# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:27:19 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-methyl-2-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](C[C@@H](C1)c2ccccc2)NC3=NC4=C(CCC4)C(=O)N3C
#
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
 JC3  JC3  "3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-one"
  ligand  51  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JC3
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
 JC3  C13   C  CH2   0  -0.463  50.8969  -26.3568  -14.1709
 JC3  C15   C  CR56  0  -0.170  52.4519  -28.1268  -13.9358
 JC3  C20   C  CR6   0   0.190  54.8973  -30.1838   -5.8037
 JC3  C21   C  CR16  0  -0.319  55.3768  -31.4901   -5.7046
 JC3  C22   C  CR16  0  -0.236  56.3097  -31.8355   -4.7369
 JC3  C24   C  CR16  0  -0.235  56.3097  -29.5769   -3.9315
 JC3  C3    C  CH2   0  -0.243  52.5293  -30.4757   -6.5718
 JC3  C4    C  CH1   0  -0.362  53.8738  -29.7983   -6.8411
 JC3  C5    C  CH2   0  -0.427  54.3381  -30.1042   -8.2660
 JC3  C6    C  CH1   0  -0.077  53.2475  -29.7267   -9.2587
 JC3  C7    C  CH2   0  -0.260  51.9325  -30.4084   -8.8892
 JC3  C9    C  CR6   0   0.776  53.2305  -29.4363  -11.6974
 JC3  C11   C  CR56  0   0.254  52.1296  -27.7329  -12.6738
 JC3  C12   C  CH2   0  -0.501  51.3276  -26.4663  -12.6983
 JC3  C14   C  CH2   0  -0.474  51.9143  -27.1941  -14.9762
 JC3  C16   C  CR6   0   0.535  53.2506  -29.2832  -14.1278
 JC3  C23   C  CR16  0  -0.272  56.7804  -30.8795   -3.8455
 JC3  C25   C  CR16  0  -0.333  55.3759  -29.2363   -4.9021
 JC3  N2    N  NT    0  -0.415  51.5371  -30.0600   -7.5423
 JC3  N8    N  NH1   0  -0.704  53.6559  -30.0884  -10.6018
 JC3  N10   N  N     0  -0.532  52.4946  -28.3574  -11.5460
 JC3  N18   N  NR6   0  -0.581  53.6094  -29.9244  -12.9195
 JC3  O17   O  O     0  -0.484  53.6240  -29.7334  -15.2037
 JC3  H131  H  HCH2  0   0.236  50.8409  -25.3247  -14.5142
 JC3  H132  H  HCH2  0   0.239  49.9024  -26.7903  -14.2883
 JC3  H221  H  HCR6  0   0.251  56.6701  -32.8548   -4.6784
 JC3  H241  H  HCR6  0   0.251  56.6687  -28.8224   -3.2430
 JC3  H012  H  HCH3  0   0.233  49.9339  -30.2697   -6.2207
 JC3  H013  H  HCH3  0   0.233  49.4885  -30.1897   -7.9247
 JC3  H011  H  HCH3  0   0.192  50.1755  -31.6807   -7.2627
 JC3  H031  H  HCH2  0   0.241  52.1777  -30.2009   -5.5738
 JC3  H032  H  HCH2  0   0.191  52.6655  -31.5727   -6.5714
 JC3  H041  H  HCH1  0   0.248  53.7105  -28.7179   -6.7661
 JC3  H051  H  HCH2  0   0.228  54.5611  -31.1731   -8.3636
 JC3  H052  H  HCH2  0   0.254  55.2581  -29.5604   -8.4922
 JC3  H061  H  HCH1  0   0.255  53.0996  -28.6467   -9.2301
 JC3  H071  H  HCH2  0   0.241  51.1522  -30.0866   -9.5832
 JC3  H072  H  HCH2  0   0.188  52.0510  -31.5005   -9.0162
 JC3  H121  H  HCH2  0   0.254  51.9654  -25.6300  -12.3941
 JC3  H122  H  HCH2  0   0.252  50.4868  -26.4894  -12.0031
 JC3  H142  H  HCH2  0   0.237  51.4452  -27.7085  -15.8168
 JC3  H141  H  HCH2  0   0.235  52.7077  -26.5676  -15.3966
 JC3  H231  H  HCR6  0   0.251  57.5088  -31.1481   -3.0913
 JC3  H251  H  HCR6  0   0.246  55.0143  -28.2160   -4.9615
 JC3  H081  H  HNH1  0   0.420  54.1252  -30.9740  -10.6984
 JC3  C19   C  CH3   0  -0.589  54.4155  -31.1328  -12.9979
 JC3  H211  H  HCR6  0   0.247  55.0214  -32.2518   -6.3885
 JC3  C1    C  CH3   0  -0.517  50.2272  -30.5816   -7.2240
 JC3  H193  H  HCH3  0   0.263  55.3709  -30.9981  -12.4900
 JC3  H191  H  HCH3  0   0.263  53.8884  -31.9817  -12.5613
 JC3  H192  H  HCH3  0   0.290  54.6104  -31.3534  -14.0400

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
 JC3  O17  C16   double    1.225  0.020  1.225
 JC3  C14  C13   single    1.544  0.020  1.544
 JC3  C14  C15   single    1.497  0.020  1.497
 JC3  C16  C15   single    1.419  0.020  1.419
 JC3  C16  N18   single    1.414  0.020  1.414
 JC3  C13  C12   single    1.538  0.020  1.538
 JC3  C15  C11   double    1.361  0.020  1.361
 JC3  C19  N18   single    1.455  0.020  1.455
 JC3  N18  C9    single    1.369  0.020  1.369
 JC3  C12  C11   single    1.499  0.020  1.499
 JC3  C11  N10   single    1.340  0.020  1.340
 JC3  C9   N10   double    1.315  0.020  1.315
 JC3  C9   N8    single    1.344  0.020  1.344
 JC3  N8   C6    single    1.450  0.020  1.450
 JC3  C6   C7    single    1.527  0.020  1.527
 JC3  C6   C5    single    1.522  0.020  1.522
 JC3  C7   N2    single    1.446  0.020  1.446
 JC3  C5   C4    single    1.530  0.020  1.530
 JC3  N2   C1    single    1.445  0.020  1.445
 JC3  N2   C3    single    1.449  0.020  1.449
 JC3  C4   C3    single    1.529  0.020  1.529
 JC3  C4   C20   single    1.507  0.020  1.507
 JC3  C20  C21   aromatic  1.395  0.020  1.395
 JC3  C20  C25   aromatic  1.393  0.020  1.393
 JC3  C21  C22   aromatic  1.388  0.020  1.388
 JC3  C25  C24   aromatic  1.389  0.020  1.389
 JC3  C22  C23   aromatic  1.389  0.020  1.389
 JC3  C24  C23   aromatic  1.388  0.020  1.388
 JC3  C13  H131  single    0.970  0.020  1.090
 JC3  C13  H132  single    0.970  0.020  1.090
 JC3  C21  H211  single    0.930  0.020  1.080
 JC3  C22  H221  single    0.930  0.020  1.080
 JC3  C24  H241  single    0.930  0.020  1.080
 JC3  C1   H012  single    0.970  0.020  1.090
 JC3  C1   H013  single    0.970  0.020  1.090
 JC3  C1   H011  single    0.970  0.020  1.090
 JC3  C3   H031  single    0.970  0.020  1.090
 JC3  C3   H032  single    0.970  0.020  1.090
 JC3  C4   H041  single    0.970  0.020  1.090
 JC3  C5   H051  single    0.970  0.020  1.090
 JC3  C5   H052  single    0.970  0.020  1.090
 JC3  C6   H061  single    0.970  0.020  1.090
 JC3  C7   H071  single    0.970  0.020  1.090
 JC3  C7   H072  single    0.970  0.020  1.090
 JC3  C12  H121  single    0.970  0.020  1.090
 JC3  C12  H122  single    0.970  0.020  1.090
 JC3  C14  H142  single    0.970  0.020  1.090
 JC3  C14  H141  single    0.970  0.020  1.090
 JC3  C19  H193  single    0.970  0.020  1.090
 JC3  C19  H191  single    0.970  0.020  1.090
 JC3  C19  H192  single    0.970  0.020  1.090
 JC3  C23  H231  single    0.930  0.020  1.080
 JC3  C25  H251  single    0.930  0.020  1.080
 JC3  N8   H081  single    0.860  0.020  1.020

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
 JC3  H132  C13  H131  107.20  3.000
 JC3  H132  C13  C14   109.21  3.000
 JC3  H131  C13  C14   112.54  3.000
 JC3  H132  C13  C12   109.26  3.000
 JC3  H131  C13  C12   112.56  3.000
 JC3  C14   C13  C12   106.03  3.000
 JC3  C16   C15  C14   128.03  3.000
 JC3  C16   C15  C11   119.66  3.000
 JC3  C14   C15  C11   112.28  3.000
 JC3  C25   C20  C4    120.32  3.000
 JC3  C25   C20  C21   118.22  3.000
 JC3  C4    C20  C21   121.45  3.000
 JC3  H211  C21  C22   119.05  3.000
 JC3  H211  C21  C20   120.04  3.000
 JC3  C22   C21  C20   120.91  3.000
 JC3  H221  C22  C23   120.02  3.000
 JC3  H221  C22  C21   119.72  3.000
 JC3  C23   C22  C21   120.25  3.000
 JC3  H241  C24  C25   119.75  3.000
 JC3  H241  C24  C23   120.15  3.000
 JC3  C25   C24  C23   120.10  3.000
 JC3  H032  C3   H031  106.79  3.000
 JC3  H032  C3   N2    111.67  3.000
 JC3  H031  C3   N2    108.61  3.000
 JC3  H032  C3   C4    109.34  3.000
 JC3  H031  C3   C4    109.40  3.000
 JC3  N2    C3   C4    110.91  3.000
 JC3  H041  C4   C5    107.84  3.000
 JC3  H041  C4   C3    107.08  3.000
 JC3  C5    C4   C3    110.02  3.000
 JC3  H041  C4   C20   107.84  3.000
 JC3  C3    C4   C20   111.25  3.000
 JC3  C5    C4   C20   112.57  3.000
 JC3  H052  C5   H051  107.20  3.000
 JC3  H052  C5   C6    110.17  3.000
 JC3  H051  C5   C6    109.24  3.000
 JC3  H052  C5   C4    110.42  3.000
 JC3  H051  C5   C4    109.86  3.000
 JC3  C6    C5   C4    109.90  3.000
 JC3  H061  C6   N8    108.04  3.000
 JC3  H061  C6   C7    108.61  3.000
 JC3  N8    C6   C7    110.82  3.000
 JC3  H061  C6   C5    109.00  3.000
 JC3  C7    C6   C5    110.40  3.000
 JC3  N8    C6   C5    109.90  3.000
 JC3  H072  C7   H071  107.13  3.000
 JC3  H072  C7   N2    111.97  3.000
 JC3  H071  C7   N2    108.98  3.000
 JC3  H072  C7   C6    108.72  3.000
 JC3  H071  C7   C6    109.26  3.000
 JC3  N2    C7   C6    110.69  3.000
 JC3  N18   C9   N10   123.38  3.000
 JC3  N10   C9   N8    118.78  3.000
 JC3  N18   C9   N8    117.83  3.000
 JC3  N10   C11  C12   123.59  3.000
 JC3  N10   C11  C15   125.53  3.000
 JC3  C12   C11  C15   110.86  3.000
 JC3  H122  C12  H121  106.73  3.000
 JC3  H122  C12  C11   112.58  3.000
 JC3  H121  C12  C11   109.22  3.000
 JC3  H122  C12  C13   113.31  3.000
 JC3  H121  C12  C13   112.01  3.000
 JC3  C11   C12  C13   103.04  3.000
 JC3  H141  C14  H142  106.58  3.000
 JC3  H141  C14  C15   111.29  3.000
 JC3  H142  C14  C15   113.32  3.000
 JC3  H141  C14  C13   111.56  3.000
 JC3  H142  C14  C13   111.96  3.000
 JC3  C15   C14  C13   102.24  3.000
 JC3  O17   C16  N18   120.44  3.000
 JC3  N18   C16  C15   113.38  3.000
 JC3  O17   C16  C15   126.18  3.000
 JC3  H231  C23  C24   120.30  3.000
 JC3  H231  C23  C22   120.28  3.000
 JC3  C24   C23  C22   119.42  3.000
 JC3  H251  C25  C24   119.56  3.000
 JC3  H251  C25  C20   119.35  3.000
 JC3  C24   C25  C20   121.09  3.000
 JC3  C7    N2   C3    111.56  3.000
 JC3  C3    N2   C1    111.69  3.000
 JC3  C7    N2   C1    111.46  3.000
 JC3  H081  N8   C9    119.74  3.000
 JC3  H081  N8   C6    116.09  3.000
 JC3  C9    N8   C6    123.02  3.000
 JC3  C11   N10  C9    115.98  3.000
 JC3  C19   N18  C16   118.11  3.000
 JC3  C19   N18  C9    119.83  3.000
 JC3  C16   N18  C9    122.05  3.000
 JC3  H192  C19  H191  108.28  3.000
 JC3  H192  C19  H193  108.40  3.000
 JC3  H191  C19  H193  109.46  3.000
 JC3  H192  C19  N18   108.71  3.000
 JC3  H191  C19  N18   110.93  3.000
 JC3  H193  C19  N18   110.97  3.000
 JC3  H011  C1   H013  107.72  3.000
 JC3  H011  C1   H012  107.76  3.000
 JC3  H013  C1   H012  107.82  3.000
 JC3  H011  C1   N2    113.27  3.000
 JC3  H013  C1   N2    110.03  3.000
 JC3  H012  C1   N2    110.06  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
 JC3  CONST_01  C23   C22  C21  C20     0.00   0.0  0
 JC3  CONST_02  C23   C24  C25  C20     0.00   0.0  0
 JC3  CONST_03  C24   C25  C20  C21     0.00   0.0  0
 JC3  CONST_04  C24   C23  C22  C21     0.00   0.0  0
 JC3  CONST_05  C25   C20  C21  C22     0.00   0.0  0
 JC3  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 JC3  CONST_07  C4    C20  C21  C22   180.00   0.0  0
 JC3  CONST_08  C4    C20  C25  C24   180.00   0.0  0
 JC3  CONST_09  C9    N18  C16  C15     0.00   0.0  0
 JC3  CONST_10  N18   C9   N10  C11     0.00   0.0  0
 JC3  CONST_11  N10   C9   N18  C16     0.00   0.0  0
 JC3  CONST_12  C19   N18  C16  C15   180.00   0.0  0
 JC3  CONST_13  N18   C9   N8   C6    180.00   0.0  0
 JC3  CONST_14  N10   C9   N8   C6      0.00   0.0  0
 JC3  CONST_15  O17   C16  N18  C9    180.00   0.0  0
 JC3  CONST_16  N8    C9   N10  C11   180.00   0.0  0
 JC3  CONST_17  N8    C9   N18  C16   180.00   0.0  0
 JC3  CONST_18  N10   C9   N18  C19   180.00   0.0  0
 JC3  CONST_19  H221  C22  C21  C20   180.00   0.0  0
 JC3  CONST_20  H241  C24  C25  C20   180.00   0.0  0
 JC3  CONST_21  H251  C25  C20  C21   180.00   0.0  0
 JC3  CONST_22  H231  C23  C22  C21   180.00   0.0  0
 JC3  CONST_23  H241  C24  C23  C22   180.00   0.0  0
 JC3  CONST_24  H221  C22  C23  C24   180.00   0.0  0
 JC3  CONST_25  H211  C21  C20  C4      0.00   0.0  0
 JC3  CONST_26  H251  C25  C20  C4      0.00   0.0  0
 JC3  CONST_27  H211  C21  C22  C23   180.00   0.0  0
 JC3  CONST_28  H251  C25  C24  C23   180.00   0.0  0
 JC3  CONST_29  H211  C21  C20  C25   180.00   0.0  0
 JC3  CONST_30  H231  C23  C24  C25   180.00   0.0  0
 JC3  CONST_31  O17   C16  N18  C19     0.00   0.0  0
 JC3  CONST_32  N8    C9   N18  C19     0.00   0.0  0
 JC3  CONST_33  H081  N8   C9   N10   180.00   0.0  0
 JC3  CONST_34  H081  N8   C9   N18     0.00   0.0  0
 JC3  Var_01    C16   C15  C14  C13   168.00  30.0  1
 JC3  Var_02    C11   C15  C14  C13   -14.12  30.0  1
 JC3  Var_03    C15   C11  C12  C13    14.53  30.0  1
 JC3  Var_04    N10   C11  C12  C13  -166.93  30.0  1
 JC3  Var_05    C12   C13  C14  C15    22.35  30.0  1
 JC3  Var_06    C6    C7   N2   C3    -60.43  30.0  1
 JC3  Var_07    C7    N2   C3   C4     60.43  30.0  1
 JC3  Var_08    C12   C11  N10  C9   -178.03  30.0  1
 JC3  Var_09    C14   C13  C12  C11   -22.64  30.0  1
 JC3  Var_10    C14   C15  C11  C12    -0.20  30.0  1
 JC3  Var_11    C16   C15  C11  C12   177.87  30.0  1
 JC3  Var_12    N18   C16  C15  C14   178.79  30.0  1
 JC3  Var_13    N10   C11  C15  C14  -178.70  30.0  1
 JC3  Var_14    C6    C7   N2   C1    173.96  30.0  1
 JC3  Var_15    C4    C3   N2   C1   -174.09  30.0  1
 JC3  Var_16    O17   C16  C15  C14    -1.29  30.0  1
 JC3  Var_17    H131  C13  C14  C15   145.81  30.0  1
 JC3  Var_18    H132  C13  C14  C15   -95.27  30.0  1
 JC3  Var_19    H121  C12  C11  C15  -104.68  30.0  1
 JC3  Var_20    H122  C12  C11  C15   136.95  30.0  1
 JC3  Var_21    H071  C7   N2   C3    179.39  30.0  1
 JC3  Var_22    H072  C7   N2   C3     61.06  30.0  1
 JC3  Var_23    H031  C3   N2   C7   -179.31  30.0  1
 JC3  Var_24    H032  C3   N2   C7    -61.81  30.0  1
 JC3  Var_25    H142  C14  C15  C11  -134.81  30.0  1
 JC3  Var_26    H141  C14  C15  C11   105.09  30.0  1
 JC3  Var_27    H131  C13  C12  C11  -146.09  30.0  1
 JC3  Var_28    H132  C13  C12  C11    94.94  30.0  1
 JC3  Var_29    H142  C14  C13  C12   143.97  30.0  1
 JC3  Var_30    H141  C14  C13  C12   -96.68  30.0  1
 JC3  Var_31    H121  C12  C13  C14    94.62  30.0  1
 JC3  Var_32    H122  C12  C13  C14  -144.56  30.0  1
 JC3  Var_33    H142  C14  C15  C16    47.32  30.0  1
 JC3  Var_34    H141  C14  C15  C16   -72.78  30.0  1
 JC3  Var_35    H121  C12  C11  N10    73.86  30.0  1
 JC3  Var_36    H122  C12  C11  N10   -44.51  30.0  1
 JC3  Var_37    H071  C7   N2   C1     53.78  30.0  1
 JC3  Var_38    H072  C7   N2   C1    -64.55  30.0  1
 JC3  Var_39    H031  C3   N2   C1    -53.83  30.0  1
 JC3  Var_40    H032  C3   N2   C1     63.67  30.0  1
 JC3  Var_41    H012  C1   N2   C3     56.90  30.0  3
 JC3  Var_42    H013  C1   N2   C3    175.57  30.0  3
 JC3  Var_43    H011  C1   N2   C3    -63.81  30.0  3
 JC3  Var_44    H012  C1   N2   C7   -177.56  30.0  3
 JC3  Var_45    H013  C1   N2   C7    -58.89  30.0  3
 JC3  Var_46    H011  C1   N2   C7     61.74  30.0  3
 JC3  Var_47    H193  C19  N18  C9    -60.79  30.0  3
 JC3  Var_48    H191  C19  N18  C9     61.12  30.0  3
 JC3  Var_49    H192  C19  N18  C9   -179.92  30.0  3
 JC3  Var_50    H193  C19  N18  C16   118.71  30.0  3
 JC3  Var_51    H191  C19  N18  C16  -119.37  30.0  3
 JC3  Var_52    H192  C19  N18  C16    -0.42  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
 JC3  chir_01  C4  C5  C3  C20  negativ
 JC3  chir_02  C6  N8  C5  C7   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
 JC3  plan-1  C20   0.020
 JC3  plan-1  C21   0.020
 JC3  plan-1  C22   0.020
 JC3  plan-1  C24   0.020
 JC3  plan-1  C4    0.020
 JC3  plan-1  C23   0.020
 JC3  plan-1  C25   0.020
 JC3  plan-1  H221  0.020
 JC3  plan-1  H241  0.020
 JC3  plan-1  H231  0.020
 JC3  plan-1  H251  0.020
 JC3  plan-1  H211  0.020
 JC3  plan-2  C15   0.020
 JC3  plan-2  C6    0.020
 JC3  plan-2  C9    0.020
 JC3  plan-2  C11   0.020
 JC3  plan-2  C16   0.020
 JC3  plan-2  N8    0.020
 JC3  plan-2  N10   0.020
 JC3  plan-2  N18   0.020
 JC3  plan-2  O17   0.020
 JC3  plan-2  H081  0.020
 JC3  plan-2  C19   0.020

