# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 17:18:03 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (1-azanyl-1-phosphono-decyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(N)([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
 NT8  NT8  '(1-azanyl-1-phosphono-decyl)phosphonic acid'  ligand  44  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NT8
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
 NT8  N01   N  NH2   0  -0.793  -2.1254  -0.0040   1.9454
 NT8  C02   C  CT    0  -0.452  -2.1287  -0.1588   0.4978
 NT8  C03   C  CH2   0  -0.471  -0.8065  -0.6859  -0.1043
 NT8  C04   C  CH2   0  -0.435   0.4398   0.1350   0.2183
 NT8  C05   C  CH2   0  -0.410   1.7014  -0.5202  -0.3327
 NT8  C06   C  CH2   0  -0.415   2.9749   0.1487   0.1677
 NT8  C07   C  CH2   0  -0.413   4.2465  -0.4830  -0.3837
 NT8  C08   C  CH2   0  -0.412   5.5153   0.1165   0.2091
 NT8  C09   C  CH2   0  -0.407   6.7931  -0.5150  -0.3278
 NT8  C10   C  CH2   0  -0.419   8.0573   0.0651   0.2942
 NT8  C11   C  CH3   0  -0.662   9.3315  -0.5702  -0.2440
 NT8  P12   P  P     0   1.403  -3.5194  -1.3378   0.1644
 NT8  O13   O  O     0  -0.689  -4.7828  -1.1046   0.8918
 NT8  O14   O  OH1   0  -0.746  -3.5625  -1.2929  -1.4358
 NT8  O15   O  OH1   0  -0.744  -2.9541  -2.7868   0.5782
 NT8  P16   P  P     0   1.393  -2.6545   1.4639  -0.2189
 NT8  O17   O  OH1   0  -0.743  -1.7422   2.4756   0.6278
 NT8  O18   O  OH1   0  -0.740  -2.1145   1.5137  -1.7289
 NT8  O19   O  O     0  -0.689  -4.1092   1.7277  -0.2022
 NT8  H011  H  HNH2  0   0.365  -1.8810  -0.8813   2.3916
 NT8  H012  H  HNH2  0   0.373  -1.4204   0.6616   2.2343
 NT8  H032  H  HCH2  0   0.251  -0.6338  -1.6857   0.3042
 NT8  H031  H  HCH2  0   0.253  -0.9014  -0.8147  -1.1850
 NT8  H041  H  HCH2  0   0.221   0.3713   1.1535  -0.1727
 NT8  H042  H  HCH2  0   0.223   0.5406   0.2341   1.3027
 NT8  H051  H  HCH2  0   0.215   1.7163  -1.5775  -0.0475
 NT8  H052  H  HCH2  0   0.217   1.6759  -0.5020  -1.4271
 NT8  H061  H  HCH2  0   0.211   2.9560   1.2144  -0.0848
 NT8  H062  H  HCH2  0   0.209   2.9943   0.0989   1.2620
 NT8  H071  H  HCH2  0   0.207   4.2303  -1.5606  -0.1854
 NT8  H072  H  HCH2  0   0.209   4.2652  -0.3777  -1.4739
 NT8  H081  H  HCH2  0   0.207   5.5343   1.1951   0.0174
 NT8  H082  H  HCH2  0   0.206   5.4885   0.0059   1.2991
 NT8  H091  H  HCH2  0   0.206   6.7659  -1.5961  -0.1505
 NT8  H092  H  HCH2  0   0.206   6.8331  -0.3898  -1.4157
 NT8  H101  H  HCH2  0   0.210   8.0837   1.1452   0.1187
 NT8  H102  H  HCH2  0   0.210   8.0153  -0.0621   1.3805
 NT8  H112  H  HCH3  0   0.226  10.2208  -0.1381   0.2163
 NT8  H111  H  HCH3  0   0.215   9.3489  -1.6447  -0.0514
 NT8  H113  H  HCH3  0   0.215   9.4169  -0.4305  -1.3234
 NT8  H2    H  HOH1  0   0.500  -4.3297  -1.7293  -1.8331
 NT8  H3    H  HOH1  0   0.493  -2.2307  -3.1401   0.0446
 NT8  H4    H  HOH1  0   0.501  -2.0091   3.4037   0.5611
 NT8  H5    H  HOH1  0   0.493  -1.1571   1.5515  -1.8501

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
 NT8  C11  C10   single  1.522  0.020  1.522
 NT8  C10  C09   single  1.524  0.020  1.524
 NT8  C09  C08   single  1.523  0.020  1.523
 NT8  C08  C07   single  1.523  0.020  1.523
 NT8  C07  C06   single  1.523  0.020  1.523
 NT8  C06  C05   single  1.523  0.020  1.523
 NT8  C05  C04   single  1.525  0.020  1.525
 NT8  C04  C03   single  1.527  0.020  1.527
 NT8  C03  C02   single  1.545  0.020  1.545
 NT8  O13  P12   double  1.476  0.020  1.476
 NT8  O15  P12   single  1.610  0.020  1.610
 NT8  C02  P12   single  1.853  0.020  1.853
 NT8  C02  N01   single  1.456  0.020  1.456
 NT8  C02  P16   single  1.850  0.020  1.850
 NT8  P12  O14   single  1.601  0.020  1.601
 NT8  O19  P16   double  1.478  0.020  1.478
 NT8  P16  O18   single  1.604  0.020  1.604
 NT8  P16  O17   single  1.604  0.020  1.604
 NT8  N01  H011  single  0.890  0.020  1.040
 NT8  N01  H012  single  0.890  0.020  1.040
 NT8  C03  H032  single  0.970  0.020  1.090
 NT8  C03  H031  single  0.970  0.020  1.090
 NT8  C04  H041  single  0.970  0.020  1.090
 NT8  C04  H042  single  0.970  0.020  1.090
 NT8  C05  H051  single  0.970  0.020  1.090
 NT8  C05  H052  single  0.970  0.020  1.090
 NT8  C06  H061  single  0.970  0.020  1.090
 NT8  C06  H062  single  0.970  0.020  1.090
 NT8  C07  H071  single  0.970  0.020  1.090
 NT8  C07  H072  single  0.970  0.020  1.090
 NT8  C08  H081  single  0.970  0.020  1.090
 NT8  C08  H082  single  0.970  0.020  1.090
 NT8  C09  H091  single  0.970  0.020  1.090
 NT8  C09  H092  single  0.970  0.020  1.090
 NT8  C10  H101  single  0.970  0.020  1.090
 NT8  C10  H102  single  0.970  0.020  1.090
 NT8  C11  H112  single  0.970  0.020  1.090
 NT8  C11  H111  single  0.970  0.020  1.090
 NT8  C11  H113  single  0.970  0.020  1.090
 NT8  O14  H2    single  0.850  0.020  0.980
 NT8  O15  H3    single  0.850  0.020  0.980
 NT8  O17  H4    single  0.850  0.020  0.980
 NT8  O18  H5    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
 NT8  H012  N01  H011  105.99  3.000
 NT8  H012  N01  C02   110.83  3.000
 NT8  H011  N01  C02   110.25  3.000
 NT8  P16   C02  P12   105.96  3.000
 NT8  P16   C02  C03   113.04  3.000
 NT8  P12   C02  C03   110.79  3.000
 NT8  P16   C02  N01   107.01  3.000
 NT8  P12   C02  N01   104.37  3.000
 NT8  C03   C02  N01   114.94  3.000
 NT8  H031  C03  H032  105.99  3.000
 NT8  H031  C03  C04   110.08  3.000
 NT8  H032  C03  C04   106.48  3.000
 NT8  H031  C03  C02   110.56  3.000
 NT8  H032  C03  C02   107.54  3.000
 NT8  C04   C03  C02   115.64  3.000
 NT8  H042  C04  H041  106.03  3.000
 NT8  H042  C04  C05   108.73  3.000
 NT8  H041  C04  C05   108.84  3.000
 NT8  H042  C04  C03   109.48  3.000
 NT8  H041  C04  C03   111.97  3.000
 NT8  C05   C04  C03   111.60  3.000
 NT8  H052  C05  H051  106.06  3.000
 NT8  H052  C05  C06   109.91  3.000
 NT8  H051  C05  C06   109.09  3.000
 NT8  H052  C05  C04   109.57  3.000
 NT8  H051  C05  C04   109.39  3.000
 NT8  C06   C05  C04   112.61  3.000
 NT8  H062  C06  H061  105.95  3.000
 NT8  H062  C06  C07   109.14  3.000
 NT8  H061  C06  C07   109.54  3.000
 NT8  H062  C06  C05   108.85  3.000
 NT8  H061  C06  C05   109.70  3.000
 NT8  C07   C06  C05   113.39  3.000
 NT8  H072  C07  H071  105.96  3.000
 NT8  H072  C07  C08   109.59  3.000
 NT8  H071  C07  C08   109.20  3.000
 NT8  H072  C07  C06   109.55  3.000
 NT8  H071  C07  C06   109.27  3.000
 NT8  C08   C07  C06   113.03  3.000
 NT8  H082  C08  H081  105.89  3.000
 NT8  H082  C08  C09   109.23  3.000
 NT8  H081  C08  C09   109.38  3.000
 NT8  H082  C08  C07   109.09  3.000
 NT8  H081  C08  C07   109.49  3.000
 NT8  C09   C08  C07   113.48  3.000
 NT8  H092  C09  H091  105.92  3.000
 NT8  H092  C09  C10   109.36  3.000
 NT8  H091  C09  C10   109.28  3.000
 NT8  H092  C09  C08   109.47  3.000
 NT8  H091  C09  C08   109.34  3.000
 NT8  C10   C09  C08   113.22  3.000
 NT8  H102  C10  H101  105.95  3.000
 NT8  H102  C10  C11   109.54  3.000
 NT8  H101  C10  C11   109.57  3.000
 NT8  H102  C10  C09   109.22  3.000
 NT8  H101  C10  C09   109.29  3.000
 NT8  C11   C10  C09   113.03  3.000
 NT8  H113  C11  H111  107.41  3.000
 NT8  H113  C11  H112  107.63  3.000
 NT8  H111  C11  H112  107.61  3.000
 NT8  H113  C11  C10   111.20  3.000
 NT8  H111  C11  C10   111.21  3.000
 NT8  H112  C11  C10   111.59  3.000
 NT8  O15   P12  O14   106.95  3.000
 NT8  O14   P12  O13   117.71  3.000
 NT8  O15   P12  O13   108.43  3.000
 NT8  O14   P12  C02   100.49  3.000
 NT8  O15   P12  C02   105.24  3.000
 NT8  O13   P12  C02   116.93  3.000
 NT8  H2    O14  P12   114.76  3.000
 NT8  H3    O15  P12   116.76  3.000
 NT8  O19   P16  O18   109.65  3.000
 NT8  O18   P16  O17   106.60  3.000
 NT8  O19   P16  O17   116.18  3.000
 NT8  O17   P16  C02   100.78  3.000
 NT8  O18   P16  C02   107.23  3.000
 NT8  O19   P16  C02   115.58  3.000
 NT8  H4    O17  P16   114.30  3.000
 NT8  H5    O18  P16   116.94  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
 NT8  Var_01  C04   C03  C02  N01   -56.47  30.0  1
 NT8  Var_02  O13   P12  C02  N01    44.38  30.0  3
 NT8  Var_03  O19   P16  C02  N01   -79.70  30.0  3
 NT8  Var_04  C05   C04  C03  C02   175.82  30.0  1
 NT8  Var_05  C06   C05  C04  C03  -170.50  30.0  1
 NT8  Var_06  C07   C06  C05  C04  -179.40  30.0  1
 NT8  Var_07  C08   C07  C06  C05  -175.28  30.0  1
 NT8  Var_08  C09   C08  C07  C06   179.58  30.0  1
 NT8  Var_09  C10   C09  C08  C07  -178.58  30.0  1
 NT8  Var_10  C11   C10  C09  C08   179.92  30.0  1
 NT8  Var_11  H011  N01  C02  C03   -56.00  30.0  3
 NT8  Var_12  H112  C11  C10  C09   179.99  30.0  3

