# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:09:44 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-(dibenzo[b,f]oxepin-10-ylmethyl)-N-methylprop-2-yn-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC#C)CC1=Cc2ccccc2Oc3ccccc13
#
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
 DB0  DB0  N-(dibenzo[b,f]oxepin-10-ylmethyl)-N-methylprop-2-yn-1-amine  ligand  38  21  .  2021-08-08  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DB0
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
 DB0  CAL   C  CR6    0   0.040   0.2090   1.5877  -0.5491
 DB0  CAM   C  CR16   0  -0.336  -0.1971   2.5366  -1.4939
 DB0  CAN   C  CR16   0  -0.240   0.5165   3.7059  -1.7005
 DB0  CAU   C  CR16   0  -0.267   1.6590   3.9628  -0.9550
 DB0  CAT   C  CR16   0  -0.311   2.0840   3.0409  -0.0106
 DB0  CAS   C  CR6    0   0.275   1.3590   1.8770   0.1902
 DB0  OAR   O  O2     0  -0.531   1.7686   1.0248   1.1866
 DB0  CAQ   C  CR6    0   0.276   2.2812  -0.1680   0.7376
 DB0  CAP   C  CR16   0  -0.314   3.6260  -0.4346   0.9357
 DB0  CAO   C  CR16   0  -0.268   4.1390  -1.6709   0.5690
 DB0  CAH   C  CR16   0  -0.246   3.3042  -2.6285   0.0057
 DB0  CAI   C  CR16   0  -0.329   1.9617  -2.3469  -0.1879
 DB0  CAJ   C  CR6    0   0.102   1.4243  -1.1038   0.1582
 DB0  CAK   C  C1     0  -0.307   0.0079  -0.8324  -0.0519
 DB0  CAG   C  C      0   0.068  -0.5570   0.3484  -0.3481
 DB0  CAF   C  CH2    0  -0.316  -2.0454   0.4341  -0.6203
 DB0  NAB   N  NT    -1  -0.423  -2.7971  -0.6662  -0.0560
 DB0  CAA   C  CH3    0  -0.536  -2.9966  -0.4992   1.3712
 DB0  CAC   C  CH2    0  -0.408  -4.0548  -0.8586  -0.7564
 DB0  CAD   C  CSP    0   0.279  -4.7138  -2.1049  -0.3720
 DB0  CAE   C  CSP1   0  -0.555  -5.2621  -3.1291  -0.0645
 DB0  HAM   H  HCR6   0   0.262  -1.0807   2.3568  -2.0923
 DB0  HAN   H  HCR6   0   0.261   0.1761   4.4177  -2.4407
 DB0  HAU   H  HCR6   0   0.264   2.2179   4.8768  -1.1051
 DB0  HAT   H  HCR6   0   0.267   2.9674   3.2274   0.5869
 DB0  HAP   H  HCR6   0   0.267   4.2590   0.3146   1.3940
 DB0  HAO   H  HCR6   0   0.263   5.1869  -1.8860   0.7305
 DB0  HAH   H  HCR6   0   0.260   3.6974  -3.5961  -0.2764
 DB0  HAI   H  HCR6   0   0.258   1.3113  -3.0977  -0.6205
 DB0  HAK   H  H      0   0.257  -0.6470  -1.6962  -0.0200
 DB0  HAF1  H  HCH2   0   0.263  -2.1954   0.4352  -1.7047
 DB0  HAF2  H  HCH2   0   0.228  -2.4210   1.4082  -0.2669
 DB0  HAA1  H  HCH3   0   0.246  -2.0408  -0.3237   1.8623
 DB0  HAA2  H  HCH3   0   0.206  -3.6608   0.3457   1.6073
 DB0  HAA3  H  HCH3   0   0.244  -3.4282  -1.4007   1.8054
 DB0  HAC1  H  HCH2   0   0.241  -4.7585  -0.0257  -0.5960
 DB0  HAC2  H  HCH2   0   0.282  -3.8593  -0.8922  -1.8312
 DB0  HAE   H  H      0   0.279  -5.7465  -4.0366   0.2148

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
 DB0  CAL  CAM   aromatic  1.399  0.020  1.399
 DB0  CAL  CAS   aromatic  1.397  0.020  1.397
 DB0  CAL  CAG   single    1.471  0.020  1.471
 DB0  CAM  CAN   aromatic  1.385  0.020  1.385
 DB0  CAM  HAM   single    0.929  0.020  1.085
 DB0  CAN  CAU   aromatic  1.388  0.020  1.388
 DB0  CAN  HAN   single    0.929  0.020  1.085
 DB0  CAU  CAT   aromatic  1.386  0.020  1.386
 DB0  CAU  HAU   single    0.929  0.020  1.085
 DB0  CAT  CAS   aromatic  1.386  0.020  1.386
 DB0  CAT  HAT   single    0.929  0.020  1.085
 DB0  CAS  OAR   single    1.374  0.020  1.374
 DB0  OAR  CAQ   single    1.374  0.020  1.374
 DB0  CAQ  CAP   aromatic  1.385  0.020  1.385
 DB0  CAQ  CAJ   aromatic  1.395  0.020  1.395
 DB0  CAP  CAO   aromatic  1.388  0.020  1.388
 DB0  CAP  HAP   single    0.929  0.020  1.085
 DB0  CAO  CAH   aromatic  1.390  0.020  1.390
 DB0  CAO  HAO   single    0.929  0.020  1.085
 DB0  CAH  CAI   aromatic  1.385  0.020  1.385
 DB0  CAH  HAH   single    0.929  0.020  1.085
 DB0  CAI  CAJ   aromatic  1.398  0.020  1.398
 DB0  CAI  HAI   single    0.929  0.020  1.085
 DB0  CAJ  CAK   single    1.457  0.020  1.457
 DB0  CAK  CAG   double    1.342  0.020  1.342
 DB0  CAK  HAK   single    0.930  0.020  1.086
 DB0  CAG  CAF   single    1.515  0.020  1.515
 DB0  CAF  NAB   single    1.447  0.020  1.447
 DB0  CAF  HAF1  single    0.939  0.020  1.096
 DB0  CAF  HAF2  single    0.939  0.020  1.096
 DB0  NAB  CAA   single    1.451  0.020  1.451
 DB0  NAB  CAC   single    1.452  0.020  1.452
 DB0  CAA  HAA1  single    0.939  0.020  1.096
 DB0  CAA  HAA2  single    0.939  0.020  1.096
 DB0  CAA  HAA3  single    0.939  0.020  1.096
 DB0  CAC  CAD   single    1.461  0.020  1.461
 DB0  CAC  HAC1  single    0.939  0.020  1.096
 DB0  CAC  HAC2  single    0.939  0.020  1.096
 DB0  CAD  CAE   triple    1.202  0.020  1.202
 DB0  CAE  HAE   single    0.913  0.020  1.066

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
 DB0  CAG   CAL  CAS   122.06  3.000
 DB0  CAG   CAL  CAM   120.83  3.000
 DB0  CAS   CAL  CAM   117.11  3.000
 DB0  HAM   CAM  CAN   118.58  3.000
 DB0  HAM   CAM  CAL   119.84  3.000
 DB0  CAN   CAM  CAL   121.58  3.000
 DB0  HAN   CAN  CAU   120.31  3.000
 DB0  HAN   CAN  CAM   119.69  3.000
 DB0  CAU   CAN  CAM   120.00  3.000
 DB0  HAU   CAU  CAT   119.86  3.000
 DB0  HAU   CAU  CAN   120.46  3.000
 DB0  CAT   CAU  CAN   119.67  3.000
 DB0  HAT   CAT  CAS   119.44  3.000
 DB0  HAT   CAT  CAU   120.76  3.000
 DB0  CAS   CAT  CAU   119.79  3.000
 DB0  OAR   CAS  CAT   118.05  3.000
 DB0  OAR   CAS  CAL   120.05  3.000
 DB0  CAT   CAS  CAL   121.85  3.000
 DB0  CAQ   OAR  CAS   114.38  3.000
 DB0  CAJ   CAQ  CAP   121.78  3.000
 DB0  CAJ   CAQ  OAR   119.28  3.000
 DB0  CAP   CAQ  OAR   118.86  3.000
 DB0  HAP   CAP  CAO   120.81  3.000
 DB0  HAP   CAP  CAQ   119.67  3.000
 DB0  CAO   CAP  CAQ   119.50  3.000
 DB0  HAO   CAO  CAH   120.36  3.000
 DB0  HAO   CAO  CAP   119.72  3.000
 DB0  CAH   CAO  CAP   119.93  3.000
 DB0  HAH   CAH  CAI   119.84  3.000
 DB0  HAH   CAH  CAO   120.24  3.000
 DB0  CAI   CAH  CAO   119.92  3.000
 DB0  HAI   CAI  CAJ   118.97  3.000
 DB0  HAI   CAI  CAH   119.78  3.000
 DB0  CAJ   CAI  CAH   121.25  3.000
 DB0  CAK   CAJ  CAI   120.24  3.000
 DB0  CAK   CAJ  CAQ   122.14  3.000
 DB0  CAI   CAJ  CAQ   117.60  3.000
 DB0  HAK   CAK  CAG   116.94  3.000
 DB0  HAK   CAK  CAJ   115.74  3.000
 DB0  CAG   CAK  CAJ   127.22  3.000
 DB0  CAF   CAG  CAK   120.19  3.000
 DB0  CAF   CAG  CAL   116.06  3.000
 DB0  CAK   CAG  CAL   123.53  3.000
 DB0  HAF2  CAF  HAF1  105.67  3.000
 DB0  HAF2  CAF  NAB   111.71  3.000
 DB0  HAF1  CAF  NAB   108.41  3.000
 DB0  HAF2  CAF  CAG   109.09  3.000
 DB0  HAF1  CAF  CAG   108.21  3.000
 DB0  NAB   CAF  CAG   113.40  3.000
 DB0  CAC   NAB  CAA   111.75  3.000
 DB0  CAC   NAB  CAF   111.26  3.000
 DB0  CAA   NAB  CAF   111.56  3.000
 DB0  HAA3  CAA  HAA2  108.10  3.000
 DB0  HAA3  CAA  HAA1  107.53  3.000
 DB0  HAA2  CAA  HAA1  108.02  3.000
 DB0  HAA3  CAA  NAB   110.56  3.000
 DB0  HAA2  CAA  NAB   112.49  3.000
 DB0  HAA1  CAA  NAB   109.97  3.000
 DB0  HAC2  CAC  HAC1  106.29  3.000
 DB0  HAC2  CAC  CAD   108.25  3.000
 DB0  HAC1  CAC  CAD   108.56  3.000
 DB0  HAC2  CAC  NAB   108.87  3.000
 DB0  HAC1  CAC  NAB   112.50  3.000
 DB0  CAD   CAC  NAB   112.13  3.000
 DB0  CAE   CAD  CAC   180.00  3.000
 DB0  HAE   CAE  CAD   180.00  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
 DB0  CONST_01  CAU   CAN  CAM  CAL     0.00   0.0  0
 DB0  CONST_02  CAU   CAT  CAS  CAL     0.00   0.0  0
 DB0  CONST_03  CAT   CAS  CAL  CAM     0.00   0.0  0
 DB0  CONST_04  CAT   CAU  CAN  CAM     0.00   0.0  0
 DB0  CONST_05  CAS   CAL  CAM  CAN     0.00   0.0  0
 DB0  CONST_06  CAS   CAT  CAU  CAN     0.00   0.0  0
 DB0  CONST_07  CAH   CAO  CAP  CAQ     0.00   0.0  0
 DB0  CONST_08  CAH   CAI  CAJ  CAQ     0.00   0.0  0
 DB0  CONST_09  CAI   CAJ  CAQ  CAP     0.00   0.0  0
 DB0  CONST_10  CAI   CAH  CAO  CAP     0.00   0.0  0
 DB0  CONST_11  CAJ   CAQ  CAP  CAO     0.00   0.0  0
 DB0  CONST_12  CAJ   CAI  CAH  CAO     0.00   0.0  0
 DB0  CONST_13  HAN   CAN  CAM  CAL   180.00   0.0  0
 DB0  CONST_14  HAT   CAT  CAS  CAL   180.00   0.0  0
 DB0  CONST_15  HAU   CAU  CAN  CAM   180.00   0.0  0
 DB0  CONST_16  HAM   CAM  CAN  CAU   180.00   0.0  0
 DB0  CONST_17  HAP   CAP  CAQ  OAR     0.00   0.0  0
 DB0  CONST_18  HAO   CAO  CAP  CAQ   180.00   0.0  0
 DB0  CONST_19  HAI   CAI  CAJ  CAQ   180.00   0.0  0
 DB0  CONST_20  HAH   CAH  CAO  CAP   180.00   0.0  0
 DB0  Var_01    CAJ   CAK  CAG  CAL     1.82  30.0  1
 DB0  Var_02    CAK   CAG  CAL  CAM   144.78  30.0  1
 DB0  Var_03    CAP   CAQ  OAR  CAS   113.13  30.0  1
 DB0  Var_04    CAG   CAK  CAJ  CAQ    33.60  30.0  1
 DB0  Var_05    NAB   CAF  CAG  CAL  -163.39  30.0  3
 DB0  Var_06    HAC1  CAC  CAD  CAE    71.36  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
 DB0  chir_01  NAB  CAF  CAA  CAC  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
 DB0  plan-1  CAL  0.020
 DB0  plan-1  CAM  0.020
 DB0  plan-1  CAN  0.020
 DB0  plan-1  CAU  0.020
 DB0  plan-1  CAT  0.020
 DB0  plan-1  CAS  0.020
 DB0  plan-1  OAR  0.020
 DB0  plan-1  CAG  0.020
 DB0  plan-1  HAM  0.020
 DB0  plan-1  HAN  0.020
 DB0  plan-1  HAU  0.020
 DB0  plan-1  HAT  0.020
 DB0  plan-2  OAR  0.020
 DB0  plan-2  CAQ  0.020
 DB0  plan-2  CAP  0.020
 DB0  plan-2  CAO  0.020
 DB0  plan-2  CAH  0.020
 DB0  plan-2  CAI  0.020
 DB0  plan-2  CAJ  0.020
 DB0  plan-2  CAK  0.020
 DB0  plan-2  HAP  0.020
 DB0  plan-2  HAO  0.020
 DB0  plan-2  HAH  0.020
 DB0  plan-2  HAI  0.020

