# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:18:10 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-serinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@H](CO)NC(=O)[C@@H](CO)N[S](=O)(=O)Cc2ccccc2)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
 7IN  7IN  N-(benzylsulfonyl)-D-seryl-N-(4-carbamimidoylbenzyl)-L-serinamide  ligand  60  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7IN
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
 7IN  O2    O  OH1   0  -0.657  -2.0810   0.4682   2.4328
 7IN  C3    C  CH2   0  -0.152  -1.3275   1.4312   1.7408
 7IN  C4    C  CH1   0  -0.242  -0.2402   0.7047   0.9535
 7IN  N5    N  NH1   0  -0.639  -0.7823  -0.1255  -0.0893
 7IN  C6    C  C     0   0.567  -1.1456   0.3526  -1.2860
 7IN  C7    C  CH1   0  -0.250  -1.7471  -0.6972  -2.2271
 7IN  N8    N  NC1   0  -0.733  -1.8343  -0.2104  -3.5880
 7IN  S9    S  S     0   1.374  -0.4435   0.1084  -4.4255
 7IN  C10   C  CH2   0  -0.691  -0.5578  -1.0341  -5.8088
 7IN  C11   C  CR6   0   0.106   0.6286  -0.8679  -6.7048
 7IN  C12   C  CR16  0  -0.279   0.5895   0.0362  -7.7626
 7IN  C13   C  CR16  0  -0.243   1.6951   0.2022  -8.5843
 7IN  C14   C  CR16  0  -0.260   2.8532  -0.5279  -8.3497
 7IN  C15   C  CR16  0  -0.242   2.9000  -1.4277  -7.2928
 7IN  C16   C  CR16  0  -0.279   1.7938  -1.5934  -6.4716
 7IN  O17   O  OS    0  -0.661  -0.4957   1.4604  -4.9610
 7IN  O18   O  OS    0  -0.662   0.6899  -0.2956  -3.6029
 7IN  C19   C  CH2   0  -0.155  -3.1409  -1.0948  -1.7610
 7IN  O20   O  OH1   0  -0.666  -3.9342   0.0649  -1.7332
 7IN  O21   O  O     0  -0.482  -1.0301   1.5209  -1.6151
 7IN  C22   C  C     0   0.560   0.5867  -0.1788   1.8889
 7IN  O23   O  O     0  -0.477   0.5429  -1.3968   1.8286
 7IN  N24   N  NH1   0  -0.632   1.3368   0.4993   2.7688
 7IN  C25   C  CH2   0  -0.345   2.1447  -0.1244   3.7858
 7IN  C26   C  CR6   0   0.090   1.5088  -0.1490   5.1556
 7IN  C27   C  CR16  0  -0.283   2.3249  -0.2003   6.2818
 7IN  C28   C  CR16  0  -0.268   1.7816  -0.2663   7.5548
 7IN  C29   C  CR6   0  -0.007   0.3995  -0.2934   7.7317
 7IN  C30   C  CR16  0  -0.276  -0.4170  -0.2374   6.6052
 7IN  C31   C  CR16  0  -0.295   0.1290  -0.1597   5.3334
 7IN  C32   C  C     0   0.327  -0.2068  -0.4008   9.0880
 7IN  N33   N  N     0  -0.641  -1.2714  -1.0559   9.3553
 7IN  N34   N  NH2   0  -0.803   0.4892   0.2228  10.0808
 7IN  HO2   H  HOH1  0   0.464  -2.7533   0.9225   2.9492
 7IN  H31A  H  HCH2  0   0.212  -0.8582   2.1549   2.4183
 7IN  H32   H  HCH2  0   0.233  -1.9395   2.0069   1.0379
 7IN  H4    H  HCH1  0   0.300   0.4113   1.4615   0.5072
 7IN  HN5   H  HNH1  0   0.403  -0.8654  -1.1118   0.1081
 7IN  H7    H  HCH1  0   0.306  -1.1327  -1.6002  -2.2090
 7IN  HN8   H  HNC1  0   0.413  -2.5333   0.5114  -3.7295
 7IN  H101  H  HCH2  0   0.321  -1.4978  -0.8156  -6.3164
 7IN  H102  H  HCH2  0   0.319  -0.6209  -2.0346  -5.3789
 7IN  H12   H  HCR6  0   0.257  -0.3125   0.6049  -7.9525
 7IN  H13   H  HCR6  0   0.260   1.6529   0.9024  -9.4082
 7IN  H14   H  HCR6  0   0.260   3.7152  -0.3989  -8.9912
 7IN  H15   H  HCR6  0   0.259   3.7984  -2.0021  -7.1076
 7IN  H16   H  HCR6  0   0.258   1.8326  -2.3005  -5.6525
 7IN  H191  H  HCH2  0   0.221  -3.0628  -1.5640  -0.7732
 7IN  H192  H  HCH2  0   0.238  -3.5336  -1.8510  -2.4492
 7IN  H20   H  HOH1  0   0.467  -4.8497  -0.1924  -1.5916
 7IN  H24   H  HNH1  0   0.410   1.3325   1.5067   2.7403
 7IN  H251  H  HCH2  0   0.276   2.3680  -1.1448   3.4711
 7IN  H252  H  HCH2  0   0.274   3.0998   0.4000   3.8370
 7IN  H27   H  HCR6  0   0.256   3.4023  -0.1892   6.1658
 7IN  H28   H  HCR6  0   0.262   2.4431  -0.3126   8.4102
 7IN  H30   H  HCR6  0   0.260  -1.4946  -0.2345   6.7164
 7IN  H31   H  HCR6  0   0.259  -0.5364  -0.0987   4.4815
 7IN  H33   H  H     0   0.332  -1.6044  -1.5469   8.5339
 7IN  H341  H  HNH2  0   0.384   0.0355   0.2661  10.9795
 7IN  H342  H  HNH2  0   0.392   1.0176   1.0467   9.8465

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
 7IN  O2   C3    single    1.405  0.020  1.405
 7IN  O2   HO2   single    0.850  0.020  0.980
 7IN  C3   C4    single    1.526  0.020  1.526
 7IN  C3   H31A  single    0.970  0.020  1.090
 7IN  C3   H32   single    0.970  0.020  1.090
 7IN  C4   N5    single    1.439  0.020  1.439
 7IN  C4   C22   single    1.530  0.020  1.530
 7IN  C4   H4    single    0.970  0.020  1.090
 7IN  N5   C6    single    1.339  0.020  1.339
 7IN  N5   HN5   single    0.860  0.020  1.020
 7IN  C6   C7    single    1.533  0.020  1.533
 7IN  C6   O21   double    1.219  0.020  1.219
 7IN  C7   N8    single    1.448  0.020  1.448
 7IN  C7   C19   single    1.522  0.020  1.522
 7IN  C7   H7    single    0.970  0.020  1.090
 7IN  N8   S9    single    1.655  0.020  1.655
 7IN  N8   HN8   single    0.890  0.020  1.040
 7IN  S9   C10   single    1.798  0.020  1.798
 7IN  S9   O17   double    1.455  0.020  1.455
 7IN  S9   O18   double    1.458  0.020  1.458
 7IN  C10  C11   single    1.496  0.020  1.496
 7IN  C10  H101  single    0.970  0.020  1.090
 7IN  C10  H102  single    0.970  0.020  1.090
 7IN  C11  C12   aromatic  1.392  0.020  1.392
 7IN  C11  C16   aromatic  1.392  0.020  1.392
 7IN  C12  C13   aromatic  1.387  0.020  1.387
 7IN  C12  H12   single    0.930  0.020  1.080
 7IN  C13  C14   aromatic  1.389  0.020  1.389
 7IN  C13  H13   single    0.930  0.020  1.080
 7IN  C14  C15   aromatic  1.389  0.020  1.389
 7IN  C14  H14   single    0.930  0.020  1.080
 7IN  C15  C16   aromatic  1.388  0.020  1.388
 7IN  C15  H15   single    0.930  0.020  1.080
 7IN  C16  H16   single    0.930  0.020  1.080
 7IN  C19  O20   single    1.405  0.020  1.405
 7IN  C19  H191  single    0.970  0.020  1.090
 7IN  C19  H192  single    0.970  0.020  1.090
 7IN  O20  H20   single    0.850  0.020  0.980
 7IN  C22  O23   double    1.220  0.020  1.220
 7IN  C22  N24   single    1.340  0.020  1.340
 7IN  N24  C25   single    1.441  0.020  1.441
 7IN  N24  H24   single    0.860  0.020  1.020
 7IN  C25  C26   single    1.510  0.020  1.510
 7IN  C25  H251  single    0.970  0.020  1.090
 7IN  C25  H252  single    0.970  0.020  1.090
 7IN  C26  C27   aromatic  1.392  0.020  1.392
 7IN  C26  C31   aromatic  1.391  0.020  1.391
 7IN  C27  C28   aromatic  1.386  0.020  1.386
 7IN  C27  H27   single    0.930  0.020  1.080
 7IN  C28  C29   aromatic  1.394  0.020  1.394
 7IN  C28  H28   single    0.930  0.020  1.080
 7IN  C29  C30   aromatic  1.392  0.020  1.392
 7IN  C29  C32   single    1.490  0.020  1.490
 7IN  C30  C31   aromatic  1.386  0.020  1.386
 7IN  C30  H30   single    0.930  0.020  1.080
 7IN  C31  H31   single    0.930  0.020  1.080
 7IN  C32  N33   double    1.278  0.020  1.278
 7IN  C32  N34   single    1.363  0.020  1.363
 7IN  N33  H33   single    0.890  0.020  1.040
 7IN  N34  H341  single    0.890  0.020  1.040
 7IN  N34  H342  single    0.890  0.020  1.040

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
 7IN  HO2   O2   C3    108.40  3.000
 7IN  H32   C3   H31A  106.78  3.000
 7IN  H32   C3   C4    108.49  3.000
 7IN  H31A  C3   C4    109.13  3.000
 7IN  H32   C3   O2    112.13  3.000
 7IN  H31A  C3   O2    112.18  3.000
 7IN  C4    C3   O2    108.05  3.000
 7IN  H4    C4   C22   109.10  3.000
 7IN  H4    C4   N5    109.14  3.000
 7IN  C22   C4   N5    108.28  3.000
 7IN  H4    C4   C3    107.79  3.000
 7IN  C22   C4   C3    110.15  3.000
 7IN  N5    C4   C3    112.33  3.000
 7IN  HN5   N5   C6    120.10  3.000
 7IN  HN5   N5   C4    116.94  3.000
 7IN  C6    N5   C4    122.95  3.000
 7IN  O21   C6   C7    121.85  3.000
 7IN  O21   C6   N5    123.90  3.000
 7IN  C7    C6   N5    114.24  3.000
 7IN  H7    C7   C19   107.10  3.000
 7IN  H7    C7   N8    109.11  3.000
 7IN  C19   C7   N8    108.69  3.000
 7IN  H7    C7   C6    109.58  3.000
 7IN  C19   C7   C6    110.50  3.000
 7IN  N8    C7   C6    111.74  3.000
 7IN  HN8   N8   S9    111.80  3.000
 7IN  HN8   N8   C7    114.31  3.000
 7IN  S9    N8   C7    119.33  3.000
 7IN  O18   S9   O17   119.55  3.000
 7IN  O18   S9   C10   107.91  3.000
 7IN  O17   S9   C10   107.76  3.000
 7IN  O18   S9   N8    108.34  3.000
 7IN  O17   S9   N8    109.58  3.000
 7IN  C10   S9   N8    102.33  3.000
 7IN  H102  C10  H101  108.51  3.000
 7IN  H102  C10  C11   112.58  3.000
 7IN  H101  C10  C11   112.50  3.000
 7IN  H102  C10  S9    106.46  3.000
 7IN  H101  C10  S9    106.59  3.000
 7IN  C11   C10  S9    109.87  3.000
 7IN  C16   C11  C12   119.28  3.000
 7IN  C16   C11  C10   120.37  3.000
 7IN  C12   C11  C10   120.33  3.000
 7IN  H12   C12  C13   119.80  3.000
 7IN  H12   C12  C11   119.84  3.000
 7IN  C13   C12  C11   120.36  3.000
 7IN  H13   C13  C14   120.08  3.000
 7IN  H13   C13  C12   119.82  3.000
 7IN  C14   C13  C12   120.10  3.000
 7IN  H14   C14  C15   120.10  3.000
 7IN  H14   C14  C13   120.09  3.000
 7IN  C15   C14  C13   119.81  3.000
 7IN  H15   C15  C16   119.81  3.000
 7IN  H15   C15  C14   120.13  3.000
 7IN  C16   C15  C14   120.06  3.000
 7IN  H16   C16  C15   119.81  3.000
 7IN  H16   C16  C11   119.80  3.000
 7IN  C15   C16  C11   120.39  3.000
 7IN  H192  C19  H191  107.23  3.000
 7IN  H192  C19  O20   112.32  3.000
 7IN  H191  C19  O20   112.06  3.000
 7IN  H192  C19  C7    108.43  3.000
 7IN  H191  C19  C7    108.80  3.000
 7IN  O20   C19  C7    107.90  3.000
 7IN  H20   O20  C19   108.64  3.000
 7IN  N24   C22  O23   123.88  3.000
 7IN  N24   C22  C4    114.32  3.000
 7IN  O23   C22  C4    121.80  3.000
 7IN  H24   N24  C25   117.07  3.000
 7IN  H24   N24  C22   118.99  3.000
 7IN  C25   N24  C22   123.93  3.000
 7IN  H252  C25  H251  106.50  3.000
 7IN  H252  C25  C26   109.51  3.000
 7IN  H251  C25  C26   109.43  3.000
 7IN  H252  C25  N24   108.42  3.000
 7IN  H251  C25  N24   108.42  3.000
 7IN  C26   C25  N24   114.28  3.000
 7IN  C31   C26  C27   118.55  3.000
 7IN  C31   C26  C25   122.25  3.000
 7IN  C27   C26  C25   119.18  3.000
 7IN  H27   C27  C28   119.26  3.000
 7IN  H27   C27  C26   119.73  3.000
 7IN  C28   C27  C26   121.01  3.000
 7IN  H28   C28  C29   120.33  3.000
 7IN  H28   C28  C27   119.24  3.000
 7IN  C29   C28  C27   120.43  3.000
 7IN  C32   C29  C30   120.06  3.000
 7IN  C32   C29  C28   121.38  3.000
 7IN  C30   C29  C28   118.56  3.000
 7IN  H30   C30  C31   119.07  3.000
 7IN  H30   C30  C29   120.03  3.000
 7IN  C31   C30  C29   120.90  3.000
 7IN  H31   C31  C30   118.88  3.000
 7IN  H31   C31  C26   120.57  3.000
 7IN  C30   C31  C26   120.55  3.000
 7IN  N34   C32  N33   120.49  3.000
 7IN  N34   C32  C29   114.98  3.000
 7IN  N33   C32  C29   124.49  3.000
 7IN  H33   N33  C32   110.65  3.000
 7IN  H342  N34  H341  114.14  3.000
 7IN  H342  N34  C32   118.22  3.000
 7IN  H341  N34  C32   116.05  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
 7IN  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 7IN  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 7IN  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 7IN  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 7IN  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 7IN  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 7IN  CONST_07  C29   C28  C27  C26     0.00   0.0  0
 7IN  CONST_08  C29   C30  C31  C26     0.00   0.0  0
 7IN  CONST_09  C30   C31  C26  C27     0.00   0.0  0
 7IN  CONST_10  C30   C29  C28  C27     0.00   0.0  0
 7IN  CONST_11  C31   C26  C27  C28     0.00   0.0  0
 7IN  CONST_12  C31   C30  C29  C28     0.00   0.0  0
 7IN  CONST_13  C13   C12  C11  C10   180.00   0.0  0
 7IN  CONST_14  C15   C16  C11  C10   180.00   0.0  0
 7IN  CONST_15  C28   C27  C26  C25   180.00   0.0  0
 7IN  CONST_16  C30   C31  C26  C25   180.00   0.0  0
 7IN  CONST_17  C32   C29  C28  C27   180.00   0.0  0
 7IN  CONST_18  C32   C29  C30  C31   180.00   0.0  0
 7IN  CONST_19  H13   C13  C12  C11   180.00   0.0  0
 7IN  CONST_20  H15   C15  C16  C11   180.00   0.0  0
 7IN  CONST_21  H16   C16  C11  C12   180.00   0.0  0
 7IN  CONST_22  H14   C14  C13  C12   180.00   0.0  0
 7IN  CONST_23  H12   C12  C13  C14   180.00   0.0  0
 7IN  CONST_24  H28   C28  C27  C26   180.00   0.0  0
 7IN  CONST_25  H30   C30  C31  C26   180.00   0.0  0
 7IN  CONST_26  H31   C31  C26  C27   180.00   0.0  0
 7IN  CONST_27  H27   C27  C28  C29   180.00   0.0  0
 7IN  CONST_28  H33   N33  C32  C29     0.00   0.0  0
 7IN  CONST_29  H341  N34  C32  C29   180.00   0.0  0
 7IN  CONST_31  C7    C6   N5   C4    180.00   0.0  0
 7IN  CONST_32  O21   C6   N5   C4      0.00   0.0  0
 7IN  CONST_33  C25   N24  C22  C4    180.00   0.0  0
 7IN  CONST_34  C25   N24  C22  O23     0.00   0.0  0
 7IN  CONST_35  H24   N24  C22  C4      0.00   0.0  0
 7IN  CONST_36  HN5   N5   C6   C7      0.00   0.0  0
 7IN  Var_01    C12   C11  C10  S9    -90.15  30.0  2
 7IN  Var_02    C27   C26  C25  N24  -154.02  30.0  2
 7IN  Var_03    N33   C32  C29  C28  -143.76  30.0  2
 7IN  Var_04    C11   C10  S9   N8    179.04  30.0  3
 7IN  Var_05    C26   C25  N24  C22   -99.28  30.0  3
 7IN  Var_06    C10   S9   N8   C7    118.68  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
 7IN  chir_01  C4  C3  N5  C22  positiv
 7IN  chir_02  C7  N8  C6  C19  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
 7IN  plan-1  C10   0.020
 7IN  plan-1  C11   0.020
 7IN  plan-1  C12   0.020
 7IN  plan-1  C13   0.020
 7IN  plan-1  C14   0.020
 7IN  plan-1  C15   0.020
 7IN  plan-1  C16   0.020
 7IN  plan-1  H12   0.020
 7IN  plan-1  H13   0.020
 7IN  plan-1  H14   0.020
 7IN  plan-1  H15   0.020
 7IN  plan-1  H16   0.020
 7IN  plan-2  C25   0.020
 7IN  plan-2  C26   0.020
 7IN  plan-2  C27   0.020
 7IN  plan-2  C28   0.020
 7IN  plan-2  C29   0.020
 7IN  plan-2  C30   0.020
 7IN  plan-2  C31   0.020
 7IN  plan-2  C32   0.020
 7IN  plan-2  H27   0.020
 7IN  plan-2  H28   0.020
 7IN  plan-2  H30   0.020
 7IN  plan-2  H31   0.020
 7IN  plan-3  C4    0.020
 7IN  plan-3  N5    0.020
 7IN  plan-3  C6    0.020
 7IN  plan-3  C7    0.020
 7IN  plan-3  O21   0.020
 7IN  plan-3  HN5   0.020
 7IN  plan-4  C4    0.020
 7IN  plan-4  C22   0.020
 7IN  plan-4  O23   0.020
 7IN  plan-4  N24   0.020
 7IN  plan-4  C25   0.020
 7IN  plan-4  H24   0.020
 7IN  plan-5  C29   0.020
 7IN  plan-5  C32   0.020
 7IN  plan-5  N33   0.020
 7IN  plan-5  N34   0.020
 7IN  plan-5  H33   0.020
 7IN  plan-5  H341  0.020
 7IN  plan-5  H342  0.020

