# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:10:01 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (3aR,4S)-4-(2-amino-4-oxo-4H-imidazol-5-yl)-2-bromo-4,5,6,7-tetrahydropyrrolo[2,3-c]azepin-8(3aH)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C(=N1)[C@H]2CCNC(=O)C3=NC(=C[C@@H]23)Br
#
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
 HMD  HMD  (3aR,4S)-4-(2-amino-4-oxo-4H-imidazol-5-yl)-2-bromo-4,5,6,7-tetrahydropyrrolo[2,3-c]azepin-8(3aH)-one  ligand  29  19  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HMD
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
 HMD  BR1   BR  BR    0  -0.025  24.1390  26.0583  27.5706
 HMD  O1    O   O     0  -0.454  24.3871  31.4545  28.3241
 HMD  O2    O   O     0  -0.396  30.8500  28.4445  26.2111
 HMD  N1    N   N     0  -0.366  24.7952  28.7857  27.7160
 HMD  N2    N   NH1   0  -0.623  26.5425  31.8797  27.8285
 HMD  N3    N   N     0  -0.523  29.4174  28.0496  24.4322
 HMD  N4    N   N     0  -0.416  27.4652  28.5449  25.6215
 HMD  N5    N   NH2   0  -0.770  27.3401  27.9038  23.3835
 HMD  C1    C   CR5   0   0.071  25.2747  27.4939  27.9248
 HMD  C2    C   CR15  0  -0.215  26.5302  27.4447  28.3777
 HMD  C3    C   CR15  0  -0.357  26.9866  28.8600  28.4822
 HMD  C4    C   CR5   0   0.176  25.7644  29.5798  27.9874
 HMD  C5    C   C     0   0.472  25.5033  31.0560  28.0367
 HMD  C6    C   CH2   0  -0.310  27.8072  31.5883  27.1730
 HMD  C7    C   CH2   0  -0.455  28.7291  30.6427  27.9265
 HMD  C8    C   CH1   0  -0.352  28.3438  29.1563  27.8383
 HMD  C9    C   CR5   0   0.198  28.4313  28.7050  26.4306
 HMD  C10   C   CR5   0   0.416  29.7544  28.3915  25.7064
 HMD  C11   C   CR5   0   0.619  28.1083  28.1438  24.4111
 HMD  HN2   H   HNH1  0   0.405  26.3113  32.8595  27.9080
 HMD  HN51  H   HNH2  0   0.432  26.3393  27.9984  23.4584
 HMD  HN52  H   HNH2  0   0.430  27.7306  27.6196  22.4984
 HMD  H2    H   HCR5  0   0.297  27.1215  26.5779  28.6286
 HMD  H3    H   HCR5  0   0.344  27.0843  29.1234  29.5480
 HMD  H61   H   HCH2  0   0.257  27.6373  31.2404  26.1503
 HMD  H62   H   HCH2  0   0.284  28.3133  32.5469  27.0818
 HMD  H71   H   HCH2  0   0.275  29.7382  30.7626  27.5283
 HMD  H72   H   HCH2  0   0.273  28.7751  30.9291  28.9792
 HMD  H8    H   HCH1  0   0.313  29.0981  28.5989  28.4018

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
 HMD  BR1  C1    single  1.864  0.020  1.864
 HMD  O1   C5    double  1.220  0.020  1.220
 HMD  O2   C10   double  1.207  0.020  1.207
 HMD  N1   C1    single  1.394  0.020  1.394
 HMD  N1   C4    double  1.282  0.020  1.282
 HMD  N2   C5    single  1.342  0.020  1.342
 HMD  N2   C6    single  1.454  0.020  1.454
 HMD  N2   HN2   single  0.860  0.020  1.020
 HMD  N3   C10   single  1.362  0.020  1.362
 HMD  N3   C11   double  1.313  0.020  1.313
 HMD  N4   C9    double  1.270  0.020  1.270
 HMD  N4   C11   single  1.428  0.020  1.428
 HMD  N5   C11   single  1.305  0.020  1.305
 HMD  N5   HN51  single  0.860  0.020  1.020
 HMD  N5   HN52  single  0.860  0.020  1.020
 HMD  C1   C2    double  1.336  0.020  1.336
 HMD  C2   C3    single  1.491  0.020  1.491
 HMD  C2   H2    single  0.930  0.020  1.080
 HMD  C3   C4    single  1.502  0.020  1.502
 HMD  C3   C8    single  1.531  0.020  1.531
 HMD  C3   H3    single  0.970  0.020  1.090
 HMD  C4   C5    single  1.500  0.020  1.500
 HMD  C6   C7    single  1.521  0.020  1.521
 HMD  C6   H61   single  0.970  0.020  1.090
 HMD  C6   H62   single  0.970  0.020  1.090
 HMD  C7   C8    single  1.538  0.020  1.538
 HMD  C7   H71   single  0.970  0.020  1.090
 HMD  C7   H72   single  0.970  0.020  1.090
 HMD  C8   C9    single  1.481  0.020  1.481
 HMD  C8   H8    single  0.970  0.020  1.090
 HMD  C9   C10   single  1.541  0.020  1.541

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
 HMD  C4    N1   C1    106.40  3.000
 HMD  HN2   N2   C6    115.41  3.000
 HMD  HN2   N2   C5    113.95  3.000
 HMD  C6    N2   C5    128.34  3.000
 HMD  C11   N3   C10   104.11  3.000
 HMD  C11   N4   C9    103.46  3.000
 HMD  HN52  N5   HN51  118.43  3.000
 HMD  HN52  N5   C11   121.00  3.000
 HMD  HN51  N5   C11   120.57  3.000
 HMD  C2    C1   N1    114.10  3.000
 HMD  C2    C1   BR1   127.50  3.000
 HMD  N1    C1   BR1   118.40  3.000
 HMD  H2    C2   C3    125.36  3.000
 HMD  H2    C2   C1    128.58  3.000
 HMD  C3    C2   C1    106.06  3.000
 HMD  H3    C3   C8    106.37  3.000
 HMD  H3    C3   C4    106.03  3.000
 HMD  C8    C3   C4    119.33  3.000
 HMD  H3    C3   C2    108.77  3.000
 HMD  C8    C3   C2    115.19  3.000
 HMD  C4    C3   C2    100.52  3.000
 HMD  C5    C4   C3    127.03  3.000
 HMD  C5    C4   N1    119.01  3.000
 HMD  C3    C4   N1    112.83  3.000
 HMD  C4    C5   N2    117.65  3.000
 HMD  C4    C5   O1    119.25  3.000
 HMD  N2    C5   O1    123.00  3.000
 HMD  H62   C6   H61   105.92  3.000
 HMD  H62   C6   C7    107.91  3.000
 HMD  H61   C6   C7    111.08  3.000
 HMD  H62   C6   N2    105.42  3.000
 HMD  H61   C6   N2    110.51  3.000
 HMD  C7    C6   N2    115.38  3.000
 HMD  H72   C7   H71   106.49  3.000
 HMD  H72   C7   C8    108.62  3.000
 HMD  H71   C7   C8    108.48  3.000
 HMD  H72   C7   C6    109.89  3.000
 HMD  H71   C7   C6    108.14  3.000
 HMD  C8    C7   C6    114.88  3.000
 HMD  H8    C8   C9    107.07  3.000
 HMD  H8    C8   C7    106.86  3.000
 HMD  C9    C8   C7    109.52  3.000
 HMD  H8    C8   C3    107.21  3.000
 HMD  C9    C8   C3    113.16  3.000
 HMD  C7    C8   C3    112.64  3.000
 HMD  C10   C9   C8    124.04  3.000
 HMD  C10   C9   N4    109.15  3.000
 HMD  C8    C9   N4    126.79  3.000
 HMD  C9    C10  N3    106.17  3.000
 HMD  C9    C10  O2    125.02  3.000
 HMD  N3    C10  O2    128.81  3.000
 HMD  N5    C11  N4    117.00  3.000
 HMD  N5    C11  N3    125.90  3.000
 HMD  N4    C11  N3    117.10  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
 HMD  CONST_01  N4    C9  C10  N3     0.00   0.0  0
 HMD  CONST_02  C9    N4  C11  N3     0.00   0.0  0
 HMD  CONST_03  C10   N3  C11  N4     0.00   0.0  0
 HMD  CONST_04  C11   N3  C10  C9     0.00   0.0  0
 HMD  CONST_05  C11   N4  C9   C10    0.00   0.0  0
 HMD  CONST_06  C10   N3  C11  N5   180.00   0.0  0
 HMD  CONST_07  C9    N4  C11  N5   180.00   0.0  0
 HMD  CONST_08  HN51  N5  C11  N3   180.00   0.0  0
 HMD  CONST_09  HN52  N5  C11  N3     0.00   0.0  0
 HMD  Var_01    C3    C2  C1   N1    -0.75  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
 HMD  chir_01  C3  C2  C4  C8  positiv
 HMD  chir_02  C8  C9  C7  C3  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
 HMD  plan-1  O2    0.020
 HMD  plan-1  N3    0.020
 HMD  plan-1  N4    0.020
 HMD  plan-1  N5    0.020
 HMD  plan-1  C8    0.020
 HMD  plan-1  C9    0.020
 HMD  plan-1  C10   0.020
 HMD  plan-1  C11   0.020
 HMD  plan-1  HN51  0.020
 HMD  plan-1  HN52  0.020
 HMD  plan-2  N1    0.020
 HMD  plan-2  C1    0.020
 HMD  plan-2  C3    0.020
 HMD  plan-2  C4    0.020
 HMD  plan-2  C5    0.020
 HMD  plan-3  O1    0.020
 HMD  plan-3  N2    0.020
 HMD  plan-3  C4    0.020
 HMD  plan-3  C5    0.020
 HMD  plan-3  C6    0.020
 HMD  plan-3  HN2   0.020

