# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 01:05:40 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](Cc2c[nH]c3ccccc23)C(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
 VB4  VB4  "(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan"  ligand  50  30  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VB4
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
 VB4  N03   N  N     0  -0.396   -7.1231  -13.0219  11.5176
 VB4  C02   C  CR6   0   0.134   -7.7035  -12.4749  10.4689
 VB4  C01   C  CH3   0  -0.720   -7.0211  -12.5600   9.1401
 VB4  C29   C  CR6   0   0.299   -8.9471  -11.8170  10.5788
 VB4  O30   O  OH1   0  -0.621   -9.4646  -11.2894   9.4780
 VB4  C12   C  CR6   0  -0.038   -9.5733  -11.7439  11.8314
 VB4  C13   C  C1    0   0.080  -10.8535  -11.0504  11.9650
 VB4  C05   C  CR6   0   0.002   -8.9278  -12.3396  12.9285
 VB4  C04   C  CR16  0  -0.140   -7.7162  -12.9599  12.7090
 VB4  C06   C  CH2   0  -0.321   -9.4962  -12.3203  14.3169
 VB4  O07   O  O2    0  -0.575  -10.7521  -13.0017  14.4080
 VB4  P08   P  P     0   1.458  -10.9349  -14.5839  14.5301
 VB4  O11   O  O     0  -0.691  -12.3489  -14.9172  14.7733
 VB4  O09   O  OH1   0  -0.740   -9.8698  -15.0772  15.6164
 VB4  O10   O  OH1   0  -0.736  -10.2680  -15.1719  13.2084
 VB4  N14   N  N     0  -0.457  -11.4113  -10.5423  10.9421
 VB4  C15   C  CH1   0  -0.205  -12.6867   -9.8907  11.0593
 VB4  C26   C  C     0   0.549  -12.6387   -8.6041  10.2546
 VB4  O28   O  O     0  -0.425  -12.1353   -8.5168   9.1653
 VB4  C16   C  CH2   0  -0.530  -13.7679  -10.8089  10.4417
 VB4  C17   C  CR5   0  -0.004  -15.0973  -10.1518  10.3036
 VB4  C18   C  CR15  0  -0.071  -15.6539   -9.6864   9.1448
 VB4  C21   C  CR56  0   0.028  -16.0263   -9.8344  11.3473
 VB4  N19   N  NR15  0  -0.686  -16.8613   -9.1056   9.4036
 VB4  C20   C  CR56  0   0.355  -17.1215   -9.1806  10.7410
 VB4  C22   C  CR16  0  -0.375  -16.0423  -10.0480  12.7305
 VB4  C25   C  CR16  0  -0.302  -18.2220   -8.7397  11.4745
 VB4  C23   C  CR16  0  -0.264  -17.1312   -9.6145  13.4611
 VB4  C24   C  CR16  0  -0.281  -18.2101   -8.9651  12.8376
 VB4  O27   O  OH1   0  -0.579  -13.2426   -7.6060  10.8784
 VB4  H011  H  HCH3  0   0.249   -6.8097  -11.5693   8.7339
 VB4  H012  H  HCH3  0   0.249   -6.0805  -13.0972   9.2392
 VB4  H013  H  HCH3  0   0.249   -7.6381  -13.0786   8.4042
 VB4  H301  H  HOH1  0   0.474  -10.3360  -10.8682   9.7272
 VB4  H131  H  H     0   0.268  -11.3120  -10.9760  12.9515
 VB4  H041  H  HCR6  0   0.259   -7.1928  -13.4330  13.5330
 VB4  H061  H  HCH2  0   0.273   -8.7730  -12.7452  15.0162
 VB4  H062  H  HCH2  0   0.272   -9.6972  -11.3001  14.6465
 VB4  H1    H  HOH1  0   0.498  -10.0935  -14.8485  16.5293
 VB4  H2    H  HOH1  0   0.501  -10.7691  -15.8916  12.8023
 VB4  H151  H  HCH1  0   0.273  -12.9431   -9.6739  12.1023
 VB4  H161  H  HCH2  0   0.266  -13.8304  -11.6983  11.0738
 VB4  H162  H  HCH2  0   0.263  -13.4115  -11.1386   9.4635
 VB4  H181  H  HCR5  0   0.284  -15.2695   -9.7312   8.1374
 VB4  H191  H  HNR5  0   0.408  -17.4696   -8.7036   8.7098
 VB4  H221  H  HCR6  0   0.240  -15.2154  -10.5475  13.2215
 VB4  H251  H  HCR6  0   0.257  -19.0546   -8.2405  10.9948
 VB4  H231  H  HCR6  0   0.244  -17.1578   -9.7749  14.5312
 VB4  H241  H  HCR6  0   0.247  -19.0492   -8.6359  13.4369
 VB4  H3    H  HOH1  0   0.480  -13.2469   -6.8150  10.3167

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
 VB4  O28  C26   double    1.203  0.020  1.203
 VB4  C26  O27   single    1.323  0.020  1.323
 VB4  C26  C15   single    1.518  0.020  1.518
 VB4  O30  C29   single    1.326  0.020  1.326
 VB4  C18  N19   aromatic  1.365  0.020  1.365
 VB4  C18  C17   aromatic  1.367  0.020  1.367
 VB4  C01  C02   single    1.496  0.020  1.496
 VB4  C16  C15   single    1.547  0.020  1.547
 VB4  C16  C17   single    1.489  0.020  1.489
 VB4  N19  C20   aromatic  1.365  0.020  1.365
 VB4  N14  C15   single    1.437  0.020  1.437
 VB4  N14  C13   double    1.271  0.020  1.271
 VB4  C17  C21   aromatic  1.433  0.020  1.433
 VB4  C29  C02   aromatic  1.411  0.020  1.411
 VB4  C29  C12   aromatic  1.402  0.020  1.402
 VB4  C02  N03   aromatic  1.318  0.020  1.318
 VB4  C13  C12   single    1.462  0.020  1.462
 VB4  C12  C05   aromatic  1.405  0.020  1.405
 VB4  C20  C21   aromatic  1.412  0.020  1.412
 VB4  C20  C25   aromatic  1.394  0.020  1.394
 VB4  C21  C22   aromatic  1.400  0.020  1.400
 VB4  N03  C04   aromatic  1.332  0.020  1.332
 VB4  C25  C24   aromatic  1.382  0.020  1.382
 VB4  C05  C04   aromatic  1.379  0.020  1.379
 VB4  C05  C06   single    1.500  0.020  1.500
 VB4  C22  C23   aromatic  1.381  0.020  1.381
 VB4  O07  C06   single    1.432  0.020  1.432
 VB4  O07  P08   single    1.597  0.020  1.597
 VB4  O11  P08   double    1.473  0.020  1.473
 VB4  O10  P08   single    1.593  0.020  1.593
 VB4  C24  C23   aromatic  1.405  0.020  1.405
 VB4  P08  O09   single    1.599  0.020  1.599
 VB4  C13  H131  single    0.930  0.020  1.080
 VB4  C15  H151  single    0.970  0.020  1.090
 VB4  C22  H221  single    0.930  0.020  1.080
 VB4  C24  H241  single    0.930  0.020  1.080
 VB4  C01  H012  single    0.970  0.020  1.090
 VB4  C01  H013  single    0.970  0.020  1.090
 VB4  C01  H011  single    0.970  0.020  1.090
 VB4  C04  H041  single    0.930  0.020  1.080
 VB4  C06  H061  single    0.970  0.020  1.090
 VB4  C06  H062  single    0.970  0.020  1.090
 VB4  C16  H162  single    0.970  0.020  1.090
 VB4  C16  H161  single    0.970  0.020  1.090
 VB4  C18  H181  single    0.930  0.020  1.080
 VB4  C23  H231  single    0.930  0.020  1.080
 VB4  C25  H251  single    0.930  0.020  1.080
 VB4  N19  H191  single    0.860  0.020  1.020
 VB4  O09  H1    single    0.850  0.020  0.980
 VB4  O10  H2    single    0.850  0.020  0.980
 VB4  O27  H3    single    0.850  0.020  0.980
 VB4  O30  H301  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
 VB4  C04   N03  C02   119.76  3.000
 VB4  C29   C02  C01   119.84  3.000
 VB4  C29   C02  N03   121.32  3.000
 VB4  C01   C02  N03   118.84  3.000
 VB4  H013  C01  H012  108.40  3.000
 VB4  H013  C01  H011  106.85  3.000
 VB4  H012  C01  H011  108.34  3.000
 VB4  H011  C01  C02   111.55  3.000
 VB4  H013  C01  C02   111.59  3.000
 VB4  H012  C01  C02   109.97  3.000
 VB4  C12   C29  O30   123.13  3.000
 VB4  C12   C29  C02   119.17  3.000
 VB4  O30   C29  C02   117.70  3.000
 VB4  H301  O30  C29   107.52  3.000
 VB4  C05   C12  C13   122.13  3.000
 VB4  C05   C12  C29   118.04  3.000
 VB4  C13   C12  C29   119.82  3.000
 VB4  H131  C13  N14   121.08  3.000
 VB4  H131  C13  C12   118.89  3.000
 VB4  N14   C13  C12   120.03  3.000
 VB4  C06   C05  C04   119.08  3.000
 VB4  C06   C05  C12   122.88  3.000
 VB4  C04   C05  C12   118.04  3.000
 VB4  H041  C04  C05   119.95  3.000
 VB4  H041  C04  N03   116.37  3.000
 VB4  C05   C04  N03   123.68  3.000
 VB4  H062  C06  H061  107.01  3.000
 VB4  H062  C06  O07   105.32  3.000
 VB4  H061  C06  O07   110.79  3.000
 VB4  H062  C06  C05   111.19  3.000
 VB4  H061  C06  C05   109.68  3.000
 VB4  O07   C06  C05   112.65  3.000
 VB4  P08   O07  C06   125.22  3.000
 VB4  O10   P08  O09    99.84  3.000
 VB4  O09   P08  O11   117.22  3.000
 VB4  O10   P08  O11   117.09  3.000
 VB4  O09   P08  O07   106.33  3.000
 VB4  O10   P08  O07   104.73  3.000
 VB4  O11   P08  O07   110.28  3.000
 VB4  H1    O09  P08   114.46  3.000
 VB4  H2    O10  P08   113.98  3.000
 VB4  C15   N14  C13   120.34  3.000
 VB4  H151  C15  C16   109.51  3.000
 VB4  H151  C15  C26   110.14  3.000
 VB4  C16   C15  C26   108.27  3.000
 VB4  H151  C15  N14   112.02  3.000
 VB4  C16   C15  N14   108.58  3.000
 VB4  C26   C15  N14   108.24  3.000
 VB4  O27   C26  O28   124.27  3.000
 VB4  O27   C26  C15   112.03  3.000
 VB4  O28   C26  C15   123.68  3.000
 VB4  H162  C16  H161  106.92  3.000
 VB4  H161  C16  C17   111.20  3.000
 VB4  H162  C16  C17   109.96  3.000
 VB4  H161  C16  C15   106.98  3.000
 VB4  H162  C16  C15   107.99  3.000
 VB4  C17   C16  C15   113.51  3.000
 VB4  C21   C17  C18   106.14  3.000
 VB4  C21   C17  C16   127.51  3.000
 VB4  C18   C17  C16   126.31  3.000
 VB4  H181  C18  N19   120.66  3.000
 VB4  H181  C18  C17   129.20  3.000
 VB4  N19   C18  C17   110.14  3.000
 VB4  C22   C21  C20   119.08  3.000
 VB4  C22   C21  C17   133.90  3.000
 VB4  C20   C21  C17   107.01  3.000
 VB4  H191  N19  C20   125.61  3.000
 VB4  H191  N19  C18   125.03  3.000
 VB4  C20   N19  C18   109.35  3.000
 VB4  C25   C20  N19   130.46  3.000
 VB4  C25   C20  C21   122.19  3.000
 VB4  N19   C20  C21   107.36  3.000
 VB4  H221  C22  C23   120.44  3.000
 VB4  H221  C22  C21   120.63  3.000
 VB4  C23   C22  C21   118.94  3.000
 VB4  H251  C25  C24   121.25  3.000
 VB4  H251  C25  C20   121.31  3.000
 VB4  C24   C25  C20   117.43  3.000
 VB4  H231  C23  C24   119.23  3.000
 VB4  H231  C23  C22   119.72  3.000
 VB4  C24   C23  C22   121.04  3.000
 VB4  H241  C24  C23   119.35  3.000
 VB4  H241  C24  C25   119.33  3.000
 VB4  C23   C24  C25   121.32  3.000
 VB4  H3    O27  C26   110.13  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
 VB4  CONST_01  C12   C29  C02  N03     0.00   0.0  0
 VB4  CONST_02  C12   C05  C04  N03     0.00   0.0  0
 VB4  CONST_03  C05   C12  C29  C02     0.00   0.0  0
 VB4  CONST_04  C05   C04  N03  C02     0.00   0.0  0
 VB4  CONST_05  C04   N03  C02  C29     0.00   0.0  0
 VB4  CONST_06  C04   C05  C12  C29     0.00   0.0  0
 VB4  CONST_07  C20   N19  C18  C17     0.00   0.0  0
 VB4  CONST_08  N19   C20  C21  C17     0.00   0.0  0
 VB4  CONST_09  C25   C20  C21  C17   180.00   0.0  0
 VB4  CONST_10  C23   C22  C21  C17   180.00   0.0  0
 VB4  CONST_11  C21   C20  N19  C18     0.00   0.0  0
 VB4  CONST_12  C25   C20  N19  C18   180.00   0.0  0
 VB4  CONST_13  C20   C21  C17  C18     0.00   0.0  0
 VB4  CONST_14  C22   C21  C17  C18   180.00   0.0  0
 VB4  CONST_15  N19   C18  C17  C21     0.00   0.0  0
 VB4  CONST_16  C24   C25  C20  C21     0.00   0.0  0
 VB4  CONST_17  C24   C23  C22  C21     0.00   0.0  0
 VB4  CONST_18  C22   C21  C20  N19   180.00   0.0  0
 VB4  CONST_19  C24   C25  C20  N19   180.00   0.0  0
 VB4  CONST_20  C23   C22  C21  C20     0.00   0.0  0
 VB4  CONST_21  C23   C24  C25  C20     0.00   0.0  0
 VB4  CONST_22  C25   C20  C21  C22     0.00   0.0  0
 VB4  CONST_23  C25   C24  C23  C22     0.00   0.0  0
 VB4  CONST_24  O30   C29  C02  N03   180.00   0.0  0
 VB4  CONST_25  C06   C05  C04  N03   180.00   0.0  0
 VB4  CONST_26  C13   C12  C29  C02   180.00   0.0  0
 VB4  CONST_27  C12   C29  C02  C01   180.00   0.0  0
 VB4  CONST_28  C04   N03  C02  C01   180.00   0.0  0
 VB4  CONST_29  C06   C05  C12  C29   180.00   0.0  0
 VB4  CONST_30  C05   C12  C29  O30   180.00   0.0  0
 VB4  CONST_31  C04   C05  C12  C13   180.00   0.0  0
 VB4  CONST_32  N19   C18  C17  C16   180.00   0.0  0
 VB4  CONST_33  C20   C21  C17  C16   180.00   0.0  0
 VB4  CONST_34  C22   C21  C17  C16     0.00   0.0  0
 VB4  CONST_35  H041  C04  N03  C02   180.00   0.0  0
 VB4  CONST_36  H041  C04  C05  C12   180.00   0.0  0
 VB4  CONST_37  H191  N19  C18  C17   180.00   0.0  0
 VB4  CONST_38  H221  C22  C21  C17     0.00   0.0  0
 VB4  CONST_39  H181  C18  C17  C21   180.00   0.0  0
 VB4  CONST_40  H191  N19  C20  C21   180.00   0.0  0
 VB4  CONST_41  H251  C25  C20  C21   180.00   0.0  0
 VB4  CONST_42  H231  C23  C22  C21   180.00   0.0  0
 VB4  CONST_43  H251  C25  C20  N19     0.00   0.0  0
 VB4  CONST_44  H181  C18  N19  C20   180.00   0.0  0
 VB4  CONST_45  H221  C22  C21  C20   180.00   0.0  0
 VB4  CONST_46  H241  C24  C25  C20   180.00   0.0  0
 VB4  CONST_47  H241  C24  C23  C22   180.00   0.0  0
 VB4  CONST_48  H191  N19  C20  C25     0.00   0.0  0
 VB4  CONST_49  H231  C23  C24  C25   180.00   0.0  0
 VB4  CONST_50  H251  C25  C24  C23   180.00   0.0  0
 VB4  CONST_51  H221  C22  C23  C24   180.00   0.0  0
 VB4  CONST_52  H3    O27  C26  C15   180.00   0.0  0
 VB4  CONST_53  H3    O27  C26  O28     0.00   0.0  0
 VB4  Var_01    N14   C13  C12  C29     1.62  30.0  2
 VB4  Var_02    O07   C06  C05  C12    62.28  30.0  2
 VB4  Var_03    N14   C13  C12  C05  -179.00  30.0  2
 VB4  Var_04    O07   C06  C05  C04  -118.09  30.0  2
 VB4  Var_05    C18   C17  C16  C15   104.47  30.0  2
 VB4  Var_06    C21   C17  C16  C15   -73.05  30.0  2
 VB4  Var_07    H012  C01  C02  N03    -0.04  30.0  2
 VB4  Var_08    H013  C01  C02  N03   120.30  30.0  2
 VB4  Var_09    H011  C01  C02  N03  -120.27  30.0  2
 VB4  Var_10    H012  C01  C02  C29  -180.00  30.0  2
 VB4  Var_11    H013  C01  C02  C29   -59.67  30.0  2
 VB4  Var_12    H011  C01  C02  C29    59.77  30.0  2
 VB4  Var_13    H131  C13  C12  C29  -178.13  30.0  2
 VB4  Var_14    H061  C06  C05  C12  -173.83  30.0  2
 VB4  Var_15    H062  C06  C05  C12   -55.68  30.0  2
 VB4  Var_16    H131  C13  C12  C05     1.25  30.0  2
 VB4  Var_17    H061  C06  C05  C04     5.81  30.0  2
 VB4  Var_18    H062  C06  C05  C04   123.96  30.0  2
 VB4  Var_19    H162  C16  C17  C18   -16.62  30.0  2
 VB4  Var_20    H161  C16  C17  C18  -134.84  30.0  2
 VB4  Var_21    H162  C16  C17  C21   165.87  30.0  2
 VB4  Var_22    H161  C16  C17  C21    47.64  30.0  2
 VB4  Var_23    C15   N14  C13  C12   178.31   0.0  2
 VB4  Var_24    P08   O07  C06  C05    80.79  30.0  1
 VB4  Var_25    O11   P08  O07  C06   172.85  30.0  3
 VB4  Var_26    O10   P08  O07  C06   -60.34  30.0  3
 VB4  Var_27    O09   P08  O07  C06    44.80  30.0  3
 VB4  Var_28    H131  C13  N14  C15    -1.94   0.0  2
 VB4  Var_29    H061  C06  O07  P08   -42.48  30.0  3
 VB4  Var_30    H062  C06  O07  P08  -157.85  30.0  3

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
 VB4  chir_01  C15  C26  C16  N14  negativ

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
 VB4  plan-1  N03   0.020
 VB4  plan-1  C02   0.020
 VB4  plan-1  C01   0.020
 VB4  plan-1  C29   0.020
 VB4  plan-1  O30   0.020
 VB4  plan-1  C12   0.020
 VB4  plan-1  C13   0.020
 VB4  plan-1  C05   0.020
 VB4  plan-1  C04   0.020
 VB4  plan-1  C06   0.020
 VB4  plan-1  H041  0.020
 VB4  plan-2  C16   0.020
 VB4  plan-2  C17   0.020
 VB4  plan-2  C18   0.020
 VB4  plan-2  C21   0.020
 VB4  plan-2  N19   0.020
 VB4  plan-2  C20   0.020
 VB4  plan-2  C22   0.020
 VB4  plan-2  C25   0.020
 VB4  plan-2  C23   0.020
 VB4  plan-2  C24   0.020
 VB4  plan-2  H181  0.020
 VB4  plan-2  H191  0.020
 VB4  plan-2  H221  0.020
 VB4  plan-2  H251  0.020
 VB4  plan-2  H231  0.020
 VB4  plan-2  H241  0.020
 VB4  plan-3  C15   0.020
 VB4  plan-3  C26   0.020
 VB4  plan-3  O28   0.020
 VB4  plan-3  O27   0.020
 VB4  plan-3  H3    0.020
 VB4  plan-4  C12   0.020
 VB4  plan-4  C13   0.020
 VB4  plan-4  N14   0.020
 VB4  plan-4  C15   0.020
 VB4  plan-4  H131  0.020

