# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:45:26 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: [(R)-{[(benzyloxy)carbonyl]amino}(4-carbamimidoylphenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)[C@H](NC(=O)OCc2ccccc2)[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
 ZAP  ZAP  '[(R)-{[(benzyloxy)carbonyl]amino}(4-carbamimidoylphenyl)methyl]phosphonic acid'  ligand  41  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZAP
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
 ZAP  C1    C  C      0   0.322   2.5294  -0.2989   4.9535
 ZAP  C2    C  CR6    0  -0.016   1.4771  -0.2333   3.9051
 ZAP  C3    C  CR16   0  -0.283   1.6661   0.5554   2.7718
 ZAP  C4    C  CR16   0  -0.298   0.6940   0.6337   1.7882
 ZAP  C5    C  CR6    0   0.190  -0.5008  -0.0762   1.8984
 ZAP  C6    C  CR16   0  -0.296  -0.6921  -0.8498   3.0421
 ZAP  C7    C  CR16   0  -0.281   0.2805  -0.9414   4.0232
 ZAP  C8    C  CH1    0  -0.442  -1.5783   0.0372   0.8708
 ZAP  C10   C  CH2    0  -0.230   0.5962  -1.2981  -3.1935
 ZAP  C11   C  CR6    0   0.075   1.0547  -0.5742  -4.4235
 ZAP  C12   C  CR16   0  -0.301   2.4047  -0.3103  -4.6278
 ZAP  C13   C  CR16   0  -0.241   2.8289   0.3703  -5.7625
 ZAP  C14   C  CR16   0  -0.263   1.9013   0.7989  -6.7015
 ZAP  C15   C  CR16   0  -0.243   0.5493   0.5421  -6.5037
 ZAP  C16   C  CR16   0  -0.284   0.1303  -0.1410  -5.3719
 ZAP  N1    N  N      0  -0.648   3.3116   0.6643   5.2664
 ZAP  N2    N  NH2    0  -0.805   2.5981  -1.4831   5.6305
 ZAP  N3    N  NH1    0  -0.657  -1.0634   0.2130  -0.4664
 ZAP  O3    O  O      0  -0.527  -0.4332  -1.9424  -0.8190
 ZAP  O4    O  O2     0  -0.487   0.0072  -0.3260  -2.3276
 ZAP  P     P  P      0   1.180  -2.6996   1.5311   1.2352
 ZAP  H3    H  HCR6   0   0.248   2.5918   1.1040   2.6427
 ZAP  H4    H  HCR6   0   0.234   0.8781   1.2447   0.9144
 ZAP  H6    H  HCR6   0   0.235  -1.6163  -1.4027   3.1595
 ZAP  H7    H  HCR6   0   0.250   0.0950  -1.5550   4.8962
 ZAP  H8    H  HCH1   0   0.227  -2.1988  -0.8620   0.9041
 ZAP  H101  H  HCH2   0   0.242   1.4393  -1.7881  -2.7019
 ZAP  H102  H  HCH2   0   0.241  -0.1361  -2.0681  -3.4479
 ZAP  H12   H  HCR6   0   0.254   3.1326  -0.6416  -3.8963
 ZAP  H13   H  HCR6   0   0.258   3.8830   0.5646  -5.9123
 ZAP  H14   H  HCR6   0   0.258   2.2293   1.3277  -7.5870
 ZAP  H15   H  HCR6   0   0.257  -0.1777   0.8707  -7.2352
 ZAP  H16   H  HCR6   0   0.254  -0.9244  -0.3442  -5.2273
 ZAP  HN1   H  H      0   0.329   3.0655   1.5024   4.7527
 ZAP  HN21  H  HNH2   0   0.380   3.3902  -1.5920   6.2441
 ZAP  HN22  H  HNH2   0   0.389   2.3467  -2.3229   5.1361
 ZAP  HN3   H  HNH1   0   0.378  -0.9899   1.1651  -0.7963
 ZAP  C9    C  C      0   0.749  -0.4917  -0.7775  -1.1629
 ZAP  O1P   O  O      0  -0.873  -2.9946   1.4389   2.7282
 ZAP  O2P   O  OP    -1  -0.883  -1.8127   2.7093   0.8140
 ZAP  O3P   O  OP    -1  -0.890  -3.9125   1.3108   0.3306

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
 ZAP  C1   C2    single    1.487  0.020  1.487
 ZAP  C1   N1    double    1.280  0.020  1.280
 ZAP  C1   N2    single    1.366  0.020  1.366
 ZAP  C2   C3    aromatic  1.394  0.020  1.394
 ZAP  C2   C7    aromatic  1.395  0.020  1.395
 ZAP  C3   C4    aromatic  1.385  0.020  1.385
 ZAP  C3   H3    single    0.930  0.020  1.080
 ZAP  C4   C5    aromatic  1.394  0.020  1.394
 ZAP  C4   H4    single    0.930  0.020  1.080
 ZAP  C5   C6    aromatic  1.394  0.020  1.394
 ZAP  C5   C8    single    1.493  0.020  1.493
 ZAP  C6   C7    aromatic  1.385  0.020  1.385
 ZAP  C6   H6    single    0.930  0.020  1.080
 ZAP  C7   H7    single    0.930  0.020  1.080
 ZAP  C8   N3    single    1.444  0.020  1.444
 ZAP  C8   P     single    1.903  0.020  1.903
 ZAP  C8   H8    single    0.970  0.020  1.090
 ZAP  C9   N3    single    1.339  0.020  1.339
 ZAP  C9   O3    double    1.216  0.020  1.216
 ZAP  C9   O4    single    1.345  0.020  1.345
 ZAP  C10  C11   single    1.499  0.020  1.499
 ZAP  C10  O4    single    1.429  0.020  1.429
 ZAP  C10  H101  single    0.970  0.020  1.090
 ZAP  C10  H102  single    0.970  0.020  1.090
 ZAP  C11  C12   aromatic  1.391  0.020  1.391
 ZAP  C11  C16   aromatic  1.393  0.020  1.393
 ZAP  C12  C13   aromatic  1.390  0.020  1.390
 ZAP  C12  H12   single    0.930  0.020  1.080
 ZAP  C13  C14   aromatic  1.388  0.020  1.388
 ZAP  C13  H13   single    0.930  0.020  1.080
 ZAP  C14  C15   aromatic  1.390  0.020  1.390
 ZAP  C14  H14   single    0.930  0.020  1.080
 ZAP  C15  C16   aromatic  1.387  0.020  1.387
 ZAP  C15  H15   single    0.930  0.020  1.080
 ZAP  C16  H16   single    0.930  0.020  1.080
 ZAP  N1   HN1   single    0.890  0.020  1.040
 ZAP  N2   HN21  single    0.890  0.020  1.040
 ZAP  N2   HN22  single    0.890  0.020  1.040
 ZAP  N3   HN3   single    0.860  0.020  1.020
 ZAP  O1P  P     deloc     1.525  0.020  1.525
 ZAP  O2P  P     deloc     1.534  0.020  1.534
 ZAP  O3P  P     deloc     1.529  0.020  1.529

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
 ZAP  N2    C1   N1    120.04  3.000
 ZAP  N2    C1   C2    115.05  3.000
 ZAP  N1    C1   C2    124.88  3.000
 ZAP  C7    C2   C3    118.18  3.000
 ZAP  C7    C2   C1    121.66  3.000
 ZAP  C3    C2   C1    120.16  3.000
 ZAP  H3    C3   C4    119.10  3.000
 ZAP  H3    C3   C2    119.94  3.000
 ZAP  C4    C3   C2    120.95  3.000
 ZAP  H4    C4   C5    119.82  3.000
 ZAP  H4    C4   C3    119.07  3.000
 ZAP  C5    C4   C3    121.11  3.000
 ZAP  C8    C5   C6    120.51  3.000
 ZAP  C8    C5   C4    121.69  3.000
 ZAP  C6    C5   C4    117.71  3.000
 ZAP  H6    C6   C7    119.25  3.000
 ZAP  H6    C6   C5    119.29  3.000
 ZAP  C7    C6   C5    121.45  3.000
 ZAP  H7    C7   C6    119.23  3.000
 ZAP  H7    C7   C2    120.17  3.000
 ZAP  C6    C7   C2    120.59  3.000
 ZAP  H8    C8   P     107.79  3.000
 ZAP  H8    C8   N3    109.32  3.000
 ZAP  P     C8   N3    106.97  3.000
 ZAP  H8    C8   C5    109.04  3.000
 ZAP  P     C8   C5    110.67  3.000
 ZAP  N3    C8   C5    112.91  3.000
 ZAP  H102  C10  H101  107.82  3.000
 ZAP  H102  C10  O4    110.14  3.000
 ZAP  H101  C10  O4    110.52  3.000
 ZAP  H102  C10  C11   110.75  3.000
 ZAP  H101  C10  C11   110.48  3.000
 ZAP  O4    C10  C11   107.15  3.000
 ZAP  C16   C11  C12   119.01  3.000
 ZAP  C16   C11  C10   120.37  3.000
 ZAP  C12   C11  C10   120.61  3.000
 ZAP  H12   C12  C13   119.73  3.000
 ZAP  H12   C12  C11   119.66  3.000
 ZAP  C13   C12  C11   120.62  3.000
 ZAP  H13   C13  C14   120.13  3.000
 ZAP  H13   C13  C12   119.89  3.000
 ZAP  C14   C13  C12   119.99  3.000
 ZAP  H14   C14  C15   120.09  3.000
 ZAP  H14   C14  C13   120.13  3.000
 ZAP  C15   C14  C13   119.78  3.000
 ZAP  H15   C15  C16   119.88  3.000
 ZAP  H15   C15  C14   120.06  3.000
 ZAP  C16   C15  C14   120.06  3.000
 ZAP  H16   C16  C15   119.68  3.000
 ZAP  H16   C16  C11   119.77  3.000
 ZAP  C15   C16  C11   120.54  3.000
 ZAP  HN1   N1   C1    110.49  3.000
 ZAP  HN22  N2   HN21  113.91  3.000
 ZAP  HN22  N2   C1    117.86  3.000
 ZAP  HN21  N2   C1    115.79  3.000
 ZAP  HN3   N3   C9    119.75  3.000
 ZAP  HN3   N3   C8    116.31  3.000
 ZAP  C9    N3   C8    122.96  3.000
 ZAP  C10   O4   C9    116.70  3.000
 ZAP  O3P   P    O2P   114.01  3.000
 ZAP  O3P   P    O1P   114.65  3.000
 ZAP  O2P   P    O1P   115.30  3.000
 ZAP  O3P   P    C8    103.94  3.000
 ZAP  O2P   P    C8    102.11  3.000
 ZAP  O1P   P    C8    104.72  3.000
 ZAP  O4    C9   O3    123.27  3.000
 ZAP  O4    C9   N3    111.13  3.000
 ZAP  O3    C9   N3    125.59  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
 ZAP  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 ZAP  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 ZAP  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 ZAP  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 ZAP  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 ZAP  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 ZAP  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 ZAP  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 ZAP  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 ZAP  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 ZAP  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 ZAP  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 ZAP  CONST_13  C4    C3   C2   C1    180.00   0.0  0
 ZAP  CONST_14  C6    C7   C2   C1    180.00   0.0  0
 ZAP  CONST_15  C8    C5   C4   C3    180.00   0.0  0
 ZAP  CONST_16  C8    C5   C6   C7    180.00   0.0  0
 ZAP  CONST_17  C13   C12  C11  C10   180.00   0.0  0
 ZAP  CONST_18  C15   C16  C11  C10   180.00   0.0  0
 ZAP  CONST_19  H4    C4   C3   C2    180.00   0.0  0
 ZAP  CONST_20  H6    C6   C7   C2    180.00   0.0  0
 ZAP  CONST_21  H7    C7   C2   C3    180.00   0.0  0
 ZAP  CONST_22  H3    C3   C4   C5    180.00   0.0  0
 ZAP  CONST_23  H13   C13  C12  C11   180.00   0.0  0
 ZAP  CONST_24  H15   C15  C16  C11   180.00   0.0  0
 ZAP  CONST_25  H16   C16  C11  C12   180.00   0.0  0
 ZAP  CONST_26  H14   C14  C13  C12   180.00   0.0  0
 ZAP  CONST_27  H12   C12  C13  C14   180.00   0.0  0
 ZAP  CONST_28  HN1   N1   C1   C2      0.00   0.0  0
 ZAP  CONST_29  HN21  N2   C1   C2    180.00   0.0  0
 ZAP  Var_01    N1    C1   C2   C3     32.64  30.0  2
 ZAP  Var_02    O4    C10  C11  C12   104.79  30.0  2
 ZAP  Var_03    C11   C10  O4   C9    179.04  30.0  1
 ZAP  Var_04    O3    C9   N3   C8      6.38  30.0  1
 ZAP  Var_05    N3    C9   O4   C10  -177.43  30.0  1

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
 ZAP  chir_01  C8  C5  N3  P  positiv

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
 ZAP  plan-1  C1    0.020
 ZAP  plan-1  C2    0.020
 ZAP  plan-1  C3    0.020
 ZAP  plan-1  C4    0.020
 ZAP  plan-1  C5    0.020
 ZAP  plan-1  C6    0.020
 ZAP  plan-1  C7    0.020
 ZAP  plan-1  C8    0.020
 ZAP  plan-1  H3    0.020
 ZAP  plan-1  H4    0.020
 ZAP  plan-1  H6    0.020
 ZAP  plan-1  H7    0.020
 ZAP  plan-2  C10   0.020
 ZAP  plan-2  C11   0.020
 ZAP  plan-2  C12   0.020
 ZAP  plan-2  C13   0.020
 ZAP  plan-2  C14   0.020
 ZAP  plan-2  C15   0.020
 ZAP  plan-2  C16   0.020
 ZAP  plan-2  H12   0.020
 ZAP  plan-2  H13   0.020
 ZAP  plan-2  H14   0.020
 ZAP  plan-2  H15   0.020
 ZAP  plan-2  H16   0.020
 ZAP  plan-3  C1    0.020
 ZAP  plan-3  C2    0.020
 ZAP  plan-3  N1    0.020
 ZAP  plan-3  N2    0.020
 ZAP  plan-3  HN1   0.020
 ZAP  plan-3  HN21  0.020
 ZAP  plan-3  HN22  0.020
 ZAP  plan-4  N3    0.020
 ZAP  plan-4  O3    0.020
 ZAP  plan-4  O4    0.020
 ZAP  plan-4  C9    0.020

