# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:04:29 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2E,6E)-3,7-dimethyl-8-(phenylamino)octa-2,6-dien-1-yl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(\CC\C=C(C)\CNc1ccccc1)=C/CO[P](O)(=O)O[P](O)(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
 A4S  A4S  '(2E,6E)-3,7-dimethyl-8-(phenylamino)octa-2,6-dien-1-yl trihydrogen diphosphate'  ligand  51  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A4S
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
 A4S  C01  C  CR16  0  -0.347   -7.3705  -1.8456  -1.2989
 A4S  C02  C  CR16  0  -0.245   -8.6577  -2.2806  -1.5547
 A4S  C03  C  CR16  0  -0.296   -9.7086  -1.9391  -0.7080
 A4S  C04  C  CR16  0  -0.245   -9.4384  -1.1435   0.3954
 A4S  C05  C  CR16  0  -0.354   -8.1515  -0.6930   0.6618
 A4S  C06  C  CR6   0   0.371   -7.0872  -1.0472  -0.1780
 A4S  N07  N  NH1   0  -0.687   -5.7883  -0.6697   0.0703
 A4S  C08  C  CH2   0  -0.327   -5.4596   0.3646   1.0268
 A4S  C09  C  C     0   0.060   -3.9674   0.4744   1.1936
 A4S  C10  C  C1    0  -0.247   -3.3564   1.6245   0.9026
 A4S  C11  C  CH2   0  -0.497   -1.8998   1.9479   1.0034
 A4S  C12  C  CH2   0  -0.487   -1.3130   2.2672  -0.3805
 A4S  C13  C  C     0   0.140    0.1466   2.6340  -0.3424
 A4S  C14  C  C1    0  -0.325    1.0399   1.8406  -0.9403
 A4S  C15  C  CH2   0  -0.235    2.5078   2.0576  -1.0365
 A4S  O16  O  O2    0  -0.576    3.1590   0.9463  -0.3654
 A4S  P17  P  P     0   1.482    4.7182   0.7212  -0.5391
 A4S  O18  O  OH1   0  -0.726    5.4762   1.7763   0.3733
 A4S  O19  O  O2    0  -0.684    4.7978  -0.6887   0.2541
 A4S  O20  O  O     0  -0.693    5.2691   0.7080  -1.9021
 A4S  P21  P  P     0   1.468    5.9941  -1.7753   0.1139
 A4S  O22  O  OH1   0  -0.724    5.6521  -2.6354  -1.1742
 A4S  O23  O  O     0  -0.691    7.3442  -1.2010   0.0276
 A4S  O24  O  OH1   0  -0.720    5.6059  -2.6184   1.4020
 A4S  C25  C  CH3   0  -0.734    0.4710   3.9075   0.3782
 A4S  C26  C  CH3   0  -0.716   -3.2897  -0.7648   1.6990
 A4S  H1   H  HCR6  0   0.252   -6.5647  -2.1258  -1.9682
 A4S  H2   H  HCR6  0   0.249   -8.8420  -2.8950  -2.4273
 A4S  H3   H  HCR6  0   0.244  -10.7144  -2.2825  -0.9096
 A4S  H4   H  HCR6  0   0.249  -10.2404  -0.8563   1.0644
 A4S  H5   H  HCR6  0   0.261   -7.9861  -0.0617   1.5246
 A4S  H6   H  HNH1  0   0.375   -5.1881  -0.6858  -0.7401
 A4S  H7   H  HCH2  0   0.229   -5.8832   1.3382   0.7458
 A4S  H8   H  HCH2  0   0.236   -5.8992   0.0965   1.9931
 A4S  H10  H  H     0   0.234   -3.9731   2.4400   0.5299
 A4S  H12  H  HCH2  0   0.242   -1.7822   2.8153   1.6594
 A4S  H13  H  HCH2  0   0.245   -1.3315   1.1342   1.4571
 A4S  H14  H  HCH2  0   0.245   -1.4600   1.4040  -1.0334
 A4S  H15  H  HCH2  0   0.238   -1.8809   3.0946  -0.8203
 A4S  H17  H  H     0   0.246    0.6802   0.9459  -1.4408
 A4S  H19  H  HCH2  0   0.254    2.8200   2.0712  -2.0838
 A4S  H20  H  HCH2  0   0.256    2.8297   2.9910  -0.5755
 A4S  H21  H  HOH1  0   0.504    5.1796   1.8459   1.2916
 A4S  H22  H  HOH1  0   0.504    4.8050  -3.1028  -1.1679
 A4S  H23  H  HOH1  0   0.511    6.2250  -3.3318   1.6116
 A4S  H24  H  HCH3  0   0.250    0.1923   3.8388   1.4313
 A4S  H25  H  HCH3  0   0.247    1.5223   4.1816   0.3376
 A4S  H26  H  HCH3  0   0.246   -0.1034   4.7357  -0.0426
 A4S  H27  H  HCH3  0   0.240   -3.3323  -1.5673   0.9600
 A4S  H28  H  HCH3  0   0.242   -2.2438  -0.6060   1.9515
 A4S  H29  H  HCH3  0   0.235   -3.7962  -1.1370   2.5923

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
 A4S  O20  P17  double    1.470  0.020  1.470
 A4S  O18  P17  single    1.588  0.020  1.588
 A4S  P17  O16  single    1.585  0.020  1.585
 A4S  P17  O19  single    1.620  0.020  1.620
 A4S  O23  P21  double    1.470  0.020  1.470
 A4S  O16  C15  single    1.452  0.020  1.452
 A4S  O22  P21  single    1.586  0.020  1.586
 A4S  O19  P21  single    1.622  0.020  1.622
 A4S  P21  O24  single    1.588  0.020  1.588
 A4S  C15  C14  single    1.487  0.020  1.487
 A4S  C25  C13  single    1.499  0.020  1.499
 A4S  C02  C01  aromatic  1.383  0.020  1.383
 A4S  C02  C03  aromatic  1.392  0.020  1.392
 A4S  C14  C13  double    1.336  0.020  1.336
 A4S  C01  C06  aromatic  1.405  0.020  1.405
 A4S  C03  C04  aromatic  1.387  0.020  1.387
 A4S  C13  C12  single    1.506  0.020  1.506
 A4S  C06  N07  single    1.375  0.020  1.375
 A4S  C06  C05  aromatic  1.401  0.020  1.401
 A4S  C04  C05  aromatic  1.389  0.020  1.389
 A4S  C12  C11  single    1.537  0.020  1.537
 A4S  N07  C08  single    1.447  0.020  1.447
 A4S  C11  C10  single    1.495  0.020  1.495
 A4S  C10  C09  double    1.335  0.020  1.335
 A4S  C08  C09  single    1.505  0.020  1.505
 A4S  C09  C26  single    1.500  0.020  1.500
 A4S  C01  H1   single    0.930  0.020  1.080
 A4S  C02  H2   single    0.930  0.020  1.080
 A4S  C03  H3   single    0.930  0.020  1.080
 A4S  C04  H4   single    0.930  0.020  1.080
 A4S  C05  H5   single    0.930  0.020  1.080
 A4S  N07  H6   single    0.890  0.020  1.040
 A4S  C08  H7   single    0.970  0.020  1.090
 A4S  C08  H8   single    0.970  0.020  1.090
 A4S  C10  H10  single    0.930  0.020  1.080
 A4S  C11  H12  single    0.970  0.020  1.090
 A4S  C11  H13  single    0.970  0.020  1.090
 A4S  C12  H14  single    0.970  0.020  1.090
 A4S  C12  H15  single    0.970  0.020  1.090
 A4S  C14  H17  single    0.930  0.020  1.080
 A4S  C15  H19  single    0.970  0.020  1.090
 A4S  C15  H20  single    0.970  0.020  1.090
 A4S  O18  H21  single    0.850  0.020  0.980
 A4S  O22  H22  single    0.850  0.020  0.980
 A4S  O24  H23  single    0.850  0.020  0.980
 A4S  C25  H24  single    0.970  0.020  1.090
 A4S  C25  H25  single    0.970  0.020  1.090
 A4S  C25  H26  single    0.970  0.020  1.090
 A4S  C26  H27  single    0.970  0.020  1.090
 A4S  C26  H28  single    0.970  0.020  1.090
 A4S  C26  H29  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
 A4S  H1   C01  C06  119.30  3.000
 A4S  H1   C01  C02  119.76  3.000
 A4S  C06  C01  C02  120.93  3.000
 A4S  H2   C02  C03  120.05  3.000
 A4S  H2   C02  C01  119.07  3.000
 A4S  C03  C02  C01  120.88  3.000
 A4S  H3   C03  C04  120.76  3.000
 A4S  H3   C03  C02  120.72  3.000
 A4S  C04  C03  C02  118.52  3.000
 A4S  H4   C04  C05  118.78  3.000
 A4S  H4   C04  C03  119.95  3.000
 A4S  C05  C04  C03  121.27  3.000
 A4S  H5   C05  C06  120.62  3.000
 A4S  H5   C05  C04  118.93  3.000
 A4S  C06  C05  C04  120.45  3.000
 A4S  N07  C06  C05  122.67  3.000
 A4S  C05  C06  C01  117.95  3.000
 A4S  N07  C06  C01  119.37  3.000
 A4S  H6   N07  C08  114.04  3.000
 A4S  H6   N07  C06  114.37  3.000
 A4S  C08  N07  C06  122.02  3.000
 A4S  H8   C08  H7   106.74  3.000
 A4S  H8   C08  C09  108.55  3.000
 A4S  H7   C08  C09  110.25  3.000
 A4S  H8   C08  N07  108.49  3.000
 A4S  H7   C08  N07  112.14  3.000
 A4S  C09  C08  N07  110.52  3.000
 A4S  C26  C09  C10  125.35  3.000
 A4S  C26  C09  C08  115.15  3.000
 A4S  C10  C09  C08  119.50  3.000
 A4S  H10  C10  C11  114.40  3.000
 A4S  H10  C10  C09  117.45  3.000
 A4S  C11  C10  C09  128.14  3.000
 A4S  H13  C11  H12  106.61  3.000
 A4S  H13  C11  C12  109.30  3.000
 A4S  H12  C11  C12  109.53  3.000
 A4S  H13  C11  C10  111.97  3.000
 A4S  H12  C11  C10  108.46  3.000
 A4S  C12  C11  C10  110.87  3.000
 A4S  H15  C12  H14  106.69  3.000
 A4S  H15  C12  C13  109.19  3.000
 A4S  H14  C12  C13  109.77  3.000
 A4S  H15  C12  C11  108.69  3.000
 A4S  H14  C12  C11  108.83  3.000
 A4S  C13  C12  C11  113.46  3.000
 A4S  C25  C13  C14  125.11  3.000
 A4S  C14  C13  C12  119.48  3.000
 A4S  C25  C13  C12  115.41  3.000
 A4S  H17  C14  C15  114.65  3.000
 A4S  H17  C14  C13  118.29  3.000
 A4S  C15  C14  C13  127.04  3.000
 A4S  H20  C15  H19  108.09  3.000
 A4S  H20  C15  O16  109.12  3.000
 A4S  H19  C15  O16  108.92  3.000
 A4S  H20  C15  C14  112.90  3.000
 A4S  H19  C15  C14  110.23  3.000
 A4S  O16  C15  C14  107.52  3.000
 A4S  P17  O16  C15  119.94  3.000
 A4S  O20  P17  O19  115.32  3.000
 A4S  O19  P17  O18  105.88  3.000
 A4S  O20  P17  O18  111.09  3.000
 A4S  O19  P17  O16   96.80  3.000
 A4S  O18  P17  O16  108.20  3.000
 A4S  O20  P17  O16  118.13  3.000
 A4S  H21  O18  P17  116.54  3.000
 A4S  P21  O19  P17  125.25  3.000
 A4S  O24  P21  O23  118.67  3.000
 A4S  O24  P21  O22  108.56  3.000
 A4S  O23  P21  O22  111.24  3.000
 A4S  O24  P21  O19   96.05  3.000
 A4S  O22  P21  O19  105.93  3.000
 A4S  O23  P21  O19  114.88  3.000
 A4S  H22  O22  P21  116.45  3.000
 A4S  H23  O24  P21  114.26  3.000
 A4S  H26  C25  H25  107.63  3.000
 A4S  H26  C25  H24  106.58  3.000
 A4S  H25  C25  H24  107.39  3.000
 A4S  H26  C25  C13  110.20  3.000
 A4S  H25  C25  C13  113.92  3.000
 A4S  H24  C25  C13  110.80  3.000
 A4S  H29  C26  H28  107.80  3.000
 A4S  H29  C26  H27  106.56  3.000
 A4S  H28  C26  H27  107.58  3.000
 A4S  H29  C26  C09  110.34  3.000
 A4S  H28  C26  C09  113.09  3.000
 A4S  H27  C26  C09  111.20  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
 A4S  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 A4S  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 A4S  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 A4S  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 A4S  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 A4S  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 A4S  CONST_07  N07  C06  C01  C02  180.00   0.0  0
 A4S  CONST_08  N07  C06  C05  C04  180.00   0.0  0
 A4S  CONST_09  H3   C03  C02  C01  180.00   0.0  0
 A4S  CONST_10  H5   C05  C06  C01  180.00   0.0  0
 A4S  CONST_11  H4   C04  C03  C02  180.00   0.0  0
 A4S  CONST_12  H1   C01  C02  C03  180.00   0.0  0
 A4S  CONST_13  H2   C02  C03  C04  180.00   0.0  0
 A4S  CONST_14  C08  N07  C06  C01  180.00   0.0  0
 A4S  CONST_15  C08  N07  C06  C05    0.00   0.0  0
 A4S  Var_01    C09  C08  N07  C06  174.41  30.0  3
 A4S  Var_02    C11  C10  C09  C08  179.62   0.0  2
 A4S  Var_03    C15  C14  C13  C12  178.28   0.0  2
 A4S  Var_04    C10  C09  C08  N07  119.67  30.0  3
 A4S  Var_05    C12  C11  C10  C09  116.71  30.0  1
 A4S  Var_06    C13  C12  C11  C10  178.62  30.0  1
 A4S  Var_07    O16  C15  C14  C13  118.74  30.0  2
 A4S  Var_08    O20  P17  O16  C15  -50.23  30.0  2
 A4S  Var_09    O23  P21  O19  P17   40.12  30.0  3
 A4S  Var_10    H27  C26  C09  C08   67.65  30.0  3
 A4S  Var_11    H24  C25  C13  C12   62.43  30.0  3

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
 A4S  chir_01  P17  O18  O16  O19  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
 A4S  plan-1  C01  0.020
 A4S  plan-1  C02  0.020
 A4S  plan-1  C03  0.020
 A4S  plan-1  C04  0.020
 A4S  plan-1  C05  0.020
 A4S  plan-1  C06  0.020
 A4S  plan-1  N07  0.020
 A4S  plan-1  H1   0.020
 A4S  plan-1  H2   0.020
 A4S  plan-1  H3   0.020
 A4S  plan-1  H4   0.020
 A4S  plan-1  H5   0.020
 A4S  plan-2  C06  0.020
 A4S  plan-2  N07  0.020
 A4S  plan-2  C08  0.020
 A4S  plan-2  H6   0.020
 A4S  plan-3  C12  0.020
 A4S  plan-3  C13  0.020
 A4S  plan-3  C14  0.020
 A4S  plan-3  C15  0.020
 A4S  plan-3  C25  0.020
 A4S  plan-3  H17  0.020
 A4S  plan-4  C08  0.020
 A4S  plan-4  C09  0.020
 A4S  plan-4  C10  0.020
 A4S  plan-4  C11  0.020
 A4S  plan-4  C26  0.020
 A4S  plan-4  H10  0.020

