# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:02:30 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2S)-{[(3-{[(2-chloro-6-methylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]amino}(phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Cl)c1NC(=O)Nc2cc3ccccc3cc2C(=O)N[C@H](C(O)=O)c4ccccc4
#
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
 055  055  '(2S)-{[(3-{[(2-chloro-6-methylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]amino}(phenyl)ethanoic acid'  ligand  57  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_055
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
 055  CL1   CL  CL    0  -0.114  -5.8255  -0.3475   0.6443
 055  C30   C   CR6   0  -0.072  -5.4075   1.0039  -0.3489
 055  C29   C   CR16  0  -0.251  -6.3811   1.5667  -1.1582
 055  C28   C   CR16  0  -0.248  -6.0609   2.6820  -1.9155
 055  C27   C   CR16  0  -0.310  -4.7852   3.2223  -1.8598
 055  C26   C   CR6   0   0.077  -3.7967   2.6499  -1.0659
 055  C31   C   CH3   0  -0.735  -2.4146   3.2300  -1.0182
 055  C25   C   CR6   0   0.348  -4.1150   1.5222  -0.3011
 055  N24   N   NH1   0  -0.770  -3.1390   0.9431   0.5259
 055  C23   C   C     0   0.692  -2.5831  -0.2726   0.2343
 055  O33   O   O     0  -0.488  -2.9587  -0.9633  -0.6925
 055  N22   N   NH1   0  -0.796  -1.5788  -0.6229   1.0991
 055  C5    C   CR6   0   0.349  -0.7502  -1.7341   0.9154
 055  C6    C   CR16  0  -0.361  -1.2682  -2.9775   0.6608
 055  C1    C   CR66  0   0.129  -0.4293  -4.0966   0.4726
 055  C7    C   CR16  0  -0.317  -0.9550  -5.3851   0.2171
 055  C8    C   CR16  0  -0.250  -0.1191  -6.4564   0.0562
 055  C9    C   CR16  0  -0.260   1.2806  -6.2945   0.1414
 055  C2    C   CR66  0   0.126   0.9753  -3.9367   0.5598
 055  C10   C   CR16  0  -0.306   1.8163  -5.0605   0.3896
 055  C3    C   CR16  0  -0.365   1.4906  -2.6498   0.8178
 055  C4    C   CR6   0  -0.085   0.6658  -1.5672   0.9842
 055  C11   C   C     0   0.564   1.2478  -0.2276   1.2782
 055  O14   O   O     0  -0.494   0.7630   0.5275   2.1149
 055  N12   N   NH1   0  -0.636   2.3417   0.1091   0.5794
 055  C13   C   CH1   0  -0.228   2.9751   1.3837   0.7950
 055  C16   C   C     0   0.551   2.0181   2.5207   0.4452
 055  O21   O   OH1   0  -0.584   2.3272   3.6192   1.1145
 055  O20   O   O     0  -0.422   1.1395   2.4423  -0.3705
 055  C46   C   CR6   0   0.088   4.2143   1.5196  -0.0605
 055  C47   C   CR16  0  -0.283   4.1319   1.4116  -1.4473
 055  C48   C   CR16  0  -0.238   5.2735   1.5349  -2.2254
 055  C49   C   CR16  0  -0.258   6.5040   1.7750  -1.6270
 055  C50   C   CR16  0  -0.239   6.5888   1.8882  -0.2464
 055  C51   C   CR16  0  -0.313   5.4474   1.7594   0.5338
 055  H29   H   HCR6  0   0.279  -7.3764   1.1453  -1.1872
 055  H28   H   HCR6  0   0.267  -6.8137   3.1319  -2.5487
 055  H27   H   HCR6  0   0.258  -4.5464   4.0965  -2.4520
 055  H31   H   HCH3  0   0.251  -2.2024   3.6828  -0.0473
 055  H31A  H   HCH3  0   0.255  -1.6484   2.4736  -1.1896
 055  H31B  H   HCH3  0   0.255  -2.2974   4.0073  -1.7710
 055  HN24  H   HNH1  0   0.405  -2.6786   1.5502   1.1869
 055  HN22  H   HNH1  0   0.409  -1.2158   0.0815   1.7266
 055  H6    H   HCR6  0   0.266  -2.3392  -3.1197   0.6212
 055  H7    H   HCR6  0   0.259  -2.0287  -5.5124   0.1522
 055  H8    H   HCR6  0   0.263  -0.5304  -7.4379  -0.1400
 055  H9    H   HCR6  0   0.262   1.9279  -7.1512   0.0092
 055  H10   H   HCR6  0   0.260   2.8895  -4.9296   0.4547
 055  H3    H   HCR6  0   0.272   2.5654  -2.5320   0.8947
 055  HN12  H   HNH1  0   0.424   2.6677  -0.4794  -0.1712
 055  H13   H   HCH1  0   0.310   3.2601   1.4826   1.8453
 055  HO21  H   HOH1  0   0.485   1.7572   4.3525   0.8366
 055  H47   H   HCR6  0   0.265   3.1781   1.2324  -1.9297
 055  H48   H   HCR6  0   0.264   5.2005   1.4489  -3.3015
 055  H49   H   HCR6  0   0.263   7.3926   1.8738  -2.2366
 055  H50   H   HCR6  0   0.263   7.5441   2.0745   0.2265
 055  H51   H   HCR6  0   0.263   5.5187   1.8396   1.6115

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
 055  C30  CL1   single    1.728  0.020  1.728
 055  C29  C30   aromatic  1.386  0.020  1.386
 055  C30  C25   aromatic  1.393  0.020  1.393
 055  C28  C29   aromatic  1.386  0.020  1.386
 055  C29  H29   single    0.930  0.020  1.080
 055  C28  C27   aromatic  1.387  0.020  1.387
 055  C28  H28   single    0.930  0.020  1.080
 055  C27  C26   aromatic  1.391  0.020  1.391
 055  C27  H27   single    0.930  0.020  1.080
 055  C26  C31   single    1.500  0.020  1.500
 055  C26  C25   aromatic  1.399  0.020  1.399
 055  C31  H31   single    0.970  0.020  1.090
 055  C31  H31A  single    0.970  0.020  1.090
 055  C31  H31B  single    0.970  0.020  1.090
 055  C25  N24   single    1.404  0.020  1.404
 055  C23  N24   single    1.368  0.020  1.368
 055  N24  HN24  single    0.860  0.020  1.020
 055  N22  C23   single    1.371  0.020  1.371
 055  C23  O33   double    1.215  0.020  1.215
 055  C5   N22   single    1.398  0.020  1.398
 055  N22  HN22  single    0.890  0.020  1.040
 055  C4   C5    aromatic  1.427  0.020  1.427
 055  C5   C6    aromatic  1.371  0.020  1.371
 055  C1   C6    aromatic  1.411  0.020  1.411
 055  C6   H6    single    0.930  0.020  1.080
 055  C2   C1    aromatic  1.416  0.020  1.416
 055  C1   C7    aromatic  1.415  0.020  1.415
 055  C8   C7    aromatic  1.368  0.020  1.368
 055  C7   H7    single    0.930  0.020  1.080
 055  C9   C8    aromatic  1.412  0.020  1.412
 055  C8   H8    single    0.930  0.020  1.080
 055  C10  C9    aromatic  1.368  0.020  1.368
 055  C9   H9    single    0.930  0.020  1.080
 055  C10  C2    aromatic  1.414  0.020  1.414
 055  C3   C2    aromatic  1.410  0.020  1.410
 055  C10  H10   single    0.930  0.020  1.080
 055  C3   C4    aromatic  1.371  0.020  1.371
 055  C3   H3    single    0.930  0.020  1.080
 055  C11  C4    single    1.490  0.020  1.490
 055  N12  C11   single    1.341  0.020  1.341
 055  C11  O14   double    1.227  0.020  1.227
 055  C13  N12   single    1.440  0.020  1.440
 055  N12  HN12  single    0.860  0.020  1.020
 055  C16  C13   single    1.527  0.020  1.527
 055  C46  C13   single    1.512  0.020  1.512
 055  C13  H13   single    0.970  0.020  1.090
 055  O20  C16   double    1.202  0.020  1.202
 055  O21  C16   single    1.323  0.020  1.323
 055  O21  HO21  single    0.850  0.020  0.980
 055  C47  C46   aromatic  1.393  0.020  1.393
 055  C46  C51   aromatic  1.390  0.020  1.390
 055  C47  C48   aromatic  1.387  0.020  1.387
 055  C47  H47   single    0.930  0.020  1.080
 055  C48  C49   aromatic  1.389  0.020  1.389
 055  C48  H48   single    0.930  0.020  1.080
 055  C49  C50   aromatic  1.388  0.020  1.388
 055  C49  H49   single    0.930  0.020  1.080
 055  C51  C50   aromatic  1.389  0.020  1.389
 055  C50  H50   single    0.930  0.020  1.080
 055  C51  H51   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
 055  C25   C30  C29   121.39  3.000
 055  C25   C30  CL1   119.70  3.000
 055  C29   C30  CL1   118.90  3.000
 055  H29   C29  C28   120.78  3.000
 055  H29   C29  C30   120.28  3.000
 055  C28   C29  C30   118.93  3.000
 055  H28   C28  C27   120.11  3.000
 055  H28   C28  C29   119.60  3.000
 055  C27   C28  C29   120.29  3.000
 055  H27   C27  C26   119.19  3.000
 055  H27   C27  C28   119.71  3.000
 055  C26   C27  C28   121.09  3.000
 055  C25   C26  C31   120.26  3.000
 055  C25   C26  C27   118.81  3.000
 055  C31   C26  C27   120.93  3.000
 055  H31B  C31  H31A  108.12  3.000
 055  H31B  C31  H31   107.33  3.000
 055  H31A  C31  H31   106.91  3.000
 055  H31B  C31  C26   110.70  3.000
 055  H31A  C31  C26   111.99  3.000
 055  H31   C31  C26   111.58  3.000
 055  N24   C25  C26   119.75  3.000
 055  N24   C25  C30   120.77  3.000
 055  C26   C25  C30   119.47  3.000
 055  HN24  N24  C23   119.28  3.000
 055  HN24  N24  C25   117.06  3.000
 055  C23   N24  C25   121.55  3.000
 055  N22   C23  O33   124.21  3.000
 055  O33   C23  N24   122.81  3.000
 055  N22   C23  N24   112.97  3.000
 055  HN22  N22  C5    114.99  3.000
 055  HN22  N22  C23   118.47  3.000
 055  C5    N22  C23   123.67  3.000
 055  C4    C5   C6    119.33  3.000
 055  C6    C5   N22   121.42  3.000
 055  C4    C5   N22   119.25  3.000
 055  H6    C6   C1    118.66  3.000
 055  H6    C6   C5    120.03  3.000
 055  C1    C6   C5    121.30  3.000
 055  C2    C1   C7    118.84  3.000
 055  C7    C1   C6    121.70  3.000
 055  C2    C1   C6    119.45  3.000
 055  H7    C7   C8    120.43  3.000
 055  H7    C7   C1    119.09  3.000
 055  C8    C7   C1    120.48  3.000
 055  H8    C8   C9    119.47  3.000
 055  H8    C8   C7    119.94  3.000
 055  C9    C8   C7    120.59  3.000
 055  H9    C9   C10   120.15  3.000
 055  H9    C9   C8    119.67  3.000
 055  C10   C9   C8    120.18  3.000
 055  C3    C2   C10   122.01  3.000
 055  C3    C2   C1    118.47  3.000
 055  C10   C2   C1    119.52  3.000
 055  H10   C10  C2    119.08  3.000
 055  H10   C10  C9    120.53  3.000
 055  C2    C10  C9    120.39  3.000
 055  H3    C3   C4    120.14  3.000
 055  H3    C3   C2    118.33  3.000
 055  C4    C3   C2    121.53  3.000
 055  C11   C4   C3    119.92  3.000
 055  C11   C4   C5    120.14  3.000
 055  C3    C4   C5    119.91  3.000
 055  N12   C11  O14   121.55  3.000
 055  O14   C11  C4    122.25  3.000
 055  N12   C11  C4    116.20  3.000
 055  HN12  N12  C13   119.09  3.000
 055  HN12  N12  C11   120.35  3.000
 055  C13   N12  C11   120.21  3.000
 055  H13   C13  C46   108.79  3.000
 055  H13   C13  C16   108.44  3.000
 055  C46   C13  C16   108.49  3.000
 055  H13   C13  N12   109.81  3.000
 055  C46   C13  N12   110.82  3.000
 055  C16   C13  N12   110.44  3.000
 055  O20   C16  O21   124.64  3.000
 055  O21   C16  C13   110.86  3.000
 055  O20   C16  C13   124.43  3.000
 055  HO21  O21  C16   110.22  3.000
 055  C51   C46  C47   119.44  3.000
 055  C51   C46  C13   120.05  3.000
 055  C47   C46  C13   120.51  3.000
 055  H47   C47  C48   119.30  3.000
 055  H47   C47  C46   120.52  3.000
 055  C48   C47  C46   120.18  3.000
 055  H48   C48  C49   120.13  3.000
 055  H48   C48  C47   119.69  3.000
 055  C49   C48  C47   120.18  3.000
 055  H49   C49  C50   120.18  3.000
 055  H49   C49  C48   120.03  3.000
 055  C50   C49  C48   119.79  3.000
 055  H50   C50  C51   119.74  3.000
 055  H50   C50  C49   120.19  3.000
 055  C51   C50  C49   120.07  3.000
 055  H51   C51  C50   119.87  3.000
 055  H51   C51  C46   119.79  3.000
 055  C50   C51  C46   120.34  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
 055  CONST_01  C27   C28  C29  C30    0.00   0.0  0
 055  CONST_02  C27   C26  C25  C30    0.00   0.0  0
 055  CONST_03  C26   C25  C30  C29    0.00   0.0  0
 055  CONST_04  C26   C27  C28  C29    0.00   0.0  0
 055  CONST_05  C25   C30  C29  C28    0.00   0.0  0
 055  CONST_06  C25   C26  C27  C28    0.00   0.0  0
 055  CONST_07  C2    C3   C4   C5     0.00   0.0  0
 055  CONST_08  C2    C1   C6   C5     0.00   0.0  0
 055  CONST_09  C7    C1   C6   C5   180.00   0.0  0
 055  CONST_10  C3    C4   C5   C6     0.00   0.0  0
 055  CONST_11  C10   C2   C1   C6   180.00   0.0  0
 055  CONST_12  C3    C2   C1   C6     0.00   0.0  0
 055  CONST_13  C8    C7   C1   C6   180.00   0.0  0
 055  CONST_14  C4    C5   C6   C1     0.00   0.0  0
 055  CONST_15  C9    C10  C2   C1     0.00   0.0  0
 055  CONST_16  C4    C3   C2   C1     0.00   0.0  0
 055  CONST_17  C9    C8   C7   C1     0.00   0.0  0
 055  CONST_18  C10   C2   C1   C7     0.00   0.0  0
 055  CONST_19  C3    C2   C1   C7   180.00   0.0  0
 055  CONST_20  C10   C9   C8   C7     0.00   0.0  0
 055  CONST_21  C2    C1   C7   C8     0.00   0.0  0
 055  CONST_22  C2    C10  C9   C8     0.00   0.0  0
 055  CONST_23  C3    C2   C10  C9   180.00   0.0  0
 055  CONST_24  C4    C3   C2   C10  180.00   0.0  0
 055  CONST_25  C49   C48  C47  C46    0.00   0.0  0
 055  CONST_26  C49   C50  C51  C46    0.00   0.0  0
 055  CONST_27  C50   C51  C46  C47    0.00   0.0  0
 055  CONST_28  C50   C49  C48  C47    0.00   0.0  0
 055  CONST_29  C51   C46  C47  C48    0.00   0.0  0
 055  CONST_30  C51   C50  C49  C48    0.00   0.0  0
 055  CONST_31  C28   C29  C30  CL1  180.00   0.0  0
 055  CONST_32  C26   C25  C30  CL1  180.00   0.0  0
 055  CONST_33  C31   C26  C25  C30  180.00   0.0  0
 055  CONST_34  N24   C25  C30  C29  180.00   0.0  0
 055  CONST_35  C31   C26  C27  C28  180.00   0.0  0
 055  CONST_36  N24   C25  C26  C27  180.00   0.0  0
 055  CONST_37  C3    C4   C5   N22  180.00   0.0  0
 055  CONST_38  C1    C6   C5   N22  180.00   0.0  0
 055  CONST_39  C11   C4   C5   C6   180.00   0.0  0
 055  CONST_40  C11   C4   C3   C2   180.00   0.0  0
 055  CONST_41  C48   C47  C46  C13  180.00   0.0  0
 055  CONST_42  C50   C51  C46  C13  180.00   0.0  0
 055  CONST_43  H28   C28  C29  C30  180.00   0.0  0
 055  CONST_44  H27   C27  C28  C29  180.00   0.0  0
 055  CONST_45  H29   C29  C28  C27  180.00   0.0  0
 055  CONST_46  H3    C3   C4   C5   180.00   0.0  0
 055  CONST_47  H7    C7   C1   C6     0.00   0.0  0
 055  CONST_48  H10   C10  C2   C1   180.00   0.0  0
 055  CONST_49  H8    C8   C7   C1   180.00   0.0  0
 055  CONST_50  H6    C6   C1   C7     0.00   0.0  0
 055  CONST_51  H9    C9   C8   C7   180.00   0.0  0
 055  CONST_52  H48   C48  C47  C46  180.00   0.0  0
 055  CONST_53  H50   C50  C51  C46  180.00   0.0  0
 055  CONST_54  H51   C51  C46  C47  180.00   0.0  0
 055  CONST_55  H49   C49  C48  C47  180.00   0.0  0
 055  CONST_56  H47   C47  C48  C49  180.00   0.0  0
 055  CONST_64  O33   C23  N24  C25    0.00   0.0  0
 055  CONST_65  C5    N22  C23  O33    0.00   0.0  0
 055  CONST_66  C13   N12  C11  C4   180.00   0.0  0
 055  CONST_67  N22   C23  N24  C25  180.00   0.0  0
 055  CONST_68  C5    N22  C23  N24  180.00   0.0  0
 055  CONST_69  HN12  N12  C11  C4     0.00   0.0  0
 055  CONST_70  C13   N12  C11  O14    0.00   0.0  0
 055  CONST_71  HO21  O21  C16  C13  180.00   0.0  0
 055  Var_01    H31   C31  C26  C27  111.00  30.0  2

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
 055  chir_01  C13  N12  C16  C46  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
 055  plan-1  CL1   0.020
 055  plan-1  C30   0.020
 055  plan-1  C29   0.020
 055  plan-1  C28   0.020
 055  plan-1  C27   0.020
 055  plan-1  C26   0.020
 055  plan-1  C31   0.020
 055  plan-1  C25   0.020
 055  plan-1  N24   0.020
 055  plan-1  H29   0.020
 055  plan-1  H28   0.020
 055  plan-1  H27   0.020
 055  plan-2  C13   0.020
 055  plan-2  C16   0.020
 055  plan-2  O21   0.020
 055  plan-2  O20   0.020
 055  plan-2  HO21  0.020
 055  plan-3  C13   0.020
 055  plan-3  C46   0.020
 055  plan-3  C47   0.020
 055  plan-3  C48   0.020
 055  plan-3  C49   0.020
 055  plan-3  C50   0.020
 055  plan-3  C51   0.020
 055  plan-3  H47   0.020
 055  plan-3  H48   0.020
 055  plan-3  H49   0.020
 055  plan-3  H50   0.020
 055  plan-3  H51   0.020
 055  plan-4  C25   0.020
 055  plan-4  N24   0.020
 055  plan-4  C23   0.020
 055  plan-4  O33   0.020
 055  plan-4  N22   0.020
 055  plan-4  C5    0.020
 055  plan-4  HN24  0.020
 055  plan-4  HN22  0.020
 055  plan-5  N22   0.020
 055  plan-5  C5    0.020
 055  plan-5  C6    0.020
 055  plan-5  C1    0.020
 055  plan-5  C7    0.020
 055  plan-5  C8    0.020
 055  plan-5  C9    0.020
 055  plan-5  C2    0.020
 055  plan-5  C10   0.020
 055  plan-5  C3    0.020
 055  plan-5  C4    0.020
 055  plan-5  C11   0.020
 055  plan-5  O14   0.020
 055  plan-5  N12   0.020
 055  plan-5  C13   0.020
 055  plan-5  H6    0.020
 055  plan-5  H7    0.020
 055  plan-5  H8    0.020
 055  plan-5  H9    0.020
 055  plan-5  H10   0.020
 055  plan-5  H3    0.020
 055  plan-5  HN12  0.020

