# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:38:17 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(2-amino-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-11-yl)-2-methylbut-3-yn-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)C#Cc1ccc2[nH]c3CCCc4cnc(N)nc4c3c2c1
#
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
 VP7  VP7  4-(2-amino-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-11-yl)-2-methylbut-3-yn-2-ol  ligand  45  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VP7
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
 VP7  N1   N  N     0  -0.455  174.6705  19.2925  47.3694
 VP7  N3   N  N     0  -0.502  176.8316  19.6205  46.4625
 VP7  C4   C  CR6   0   0.525  175.6482  19.0159  46.5063
 VP7  C5   C  CR6   0   0.219  177.0965  20.5822  47.3469
 VP7  C6   C  CR5   0  -0.115  178.4210  21.1779  47.2435
 VP7  C7   C  CR56  0   0.118  179.5374  20.5949  46.5282
 VP7  C8   C  CR16  0  -0.423  179.7405  19.4217  45.7989
 VP7  C13  C  CH3   0  -0.653  180.9971  15.8334  41.7251
 VP7  C15  C  CR16  0  -0.320  182.0558  20.0778  45.4198
 VP7  C17  C  CR56  0   0.332  180.6231  21.4782  46.6829
 VP7  C20  C  CH2   0  -0.444  176.7516  23.3500  48.7872
 VP7  C1   C  CH2   0  -0.539  176.3406  21.9946  49.3592
 VP7  C11  C  CSP   0   0.069  181.4043  16.9626  43.8657
 VP7  C12  C  CT    0   0.025  181.6447  15.7226  43.1034
 VP7  C14  C  CH3   0  -0.667  181.0625  14.5346  43.8718
 VP7  C16  C  CR16  0  -0.295  181.8813  21.2396  46.1394
 VP7  C18  C  CR5   0   0.354  178.8805  22.3743  47.7724
 VP7  C19  C  CH2   0  -0.547  178.2496  23.4605  48.5769
 VP7  C2   C  CR6   0  -0.018  176.1408  20.9433  48.3131
 VP7  C3   C  CR16  0  -0.082  174.9458  20.2478  48.2447
 VP7  C9   C  CR6   0  -0.126  180.9942  19.1653  45.2500
 VP7  N2   N  NH2   0  -0.831  175.4025  18.0675  45.5673
 VP7  N4   N  NR15  0  -0.733  180.1862  22.5319  47.4291
 VP7  O1   O  OH1   0  -0.653  183.0321  15.5530  42.8839
 VP7  H1   H  HCR6  0   0.257  178.9353  18.7186  45.6509
 VP7  H2   H  HCH3  0   0.234  179.9230  15.9833  41.8215
 VP7  H3   H  HCH3  0   0.240  181.4096  16.6714  41.1632
 VP7  H4   H  HCH3  0   0.239  181.1642  14.9170  41.1569
 VP7  H5   H  HCR6  0   0.252  183.0188  19.8577  44.9787
 VP7  H6   H  HCH2  0   0.251  176.4559  24.1439  49.4746
 VP7  H7   H  HCH2  0   0.239  176.2194  23.5371  47.8516
 VP7  H8   H  HCH2  0   0.256  175.4065  22.1001  49.9143
 VP7  H9   H  HCH2  0   0.245  177.0896  21.6715  50.0914
 VP7  H10  H  HCH3  0   0.237  181.5296  14.4346  44.8532
 VP7  H11  H  HCH3  0   0.234  179.9898  14.6534  44.0219
 VP7  H12  H  HCH3  0   0.240  181.2308  13.6127  43.3132
 VP7  H13  H  HCR6  0   0.265  182.6946  21.9406  46.2761
 VP7  H14  H  HCH2  0   0.266  178.7474  23.4872  49.5524
 VP7  H15  H  HCH2  0   0.271  178.4840  24.4180  48.1018
 VP7  H16  H  HCR6  0   0.255  174.1592  20.4799  48.9585
 VP7  H17  H  HNH2  0   0.389  176.1937  17.6775  45.0838
 VP7  H18  H  HNH2  0   0.387  174.6387  17.4351  45.7360
 VP7  H19  H  HNR5  0   0.415  180.7437  23.3340  47.6793
 VP7  H20  H  HOH1  0   0.448  183.4610  15.4073  43.7346
 VP7  C10  C  CSP   0   0.141  181.2101  17.9695  44.5010

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
 VP7  C13  C12  single    1.527  0.020  1.527
 VP7  O1   C12  single    1.415  0.020  1.415
 VP7  C12  C14  single    1.530  0.020  1.530
 VP7  C12  C11  single    1.475  0.020  1.475
 VP7  C11  C10  triple    1.206  0.020  1.206
 VP7  C10  C9   single    1.427  0.020  1.427
 VP7  C9   C15  aromatic  1.410  0.020  1.410
 VP7  C9   C8   aromatic  1.392  0.020  1.392
 VP7  C15  C16  aromatic  1.378  0.020  1.378
 VP7  C8   C7   aromatic  1.396  0.020  1.396
 VP7  N2   C4   single    1.357  0.020  1.357
 VP7  C16  C17  aromatic  1.391  0.020  1.391
 VP7  C7   C17  aromatic  1.408  0.020  1.408
 VP7  C7   C6   aromatic  1.448  0.020  1.448
 VP7  N3   C4   aromatic  1.330  0.020  1.330
 VP7  N3   C5   aromatic  1.333  0.020  1.333
 VP7  C4   N1   aromatic  1.333  0.020  1.333
 VP7  C17  N4   aromatic  1.363  0.020  1.363
 VP7  C6   C5   aromatic  1.456  0.020  1.456
 VP7  C6   C18  aromatic  1.386  0.020  1.386
 VP7  C5   C2   aromatic  1.406  0.020  1.406
 VP7  N1   C3   aromatic  1.325  0.020  1.325
 VP7  N4   C18  aromatic  1.359  0.020  1.359
 VP7  C18  C19  single    1.492  0.020  1.492
 VP7  C3   C2   aromatic  1.384  0.020  1.384
 VP7  C2   C1   single    1.496  0.020  1.496
 VP7  C20  C19  single    1.517  0.020  1.517
 VP7  C20  C1   single    1.528  0.020  1.528
 VP7  C8   H1   single    0.930  0.020  1.080
 VP7  C13  H2   single    0.970  0.020  1.090
 VP7  C13  H3   single    0.970  0.020  1.090
 VP7  C13  H4   single    0.970  0.020  1.090
 VP7  C15  H5   single    0.930  0.020  1.080
 VP7  C20  H6   single    0.970  0.020  1.090
 VP7  C20  H7   single    0.970  0.020  1.090
 VP7  C1   H8   single    0.970  0.020  1.090
 VP7  C1   H9   single    0.970  0.020  1.090
 VP7  C14  H10  single    0.970  0.020  1.090
 VP7  C14  H11  single    0.970  0.020  1.090
 VP7  C14  H12  single    0.970  0.020  1.090
 VP7  C16  H13  single    0.930  0.020  1.080
 VP7  C19  H14  single    0.970  0.020  1.090
 VP7  C19  H15  single    0.970  0.020  1.090
 VP7  C3   H16  single    0.930  0.020  1.080
 VP7  N2   H17  single    0.890  0.020  1.040
 VP7  N2   H18  single    0.890  0.020  1.040
 VP7  N4   H19  single    0.860  0.020  1.020
 VP7  O1   H20  single    0.850  0.020  0.980

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
 VP7  C3   N1   C4   115.15  3.000
 VP7  C5   N3   C4   118.88  3.000
 VP7  N2   C4   N3   117.14  3.000
 VP7  N3   C4   N1   125.43  3.000
 VP7  N2   C4   N1   117.40  3.000
 VP7  C2   C5   C6   124.20  3.000
 VP7  C2   C5   N3   120.40  3.000
 VP7  C6   C5   N3   115.39  3.000
 VP7  C18  C6   C7   106.28  3.000
 VP7  C18  C6   C5   128.86  3.000
 VP7  C7   C6   C5   124.86  3.000
 VP7  C17  C7   C8   118.19  3.000
 VP7  C17  C7   C6   106.71  3.000
 VP7  C8   C7   C6   135.09  3.000
 VP7  H1   C8   C9   119.85  3.000
 VP7  H1   C8   C7   120.71  3.000
 VP7  C9   C8   C7   119.44  3.000
 VP7  H4   C13  H3   108.62  3.000
 VP7  H4   C13  H2   108.23  3.000
 VP7  H3   C13  H2   108.24  3.000
 VP7  H4   C13  C12  110.14  3.000
 VP7  H3   C13  C12  111.14  3.000
 VP7  H2   C13  C12  110.40  3.000
 VP7  H5   C15  C9   119.30  3.000
 VP7  H5   C15  C16  119.82  3.000
 VP7  C9   C15  C16  120.88  3.000
 VP7  N4   C17  C16  129.52  3.000
 VP7  N4   C17  C7   107.34  3.000
 VP7  C16  C17  C7   123.15  3.000
 VP7  H7   C20  H6   106.43  3.000
 VP7  H7   C20  C19  110.48  3.000
 VP7  H6   C20  C19  107.58  3.000
 VP7  H7   C20  C1   109.97  3.000
 VP7  H6   C20  C1   109.68  3.000
 VP7  C19  C20  C1   112.48  3.000
 VP7  H9   C1   H8   105.87  3.000
 VP7  H9   C1   C2   110.56  3.000
 VP7  H8   C1   C2   108.00  3.000
 VP7  H9   C1   C20  109.14  3.000
 VP7  H8   C1   C20  109.56  3.000
 VP7  C2   C1   C20  113.42  3.000
 VP7  C12  C11  C10  180.00  3.000
 VP7  O1   C12  C14  110.98  3.000
 VP7  C14  C12  C11  109.34  3.000
 VP7  O1   C12  C11  109.92  3.000
 VP7  C11  C12  C13  109.65  3.000
 VP7  C14  C12  C13  110.39  3.000
 VP7  O1   C12  C13  106.53  3.000
 VP7  H12  C14  H11  108.34  3.000
 VP7  H12  C14  H10  108.48  3.000
 VP7  H11  C14  H10  107.90  3.000
 VP7  H12  C14  C12  109.90  3.000
 VP7  H11  C14  C12  111.05  3.000
 VP7  H10  C14  C12  111.09  3.000
 VP7  H13  C16  C17  121.28  3.000
 VP7  H13  C16  C15  121.12  3.000
 VP7  C17  C16  C15  117.59  3.000
 VP7  N4   C18  C19  117.26  3.000
 VP7  C19  C18  C6   133.94  3.000
 VP7  N4   C18  C6   108.79  3.000
 VP7  H15  C19  H14  105.54  3.000
 VP7  H15  C19  C18  108.21  3.000
 VP7  H14  C19  C18  107.80  3.000
 VP7  H15  C19  C20  109.60  3.000
 VP7  H14  C19  C20  109.09  3.000
 VP7  C18  C19  C20  116.07  3.000
 VP7  C3   C2   C1   120.18  3.000
 VP7  C1   C2   C5   124.75  3.000
 VP7  C3   C2   C5   115.07  3.000
 VP7  H16  C3   C2   119.00  3.000
 VP7  H16  C3   N1   115.94  3.000
 VP7  C2   C3   N1   125.06  3.000
 VP7  C15  C9   C10  119.43  3.000
 VP7  C15  C9   C8   120.75  3.000
 VP7  C10  C9   C8   119.82  3.000
 VP7  H18  N2   H17  115.72  3.000
 VP7  H18  N2   C4   117.44  3.000
 VP7  H17  N2   C4   117.46  3.000
 VP7  H19  N4   C18  124.10  3.000
 VP7  H19  N4   C17  125.00  3.000
 VP7  C18  N4   C17  110.89  3.000
 VP7  H20  O1   C12  108.52  3.000
 VP7  C9   C10  C11  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
 VP7  CONST_01  C5   N3   C4   N1     0.00   0.0  0
 VP7  CONST_02  C5   C2   C3   N1     0.00   0.0  0
 VP7  CONST_03  C3   N1   C4   N3     0.00   0.0  0
 VP7  CONST_06  C3   C2   C5   N3     0.00   0.0  0
 VP7  CONST_07  C6   C5   N3   C4   180.00   0.0  0
 VP7  CONST_08  C2   C5   N3   C4     0.00   0.0  0
 VP7  CONST_09  C2   C3   N1   C4     0.00   0.0  0
 VP7  CONST_10  C8   C7   C6   C5     0.00   0.0  0
 VP7  CONST_11  C17  C7   C6   C5   180.00   0.0  0
 VP7  CONST_12  N4   C18  C6   C5   180.00   0.0  0
 VP7  CONST_13  C9   C8   C7   C6   180.00   0.0  0
 VP7  CONST_14  C16  C17  C7   C6   180.00   0.0  0
 VP7  CONST_15  N4   C17  C7   C6     0.00   0.0  0
 VP7  CONST_16  C3   C2   C5   C6   180.00   0.0  0
 VP7  CONST_17  C17  N4   C18  C6     0.00   0.0  0
 VP7  CONST_18  C15  C9   C8   C7     0.00   0.0  0
 VP7  CONST_19  C15  C16  C17  C7     0.00   0.0  0
 VP7  CONST_20  C18  N4   C17  C7     0.00   0.0  0
 VP7  CONST_22  N4   C18  C6   C7     0.00   0.0  0
 VP7  CONST_23  C16  C15  C9   C8     0.00   0.0  0
 VP7  CONST_24  C16  C17  C7   C8     0.00   0.0  0
 VP7  CONST_25  N4   C17  C7   C8   180.00   0.0  0
 VP7  CONST_26  C18  C6   C7   C8   180.00   0.0  0
 VP7  CONST_27  N4   C17  C16  C15  180.00   0.0  0
 VP7  CONST_28  C9   C15  C16  C17    0.00   0.0  0
 VP7  CONST_29  C9   C8   C7   C17    0.00   0.0  0
 VP7  CONST_30  C18  C6   C7   C17    0.00   0.0  0
 VP7  CONST_31  C18  N4   C17  C16  180.00   0.0  0
 VP7  CONST_33  N2   C4   N3   C5   180.00   0.0  0
 VP7  CONST_34  C10  C9   C8   C7   180.00   0.0  0
 VP7  CONST_35  C16  C15  C9   C10  180.00   0.0  0
 VP7  CONST_36  N2   C4   N1   C3   180.00   0.0  0
 VP7  CONST_37  H16  C3   N1   C4   180.00   0.0  0
 VP7  CONST_38  H1   C8   C7   C6     0.00   0.0  0
 VP7  CONST_39  H19  N4   C18  C6   180.00   0.0  0
 VP7  CONST_40  H13  C16  C17  C7   180.00   0.0  0
 VP7  CONST_41  H5   C15  C9   C8   180.00   0.0  0
 VP7  Var_01    C20  C1   C2   C5    54.40  30.0  1
 VP7  Var_02    C20  C19  C18  C6    -6.79  30.0  1
 VP7  Var_03    C18  C19  C20  C1    53.10  30.0  1
 VP7  Var_04    C2   C1   C20  C19  -85.55  30.0  1
 VP7  Var_05    C13  C12  C11  C10  158.59  30.0  2
 VP7  Var_06    H10  C14  C12  C13  179.05  30.0  3
 VP7  Var_07    H2   C13  C12  C11  -60.15  30.0  3

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
 VP7  plan-1  C5   0.020
 VP7  plan-1  C6   0.020
 VP7  plan-1  C7   0.020
 VP7  plan-1  C8   0.020
 VP7  plan-1  C15  0.020
 VP7  plan-1  C17  0.020
 VP7  plan-1  C11  0.020
 VP7  plan-1  C16  0.020
 VP7  plan-1  C18  0.020
 VP7  plan-1  C19  0.020
 VP7  plan-1  C9   0.020
 VP7  plan-1  N4   0.020
 VP7  plan-1  H1   0.020
 VP7  plan-1  H5   0.020
 VP7  plan-1  H13  0.020
 VP7  plan-1  H19  0.020
 VP7  plan-1  C10  0.020
 VP7  plan-2  C4   0.020
 VP7  plan-2  N2   0.020
 VP7  plan-2  H17  0.020
 VP7  plan-2  H18  0.020
 VP7  plan-3  N1   0.020
 VP7  plan-3  N3   0.020
 VP7  plan-3  C4   0.020
 VP7  plan-3  C5   0.020
 VP7  plan-3  C6   0.020
 VP7  plan-3  C1   0.020
 VP7  plan-3  C2   0.020
 VP7  plan-3  C3   0.020
 VP7  plan-3  N2   0.020
 VP7  plan-3  H16  0.020

