# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:37:06 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-(1H-indol-3-yl)propyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)OCCCc1c[nH]c2ccccc12
#
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
 IPL  IPL  '3-(1H-indol-3-yl)propyl dihydrogen phosphate'  ligand  31  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IPL
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
 IPL  N1    N  NR15  0  -0.687  -1.8982  -0.2735  -3.9012
 IPL  C2    C  CR15  0  -0.092  -2.1743   0.2442  -2.6654
 IPL  C3    C  CR5   0   0.024  -1.0156   0.5623  -2.0159
 IPL  C4    C  CR16  0  -0.376   1.4426   0.3072  -2.8425
 IPL  C5    C  CR16  0  -0.269   2.1977  -0.1199  -3.9173
 IPL  C6    C  CR16  0  -0.284   1.5852  -0.6391  -5.0707
 IPL  C7    C  CR16  0  -0.306   0.2106  -0.7373  -5.1719
 IPL  C8    C  CR56  0   0.354  -0.5478  -0.3051  -4.0844
 IPL  C9    C  CR56  0   0.028   0.0474   0.2159  -2.9134
 IPL  C1'   C  CH2   0  -0.163  -0.2266   0.7253   1.7437
 IPL  C2'   C  CH2   0  -0.458  -0.3641   0.1013   0.3730
 IPL  C3'   C  CH2   0  -0.544  -0.8757   1.1268  -0.6414
 IPL  P     P  P     0   1.452   0.2325   0.0067   4.2188
 IPL  O1P   O  O     0  -0.714   0.6915   1.3293   4.6833
 IPL  O2P   O  OH1   0  -0.732   1.0711  -1.2732   4.6674
 IPL  O3P   O  OH1   0  -0.742  -1.2832  -0.2206   4.6760
 IPL  O4P   O  O2    0  -0.592   0.2903  -0.2643   2.6494
 IPL  HN1   H  HNR5  0   0.407  -2.5891  -0.5805  -4.5648
 IPL  H2    H  HCR5  0   0.279  -3.1953   0.3538  -2.3334
 IPL  H4    H  HCR6  0   0.239   1.9245   0.7106  -1.9596
 IPL  H5    H  HCR6  0   0.245   3.2774  -0.0550  -3.8755
 IPL  H6    H  HCR6  0   0.248   2.2020  -0.9671  -5.8975
 IPL  H7    H  HCR6  0   0.258  -0.2580  -1.1349  -6.0632
 IPL  H1'1  H  HCH2  0   0.231  -1.1995   1.0885   2.0889
 IPL  H1'2  H  HCH2  0   0.237   0.4572   1.5770   1.7126
 IPL  H2'1  H  HCH2  0   0.240   0.6040  -0.2908   0.0505
 IPL  H2'2  H  HCH2  0   0.239  -1.0563  -0.7428   0.4173
 IPL  H3'1  H  HCH2  0   0.245  -1.8418   1.5151  -0.3074
 IPL  H3'2  H  HCH2  0   0.236  -0.1926   1.9828  -0.6620
 IPL  HOP2  H  HOH1  0   0.503   1.2992  -1.2826   5.6067
 IPL  HOP3  H  HOH1  0   0.495  -1.6639  -1.0786   4.4452

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
 IPL  N1   C2    aromatic  1.368  0.020  1.368
 IPL  N1   C8    aromatic  1.363  0.020  1.363
 IPL  N1   HN1   single    0.860  0.020  1.020
 IPL  C2   C3    aromatic  1.366  0.020  1.366
 IPL  C2   H2    single    0.930  0.020  1.080
 IPL  C3   C9    aromatic  1.434  0.020  1.434
 IPL  C3   C3'   single    1.492  0.020  1.492
 IPL  C4   C5    aromatic  1.381  0.020  1.381
 IPL  C4   C9    aromatic  1.400  0.020  1.400
 IPL  C4   H4    single    0.930  0.020  1.080
 IPL  C5   C6    aromatic  1.405  0.020  1.405
 IPL  C5   H5    single    0.930  0.020  1.080
 IPL  C6   C7    aromatic  1.382  0.020  1.382
 IPL  C6   H6    single    0.930  0.020  1.080
 IPL  C7   C8    aromatic  1.394  0.020  1.394
 IPL  C7   H7    single    0.930  0.020  1.080
 IPL  C8   C9    aromatic  1.413  0.020  1.413
 IPL  C1'  C2'   single    1.512  0.020  1.512
 IPL  C1'  O4P   single    1.438  0.020  1.438
 IPL  C1'  H1'1  single    0.970  0.020  1.090
 IPL  C1'  H1'2  single    0.970  0.020  1.090
 IPL  C2'  C3'   single    1.531  0.020  1.531
 IPL  C2'  H2'1  single    0.970  0.020  1.090
 IPL  C2'  H2'2  single    0.970  0.020  1.090
 IPL  C3'  H3'1  single    0.970  0.020  1.090
 IPL  C3'  H3'2  single    0.970  0.020  1.090
 IPL  P    O1P   double    1.475  0.020  1.475
 IPL  P    O2P   single    1.595  0.020  1.595
 IPL  P    O3P   single    1.599  0.020  1.599
 IPL  P    O4P   single    1.594  0.020  1.594
 IPL  O2P  HOP2  single    0.850  0.020  0.980
 IPL  O3P  HOP3  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
 IPL  HN1   N1   C8    125.78  3.000
 IPL  HN1   N1   C2    124.95  3.000
 IPL  C8    N1   C2    109.28  3.000
 IPL  H2    C2   C3    129.25  3.000
 IPL  H2    C2   N1    120.48  3.000
 IPL  C3    C2   N1    110.27  3.000
 IPL  C3'   C3   C9    126.76  3.000
 IPL  C3'   C3   C2    127.26  3.000
 IPL  C9    C3   C2    105.97  3.000
 IPL  H4    C4   C9    120.58  3.000
 IPL  H4    C4   C5    120.39  3.000
 IPL  C9    C4   C5    119.03  3.000
 IPL  H5    C5   C6    119.25  3.000
 IPL  H5    C5   C4    119.78  3.000
 IPL  C6    C5   C4    120.97  3.000
 IPL  H6    C6   C7    119.30  3.000
 IPL  H6    C6   C5    119.37  3.000
 IPL  C7    C6   C5    121.33  3.000
 IPL  H7    C7   C8    121.36  3.000
 IPL  H7    C7   C6    121.13  3.000
 IPL  C8    C7   C6    117.51  3.000
 IPL  C9    C8   C7    122.10  3.000
 IPL  C9    C8   N1    107.30  3.000
 IPL  C7    C8   N1    130.60  3.000
 IPL  C8    C9   C4    119.06  3.000
 IPL  C8    C9   C3    107.19  3.000
 IPL  C4    C9   C3    133.75  3.000
 IPL  H1'2  C1'  H1'1  107.86  3.000
 IPL  H1'2  C1'  O4P   109.23  3.000
 IPL  H1'1  C1'  O4P   110.45  3.000
 IPL  H1'2  C1'  C2'   110.66  3.000
 IPL  H1'1  C1'  C2'   110.00  3.000
 IPL  O4P   C1'  C2'   108.65  3.000
 IPL  H2'2  C2'  H2'1  107.21  3.000
 IPL  H2'2  C2'  C3'   109.43  3.000
 IPL  H2'1  C2'  C3'   109.93  3.000
 IPL  H2'2  C2'  C1'   109.86  3.000
 IPL  H2'1  C2'  C1'   109.57  3.000
 IPL  C3'   C2'  C1'   110.77  3.000
 IPL  H3'2  C3'  H3'1  106.22  3.000
 IPL  H3'2  C3'  C2'   109.12  3.000
 IPL  H3'1  C3'  C2'   109.32  3.000
 IPL  H3'2  C3'  C3    109.67  3.000
 IPL  H3'1  C3'  C3    109.44  3.000
 IPL  C2'   C3'  C3    112.85  3.000
 IPL  O4P   P    O3P   106.96  3.000
 IPL  O4P   P    O2P    96.98  3.000
 IPL  O3P   P    O2P   107.69  3.000
 IPL  O4P   P    O1P   116.83  3.000
 IPL  O3P   P    O1P   109.41  3.000
 IPL  O2P   P    O1P   117.87  3.000
 IPL  HOP2  O2P  P     113.91  3.000
 IPL  HOP3  O3P  P     115.54  3.000
 IPL  P     O4P  C1'   119.36  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
 IPL  CONST_01  C9   C3   C2   N1      0.00   0.0  0
 IPL  CONST_02  C6   C7   C8   N1    180.00   0.0  0
 IPL  CONST_03  C3   C9   C8   N1      0.00   0.0  0
 IPL  CONST_04  C4   C9   C8   N1    180.00   0.0  0
 IPL  CONST_05  C7   C8   N1   C2    180.00   0.0  0
 IPL  CONST_06  C9   C8   N1   C2      0.00   0.0  0
 IPL  CONST_07  C4   C9   C3   C2    180.00   0.0  0
 IPL  CONST_08  C8   C9   C3   C2      0.00   0.0  0
 IPL  CONST_09  C8   N1   C2   C3      0.00   0.0  0
 IPL  CONST_10  C5   C4   C9   C3    180.00   0.0  0
 IPL  CONST_11  C7   C8   C9   C3    180.00   0.0  0
 IPL  CONST_12  C7   C6   C5   C4      0.00   0.0  0
 IPL  CONST_13  C7   C8   C9   C4      0.00   0.0  0
 IPL  CONST_14  C8   C9   C4   C5      0.00   0.0  0
 IPL  CONST_15  C8   C7   C6   C5      0.00   0.0  0
 IPL  CONST_16  C9   C4   C5   C6      0.00   0.0  0
 IPL  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 IPL  CONST_18  C3'  C3   C2   N1    180.00   0.0  0
 IPL  CONST_19  C3'  C3   C9   C4      0.00   0.0  0
 IPL  CONST_20  C3'  C3   C9   C8    180.00   0.0  0
 IPL  CONST_21  H7   C7   C8   N1      0.00   0.0  0
 IPL  CONST_22  HN1  N1   C2   C3    180.00   0.0  0
 IPL  CONST_23  H4   C4   C9   C3      0.00   0.0  0
 IPL  CONST_24  H6   C6   C5   C4    180.00   0.0  0
 IPL  CONST_25  H5   C5   C6   C7    180.00   0.0  0
 IPL  CONST_26  H2   C2   N1   C8    180.00   0.0  0
 IPL  Var_01    C2'  C3'  C3   C2    106.44  30.0  2
 IPL  Var_02    C1'  C2'  C3'  C3    179.41  30.0  1
 IPL  Var_03    O1P  P    O4P  C1'   -47.22  30.0  1
 IPL  Var_04    O4P  C1'  C2'  C3'  -178.43  30.0  1

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
 IPL  plan-1  N1   0.020
 IPL  plan-1  C2   0.020
 IPL  plan-1  C3   0.020
 IPL  plan-1  C4   0.020
 IPL  plan-1  C5   0.020
 IPL  plan-1  C6   0.020
 IPL  plan-1  C7   0.020
 IPL  plan-1  C8   0.020
 IPL  plan-1  C9   0.020
 IPL  plan-1  C3'  0.020
 IPL  plan-1  HN1  0.020
 IPL  plan-1  H2   0.020
 IPL  plan-1  H4   0.020
 IPL  plan-1  H5   0.020
 IPL  plan-1  H6   0.020
 IPL  plan-1  H7   0.020

