# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:35:03 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (3R)-1-(cyclopropylmethyl)-3-methyl-3-(4-methylsulfanylphenoxy)pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc(O[C@]2(C)CCN(CC3CC3)C2)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
 7GM  7GM  (3R)-1-(cyclopropylmethyl)-3-methyl-3-(4-methylsulfanylphenoxy)pyrrolidine  ligand  42  19  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7GM
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
 7GM  C13   C  CR16  0  -0.355  -1.7250  -0.4325   0.9574
 7GM  C17   C  CR16  0  -0.340  -1.9876  -0.0917  -1.3979
 7GM  C14   C  CR16  0  -0.255  -3.0409  -0.0360   1.1455
 7GM  C16   C  CR16  0  -0.243  -3.3007   0.3034  -1.2046
 7GM  C12   C  CR6   0   0.371  -1.1776  -0.4668  -0.3258
 7GM  C15   C  CR6   0  -0.134  -3.8495   0.3354   0.0751
 7GM  C9    C  CH2   0  -0.497   6.5017   1.3722  -0.5796
 7GM  C10   C  CH2   0  -0.481   5.7436   1.6479   0.6831
 7GM  C3    C  CH2   0  -0.505   1.3496  -0.2615   1.4030
 7GM  C4    C  CH2   0  -0.274   2.8200   0.0901   1.1902
 7GM  C6    C  CH2   0  -0.279   2.3552  -1.4053  -0.4608
 7GM  C8    C  CH1   0  -0.255   5.0097   1.2498  -0.5612
 7GM  C2    C  CR5   0   0.218   1.0306  -1.3103   0.3077
 7GM  C1    C  CH3   0  -0.696   0.6167  -2.6776   0.8322
 7GM  C19   C  CH3   0  -0.794  -6.1845   1.2668  -1.1624
 7GM  N5    N  NR5   0  -0.426   3.0107  -0.1367  -0.2300
 7GM  O11   O  O2    0  -0.503   0.0818  -0.8207  -0.6492
 7GM  S18   S  S2    0   0.027  -5.5094   0.8079   0.4431
 7GM  H13   H  HCR6  0   0.283  -1.1527  -0.7025   1.8326
 7GM  H14   H  HCR6  0   0.264  -3.4330  -0.0191   2.1556
 7GM  H17   H  HCR6  0   0.262  -1.5811  -0.1121  -2.4016
 7GM  H16   H  HCR6  0   0.263  -3.8821   0.5837  -2.0722
 7GM  H92C  H  HCH2  0   0.241   7.0848   0.4602  -0.6318
 7GM  H101  H  HCH2  0   0.240   5.8149   0.9218   1.4845
 7GM  H102  H  HCH2  0   0.247   5.6620   2.6733   1.0206
 7GM  H8    H  HCH1  0   0.250   4.4588   2.0378  -1.0649
 7GM  H31C  H  HCH2  0   0.250   1.1622  -0.6416   2.4077
 7GM  H32C  H  HCH2  0   0.261   0.7324   0.6285   1.2781
 7GM  H41C  H  HCH2  0   0.245   3.0503   1.1170   1.4731
 7GM  H42C  H  HCH2  0   0.192   3.4648  -0.5716   1.7944
 7GM  H61C  H  HCH2  0   0.203   2.9423  -2.2445  -0.0476
 7GM  H62C  H  HCH2  0   0.249   2.2067  -1.6063  -1.5242
 7GM  H11C  H  HCH3  0   0.245  -0.3418  -2.6673   1.3494
 7GM  H12C  H  HCH3  0   0.242   0.5510  -3.4006   0.0171
 7GM  H13C  H  HCH3  0   0.240   1.3638  -3.0408   1.5383
 7GM  H191  H  HCH3  0   0.293  -7.2093   1.5828  -0.9770
 7GM  H192  H  HCH3  0   0.272  -5.6398   2.0988  -1.6048
 7GM  H193  H  HCH3  0   0.272  -6.2012   0.4241  -1.8508
 7GM  C7    C  CH2   0  -0.269   4.3838  -0.1135  -0.6803
 7GM  H91C  H  HCH2  0   0.249   6.9421   2.2072  -1.1090
 7GM  H71C  H  HCH2  0   0.236   4.3960  -0.4223  -1.7302
 7GM  H72C  H  HCH2  0   0.187   5.0012  -0.8489  -0.1314

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
 7GM  C13  C14   aromatic  1.387  0.020  1.387
 7GM  C13  C12   aromatic  1.395  0.020  1.395
 7GM  C17  C16   aromatic  1.385  0.020  1.385
 7GM  C17  C12   aromatic  1.395  0.020  1.395
 7GM  C14  C15   aromatic  1.392  0.020  1.392
 7GM  C16  C15   aromatic  1.393  0.020  1.393
 7GM  C12  O11   single    1.348  0.020  1.348
 7GM  C15  S18   single    1.765  0.020  1.765
 7GM  C9   C10   single    1.498  0.020  1.498
 7GM  C9   C8    single    1.497  0.020  1.497
 7GM  C10  C8    single    1.498  0.020  1.498
 7GM  C3   C4    single    1.527  0.020  1.527
 7GM  C3   C2    single    1.550  0.020  1.550
 7GM  C4   N5    single    1.451  0.020  1.451
 7GM  C6   C2    single    1.534  0.020  1.534
 7GM  C6   N5    single    1.446  0.020  1.446
 7GM  C8   C7    single    1.505  0.020  1.505
 7GM  C2   C1    single    1.522  0.020  1.522
 7GM  C2   O11   single    1.434  0.020  1.434
 7GM  C19  S18   single    1.801  0.020  1.801
 7GM  C7   N5    single    1.445  0.020  1.445
 7GM  C13  H13   single    0.930  0.020  1.080
 7GM  C14  H14   single    0.930  0.020  1.080
 7GM  C17  H17   single    0.930  0.020  1.080
 7GM  C16  H16   single    0.930  0.020  1.080
 7GM  C9   H91C  single    0.970  0.020  1.090
 7GM  C9   H92C  single    0.970  0.020  1.090
 7GM  C10  H101  single    0.970  0.020  1.090
 7GM  C10  H102  single    0.970  0.020  1.090
 7GM  C8   H8    single    0.970  0.020  1.090
 7GM  C3   H31C  single    0.970  0.020  1.090
 7GM  C3   H32C  single    0.970  0.020  1.090
 7GM  C4   H41C  single    0.970  0.020  1.090
 7GM  C4   H42C  single    0.970  0.020  1.090
 7GM  C6   H61C  single    0.970  0.020  1.090
 7GM  C6   H62C  single    0.970  0.020  1.090
 7GM  C7   H71C  single    0.970  0.020  1.090
 7GM  C7   H72C  single    0.970  0.020  1.090
 7GM  C1   H11C  single    0.970  0.020  1.090
 7GM  C1   H12C  single    0.970  0.020  1.090
 7GM  C1   H13C  single    0.970  0.020  1.090
 7GM  C19  H191  single    0.970  0.020  1.090
 7GM  C19  H192  single    0.970  0.020  1.090
 7GM  C19  H193  single    0.970  0.020  1.090

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
 7GM  H13   C13  C12   122.08  3.000
 7GM  H13   C13  C14   117.66  3.000
 7GM  C12   C13  C14   120.26  3.000
 7GM  H17   C17  C12   119.29  3.000
 7GM  H17   C17  C16   119.38  3.000
 7GM  C12   C17  C16   121.33  3.000
 7GM  H14   C14  C15   120.16  3.000
 7GM  H14   C14  C13   118.30  3.000
 7GM  C15   C14  C13   121.54  3.000
 7GM  H16   C16  C15   121.29  3.000
 7GM  H16   C16  C17   118.16  3.000
 7GM  C15   C16  C17   120.56  3.000
 7GM  O11   C12  C17   115.39  3.000
 7GM  O11   C12  C13   126.43  3.000
 7GM  C17   C12  C13   118.18  3.000
 7GM  S18   C15  C16   124.64  3.000
 7GM  S18   C15  C14   117.22  3.000
 7GM  C16   C15  C14   118.13  3.000
 7GM  H92C  C9   H91C  114.00  3.000
 7GM  H92C  C9   C8    117.90  3.000
 7GM  H91C  C9   C8    118.33  3.000
 7GM  H92C  C9   C10   117.88  3.000
 7GM  H91C  C9   C10   118.43  3.000
 7GM  C8    C9   C10    60.03  3.000
 7GM  H102  C10  H101  114.14  3.000
 7GM  H102  C10  C8    118.27  3.000
 7GM  H101  C10  C8    117.92  3.000
 7GM  H102  C10  C9    118.37  3.000
 7GM  H101  C10  C9    117.81  3.000
 7GM  C8    C10  C9     59.94  3.000
 7GM  H32C  C3   H31C  107.03  3.000
 7GM  H32C  C3   C2    110.80  3.000
 7GM  H31C  C3   C2    112.33  3.000
 7GM  H32C  C3   C4    109.96  3.000
 7GM  H31C  C3   C4    111.97  3.000
 7GM  C2    C3   C4    104.81  3.000
 7GM  H42C  C4   H41C  107.41  3.000
 7GM  H42C  C4   N5    111.43  3.000
 7GM  H41C  C4   N5    111.95  3.000
 7GM  H42C  C4   C3    110.38  3.000
 7GM  H41C  C4   C3    112.60  3.000
 7GM  N5    C4   C3    103.12  3.000
 7GM  H62C  C6   H61C  107.26  3.000
 7GM  H62C  C6   N5    112.23  3.000
 7GM  H61C  C6   N5    111.46  3.000
 7GM  H62C  C6   C2    112.44  3.000
 7GM  H61C  C6   C2    108.58  3.000
 7GM  N5    C6   C2    104.89  3.000
 7GM  H8    C8   C7    114.19  3.000
 7GM  H8    C8   C10   116.17  3.000
 7GM  C7    C8   C10   120.67  3.000
 7GM  H8    C8   C9    116.15  3.000
 7GM  C7    C8   C9    119.18  3.000
 7GM  C10   C8   C9     60.03  3.000
 7GM  O11   C2   C1    110.91  3.000
 7GM  O11   C2   C6    104.96  3.000
 7GM  C1    C2   C6    110.60  3.000
 7GM  O11   C2   C3    112.14  3.000
 7GM  C1    C2   C3    114.87  3.000
 7GM  C6    C2   C3    102.60  3.000
 7GM  H13C  C1   H12C  107.71  3.000
 7GM  H13C  C1   H11C  107.38  3.000
 7GM  H12C  C1   H11C  107.93  3.000
 7GM  H13C  C1   C2    109.64  3.000
 7GM  H12C  C1   C2    110.74  3.000
 7GM  H11C  C1   C2    113.24  3.000
 7GM  H193  C19  H192  110.03  3.000
 7GM  H193  C19  H191  108.55  3.000
 7GM  H192  C19  H191  108.57  3.000
 7GM  H193  C19  S18   111.86  3.000
 7GM  H192  C19  S18   111.69  3.000
 7GM  H191  C19  S18   105.97  3.000
 7GM  C7    N5   C6    113.26  3.000
 7GM  C7    N5   C4    115.30  3.000
 7GM  C6    N5   C4    103.52  3.000
 7GM  C2    O11  C12   123.23  3.000
 7GM  C19   S18  C15   103.59  3.000
 7GM  H72C  C7   H71C  106.40  3.000
 7GM  H72C  C7   N5    111.41  3.000
 7GM  H71C  C7   N5    107.75  3.000
 7GM  H72C  C7   C8    109.32  3.000
 7GM  H71C  C7   C8    109.08  3.000
 7GM  N5    C7   C8    112.65  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
 7GM  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 7GM  CONST_02  C16   C17  C12  C13     0.00   0.0  0
 7GM  CONST_03  C14   C15  C16  C17     0.00   0.0  0
 7GM  CONST_04  C14   C13  C12  C17     0.00   0.0  0
 7GM  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 7GM  CONST_06  C15   C16  C17  C12     0.00   0.0  0
 7GM  CONST_07  S18   C15  C14  C13   180.00   0.0  0
 7GM  CONST_08  S18   C15  C16  C17   180.00   0.0  0
 7GM  CONST_09  O11   C12  C13  C14   180.00   0.0  0
 7GM  CONST_10  O11   C12  C17  C16   180.00   0.0  0
 7GM  CONST_11  H17   C17  C12  C13   180.00   0.0  0
 7GM  CONST_12  H13   C13  C12  C17   180.00   0.0  0
 7GM  CONST_13  H16   C16  C15  C14   180.00   0.0  0
 7GM  CONST_14  H14   C14  C15  C16   180.00   0.0  0
 7GM  Var_01    C6    N5   C4   C3    -45.03  30.0  1
 7GM  Var_02    C2    C6   N5   C4     44.21  30.0  1
 7GM  Var_03    N5    C4   C3   C2     28.34  30.0  1
 7GM  Var_04    C7    C8   C10  C9    108.20  30.0  1
 7GM  Var_05    N5    C7   C8   C9    161.53  30.0  3
 7GM  Var_06    C8    C7   N5   C4    -66.77  30.0  1
 7GM  Var_07    H191  C19  S18  C15  -179.08  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
 7GM  chir_02  C2  C6  C3   O11  negativ
 7GM  chir_03  C8  C9  C10  C7   both

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
 7GM  plan-1  C13  0.020
 7GM  plan-1  C17  0.020
 7GM  plan-1  C14  0.020
 7GM  plan-1  C16  0.020
 7GM  plan-1  C12  0.020
 7GM  plan-1  C15  0.020
 7GM  plan-1  O11  0.020
 7GM  plan-1  S18  0.020
 7GM  plan-1  H13  0.020
 7GM  plan-1  H14  0.020
 7GM  plan-1  H17  0.020
 7GM  plan-1  H16  0.020

