# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:56:16 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2S,3S,6R,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H](Cc1ccccc1)[C@@H](C)C[C@H](C)CC[C@H](N)[C@H](C)C(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
 ADD  ADD  '(2S,3S,6R,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldecanoic acid'  L-peptide  56  24  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ADD
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
 ADD  C1    C  C      0   0.421   0.9008   0.5750   7.0010
 ADD  O1    O  O      0  -0.625   0.9051   1.8228   7.0611
 ADD  O2    O  OC    -1  -0.624   1.5511  -0.1958   7.7375
 ADD  C2    C  CH1    0  -0.325  -0.0267  -0.0531   5.9437
 ADD  CM2   C  CH3    0  -0.673  -1.4758   0.3201   6.2526
 ADD  C3    C  CH1    0  -0.065   0.4077   0.3788   4.5389
 ADD  N3    N  NH2    0  -0.793   1.8308   0.0842   4.3882
 ADD  C4    C  CH2    0  -0.429  -0.4677  -0.2372   3.4403
 ADD  C5    C  CH2    0  -0.413  -0.0537   0.1637   2.0280
 ADD  C6    C  CH1    0  -0.225  -0.9973  -0.3239   0.9233
 ADD  CM6   C  CH3    0  -0.674  -2.3321   0.4162   0.9610
 ADD  C7    C  CH2    0  -0.398  -0.3031  -0.1662  -0.4334
 ADD  C8    C  CH1    0  -0.248  -1.1183  -0.5625  -1.6677
 ADD  CM8   C  CH3    0  -0.673  -1.5331  -2.0297  -1.6198
 ADD  C9    C  CH1    0   0.085  -0.3437  -0.2007  -2.9412
 ADD  O9    O  O2     0  -0.497   0.8104  -1.0087  -3.0587
 ADD  CM9   C  CH3    0  -0.403   2.0234  -0.3057  -3.1570
 ADD  C'    C  CH2    0  -0.537  -1.1935  -0.3213  -4.2107
 ADD  C1'   C  CR6    0   0.143  -0.4402   0.1217  -5.4319
 ADD  C2'   C  CR16   0  -0.302   0.2699  -0.7919  -6.2072
 ADD  C3'   C  CR16   0  -0.243   1.0087  -0.3721  -7.3055
 ADD  C4'   C  CR16   0  -0.274   1.0490   0.9734  -7.6472
 ADD  C5'   C  CR16   0  -0.241   0.3411   1.8940  -6.8848
 ADD  C6'   C  CR16   0  -0.307  -0.3956   1.4685  -5.7879
 ADD  H2    H  HCH1   0   0.183   0.0672  -1.1457   6.0005
 ADD  HM21  H  HCH3   0   0.212  -1.6403   1.3892   6.1101
 ADD  HM22  H  HCH3   0   0.219  -2.1871  -0.2156   5.6237
 ADD  HM23  H  HCH3   0   0.223  -1.7266   0.0828   7.2884
 ADD  H3    H  HCH1   0   0.198   0.3016   1.4689   4.4818
 ADD  HN31  H  HNH2   0   0.327   1.9630  -0.9219   4.3946
 ADD  HN32  H  HNH2   0   0.343   2.1533   0.3958   3.4801
 ADD  H41   H  HCH2   0   0.217  -1.5071   0.0548   3.6057
 ADD  H42   H  HCH2   0   0.200  -0.4402  -1.3308   3.5299
 ADD  H51   H  HCH2   0   0.209   0.9482  -0.2263   1.8219
 ADD  H52   H  HCH2   0   0.204   0.0275   1.2566   1.9650
 ADD  H6    H  HCH1   0   0.210  -1.1875  -1.3896   1.0999
 ADD  HM61  H  HCH3   0   0.213  -2.2014   1.4625   0.6717
 ADD  HM62  H  HCH3   0   0.228  -3.0651  -0.0242   0.2838
 ADD  HM63  H  HCH3   0   0.230  -2.7765   0.4053   1.9569
 ADD  H71   H  HCH2   0   0.218   0.6203  -0.7549  -0.4180
 ADD  H72   H  HCH2   0   0.207   0.0014   0.8830  -0.5387
 ADD  H8    H  HCH1   0   0.221  -2.0233   0.0543  -1.6930
 ADD  HM81  H  HCH3   0   0.220  -0.6647  -2.6818  -1.5144
 ADD  HM82  H  HCH3   0   0.231  -2.1958  -2.2222  -0.7757
 ADD  HM83  H  HCH3   0   0.229  -2.0722  -2.3369  -2.5168
 ADD  H9    H  HCH1   0   0.218  -0.0542   0.8564  -2.8457
 ADD  HM91  H  HCH3   0   0.225   2.8301  -1.0381  -3.1961
 ADD  HM92  H  HCH3   0   0.209   2.0801   0.3104  -4.0608
 ADD  HM93  H  HCH3   0   0.203   2.1951   0.3442  -2.2912
 ADD  H'1   H  HCH2   0   0.245  -1.5323  -1.3517  -4.3400
 ADD  H'2   H  HCH2   0   0.243  -2.0884   0.2938  -4.0820
 ADD  H2'   H  HCR6   0   0.240   0.2430  -1.8440  -5.9500
 ADD  H3'   H  HCR6   0   0.250   1.5548  -1.0969  -7.8961
 ADD  H4'   H  HCR6   0   0.251   1.6218   1.3018  -8.5051
 ADD  H5'   H  HCR6   0   0.251   0.3598   2.9443  -7.1469
 ADD  H6'   H  HCR6   0   0.243  -0.9485   2.1936  -5.2010

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
 ADD  C1   O1    deloc     1.249  0.020  1.249
 ADD  C1   O2    deloc     1.249  0.020  1.249
 ADD  C1   C2    single    1.540  0.020  1.540
 ADD  C2   CM2   single    1.528  0.020  1.528
 ADD  C2   C3    single    1.533  0.020  1.533
 ADD  C2   H2    single    0.970  0.020  1.090
 ADD  CM2  HM21  single    0.970  0.020  1.090
 ADD  CM2  HM22  single    0.970  0.020  1.090
 ADD  CM2  HM23  single    0.970  0.020  1.090
 ADD  C3   N3    single    1.461  0.020  1.461
 ADD  C3   C4    single    1.534  0.020  1.534
 ADD  C3   H3    single    0.970  0.020  1.090
 ADD  N3   HN31  single    0.890  0.020  1.040
 ADD  N3   HN32  single    0.890  0.020  1.040
 ADD  C4   C5    single    1.525  0.020  1.525
 ADD  C4   H41   single    0.970  0.020  1.090
 ADD  C4   H42   single    0.970  0.020  1.090
 ADD  C5   C6    single    1.533  0.020  1.533
 ADD  C5   H51   single    0.970  0.020  1.090
 ADD  C5   H52   single    0.970  0.020  1.090
 ADD  C6   CM6   single    1.527  0.020  1.527
 ADD  C6   C7    single    1.532  0.020  1.532
 ADD  C6   H6    single    0.970  0.020  1.090
 ADD  CM6  HM61  single    0.970  0.020  1.090
 ADD  CM6  HM62  single    0.970  0.020  1.090
 ADD  CM6  HM63  single    0.970  0.020  1.090
 ADD  C7   C8    single    1.531  0.020  1.531
 ADD  C7   H71   single    0.970  0.020  1.090
 ADD  C7   H72   single    0.970  0.020  1.090
 ADD  C8   CM8   single    1.526  0.020  1.526
 ADD  C8   C9    single    1.534  0.020  1.534
 ADD  C8   H8    single    0.970  0.020  1.090
 ADD  CM8  HM81  single    0.970  0.020  1.090
 ADD  CM8  HM82  single    0.970  0.020  1.090
 ADD  CM8  HM83  single    0.970  0.020  1.090
 ADD  C9   O9    single    1.414  0.020  1.414
 ADD  C9   C'    single    1.532  0.020  1.532
 ADD  C9   H9    single    0.970  0.020  1.090
 ADD  O9   CM9   single    1.405  0.020  1.405
 ADD  CM9  HM91  single    0.970  0.020  1.090
 ADD  CM9  HM92  single    0.970  0.020  1.090
 ADD  CM9  HM93  single    0.970  0.020  1.090
 ADD  C'   C1'   single    1.502  0.020  1.502
 ADD  C'   H'1   single    0.970  0.020  1.090
 ADD  C'   H'2   single    0.970  0.020  1.090
 ADD  C1'  C2'   aromatic  1.393  0.020  1.393
 ADD  C1'  C6'   aromatic  1.394  0.020  1.394
 ADD  C2'  C3'   aromatic  1.389  0.020  1.389
 ADD  C2'  H2'   single    0.930  0.020  1.080
 ADD  C3'  C4'   aromatic  1.389  0.020  1.389
 ADD  C3'  H3'   single    0.930  0.020  1.080
 ADD  C4'  C5'   aromatic  1.389  0.020  1.389
 ADD  C4'  H4'   single    0.930  0.020  1.080
 ADD  C5'  C6'   aromatic  1.388  0.020  1.388
 ADD  C5'  H5'   single    0.930  0.020  1.080
 ADD  C6'  H6'   single    0.930  0.020  1.080

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
 ADD  C2    C1   O2    117.82  3.000
 ADD  C2    C1   O1    116.26  3.000
 ADD  O2    C1   O1    125.90  3.000
 ADD  H2    C2   C3    107.67  3.000
 ADD  H2    C2   CM2   108.28  3.000
 ADD  C3    C2   CM2   112.66  3.000
 ADD  H2    C2   C1    108.59  3.000
 ADD  C3    C2   C1    110.10  3.000
 ADD  CM2   C2   C1    109.43  3.000
 ADD  HM23  CM2  HM22  106.89  3.000
 ADD  HM23  CM2  HM21  107.59  3.000
 ADD  HM22  CM2  HM21  107.93  3.000
 ADD  HM23  CM2  C2    110.89  3.000
 ADD  HM22  CM2  C2    112.47  3.000
 ADD  HM21  CM2  C2    110.85  3.000
 ADD  H3    C3   C4    107.87  3.000
 ADD  H3    C3   N3    106.81  3.000
 ADD  C4    C3   N3    113.64  3.000
 ADD  H3    C3   C2    107.48  3.000
 ADD  C4    C3   C2    112.43  3.000
 ADD  N3    C3   C2    108.28  3.000
 ADD  HN32  N3   HN31  105.62  3.000
 ADD  HN32  N3   C3    109.91  3.000
 ADD  HN31  N3   C3    109.03  3.000
 ADD  H42   C4   H41   106.13  3.000
 ADD  H42   C4   C5    109.31  3.000
 ADD  H41   C4   C5    109.16  3.000
 ADD  H42   C4   C3    109.12  3.000
 ADD  H41   C4   C3    109.10  3.000
 ADD  C5    C4   C3    113.75  3.000
 ADD  H52   C5   H51   106.03  3.000
 ADD  H52   C5   C6    108.72  3.000
 ADD  H51   C5   C6    108.33  3.000
 ADD  H52   C5   C4    109.57  3.000
 ADD  H51   C5   C4    109.21  3.000
 ADD  C6    C5   C4    114.63  3.000
 ADD  H6    C6   C7    108.74  3.000
 ADD  H6    C6   CM6   108.39  3.000
 ADD  C7    C6   CM6   111.60  3.000
 ADD  H6    C6   C5    107.45  3.000
 ADD  C7    C6   C5    109.06  3.000
 ADD  CM6   C6   C5    111.48  3.000
 ADD  HM63  CM6  HM62  106.80  3.000
 ADD  HM63  CM6  HM61  107.46  3.000
 ADD  HM62  CM6  HM61  107.61  3.000
 ADD  HM63  CM6  C6    111.96  3.000
 ADD  HM62  CM6  C6    112.11  3.000
 ADD  HM61  CM6  C6    110.66  3.000
 ADD  H72   C7   H71   106.33  3.000
 ADD  H72   C7   C8    108.53  3.000
 ADD  H71   C7   C8    108.73  3.000
 ADD  H72   C7   C6    108.00  3.000
 ADD  H71   C7   C6    108.31  3.000
 ADD  C8    C7   C6    116.48  3.000
 ADD  H8    C8   C9    105.38  3.000
 ADD  H8    C8   CM8   108.52  3.000
 ADD  C9    C8   CM8   112.97  3.000
 ADD  H8    C8   C7    108.22  3.000
 ADD  C9    C8   C7    109.84  3.000
 ADD  CM8   C8   C7    111.61  3.000
 ADD  HM83  CM8  HM82  106.65  3.000
 ADD  HM83  CM8  HM81  107.73  3.000
 ADD  HM82  CM8  HM81  107.67  3.000
 ADD  HM83  CM8  C8    112.30  3.000
 ADD  HM82  CM8  C8    111.06  3.000
 ADD  HM81  CM8  C8    111.18  3.000
 ADD  H9    C9   C'    107.06  3.000
 ADD  H9    C9   O9    109.97  3.000
 ADD  C'    C9   O9    109.81  3.000
 ADD  H9    C9   C8    106.70  3.000
 ADD  C'    C9   C8    112.91  3.000
 ADD  O9    C9   C8    110.27  3.000
 ADD  CM9   O9   C9    115.12  3.000
 ADD  HM93  CM9  HM92  108.07  3.000
 ADD  HM93  CM9  HM91  108.10  3.000
 ADD  HM92  CM9  HM91  108.05  3.000
 ADD  HM93  CM9  O9    112.12  3.000
 ADD  HM92  CM9  O9    112.57  3.000
 ADD  HM91  CM9  O9    107.76  3.000
 ADD  H'2   C'   H'1   106.90  3.000
 ADD  H'2   C'   C1'   109.90  3.000
 ADD  H'1   C'   C1'   109.73  3.000
 ADD  H'2   C'   C9    108.18  3.000
 ADD  H'1   C'   C9    110.14  3.000
 ADD  C1'   C'   C9    111.86  3.000
 ADD  C6'   C1'  C2'   118.38  3.000
 ADD  C6'   C1'  C'    120.58  3.000
 ADD  C2'   C1'  C'    120.99  3.000
 ADD  H2'   C2'  C3'   119.64  3.000
 ADD  H2'   C2'  C1'   119.48  3.000
 ADD  C3'   C2'  C1'   120.88  3.000
 ADD  H3'   C3'  C4'   119.98  3.000
 ADD  H3'   C3'  C2'   119.82  3.000
 ADD  C4'   C3'  C2'   120.20  3.000
 ADD  H4'   C4'  C5'   120.24  3.000
 ADD  H4'   C4'  C3'   120.28  3.000
 ADD  C5'   C4'  C3'   119.48  3.000
 ADD  H5'   C5'  C6'   119.86  3.000
 ADD  H5'   C5'  C4'   120.07  3.000
 ADD  C6'   C5'  C4'   120.07  3.000
 ADD  H6'   C6'  C5'   119.56  3.000
 ADD  H6'   C6'  C1'   119.44  3.000
 ADD  C5'   C6'  C1'   121.00  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
 ADD  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 ADD  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 ADD  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 ADD  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 ADD  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 ADD  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 ADD  CONST_07  C3'   C2'  C1'  C'    180.00   0.0  0
 ADD  CONST_08  C5'   C6'  C1'  C'    180.00   0.0  0
 ADD  CONST_09  H3'   C3'  C2'  C1'   180.00   0.0  0
 ADD  CONST_10  H5'   C5'  C6'  C1'   180.00   0.0  0
 ADD  CONST_11  H6'   C6'  C1'  C2'   180.00   0.0  0
 ADD  CONST_12  H4'   C4'  C3'  C2'   180.00   0.0  0
 ADD  CONST_13  H2'   C2'  C3'  C4'   180.00   0.0  0
 ADD  Var_01    C2'   C1'  C'   C9     92.76  30.0  2
 ADD  Var_02    C6    C5   C4   C3   -174.11  30.0  3
 ADD  Var_03    HM91  CM9  O9   C9    177.49  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
 ADD  chir_01  C2  C1  CM2  C3  negativ
 ADD  chir_02  C3  N3  C2   C4  positiv
 ADD  chir_03  C6  C5  CM6  C7  negativ
 ADD  chir_04  C8  C9  CM8  C7  negativ
 ADD  chir_05  C9  O9  C'   C8  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
 ADD  plan-1  C'   0.020
 ADD  plan-1  C1'  0.020
 ADD  plan-1  C2'  0.020
 ADD  plan-1  C3'  0.020
 ADD  plan-1  C4'  0.020
 ADD  plan-1  C5'  0.020
 ADD  plan-1  C6'  0.020
 ADD  plan-1  H2'  0.020
 ADD  plan-1  H3'  0.020
 ADD  plan-1  H4'  0.020
 ADD  plan-1  H5'  0.020
 ADD  plan-1  H6'  0.020
 ADD  plan-2  C1   0.020
 ADD  plan-2  O1   0.020
 ADD  plan-2  O2   0.020
 ADD  plan-2  C2   0.020

