# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 17:16:25 2019
#
#   Inital geometry file: a 96 line input string
#   Ligand name: N-naphthalen-2-yl-D-histidinamide
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1[nH]cnc1)C(=O)Nc2ccc3ccccc3c2
#
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
HBN        HBN 'N-naphthalen-2-yl-D-histidinamide' L-peptide 37 21 .
2019-03-22 2019-03-22
;
CIF prepared directly in eLBOW
;
#
data_comp_HBN
#
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
HBN         C1     C   CR16   0  -0.120    1.5188    0.1210   -4.5041
HBN         C2     C   CR16   0  -0.122    1.3724   -0.1069   -5.8503
HBN         C3     C   CR16   0  -0.132    0.1082   -0.4517   -6.3864
HBN         C4     C   CR16   0  -0.112   -0.9862   -0.5618   -5.5637
HBN         C4A    C   CR66   0  -0.058   -0.8618   -0.3313   -4.1675
HBN         C8A    C   CR66   0  -0.013    0.4019    0.0139   -3.6284
HBN         C8     C   CR16   0  -0.149    0.5412    0.2466   -2.2350
HBN         C7     C   CR6    0   0.064   -0.5537    0.1399   -1.3880
HBN         C6     C   CR16   0  -0.165   -1.8333   -0.2114   -1.9440
HBN         C5     C   CR16   0  -0.091   -1.9717   -0.4367   -3.2864
HBN         N1     N   NH1    0  -0.315   -0.4912    0.3561    0.0006
HBN         N      N   NH2    0  -0.333    1.3536    1.7612    2.9012
HBN         CA     C   CH1    0  -0.048    0.3826    0.8902    2.2761
HBN         C      C   C      0   0.261    0.6115    0.7266    0.7462
HBN         O      O   O      0  -0.359    1.7383    0.9345    0.2584
HBN         CB     C   CH2    0  -0.084    0.3751   -0.5210    2.8923
HBN         CG     C   CR5    0  -0.130   -0.2097   -0.5386    4.2443
HBN         ND1    N   NR15   0  -0.181    0.1442    0.3139    5.2945
HBN         CD2    C   CR15   0  -0.172   -1.1929   -1.4096    4.7698
HBN         CE1    C   CR15   0  -0.106   -0.6304   -0.0590    6.3949
HBN         NE2    N   N      0  -0.142   -1.4420   -1.1021    6.1014
HBN         H1     H   HCR6   0   0.138    2.4977    0.3894   -4.0787
HBN         HC2    H   HCR6   0   0.133    2.2346   -0.0247   -6.5287
HBN         H3     H   HCR6   0   0.133    0.0170   -0.6293   -7.4680
HBN         H4     H   HCR6   0   0.132   -1.9734   -0.8293   -5.9690
HBN         H8     H   HCR6   0   0.173    1.5413    0.5131   -1.8538
HBN         H6     H   HCR6   0   0.130   -2.7097   -0.2994   -1.2831
HBN         H5     H   HCR6   0   0.135   -2.9538   -0.7051   -3.7063
HBN         HN1    H   HNH1   0   0.233   -1.3445    0.2114    0.4943
HBN         H2     H   HNH2   0   0.160    1.2967    2.6802    2.5058
HBN         HA     H   HCH1   0   0.120   -0.6328    1.3606    2.4438
HBN         HB2    H   HCH2   0   0.106   -0.2367   -1.2030    2.2428
HBN         HB3    H   HCH2   0   0.110    1.4216   -0.9321    2.9188
HBN         HD1    H   HNR5   0   0.269    0.7848    1.0629    5.2406
HBN         HD2    H   HCR5   0   0.176   -1.7110   -2.2215    4.2626
HBN         HE1    H   HCR5   0   0.198   -0.5633    0.4449    7.3640
HBN         H      H   HNH2   0   0.163    2.2827    1.4092    2.7591
#
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
HBN   C1      C2    aromatic      1.373 0.020     1.373
HBN   C1      C8A   aromatic      1.423 0.020     1.423
HBN   C1      H1    single        0.930 0.020     1.080
HBN   C2      C3    aromatic      1.416 0.020     1.416
HBN   C2      HC2   single        0.930 0.020     1.080
HBN   C3      C4    aromatic      1.374 0.020     1.374
HBN   C3      H3    single        0.930 0.020     1.080
HBN   C4      C4A   aromatic      1.421 0.020     1.421
HBN   C4      H4    single        0.930 0.020     1.080
HBN   C4A     C8A   aromatic      1.417 0.020     1.417
HBN   C4A     C5    aromatic      1.421 0.020     1.421
HBN   C8A     C8    aromatic      1.420 0.020     1.420
HBN   C8      C7    aromatic      1.388 0.020     1.388
HBN   C8      H8    single        0.930 0.020     1.080
HBN   C7      C6    aromatic      1.439 0.020     1.439
HBN   C7      N1    single        1.407 0.020     1.407
HBN   C6      C5    aromatic      1.368 0.020     1.368
HBN   C6      H6    single        0.930 0.020     1.080
HBN   C5      H5    single        0.930 0.020     1.080
HBN   N1      C     single        1.382 0.020     1.382
HBN   N1      HN1   single        0.860 0.020     1.020
HBN   N       CA    single        1.446 0.020     1.446
HBN   N       H     single        0.860 0.020     1.020
HBN   N       H2    single        0.890 0.020     1.040
HBN   CA      C     single        1.556 0.020     1.556
HBN   CA      CB    single        1.540 0.020     1.540
HBN   CA      HA    single        0.970 0.020     1.090
HBN   C       O     double        1.245 0.020     1.245
HBN   CB      CG    single        1.473 0.020     1.473
HBN   CB      HB2   single        0.970 0.020     1.090
HBN   CB      HB3   single        0.970 0.020     1.090
HBN   CG      ND1   aromatic      1.398 0.020     1.398
HBN   CG      CD2   aromatic      1.415 0.020     1.415
HBN   ND1     CE1   aromatic      1.396 0.020     1.396
HBN   ND1     HD1   single        0.860 0.020     1.020
HBN   CD2     NE2   aromatic      1.389 0.020     1.389
HBN   CD2     HD2   single        0.930 0.020     1.080
HBN   CE1     NE2   aromatic      1.354 0.020     1.354
HBN   CE1     HE1   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
HBN   H1      C1      C8A         118.59 3.000
HBN   H1      C1      C2          120.95 3.000
HBN   C8A     C1      C2          120.46 3.000
HBN   HC2     C2      C3          118.98 3.000
HBN   HC2     C2      C1          120.57 3.000
HBN   C3      C2      C1          120.45 3.000
HBN   H3      C3      C4          120.67 3.000
HBN   H3      C3      C2          119.06 3.000
HBN   C4      C3      C2          120.27 3.000
HBN   H4      C4      C4A         118.69 3.000
HBN   H4      C4      C3          120.91 3.000
HBN   C4A     C4      C3          120.40 3.000
HBN   C5      C4A     C8A         118.62 3.000
HBN   C5      C4A     C4          121.94 3.000
HBN   C8A     C4A     C4          119.45 3.000
HBN   C8      C8A     C4A         120.07 3.000
HBN   C8      C8A     C1          120.97 3.000
HBN   C4A     C8A     C1          118.97 3.000
HBN   H8      C8      C7          121.51 3.000
HBN   H8      C8      C8A         117.90 3.000
HBN   C7      C8      C8A         120.59 3.000
HBN   N1      C7      C6          117.29 3.000
HBN   N1      C7      C8          123.74 3.000
HBN   C6      C7      C8          118.97 3.000
HBN   H6      C6      C5          119.69 3.000
HBN   H6      C6      C7          119.69 3.000
HBN   C5      C6      C7          120.62 3.000
HBN   H5      C5      C6          120.29 3.000
HBN   H5      C5      C4A         118.57 3.000
HBN   C6      C5      C4A         121.14 3.000
HBN   HN1     N1      C           117.07 3.000
HBN   HN1     N1      C7          115.39 3.000
HBN   C       N1      C7          127.54 3.000
HBN   H2      N       H           108.56 3.000
HBN   H2      N       CA          110.09 3.000
HBN   H       N       CA          110.43 3.000
HBN   HA      CA      CB          108.50 3.000
HBN   HA      CA      C           108.75 3.000
HBN   CB      CA      C           107.33 3.000
HBN   HA      CA      N           106.74 3.000
HBN   CB      CA      N           112.47 3.000
HBN   C       CA      N           112.93 3.000
HBN   O       C       CA          120.05 3.000
HBN   O       C       N1          123.75 3.000
HBN   CA      C       N1          116.20 3.000
HBN   HB3     CB      HB2         107.37 3.000
HBN   HB3     CB      CG          110.08 3.000
HBN   HB2     CB      CG          107.89 3.000
HBN   HB3     CB      CA          109.87 3.000
HBN   HB2     CB      CA          109.14 3.000
HBN   CG      CB      CA          112.34 3.000
HBN   CD2     CG      ND1         105.80 3.000
HBN   CD2     CG      CB          128.62 3.000
HBN   ND1     CG      CB          125.56 3.000
HBN   HD1     ND1     CE1         127.28 3.000
HBN   HD1     ND1     CG          125.86 3.000
HBN   CE1     ND1     CG          106.78 3.000
HBN   HD2     CD2     NE2         121.76 3.000
HBN   HD2     CD2     CG          128.09 3.000
HBN   NE2     CD2     CG          110.14 3.000
HBN   HE1     CE1     NE2         125.70 3.000
HBN   HE1     CE1     ND1         122.74 3.000
HBN   NE2     CE1     ND1         111.56 3.000
HBN   CE1     NE2     CD2         105.71 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
HBN CONST_01       C4      C3      C2      C1           -0.00   0.0 0
HBN CONST_02       C4      C4A     C8A     C1           -0.01   0.0 0
HBN CONST_03       C5      C4A     C8A     C1          179.98   0.0 0
HBN CONST_04       C7      C8      C8A     C1         -180.00   0.0 0
HBN CONST_05       C4A     C8A     C1      C2           -0.00   0.0 0
HBN CONST_06       C8      C8A     C1      C2          179.97   0.0 0
HBN CONST_07       C4A     C4      C3      C2           -0.00   0.0 0
HBN CONST_08       C8A     C1      C2      C3            0.00   0.0 0
HBN CONST_09       C8A     C4A     C4      C3            0.01   0.0 0
HBN CONST_10       C5      C4A     C4      C3         -179.98   0.0 0
HBN CONST_11       C8      C8A     C4A     C4         -179.98   0.0 0
HBN CONST_12       C6      C5      C4A     C4          179.99   0.0 0
HBN CONST_13       C7      C8      C8A     C4A          -0.03   0.0 0
HBN CONST_14       C7      C6      C5      C4A           0.01   0.0 0
HBN CONST_15       C6      C5      C4A     C8A           0.00   0.0 0
HBN CONST_16       C6      C7      C8      C8A           0.04   0.0 0
HBN CONST_17       C5      C4A     C8A     C8            0.01   0.0 0
HBN CONST_18       C5      C6      C7      C8           -0.03   0.0 0
HBN CONST_19       NE2     CE1     ND1     CG            0.50   0.0 0
HBN CONST_20       CE1     NE2     CD2     CG            0.10   0.0 0
HBN CONST_21       NE2     CD2     CG      ND1           0.20   0.0 0
HBN CONST_22       CD2     NE2     CE1     ND1          -0.37   0.0 0
HBN CONST_23       CE1     ND1     CG      CD2          -0.41   0.0 0
HBN CONST_24       N1      C7      C8      C8A        -179.98   0.0 0
HBN CONST_25       N1      C7      C6      C5          179.99   0.0 0
HBN CONST_26       CE1     ND1     CG      CB         -178.93   0.0 0
HBN CONST_27       NE2     CD2     CG      CB          178.66   0.0 0
HBN CONST_28       H3      C3      C2      C1         -180.00   0.0 0
HBN CONST_29       H8      C8      C8A     C1            0.03   0.0 0
HBN CONST_30       H4      C4      C3      C2         -179.99   0.0 0
HBN CONST_31       H1      C1      C2      C3          180.00   0.0 0
HBN CONST_32       HC2     C2      C3      C4          179.99   0.0 0
HBN CONST_33       H5      C5      C4A     C4           -0.01   0.0 0
HBN CONST_34       H6      C6      C5      C4A         179.99   0.0 0
HBN CONST_35       HE1     CE1     ND1     CG         -179.84   0.0 0
HBN CONST_36       HD2     CD2     CG      ND1        -179.49   0.0 0
HBN CONST_37       HD1     ND1     CG      CD2        -177.43   0.0 0
HBN CONST_38       C       N1      C7      C8            1.48   0.0 0
HBN CONST_39       C       N1      C7      C6         -178.54   0.0 0
HBN CONST_40       HN1     N1      C7      C8         -177.71   0.0 0
HBN CONST_41       CA      C       N1      C7         -179.85   0.0 0
HBN CONST_42       O       C       N1      C7            0.56   0.0 0
HBN Var_01         ND1     CG      CB      CA          -50.31  30.0 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
HBN chir_01   CA      N       C       CB    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
HBN plan-1     CB 0.020
HBN plan-1     CG 0.020
HBN plan-1    ND1 0.020
HBN plan-1    CD2 0.020
HBN plan-1    CE1 0.020
HBN plan-1    NE2 0.020
HBN plan-1    HD1 0.020
HBN plan-1    HD2 0.020
HBN plan-1    HE1 0.020
HBN plan-2     C1 0.020
HBN plan-2     C2 0.020
HBN plan-2     C3 0.020
HBN plan-2     C4 0.020
HBN plan-2    C4A 0.020
HBN plan-2    C8A 0.020
HBN plan-2     C8 0.020
HBN plan-2     C7 0.020
HBN plan-2     C6 0.020
HBN plan-2     C5 0.020
HBN plan-2     N1 0.020
HBN plan-2     H1 0.020
HBN plan-2    HC2 0.020
HBN plan-2     H3 0.020
HBN plan-2     H4 0.020
HBN plan-2     H8 0.020
HBN plan-2     H6 0.020
HBN plan-2     H5 0.020
HBN plan-3     C7 0.020
HBN plan-3     N1 0.020
HBN plan-3     CA 0.020
HBN plan-3      C 0.020
HBN plan-3      O 0.020
HBN plan-3    HN1 0.020
