# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 17:19:13 2019
#
#   Inital geometry file: a 100 line input string
#   Ligand name: (3~{R})-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
HLY        HLY '(3~{R})-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_HLY
#
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
HLY         O      O   O      0  -0.597   -7.3738   -1.4232   -0.8956
HLY         C      C   C      0   0.306   -6.5404   -0.4709   -0.8380
HLY         CA     C   CH1    0  -0.124   -5.4034   -0.5453    0.2331
HLY         N      N   NH2    0  -0.326   -5.4511   -1.7367    1.0726
HLY         CB     C   CH2    0  -0.143   -4.0569   -0.3433   -0.4659
HLY         CG     C   CH2    0  -0.154   -2.9320   -0.0830    0.5129
HLY         CD     C   CH2    0  -0.172   -1.6155    0.1650   -0.1961
HLY         CE     C   CH2    0  -0.031   -0.5264    0.4810    0.8319
HLY         NZ     N   NH1    0  -0.354    0.7738    0.7113    0.2604
HLY         CAK    C   C      0   0.321    1.5653    1.7700    0.6384
HLY         OAT    O   O      0  -0.433    1.1379    2.6685    1.4034
HLY         CAL    C   CH2    0  -0.178    2.9481    1.9183    0.0299
HLY         CAM    C   CT     0   0.111    3.8208    0.6614   -0.1174
HLY         CAS    C   CH3    0  -0.236    5.2658    1.0277    0.2306
HLY         OAR    O   OH1    0  -0.377    3.3542   -0.3080    0.8141
HLY         CAN    C   CH2    0  -0.259    3.7608    0.1184   -1.5469
HLY         CAO    C   C      0   0.329    4.7484   -1.0345   -1.7940
HLY         OAQ    O   O      0  -0.601    4.8817   -1.9221   -0.8959
HLY         OAP    O   OC    -1  -0.567    5.3786   -1.0506   -2.8873
HLY         H2     H   HCH1   0   0.080   -5.5710    0.3312    0.9264
HLY         H3     H   HNH2   0   0.138   -6.4217   -1.9802    1.1918
HLY         H4     H   HNH2   0   0.109   -5.0283   -2.4995    0.5737
HLY         H6     H   HCH2   0   0.064   -3.8109   -1.2384   -1.0944
HLY         H7     H   HCH2   0   0.106   -4.1733    0.5319   -1.1600
HLY         H8     H   HCH2   0   0.072   -3.1898    0.8082    1.1443
HLY         H9     H   HCH2   0   0.078   -2.8214   -0.9569    1.2074
HLY         H10    H   HCH2   0   0.074   -1.3328   -0.7389   -0.7954
HLY         H11    H   HCH2   0   0.084   -1.7267    1.0194   -0.9127
HLY         H12    H   HCH2   0   0.109   -0.8328    1.3973    1.4144
HLY         H13    H   HCH2   0   0.063   -0.4644   -0.3813    1.5593
HLY         H14    H   HNH1   0   0.239    1.2151   -0.0524   -0.2014
HLY         H15    H   HCH2   0   0.099    2.8118    2.3818   -0.9834
HLY         H16    H   HCH2   0   0.099    3.4865    2.6633    0.6753
HLY         H17    H   HCH3   0   0.057    5.3337    1.3584    1.2936
HLY         H18    H   HCH3   0   0.114    5.9131    0.1271    0.0876
HLY         H19    H   HCH3   0   0.060    5.6247    1.8458   -0.4355
HLY         H20    H   HOH1   0   0.256    3.8071   -1.1425    0.5935
HLY         H21    H   HCH2   0   0.077    2.7313   -0.2656   -1.7557
HLY         H22    H   HCH2   0   0.078    3.9851    0.9423   -2.2684
HLY         OXT    O   OC    -1  -0.574   -6.5906    0.5530   -1.5747
#
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
HLY   OAQ     CAO   deloc         1.270 0.020     1.270
HLY   CAO     OAP   deloc         1.262 0.020     1.262
HLY   CAO     CAN   single        1.538 0.020     1.538
HLY   CAN     CAM   single        1.530 0.020     1.530
HLY   OAR     CAM   single        1.423 0.020     1.423
HLY   CAM     CAL   single        1.537 0.020     1.537
HLY   CAM     CAS   single        1.531 0.020     1.531
HLY   CAL     CAK   single        1.518 0.020     1.518
HLY   OAT     CAK   double        1.255 0.020     1.255
HLY   CAK     NZ    single        1.375 0.020     1.375
HLY   NZ      CE    single        1.439 0.020     1.439
HLY   CE      CD    single        1.531 0.020     1.531
HLY   CD      CG    single        1.516 0.020     1.516
HLY   CG      CB    single        1.514 0.020     1.514
HLY   O       C     deloc         1.267 0.020     1.267
HLY   CB      CA    single        1.531 0.020     1.531
HLY   C       CA    single        1.564 0.020     1.564
HLY   CA      N     single        1.458 0.020     1.458
HLY   CA      H2    single        0.970 0.020     1.090
HLY   N       H3    single        0.890 0.020     1.040
HLY   N       H4    single        0.890 0.020     1.040
HLY   CB      H6    single        0.970 0.020     1.090
HLY   CB      H7    single        0.970 0.020     1.090
HLY   CG      H8    single        0.970 0.020     1.090
HLY   CG      H9    single        0.970 0.020     1.090
HLY   CD      H10   single        0.970 0.020     1.090
HLY   CD      H11   single        0.970 0.020     1.090
HLY   CE      H12   single        0.970 0.020     1.090
HLY   CE      H13   single        0.970 0.020     1.090
HLY   NZ      H14   single        0.860 0.020     1.020
HLY   CAL     H15   single        0.970 0.020     1.090
HLY   CAL     H16   single        0.970 0.020     1.090
HLY   CAS     H17   single        0.970 0.020     1.090
HLY   CAS     H18   single        0.970 0.020     1.090
HLY   CAS     H19   single        0.970 0.020     1.090
HLY   OAR     H20   single        0.850 0.020     0.980
HLY   CAN     H21   single        0.970 0.020     1.090
HLY   CAN     H22   single        0.970 0.020     1.090
HLY   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
HLY   OXT     C       CA          117.85 3.000
HLY   OXT     C       O           123.85 3.000
HLY   CA      C       O           118.28 3.000
HLY   H2      CA      CB          107.96 3.000
HLY   H2      CA      N           106.00 3.000
HLY   CB      CA      N           113.55 3.000
HLY   H2      CA      C           105.99 3.000
HLY   N       CA      C           114.17 3.000
HLY   CB      CA      C           108.70 3.000
HLY   H4      N       H3          106.29 3.000
HLY   H4      N       CA          108.70 3.000
HLY   H3      N       CA          107.28 3.000
HLY   H7      CB      H6          107.37 3.000
HLY   H7      CB      CG          110.04 3.000
HLY   H6      CB      CG          109.68 3.000
HLY   H7      CB      CA          107.09 3.000
HLY   H6      CB      CA          110.10 3.000
HLY   CG      CB      CA          112.40 3.000
HLY   H9      CG      H8          107.04 3.000
HLY   H9      CG      CD          109.36 3.000
HLY   H8      CG      CD          109.44 3.000
HLY   H9      CG      CB          109.86 3.000
HLY   H8      CG      CB          109.25 3.000
HLY   CD      CG      CB          111.78 3.000
HLY   H11     CD      H10         107.34 3.000
HLY   H11     CD      CE          110.04 3.000
HLY   H10     CD      CE          110.25 3.000
HLY   H11     CD      CG          109.73 3.000
HLY   H10     CD      CG          109.71 3.000
HLY   CE      CD      CG          109.73 3.000
HLY   H13     CE      H12         107.60 3.000
HLY   H13     CE      NZ          109.17 3.000
HLY   H12     CE      NZ          108.69 3.000
HLY   H13     CE      CD          108.30 3.000
HLY   H12     CE      CD          108.73 3.000
HLY   NZ      CE      CD          114.15 3.000
HLY   H14     NZ      CAK         117.58 3.000
HLY   H14     NZ      CE          117.52 3.000
HLY   CAK     NZ      CE          122.30 3.000
HLY   CAL     CAK     OAT         118.99 3.000
HLY   OAT     CAK     NZ          121.52 3.000
HLY   CAL     CAK     NZ          119.30 3.000
HLY   H16     CAL     H15         107.64 3.000
HLY   H16     CAL     CAM         108.98 3.000
HLY   H15     CAL     CAM         108.67 3.000
HLY   H16     CAL     CAK         105.73 3.000
HLY   H15     CAL     CAK         106.96 3.000
HLY   CAM     CAL     CAK         118.40 3.000
HLY   CAN     CAM     OAR         110.91 3.000
HLY   OAR     CAM     CAS         108.89 3.000
HLY   CAN     CAM     CAS         109.53 3.000
HLY   CAS     CAM     CAL         108.57 3.000
HLY   OAR     CAM     CAL         107.95 3.000
HLY   CAN     CAM     CAL         110.94 3.000
HLY   H19     CAS     H18         109.17 3.000
HLY   H19     CAS     H17         109.41 3.000
HLY   H18     CAS     H17         108.99 3.000
HLY   H19     CAS     CAM         110.11 3.000
HLY   H18     CAS     CAM         108.95 3.000
HLY   H17     CAS     CAM         110.19 3.000
HLY   H20     OAR     CAM         106.42 3.000
HLY   H22     CAN     H21         108.50 3.000
HLY   H22     CAN     CAO         108.66 3.000
HLY   H21     CAN     CAO         107.68 3.000
HLY   H22     CAN     CAM         109.48 3.000
HLY   H21     CAN     CAM         109.41 3.000
HLY   CAO     CAN     CAM         113.01 3.000
HLY   OAP     CAO     OAQ         123.46 3.000
HLY   OAP     CAO     CAN         117.99 3.000
HLY   OAQ     CAO     CAN         118.54 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
HLY CONST_01       CAL     CAK     NZ      CE          177.66   0.0 0
HLY CONST_02       OAT     CAK     NZ      CE           -7.41   0.0 0
HLY CONST_03       H14     NZ      CAK     OAT        -168.62   0.0 0
HLY Var_01         CD      CG      CB      CA         -177.92  30.0 1
HLY Var_02         CE      CD      CG      CB          177.60  30.0 1
HLY Var_03         NZ      CE      CD      CG          179.01  30.0 1
HLY Var_04         CAK     NZ      CE      CD          133.88  30.0 1
HLY Var_05         CAM     CAL     CAK     NZ          -42.91  30.0 2
HLY Var_06         OAQ     CAO     CAN     CAM          41.72  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
HLY chir_01   CA      CB      C       N     negativ
HLY chir_02   CAM     OAR     CAL     CAS   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
HLY plan-1     CE 0.020
HLY plan-1     NZ 0.020
HLY plan-1    CAK 0.020
HLY plan-1    OAT 0.020
HLY plan-1    CAL 0.020
HLY plan-1    H14 0.020
HLY plan-2      O 0.020
HLY plan-2      C 0.020
HLY plan-2     CA 0.020
HLY plan-2    OXT 0.020
HLY plan-3    CAN 0.020
HLY plan-3    CAO 0.020
HLY plan-3    OAQ 0.020
HLY plan-3    OAP 0.020
