# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:42:40 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: methyl (7-carbamimidoylnaphthalen-1-yl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1cccc2ccc(cc12)C(N)=N
#
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
 9UP  9UP  'methyl (7-carbamimidoylnaphthalen-1-yl)carbamate'  ligand  31  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9UP
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
 9UP  CAA  C  CH3   0  -0.417   4.5323  -2.3422  -0.2527
 9UP  OAL  O  O2    0  -0.475   3.3374  -1.8404   0.3398
 9UP  CAN  C  C     0   0.730   2.9067  -0.6535  -0.0833
 9UP  OAD  O  O     0  -0.497   3.4598   0.0159  -0.9254
 9UP  N1   N  NH1   0  -0.769   1.7630  -0.3171   0.5674
 9UP  CAP  C  CR6   0   0.306   1.0500   0.8720   0.3451
 9UP  CAR  C  CR66  0   0.105  -0.3521   0.7978   0.0988
 9UP  CAJ  C  CR16  0  -0.343  -1.0433  -0.4293   0.0087
 9UP  CAF  C  CR16  0  -0.293   1.6769   2.0903   0.3898
 9UP  CAE  C  CR16  0  -0.262   0.9505   3.2794   0.1895
 9UP  CAH  C  CR16  0  -0.320  -0.3986   3.2449  -0.0259
 9UP  CAQ  C  CR66  0   0.092  -1.0780   2.0070  -0.0673
 9UP  CAI  C  CR16  0  -0.301  -2.4720   1.9379  -0.2875
 9UP  CAG  C  CR16  0  -0.290  -3.1198   0.7363  -0.3412
 9UP  CAO  C  CR6   0   0.051  -2.3999  -0.4724  -0.1968
 9UP  CAM  C  C     0   0.337  -3.0824  -1.7948  -0.2725
 9UP  N2   N  NH2   0  -0.822  -4.4069  -1.7819   0.0610
 9UP  N3   N  N     0  -0.651  -2.4152  -2.8087  -0.6706
 9UP  H1   H  HCH3  0   0.238   4.4124  -2.5043  -1.3237
 9UP  H2   H  HCH3  0   0.238   5.3765  -1.6746  -0.0815
 9UP  H3   H  HCH3  0   0.251   4.7257  -3.2942   0.2329
 9UP  H4   H  HNH1  0   0.413   1.3673  -0.9963   1.2000
 9UP  H5   H  HCR6  0   0.246  -0.5079  -1.3648   0.0986
 9UP  H6   H  HCR6  0   0.271   2.7360   2.1493   0.5982
 9UP  H7   H  HCR6  0   0.265   1.4729   4.2260   0.2290
 9UP  H8   H  HCR6  0   0.260  -0.9600   4.1601  -0.1668
 9UP  H9   H  HCR6  0   0.261  -3.0264   2.8585  -0.4221
 9UP  H10  H  HCR6  0   0.262  -4.1860   0.7182  -0.5248
 9UP  H11  H  HNH2  0   0.396  -4.7279  -1.0826   0.7106
 9UP  H12  H  HNH2  0   0.392  -4.8576  -2.6752   0.1837
 9UP  H13  H  H     0   0.325  -2.9791  -3.6539  -0.6386

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
 9UP  CAI  CAG  aromatic  1.366  0.020  1.366
 9UP  CAI  CAQ  aromatic  1.413  0.020  1.413
 9UP  CAH  CAQ  aromatic  1.413  0.020  1.413
 9UP  CAH  CAE  aromatic  1.367  0.020  1.367
 9UP  CAG  CAO  aromatic  1.414  0.020  1.414
 9UP  CAQ  CAR  aromatic  1.420  0.020  1.420
 9UP  CAE  CAF  aromatic  1.408  0.020  1.408
 9UP  CAO  CAM  single    1.490  0.020  1.490
 9UP  CAO  CAJ  aromatic  1.373  0.020  1.373
 9UP  N3   CAM  double    1.277  0.020  1.277
 9UP  CAR  CAJ  aromatic  1.411  0.020  1.411
 9UP  CAR  CAP  aromatic  1.425  0.020  1.425
 9UP  CAM  N2   single    1.366  0.020  1.366
 9UP  CAF  CAP  aromatic  1.371  0.020  1.371
 9UP  CAP  N1   single    1.404  0.020  1.404
 9UP  N1   CAN  single    1.358  0.020  1.358
 9UP  CAN  OAL  single    1.332  0.020  1.332
 9UP  CAN  OAD  double    1.210  0.020  1.210
 9UP  OAL  CAA  single    1.425  0.020  1.425
 9UP  CAA  H1   single    0.970  0.020  1.090
 9UP  CAA  H2   single    0.970  0.020  1.090
 9UP  CAA  H3   single    0.970  0.020  1.090
 9UP  N1   H4   single    0.860  0.020  1.020
 9UP  CAJ  H5   single    0.930  0.020  1.080
 9UP  CAF  H6   single    0.930  0.020  1.080
 9UP  CAE  H7   single    0.930  0.020  1.080
 9UP  CAH  H8   single    0.930  0.020  1.080
 9UP  CAI  H9   single    0.930  0.020  1.080
 9UP  CAG  H10  single    0.930  0.020  1.080
 9UP  N2   H11  single    0.890  0.020  1.040
 9UP  N2   H12  single    0.890  0.020  1.040
 9UP  N3   H13  single    0.890  0.020  1.040

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
 9UP  H3   CAA  H2   109.19  3.000
 9UP  H3   CAA  H1   109.19  3.000
 9UP  H2   CAA  H1   109.31  3.000
 9UP  H3   CAA  OAL  105.79  3.000
 9UP  H2   CAA  OAL  111.62  3.000
 9UP  H1   CAA  OAL  111.64  3.000
 9UP  CAN  OAL  CAA  116.93  3.000
 9UP  N1   CAN  OAD  125.56  3.000
 9UP  OAD  CAN  OAL  124.51  3.000
 9UP  N1   CAN  OAL  109.93  3.000
 9UP  H4   N1   CAP  118.04  3.000
 9UP  H4   N1   CAN  117.64  3.000
 9UP  CAP  N1   CAN  124.15  3.000
 9UP  CAF  CAP  CAR  120.11  3.000
 9UP  CAF  CAP  N1   121.01  3.000
 9UP  CAR  CAP  N1   118.86  3.000
 9UP  CAQ  CAR  CAJ  118.85  3.000
 9UP  CAJ  CAR  CAP  122.55  3.000
 9UP  CAQ  CAR  CAP  118.60  3.000
 9UP  H5   CAJ  CAO  118.32  3.000
 9UP  H5   CAJ  CAR  120.28  3.000
 9UP  CAO  CAJ  CAR  121.40  3.000
 9UP  H6   CAF  CAE  119.14  3.000
 9UP  H6   CAF  CAP  120.19  3.000
 9UP  CAE  CAF  CAP  120.67  3.000
 9UP  H7   CAE  CAH  120.30  3.000
 9UP  H7   CAE  CAF  118.99  3.000
 9UP  CAH  CAE  CAF  120.70  3.000
 9UP  H8   CAH  CAQ  119.17  3.000
 9UP  H8   CAH  CAE  120.73  3.000
 9UP  CAQ  CAH  CAE  120.10  3.000
 9UP  CAI  CAQ  CAH  121.46  3.000
 9UP  CAH  CAQ  CAR  119.79  3.000
 9UP  CAI  CAQ  CAR  118.74  3.000
 9UP  H9   CAI  CAG  120.00  3.000
 9UP  H9   CAI  CAQ  118.87  3.000
 9UP  CAG  CAI  CAQ  121.13  3.000
 9UP  H10  CAG  CAO  120.30  3.000
 9UP  H10  CAG  CAI  119.25  3.000
 9UP  CAO  CAG  CAI  120.42  3.000
 9UP  CAM  CAO  CAG  121.35  3.000
 9UP  CAM  CAO  CAJ  119.22  3.000
 9UP  CAG  CAO  CAJ  119.43  3.000
 9UP  N3   CAM  N2   126.16  3.000
 9UP  N2   CAM  CAO  115.05  3.000
 9UP  N3   CAM  CAO  118.76  3.000
 9UP  H12  N2   H11  113.22  3.000
 9UP  H12  N2   CAM  117.06  3.000
 9UP  H11  N2   CAM  118.24  3.000
 9UP  H13  N3   CAM  111.12  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
 9UP  CONST_01  CAI  CAQ  CAR  CAP  180.00   0.0  0
 9UP  CONST_02  CAH  CAQ  CAR  CAP    0.00   0.0  0
 9UP  CONST_03  CAO  CAJ  CAR  CAP  180.00   0.0  0
 9UP  CONST_04  CAH  CAE  CAF  CAP    0.00   0.0  0
 9UP  CONST_05  CAG  CAI  CAQ  CAR    0.00   0.0  0
 9UP  CONST_06  CAE  CAH  CAQ  CAR    0.00   0.0  0
 9UP  CONST_07  CAG  CAO  CAJ  CAR    0.00   0.0  0
 9UP  CONST_08  CAE  CAF  CAP  CAR    0.00   0.0  0
 9UP  CONST_09  CAI  CAG  CAO  CAJ    0.00   0.0  0
 9UP  CONST_10  CAI  CAQ  CAR  CAJ    0.00   0.0  0
 9UP  CONST_11  CAH  CAQ  CAR  CAJ  180.00   0.0  0
 9UP  CONST_12  CAF  CAP  CAR  CAJ  180.00   0.0  0
 9UP  CONST_13  CAQ  CAH  CAE  CAF    0.00   0.0  0
 9UP  CONST_14  CAQ  CAR  CAP  CAF    0.00   0.0  0
 9UP  CONST_15  CAI  CAQ  CAH  CAE  180.00   0.0  0
 9UP  CONST_16  CAG  CAI  CAQ  CAH  180.00   0.0  0
 9UP  CONST_17  CAO  CAG  CAI  CAQ    0.00   0.0  0
 9UP  CONST_18  CAO  CAJ  CAR  CAQ    0.00   0.0  0
 9UP  CONST_19  CAQ  CAR  CAP  N1   180.00   0.0  0
 9UP  CONST_20  CAJ  CAR  CAP  N1     0.00   0.0  0
 9UP  CONST_21  CAE  CAF  CAP  N1   180.00   0.0  0
 9UP  CONST_22  CAM  CAO  CAJ  CAR  180.00   0.0  0
 9UP  CONST_23  CAM  CAO  CAG  CAI  180.00   0.0  0
 9UP  CONST_24  H5   CAJ  CAR  CAP    0.00   0.0  0
 9UP  CONST_25  H7   CAE  CAF  CAP  180.00   0.0  0
 9UP  CONST_26  H9   CAI  CAQ  CAR  180.00   0.0  0
 9UP  CONST_27  H8   CAH  CAQ  CAR  180.00   0.0  0
 9UP  CONST_28  H6   CAF  CAP  CAR  180.00   0.0  0
 9UP  CONST_29  H10  CAG  CAO  CAJ  180.00   0.0  0
 9UP  CONST_33  CAP  N1   CAN  OAL  180.00   0.0  0
 9UP  CONST_34  CAP  N1   CAN  OAD    0.00   0.0  0
 9UP  CONST_35  H13  N3   CAM  CAO  180.00   0.0  0
 9UP  CONST_37  H12  N2   CAM  CAO  180.00   0.0  0
 9UP  Var_01    N3   CAM  CAO  CAJ  -27.38  30.0  2
 9UP  Var_02    N1   CAN  OAL  CAA  179.76  30.0  1
 9UP  Var_03    H1   CAA  OAL  CAN  -62.52  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
 9UP  plan-1  N1   0.020
 9UP  plan-1  CAP  0.020
 9UP  plan-1  CAR  0.020
 9UP  plan-1  CAJ  0.020
 9UP  plan-1  CAF  0.020
 9UP  plan-1  CAE  0.020
 9UP  plan-1  CAH  0.020
 9UP  plan-1  CAQ  0.020
 9UP  plan-1  CAI  0.020
 9UP  plan-1  CAG  0.020
 9UP  plan-1  CAO  0.020
 9UP  plan-1  CAM  0.020
 9UP  plan-1  H5   0.020
 9UP  plan-1  H6   0.020
 9UP  plan-1  H7   0.020
 9UP  plan-1  H8   0.020
 9UP  plan-1  H9   0.020
 9UP  plan-1  H10  0.020
 9UP  plan-2  CAN  0.020
 9UP  plan-2  N1   0.020
 9UP  plan-2  CAP  0.020
 9UP  plan-2  H4   0.020
 9UP  plan-3  CAO  0.020
 9UP  plan-3  CAM  0.020
 9UP  plan-3  N2   0.020
 9UP  plan-3  N3   0.020
 9UP  plan-3  H11  0.020
 9UP  plan-3  H12  0.020
 9UP  plan-3  H13  0.020
 9UP  plan-4  OAL  0.020
 9UP  plan-4  CAN  0.020
 9UP  plan-4  OAD  0.020
 9UP  plan-4  N1   0.020

