# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:28:22 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: (7R)-7-methyl-2-({[(3R)-1-methylpiperidin-3-yl]methyl}sulfanyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCc2c(C1)sc3nc(SC[C@@H]4CCCN(C)C4)nc(N)c23
#
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
 RNM  RNM  (7R)-7-methyl-2-({[(3R)-1-methylpiperidin-3-yl]methyl}sulfanyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine  ligand  50  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RNM
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
 RNM  N01  N  NH2   0  -0.835  22.3600  -11.4464  37.7206
 RNM  C02  C  CR6   0   0.473  21.1879  -10.9847  37.2731
 RNM  N03  N  N     0  -0.447  20.5993  -10.0335  38.0009
 RNM  C04  C  CR6   0   0.209  19.4350   -9.5556  37.6033
 RNM  S05  S  S2    0   0.036  18.6453   -8.2891  38.5379
 RNM  C06  C  CH2   0  -0.577  19.6721   -8.1015  40.0224
 RNM  C07  C  CH1   0  -0.224  19.1513   -8.8527  41.2412
 RNM  C08  C  CH2   0  -0.426  19.9498   -8.4481  42.4791
 RNM  C09  C  CH2   0  -0.440  19.4761   -9.2301  43.6970
 RNM  C10  C  CH2   0  -0.275  19.5078  -10.7241  43.4208
 RNM  N11  N  NT    0  -0.410  18.7199  -11.0531  42.2475
 RNM  C12  C  CH3   0  -0.517  18.6698  -12.4809  42.0328
 RNM  C13  C  CH2   0  -0.243  19.2106  -10.3656  41.0676
 RNM  N14  N  N     0  -0.459  18.7523   -9.8958  36.5243
 RNM  C15  C  CR56  0  -0.029  19.3471  -10.8381  35.7983
 RNM  C16  C  CR56  0  -0.022  20.5603  -11.4587  36.0929
 RNM  C17  C  CR5   0   0.230  20.9285  -12.4503  35.1156
 RNM  C18  C  CR5   0  -0.273  20.0172  -12.5359  34.1161
 RNM  C19  C  CH2   0  -0.461  20.1057  -13.4341  32.9272
 RNM  C20  C  CH1   0  -0.248  21.5336  -13.9560  32.7539
 RNM  C21  C  CH3   0  -0.660  21.5827  -15.0546  31.7021
 RNM  C22  C  CH2   0  -0.422  22.0709  -14.4372  34.0985
 RNM  C23  C  CH2   0  -0.553  22.1542  -13.3152  35.1305
 RNM  S24  S  S2    0   0.199  18.6729  -11.4480  34.3280
 RNM  H1   H  HNH2  0   0.405  22.7840  -11.0000  38.5163
 RNM  H2   H  HNH2  0   0.426  22.9349  -12.0660  37.1793
 RNM  H3   H  HCH2  0   0.284  20.6913   -8.3972  39.7726
 RNM  H4   H  HCH2  0   0.285  19.6789   -7.0290  40.2251
 RNM  H5   H  HCH1  0   0.227  18.1038   -8.5708  41.4012
 RNM  H6   H  HCH2  0   0.212  21.0124   -8.6551  42.3043
 RNM  H7   H  HCH2  0   0.234  19.8618   -7.3723  42.6520
 RNM  H8   H  HCH2  0   0.231  20.1022   -9.0055  44.5632
 RNM  H9   H  HCH2  0   0.217  18.4550   -8.9321  43.9519
 RNM  H10  H  HCH2  0   0.231  19.1044  -11.2710  44.2768
 RNM  H11  H  HCH2  0   0.180  20.5581  -11.0507  43.3030
 RNM  H13  H  HCH3  0   0.230  18.2662  -12.9801  42.9154
 RNM  H14  H  HCH3  0   0.230  18.0159  -12.7129  41.1905
 RNM  H15  H  HCH3  0   0.188  19.6566  -12.9238  41.8215
 RNM  H16  H  HCH2  0   0.227  18.5960  -10.6677  40.2149
 RNM  H17  H  HCH2  0   0.184  20.2489  -10.6611  40.8271
 RNM  H18  H  HCH2  0   0.256  19.7917  -12.9033  32.0242
 RNM  H19  H  HCH2  0   0.247  19.4124  -14.2763  33.0395
 RNM  H20  H  HCH1  0   0.231  22.1569  -13.1198  32.4146
 RNM  H21  H  HCH3  0   0.232  22.6078  -15.3771  31.5153
 RNM  H22  H  HCH3  0   0.218  21.0121  -15.9290  32.0237
 RNM  H23  H  HCH3  0   0.229  21.1635  -14.7162  30.7531
 RNM  H24  H  HCH2  0   0.226  21.4196  -15.2331  34.4753
 RNM  H25  H  HCH2  0   0.240  23.0616  -14.8799  33.9738
 RNM  H26  H  HCH2  0   0.251  22.2931  -13.7578  36.1210
 RNM  H27  H  HCH2  0   0.252  23.0395  -12.6982  34.9403

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
 RNM  C21  C20  single    1.522  0.020  1.522
 RNM  C20  C19  single    1.530  0.020  1.530
 RNM  C20  C22  single    1.526  0.020  1.526
 RNM  C19  C18  single    1.493  0.020  1.493
 RNM  C18  S24  aromatic  1.742  0.020  1.742
 RNM  C18  C17  aromatic  1.355  0.020  1.355
 RNM  C22  C23  single    1.527  0.020  1.527
 RNM  S24  C15  aromatic  1.729  0.020  1.729
 RNM  C17  C23  single    1.500  0.020  1.500
 RNM  C17  C16  aromatic  1.440  0.020  1.440
 RNM  C15  C16  aromatic  1.394  0.020  1.394
 RNM  C15  N14  aromatic  1.330  0.020  1.330
 RNM  C16  C02  aromatic  1.418  0.020  1.418
 RNM  N14  C04  aromatic  1.321  0.020  1.321
 RNM  C02  N01  single    1.337  0.020  1.337
 RNM  C02  N03  aromatic  1.334  0.020  1.334
 RNM  C04  N03  aromatic  1.320  0.020  1.320
 RNM  C04  S05  single    1.761  0.020  1.761
 RNM  S05  C06  single    1.815  0.020  1.815
 RNM  C06  C07  single    1.523  0.020  1.523
 RNM  C13  C07  single    1.524  0.020  1.524
 RNM  C13  N11  single    1.451  0.020  1.451
 RNM  C12  N11  single    1.445  0.020  1.445
 RNM  C07  C08  single    1.528  0.020  1.528
 RNM  N11  C10  single    1.451  0.020  1.451
 RNM  C08  C09  single    1.523  0.020  1.523
 RNM  C10  C09  single    1.520  0.020  1.520
 RNM  N01  H1   single    0.860  0.020  1.020
 RNM  N01  H2   single    0.860  0.020  1.020
 RNM  C06  H3   single    0.970  0.020  1.090
 RNM  C06  H4   single    0.970  0.020  1.090
 RNM  C07  H5   single    0.970  0.020  1.090
 RNM  C08  H6   single    0.970  0.020  1.090
 RNM  C08  H7   single    0.970  0.020  1.090
 RNM  C09  H8   single    0.970  0.020  1.090
 RNM  C09  H9   single    0.970  0.020  1.090
 RNM  C10  H10  single    0.970  0.020  1.090
 RNM  C10  H11  single    0.970  0.020  1.090
 RNM  C12  H13  single    0.970  0.020  1.090
 RNM  C12  H14  single    0.970  0.020  1.090
 RNM  C12  H15  single    0.970  0.020  1.090
 RNM  C13  H16  single    0.970  0.020  1.090
 RNM  C13  H17  single    0.970  0.020  1.090
 RNM  C19  H18  single    0.970  0.020  1.090
 RNM  C19  H19  single    0.970  0.020  1.090
 RNM  C20  H20  single    0.970  0.020  1.090
 RNM  C21  H21  single    0.970  0.020  1.090
 RNM  C21  H22  single    0.970  0.020  1.090
 RNM  C21  H23  single    0.970  0.020  1.090
 RNM  C22  H24  single    0.970  0.020  1.090
 RNM  C22  H25  single    0.970  0.020  1.090
 RNM  C23  H26  single    0.970  0.020  1.090
 RNM  C23  H27  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
 RNM  H2   N01  H1   117.32  3.000
 RNM  H2   N01  C02  122.34  3.000
 RNM  H1   N01  C02  118.75  3.000
 RNM  C16  C02  N03  119.79  3.000
 RNM  N03  C02  N01  116.76  3.000
 RNM  C16  C02  N01  123.44  3.000
 RNM  C04  N03  C02  118.87  3.000
 RNM  N14  C04  S05  112.76  3.000
 RNM  S05  C04  N03  119.74  3.000
 RNM  N14  C04  N03  127.48  3.000
 RNM  C06  S05  C04  104.76  3.000
 RNM  H4   C06  H3   107.65  3.000
 RNM  H4   C06  C07  109.76  3.000
 RNM  H3   C06  C07  111.66  3.000
 RNM  H4   C06  S05  104.89  3.000
 RNM  H3   C06  S05  108.27  3.000
 RNM  C07  C06  S05  114.21  3.000
 RNM  H5   C07  C13  108.00  3.000
 RNM  H5   C07  C08  108.24  3.000
 RNM  C13  C07  C08  109.57  3.000
 RNM  H5   C07  C06  108.45  3.000
 RNM  C08  C07  C06  109.81  3.000
 RNM  C13  C07  C06  112.65  3.000
 RNM  H7   C08  H6   106.80  3.000
 RNM  H7   C08  C09  110.72  3.000
 RNM  H6   C08  C09  109.38  3.000
 RNM  H7   C08  C07  110.29  3.000
 RNM  H6   C08  C07  109.10  3.000
 RNM  C09  C08  C07  110.45  3.000
 RNM  H9   C09  H8   107.12  3.000
 RNM  H9   C09  C10  109.24  3.000
 RNM  H8   C09  C10  109.54  3.000
 RNM  H9   C09  C08  109.69  3.000
 RNM  H8   C09  C08  110.51  3.000
 RNM  C10  C09  C08  110.67  3.000
 RNM  H11  C10  H10  106.62  3.000
 RNM  H11  C10  N11  111.25  3.000
 RNM  H10  C10  N11  108.63  3.000
 RNM  H11  C10  C09  109.23  3.000
 RNM  H10  C10  C09  109.99  3.000
 RNM  N11  C10  C09  111.01  3.000
 RNM  C13  N11  C12  111.05  3.000
 RNM  C12  N11  C10  111.29  3.000
 RNM  C13  N11  C10  111.50  3.000
 RNM  H15  C12  H14  107.64  3.000
 RNM  H15  C12  H13  107.60  3.000
 RNM  H14  C12  H13  107.78  3.000
 RNM  H15  C12  N11  113.24  3.000
 RNM  H14  C12  N11  110.22  3.000
 RNM  H13  C12  N11  110.17  3.000
 RNM  H17  C13  H16  106.51  3.000
 RNM  H17  C13  N11  111.57  3.000
 RNM  H16  C13  N11  108.25  3.000
 RNM  H17  C13  C07  109.06  3.000
 RNM  H16  C13  C07  109.95  3.000
 RNM  N11  C13  C07  111.38  3.000
 RNM  C15  N14  C04  113.40  3.000
 RNM  S24  C15  C16  111.23  3.000
 RNM  C16  C15  N14  126.10  3.000
 RNM  S24  C15  N14  122.67  3.000
 RNM  C17  C16  C15  112.68  3.000
 RNM  C15  C16  C02  114.34  3.000
 RNM  C17  C16  C02  132.98  3.000
 RNM  C23  C17  C18  121.36  3.000
 RNM  C23  C17  C16  126.80  3.000
 RNM  C18  C17  C16  111.84  3.000
 RNM  S24  C18  C19  121.22  3.000
 RNM  S24  C18  C17  112.94  3.000
 RNM  C19  C18  C17  125.84  3.000
 RNM  H19  C19  H18  106.01  3.000
 RNM  H19  C19  C20  109.85  3.000
 RNM  H18  C19  C20  109.88  3.000
 RNM  H19  C19  C18  110.06  3.000
 RNM  H18  C19  C18  110.40  3.000
 RNM  C20  C19  C18  110.54  3.000
 RNM  H20  C20  C22  108.23  3.000
 RNM  H20  C20  C21  108.56  3.000
 RNM  C22  C20  C21  111.72  3.000
 RNM  H20  C20  C19  107.78  3.000
 RNM  C22  C20  C19  109.66  3.000
 RNM  C21  C20  C19  110.77  3.000
 RNM  H23  C21  H22  107.67  3.000
 RNM  H23  C21  H21  107.68  3.000
 RNM  H22  C21  H21  107.74  3.000
 RNM  H23  C21  C20  111.40  3.000
 RNM  H22  C21  C20  110.94  3.000
 RNM  H21  C21  C20  111.23  3.000
 RNM  H25  C22  H24  106.51  3.000
 RNM  H25  C22  C23  109.00  3.000
 RNM  H24  C22  C23  109.50  3.000
 RNM  H25  C22  C20  110.28  3.000
 RNM  H24  C22  C20  108.84  3.000
 RNM  C23  C22  C20  112.53  3.000
 RNM  H27  C23  H26  106.41  3.000
 RNM  H27  C23  C22  109.91  3.000
 RNM  H26  C23  C22  108.76  3.000
 RNM  H27  C23  C17  109.50  3.000
 RNM  H26  C23  C17  110.25  3.000
 RNM  C22  C23  C17  111.86  3.000
 RNM  C18  S24  C15   91.31  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
 RNM  CONST_01  C18  C17  C16  C02  180.00   0.0  0
 RNM  CONST_02  S24  C15  C16  C02  180.00   0.0  0
 RNM  CONST_03  N14  C15  C16  C02    0.00   0.0  0
 RNM  CONST_04  N14  C04  N03  C02    0.00   0.0  0
 RNM  CONST_05  C17  C16  C02  N03  180.00   0.0  0
 RNM  CONST_06  C15  C16  C02  N03    0.00   0.0  0
 RNM  CONST_07  C15  N14  C04  N03    0.00   0.0  0
 RNM  CONST_08  S24  C15  N14  C04  180.00   0.0  0
 RNM  CONST_09  C16  C15  N14  C04    0.00   0.0  0
 RNM  CONST_10  C16  C02  N03  C04    0.00   0.0  0
 RNM  CONST_11  C18  S24  C15  N14  180.00   0.0  0
 RNM  CONST_12  C17  C16  C15  N14  180.00   0.0  0
 RNM  CONST_13  C17  C18  S24  C15    0.00   0.0  0
 RNM  CONST_14  C18  C17  C16  C15    0.00   0.0  0
 RNM  CONST_15  S24  C18  C17  C16    0.00   0.0  0
 RNM  CONST_16  C18  S24  C15  C16    0.00   0.0  0
 RNM  CONST_17  S24  C15  C16  C17    0.00   0.0  0
 RNM  CONST_18  C17  C16  C02  N01    0.00   0.0  0
 RNM  CONST_19  C15  C16  C02  N01  180.00   0.0  0
 RNM  CONST_20  C04  N03  C02  N01  180.00   0.0  0
 RNM  CONST_21  S05  C04  N03  C02  180.00   0.0  0
 RNM  CONST_22  C15  N14  C04  S05  180.00   0.0  0
 RNM  CONST_23  H1   N01  C02  N03    0.00   0.0  0
 RNM  CONST_24  H2   N01  C02  N03  180.00   0.0  0
 RNM  Var_01    C10  N11  C13  C07  -60.27  30.0  1
 RNM  Var_02    C10  C09  C08  C07   53.60  30.0  1
 RNM  Var_03    N11  C10  C09  C08  -56.04  30.0  1
 RNM  Var_04    C13  N11  C10  C09   59.38  30.0  1
 RNM  Var_05    C22  C23  C17  C16  168.32  30.0  1
 RNM  Var_06    C20  C19  C18  C17  -16.51  30.0  1
 RNM  Var_07    C20  C22  C23  C17   43.58  30.0  1
 RNM  Var_08    C07  C06  S05  C04  -97.74  30.0  3
 RNM  Var_09    N14  C04  S05  C06  175.03  30.0  1
 RNM  Var_10    H13  C12  N11  C10   57.14  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
 RNM  chir_01  C07  C06  C13  C08  negativ
 RNM  chir_02  C20  C21  C19  C22  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
 RNM  plan-1  N01  0.020
 RNM  plan-1  C02  0.020
 RNM  plan-1  N03  0.020
 RNM  plan-1  C04  0.020
 RNM  plan-1  S05  0.020
 RNM  plan-1  N14  0.020
 RNM  plan-1  C15  0.020
 RNM  plan-1  C16  0.020
 RNM  plan-1  C17  0.020
 RNM  plan-1  C18  0.020
 RNM  plan-1  C19  0.020
 RNM  plan-1  C23  0.020
 RNM  plan-1  S24  0.020
 RNM  plan-2  N01  0.020
 RNM  plan-2  C02  0.020
 RNM  plan-2  H1   0.020
 RNM  plan-2  H2   0.020

