# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:51:23 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: benzyl (2-{[(2-amino-4-oxo-3,4-dihydropteridin-7-yl)carbonyl]amino}ethyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2nc(cnc2C(=O)N1)C(=O)NCCNC(=O)OCc3ccccc3
#
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
 5MX  5MX  'benzyl (2-{[(2-amino-4-oxo-3,4-dihydropteridin-7-yl)carbonyl]amino}ethyl)carbamate'  ligand  45  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5MX
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
 5MX  N1    N  N     0  -0.506  -5.2762  -0.8145  -1.4262
 5MX  C2    C  CR6   0   0.706  -6.5687  -1.0034  -1.4696
 5MX  N2    N  NH2   0  -0.820  -7.1361  -1.4789  -2.5727
 5MX  N3    N  NR16  0  -0.716  -7.4020  -0.7370  -0.4168
 5MX  C4    C  CR6   0   0.548  -6.9877  -0.2431   0.8005
 5MX  O4    O  O     0  -0.429  -7.7668  -0.0209   1.7006
 5MX  N5    N  N     0  -0.348  -5.0144   0.4453   1.9783
 5MX  C6    C  CR16  0  -0.105  -3.7129   0.6373   2.0061
 5MX  C7    C  CR6   0   0.091  -2.9274   0.3479   0.8826
 5MX  N8    N  N     0  -0.426  -3.4399  -0.1257  -0.2307
 5MX  C4A   C  CR66  0  -0.029  -5.5387  -0.0287   0.8580
 5MX  C8A   C  CR66  0   0.403  -4.7625  -0.3300  -0.2787
 5MX  CAM   C  C     0   0.539  -1.4415   0.5863   0.9400
 5MX  OAN   O  O     0  -0.471  -0.9214   1.0041   1.9638
 5MX  NAO   N  NH1   0  -0.640  -0.7923   0.3219  -0.1958
 5MX  CAP   C  CH2   0  -0.297   0.6385   0.4361  -0.3385
 5MX  CAQ   C  CH2   0  -0.298   1.3541  -0.8651   0.0303
 5MX  NAR   N  NH1   0  -0.660   2.7746  -0.7897  -0.2036
 5MX  CAS   C  C     0   0.761   3.6257  -0.2767   0.7029
 5MX  OAT   O  O2    0  -0.482   4.8725  -0.2307   0.2183
 5MX  OAU   O  O     0  -0.519   3.3192   0.0876   1.8202
 5MX  HN2   H  HNH2  0   0.422  -6.5599  -1.6759  -3.3730
 5MX  HN2A  H  HNH2  0   0.425  -8.1286  -1.6143  -2.6601
 5MX  HN3   H  HNR6  0   0.435  -8.3958  -0.9018  -0.5230
 5MX  H6    H  HCR6  0   0.283  -3.2757   1.0253   2.9155
 5MX  HNAO  H  HNH1  0   0.412  -1.3267  -0.0596  -0.9624
 5MX  HAP   H  HCH2  0   0.261   0.8557   0.6965  -1.3746
 5MX  HAPA  H  HCH2  0   0.253   1.0000   1.2500   0.2896
 5MX  HAQ   H  HCH2  0   0.253   1.1686  -1.1061   1.0767
 5MX  HAQA  H  HCH2  0   0.260   0.9567  -1.6862  -0.5664
 5MX  HNAR  H  HNH1  0   0.403   3.1196  -1.0145  -1.1229
 5MX  C11   C  CH2   0  -0.237   5.8929   0.2332   1.1094
 5MX  H11   H  HCH2  0   0.248   5.6806   1.2548   1.4314
 5MX  H12   H  HCH2  0   0.247   5.9267  -0.4025   1.9972
 5MX  C12   C  CR6   0   0.075   7.1923   0.1718   0.3651
 5MX  C13   C  CR16  0  -0.302   7.8163   1.3356  -0.0699
 5MX  C14   C  CR16  0  -0.241   9.0193   1.2770  -0.7630
 5MX  C15   C  CR16  0  -0.262   9.6039   0.0484  -1.0348
 5MX  C16   C  CR16  0  -0.243   8.9847  -1.1205  -0.6063
 5MX  C17   C  CR16  0  -0.282   7.7875  -1.0580   0.0905
 5MX  H13   H  HCR6  0   0.256   7.3627   2.2975   0.1377
 5MX  H14   H  HCR6  0   0.258   9.4978   2.1916  -1.0883
 5MX  H15   H  HCR6  0   0.258  10.5405  -0.0005  -1.5751
 5MX  H16   H  HCR6  0   0.258   9.4391  -2.0812  -0.8110
 5MX  H17   H  HCR6  0   0.255   7.3153  -1.9732   0.4277

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
 5MX  N1   C2    double    1.307  0.020  1.307
 5MX  N1   C8A   single    1.347  0.020  1.347
 5MX  C2   N2    single    1.328  0.020  1.328
 5MX  C2   N3    single    1.369  0.020  1.369
 5MX  N2   HN2   single    0.860  0.020  1.020
 5MX  N2   HN2A  single    0.860  0.020  1.020
 5MX  N3   C4    single    1.378  0.020  1.378
 5MX  N3   HN3   single    0.860  0.020  1.020
 5MX  C4   O4    double    1.211  0.020  1.211
 5MX  C4   C4A   single    1.466  0.020  1.466
 5MX  N5   C6    aromatic  1.316  0.020  1.316
 5MX  N5   C4A   aromatic  1.325  0.020  1.325
 5MX  C6   C7    aromatic  1.401  0.020  1.401
 5MX  C6   H6    single    0.930  0.020  1.080
 5MX  C7   N8    aromatic  1.314  0.020  1.314
 5MX  C7   CAM   single    1.506  0.020  1.506
 5MX  N8   C8A   aromatic  1.339  0.020  1.339
 5MX  C4A  C8A   aromatic  1.409  0.020  1.409
 5MX  CAM  OAN   double    1.222  0.020  1.222
 5MX  CAM  NAO   single    1.335  0.020  1.335
 5MX  NAO  CAP   single    1.442  0.020  1.442
 5MX  NAO  HNAO  single    0.860  0.020  1.020
 5MX  CAP  CAQ   single    1.530  0.020  1.530
 5MX  CAP  HAP   single    0.970  0.020  1.090
 5MX  CAP  HAPA  single    0.970  0.020  1.090
 5MX  CAQ  NAR   single    1.442  0.020  1.442
 5MX  CAQ  HAQ   single    0.970  0.020  1.090
 5MX  CAQ  HAQA  single    0.970  0.020  1.090
 5MX  NAR  CAS   single    1.345  0.020  1.345
 5MX  NAR  HNAR  single    0.860  0.020  1.020
 5MX  CAS  OAT   single    1.338  0.020  1.338
 5MX  CAS  OAU   double    1.214  0.020  1.214
 5MX  OAT  C11   single    1.432  0.020  1.432
 5MX  C11  C12   single    1.499  0.020  1.499
 5MX  C11  H11   single    0.970  0.020  1.090
 5MX  C11  H12   single    0.970  0.020  1.090
 5MX  C12  C13   aromatic  1.390  0.020  1.390
 5MX  C13  C14   aromatic  1.390  0.020  1.390
 5MX  C14  C15   aromatic  1.387  0.020  1.387
 5MX  C15  C16   aromatic  1.390  0.020  1.390
 5MX  C16  C17   aromatic  1.387  0.020  1.387
 5MX  C12  C17   aromatic  1.394  0.020  1.394
 5MX  C13  H13   single    0.930  0.020  1.080
 5MX  C14  H14   single    0.930  0.020  1.080
 5MX  C15  H15   single    0.930  0.020  1.080
 5MX  C16  H16   single    0.930  0.020  1.080
 5MX  C17  H17   single    0.930  0.020  1.080

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
 5MX  C8A   N1   C2   117.21  3.000
 5MX  N3    C2   N2   116.64  3.000
 5MX  N3    C2   N1   123.25  3.000
 5MX  N2    C2   N1   120.11  3.000
 5MX  HN2A  N2   HN2  118.04  3.000
 5MX  HN2A  N2   C2   122.81  3.000
 5MX  HN2   N2   C2   119.09  3.000
 5MX  HN3   N3   C4   116.49  3.000
 5MX  HN3   N3   C2   119.01  3.000
 5MX  C4    N3   C2   124.50  3.000
 5MX  C4A   C4   O4   125.45  3.000
 5MX  C4A   C4   N3   112.61  3.000
 5MX  O4    C4   N3   121.94  3.000
 5MX  C4A   N5   C6   117.48  3.000
 5MX  H6    C6   C7   121.47  3.000
 5MX  H6    C6   N5   118.04  3.000
 5MX  C7    C6   N5   120.49  3.000
 5MX  CAM   C7   N8   118.31  3.000
 5MX  CAM   C7   C6   119.33  3.000
 5MX  N8    C7   C6   122.36  3.000
 5MX  C8A   N8   C7   118.08  3.000
 5MX  C8A   C4A  N5   122.74  3.000
 5MX  C8A   C4A  C4   118.79  3.000
 5MX  N5    C4A  C4   118.47  3.000
 5MX  C4A   C8A  N8   118.85  3.000
 5MX  C4A   C8A  N1   123.64  3.000
 5MX  N8    C8A  N1   117.51  3.000
 5MX  NAO   CAM  OAN  125.00  3.000
 5MX  NAO   CAM  C7   114.59  3.000
 5MX  OAN   CAM  C7   120.40  3.000
 5MX  HNAO  NAO  CAP  118.68  3.000
 5MX  HNAO  NAO  CAM  117.62  3.000
 5MX  CAP   NAO  CAM  123.44  3.000
 5MX  HAPA  CAP  HAP  107.66  3.000
 5MX  HAPA  CAP  CAQ  109.94  3.000
 5MX  HAP   CAP  CAQ  109.82  3.000
 5MX  HAPA  CAP  NAO  109.34  3.000
 5MX  HAP   CAP  NAO  108.10  3.000
 5MX  CAQ   CAP  NAO  111.88  3.000
 5MX  HAQA  CAQ  HAQ  107.28  3.000
 5MX  HAQA  CAQ  NAR  108.05  3.000
 5MX  HAQ   CAQ  NAR  109.57  3.000
 5MX  HAQA  CAQ  CAP  109.77  3.000
 5MX  HAQ   CAQ  CAP  109.87  3.000
 5MX  NAR   CAQ  CAP  112.17  3.000
 5MX  HNAR  NAR  CAS  118.91  3.000
 5MX  HNAR  NAR  CAQ  118.29  3.000
 5MX  CAS   NAR  CAQ  122.28  3.000
 5MX  OAU   CAS  OAT  123.91  3.000
 5MX  OAU   CAS  NAR  125.08  3.000
 5MX  OAT   CAS  NAR  111.01  3.000
 5MX  C11   OAT  CAS  116.72  3.000
 5MX  C12   C11  H12  110.67  3.000
 5MX  H12   C11  H11  108.10  3.000
 5MX  C12   C11  H11  110.69  3.000
 5MX  H12   C11  OAT  109.83  3.000
 5MX  H11   C11  OAT  110.37  3.000
 5MX  C12   C11  OAT  107.19  3.000
 5MX  C17   C12  C13  119.04  3.000
 5MX  C17   C12  C11  120.28  3.000
 5MX  C13   C12  C11  120.68  3.000
 5MX  H13   C13  C14  119.69  3.000
 5MX  H13   C13  C12  119.69  3.000
 5MX  C14   C13  C12  120.61  3.000
 5MX  H14   C14  C15  120.21  3.000
 5MX  H14   C14  C13  119.80  3.000
 5MX  C15   C14  C13  119.99  3.000
 5MX  H15   C15  C16  120.08  3.000
 5MX  H15   C15  C14  120.16  3.000
 5MX  C16   C15  C14  119.76  3.000
 5MX  H16   C16  C17  119.84  3.000
 5MX  H16   C16  C15  120.07  3.000
 5MX  C17   C16  C15  120.09  3.000
 5MX  H17   C17  C16  119.63  3.000
 5MX  H17   C17  C12  119.86  3.000
 5MX  C16   C17  C12  120.50  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
 5MX  CONST_01  N8    C7   C6   N5      0.00   0.0  0
 5MX  CONST_02  N8    C8A  C4A  N5      0.00   0.0  0
 5MX  CONST_03  C8A   C4A  N5   C6      0.00   0.0  0
 5MX  CONST_04  C8A   N8   C7   C6      0.00   0.0  0
 5MX  CONST_05  C4A   N5   C6   C7      0.00   0.0  0
 5MX  CONST_06  C4A   C8A  N8   C7      0.00   0.0  0
 5MX  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 5MX  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 5MX  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 5MX  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 5MX  CONST_11  C17   C12  C13  C14     0.00   0.0  0
 5MX  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 5MX  CONST_13  C4    N3   C2   N1      0.00   0.0  0
 5MX  CONST_14  C4A   C4   N3   C2      0.00   0.0  0
 5MX  CONST_15  C8A   N1   C2   N3      0.00   0.0  0
 5MX  CONST_16  CAM   C7   C6   N5    180.00   0.0  0
 5MX  CONST_17  CAM   C7   N8   C8A   180.00   0.0  0
 5MX  CONST_18  C14   C13  C12  C11   180.00   0.0  0
 5MX  CONST_19  C16   C17  C12  C11   180.00   0.0  0
 5MX  CONST_20  O4    C4   N3   C2    180.00   0.0  0
 5MX  CONST_21  C8A   N1   C2   N2    180.00   0.0  0
 5MX  CONST_22  C4    N3   C2   N2    180.00   0.0  0
 5MX  CONST_23  H6    C6   C7   N8    180.00   0.0  0
 5MX  CONST_24  H14   C14  C13  C12   180.00   0.0  0
 5MX  CONST_25  H16   C16  C17  C12   180.00   0.0  0
 5MX  CONST_26  H17   C17  C12  C13   180.00   0.0  0
 5MX  CONST_27  H15   C15  C14  C13   180.00   0.0  0
 5MX  CONST_28  H13   C13  C14  C15   180.00   0.0  0
 5MX  CONST_29  HN3   N3   C2   N1    180.00   0.0  0
 5MX  CONST_30  HN2   N2   C2   N1      0.00   0.0  0
 5MX  CONST_31  HN2A  N2   C2   N1    180.00   0.0  0
 5MX  CONST_32  CAP   NAO  CAM  C7    180.00   0.0  0
 5MX  CONST_33  HNAO  NAO  CAM  C7      0.00   0.0  0
 5MX  CONST_34  CAP   NAO  CAM  OAN     0.00   0.0  0
 5MX  Var_01    OAN   CAM  C7   C6      1.37  30.0  2
 5MX  Var_02    C13   C12  C11  OAT   107.39  30.0  2
 5MX  Var_03    C12   C11  OAT  CAS   178.87  30.0  3
 5MX  Var_04    CAQ   CAP  NAO  CAM    88.92  30.0  3
 5MX  Var_05    NAR   CAQ  CAP  NAO   175.74  30.0  3
 5MX  Var_06    CAS   NAR  CAQ  CAP    85.05  30.0  3
 5MX  Var_07    OAT   CAS  NAR  CAQ  -175.64  30.0  2

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
 5MX  plan-1  C11   0.020
 5MX  plan-1  C12   0.020
 5MX  plan-1  C13   0.020
 5MX  plan-1  C14   0.020
 5MX  plan-1  C15   0.020
 5MX  plan-1  C16   0.020
 5MX  plan-1  C17   0.020
 5MX  plan-1  H13   0.020
 5MX  plan-1  H14   0.020
 5MX  plan-1  H15   0.020
 5MX  plan-1  H16   0.020
 5MX  plan-1  H17   0.020
 5MX  plan-2  N1    0.020
 5MX  plan-2  C2    0.020
 5MX  plan-2  N2    0.020
 5MX  plan-2  N3    0.020
 5MX  plan-2  C4    0.020
 5MX  plan-2  O4    0.020
 5MX  plan-2  N5    0.020
 5MX  plan-2  C6    0.020
 5MX  plan-2  C7    0.020
 5MX  plan-2  N8    0.020
 5MX  plan-2  C4A   0.020
 5MX  plan-2  C8A   0.020
 5MX  plan-2  CAM   0.020
 5MX  plan-2  HN2   0.020
 5MX  plan-2  HN2A  0.020
 5MX  plan-2  HN3   0.020
 5MX  plan-2  H6    0.020
 5MX  plan-3  C7    0.020
 5MX  plan-3  CAM   0.020
 5MX  plan-3  OAN   0.020
 5MX  plan-3  NAO   0.020
 5MX  plan-3  CAP   0.020
 5MX  plan-3  HNAO  0.020
 5MX  plan-4  NAR   0.020
 5MX  plan-4  CAS   0.020
 5MX  plan-4  OAT   0.020
 5MX  plan-4  OAU   0.020

