# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 16:23:16 2019
#
#   Inital geometry file: a 77 line input string
#   Ligand name: 4-carboxy-N-methyl-D-phenylalanine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CN[C@H](Cc1ccc(cc1)C(O)=O)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
1JM        1JM '4-carboxy-N-methyl-D-phenylalanine' ligand 27 16 .
2019-03-22 2019-03-22
;
CIF prepared directly in eLBOW
;
#
data_comp_1JM
#
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
1JM         CAA    C   CH3    0  -0.127   -2.6987    2.2131    1.2397
1JM         N      N   NH1    0  -0.282   -2.1460    1.4914    0.1270
1JM         CA     C   CH1    0  -0.086   -2.3114    0.0430    0.2303
1JM         C      C   C      0   0.344   -3.8011   -0.3929    0.0319
1JM         O      O   OC    -1  -0.579   -4.1228   -1.0222   -1.0138
1JM         CB     C   CH2    0  -0.114   -1.4195   -0.7086   -0.7680
1JM         CG     C   C      0  -0.079    0.0380   -0.5255   -0.5233
1JM         CD1    C   C1     0  -0.165    0.7241   -1.3604    0.3685
1JM         CE1    C   C1     0  -0.115    2.0960   -1.2163    0.5661
1JM         CZ     C   C      0  -0.119    2.8181   -0.2351   -0.1209
1JM         CAL    C   C      0   0.355    4.3129   -0.0931    0.0793
1JM         OAB    O   OC    -1  -0.588    4.9297    0.8076   -0.5643
1JM         OAD    O   O      0  -0.588    4.8968   -0.8828    0.8803
1JM         CE2    C   C1     0  -0.116    2.1326    0.6070   -1.0019
1JM         CD2    C   C1     0  -0.168    0.7604    0.4649   -1.2015
1JM         H1     H   HCH3   0   0.130   -3.7562    1.8687    1.4086
1JM         H2     H   HCH3   0   0.009   -2.1288    2.0783    2.2026
1JM         H3     H   HCH3   0   0.033   -2.6934    3.3077    0.9905
1JM         H4     H   HNH1   0   0.132   -1.1651    1.6987    0.0366
1JM         H6     H   HCH1   0   0.043   -2.0235   -0.3103    1.2694
1JM         H10    H   HCH2   0   0.091   -1.6882   -1.7957   -0.6877
1JM         H11    H   HCH2   0   0.096   -1.6854   -0.3841   -1.8086
1JM         H12    H   H      0   0.109    0.1673   -2.1354    0.9144
1JM         H13    H   H      0   0.135    2.6399   -1.8723    1.2633
1JM         H15    H   H      0   0.135    2.7050    1.3818   -1.5352
1JM         H16    H   H      0   0.113    0.2331    1.1311   -1.8997
1JM         O1     O   O      0  -0.601   -4.6130   -0.1316    0.9681
#
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
1JM   OAD     CAL   deloc         1.267 0.020     1.267
1JM   CE2     CD2   aromatic      1.394 0.020     1.394
1JM   CE2     CZ    aromatic      1.398 0.020     1.398
1JM   CD2     CG    aromatic      1.401 0.020     1.401
1JM   CAL     CZ    single        1.515 0.020     1.515
1JM   CAL     OAB   deloc         1.267 0.020     1.267
1JM   CZ      CE1   aromatic      1.399 0.020     1.399
1JM   C       CA    single        1.565 0.020     1.565
1JM   C       O     deloc         1.262 0.020     1.262
1JM   CA      N     single        1.461 0.020     1.461
1JM   CA      CB    single        1.535 0.020     1.535
1JM   CG      CB    single        1.489 0.020     1.489
1JM   CG      CD1   aromatic      1.401 0.020     1.401
1JM   N       CAA   single        1.437 0.020     1.437
1JM   CE1     CD1   aromatic      1.393 0.020     1.393
1JM   CAA     H1    single        0.970 0.020     1.090
1JM   CAA     H2    single        0.970 0.020     1.090
1JM   CAA     H3    single        0.970 0.020     1.090
1JM   N       H4    single        0.890 0.020     1.040
1JM   CA      H6    single        0.970 0.020     1.090
1JM   CB      H10   single        0.970 0.020     1.090
1JM   CB      H11   single        0.970 0.020     1.090
1JM   CD1     H12   single        0.930 0.020     1.080
1JM   CE1     H13   single        0.930 0.020     1.080
1JM   CE2     H15   single        0.930 0.020     1.080
1JM   CD2     H16   single        0.930 0.020     1.080
1JM   C       O1    deloc         1.267 0.020     1.267
#
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
1JM   H3      CAA     H2          107.69 3.000
1JM   H3      CAA     H1          109.65 3.000
1JM   H2      CAA     H1          108.08 3.000
1JM   H3      CAA     N           108.42 3.000
1JM   H2      CAA     N           114.02 3.000
1JM   H1      CAA     N           108.91 3.000
1JM   H4      N       CA          108.71 3.000
1JM   H4      N       CAA         109.94 3.000
1JM   CA      N       CAA         113.55 3.000
1JM   H6      CA      CB          107.20 3.000
1JM   H6      CA      C           105.72 3.000
1JM   CB      CA      C           109.53 3.000
1JM   H6      CA      N           110.16 3.000
1JM   CB      CA      N           111.93 3.000
1JM   C       CA      N           112.02 3.000
1JM   O1      C       O           123.50 3.000
1JM   O1      C       CA          117.33 3.000
1JM   O       C       CA          119.11 3.000
1JM   H11     CB      H10         106.84 3.000
1JM   H11     CB      CG          110.41 3.000
1JM   H10     CB      CG          109.97 3.000
1JM   H11     CB      CA          108.89 3.000
1JM   H10     CB      CA          106.77 3.000
1JM   CG      CB      CA          113.67 3.000
1JM   CD2     CG      CD1         118.48 3.000
1JM   CD1     CG      CB          120.70 3.000
1JM   CD2     CG      CB          120.80 3.000
1JM   H12     CD1     CE1         120.07 3.000
1JM   H12     CD1     CG          119.22 3.000
1JM   CE1     CD1     CG          120.71 3.000
1JM   H13     CE1     CZ          118.29 3.000
1JM   H13     CE1     CD1         120.97 3.000
1JM   CZ      CE1     CD1         120.75 3.000
1JM   CE2     CZ      CAL         120.70 3.000
1JM   CAL     CZ      CE1         120.69 3.000
1JM   CE2     CZ      CE1         118.61 3.000
1JM   OAD     CAL     OAB         122.66 3.000
1JM   OAB     CAL     CZ          118.67 3.000
1JM   OAD     CAL     CZ          118.67 3.000
1JM   H15     CE2     CD2         120.94 3.000
1JM   H15     CE2     CZ          118.30 3.000
1JM   CD2     CE2     CZ          120.76 3.000
1JM   H16     CD2     CE2         120.08 3.000
1JM   H16     CD2     CG          119.23 3.000
1JM   CE2     CD2     CG          120.69 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
1JM CONST_01       CZ      CE2     CD2     CG           -0.00   0.0 0
1JM CONST_02       CZ      CE1     CD1     CG            0.02   0.0 0
1JM CONST_03       CE2     CD2     CG      CD1           0.59   0.0 0
1JM CONST_04       CE2     CZ      CE1     CD1           0.57   0.0 0
1JM CONST_05       CD2     CE2     CZ      CE1          -0.57   0.0 0
1JM CONST_06       CD2     CG      CD1     CE1          -0.59   0.0 0
1JM CONST_07       CE2     CD2     CG      CB         -177.98   0.0 0
1JM CONST_08       CE1     CD1     CG      CB          177.98   0.0 0
1JM CONST_09       CAL     CZ      CE1     CD1        -179.08   0.0 0
1JM CONST_10       CD2     CE2     CZ      CAL         179.07   0.0 0
1JM CONST_11       H15     CE2     CD2     CG          179.81   0.0 0
1JM CONST_12       H13     CE1     CD1     CG         -179.79   0.0 0
1JM CONST_13       H16     CD2     CG      CD1        -179.62   0.0 0
1JM CONST_14       H12     CD1     CE1     CZ         -180.00   0.0 0
1JM Var_01         CD2     CG      CB      CA          -94.57  30.0 2
1JM Var_02         OAD     CAL     CZ      CE1           0.12  30.0 2
1JM Var_03         H1      CAA     N       CA          -50.64  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
1JM chir_01   CA      C       N       CB    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
1JM plan-1     CB 0.020
1JM plan-1     CG 0.020
1JM plan-1    CD1 0.020
1JM plan-1    CE1 0.020
1JM plan-1     CZ 0.020
1JM plan-1    CAL 0.020
1JM plan-1    CE2 0.020
1JM plan-1    CD2 0.020
1JM plan-1    H12 0.020
1JM plan-1    H13 0.020
1JM plan-1    H15 0.020
1JM plan-1    H16 0.020
1JM plan-2     CA 0.020
1JM plan-2      C 0.020
1JM plan-2      O 0.020
1JM plan-2     O1 0.020
1JM plan-3     CZ 0.020
1JM plan-3    CAL 0.020
1JM plan-3    OAB 0.020
1JM plan-3    OAD 0.020
