# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:59:59 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: O-benzyl-N-methyl-L-tyrosinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H](N)Cc1ccc(OCc2ccccc2)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
 MS7  MS7  O-benzyl-N-methyl-L-tyrosinamide  ligand  41  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MS7
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
 MS7  N1    N  NH2   0  -0.786   3.5801   1.3525   1.3379
 MS7  C4    C  CH1   0  -0.213   3.8909   0.1692   0.5653
 MS7  C6    C  CH2   0  -0.523   3.2457   0.1090  -0.8408
 MS7  C9    C  CR6   0   0.102   1.7474   0.1275  -0.7626
 MS7  C10   C  CR16  0  -0.303   1.0241   1.3167  -0.8590
 MS7  C12   C  CR16  0  -0.334  -0.3527   1.3385  -0.7207
 MS7  C14   C  CR6   0   0.371  -1.0528   0.1566  -0.4783
 MS7  C15   C  CR16  0  -0.367  -0.3497  -1.0423  -0.3870
 MS7  C17   C  CR16  0  -0.286   1.0329  -1.0410  -0.5266
 MS7  O19   O  O2    0  -0.470  -2.3924   0.2693  -0.3538
 MS7  C20   C  CH2   0  -0.267  -3.1467  -0.8984  -0.0613
 MS7  C23   C  CR6   0   0.101  -4.5777  -0.4843   0.1034
 MS7  C24   C  CR16  0  -0.303  -5.5254  -0.7920  -0.8660
 MS7  C26   C  CR16  0  -0.241  -6.8491  -0.3981  -0.7100
 MS7  C28   C  CR16  0  -0.262  -7.2325   0.3150   0.4168
 MS7  C30   C  CR16  0  -0.243  -6.2898   0.6295   1.3895
 MS7  C32   C  CR16  0  -0.285  -4.9710   0.2310   1.2329
 MS7  C34   C  C     0   0.548   5.4011   0.0820   0.3940
 MS7  O35   O  O     0  -0.502   6.0752   1.0759   0.1548
 MS7  N36   N  NH1   0  -0.622   5.9237  -1.1469   0.4692
 MS7  C38   C  CH3   0  -0.513   7.3253  -1.4123   0.2433
 MS7  HN1   H  HNH2  0   0.342   3.9350   2.1727   0.8612
 MS7  HN1A  H  HNH2  0   0.354   2.5757   1.4663   1.3968
 MS7  H4    H  HCH1  0   0.257   3.5382  -0.7015   1.1270
 MS7  H6    H  HCH2  0   0.253   3.6080   0.9564  -1.4292
 MS7  H6A   H  HCH2  0   0.251   3.5816  -0.7988  -1.3488
 MS7  H10   H  HCR6  0   0.253   1.5444   2.2468  -1.0559
 MS7  H12   H  HCR6  0   0.260  -0.8946   2.2730  -0.8004
 MS7  H15   H  HCR6  0   0.279  -0.8535  -1.9829  -0.2107
 MS7  H17   H  HCR6  0   0.250   1.5611  -1.9848  -0.4495
 MS7  H20   H  HCH2  0   0.243  -3.0474  -1.6338  -0.8666
 MS7  H20A  H  HCH2  0   0.240  -2.7802  -1.3638   0.8605
 MS7  H24   H  HCR6  0   0.255  -5.2294  -1.3453  -1.7494
 MS7  H26   H  HCR6  0   0.258  -7.5790  -0.6497  -1.4684
 MS7  H28   H  HCR6  0   0.259  -8.2626   0.6225   0.5409
 MS7  H30   H  HCR6  0   0.258  -6.5851   1.1820   2.2721
 MS7  H32   H  HCR6  0   0.254  -4.2422   0.4715   1.9980
 MS7  HN36  H  HNH1  0   0.405   5.3227  -1.9233   0.6879
 MS7  H38   H  HCH3  0   0.238   7.6321  -1.1303  -0.7644
 MS7  H38A  H  HCH3  0   0.239   7.9556  -0.8793   0.9555
 MS7  H38B  H  HCH3  0   0.251   7.4966  -2.4775   0.3667

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
 MS7  N1   C4    single    1.447  0.020  1.447
 MS7  C4   C6    single    1.548  0.020  1.548
 MS7  C4   C34   single    1.522  0.020  1.522
 MS7  C6   C9    single    1.500  0.020  1.500
 MS7  C9   C10   aromatic  1.395  0.020  1.395
 MS7  C9   C17   aromatic  1.390  0.020  1.390
 MS7  C10  C12   aromatic  1.384  0.020  1.384
 MS7  C12  C14   aromatic  1.395  0.020  1.395
 MS7  C14  C15   aromatic  1.393  0.020  1.393
 MS7  C14  O19   single    1.350  0.020  1.350
 MS7  C15  C17   aromatic  1.390  0.020  1.390
 MS7  O19  C20   single    1.421  0.020  1.421
 MS7  C20  C23   single    1.499  0.020  1.499
 MS7  C23  C24   aromatic  1.390  0.020  1.390
 MS7  C23  C32   aromatic  1.394  0.020  1.394
 MS7  C24  C26   aromatic  1.390  0.020  1.390
 MS7  C26  C28   aromatic  1.388  0.020  1.388
 MS7  C28  C30   aromatic  1.391  0.020  1.391
 MS7  C30  C32   aromatic  1.387  0.020  1.387
 MS7  C34  O35   double    1.225  0.020  1.225
 MS7  C34  N36   single    1.338  0.020  1.338
 MS7  N36  C38   single    1.444  0.020  1.444
 MS7  N1   HN1   single    0.890  0.020  1.040
 MS7  N1   HN1A  single    0.890  0.020  1.040
 MS7  C4   H4    single    0.970  0.020  1.090
 MS7  C6   H6    single    0.970  0.020  1.090
 MS7  C6   H6A   single    0.970  0.020  1.090
 MS7  C10  H10   single    0.930  0.020  1.080
 MS7  C12  H12   single    0.930  0.020  1.080
 MS7  C15  H15   single    0.930  0.020  1.080
 MS7  C17  H17   single    0.930  0.020  1.080
 MS7  C20  H20   single    0.970  0.020  1.090
 MS7  C20  H20A  single    0.970  0.020  1.090
 MS7  C24  H24   single    0.930  0.020  1.080
 MS7  C26  H26   single    0.930  0.020  1.080
 MS7  C28  H28   single    0.930  0.020  1.080
 MS7  C30  H30   single    0.930  0.020  1.080
 MS7  C32  H32   single    0.930  0.020  1.080
 MS7  N36  HN36  single    0.860  0.020  1.020
 MS7  C38  H38   single    0.970  0.020  1.090
 MS7  C38  H38A  single    0.970  0.020  1.090
 MS7  C38  H38B  single    0.970  0.020  1.090

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
 MS7  HN1A  N1   HN1   106.50  3.000
 MS7  HN1A  N1   C4    109.64  3.000
 MS7  HN1   N1   C4    109.61  3.000
 MS7  H4    C4   C34   109.38  3.000
 MS7  H4    C4   C6    107.51  3.000
 MS7  C34   C4   C6    108.00  3.000
 MS7  H4    C4   N1    107.90  3.000
 MS7  C34   C4   N1    108.66  3.000
 MS7  C6    C4   N1    115.29  3.000
 MS7  H6A   C6   H6    106.96  3.000
 MS7  H6A   C6   C9    109.95  3.000
 MS7  H6    C6   C9    110.45  3.000
 MS7  H6A   C6   C4    109.04  3.000
 MS7  H6    C6   C4    108.70  3.000
 MS7  C9    C6   C4    111.61  3.000
 MS7  C17   C9   C10   117.50  3.000
 MS7  C17   C9   C6    120.79  3.000
 MS7  C10   C9   C6    121.64  3.000
 MS7  H10   C10  C12   118.83  3.000
 MS7  H10   C10  C9    119.68  3.000
 MS7  C12   C10  C9    121.49  3.000
 MS7  H12   C12  C14   119.52  3.000
 MS7  H12   C12  C10   120.26  3.000
 MS7  C14   C12  C10   120.22  3.000
 MS7  O19   C14  C15   124.52  3.000
 MS7  O19   C14  C12   116.32  3.000
 MS7  C15   C14  C12   119.16  3.000
 MS7  H15   C15  C17   118.73  3.000
 MS7  H15   C15  C14   121.61  3.000
 MS7  C17   C15  C14   119.66  3.000
 MS7  H17   C17  C15   118.47  3.000
 MS7  H17   C17  C9    119.56  3.000
 MS7  C15   C17  C9    121.96  3.000
 MS7  C20   O19  C14   118.50  3.000
 MS7  H20A  C20  H20   107.64  3.000
 MS7  H20A  C20  C23   110.14  3.000
 MS7  H20   C20  C23   110.66  3.000
 MS7  H20A  C20  O19   110.17  3.000
 MS7  H20   C20  O19   110.64  3.000
 MS7  C23   C20  O19   107.61  3.000
 MS7  C32   C23  C24   119.11  3.000
 MS7  C32   C23  C20   120.02  3.000
 MS7  C24   C23  C20   120.87  3.000
 MS7  H24   C24  C26   119.76  3.000
 MS7  H24   C24  C23   119.69  3.000
 MS7  C26   C24  C23   120.55  3.000
 MS7  H26   C26  C28   120.14  3.000
 MS7  H26   C26  C24   119.86  3.000
 MS7  C28   C26  C24   119.99  3.000
 MS7  H28   C28  C30   120.06  3.000
 MS7  H28   C28  C26   120.14  3.000
 MS7  C30   C28  C26   119.80  3.000
 MS7  H30   C30  C32   119.89  3.000
 MS7  H30   C30  C28   120.06  3.000
 MS7  C32   C30  C28   120.05  3.000
 MS7  H32   C32  C30   119.74  3.000
 MS7  H32   C32  C23   119.76  3.000
 MS7  C30   C32  C23   120.49  3.000
 MS7  N36   C34  O35   122.79  3.000
 MS7  N36   C34  C4    115.72  3.000
 MS7  O35   C34  C4    121.44  3.000
 MS7  HN36  N36  C38   118.16  3.000
 MS7  HN36  N36  C34   119.20  3.000
 MS7  C38   N36  C34   122.63  3.000
 MS7  H38B  C38  H38A  108.30  3.000
 MS7  H38B  C38  H38   108.31  3.000
 MS7  H38A  C38  H38   108.34  3.000
 MS7  H38B  C38  N36   108.40  3.000
 MS7  H38A  C38  N36   111.66  3.000
 MS7  H38   C38  N36   111.72  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
 MS7  CONST_01  C14   C12  C10  C9     0.00   0.0  0
 MS7  CONST_02  C14   C15  C17  C9     0.00   0.0  0
 MS7  CONST_03  C15   C17  C9   C10    0.00   0.0  0
 MS7  CONST_04  C15   C14  C12  C10    0.00   0.0  0
 MS7  CONST_05  C17   C9   C10  C12    0.00   0.0  0
 MS7  CONST_06  C17   C15  C14  C12    0.00   0.0  0
 MS7  CONST_07  C28   C26  C24  C23    0.00   0.0  0
 MS7  CONST_08  C28   C30  C32  C23    0.00   0.0  0
 MS7  CONST_09  C30   C32  C23  C24    0.00   0.0  0
 MS7  CONST_10  C30   C28  C26  C24    0.00   0.0  0
 MS7  CONST_11  C32   C23  C24  C26    0.00   0.0  0
 MS7  CONST_12  C32   C30  C28  C26    0.00   0.0  0
 MS7  CONST_13  C12   C10  C9   C6   180.00   0.0  0
 MS7  CONST_14  C15   C17  C9   C6   180.00   0.0  0
 MS7  CONST_15  O19   C14  C12  C10  180.00   0.0  0
 MS7  CONST_16  O19   C14  C15  C17  180.00   0.0  0
 MS7  CONST_17  C26   C24  C23  C20  180.00   0.0  0
 MS7  CONST_18  C30   C32  C23  C20  180.00   0.0  0
 MS7  CONST_19  H12   C12  C10  C9   180.00   0.0  0
 MS7  CONST_20  H15   C15  C17  C9   180.00   0.0  0
 MS7  CONST_21  H17   C17  C9   C10  180.00   0.0  0
 MS7  CONST_22  H10   C10  C12  C14  180.00   0.0  0
 MS7  CONST_23  H26   C26  C24  C23  180.00   0.0  0
 MS7  CONST_24  H30   C30  C32  C23  180.00   0.0  0
 MS7  CONST_25  H32   C32  C23  C24  180.00   0.0  0
 MS7  CONST_26  H28   C28  C26  C24  180.00   0.0  0
 MS7  CONST_27  H24   C24  C26  C28  180.00   0.0  0
 MS7  CONST_28  C38   N36  C34  C4   180.00   0.0  0
 MS7  CONST_29  C38   N36  C34  O35    0.00   0.0  0
 MS7  CONST_30  HN36  N36  C34  C4     0.00   0.0  0
 MS7  Var_01    C10   C9   C6   C4    93.80  30.0  2
 MS7  Var_02    C23   C20  O19  C14  176.67  30.0  3
 MS7  Var_03    C24   C23  C20  O19  107.43  30.0  2
 MS7  Var_04    H38   C38  N36  C34  -61.01  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
 MS7  chir_01  C4  N1  C6  C34  negativ

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
 MS7  plan-1  C6    0.020
 MS7  plan-1  C9    0.020
 MS7  plan-1  C10   0.020
 MS7  plan-1  C12   0.020
 MS7  plan-1  C14   0.020
 MS7  plan-1  C15   0.020
 MS7  plan-1  C17   0.020
 MS7  plan-1  O19   0.020
 MS7  plan-1  H10   0.020
 MS7  plan-1  H12   0.020
 MS7  plan-1  H15   0.020
 MS7  plan-1  H17   0.020
 MS7  plan-2  C20   0.020
 MS7  plan-2  C23   0.020
 MS7  plan-2  C24   0.020
 MS7  plan-2  C26   0.020
 MS7  plan-2  C28   0.020
 MS7  plan-2  C30   0.020
 MS7  plan-2  C32   0.020
 MS7  plan-2  H24   0.020
 MS7  plan-2  H26   0.020
 MS7  plan-2  H28   0.020
 MS7  plan-2  H30   0.020
 MS7  plan-2  H32   0.020
 MS7  plan-3  C4    0.020
 MS7  plan-3  C34   0.020
 MS7  plan-3  O35   0.020
 MS7  plan-3  N36   0.020
 MS7  plan-3  C38   0.020
 MS7  plan-3  HN36  0.020

