# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:14:34 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-{[(2S)-1-amino-5-{[(1Z)-2-chloroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](CCCNC(=N)CCl)NC(=O)c1ccccc1C(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
 YCL  YCL  '2-{[(2S)-1-amino-5-{[(1Z)-2-chloroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid'  ligand  42  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YCL
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
 YCL  CL    CL  CL     0  -0.141   7.7712  -1.3184  -0.1225
 YCL  O1    O   OC    -1  -0.590  -5.4748   0.6511  -1.1269
 YCL  O2    O   O      0  -0.572  -4.0566   1.1492   0.5217
 YCL  NAA   N   NH2    0  -0.801  -1.6248   3.9997   0.6351
 YCL  NAC   N   N      0  -0.662   5.8303   0.4322  -1.4446
 YCL  OAE   O   O      0  -0.495  -1.8182   3.0576  -1.4074
 YCL  OAF   O   O      0  -0.491  -1.5954  -0.1987   1.9575
 YCL  CAH   C   CR16   0  -0.247  -4.1104  -3.3173  -1.0794
 YCL  CAI   C   CR16   0  -0.289  -4.6136  -2.0250  -1.0576
 YCL  CAJ   C   CR16   0  -0.255  -2.8801  -3.5900  -0.4963
 YCL  CAK   C   CR6    0  -0.099  -3.9105  -0.9868  -0.4515
 YCL  CAL   C   CR16   0  -0.278  -2.1610  -2.5643   0.0994
 YCL  CAM   C   CH2    0  -0.464   1.7629   0.8641   0.1514
 YCL  CAN   C   CH2    0  -0.263   3.1441   1.0032  -0.4678
 YCL  CAO   C   CH2    0  -0.418   0.8254   1.9512  -0.3529
 YCL  CAP   C   CH2    0  -0.529   6.0327  -1.2969   0.2416
 YCL  NAR   N   NH1    0  -0.643   4.0326  -0.0300   0.0139
 YCL  NAS   N   NH1    0  -0.597  -1.2292   0.6173  -0.1291
 YCL  CAU   C   C      0   0.552  -1.4211   3.0213  -0.2522
 YCL  CAV   C   C      0   0.424   5.2919  -0.1876  -0.4716
 YCL  CAW   C   C      0   0.506  -1.8232  -0.2062   0.7579
 YCL  CAX   C   CR6    0  -0.063  -2.6679  -1.2685   0.1197
 YCL  CAZ   C   CH1    0  -0.224  -0.5786   1.8473   0.2457
 YCL  HNAA  H   HNH2   0   0.402  -2.1489   4.8216   0.3803
 YCL  HNAB  H   HNH2   0   0.409  -1.3247   3.9218   1.5911
 YCL  HNAC  H   H      0   0.337   5.2105   1.1368  -1.8325
 YCL  HAH   H   HCR6   0   0.254  -4.6777  -4.1120  -1.5469
 YCL  HAI   H   HCR6   0   0.250  -5.5745  -1.8131  -1.5075
 YCL  HAJ   H   HCR6   0   0.257  -2.4804  -4.5956  -0.5064
 YCL  HAL   H   HCR6   0   0.256  -1.1948  -2.7753   0.5418
 YCL  HAM   H   HCH2   0   0.241   1.3584  -0.1218  -0.0895
 YCL  HAMA  H   HCH2   0   0.234   1.8419   0.9217   1.2418
 YCL  HAN   H   HCH2   0   0.235   3.0575   0.9231  -1.5556
 YCL  HANA  H   HCH2   0   0.229   3.5488   2.0006  -0.2537
 YCL  HAO   H   HCH2   0   0.242   1.2342   2.9348  -0.1038
 YCL  HAOA  H   HCH2   0   0.235   0.7555   1.9093  -1.4440
 YCL  HAP   H   HCH2   0   0.311   5.6201  -2.2616  -0.0523
 YCL  HAPA  H   HCH2   0   0.298   5.9228  -1.2012   1.3210
 YCL  HNAS  H   HNH1   0   0.391  -1.5383   0.5633  -1.0879
 YCL  HAZ   H   HCH1   0   0.268  -0.5016   1.8641   1.3334
 YCL  HAR   H   HNH1   0   0.394   3.8261  -0.4152   0.9221
 YCL  C1    C   C      0   0.397  -4.5339   0.4013  -0.3520

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
 YCL  CL   CAP   single    1.776  0.020  1.776
 YCL  C1   O1    deloc     1.244  0.020  1.244
 YCL  C1   O2    deloc     1.245  0.020  1.245
 YCL  C1   CAK   single    1.525  0.020  1.525
 YCL  NAA  CAU   single    1.336  0.020  1.336
 YCL  NAC  CAV   double    1.273  0.020  1.273
 YCL  OAE  CAU   double    1.222  0.020  1.222
 YCL  OAF  CAW   double    1.221  0.020  1.221
 YCL  CAH  CAI   aromatic  1.387  0.020  1.387
 YCL  CAH  CAJ   aromatic  1.388  0.020  1.388
 YCL  CAI  CAK   aromatic  1.393  0.020  1.393
 YCL  CAJ  CAL   aromatic  1.387  0.020  1.387
 YCL  CAK  CAX   aromatic  1.396  0.020  1.396
 YCL  CAL  CAX   aromatic  1.392  0.020  1.392
 YCL  CAM  CAN   single    1.520  0.020  1.520
 YCL  CAM  CAO   single    1.522  0.020  1.522
 YCL  CAN  NAR   single    1.445  0.020  1.445
 YCL  CAO  CAZ   single    1.530  0.020  1.530
 YCL  CAP  CAV   single    1.513  0.020  1.513
 YCL  NAR  CAV   single    1.359  0.020  1.359
 YCL  NAS  CAW   single    1.348  0.020  1.348
 YCL  NAS  CAZ   single    1.441  0.020  1.441
 YCL  CAU  CAZ   single    1.528  0.020  1.528
 YCL  CAW  CAX   single    1.500  0.020  1.500
 YCL  NAA  HNAA  single    0.860  0.020  1.020
 YCL  NAA  HNAB  single    0.860  0.020  1.020
 YCL  NAC  HNAC  single    0.890  0.020  1.040
 YCL  CAH  HAH   single    0.930  0.020  1.080
 YCL  CAI  HAI   single    0.930  0.020  1.080
 YCL  CAJ  HAJ   single    0.930  0.020  1.080
 YCL  CAL  HAL   single    0.930  0.020  1.080
 YCL  CAM  HAM   single    0.970  0.020  1.090
 YCL  CAM  HAMA  single    0.970  0.020  1.090
 YCL  CAN  HAN   single    0.970  0.020  1.090
 YCL  CAN  HANA  single    0.970  0.020  1.090
 YCL  CAO  HAO   single    0.970  0.020  1.090
 YCL  CAO  HAOA  single    0.970  0.020  1.090
 YCL  CAP  HAP   single    0.970  0.020  1.090
 YCL  CAP  HAPA  single    0.970  0.020  1.090
 YCL  NAS  HNAS  single    0.890  0.020  1.040
 YCL  CAZ  HAZ   single    0.970  0.020  1.090
 YCL  NAR  HAR   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
 YCL  HNAB  NAA  HNAA  117.32  3.000
 YCL  HNAB  NAA  CAU   121.96  3.000
 YCL  HNAA  NAA  CAU   120.58  3.000
 YCL  HNAC  NAC  CAV   111.81  3.000
 YCL  HAH   CAH  CAJ   120.10  3.000
 YCL  HAH   CAH  CAI   120.04  3.000
 YCL  CAJ   CAH  CAI   119.86  3.000
 YCL  HAI   CAI  CAK   118.90  3.000
 YCL  HAI   CAI  CAH   119.88  3.000
 YCL  CAK   CAI  CAH   121.22  3.000
 YCL  HAJ   CAJ  CAL   119.97  3.000
 YCL  HAJ   CAJ  CAH   120.39  3.000
 YCL  CAL   CAJ  CAH   119.64  3.000
 YCL  CAX   CAK  CAI   118.48  3.000
 YCL  CAX   CAK  C1    121.39  3.000
 YCL  CAI   CAK  C1    120.04  3.000
 YCL  HAL   CAL  CAX   120.02  3.000
 YCL  HAL   CAL  CAJ   119.59  3.000
 YCL  CAX   CAL  CAJ   120.39  3.000
 YCL  HAMA  CAM  HAM   107.09  3.000
 YCL  HAMA  CAM  CAO   109.69  3.000
 YCL  HAM   CAM  CAO   110.09  3.000
 YCL  HAMA  CAM  CAN   109.60  3.000
 YCL  HAM   CAM  CAN   109.22  3.000
 YCL  CAO   CAM  CAN   111.07  3.000
 YCL  HANA  CAN  HAN   106.84  3.000
 YCL  HANA  CAN  NAR   110.97  3.000
 YCL  HAN   CAN  NAR   109.12  3.000
 YCL  HANA  CAN  CAM   109.80  3.000
 YCL  HAN   CAN  CAM   109.05  3.000
 YCL  NAR   CAN  CAM   110.94  3.000
 YCL  HAOA  CAO  HAO   106.58  3.000
 YCL  HAOA  CAO  CAZ   109.21  3.000
 YCL  HAO   CAO  CAZ   108.36  3.000
 YCL  HAOA  CAO  CAM   110.03  3.000
 YCL  HAO   CAO  CAM   109.67  3.000
 YCL  CAZ   CAO  CAM   112.79  3.000
 YCL  HAPA  CAP  HAP   107.87  3.000
 YCL  HAPA  CAP  CAV   110.70  3.000
 YCL  HAP   CAP  CAV   109.67  3.000
 YCL  HAPA  CAP  CL    107.64  3.000
 YCL  HAP   CAP  CL    107.73  3.000
 YCL  CAV   CAP  CL    113.05  3.000
 YCL  HAR   NAR  CAV   117.88  3.000
 YCL  HAR   NAR  CAN   116.58  3.000
 YCL  CAV   NAR  CAN   122.25  3.000
 YCL  HNAS  NAS  CAZ   115.54  3.000
 YCL  HNAS  NAS  CAW   117.24  3.000
 YCL  CAZ   NAS  CAW   123.30  3.000
 YCL  CAZ   CAU  OAE   120.65  3.000
 YCL  CAZ   CAU  NAA   115.47  3.000
 YCL  OAE   CAU  NAA   123.80  3.000
 YCL  NAR   CAV  CAP   111.75  3.000
 YCL  NAR   CAV  NAC   127.49  3.000
 YCL  CAP   CAV  NAC   120.68  3.000
 YCL  CAX   CAW  NAS   113.63  3.000
 YCL  CAX   CAW  OAF   121.83  3.000
 YCL  NAS   CAW  OAF   124.09  3.000
 YCL  CAW   CAX  CAL   117.42  3.000
 YCL  CAW   CAX  CAK   122.16  3.000
 YCL  CAL   CAX  CAK   120.41  3.000
 YCL  HAZ   CAZ  CAU   110.61  3.000
 YCL  HAZ   CAZ  NAS   107.72  3.000
 YCL  CAU   CAZ  NAS   108.79  3.000
 YCL  HAZ   CAZ  CAO   108.93  3.000
 YCL  CAU   CAZ  CAO   109.04  3.000
 YCL  NAS   CAZ  CAO   111.75  3.000
 YCL  CAK   C1   O2    115.84  3.000
 YCL  CAK   C1   O1    116.82  3.000
 YCL  O2    C1   O1    127.32  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
 YCL  CONST_01  CAX   CAK  CAI  CAH    0.00   0.0  0
 YCL  CONST_02  CAX   CAL  CAJ  CAH    0.00   0.0  0
 YCL  CONST_03  CAL   CAJ  CAH  CAI    0.00   0.0  0
 YCL  CONST_04  CAL   CAX  CAK  CAI    0.00   0.0  0
 YCL  CONST_05  CAK   CAI  CAH  CAJ    0.00   0.0  0
 YCL  CONST_06  CAK   CAX  CAL  CAJ    0.00   0.0  0
 YCL  CONST_07  CAH   CAI  CAK  C1   180.00   0.0  0
 YCL  CONST_08  CAL   CAX  CAK  C1   180.00   0.0  0
 YCL  CONST_09  CAW   CAX  CAK  CAI  180.00   0.0  0
 YCL  CONST_10  CAW   CAX  CAL  CAJ  180.00   0.0  0
 YCL  CONST_11  HAL   CAL  CAJ  CAH  180.00   0.0  0
 YCL  CONST_12  HAJ   CAJ  CAH  CAI  180.00   0.0  0
 YCL  CONST_13  HAI   CAI  CAH  CAJ  180.00   0.0  0
 YCL  CONST_14  HAH   CAH  CAI  CAK  180.00   0.0  0
 YCL  CONST_15  CAZ   NAS  CAW  CAX  180.00   0.0  0
 YCL  CONST_16  HNAS  NAS  CAW  CAX    0.00   0.0  0
 YCL  CONST_18  CAN   NAR  CAV  NAC    0.00   0.0  0
 YCL  CONST_19  CAP   CAV  NAR  CAN  180.00   0.0  0
 YCL  CONST_20  HNAA  NAA  CAU  OAE    0.00   0.0  0
 YCL  CONST_21  HNAB  NAA  CAU  OAE  180.00   0.0  0
 YCL  CONST_23  HNAC  NAC  CAV  CAP  180.00   0.0  0
 YCL  Var_01    CAI   CAK  C1   O1   -19.31  30.0  2
 YCL  Var_02    CAK   CAX  CAW  OAF  113.42  30.0  2
 YCL  Var_03    NAC   CAV  CAP  CL    14.97  30.0  3
 YCL  Var_04    CAV   NAR  CAN  CAM  174.57  30.0  3
 YCL  Var_05    CAZ   CAO  CAM  CAN  179.95  30.0  3
 YCL  Var_06    NAR   CAN  CAM  CAO  179.95  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
 YCL  chir_01  CAZ  CAO  NAS  CAU  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
 YCL  plan-1  CAH   0.020
 YCL  plan-1  CAI   0.020
 YCL  plan-1  CAJ   0.020
 YCL  plan-1  CAK   0.020
 YCL  plan-1  CAL   0.020
 YCL  plan-1  CAW   0.020
 YCL  plan-1  CAX   0.020
 YCL  plan-1  HAH   0.020
 YCL  plan-1  HAI   0.020
 YCL  plan-1  HAJ   0.020
 YCL  plan-1  HAL   0.020
 YCL  plan-1  C1    0.020
 YCL  plan-2  NAA   0.020
 YCL  plan-2  OAE   0.020
 YCL  plan-2  CAU   0.020
 YCL  plan-2  CAZ   0.020
 YCL  plan-2  HNAA  0.020
 YCL  plan-2  HNAB  0.020
 YCL  plan-3  OAF   0.020
 YCL  plan-3  NAS   0.020
 YCL  plan-3  CAW   0.020
 YCL  plan-3  CAX   0.020
 YCL  plan-3  CAZ   0.020
 YCL  plan-3  HNAS  0.020
 YCL  plan-4  NAC   0.020
 YCL  plan-4  CAN   0.020
 YCL  plan-4  CAP   0.020
 YCL  plan-4  NAR   0.020
 YCL  plan-4  CAV   0.020
 YCL  plan-4  HNAC  0.020
 YCL  plan-4  HAR   0.020
 YCL  plan-5  O1    0.020
 YCL  plan-5  O2    0.020
 YCL  plan-5  CAK   0.020
 YCL  plan-5  C1    0.020

