# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jan 24 21:11:02 2023
#   Inital geometry file: a 101 line input string
#   Ligand name: [(~{E})-3-[(3~{S},4~{R})-4-azanyl-1-[(2~{S})-2-azanylpropanoyl]-4-carboxy-pyrrolidin-3-yl]prop-1-enyl]-tris(oxidanyl)boranium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)N1C[C@H](C/C=C/[B+](O)(O)O)[C@@](N)(C1)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
 XC3  XC3  "[(~{E})-3-[(3~{S},4~{R})-4-azanyl-1-[(2~{S})-2-azanylpropanoyl]-4-carboxy-pyrrolidin-3-yl]prop-1-enyl]-tris(oxidanyl)boranium"  ligand  42  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XC3
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
 XC3  O21  O  O     0  -0.498   2.7267  -2.4341   1.0189
 XC3  C17  C  C     0   0.543   2.9288  -1.3386   0.5132
 XC3  C18  C  CH1   0  -0.202   4.1784  -1.0530  -0.3134
 XC3  N20  N  NH2   0  -0.792   5.2078  -2.0218   0.0141
 XC3  C19  C  CH3   0  -0.665   3.8346  -1.1755  -1.7983
 XC3  N2   N  NR5   0  -0.461   2.0315  -0.3424   0.6302
 XC3  C3   C  CH2   0  -0.254   2.1829   1.0333   0.1836
 XC3  C4   C  CR5   0  -0.061   1.0741   1.7600   0.9413
 XC3  N13  N  NH2   0  -0.776   1.5285   2.0097   2.2983
 XC3  C14  C  C     0   0.559   0.6664   3.0545   0.2522
 XC3  O16  O  OH1   0  -0.590  -0.3857   3.6052   0.8420
 XC3  O15  O  O     0  -0.426   1.2457   3.5531  -0.6798
 XC3  C5   C  CR15  0  -0.299  -0.0379   0.6942   1.0034
 XC3  C1   C  CH2   0  -0.248   0.7711  -0.5597   1.3290
 XC3  C6   C  CH2   0  -0.530  -0.8107   0.5496  -0.3163
 XC3  C7   C  C1    0  -0.194  -1.9605  -0.3918  -0.1667
 XC3  C8   C  C1    0   0.017  -3.2067   0.0189  -0.2615
 XC3  B9   B  B     1   0.644  -5.1515  -1.4012  -1.1297
 XC3  O12  O  OB    0  -0.588  -6.1520  -2.1344  -0.6528
 XC3  O11  O  OB    0  -0.587  -4.7578  -0.9998  -2.3321
 XC3  O10  O  OB    0  -0.571  -4.2625  -0.9305  -0.0715
 XC3  H1   H  HCH1  0   0.235   4.5019  -0.0207  -0.1240
 XC3  H2   H  HNH2  0   0.348   6.0439  -1.7799  -0.5036
 XC3  H3   H  HNH2  0   0.346   5.4608  -1.9458   0.9915
 XC3  H5   H  HCH3  0   0.234   3.4657  -2.1770  -2.0215
 XC3  H6   H  HCH3  0   0.236   3.0808  -0.4539  -2.1104
 XC3  H7   H  HCH3  0   0.244   4.7249  -0.9978  -2.4026
 XC3  H8   H  HCH2  0   0.273   3.1626   1.4421   0.4348
 XC3  H9   H  HCH2  0   0.256   2.0560   1.1258  -0.8974
 XC3  H10  H  HNH2  0   0.363   2.3093   2.6545   2.3101
 XC3  H11  H  HNH2  0   0.362   0.7923   2.4128   2.8642
 XC3  H13  H  HOH1  0   0.487  -0.6040   4.4522   0.4239
 XC3  H14  H  HCR5  0   0.287  -0.7440   0.9212   1.8053
 XC3  H15  H  HCH2  0   0.251   0.2881  -1.4737   0.9816
 XC3  H16  H  HCH2  0   0.256   0.9300  -0.6623   2.4035
 XC3  H17  H  HCH2  0   0.277  -1.1849   1.5148  -0.6616
 XC3  H18  H  HCH2  0   0.277  -0.1548   0.1613  -1.1013
 XC3  H19  H  H     0   0.310  -1.7553  -1.4368   0.0400
 XC3  H20  H  H     0   0.323  -3.5701   1.0161  -0.4609
 XC3  H21  H  H     0   0.521  -6.7718  -2.4899  -1.2999
 XC3  H22  H  H     0   0.519  -5.3076  -1.2694  -3.0763
 XC3  H23  H  H     0   0.573  -4.5234  -1.0765   0.8578

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
 XC3  N13  C4   single  1.453  0.020  1.453
 XC3  O12  B9   single  1.329  0.020  1.329
 XC3  O15  C14  double  1.205  0.020  1.205
 XC3  O10  B9   single  1.460  0.020  1.460
 XC3  C4   C5   single  1.542  0.020  1.542
 XC3  C4   C14  single  1.522  0.020  1.522
 XC3  C4   C3   single  1.527  0.020  1.527
 XC3  B9   C8   single  2.560  0.020  2.560
 XC3  B9   O11  single  1.327  0.020  1.327
 XC3  C6   C5   single  1.536  0.020  1.536
 XC3  C6   C7   single  1.493  0.020  1.493
 XC3  C5   C1   single  1.527  0.020  1.527
 XC3  C8   C7   double  1.316  0.020  1.316
 XC3  C14  O16  single  1.326  0.020  1.326
 XC3  C3   N2   single  1.454  0.020  1.454
 XC3  C1   N2   single  1.457  0.020  1.457
 XC3  N2   C17  single  1.346  0.020  1.346
 XC3  C17  O21  double  1.223  0.020  1.223
 XC3  C17  C18  single  1.525  0.020  1.525
 XC3  N20  C18  single  1.451  0.020  1.451
 XC3  C18  C19  single  1.529  0.020  1.529
 XC3  C18  H1   single  0.939  0.020  1.096
 XC3  N20  H2   single  0.868  0.020  1.013
 XC3  N20  H3   single  0.868  0.020  1.013
 XC3  C19  H5   single  0.939  0.020  1.096
 XC3  C19  H6   single  0.939  0.020  1.096
 XC3  C19  H7   single  0.939  0.020  1.096
 XC3  C3   H8   single  0.939  0.020  1.096
 XC3  C3   H9   single  0.939  0.020  1.096
 XC3  N13  H10  single  0.868  0.020  1.013
 XC3  N13  H11  single  0.868  0.020  1.013
 XC3  O16  H13  single  0.832  0.020  0.971
 XC3  C5   H14  single  0.939  0.020  1.096
 XC3  C1   H15  single  0.939  0.020  1.096
 XC3  C1   H16  single  0.939  0.020  1.096
 XC3  C6   H17  single  0.939  0.020  1.096
 XC3  C6   H18  single  0.939  0.020  1.096
 XC3  C7   H19  single  0.930  0.020  1.086
 XC3  C8   H20  single  0.930  0.020  1.086
 XC3  O12  H21  single  0.832  0.020  0.971
 XC3  O11  H22  single  0.832  0.020  0.971
 XC3  O10  H23  single  0.832  0.020  0.971

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
 XC3  N2   C17  C18  117.05  3.000
 XC3  C18  C17  O21  121.80  3.000
 XC3  N2   C17  O21  121.12  3.000
 XC3  H1   C18  C19  108.00  3.000
 XC3  H1   C18  N20  112.31  3.000
 XC3  C19  C18  N20  108.98  3.000
 XC3  H1   C18  C17  108.90  3.000
 XC3  C19  C18  C17  109.09  3.000
 XC3  N20  C18  C17  109.50  3.000
 XC3  H3   N20  H2   105.62  3.000
 XC3  H3   N20  C18  110.19  3.000
 XC3  H2   N20  C18  108.11  3.000
 XC3  H7   C19  H6   107.35  3.000
 XC3  H7   C19  H5   108.20  3.000
 XC3  H6   C19  H5   108.40  3.000
 XC3  H7   C19  C18  109.97  3.000
 XC3  H6   C19  C18  112.39  3.000
 XC3  H5   C19  C18  110.39  3.000
 XC3  C1   N2   C3   112.23  3.000
 XC3  C1   N2   C17  120.52  3.000
 XC3  C3   N2   C17  127.17  3.000
 XC3  H9   C3   H8   107.49  3.000
 XC3  H9   C3   C4   111.49  3.000
 XC3  H8   C3   C4   111.07  3.000
 XC3  H9   C3   N2   111.83  3.000
 XC3  H8   C3   N2   112.17  3.000
 XC3  C4   C3   N2   102.84  3.000
 XC3  C5   C4   C14  114.39  3.000
 XC3  C14  C4   N13  111.13  3.000
 XC3  C5   C4   N13  107.87  3.000
 XC3  C14  C4   C3   112.00  3.000
 XC3  C5   C4   C3   102.40  3.000
 XC3  N13  C4   C3   108.55  3.000
 XC3  H11  N13  H10  107.50  3.000
 XC3  H11  N13  C4   111.29  3.000
 XC3  H10  N13  C4   111.19  3.000
 XC3  O15  C14  O16  123.61  3.000
 XC3  O16  C14  C4   111.37  3.000
 XC3  O15  C14  C4   124.97  3.000
 XC3  H13  O16  C14  110.47  3.000
 XC3  H14  C5   C6   108.97  3.000
 XC3  H14  C5   C1   110.88  3.000
 XC3  C6   C5   C1   111.86  3.000
 XC3  H14  C5   C4   110.62  3.000
 XC3  C1   C5   C4   101.19  3.000
 XC3  C6   C5   C4   113.17  3.000
 XC3  H16  C1   H15  107.42  3.000
 XC3  H16  C1   C5   111.37  3.000
 XC3  H15  C1   C5   112.68  3.000
 XC3  H16  C1   N2   111.12  3.000
 XC3  H15  C1   N2   110.81  3.000
 XC3  C5   C1   N2   103.50  3.000
 XC3  H18  C6   H17  107.01  3.000
 XC3  H18  C6   C7   108.04  3.000
 XC3  H17  C6   C7   108.98  3.000
 XC3  H18  C6   C5   110.38  3.000
 XC3  H17  C6   C5   111.16  3.000
 XC3  C7   C6   C5   111.14  3.000
 XC3  H19  C7   C8   119.57  3.000
 XC3  H19  C7   C6   118.73  3.000
 XC3  C8   C7   C6   121.69  3.000
 XC3  H20  C8   B9   101.19  3.000
 XC3  H20  C8   C7   128.33  3.000
 XC3  B9   C8   C7   124.82  3.000
 XC3  O10  B9   O11  112.24  3.000
 XC3  O11  B9   O12  135.66  3.000
 XC3  O10  B9   O12  112.09  3.000
 XC3  O11  B9   C8    85.07  3.000
 XC3  O10  B9   C8    27.47  3.000
 XC3  O12  B9   C8   139.14  3.000
 XC3  H21  O12  B9   116.52  3.000
 XC3  H22  O11  B9   116.47  3.000
 XC3  H23  O10  B9   118.62  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
 XC3  CONST_01  C3   N2   C17  O21   180.00   0.0  0
 XC3  CONST_02  C1   N2   C17  O21     0.00   0.0  0
 XC3  CONST_03  C3   N2   C17  C18     0.00   0.0  0
 XC3  CONST_04  C1   N2   C17  C18   180.00   0.0  0
 XC3  CONST_05  H13  O16  C14  C4    180.00   0.0  0
 XC3  CONST_06  H13  O16  C14  O15     0.00   0.0  0
 XC3  Var_01    C5   C1   N2   C3     13.49  30.0  1
 XC3  Var_02    C1   N2   C3   C4     13.11  30.0  1
 XC3  Var_03    C4   C3   N2   C17  -163.59  30.0  1
 XC3  Var_04    C5   C1   N2   C17  -169.56  30.0  1
 XC3  Var_05    H15  C1   N2   C3    134.52  30.0  1
 XC3  Var_06    H16  C1   N2   C3   -106.13  30.0  1
 XC3  Var_07    H8   C3   N2   C1    132.52  30.0  1
 XC3  Var_08    H9   C3   N2   C1   -106.63  30.0  1
 XC3  Var_09    H8   C3   N2   C17   -44.18  30.0  1
 XC3  Var_10    H9   C3   N2   C17    76.67  30.0  1
 XC3  Var_11    H15  C1   N2   C17   -48.53  30.0  1
 XC3  Var_12    H16  C1   N2   C17    70.81  30.0  1
 XC3  Var_13    C8   C7   C6   C5    113.75  30.0  3
 XC3  Var_14    H19  C7   C6   C5    -65.32  30.0  3
 XC3  Var_15    B9   C8   C7   C6    149.30   0.0  2
 XC3  Var_16    O12  B9   C8   C7     98.92  30.0  3
 XC3  Var_17    O10  B9   C8   C7     86.70  30.0  3
 XC3  Var_18    O11  B9   C8   C7    -84.93  30.0  3
 XC3  Var_19    H20  C8   C7   C6      0.94   0.0  2
 XC3  Var_20    H19  C7   C8   B9    -31.64   0.0  2
 XC3  Var_21    H17  C6   C7   C8     -9.09  30.0  1
 XC3  Var_22    H18  C6   C7   C8   -125.02  30.0  1
 XC3  Var_23    H20  C8   B9   O12  -105.88  30.0  3
 XC3  Var_24    H20  C8   B9   O11    70.26  30.0  3
 XC3  Var_25    H20  C8   B9   O10  -118.10  30.0  3
 XC3  Var_26    H20  C8   C7   H19  -179.99   0.0  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
 XC3  chir_01  C18  C17  N20  C19  negativ
 XC3  chir_02  C4   C5   C14  C3   positiv
 XC3  chir_03  C5   C1   C6   C4   positiv

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
 XC3  plan-1  O21  0.020
 XC3  plan-1  C17  0.020
 XC3  plan-1  C18  0.020
 XC3  plan-1  N2   0.020
 XC3  plan-1  C3   0.020
 XC3  plan-1  C1   0.020
 XC3  plan-2  C4   0.020
 XC3  plan-2  C14  0.020
 XC3  plan-2  O16  0.020
 XC3  plan-2  O15  0.020
 XC3  plan-2  H13  0.020
 XC3  plan-3  C6   0.020
 XC3  plan-3  C7   0.020
 XC3  plan-3  C8   0.020
 XC3  plan-3  B9   0.020
 XC3  plan-3  H19  0.020
 XC3  plan-3  H20  0.020

