# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:37:59 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: N-[(1R)-2-{(2S)-2-[(4-carbamimidoylbenzyl)carbamoyl]azetidin-1-yl}-1-cyclohexyl-2-oxoethyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCN2C(=O)[C@H](NCC(O)=O)C3CCCCC3)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
 MEL  MEL  N-[(1R)-2-{(2S)-2-[(4-carbamimidoylbenzyl)carbamoyl]azetidin-1-yl}-1-cyclohexyl-2-oxoethyl]glycine  ligand  62  31  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MEL
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
 MEL  C1    C  CH1   0  -0.243  40.3545  23.9978  55.6533
 MEL  C2    C  CH2   0  -0.432  39.1427  24.7266  55.0679
 MEL  C3    C  CH2   0  -0.428  37.8585  24.3773  55.8135
 MEL  C4    C  CH2   0  -0.429  37.9832  24.6614  57.3058
 MEL  C5    C  CH2   0  -0.434  39.1887  23.9393  57.8967
 MEL  C6    C  CH2   0  -0.409  40.4723  24.2867  57.1500
 MEL  N7    N  NH1   0  -0.579  42.7815  23.6579  55.4559
 MEL  C8    C  CH1   0  -0.173  41.6408  24.3730  54.9115
 MEL  C9    C  C     0   0.510  41.5066  24.0744  53.4196
 MEL  O0    O  O     0  -0.480  41.3389  22.9319  53.0120
 MEL  N11   N  N     0  -0.446  41.6307  25.1028  52.5748
 MEL  C12   C  C     0  -0.200  41.8318  25.0518  51.1345
 MEL  C13   C  C     0   0.593  43.1305  24.3144  50.8322
 MEL  O14   O  O     0  -0.477  44.2038  24.7615  51.2060
 MEL  N15   N  NH1   0  -0.618  43.0101  23.1562  50.1703
 MEL  C16   C  CH2   0  -0.386  44.1295  22.2441  50.0551
 MEL  C17   C  CR6   0   0.110  44.5090  21.6291  51.3808
 MEL  C18   C  CR16  0  -0.281  45.7453  21.8778  51.9660
 MEL  C19   C  CR16  0  -0.261  46.0845  21.3095  53.1836
 MEL  C20   C  CR6   0   0.025  45.1842  20.4879  53.8575
 MEL  C21   C  CR16  0  -0.288  43.9424  20.2412  53.2720
 MEL  C22   C  CR16  0  -0.240  43.6120  20.8052  52.0511
 MEL  C23   C  C     0   0.331  45.5757  19.8744  55.1561
 MEL  N24   N  N     0  -0.650  46.8183  19.7527  55.4279
 MEL  N25   N  NH2   0  -0.821  44.5402  19.4305  55.9315
 MEL  C26   C  C     0  -0.509  41.9677  26.5901  51.1561
 MEL  C27   C  C     0  -0.256  41.9291  26.5262  52.6954
 MEL  C28   C  CH2   0  -0.414  44.0468  24.0444  54.8736
 MEL  C29   C  C     0   0.540  45.2536  23.5518  55.6334
 MEL  O30   O  OH1   0  -0.581  44.9679  22.6388  56.5487
 MEL  O31   O  O     0  -0.455  46.3735  23.9381  55.4056
 MEL  H11   H  HCH1  0   0.218  40.1966  22.9186  55.5217
 MEL  H21   H  HCH2  0   0.236  39.0207  24.4897  54.0075
 MEL  H22   H  HCH2  0   0.211  39.3117  25.8090  55.1284
 MEL  H31   H  HCH2  0   0.210  37.6337  23.3156  55.6645
 MEL  H32   H  HCH2  0   0.228  37.0198  24.9334  55.3879
 MEL  H41   H  HCH2  0   0.225  37.0686  24.3654  57.8258
 MEL  H42   H  HCH2  0   0.208  38.0953  25.7403  57.4601
 MEL  H51   H  HCH2  0   0.208  39.0228  22.8574  57.8442
 MEL  H52   H  HCH2  0   0.226  39.2979  24.1835  58.9562
 MEL  H61   H  HCH2  0   0.203  40.6973  25.3514  57.2879
 MEL  H62   H  HCH2  0   0.234  41.3150  23.7359  57.5696
 MEL  H71   H  HNH1  0   0.345  42.6325  22.6619  55.3399
 MEL  H81   H  HCH1  0   0.251  41.8214  25.4437  55.0644
 MEL  H121  H  H     0   0.277  40.9827  24.6543  50.5738
 MEL  H151  H  HNH1  0   0.405  42.0864  22.7889  50.0101
 MEL  H161  H  HCH2  0   0.264  44.9820  22.7681  49.6230
 MEL  H162  H  HCH2  0   0.276  43.8395  21.4664  49.3486
 MEL  H181  H  HCR6  0   0.248  46.4538  22.5254  51.4648
 MEL  H191  H  HCR6  0   0.250  47.0511  21.5127  53.6235
 MEL  H211  H  HCR6  0   0.253  43.2288  19.5821  53.7498
 MEL  H221  H  HCR6  0   0.244  42.6432  20.5922  51.6171
 MEL  H241  H  H     0   0.323  46.9555  19.3469  56.3496
 MEL  H251  H  HNH2  0   0.388  43.6660  19.9274  55.8805
 MEL  H252  H  HNH2  0   0.389  44.7677  19.1314  56.8669
 MEL  H261  H  H     0   0.268  41.1067  27.0923  50.7217
 MEL  H262  H  H     0   0.266  42.8803  26.9900  50.7236
 MEL  H271  H  H     0   0.248  42.8856  26.7356  53.1773
 MEL  H272  H  H     0   0.255  41.1458  27.1091  53.1800
 MEL  H281  H  HCH2  0   0.273  44.1119  25.1360  54.8567
 MEL  H282  H  HCH2  0   0.275  44.1956  23.7225  53.8309
 MEL  H301  H  HOH1  0   0.479  45.7859  22.3256  56.9635

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
 MEL  C1   C2    single    1.530  0.020  1.530
 MEL  C1   C6    single    1.529  0.020  1.529
 MEL  C1   C8    single    1.532  0.020  1.532
 MEL  C1   H11   single    0.970  0.020  1.090
 MEL  C2   C3    single    1.525  0.020  1.525
 MEL  C2   H21   single    0.970  0.020  1.090
 MEL  C2   H22   single    0.970  0.020  1.090
 MEL  C3   C4    single    1.524  0.020  1.524
 MEL  C3   H31   single    0.970  0.020  1.090
 MEL  C3   H32   single    0.970  0.020  1.090
 MEL  C4   C5    single    1.524  0.020  1.524
 MEL  C4   H41   single    0.970  0.020  1.090
 MEL  C4   H42   single    0.970  0.020  1.090
 MEL  C5   C6    single    1.525  0.020  1.525
 MEL  C5   H51   single    0.970  0.020  1.090
 MEL  C5   H52   single    0.970  0.020  1.090
 MEL  C6   H61   single    0.970  0.020  1.090
 MEL  C6   H62   single    0.970  0.020  1.090
 MEL  N7   C8    single    1.452  0.020  1.452
 MEL  N7   C28   single    1.445  0.020  1.445
 MEL  N7   H71   single    0.890  0.020  1.040
 MEL  C8   C9    single    1.527  0.020  1.527
 MEL  C8   H81   single    0.970  0.020  1.090
 MEL  C9   O0    double    1.225  0.020  1.225
 MEL  C9   N11   single    1.337  0.020  1.337
 MEL  N11  C12   single    1.455  0.020  1.455
 MEL  N11  C27   single    1.459  0.020  1.459
 MEL  C12  C13   single    1.524  0.020  1.524
 MEL  C12  C26   single    1.544  0.020  1.544
 MEL  C12  H121  single    0.970  0.020  1.090
 MEL  C13  O14   double    1.221  0.020  1.221
 MEL  C13  N15   single    1.339  0.020  1.339
 MEL  N15  C16   single    1.449  0.020  1.449
 MEL  N15  H151  single    0.860  0.020  1.020
 MEL  C16  C17   single    1.510  0.020  1.510
 MEL  C16  H161  single    0.970  0.020  1.090
 MEL  C16  H162  single    0.970  0.020  1.090
 MEL  C17  C18   aromatic  1.390  0.020  1.390
 MEL  C17  C22   aromatic  1.390  0.020  1.390
 MEL  C18  C19   aromatic  1.386  0.020  1.386
 MEL  C18  H181  single    0.930  0.020  1.080
 MEL  C19  C20   aromatic  1.393  0.020  1.393
 MEL  C19  H191  single    0.930  0.020  1.080
 MEL  C20  C21   aromatic  1.395  0.020  1.395
 MEL  C20  C23   single    1.489  0.020  1.489
 MEL  C21  C22   aromatic  1.385  0.020  1.385
 MEL  C21  H211  single    0.930  0.020  1.080
 MEL  C22  H221  single    0.930  0.020  1.080
 MEL  C23  N24   double    1.278  0.020  1.278
 MEL  C23  N25   single    1.368  0.020  1.368
 MEL  N24  H241  single    0.890  0.020  1.040
 MEL  N25  H251  single    0.890  0.020  1.040
 MEL  N25  H252  single    0.890  0.020  1.040
 MEL  C26  C27   single    1.541  0.020  1.541
 MEL  C26  H261  single    0.970  0.020  1.090
 MEL  C26  H262  single    0.970  0.020  1.090
 MEL  C27  H271  single    0.970  0.020  1.090
 MEL  C27  H272  single    0.970  0.020  1.090
 MEL  C28  C29   single    1.509  0.020  1.509
 MEL  C28  H281  single    0.970  0.020  1.090
 MEL  C28  H282  single    0.970  0.020  1.090
 MEL  C29  O30   single    1.324  0.020  1.324
 MEL  C29  O31   double    1.206  0.020  1.206
 MEL  O30  H301  single    0.850  0.020  0.980

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
 MEL  H11   C1   C8    107.66  3.000
 MEL  H11   C1   C6    108.30  3.000
 MEL  C8    C1   C6    111.29  3.000
 MEL  H11   C1   C2    107.96  3.000
 MEL  C8    C1   C2    111.29  3.000
 MEL  C6    C1   C2    110.21  3.000
 MEL  H22   C2   H21   106.53  3.000
 MEL  H22   C2   C3    109.19  3.000
 MEL  H21   C2   C3    109.30  3.000
 MEL  H22   C2   C1    109.07  3.000
 MEL  H21   C2   C1    110.86  3.000
 MEL  C3    C2   C1    111.75  3.000
 MEL  H32   C3   H31   106.42  3.000
 MEL  H32   C3   C4    110.44  3.000
 MEL  H31   C3   C4    109.31  3.000
 MEL  H32   C3   C2    109.83  3.000
 MEL  H31   C3   C2    109.16  3.000
 MEL  C4    C3   C2    111.53  3.000
 MEL  H42   C4   H41   106.58  3.000
 MEL  H42   C4   C5    109.33  3.000
 MEL  H41   C4   C5    110.43  3.000
 MEL  H42   C4   C3    109.25  3.000
 MEL  H41   C4   C3    110.30  3.000
 MEL  C5    C4   C3    110.85  3.000
 MEL  H52   C5   H51   106.40  3.000
 MEL  H52   C5   C6    109.86  3.000
 MEL  H51   C5   C6    109.20  3.000
 MEL  H52   C5   C4    110.43  3.000
 MEL  H51   C5   C4    109.23  3.000
 MEL  C6    C5   C4    111.58  3.000
 MEL  H62   C6   H61   106.45  3.000
 MEL  H62   C6   C5    110.30  3.000
 MEL  H61   C6   C5    109.40  3.000
 MEL  H62   C6   C1    109.92  3.000
 MEL  H61   C6   C1    108.81  3.000
 MEL  C5    C6   C1    111.80  3.000
 MEL  H71   N7   C28   110.20  3.000
 MEL  H71   N7   C8    108.99  3.000
 MEL  C28   N7   C8    113.88  3.000
 MEL  H81   C8   C9    109.97  3.000
 MEL  H81   C8   N7    107.40  3.000
 MEL  C9    C8   N7    109.81  3.000
 MEL  H81   C8   C1    108.06  3.000
 MEL  C9    C8   C1    110.57  3.000
 MEL  N7    C8   C1    110.95  3.000
 MEL  N11   C9   O0    121.35  3.000
 MEL  N11   C9   C8    117.31  3.000
 MEL  O0    C9   C8    121.30  3.000
 MEL  C27   N11  C12    95.03  3.000
 MEL  C27   N11  C9    135.82  3.000
 MEL  C12   N11  C9    127.69  3.000
 MEL  H121  C12  C26   115.98  3.000
 MEL  H121  C12  C13   112.61  3.000
 MEL  C26   C12  C13   114.19  3.000
 MEL  H121  C12  N11   114.42  3.000
 MEL  C26   C12  N11    87.90  3.000
 MEL  C13   C12  N11   109.34  3.000
 MEL  N15   C13  O14   123.15  3.000
 MEL  N15   C13  C12   116.10  3.000
 MEL  O14   C13  C12   120.74  3.000
 MEL  H151  N15  C16   117.81  3.000
 MEL  H151  N15  C13   118.46  3.000
 MEL  C16   N15  C13   120.95  3.000
 MEL  H162  C16  H161  107.10  3.000
 MEL  H162  C16  C17   110.21  3.000
 MEL  H161  C16  C17   110.32  3.000
 MEL  H162  C16  N15   107.17  3.000
 MEL  H161  C16  N15   109.46  3.000
 MEL  C17   C16  N15   112.39  3.000
 MEL  C22   C17  C18   118.47  3.000
 MEL  C22   C17  C16   120.17  3.000
 MEL  C18   C17  C16   121.35  3.000
 MEL  H181  C18  C19   119.46  3.000
 MEL  H181  C18  C17   119.60  3.000
 MEL  C19   C18  C17   120.94  3.000
 MEL  H191  C19  C20   119.46  3.000
 MEL  H191  C19  C18   119.94  3.000
 MEL  C20   C19  C18   120.59  3.000
 MEL  C23   C20  C21   121.83  3.000
 MEL  C23   C20  C19   119.69  3.000
 MEL  C21   C20  C19   118.47  3.000
 MEL  H211  C21  C22   118.67  3.000
 MEL  H211  C21  C20   120.62  3.000
 MEL  C22   C21  C20   120.69  3.000
 MEL  H221  C22  C21   119.12  3.000
 MEL  H221  C22  C17   120.04  3.000
 MEL  C21   C22  C17   120.83  3.000
 MEL  N25   C23  N24   125.78  3.000
 MEL  N25   C23  C20   115.42  3.000
 MEL  N24   C23  C20   118.72  3.000
 MEL  H241  N24  C23   111.23  3.000
 MEL  H252  N25  H251  112.92  3.000
 MEL  H252  N25  C23   116.84  3.000
 MEL  H251  N25  C23   117.93  3.000
 MEL  H262  C26  H261  109.64  3.000
 MEL  H262  C26  C27   115.73  3.000
 MEL  H261  C26  C27   113.47  3.000
 MEL  H262  C26  C12   115.79  3.000
 MEL  H261  C26  C12   112.63  3.000
 MEL  C27   C26  C12    88.31  3.000
 MEL  H272  C27  H271  109.32  3.000
 MEL  H272  C27  C26   116.10  3.000
 MEL  H271  C27  C26   114.28  3.000
 MEL  H272  C27  N11   114.29  3.000
 MEL  H271  C27  N11   113.75  3.000
 MEL  C26   C27  N11    87.88  3.000
 MEL  H282  C28  H281  105.61  3.000
 MEL  H282  C28  C29   105.86  3.000
 MEL  H281  C28  C29   106.62  3.000
 MEL  H282  C28  N7    114.93  3.000
 MEL  H281  C28  N7    108.98  3.000
 MEL  C29   C28  N7    114.20  3.000
 MEL  O31   C29  O30   123.48  3.000
 MEL  O31   C29  C28   122.88  3.000
 MEL  O30   C29  C28   113.63  3.000
 MEL  H301  O30  C29   109.67  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
 MEL  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 MEL  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 MEL  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 MEL  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 MEL  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 MEL  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 MEL  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 MEL  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 MEL  CONST_09  C23   C20  C19  C18   180.00   0.0  0
 MEL  CONST_10  C23   C20  C21  C22   180.00   0.0  0
 MEL  CONST_11  H191  C19  C18  C17   180.00   0.0  0
 MEL  CONST_12  H211  C21  C22  C17   180.00   0.0  0
 MEL  CONST_13  H221  C22  C17  C18   180.00   0.0  0
 MEL  CONST_14  H181  C18  C19  C20   180.00   0.0  0
 MEL  CONST_15  C12   N11  C9   C8    180.00   0.0  0
 MEL  CONST_16  C27   N11  C9   C8      0.00   0.0  0
 MEL  CONST_17  C12   N11  C9   O0      0.00   0.0  0
 MEL  CONST_18  C27   N11  C9   O0    180.00   0.0  0
 MEL  CONST_19  C16   N15  C13  C12   180.00   0.0  0
 MEL  CONST_20  H151  N15  C13  C12     0.00   0.0  0
 MEL  CONST_21  H241  N24  C23  C20   180.00   0.0  0
 MEL  CONST_23  H252  N25  C23  C20   180.00   0.0  0
 MEL  CONST_24  C16   N15  C13  O14     0.00   0.0  0
 MEL  CONST_25  H301  O30  C29  C28   180.00   0.0  0
 MEL  Var_01    C4    C3   C2   C1     55.74  30.0  1
 MEL  Var_02    C4    C5   C6   C1    -55.62  30.0  1
 MEL  Var_03    C5    C4   C3   C2    -55.02  30.0  1
 MEL  Var_04    C6    C5   C4   C3     54.96  30.0  1
 MEL  Var_05    C12   C26  C27  N11    -6.85  30.0  1
 MEL  Var_06    C18   C17  C16  N15  -115.74  30.0  2
 MEL  Var_07    N24   C23  C20  C19   -21.78  30.0  2
 MEL  Var_08    C17   C16  N15  C13    67.75  30.0  3
 MEL  Var_09    O30   C29  C28  N7     12.44  30.0  3
 MEL  Var_10    C29   C28  N7   C8    166.77  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
 MEL  chir_01  C1   C2   C6   C8   positiv
 MEL  chir_02  C8   N7   C1   C9   positiv
 MEL  chir_03  C12  N11  C13  C26  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
 MEL  plan-1  C8    0.020
 MEL  plan-1  C9    0.020
 MEL  plan-1  O0    0.020
 MEL  plan-1  N11   0.020
 MEL  plan-1  C12   0.020
 MEL  plan-1  C27   0.020
 MEL  plan-2  C16   0.020
 MEL  plan-2  C17   0.020
 MEL  plan-2  C18   0.020
 MEL  plan-2  C19   0.020
 MEL  plan-2  C20   0.020
 MEL  plan-2  C21   0.020
 MEL  plan-2  C22   0.020
 MEL  plan-2  C23   0.020
 MEL  plan-2  H181  0.020
 MEL  plan-2  H191  0.020
 MEL  plan-2  H211  0.020
 MEL  plan-2  H221  0.020
 MEL  plan-3  C12   0.020
 MEL  plan-3  C13   0.020
 MEL  plan-3  O14   0.020
 MEL  plan-3  N15   0.020
 MEL  plan-3  C16   0.020
 MEL  plan-3  H151  0.020
 MEL  plan-4  C20   0.020
 MEL  plan-4  C23   0.020
 MEL  plan-4  N24   0.020
 MEL  plan-4  N25   0.020
 MEL  plan-4  H241  0.020
 MEL  plan-4  H251  0.020
 MEL  plan-4  H252  0.020
 MEL  plan-5  C28   0.020
 MEL  plan-5  C29   0.020
 MEL  plan-5  O30   0.020
 MEL  plan-5  O31   0.020
 MEL  plan-5  H301  0.020

