   C8   C4    106.95  3.000
 3LV  H8    C8   C4    110.75  3.000
 3LV  N8    C8   C4    112.63  3.000
 3LV  C12   N8   C9    113.53  3.000
 3LV  C12   N8   C8    111.81  3.000
 3LV  C9    N8   C8    111.12  3.000
 3LV  H9A   C9   H9    106.01  3.000
 3LV  H9A   C9   C10   109.77  3.000
 3LV  H9    C9   C10   107.61  3.000
 3LV  H9A   C9   N8    111.50  3.000
 3LV  H9    C9   N8    107.75  3.000
 3LV  C10   C9   N8    113.80  3.000
 3LV  H10A  C10  H10   106.46  3.000
 3LV  H10A  C10  C11   110.17  3.000
 3LV  H10   C10  C11   109.17  3.000
 3LV  H10A  C10  C9    108.71  3.000
 3LV  H10   C10  C9    110.61  3.000
 3LV  C11   C10  C9    111.58  3.000
 3LV  H11B  C11  H11A  107.57  3.000
 3LV  H11B  C11  H11   107.59  3.000
 3LV  H11A  C11  H11   107.63  3.000
 3LV  H11B  C11  C10   111.30  3.000
 3LV  H11A  C11  C10   111.29  3.000
 3LV  H11   C11  C10   111.27  3.000
 3LV  H12A  C12  H12   105.85  3.000
 3LV  H12A  C12  C13   109.86  3.000
 3LV  H12   C12  C13   107.76  3.000
 3LV  H12A  C12  N8    111.63  3.000
 3LV  H12   C12  N8    108.55  3.000
 3LV  C13   C12  N8    112.86  3.000
 3LV  H13A  C13  H13   106.30  3.000
 3LV  H13A  C13  C14   110.28  3.000
 3LV  H13   C13  C14   109.20  3.000
 3LV  H13A  C13  C12   108.43  3.000
 3LV  H13   C13  C12   110.54  3.000
 3LV  C14   C13  C12   111.94  3.000
 3LV  H14B  C14  H14A  107.60  3.000
 3LV  H14B  C14  H14   107.60  3.000
 3LV  H14A  C14  H14   107.56  3.000
 3LV  H14B  C14  C13   111.32  3.000
 3LV  H14A  C14  C13   111.28  3.000
 3LV  H14   C14  C13   111.28  3.000
 3LV  C16   C15  O15   127.42  3.000
 3LV  O15   C15  N5    124.60  3.000
 3LV  C16   C15  N5    107.97  3.000
 3LV  H16A  C16  H16   107.12  3.000
 3LV  H16A  C16  C17   112.39  3.000
 3LV  H16   C16  C17   113.86  3.000
 3LV  H16A  C16  C15   108.13  3.000
 3LV  H16   C16  C15   111.18  3.000
 3LV  C17   C16  C15   104.07  3.000
 3LV  H17A  C17  H17   107.43  3.000
 3LV  H17A  C17  C18   111.85  3.000
 3LV  H17   C17  C18   109.60  3.000
 3LV  H17A  C17  C16   113.31  3.000
 3LV  H17   C17  C16   109.67  3.000
 3LV  C18   C17  C16   104.95  3.000
 3LV  C20   C18  C19   113.05  3.000
 3LV  C19   C18  C17   112.10  3.000
 3LV  C20   C18  C17   111.16  3.000
 3LV  C19   C18  N5    107.43  3.000
 3LV  C20   C18  N5    110.74  3.000
 3LV  C17   C18  N5    101.71  3.000
 3LV  H19A  C19  H19   106.88  3.000
 3LV  H19A  C19  O19   111.42  3.000
 3LV  H19   C19  O19   111.05  3.000
 3LV  H19A  C19  C18   108.61  3.000
 3LV  H19   C19  C18   108.18  3.000
 3LV  O19   C19  C18   110.56  3.000
 3LV  HO19  O19  C19   107.68  3.000
 3LV  H20A  C20  H20   107.31  3.000
 3LV  H20A  C20  O20   110.61  3.000
 3LV  H20   C20  O20   111.47  3.000
 3LV  H20A  C20  C18   107.34  3.000
 3LV  H20   C20  C18   110.21  3.000
 3LV  O20   C20  C18   109.79  3.000
 3LV  HO20  O20  C20   107.49  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
 3LV  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 3LV  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 3LV  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 3LV  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 3LV  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 3LV  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 3LV  CONST_07  N5   C5   C4   C3    180.00   0.0  0
 3LV  CONST_08  C7   C6   C5   N5    180.00   0.0  0
 3LV  CONST_09  C16  C15  N5   C5    180.00   0.0  0
 3LV  CONST_10  C18  N5   C15  C16     0.00   0.0  0
 3LV  CONST_11  C4   C3   C2   C1    180.00   0.0  0
 3LV  CONST_12  C6   C7   C2   C1    180.00   0.0  0
 3LV  CONST_13  C8   C4   C3   C2    180.00   0.0  0
 3LV  CONST_14  C8   C4   C5   N5      0.00   0.0  0
 3LV  CONST_15  C8   C4   C5   C6    180.00   0.0  0
 3LV  CONST_16  O15  C15  N5   C5      0.00   0.0  0
 3LV  CONST_17  C18  N5   C15  O15   180.00   0.0  0
 3LV  CONST_18  H6   C6   C7   C2    180.00   0.0  0
 3LV  CONST_19  H7   C7   C2   C3    180.00   0.0  0
 3LV  CONST_20  H3   C3   C4   C5    180.00   0.0  0
 3LV  CONST_21  HO1  O1   C1   C2    180.00   0.0  0
 3LV  Var_01    C18  N5   C5   C4    106.28  30.0  2
 3LV  Var_02    C17  C18  N5   C5    170.74  30.0  1
 3LV  Var_03    C16  C17  C18  N5     25.41  30.0  1
 3LV  Var_04    C17  C16  C15  N5     16.90  30.0  1
 3LV  Var_05    C18  C17  C16  C15   -26.21  30.0  1
 3LV  Var_06    C3   C2   C1   O1    178.95  30.0  2
 3LV  Var_07    N8   C8   C4   C3     32.77  30.0  1
 3LV  Var_08    O20  C20  C18  N5    166.19  30.0  1
 3LV  Var_09    O19  C19  C18  N5   -179.65  30.0  3
 3LV  Var_10    C9   N8   C8   C4     75.17  30.0  3
 3LV  Var_11    C10  C9   N8   C8   -160.43  30.0  2
 3LV  Var_12    C13  C12  N8   C8     77.46  30.0  3
 3LV  Var_13    C11  C10  C9   N8    177.88  30.0  3
 3LV  Var_14    C14  C13  C12  N8    178.30  30.0  2
 3LV  Var_15    H11  C11  C10  C9    179.88  30.0  3
 3LV  Var_16    H14  C14  C13  C12   -60.32  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
 3LV  plan-1  C1   0.020
 3LV  plan-1  C2   0.020
 3LV  plan-1  C3   0.020
 3LV  plan-1  C4   0.020
 3LV  plan-1  C5   0.020
 3LV  plan-1  N5   0.020
 3LV  plan-1  C6   0.020
 3LV  plan-1  C7   0.020
 3LV  plan-1  C8   0.020
 3LV  plan-1  H3   0.020
 3LV  plan-1  H6   0.020
 3LV  plan-1  H7   0.020
 3LV  plan-2  C1   0.020
 3LV  plan-2  O1   0.020
 3LV  plan-2  C2   0.020
 3LV  plan-2  O2   0.020
 3LV  plan-2  HO1  0.020
 3LV  plan-3  C5   0.020
 3LV  plan-3  N5   0.020
 3LV  plan-3  C15  0.020
 3LV  plan-3  O15  0.020
 3LV  plan-3  C16  0.020
 3LV  plan-3  C18  0.020

