# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:05:40 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: (Z)-N-[(1E)-1-carboxy-2-(2,3-dihydro-1H-indol-1-yl)ethylidene]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)\C(=C/[NH+]=C(CN2CCc3ccccc23)C(O)=O)C(=CN1)CO[P](O)(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
 7MN  7MN  (Z)-N-[(1E)-1-carboxy-2-(2,3-dihydro-1H-indol-1-yl)ethylidene]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methanaminium  peptide  50  30  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7MN
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
 7MN  C     C  C      0   0.401  80.4539  18.6966   8.5816
 7MN  N     N  NC1    1  -0.533  81.1726  17.0827  10.1739
 7MN  O     O  O      0  -0.587  81.4592  18.3463   7.9314
 7MN  P     P  P      0   1.222  79.5011  12.4768  13.5158
 7MN  N1    N  NH1    0  -0.644  84.4549  13.6242  11.9994
 7MN  C2    C  C      0   0.249  84.5332  14.3792  10.8771
 7MN  C3    C  C      0   0.248  83.5091  15.2422  10.5975
 7MN  O3    O  OH1    0  -0.653  83.5249  16.0253   9.4938
 7MN  C4    C  C      0   0.103  82.3683  15.3782  11.4530
 7MN  C5    C  C      0  -0.066  82.3598  14.5316  12.6138
 7MN  C6    C  C1     0  -0.019  83.4033  13.6892  12.8359
 7MN  CA    C  C      0   0.112  80.2645  17.9735   9.9061
 7MN  CB    C  CH2    0  -0.364  79.1696  18.3057  10.8640
 7MN  CG    C  CH2    0  -0.507  76.8569  15.4047  11.1769
 7MN  O1P   O  OP    -1  -0.892  79.4331  12.5717  15.0371
 7MN  O2P   O  O      0  -0.877  78.1501  12.4073  12.8111
 7MN  O3P   O  OP    -1  -0.889  80.5566  11.5095  12.9924
 7MN  C4A   C  C1     0  -0.135  81.3125  16.2618  11.2525
 7MN  C5A   C  CH2    0  -0.267  81.2090  14.5338  13.5855
 7MN  CD1   C  CH2    0  -0.280  77.6527  16.3982  10.3224
 7MN  CD2   C  CR56   0  -0.014  76.8075  16.0993  12.5091
 7MN  NE1   N  NR5    0  -0.548  78.4295  17.1509  11.3010
 7MN  CE2   C  CR56   0   0.429  77.7711  17.1154  12.5148
 7MN  CE3   C  CR16   0  -0.334  76.0561  15.8403  13.6336
 7MN  CH2   C  CR16   0  -0.258  77.1970  17.6255  14.7777
 7MN  OXT   O  OC    -1  -0.557  79.6010  19.5488   8.2930
 7MN  CZ2   C  CR16   0  -0.348  77.9696  17.8943  13.6478
 7MN  CZ3   C  CR16   0  -0.280  76.2484  16.6140  14.7820
 7MN  H6    H  H      0   0.307  83.4391  13.0308  13.6916
 7MN  HB    H  HCH2   0   0.280  79.6255  18.7789  11.7412
 7MN  HBA   H  HCH2   0   0.262  78.5227  19.0566  10.3997
 7MN  HG    H  HCH2   0   0.254  77.3822  14.4515  11.2802
 7MN  H2A   H  HCH3   0   0.276  85.4735  13.9723   8.9878
 7MN  H2AA  H  HCH3   0   0.279  86.3239  15.1577   9.9832
 7MN  H4A   H  H      0   0.300  80.4998  16.2937  11.9544
 7MN  H5A   H  HCH2   0   0.208  81.5097  13.9703  14.4755
 7MN  H5AA  H  HCH2   0   0.195  81.0418  15.5637  13.9324
 7MN  HD1   H  HCH2   0   0.245  78.3047  15.9104   9.5967
 7MN  HE3   H  HCR6   0   0.242  75.3163  15.0487  13.6262
 7MN  HH2   H  HCR6   0   0.245  77.3420  18.2289  15.6651
 7MN  HZ2   H  HCR6   0   0.253  78.6969  18.6957  13.6741
 7MN  HZ3   H  HCR6   0   0.240  75.6579  16.4261  15.6688
 7MN  H     H  HNC1   0   0.438  81.8734  17.0265   9.4270
 7MN  H19   H  HNH1   0   0.433  85.2055  12.9826  12.2086
 7MN  H20   H  HOH1   0   0.494  84.3347  15.9394   8.9776
 7MN  H21   H  HCH2   0   0.253  75.8749  15.1946  10.7539
 7MN  H22   H  HCH3   0   0.285  86.4004  13.4498  10.3818
 7MN  H23   H  HCH2   0   0.223  76.9790  17.0689   9.7716
 7MN  C2A   C  CH3    0  -0.778  85.7429  14.2339  10.0124
 7MN  O4P   O  O2     0  -0.645  80.0342  14.0394  13.0162

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
 7MN  C    CA    single    1.525  0.021  1.525
 7MN  N    C4A   single    1.363  0.020  1.363
 7MN  O    C     deloc     1.231  0.020  1.231
 7MN  P    O1P   deloc     1.526  0.020  1.526
 7MN  N1   C6    single    1.345  0.020  1.345
 7MN  C2   N1    single    1.355  0.020  1.355
 7MN  C3   C2    double    1.368  0.020  1.368
 7MN  C3   C4    single    1.432  0.020  1.432
 7MN  O3   C3    single    1.353  0.020  1.353
 7MN  C4   C5    single    1.437  0.020  1.437
 7MN  C5   C6    double    1.359  0.020  1.359
 7MN  C5   C5A   single    1.506  0.020  1.506
 7MN  C6   H6    single    0.930  0.020  1.080
 7MN  CA   N     double    1.458  0.019  1.458
 7MN  CA   CB    single    1.521  0.033  1.521
 7MN  CB   HB    single    0.970  0.020  1.090
 7MN  CB   HBA   single    0.970  0.020  1.090
 7MN  CG   CD2   single    1.503  0.020  1.503
 7MN  CG   HG    single    0.970  0.020  1.090
 7MN  C2A  C2    single    1.494  0.020  1.494
 7MN  C2A  H2A   single    0.970  0.020  1.090
 7MN  C2A  H2AA  single    0.970  0.020  1.090
 7MN  O2P  P     deloc     1.525  0.020  1.525
 7MN  O3P  P     deloc     1.524  0.020  1.524
 7MN  C4A  C4    double    1.391  0.020  1.391
 7MN  C4A  H4A   single    0.930  0.020  1.080
 7MN  O4P  P     single    1.725  0.020  1.725
 7MN  O4P  C5A   single    1.396  0.020  1.396
 7MN  C5A  H5A   single    0.970  0.020  1.090
 7MN  C5A  H5AA  single    0.970  0.020  1.090
 7MN  CD1  CG    single    1.533  0.020  1.533
 7MN  CD1  NE1   single    1.459  0.020  1.459
 7MN  CD1  HD1   single    0.970  0.020  1.090
 7MN  CD2  CE2   aromatic  1.400  0.020  1.400
 7MN  CD2  CE3   aromatic  1.377  0.020  1.377
 7MN  NE1  CB    single    1.440  0.020  1.440
 7MN  NE1  CE2   single    1.381  0.020  1.381
 7MN  CE2  CZ2   aromatic  1.389  0.020  1.389
 7MN  CE3  CZ3   aromatic  1.398  0.020  1.398
 7MN  CE3  HE3   single    0.930  0.020  1.080
 7MN  CH2  HH2   single    0.930  0.020  1.080
 7MN  OXT  C     deloc     1.240  0.020  1.240
 7MN  CZ2  CH2   aromatic  1.395  0.020  1.395
 7MN  CZ2  HZ2   single    0.930  0.020  1.080
 7MN  CZ3  CH2   aromatic  1.387  0.020  1.387
 7MN  CZ3  HZ3   single    0.930  0.020  1.080
 7MN  N    H     single    0.860  0.020  0.860
 7MN  N1   H19   single    0.860  0.020  1.020
 7MN  O3   H20   single    0.850  0.020  0.980
 7MN  CG   H21   single    0.970  0.020  1.090
 7MN  C2A  H22   single    0.970  0.020  1.090
 7MN  CD1  H23   single    0.970  0.020  1.090

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
 7MN  OXT   C    CA    120.80  1.700
 7MN  OXT   C    O     128.77  3.000
 7MN  CA    C    O     120.80  1.700
 7MN  H     N    C4A   118.24  3.000
 7MN  H     N    CA    114.00  3.000
 7MN  C4A   N    CA    130.36  3.000
 7MN  O4P   P    O3P   105.15  3.000
 7MN  O4P   P    O2P   100.44  3.000
 7MN  O3P   P    O2P   115.20  3.000
 7MN  O4P   P    O1P   104.25  3.000
 7MN  O3P   P    O1P   114.37  3.000
 7MN  O2P   P    O1P   115.09  3.000
 7MN  H19   N1   C6    118.88  3.000
 7MN  H19   N1   C2    118.88  3.000
 7MN  C6    N1   C2    122.23  3.000
 7MN  C2A   C2   C3    123.31  3.000
 7MN  C2A   C2   N1    118.16  3.000
 7MN  C3    C2   N1    118.53  3.000
 7MN  C4    C3   O3    116.19  3.000
 7MN  O3    C3   C2    121.53  3.000
 7MN  C4    C3   C2    122.27  3.000
 7MN  H20   O3   C3    113.26  3.000
 7MN  C4A   C4   C5    119.09  3.000
 7MN  C4A   C4   C3    125.35  3.000
 7MN  C5    C4   C3    115.55  3.000
 7MN  C5A   C5   C6    118.82  3.000
 7MN  C5A   C5   C4    121.66  3.000
 7MN  C6    C5   C4    119.51  3.000
 7MN  H6    C6   C5    122.18  3.000
 7MN  H6    C6   N1    115.92  3.000
 7MN  C5    C6   N1    121.90  3.000
 7MN  CB    CA   N     110.40  1.500
 7MN  CB    CA   C     110.50  1.500
 7MN  N     CA   C     111.00  2.800
 7MN  HBA   CB   HB    106.80  3.000
 7MN  HBA   CB   NE1   112.04  3.000
 7MN  HB    CB   NE1   108.49  3.000
 7MN  NE1   CB   CA    113.17  3.000
 7MN  HBA   CB   CA    108.31  3.000
 7MN  HB    CB   CA    107.74  3.000
 7MN  H21   CG   HG    107.54  3.000
 7MN  H21   CG   CD2   113.80  3.000
 7MN  HG    CG   CD2   109.57  3.000
 7MN  H21   CG   CD1   112.11  3.000
 7MN  HG    CG   CD1   111.61  3.000
 7MN  CD2   CG   CD1   102.22  3.000
 7MN  H4A   C4A  C4    119.92  3.000
 7MN  H4A   C4A  N     114.93  3.000
 7MN  C4    C4A  N     125.08  3.000
 7MN  H5AA  C5A  H5A   105.50  3.000
 7MN  H5AA  C5A  O4P   109.42  3.000
 7MN  H5A   C5A  O4P   112.34  3.000
 7MN  H5AA  C5A  C5    108.73  3.000
 7MN  H5A   C5A  C5    108.28  3.000
 7MN  O4P   C5A  C5    112.29  3.000
 7MN  H23   CD1  HD1   107.83  3.000
 7MN  H23   CD1  NE1   110.36  3.000
 7MN  HD1   CD1  NE1   111.03  3.000
 7MN  H23   CD1  CG    110.90  3.000
 7MN  HD1   CD1  CG    113.03  3.000
 7MN  NE1   CD1  CG    103.70  3.000
 7MN  CE3   CD2  CE2   120.57  3.000
 7MN  CE3   CD2  CG    130.90  3.000
 7MN  CE2   CD2  CG    108.43  3.000
 7MN  CE2   NE1  CD1   108.81  3.000
 7MN  CE2   NE1  CB    122.17  3.000
 7MN  CD1   NE1  CB    118.95  3.000
 7MN  CZ2   CE2  NE1   129.36  3.000
 7MN  CZ2   CE2  CD2   120.56  3.000
 7MN  NE1   CE2  CD2   110.06  3.000
 7MN  HE3   CE3  CZ3   120.26  3.000
 7MN  HE3   CE3  CD2   120.29  3.000
 7MN  CZ3   CE3  CD2   119.45  3.000
 7MN  HH2   CH2  CZ3   119.70  3.000
 7MN  CZ3   CH2  CZ2   121.46  3.000
 7MN  HH2   CH2  CZ2   118.83  3.000
 7MN  HZ2   CZ2  CH2   119.67  3.000
 7MN  HZ2   CZ2  CE2   122.07  3.000
 7MN  CH2   CZ2  CE2   118.26  3.000
 7MN  HZ3   CZ3  CH2   120.17  3.000
 7MN  HZ3   CZ3  CE3   120.14  3.000
 7MN  CH2   CZ3  CE3   119.69  3.000
 7MN  H22   C2A  H2AA  107.30  3.000
 7MN  H22   C2A  H2A   107.17  3.000
 7MN  H2AA  C2A  H2A   108.01  3.000
 7MN  H22   C2A  C2    111.28  3.000
 7MN  H2AA  C2A  C2    111.35  3.000
 7MN  H2A   C2A  C2    111.52  3.000
 7MN  C5A   O4P  P     117.57  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
 7MN  CONST_01  CH2  CZ2  CE2  CD2     0.00   0.0  0
 7MN  CONST_02  CH2  CZ3  CE3  CD2     0.00   0.0  0
 7MN  CONST_03  CZ3  CE3  CD2  CE2     0.00   0.0  0
 7MN  CONST_04  CZ3  CH2  CZ2  CE2     0.00   0.0  0
 7MN  CONST_05  CZ2  CE2  CD2  CE3     0.00   0.0  0
 7MN  CONST_06  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 7MN  CONST_07  HE3  CE3  CD2  CG      0.00   0.0  0
 7MN  CONST_08  HZ2  CZ2  CE2  CD2   180.00   0.0  0
 7MN  CONST_09  HZ3  CZ3  CE3  CD2   180.00   0.0  0
 7MN  CONST_10  HH2  CH2  CZ2  CE2   180.00   0.0  0
 7MN  Var_01    CE2  NE1  CD1  CG    -25.48  30.0  1
 7MN  Var_02    CE2  CD2  CG   CD1   -15.83  30.0  1
 7MN  Var_03    CD2  CE2  NE1  CD1    16.11  30.0  1
 7MN  Var_04    NE1  CD1  CG   CD2    24.27  30.0  1
 7MN  Var_05    C3   C4   C4A  N       3.57   0.0  2
 7MN  Var_06    O4P  C5A  C5   C4     66.43  30.0  3
 7MN  Var_07    CD1  NE1  CB   CA    -64.58  30.0  3
 7MN  Var_08    H2A  C2A  C2   N1    123.85  30.0  3
 7MN  Var_09    NE1  CB   CA   C     129.99  30.0  3
 7MN  Var_10    C5   C5A  O4P  P     107.46  30.0  3
 7MN  Var_11    CA   N    C4A  C4   -177.23  30.0  1
 7MN  Var_12    C4A  N    CA   C    -179.98   0.0  2
 7MN  Var_13    O    C    CA   N      -0.44  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
 7MN  plan-1  N    0.020
 7MN  plan-1  N1   0.020
 7MN  plan-1  C2   0.020
 7MN  plan-1  C3   0.020
 7MN  plan-1  O3   0.020
 7MN  plan-1  C4   0.020
 7MN  plan-1  C5   0.020
 7MN  plan-1  C6   0.020
 7MN  plan-1  C4A  0.020
 7MN  plan-1  C5A  0.020
 7MN  plan-1  H6   0.020
 7MN  plan-1  H4A  0.020
 7MN  plan-1  H19  0.020
 7MN  plan-1  C2A  0.020
 7MN  plan-2  CG   0.020
 7MN  plan-2  CD2  0.020
 7MN  plan-2  NE1  0.020
 7MN  plan-2  CE2  0.020
 7MN  plan-2  CE3  0.020
 7MN  plan-2  CH2  0.020
 7MN  plan-2  CZ2  0.020
 7MN  plan-2  CZ3  0.020
 7MN  plan-2  HE3  0.020
 7MN  plan-2  HH2  0.020
 7MN  plan-2  HZ2  0.020
 7MN  plan-2  HZ3  0.020
 7MN  plan-3  C    0.020
 7MN  plan-3  O    0.020
 7MN  plan-3  CA   0.020
 7MN  plan-3  OXT  0.020
 7MN  plan-4  C    0.020
 7MN  plan-4  N    0.020
 7MN  plan-4  CA   0.020
 7MN  plan-4  CB   0.020
 7MN  plan-4  C4A  0.020
 7MN  plan-4  H    0.020

