# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 02:46:48 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: {4-[(2-aminophenyl)sulfanyl]butyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1SCCCC[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
 NHP  NHP  '{4-[(2-aminophenyl)sulfanyl]butyl}phosphonic acid'  ligand  32  16  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NHP
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
 NHP  C1    C  CR16  0  -0.230  -1.4904  -1.2352   3.7667
 NHP  C2    C  CR6   0  -0.202  -0.2489  -0.7304   3.3881
 NHP  C3    C  CR6   0   0.349   0.3375   0.3259   4.1126
 NHP  C4    C  CR16  0  -0.327  -0.3774   0.8497   5.2019
 NHP  C5    C  CR16  0  -0.250  -1.6124   0.3413   5.5565
 NHP  C6    C  CR16  0  -0.287  -2.1834  -0.7096   4.8447
 NHP  N1    N  NH2   0  -0.854   1.5797   0.8110   3.8082
 NHP  S1    S  S2    0  -0.035   0.5981  -1.4311   2.0001
 NHP  C7    C  CH2   0  -0.539  -0.0670  -0.4153   0.6349
 NHP  C8    C  CH2   0  -0.416   0.7009  -0.7169  -0.6420
 NHP  C9    C  CH2   0  -0.430   0.1238   0.0388  -1.8340
 NHP  C10   C  CH2   0  -0.757   0.9406  -0.2151  -3.0995
 NHP  P1    P  P     0   1.373   0.2842   0.6627  -4.5270
 NHP  O1    O  OH1   0  -0.746   1.3017   0.1923  -5.6807
 NHP  O2    O  OH1   0  -0.753  -1.1460   0.0057  -4.8724
 NHP  O3    O  O     0  -0.720   0.1133   2.1279  -4.3707
 NHP  H1    H  HCR6  0   0.259  -1.9145  -2.0508   3.1939
 NHP  H4    H  HCR6  0   0.258   0.0542   1.6643   5.7719
 NHP  H5    H  HCR6  0   0.255  -2.1364   0.7715   6.4007
 NHP  H6    H  HCR6  0   0.249  -3.1488  -1.1091   5.1241
 NHP  HN11  H  HNH2  0   0.385   1.7907   1.7453   4.1163
 NHP  HN12  H  HNH2  0   0.382   1.9474   0.5887   2.8971
 NHP  H71   H  HCH2  0   0.266  -1.1278  -0.6407   0.5148
 NHP  H72   H  HCH2  0   0.266   0.0302   0.6382   0.9010
 NHP  H81   H  HCH2  0   0.237   1.7519  -0.4469  -0.5081
 NHP  H82   H  HCH2  0   0.236   0.6748  -1.7914  -0.8462
 NHP  H91   H  HCH2  0   0.239  -0.9144  -0.2661  -1.9876
 NHP  H92   H  HCH2  0   0.240   0.1081   1.1097  -1.6170
 NHP  H101  H  HCH2  0   0.286   1.9721   0.1165  -2.9540
 NHP  H102  H  HCH2  0   0.283   0.9824  -1.2844  -3.3236
 NHP  HO1   H  HOH1  0   0.493   1.1881   0.6569  -6.5214
 NHP  HO2   H  HOH1  0   0.489  -1.1364  -0.9485  -5.0225

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
 NHP  C1   C2    aromatic  1.393  0.020  1.393
 NHP  C1   C6    aromatic  1.385  0.020  1.385
 NHP  C1   H1    single    0.930  0.020  1.080
 NHP  C2   C3    aromatic  1.409  0.020  1.409
 NHP  C2   S1    single    1.771  0.020  1.771
 NHP  C3   C4    aromatic  1.404  0.020  1.404
 NHP  C3   N1    single    1.368  0.020  1.368
 NHP  C4   C5    aromatic  1.382  0.020  1.382
 NHP  C4   H4    single    0.930  0.020  1.080
 NHP  C5   C6    aromatic  1.392  0.020  1.392
 NHP  C5   H5    single    0.930  0.020  1.080
 NHP  C6   H6    single    0.930  0.020  1.080
 NHP  N1   HN11  single    0.890  0.020  1.040
 NHP  N1   HN12  single    0.890  0.020  1.040
 NHP  S1   C7    single    1.827  0.020  1.827
 NHP  C7   C8    single    1.520  0.020  1.520
 NHP  C7   H71   single    0.970  0.020  1.090
 NHP  C7   H72   single    0.970  0.020  1.090
 NHP  C8   C9    single    1.525  0.020  1.525
 NHP  C8   H81   single    0.970  0.020  1.090
 NHP  C8   H82   single    0.970  0.020  1.090
 NHP  C9   C10   single    1.528  0.020  1.528
 NHP  C9   H91   single    0.970  0.020  1.090
 NHP  C9   H92   single    0.970  0.020  1.090
 NHP  C10  P1    single    1.800  0.020  1.800
 NHP  C10  H101  single    0.970  0.020  1.090
 NHP  C10  H102  single    0.970  0.020  1.090
 NHP  P1   O1    single    1.609  0.020  1.609
 NHP  P1   O2    single    1.611  0.020  1.611
 NHP  P1   O3    double    1.483  0.020  1.483
 NHP  O1   HO1   single    0.850  0.020  0.980
 NHP  O2   HO2   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
 NHP  H1    C1   C6    120.09  3.000
 NHP  H1    C1   C2    118.57  3.000
 NHP  C6    C1   C2    121.34  3.000
 NHP  S1    C2   C3    120.05  3.000
 NHP  S1    C2   C1    119.74  3.000
 NHP  C3    C2   C1    120.20  3.000
 NHP  N1    C3   C4    120.17  3.000
 NHP  N1    C3   C2    121.97  3.000
 NHP  C4    C3   C2    117.82  3.000
 NHP  H4    C4   C5    119.83  3.000
 NHP  H4    C4   C3    119.05  3.000
 NHP  C5    C4   C3    121.12  3.000
 NHP  H5    C5   C6    120.01  3.000
 NHP  H5    C5   C4    119.11  3.000
 NHP  C6    C5   C4    120.88  3.000
 NHP  H6    C6   C5    120.86  3.000
 NHP  H6    C6   C1    120.50  3.000
 NHP  C5    C6   C1    118.64  3.000
 NHP  HN12  N1   HN11  113.92  3.000
 NHP  HN12  N1   C3    117.03  3.000
 NHP  HN11  N1   C3    116.85  3.000
 NHP  C7    S1   C2    101.05  3.000
 NHP  H72   C7   H71   108.23  3.000
 NHP  H72   C7   C8    110.58  3.000
 NHP  H71   C7   C8    110.95  3.000
 NHP  H72   C7   S1    108.80  3.000
 NHP  H71   C7   S1    108.74  3.000
 NHP  C8    C7   S1    109.48  3.000
 NHP  H82   C8   H81   106.76  3.000
 NHP  H82   C8   C9    109.38  3.000
 NHP  H81   C8   C9    109.70  3.000
 NHP  H82   C8   C7    109.85  3.000
 NHP  H81   C8   C7    109.49  3.000
 NHP  C9    C8   C7    111.54  3.000
 NHP  H92   C9   H91   106.72  3.000
 NHP  H92   C9   C10   109.58  3.000
 NHP  H91   C9   C10   110.19  3.000
 NHP  H92   C9   C8    109.63  3.000
 NHP  H91   C9   C8    109.34  3.000
 NHP  C10   C9   C8    111.28  3.000
 NHP  H102  C10  H101  106.73  3.000
 NHP  H102  C10  P1    109.17  3.000
 NHP  H101  C10  P1    107.56  3.000
 NHP  H102  C10  C9    110.66  3.000
 NHP  H101  C10  C9    110.11  3.000
 NHP  P1    C10  C9    112.40  3.000
 NHP  O3    P1   O2    108.85  3.000
 NHP  O3    P1   O1    115.93  3.000
 NHP  O2    P1   O1    106.77  3.000
 NHP  O3    P1   C10   116.12  3.000
 NHP  O2    P1   C10   107.14  3.000
 NHP  O1    P1   C10   101.28  3.000
 NHP  HO1   O1   P1    114.12  3.000
 NHP  HO2   O2   P1    115.30  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
 NHP  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NHP  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 NHP  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 NHP  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 NHP  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 NHP  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 NHP  CONST_07  N1   C3   C2   C1   180.00   0.0  0
 NHP  CONST_08  S1   C2   C3   C4   180.00   0.0  0
 NHP  CONST_09  N1   C3   C4   C5   180.00   0.0  0
 NHP  CONST_10  S1   C2   C1   C6   180.00   0.0  0
 NHP  CONST_11  H5   C5   C6   C1   180.00   0.0  0
 NHP  CONST_12  H6   C6   C1   C2   180.00   0.0  0
 NHP  CONST_13  H4   C4   C3   C2   180.00   0.0  0
 NHP  CONST_14  H1   C1   C2   C3   180.00   0.0  0
 NHP  Var_01    C8   C7   S1   C2   171.32  30.0  3
 NHP  Var_02    C9   C8   C7   S1   176.25  30.0  3
 NHP  Var_03    C10  C9   C8   C7   177.23  30.0  3
 NHP  Var_04    P1   C10  C9   C8   179.96  30.0  3
 NHP  Var_05    O1   P1   C10  C9  -178.93  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
 NHP  plan-1  C1    0.020
 NHP  plan-1  C2    0.020
 NHP  plan-1  C3    0.020
 NHP  plan-1  C4    0.020
 NHP  plan-1  C5    0.020
 NHP  plan-1  C6    0.020
 NHP  plan-1  N1    0.020
 NHP  plan-1  S1    0.020
 NHP  plan-1  H1    0.020
 NHP  plan-1  H4    0.020
 NHP  plan-1  H5    0.020
 NHP  plan-1  H6    0.020
 NHP  plan-2  C3    0.020
 NHP  plan-2  N1    0.020
 NHP  plan-2  HN11  0.020
 NHP  plan-2  HN12  0.020

