# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 18:18:55 2019
#
#   Inital geometry file: a 100 line input string
#   Ligand name: (3~{S})-5-[[(5~{S})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic acid
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: C[C@@](O)(CC(O)=O)CC(=O)NCCCC[C@H](N)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
SKH        SKH '(3~{S})-5-[[(5~{S})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic acid' ligand 40 20 .
2019-03-22 2019-03-22
;
CIF prepared directly in eLBOW
;
#
data_comp_SKH
#
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
SKH         O      O   O      0  -0.597   -7.4718   -0.7998   -0.6924
SKH         C      C   C      0   0.306   -6.3733   -0.4741   -1.2322
SKH         CA     C   CH1    0  -0.125   -5.3950    0.4421   -0.4263
SKH         N      N   NH2    0  -0.325   -5.9000    0.8511    0.8793
SKH         CB     C   CH2    0  -0.143   -4.0256   -0.2387   -0.3661
SKH         CG     C   CH2    0  -0.154   -2.9362    0.6975    0.1117
SKH         CD     C   CH2    0  -0.170   -1.5829    0.0152    0.1424
SKH         CE     C   CH2    0  -0.024   -0.5160    1.0029    0.6138
SKH         NZ     N   NH1    0  -0.370    0.8073    0.4444    0.6958
SKH         CAK    C   C      0   0.303    1.8224    1.1061    1.3532
SKH         OAT    O   O      0  -0.429    1.5871    2.1320    2.0352
SKH         CAL    C   CH2    0  -0.211    3.2194    0.5241    1.2861
SKH         CAM    C   CT     0   0.113    3.7612    0.3195   -0.1341
SKH         CAR    C   CH3    0  -0.210    3.5607    1.5732   -0.9823
SKH         OAS    O   OH1    0  -0.381    3.0359   -0.7194   -0.7864
SKH         CAN    C   CH2    0  -0.254    5.2525   -0.0161   -0.0644
SKH         CAO    C   C      0   0.328    5.5898   -1.2469    0.7895
SKH         OAQ    O   O      0  -0.599    4.7220   -2.1656    0.9092
SKH         OAP    O   OC    -1  -0.570    6.7356   -1.2984    1.3175
SKH         H2     H   HCH1   0   0.080   -5.2864    1.3909   -1.0303
SKH         H3     H   HNH2   0   0.138   -6.8992    0.9523    0.7951
SKH         H4     H   HNH2   0   0.109   -5.7477    0.1022    1.5316
SKH         H6     H   HCH2   0   0.064   -4.0715   -1.1370    0.3031
SKH         H7     H   HCH2   0   0.105   -3.7923   -0.6038   -1.4021
SKH         H8     H   HCH2   0   0.071   -2.8902    1.5896   -0.5673
SKH         H9     H   HCH2   0   0.081   -3.1830    1.0778    1.1377
SKH         H10    H   HCH2   0   0.082   -1.6213   -0.8685    0.8307
SKH         H11    H   HCH2   0   0.079   -1.3300   -0.3687   -0.8803
SKH         H12    H   HCH2   0   0.057   -0.5105    1.8877   -0.0897
SKH         H13    H   HCH2   0   0.095   -0.7950    1.3964    1.6338
SKH         H14    H   HNH1   0   0.245    1.0573   -0.2695    0.0467
SKH         H15    H   HCH2   0   0.110    3.9018    1.2191    1.8404
SKH         H16    H   HCH2   0   0.149    3.2368   -0.4742    1.8063
SKH         H17    H   HCH3   0   0.068    4.0411    2.4443   -0.4790
SKH         H18    H   HCH3   0   0.068    4.0227    1.4269   -1.9869
SKH         H19    H   HCH3   0   0.076    2.4737    1.7822   -1.1201
SKH         H20    H   HOH1   0   0.255    3.3285   -1.5580   -0.3859
SKH         H21    H   HCH2   0   0.076    5.6178   -0.2225   -1.1024
SKH         H22    H   HCH2   0   0.077    5.8099    0.8663    0.3357
SKH         OXT    O   OC    -1  -0.574   -6.0314   -0.8203   -2.3970
#
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
SKH   OAQ     CAO   deloc         1.269 0.020     1.269
SKH   CAO     OAP   deloc         1.263 0.020     1.263
SKH   CAO     CAN   single        1.536 0.020     1.536
SKH   CAN     CAM   single        1.530 0.020     1.530
SKH   CAM     CAR   single        1.527 0.020     1.527
SKH   CAM     CAL   single        1.534 0.020     1.534
SKH   CAM     OAS   single        1.425 0.020     1.425
SKH   CAL     CAK   single        1.515 0.020     1.515
SKH   OAT     CAK   double        1.254 0.020     1.254
SKH   CAK     NZ    single        1.379 0.020     1.379
SKH   NZ      CE    single        1.439 0.020     1.439
SKH   CE      CD    single        1.528 0.020     1.528
SKH   CD      CG    single        1.516 0.020     1.516
SKH   CG      CB    single        1.514 0.020     1.514
SKH   O       C     deloc         1.267 0.020     1.267
SKH   CB      CA    single        1.531 0.020     1.531
SKH   C       CA    single        1.564 0.020     1.564
SKH   CA      N     single        1.458 0.020     1.458
SKH   CA      H2    single        0.970 0.020     1.090
SKH   N       H3    single        0.890 0.020     1.040
SKH   N       H4    single        0.890 0.020     1.040
SKH   CB      H6    single        0.970 0.020     1.090
SKH   CB      H7    single        0.970 0.020     1.090
SKH   CG      H8    single        0.970 0.020     1.090
SKH   CG      H9    single        0.970 0.020     1.090
SKH   CD      H10   single        0.970 0.020     1.090
SKH   CD      H11   single        0.970 0.020     1.090
SKH   CE      H12   single        0.970 0.020     1.090
SKH   CE      H13   single        0.970 0.020     1.090
SKH   NZ      H14   single        0.860 0.020     1.020
SKH   CAL     H15   single        0.970 0.020     1.090
SKH   CAL     H16   single        0.970 0.020     1.090
SKH   CAR     H17   single        0.970 0.020     1.090
SKH   CAR     H18   single        0.970 0.020     1.090
SKH   CAR     H19   single        0.970 0.020     1.090
SKH   OAS     H20   single        0.850 0.020     0.980
SKH   CAN     H21   single        0.970 0.020     1.090
SKH   CAN     H22   single        0.970 0.020     1.090
SKH   C       OXT   deloc         1.262 0.020     1.262
#
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
SKH   OXT     C       CA          117.83 3.000
SKH   OXT     C       O           123.89 3.000
SKH   CA      C       O           118.26 3.000
SKH   H2      CA      CB          107.97 3.000
SKH   H2      CA      N           106.04 3.000
SKH   CB      CA      N           113.54 3.000
SKH   H2      CA      C           106.06 3.000
SKH   N       CA      C           114.15 3.000
SKH   CB      CA      C           108.63 3.000
SKH   H4      N       H3          106.22 3.000
SKH   H4      N       CA          108.64 3.000
SKH   H3      N       CA          107.25 3.000
SKH   H7      CB      H6          107.38 3.000
SKH   H7      CB      CG          110.05 3.000
SKH   H6      CB      CG          109.67 3.000
SKH   H7      CB      CA          107.11 3.000
SKH   H6      CB      CA          110.07 3.000
SKH   CG      CB      CA          112.41 3.000
SKH   H9      CG      H8          107.03 3.000
SKH   H9      CG      CD          109.30 3.000
SKH   H8      CG      CD          109.48 3.000
SKH   H9      CG      CB          109.88 3.000
SKH   H8      CG      CB          109.28 3.000
SKH   CD      CG      CB          111.75 3.000
SKH   H11     CD      H10         107.33 3.000
SKH   H11     CD      CE          110.19 3.000
SKH   H10     CD      CE          110.12 3.000
SKH   H11     CD      CG          109.70 3.000
SKH   H10     CD      CG          109.68 3.000
SKH   CE      CD      CG          109.79 3.000
SKH   H13     CE      H12         106.91 3.000
SKH   H13     CE      NZ          108.13 3.000
SKH   H12     CE      NZ          109.57 3.000
SKH   H13     CE      CD          109.37 3.000
SKH   H12     CE      CD          108.50 3.000
SKH   NZ      CE      CD          114.13 3.000
SKH   H14     NZ      CAK         118.01 3.000
SKH   H14     NZ      CE          118.14 3.000
SKH   CAK     NZ      CE          121.21 3.000
SKH   CAL     CAK     OAT         120.75 3.000
SKH   OAT     CAK     NZ          120.92 3.000
SKH   CAL     CAK     NZ          118.27 3.000
SKH   H16     CAL     H15         108.18 3.000
SKH   H16     CAL     CAM         107.70 3.000
SKH   H15     CAL     CAM         109.01 3.000
SKH   H16     CAL     CAK         109.54 3.000
SKH   H15     CAL     CAK         107.54 3.000
SKH   CAM     CAL     CAK         114.71 3.000
SKH   CAN     CAM     OAS         110.92 3.000
SKH   OAS     CAM     CAR         106.11 3.000
SKH   CAN     CAM     CAR         109.47 3.000
SKH   OAS     CAM     CAL         109.96 3.000
SKH   CAR     CAM     CAL         111.00 3.000
SKH   CAN     CAM     CAL         109.35 3.000
SKH   H19     CAR     H18         108.48 3.000
SKH   H19     CAR     H17         109.23 3.000
SKH   H18     CAR     H17         109.31 3.000
SKH   H19     CAR     CAM         110.52 3.000
SKH   H18     CAR     CAM         109.77 3.000
SKH   H17     CAR     CAM         109.52 3.000
SKH   H20     OAS     CAM         106.64 3.000
SKH   H22     CAN     H21         108.34 3.000
SKH   H22     CAN     CAO         108.91 3.000
SKH   H21     CAN     CAO         107.23 3.000
SKH   H22     CAN     CAM         109.22 3.000
SKH   H21     CAN     CAM         108.44 3.000
SKH   CAO     CAN     CAM         114.53 3.000
SKH   OAP     CAO     OAQ         123.47 3.000
SKH   OAP     CAO     CAN         117.68 3.000
SKH   OAQ     CAO     CAN         118.84 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
SKH CONST_01       CAL     CAK     NZ      CE         -174.22   0.0 0
SKH CONST_02       OAT     CAK     NZ      CE            8.70   0.0 0
SKH CONST_03       H14     NZ      CAK     OAT         169.93   0.0 0
SKH Var_01         CD      CG      CB      CA         -179.00  30.0 1
SKH Var_02         CE      CD      CG      CB          179.32  30.0 1
SKH Var_03         NZ      CE      CD      CG          179.16  30.0 1
SKH Var_04         CAK     NZ      CE      CD         -166.64  30.0 1
SKH Var_05         CAM     CAL     CAK     NZ           56.34  30.0 2
SKH Var_06         OAQ     CAO     CAN     CAM          28.02  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
SKH chir_01   CA      CB      C       N     negativ
SKH chir_02   CAM     CAR     CAL     OAS   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
SKH plan-1     CE 0.020
SKH plan-1     NZ 0.020
SKH plan-1    CAK 0.020
SKH plan-1    OAT 0.020
SKH plan-1    CAL 0.020
SKH plan-1    H14 0.020
SKH plan-2      O 0.020
SKH plan-2      C 0.020
SKH plan-2     CA 0.020
SKH plan-2    OXT 0.020
SKH plan-3    CAN 0.020
SKH plan-3    CAO 0.020
SKH plan-3    OAQ 0.020
SKH plan-3    OAP 0.020
