# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:45:28 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNCCCCC(O)=O)c1O
#
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
 I3B  I3B  "5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid"  ligand  41  23  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I3B
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
 I3B  C02  C  CR6    0   0.094  69.3310  -25.4152  47.4078
 I3B  C03  C  CR6    0  -0.022  68.0455  -24.8944  47.2314
 I3B  C05  C  CR16   0  -0.160  67.5134  -24.1227  48.2562
 I3B  C07  C  CR6    0   0.114  69.3691  -24.3240  49.5731
 I3B  C09  C  CR6    0   0.258  69.9931  -25.1151  48.5995
 I3B  C27  C  CH2    0  -0.574  72.3326  -22.5094  41.9066
 I3B  C29  C  CH2    0  -0.435  71.7368  -24.0143  43.8740
 I3B  O13  O  O2     0  -0.652  66.8214  -26.4610  45.8975
 I3B  O32  O  OC    -1  -0.607  72.2986  -24.5467  40.6499
 I3B  C01  C  CH2    0  -0.403  70.0223  -26.2628  46.3695
 I3B  C04  C  CH2    0  -0.224  67.2285  -25.1284  45.9863
 I3B  C08  C  CH3    0  -0.780  70.0657  -23.9960  50.8620
 I3B  C26  C  C      0   0.403  72.9672  -23.5333  40.9392
 I3B  C28  C  CH2    0  -0.403  71.2340  -23.0397  42.8164
 I3B  C30  C  CH2    0  -0.255  70.6034  -24.6074  44.6925
 I3B  N06  N  N      0  -0.408  68.1477  -23.8436  49.3864
 I3B  N33  N  NH1    0  -0.594  71.0910  -25.5333  45.6991
 I3B  O10  O  OH1    0  -0.618  71.2310  -25.6200  48.7793
 I3B  O12  O  OP    -1  -0.883  65.8659  -28.4147  44.6607
 I3B  O14  O  O      0  -0.886  67.7057  -27.0126  43.5353
 I3B  O15  O  OP    -1  -0.895  65.3602  -26.0237  43.8271
 I3B  O31  O  O      0  -0.622  74.0956  -23.2375  40.4931
 I3B  P11  P  P      0   1.233  66.3959  -27.0275  44.3265
 I3B  H1   H  HCR6   0   0.241  66.5162  -23.7058  48.1507
 I3B  H2   H  HCH2   0   0.201  73.1223  -22.0461  42.5066
 I3B  H3   H  HCH2   0   0.224  71.9248  -21.6977  41.2921
 I3B  H4   H  HCH2   0   0.210  72.2868  -24.8249  43.3866
 I3B  H5   H  HCH2   0   0.204  72.4448  -23.5101  44.5396
 I3B  H7   H  HCH2   0   0.248  69.2845  -26.6590  45.6653
 I3B  H8   H  HCH2   0   0.240  70.4690  -27.1265  46.8675
 I3B  H9   H  HCH2   0   0.187  67.8241  -24.8225  45.1170
 I3B  H10  H  HCH2   0   0.188  66.3664  -24.4454  46.0132
 I3B  H11  H  HCH3   0   0.265  69.4132  -23.3953  51.4913
 I3B  H12  H  HCH3   0   0.251  70.3343  -24.8917  51.4286
 I3B  H13  H  HCH3   0   0.254  70.9842  -23.4257  50.7000
 I3B  H14  H  HCH2   0   0.201  70.7386  -22.2016  43.3177
 I3B  H15  H  HCH2   0   0.200  70.4653  -23.5260  42.2101
 I3B  H16  H  HCH2   0   0.206  70.0564  -23.8008  45.1926
 I3B  H17  H  HCH2   0   0.177  69.8838  -25.0855  44.0095
 I3B  H18  H  HNH1   0   0.340  71.6902  -26.2117  45.2443
 I3B  H20  H  HOH1   0   0.480  71.5762  -25.3997  49.6513

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
 I3B  O31  C26  deloc     1.249  0.020  1.249
 I3B  C26  O32  deloc     1.248  0.020  1.248
 I3B  C26  C27  single    1.545  0.020  1.545
 I3B  C27  C28  single    1.522  0.020  1.522
 I3B  C28  C29  single    1.523  0.020  1.523
 I3B  O14  P11  deloc     1.530  0.020  1.530
 I3B  O15  P11  deloc     1.526  0.020  1.526
 I3B  O12  P11  deloc     1.522  0.020  1.522
 I3B  C29  C30  single    1.519  0.020  1.519
 I3B  P11  O13  single    1.723  0.020  1.723
 I3B  C30  N33  single    1.452  0.020  1.452
 I3B  O13  C04  single    1.396  0.020  1.396
 I3B  C04  C03  single    1.507  0.020  1.507
 I3B  N33  C01  single    1.457  0.020  1.457
 I3B  C01  C02  single    1.508  0.020  1.508
 I3B  C03  C02  aromatic  1.398  0.020  1.398
 I3B  C03  C05  aromatic  1.389  0.020  1.389
 I3B  C02  C09  aromatic  1.396  0.020  1.396
 I3B  C05  N06  aromatic  1.326  0.020  1.326
 I3B  C09  O10  single    1.349  0.020  1.349
 I3B  C09  C07  aromatic  1.401  0.020  1.401
 I3B  N06  C07  aromatic  1.326  0.020  1.326
 I3B  C07  C08  single    1.501  0.020  1.501
 I3B  C05  H1   single    0.930  0.020  1.080
 I3B  C27  H2   single    0.970  0.020  1.090
 I3B  C27  H3   single    0.970  0.020  1.090
 I3B  C29  H4   single    0.970  0.020  1.090
 I3B  C29  H5   single    0.970  0.020  1.090
 I3B  C01  H7   single    0.970  0.020  1.090
 I3B  C01  H8   single    0.970  0.020  1.090
 I3B  C04  H9   single    0.970  0.020  1.090
 I3B  C04  H10  single    0.970  0.020  1.090
 I3B  C08  H11  single    0.970  0.020  1.090
 I3B  C08  H12  single    0.970  0.020  1.090
 I3B  C08  H13  single    0.970  0.020  1.090
 I3B  C28  H14  single    0.970  0.020  1.090
 I3B  C28  H15  single    0.970  0.020  1.090
 I3B  C30  H16  single    0.970  0.020  1.090
 I3B  C30  H17  single    0.970  0.020  1.090
 I3B  N33  H18  single    0.890  0.020  1.040
 I3B  O10  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
 I3B  C01  C02  C09  119.42  3.000
 I3B  C09  C02  C03  117.63  3.000
 I3B  C01  C02  C03  122.95  3.000
 I3B  C04  C03  C05  119.21  3.000
 I3B  C05  C03  C02  117.78  3.000
 I3B  C04  C03  C02  123.01  3.000
 I3B  H1   C05  N06  116.19  3.000
 I3B  H1   C05  C03  119.56  3.000
 I3B  N06  C05  C03  124.24  3.000
 I3B  N06  C07  C08  117.98  3.000
 I3B  C08  C07  C09  120.88  3.000
 I3B  N06  C07  C09  121.14  3.000
 I3B  O10  C09  C07  121.83  3.000
 I3B  C07  C09  C02  120.22  3.000
 I3B  O10  C09  C02  117.94  3.000
 I3B  H3   C27  H2   105.19  3.000
 I3B  H3   C27  C28  108.93  3.000
 I3B  H2   C27  C28  109.92  3.000
 I3B  H3   C27  C26  107.00  3.000
 I3B  H2   C27  C26  109.11  3.000
 I3B  C28  C27  C26  116.10  3.000
 I3B  H5   C29  H4   106.67  3.000
 I3B  H5   C29  C30  109.56  3.000
 I3B  H4   C29  C30  109.02  3.000
 I3B  H5   C29  C28  109.93  3.000
 I3B  H4   C29  C28  109.30  3.000
 I3B  C30  C29  C28  112.19  3.000
 I3B  P11  O13  C04  116.34  3.000
 I3B  H8   C01  H7   106.43  3.000
 I3B  H8   C01  N33  107.79  3.000
 I3B  H7   C01  N33  112.31  3.000
 I3B  H8   C01  C02  108.54  3.000
 I3B  H7   C01  C02  109.73  3.000
 I3B  N33  C01  C02  111.81  3.000
 I3B  H10  C04  H9   105.76  3.000
 I3B  H10  C04  O13  111.44  3.000
 I3B  H9   C04  O13  111.96  3.000
 I3B  H10  C04  C03  107.95  3.000
 I3B  H9   C04  C03  108.47  3.000
 I3B  O13  C04  C03  111.02  3.000
 I3B  H13  C08  H12  107.32  3.000
 I3B  H13  C08  H11  107.56  3.000
 I3B  H12  C08  H11  107.46  3.000
 I3B  H13  C08  C07  112.12  3.000
 I3B  H12  C08  C07  112.32  3.000
 I3B  H11  C08  C07  109.82  3.000
 I3B  O31  C26  O32  126.40  3.000
 I3B  O32  C26  C27  117.59  3.000
 I3B  O31  C26  C27  115.97  3.000
 I3B  H15  C28  H14  106.04  3.000
 I3B  H15  C28  C29  109.42  3.000
 I3B  H14  C28  C29  108.73  3.000
 I3B  H15  C28  C27  109.33  3.000
 I3B  H14  C28  C27  109.48  3.000
 I3B  C29  C28  C27  113.56  3.000
 I3B  H17  C30  H16  106.05  3.000
 I3B  H17  C30  N33  111.87  3.000
 I3B  H16  C30  N33  108.71  3.000
 I3B  H17  C30  C29  108.84  3.000
 I3B  H16  C30  C29  109.34  3.000
 I3B  N33  C30  C29  111.85  3.000
 I3B  C07  N06  C05  118.98  3.000
 I3B  H18  N33  C30  108.33  3.000
 I3B  H18  N33  C01  107.76  3.000
 I3B  C30  N33  C01  113.07  3.000
 I3B  H20  O10  C09  111.34  3.000
 I3B  O15  P11  O14  113.91  3.000
 I3B  O15  P11  O12  115.78  3.000
 I3B  O14  P11  O12  114.86  3.000
 I3B  O12  P11  O13  100.68  3.000
 I3B  O15  P11  O13  104.46  3.000
 I3B  O14  P11  O13  104.88  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
 I3B  CONST_01  N06  C05  C03  C02     0.00   0.0  0
 I3B  CONST_02  N06  C07  C09  C02     0.00   0.0  0
 I3B  CONST_03  C07  C09  C02  C03     0.00   0.0  0
 I3B  CONST_04  C07  N06  C05  C03     0.00   0.0  0
 I3B  CONST_05  C09  C02  C03  C05     0.00   0.0  0
 I3B  CONST_06  C09  C07  N06  C05     0.00   0.0  0
 I3B  CONST_07  C08  C07  C09  C02   180.00   0.0  0
 I3B  CONST_08  O10  C09  C02  C03   180.00   0.0  0
 I3B  CONST_09  C01  C02  C03  C05   180.00   0.0  0
 I3B  CONST_10  C08  C07  N06  C05   180.00   0.0  0
 I3B  CONST_11  C01  C02  C09  C07   180.00   0.0  0
 I3B  CONST_12  C04  C03  C02  C09   180.00   0.0  0
 I3B  CONST_13  N06  C05  C03  C04   180.00   0.0  0
 I3B  CONST_14  O10  C09  C07  N06   180.00   0.0  0
 I3B  CONST_15  H1   C05  C03  C02   180.00   0.0  0
 I3B  CONST_16  H1   C05  N06  C07   180.00   0.0  0
 I3B  Var_01    O13  C04  C03  C02    69.44  30.0  2
 I3B  Var_02    N33  C01  C02  C03   106.99  30.0  2
 I3B  Var_03    O13  C04  C03  C05  -110.89  30.0  2
 I3B  Var_04    N33  C01  C02  C09   -72.35  30.0  2
 I3B  Var_05    H9   C04  C03  C02   -53.97  30.0  2
 I3B  Var_06    H10  C04  C03  C02  -168.13  30.0  2
 I3B  Var_07    H7   C01  C02  C03   -18.31  30.0  2
 I3B  Var_08    H8   C01  C02  C03  -134.24  30.0  2
 I3B  Var_09    H9   C04  C03  C05   125.70  30.0  2
 I3B  Var_10    H10  C04  C03  C05    11.53  30.0  2
 I3B  Var_11    H7   C01  C02  C09   162.35  30.0  2
 I3B  Var_12    H8   C01  C02  C09    46.42  30.0  2
 I3B  Var_13    H11  C08  C07  C09  -178.70  30.0  2
 I3B  Var_14    H12  C08  C07  C09   -59.17  30.0  2
 I3B  Var_15    H13  C08  C07  C09    61.78  30.0  2
 I3B  Var_16    H11  C08  C07  N06     1.25  30.0  2
 I3B  Var_17    H12  C08  C07  N06   120.78  30.0  2
 I3B  Var_18    H13  C08  C07  N06  -118.27  30.0  2
 I3B  Var_19    C30  N33  C01  C02   -77.79  30.0  1
 I3B  Var_20    P11  O13  C04  C03  -158.55  30.0  1
 I3B  Var_21    H18  N33  C01  C02   162.51  30.0  1
 I3B  Var_22    C30  C29  C28  C27  -175.49  30.0  3
 I3B  Var_23    C26  C27  C28  C29    68.57  30.0  2
 I3B  Var_24    C01  N33  C30  C29  -171.66  30.0  3
 I3B  Var_25    C28  C27  C26  O32    22.58  30.0  3
 I3B  Var_26    O14  P11  O13  C04    66.90  30.0  3
 I3B  Var_27    O15  P11  O13  C04   -53.20  30.0  3
 I3B  Var_28    O12  P11  O13  C04  -173.58  30.0  3
 I3B  Var_29    O31  C26  C27  C28  -159.39  30.0  3
 I3B  Var_30    N33  C30  C29  C28  -179.92  30.0  3
 I3B  Var_31    H4   C29  C28  C27   -54.43  30.0  3
 I3B  Var_32    H5   C29  C28  C27    62.33  30.0  3
 I3B  Var_33    H2   C27  C28  C29   -55.84  30.0  2
 I3B  Var_34    H3   C27  C28  C29  -170.61  30.0  2
 I3B  Var_35    H18  N33  C30  C29   -52.29  30.0  3
 I3B  Var_36    H2   C27  C26  O32   147.41  30.0  3
 I3B  Var_37    H3   C27  C26  O32   -99.27  30.0  3
 I3B  Var_38    H16  C30  N33  C01    67.51  30.0  1
 I3B  Var_39    H17  C30  N33  C01   -49.26  30.0  1
 I3B  Var_40    H14  C28  C27  C26  -169.70  30.0  3
 I3B  Var_41    H15  C28  C27  C26   -53.93  30.0  3
 I3B  Var_42    H16  C30  C29  C28   -59.45  30.0  3
 I3B  Var_43    H17  C30  C29  C28    55.97  30.0  3
 I3B  Var_44    H14  C28  C29  C30    62.36  30.0  1
 I3B  Var_45    H15  C28  C29  C30   -53.03  30.0  1
 I3B  Var_46    H7   C01  N33  C30    46.07  30.0  3
 I3B  Var_47    H8   C01  N33  C30   162.99  30.0  3
 I3B  Var_48    H4   C29  C30  N33    58.87  30.0  1
 I3B  Var_49    H5   C29  C30  N33   -57.53  30.0  1
 I3B  Var_50    H2   C27  C26  O31   -34.56  30.0  3
 I3B  Var_51    H3   C27  C26  O31    78.76  30.0  3
 I3B  Var_52    H9   C04  O13  P11   -37.15  30.0  3
 I3B  Var_53    H10  C04  O13  P11    81.08  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
 I3B  plan-1  C02  0.020
 I3B  plan-1  C03  0.020
 I3B  plan-1  C05  0.020
 I3B  plan-1  C07  0.020
 I3B  plan-1  C09  0.020
 I3B  plan-1  C01  0.020
 I3B  plan-1  C04  0.020
 I3B  plan-1  C08  0.020
 I3B  plan-1  N06  0.020
 I3B  plan-1  O10  0.020
 I3B  plan-1  H1   0.020
 I3B  plan-2  C27  0.020
 I3B  plan-2  O32  0.020
 I3B  plan-2  C26  0.020
 I3B  plan-2  O31  0.020

