# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:13:54 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: phenyl hydrogen (R)-(4-carbamimidoylbenzyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(C[P](O)(=O)Oc2ccccc2)cc1
#
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
 CCZ  CCZ  'phenyl hydrogen (R)-(4-carbamimidoylbenzyl)phosphonate'  ligand  35  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CCZ
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
 CCZ  P     P  P     0   1.371  -1.0143   0.0147   0.1045
 CCZ  N1    N  N     0  -0.651   5.9348  -0.6484  -1.5540
 CCZ  C2    C  CR6   0   0.037   4.1688   0.0797  -0.1331
 CCZ  N2    N  NH2   0  -0.822   6.2608   1.2768  -0.2346
 CCZ  C3    C  CR16  0  -0.278   3.4749   1.1792   0.3679
 CCZ  C4    C  CR16  0  -0.270   2.1889   1.0364   0.8655
 CCZ  C5    C  CR6   0   0.106   1.5704  -0.2089   0.8872
 CCZ  C6    C  CR16  0  -0.285   2.2617  -1.3063   0.3802
 CCZ  C7    C  CR16  0  -0.258   3.5422  -1.1643  -0.1260
 CCZ  C8    C  CH2   0  -0.829   0.1714  -0.3589   1.4122
 CCZ  C01   C  CR6   0   0.359  -3.6171  -0.0755   0.2285
 CCZ  C02   C  CR16  0  -0.308  -4.1813   1.1895   0.2941
 CCZ  C03   C  CR16  0  -0.252  -5.4123   1.4119  -0.3075
 CCZ  C04   C  CR16  0  -0.259  -6.0664   0.3830  -0.9728
 CCZ  C05   C  CR16  0  -0.251  -5.4869  -0.8775  -1.0311
 CCZ  C06   C  CR16  0  -0.317  -4.2562  -1.1131  -0.4326
 CCZ  OP1   O  O     0  -0.683  -0.9371   1.3637  -0.4947
 CCZ  OP2   O  O2    0  -0.625  -2.4135  -0.3191   0.8602
 CCZ  OP3   O  OH1   0  -0.735  -0.8518  -1.0987  -1.0378
 CCZ  HN1   H  H     0   0.324   6.8972  -0.4766  -1.8326
 CCZ  HN2   H  HNH2  0   0.391   7.2384   1.3140  -0.4759
 CCZ  HN2A  H  HNH2  0   0.395   6.0616   1.6317   0.6864
 CCZ  H3    H  HCR6  0   0.260   3.9217   2.1652   0.3558
 CCZ  H4    H  HCR6  0   0.259   1.6672   1.9054   1.2459
 CCZ  H6    H  HCR6  0   0.256   1.8016  -2.2869   0.3946
 CCZ  H7    H  HCR6  0   0.257   4.0682  -2.0271  -0.5115
 CCZ  H8    H  HCH2  0   0.323  -0.0208   0.3361   2.2323
 CCZ  H8A   H  HCH2  0   0.320  -0.0097  -1.3679   1.7887
 CCZ  H02   H  HCR6  0   0.274  -3.6724   1.9862   0.8201
 CCZ  H03   H  HCR6  0   0.265  -5.8578   2.3967  -0.2577
 CCZ  H04   H  HCR6  0   0.261  -7.0251   0.5627  -1.4405
 CCZ  H05   H  HCR6  0   0.265  -5.9902  -1.6843  -1.5474
 CCZ  H06   H  HCR6  0   0.272  -3.8067  -2.0972  -0.4681
 CCZ  HOP3  H  HOH1  0   0.494  -0.8925  -2.0193  -0.7469
 CCZ  C1    C  C     0   0.333   5.5462   0.2041  -0.6853

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
 CCZ  OP2  P     single    1.625  0.020  1.625
 CCZ  C8   P     single    1.804  0.020  1.804
 CCZ  P    OP3   single    1.603  0.020  1.603
 CCZ  P    OP1   double    1.478  0.020  1.478
 CCZ  C2   C1    single    1.489  0.020  1.489
 CCZ  N1   C1    double    1.278  0.020  1.278
 CCZ  C1   N2    single    1.366  0.020  1.366
 CCZ  N1   HN1   single    0.890  0.020  1.040
 CCZ  C3   C2    aromatic  1.393  0.020  1.393
 CCZ  C2   C7    aromatic  1.393  0.020  1.393
 CCZ  N2   HN2   single    0.890  0.020  1.040
 CCZ  N2   HN2A  single    0.890  0.020  1.040
 CCZ  C4   C3    aromatic  1.386  0.020  1.386
 CCZ  C3   H3    single    0.930  0.020  1.080
 CCZ  C4   C5    aromatic  1.391  0.020  1.391
 CCZ  C4   H4    single    0.930  0.020  1.080
 CCZ  C8   C5    single    1.502  0.020  1.502
 CCZ  C5   C6    aromatic  1.393  0.020  1.393
 CCZ  C6   C7    aromatic  1.384  0.020  1.384
 CCZ  C6   H6    single    0.930  0.020  1.080
 CCZ  C7   H7    single    0.930  0.020  1.080
 CCZ  C8   H8    single    0.970  0.020  1.090
 CCZ  C8   H8A   single    0.970  0.020  1.090
 CCZ  C02  C01   aromatic  1.387  0.020  1.387
 CCZ  C01  OP2   single    1.381  0.020  1.381
 CCZ  C01  C06   aromatic  1.386  0.020  1.386
 CCZ  C03  C02   aromatic  1.388  0.020  1.388
 CCZ  C02  H02   single    0.930  0.020  1.080
 CCZ  C03  C04   aromatic  1.389  0.020  1.389
 CCZ  C03  H03   single    0.930  0.020  1.080
 CCZ  C04  C05   aromatic  1.389  0.020  1.389
 CCZ  C04  H04   single    0.930  0.020  1.080
 CCZ  C05  C06   aromatic  1.389  0.020  1.389
 CCZ  C05  H05   single    0.930  0.020  1.080
 CCZ  C06  H06   single    0.930  0.020  1.080
 CCZ  OP3  HOP3  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
 CCZ  OP3   P    OP2  106.02  3.000
 CCZ  OP3   P    OP1  109.85  3.000
 CCZ  OP2   P    OP1  114.90  3.000
 CCZ  OP1   P    C8   116.65  3.000
 CCZ  OP3   P    C8   107.81  3.000
 CCZ  OP2   P    C8   100.73  3.000
 CCZ  HN1   N1   C1   111.20  3.000
 CCZ  C7    C2   C3   118.61  3.000
 CCZ  C7    C2   C1   119.51  3.000
 CCZ  C3    C2   C1   121.87  3.000
 CCZ  HN2A  N2   HN2  113.45  3.000
 CCZ  HN2A  N2   C1   118.38  3.000
 CCZ  HN2   N2   C1   117.24  3.000
 CCZ  H3    C3   C4   118.73  3.000
 CCZ  H3    C3   C2   120.61  3.000
 CCZ  C4    C3   C2   120.64  3.000
 CCZ  H4    C4   C5   119.94  3.000
 CCZ  H4    C4   C3   119.37  3.000
 CCZ  C5    C4   C3   120.70  3.000
 CCZ  C8    C5   C6   120.73  3.000
 CCZ  C6    C5   C4   118.64  3.000
 CCZ  C8    C5   C4   120.61  3.000
 CCZ  H6    C6   C7   119.38  3.000
 CCZ  H6    C6   C5   119.85  3.000
 CCZ  C7    C6   C5   120.77  3.000
 CCZ  H7    C7   C6   119.90  3.000
 CCZ  H7    C7   C2   119.46  3.000
 CCZ  C6    C7   C2   120.64  3.000
 CCZ  H8A   C8   H8   107.45  3.000
 CCZ  H8A   C8   C5   111.55  3.000
 CCZ  H8    C8   C5   111.28  3.000
 CCZ  H8A   C8   P    109.40  3.000
 CCZ  H8    C8   P    107.27  3.000
 CCZ  C5    C8   P    109.76  3.000
 CCZ  OP2   C01  C06  119.20  3.000
 CCZ  C06   C01  C02  121.18  3.000
 CCZ  OP2   C01  C02  119.60  3.000
 CCZ  H02   C02  C03  120.66  3.000
 CCZ  H02   C02  C01  120.22  3.000
 CCZ  C03   C02  C01  119.11  3.000
 CCZ  H03   C03  C04  120.16  3.000
 CCZ  H03   C03  C02  119.41  3.000
 CCZ  C04   C03  C02  120.43  3.000
 CCZ  H04   C04  C05  120.17  3.000
 CCZ  H04   C04  C03  120.10  3.000
 CCZ  C05   C04  C03  119.74  3.000
 CCZ  H05   C05  C06  119.43  3.000
 CCZ  H05   C05  C04  120.18  3.000
 CCZ  C06   C05  C04  120.38  3.000
 CCZ  H06   C06  C05  120.54  3.000
 CCZ  H06   C06  C01  120.30  3.000
 CCZ  C05   C06  C01  119.15  3.000
 CCZ  C01   OP2  P    120.10  3.000
 CCZ  HOP3  OP3  P    116.28  3.000
 CCZ  N2    C1   C2   115.29  3.000
 CCZ  N2    C1   N1   126.12  3.000
 CCZ  C2    C1   N1   118.54  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
 CCZ  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 CCZ  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 CCZ  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 CCZ  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 CCZ  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 CCZ  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 CCZ  CONST_07  C04  C03  C02  C01     0.00   0.0  0
 CCZ  CONST_08  C04  C05  C06  C01     0.00   0.0  0
 CCZ  CONST_09  C05  C06  C01  C02     0.00   0.0  0
 CCZ  CONST_10  C05  C04  C03  C02     0.00   0.0  0
 CCZ  CONST_11  C06  C01  C02  C03     0.00   0.0  0
 CCZ  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 CCZ  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 CCZ  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 CCZ  CONST_15  C8   C5   C4   C3    180.00   0.0  0
 CCZ  CONST_16  C8   C5   C6   C7    180.00   0.0  0
 CCZ  CONST_17  OP2  C01  C02  C03   180.00   0.0  0
 CCZ  CONST_18  OP2  C01  C06  C05   180.00   0.0  0
 CCZ  CONST_19  H4   C4   C3   C2    180.00   0.0  0
 CCZ  CONST_20  H6   C6   C7   C2    180.00   0.0  0
 CCZ  CONST_21  H7   C7   C2   C3    180.00   0.0  0
 CCZ  CONST_22  H3   C3   C4   C5    180.00   0.0  0
 CCZ  CONST_23  H03  C03  C02  C01   180.00   0.0  0
 CCZ  CONST_24  H05  C05  C06  C01   180.00   0.0  0
 CCZ  CONST_25  H06  C06  C01  C02   180.00   0.0  0
 CCZ  CONST_26  H04  C04  C03  C02   180.00   0.0  0
 CCZ  CONST_27  H02  C02  C03  C04   180.00   0.0  0
 CCZ  CONST_28  HN1  N1   C1   C2    180.00   0.0  0
 CCZ  CONST_29  HN2  N2   C1   C2    180.00   0.0  0
 CCZ  Var_01    C02  C01  OP2  P     -85.21  30.0  2
 CCZ  Var_02    C4   C5   C8   P      84.57  30.0  2
 CCZ  Var_03    C3   C2   C1   N1   -153.94  30.0  2
 CCZ  Var_04    OP2  P    C8   C5    175.93  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
 CCZ  chir_01  P  C8  OP3  OP1  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
 CCZ  plan-1  C2    0.020
 CCZ  plan-1  C3    0.020
 CCZ  plan-1  C4    0.020
 CCZ  plan-1  C5    0.020
 CCZ  plan-1  C6    0.020
 CCZ  plan-1  C7    0.020
 CCZ  plan-1  C8    0.020
 CCZ  plan-1  H3    0.020
 CCZ  plan-1  H4    0.020
 CCZ  plan-1  H6    0.020
 CCZ  plan-1  H7    0.020
 CCZ  plan-1  C1    0.020
 CCZ  plan-2  C01   0.020
 CCZ  plan-2  C02   0.020
 CCZ  plan-2  C03   0.020
 CCZ  plan-2  C04   0.020
 CCZ  plan-2  C05   0.020
 CCZ  plan-2  C06   0.020
 CCZ  plan-2  OP2   0.020
 CCZ  plan-2  H02   0.020
 CCZ  plan-2  H03   0.020
 CCZ  plan-2  H04   0.020
 CCZ  plan-2  H05   0.020
 CCZ  plan-2  H06   0.020
 CCZ  plan-3  N1    0.020
 CCZ  plan-3  C2    0.020
 CCZ  plan-3  N2    0.020
 CCZ  plan-3  HN1   0.020
 CCZ  plan-3  HN2   0.020
 CCZ  plan-3  HN2A  0.020
 CCZ  plan-3  C1    0.020

