# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 02:40:40 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  34  20  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   1.270  -0.9632  -0.3350  -0.0634
 CCZ  N1    N  N      0  -0.654   6.0367  -1.0025  -1.2564
 CCZ  C2    C  CR6    0   0.031   4.2120   0.0276  -0.1200
 CCZ  N2    N  NH2    0  -0.822   6.2984   1.1930  -0.4431
 CCZ  C3    C  CR16   0  -0.280   3.4951   1.2073   0.0695
 CCZ  C4    C  CR16   0  -0.285   2.1934   1.1749   0.5468
 CCZ  C5    C  CR6    0   0.114   1.5748  -0.0302   0.8659
 CCZ  C6    C  CR16   0  -0.279   2.2912  -1.2095   0.6623
 CCZ  C7    C  CR16   0  -0.264   3.5872  -1.1823   0.1772
 CCZ  C8    C  CH2    0  -0.786   0.1610  -0.0599   1.3568
 CCZ  C01   C  CR6    0   0.394  -3.5988  -0.0435   0.2368
 CCZ  C02   C  CR16   0  -0.347  -4.4961   0.7996   0.8896
 CCZ  C03   C  CR16   0  -0.247  -5.7546   1.0299   0.3528
 CCZ  C04   C  CR16   0  -0.279  -6.1313   0.4345  -0.8443
 CCZ  C05   C  CR16   0  -0.248  -5.2334  -0.4018  -1.4947
 CCZ  C06   C  CR16   0  -0.363  -3.9744  -0.6465  -0.9636
 CCZ  OP1   O  O      0  -0.781  -0.9346   0.8401  -0.9938
 CCZ  OP2   O  O2     0  -0.644  -2.3998  -0.2643   0.8232
 CCZ  OP3   O  OP    -1  -0.780  -0.7967  -1.7323  -0.5880
 CCZ  HN1   H  H      0   0.321   7.0071  -0.8845  -1.5355
 CCZ  HN2   H  HNH2   0   0.390   7.2854   1.1800  -0.6459
 CCZ  HN2A  H  HNH2   0   0.393   6.0605   1.7607   0.3534
 CCZ  H3    H  HCR6   0   0.253   3.9364   2.1655  -0.1739
 CCZ  H4    H  HCR6   0   0.248   1.6553   2.1049   0.6819
 CCZ  H6    H  HCR6   0   0.247   1.8312  -2.1613   0.8958
 CCZ  H7    H  HCR6   0   0.250   4.1278  -2.1078   0.0307
 CCZ  H8    H  HCH2   0   0.269  -0.0952   0.8846   1.8397
 CCZ  H8A   H  HCH2   0   0.271   0.0203  -0.8577   2.0890
 CCZ  H02   H  HCR6   0   0.257  -4.2043   1.2685   1.8214
 CCZ  H03   H  HCR6   0   0.254  -6.4410   1.6863   0.8724
 CCZ  H04   H  HCR6   0   0.251  -7.1125   0.6166  -1.2623
 CCZ  H05   H  HCR6   0   0.255  -5.5131  -0.8755  -2.4271
 CCZ  H06   H  HCR6   0   0.263  -3.2949  -1.3178  -1.4718
 CCZ  C1    C  C      0   0.328   5.6065   0.0307  -0.6385

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    1.690  0.020  1.690
 CCZ  C8   P     single    1.832  0.020  1.832
 CCZ  P    OP3   deloc     1.502  0.020  1.502
 CCZ  P    OP1   deloc     1.499  0.020  1.499
 CCZ  C2   C1    single    1.488  0.020  1.488
 CCZ  N1   C1    double    1.278  0.020  1.278
 CCZ  C1   N2    single    1.367  0.020  1.367
 CCZ  N1   HN1   single    0.890  0.020  1.040
 CCZ  C3   C2    aromatic  1.393  0.020  1.393
 CCZ  C2   C7    aromatic  1.394  0.020  1.394
 CCZ  N2   HN2   single    0.890  0.020  1.040
 CCZ  N2   HN2A  single    0.890  0.020  1.040
 CCZ  C4   C3    aromatic  1.387  0.020  1.387
 CCZ  C3   H3    single    0.930  0.020  1.080
 CCZ  C4   C5    aromatic  1.392  0.020  1.392
 CCZ  C4   H4    single    0.930  0.020  1.080
 CCZ  C8   C5    single    1.497  0.020  1.497
 CCZ  C5   C6    aromatic  1.395  0.020  1.395
 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  1.394  0.020  1.394
 CCZ  C01  OP2   single    1.353  0.020  1.353
 CCZ  C01  C06   aromatic  1.395  0.020  1.395
 CCZ  C03  C02   aromatic  1.387  0.020  1.387
 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  1.388  0.020  1.388
 CCZ  C05  H05   single    0.930  0.020  1.080
 CCZ  C06  H06   single    0.930  0.020  1.080

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  108.45  3.000
 CCZ  OP3   P    OP1  120.69  3.000
 CCZ  OP2   P    OP1  108.00  3.000
 CCZ  OP1   P    C8   110.59  3.000
 CCZ  OP3   P    C8   110.03  3.000
 CCZ  OP2   P    C8    96.24  3.000
 CCZ  HN1   N1   C1   111.11  3.000
 CCZ  C7    C2   C3   118.38  3.000
 CCZ  C7    C2   C1   119.75  3.000
 CCZ  C3    C2   C1   121.87  3.000
 CCZ  HN2A  N2   HN2  113.45  3.000
 CCZ  HN2A  N2   C1   118.24  3.000
 CCZ  HN2   N2   C1   117.14  3.000
 CCZ  H3    C3   C4   118.73  3.000
 CCZ  H3    C3   C2   120.60  3.000
 CCZ  C4    C3   C2   120.66  3.000
 CCZ  H4    C4   C5   119.62  3.000
 CCZ  H4    C4   C3   119.29  3.000
 CCZ  C5    C4   C3   121.09  3.000
 CCZ  C8    C5   C6   121.08  3.000
 CCZ  C6    C5   C4   118.06  3.000
 CCZ  C8    C5   C4   120.81  3.000
 CCZ  H6    C6   C7   119.39  3.000
 CCZ  H6    C6   C5   119.58  3.000
 CCZ  C7    C6   C5   121.03  3.000
 CCZ  H7    C7   C6   119.91  3.000
 CCZ  H7    C7   C2   119.32  3.000
 CCZ  C6    C7   C2   120.77  3.000
 CCZ  H8A   C8   H8   107.78  3.000
 CCZ  H8A   C8   C5   110.86  3.000
 CCZ  H8    C8   C5   110.47  3.000
 CCZ  H8A   C8   P    109.33  3.000
 CCZ  H8    C8   P    109.20  3.000
 CCZ  C5    C8   P    109.17  3.000
 CCZ  OP2   C01  C06  122.76  3.000
 CCZ  C06   C01  C02  119.42  3.000
 CCZ  OP2   C01  C02  117.80  3.000
 CCZ  H02   C02  C03  120.35  3.000
 CCZ  H02   C02  C01  119.43  3.000
 CCZ  C03   C02  C01  120.21  3.000
 CCZ  H03   C03  C04  120.11  3.000
 CCZ  H03   C03  C02  119.35  3.000
 CCZ  C04   C03  C02  120.55  3.000
 CCZ  H04   C04  C05  120.45  3.000
 CCZ  H04   C04  C03  120.45  3.000
 CCZ  C05   C04  C03  119.10  3.000
 CCZ  H05   C05  C06  119.13  3.000
 CCZ  H05   C05  C04  119.99  3.000
 CCZ  C06   C05  C04  120.89  3.000
 CCZ  H06   C06  C05  119.95  3.000
 CCZ  H06   C06  C01  120.22  3.000
 CCZ  C05   C06  C01  119.82  3.000
 CCZ  C01   OP2  P    122.21  3.000
 CCZ  N2    C1   C2   115.24  3.000
 CCZ  N2    C1   N1   125.88  3.000
 CCZ  C2    C1   N1   118.83  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    -139.60  30.0  2
 CCZ  Var_02    C4   C5   C8   P      94.02  30.0  2
 CCZ  Var_03    C3   C2   C1   N1   -153.96  30.0  2
 CCZ  Var_04    OP2  P    C8   C5   -178.42  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
 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

