# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 16:53:22 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-carbamimidamidobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)Nc1cc(ccc1N2C(=O)CCC2(CO)CO)C(O)=O
#
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
 RAI  RAI  '4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-carbamimidamidobenzoic acid'  ligand  41  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RAI
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
 RAI  C1    C  CR16  0  -0.249  -1.8476   0.0224   0.7652
 RAI  C2    C  CR6   0   0.335  -0.7035   0.2845   0.0236
 RAI  C3    C  CR6   0   0.264   0.4972   0.5729   0.6824
 RAI  C4    C  CR16  0  -0.309   0.5256   0.5588   2.0730
 RAI  C5    C  CR6   0  -0.078  -0.6131   0.2526   2.8062
 RAI  C6    C  CR16  0  -0.282  -1.8120  -0.0090   2.1464
 RAI  C10   C  C     0   0.540  -0.5053   0.2504   4.2878
 RAI  O11   O  OH1   0  -0.592  -1.6627   0.0195   4.8884
 RAI  N12   N  NH1   0  -0.716   1.6476   0.9144  -0.0395
 RAI  C13   C  C     0   0.506   2.8337   0.2013  -0.0381
 RAI  N14   N  NH2   0  -0.805   2.9121  -0.8308   0.8506
 RAI  N15   N  NT    0  -0.587  -0.7851   0.3049  -1.3881
 RAI  C16   C  CT    0   0.048  -0.6347  -0.8698  -2.2601
 RAI  C17   C  CH2   0  -0.473  -1.2125  -0.3402  -3.5883
 RAI  C18   C  CH2   0  -0.573  -1.0746   1.1746  -3.5256
 RAI  C19   C  C     0   0.517  -0.9647   1.4753  -2.0540
 RAI  C24   C  CH2   0  -0.140   0.8336  -1.2689  -2.4003
 RAI  O25   O  OH1   0  -0.669   1.5552  -0.2016  -2.9658
 RAI  C28   C  CH2   0  -0.156  -1.4594  -2.0618  -1.7964
 RAI  O29   O  OH1   0  -0.658  -0.8788  -2.6501  -0.6611
 RAI  O32   O  O     0  -0.434   0.5265   0.4409   4.8854
 RAI  N33   N  N     0  -0.705   3.8349   0.4904  -0.7870
 RAI  O34   O  O     0  -0.482  -1.0183   2.5683  -1.5214
 RAI  H1    H  HCR6  0   0.271  -2.7762  -0.1731   0.2460
 RAI  H4    H  HCR6  0   0.281   1.4460   0.8071   2.5836
 RAI  H6    H  HCR6  0   0.271  -2.7168  -0.2326   2.6931
 RAI  H11   H  HOH1  0   0.490  -1.5449   0.0292   5.8499
 RAI  H12   H  HNH1  0   0.402   1.4898   1.4305  -0.8912
 RAI  H141  H  HNH2  0   0.393   3.7357  -1.4015   0.7488
 RAI  H142  H  HNH2  0   0.396   2.0796  -1.3599   1.0579
 RAI  H171  H  HCH2  0   0.259  -2.2696  -0.6092  -3.6512
 RAI  H172  H  HCH2  0   0.265  -0.7166  -0.7861  -4.4486
 RAI  H181  H  HCH2  0   0.277  -1.9250   1.7051  -3.9534
 RAI  H182  H  HCH2  0   0.280  -0.1769   1.5401  -4.0260
 RAI  H241  H  HCH2  0   0.218   1.2376  -1.5578  -1.4255
 RAI  H242  H  HCH2  0   0.215   0.8777  -2.1621  -3.0385
 RAI  H25   H  HOH1  0   0.452   2.4764  -0.2745  -2.6933
 RAI  H281  H  HCH2  0   0.220  -2.4850  -1.7202  -1.6079
 RAI  H282  H  HCH2  0   0.222  -1.5111  -2.7704  -2.6352
 RAI  H29   H  HOH1  0   0.460  -1.4831  -3.3176  -0.3239
 RAI  H33   H  H     0   0.325   3.6798   1.3573  -1.2887

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
 RAI  C1   C2    aromatic  1.388  0.020  1.388
 RAI  C1   C6    aromatic  1.382  0.020  1.382
 RAI  C1   H1    single    0.930  0.020  1.080
 RAI  C2   C3    aromatic  1.400  0.020  1.400
 RAI  C2   N15   single    1.414  0.020  1.414
 RAI  C3   C4    aromatic  1.391  0.020  1.391
 RAI  C3   N12   single    1.400  0.020  1.400
 RAI  C4   C5    aromatic  1.389  0.020  1.389
 RAI  C4   H4    single    0.930  0.020  1.080
 RAI  C5   C6    aromatic  1.393  0.020  1.393
 RAI  C5   C10   single    1.486  0.020  1.486
 RAI  C6   H6    single    0.930  0.020  1.080
 RAI  C10  O11   single    1.324  0.020  1.324
 RAI  C10  O32   double    1.207  0.020  1.207
 RAI  O11  H11   single    0.850  0.020  0.980
 RAI  N12  C13   single    1.384  0.020  1.384
 RAI  N12  H12   single    0.890  0.020  1.040
 RAI  C13  N14   single    1.364  0.020  1.364
 RAI  C13  N33   double    1.283  0.020  1.283
 RAI  N14  H141  single    0.890  0.020  1.040
 RAI  N14  H142  single    0.890  0.020  1.040
 RAI  N15  C16   single    1.471  0.020  1.471
 RAI  N15  C19   single    1.359  0.020  1.359
 RAI  C16  C17   single    1.542  0.020  1.542
 RAI  C16  C24   single    1.528  0.020  1.528
 RAI  C16  C28   single    1.522  0.020  1.522
 RAI  C17  C18   single    1.522  0.020  1.522
 RAI  C17  H171  single    0.970  0.020  1.090
 RAI  C17  H172  single    0.970  0.020  1.090
 RAI  C18  C19   single    1.506  0.020  1.506
 RAI  C18  H181  single    0.970  0.020  1.090
 RAI  C18  H182  single    0.970  0.020  1.090
 RAI  C19  O34   double    1.217  0.020  1.217
 RAI  C24  O25   single    1.407  0.020  1.407
 RAI  C24  H241  single    0.970  0.020  1.090
 RAI  C24  H242  single    0.970  0.020  1.090
 RAI  O25  H25   single    0.850  0.020  0.980
 RAI  C28  O29   single    1.404  0.020  1.404
 RAI  C28  H281  single    0.970  0.020  1.090
 RAI  C28  H282  single    0.970  0.020  1.090
 RAI  O29  H29   single    0.850  0.020  0.980
 RAI  N33  H33   single    0.890  0.020  1.040

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
 RAI  H1    C1   C6    119.85  3.000
 RAI  H1    C1   C2    119.02  3.000
 RAI  C6    C1   C2    121.13  3.000
 RAI  N15   C2   C3    121.09  3.000
 RAI  N15   C2   C1    119.23  3.000
 RAI  C3    C2   C1    119.63  3.000
 RAI  N12   C3   C4    120.07  3.000
 RAI  N12   C3   C2    120.82  3.000
 RAI  C4    C3   C2    119.08  3.000
 RAI  H4    C4   C5    119.95  3.000
 RAI  H4    C4   C3    119.15  3.000
 RAI  C5    C4   C3    120.89  3.000
 RAI  C10   C5   C6    122.31  3.000
 RAI  C10   C5   C4    117.87  3.000
 RAI  C6    C5   C4    119.80  3.000
 RAI  H6    C6   C5    121.32  3.000
 RAI  H6    C6   C1    119.26  3.000
 RAI  C5    C6   C1    119.42  3.000
 RAI  O32   C10  O11   123.36  3.000
 RAI  O32   C10  C5    123.74  3.000
 RAI  O11   C10  C5    112.90  3.000
 RAI  H11   O11  C10   110.01  3.000
 RAI  H12   N12  C13   113.49  3.000
 RAI  H12   N12  C3    115.58  3.000
 RAI  C13   N12  C3    125.30  3.000
 RAI  N33   C13  N14   120.38  3.000
 RAI  N33   C13  N12   123.51  3.000
 RAI  N14   C13  N12   116.09  3.000
 RAI  H142  N14  H141  113.50  3.000
 RAI  H142  N14  C13   118.92  3.000
 RAI  H141  N14  C13   114.19  3.000
 RAI  C19   N15  C16   114.27  3.000
 RAI  C19   N15  C2    120.62  3.000
 RAI  C16   N15  C2    125.06  3.000
 RAI  C28   C16  C24   110.13  3.000
 RAI  C28   C16  C17   109.17  3.000
 RAI  C24   C16  C17   111.75  3.000
 RAI  C28   C16  N15   112.93  3.000
 RAI  C24   C16  N15   111.18  3.000
 RAI  C17   C16  N15   101.42  3.000
 RAI  H172  C17  H171  107.13  3.000
 RAI  H172  C17  C18   113.51  3.000
 RAI  H171  C17  C18   109.57  3.000
 RAI  H172  C17  C16   111.68  3.000
 RAI  H171  C17  C16   109.11  3.000
 RAI  C18   C17  C16   105.80  3.000
 RAI  H182  C18  H181  107.39  3.000
 RAI  H182  C18  C19   108.75  3.000
 RAI  H181  C18  C19   110.08  3.000
 RAI  H182  C18  C17   112.89  3.000
 RAI  H181  C18  C17   113.42  3.000
 RAI  C19   C18  C17   104.22  3.000
 RAI  O34   C19  C18   127.14  3.000
 RAI  O34   C19  N15   124.40  3.000
 RAI  C18   C19  N15   108.46  3.000
 RAI  H242  C24  H241  106.74  3.000
 RAI  H242  C24  O25   111.27  3.000
 RAI  H241  C24  O25   111.66  3.000
 RAI  H242  C24  C16   107.71  3.000
 RAI  H241  C24  C16   110.00  3.000
 RAI  O25   C24  C16   109.37  3.000
 RAI  H25   O25  C24   108.62  3.000
 RAI  H282  C28  H281  106.73  3.000
 RAI  H282  C28  O29   111.49  3.000
 RAI  H281  C28  O29   112.21  3.000
 RAI  H282  C28  C16   107.33  3.000
 RAI  H281  C28  C16   108.36  3.000
 RAI  O29   C28  C16   110.51  3.000
 RAI  H29   O29  C28   108.33  3.000
 RAI  H33   N33  C13   111.23  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
 RAI  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 RAI  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 RAI  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 RAI  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 RAI  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 RAI  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 RAI  CONST_07  N15   C2   C3   C4   180.00   0.0  0
 RAI  CONST_08  N15   C2   C1   C6   180.00   0.0  0
 RAI  CONST_09  C18   C19  N15  C2   180.00   0.0  0
 RAI  CONST_10  C18   C19  N15  C16    0.00   0.0  0
 RAI  CONST_11  N12   C3   C2   C1   180.00   0.0  0
 RAI  CONST_12  C10   C5   C6   C1   180.00   0.0  0
 RAI  CONST_13  C10   C5   C4   C3   180.00   0.0  0
 RAI  CONST_14  N12   C3   C4   C5   180.00   0.0  0
 RAI  CONST_15  N15   C2   C3   N12    0.00   0.0  0
 RAI  CONST_16  O34   C19  N15  C2     0.00   0.0  0
 RAI  CONST_17  O34   C19  N15  C16  180.00   0.0  0
 RAI  CONST_18  H6    C6   C1   C2   180.00   0.0  0
 RAI  CONST_19  H4    C4   C3   C2   180.00   0.0  0
 RAI  CONST_20  H1    C1   C2   C3   180.00   0.0  0
 RAI  CONST_24  N14   C13  N12  C3     0.00   0.0  0
 RAI  CONST_25  N33   C13  N12  C3   180.00   0.0  0
 RAI  CONST_26  H11   O11  C10  C5   180.00   0.0  0
 RAI  CONST_27  H141  N14  C13  N12  180.00   0.0  0
 RAI  CONST_29  H33   N33  C13  N12    0.00   0.0  0
 RAI  Var_01    C16   N15  C2   C1   -87.57  30.0  2
 RAI  Var_02    C17   C16  N15  C2   164.33  30.0  1
 RAI  Var_03    C18   C17  C16  N15   23.66  30.0  1
 RAI  Var_04    C17   C18  C19  N15   10.93  30.0  1
 RAI  Var_05    C19   C18  C17  C16  -21.61  30.0  1
 RAI  Var_06    O11   C10  C5   C4   176.48  30.0  2
 RAI  Var_07    O25   C24  C16  N15  -60.36  30.0  3
 RAI  Var_08    O29   C28  C16  N15  -73.92  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
 RAI  plan-1  C1    0.020
 RAI  plan-1  C2    0.020
 RAI  plan-1  C3    0.020
 RAI  plan-1  C4    0.020
 RAI  plan-1  C5    0.020
 RAI  plan-1  C6    0.020
 RAI  plan-1  C10   0.020
 RAI  plan-1  N12   0.020
 RAI  plan-1  N15   0.020
 RAI  plan-1  H1    0.020
 RAI  plan-1  H4    0.020
 RAI  plan-1  H6    0.020
 RAI  plan-2  C3    0.020
 RAI  plan-2  N12   0.020
 RAI  plan-2  C13   0.020
 RAI  plan-2  N14   0.020
 RAI  plan-2  N33   0.020
 RAI  plan-2  H12   0.020
 RAI  plan-2  H141  0.020
 RAI  plan-2  H142  0.020
 RAI  plan-2  H33   0.020
 RAI  plan-3  C2    0.020
 RAI  plan-3  N15   0.020
 RAI  plan-3  C16   0.020
 RAI  plan-3  C18   0.020
 RAI  plan-3  C19   0.020
 RAI  plan-3  O34   0.020
 RAI  plan-4  C5    0.020
 RAI  plan-4  C10   0.020
 RAI  plan-4  O11   0.020
 RAI  plan-4  O32   0.020
 RAI  plan-4  H11   0.020

