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New data for testing ref alignment
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@ConorFWild
ConorFWild committed May 20, 2024
1 parent 2f6ec68 commit 5c9b0cc
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2 changes: 2 additions & 0 deletions test-data/config_1.yaml
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Expand Up @@ -4,8 +4,10 @@ output_dir: test-data/outputs
ref_datasets:
- Mpro-IBM0045
- Mpro-x0107_fake_P1
- Mpro-x0107_fake_P1_conf_change
panddas_missing_ok:
- Mpro-x0107_fake_P1
- Mpro-x0107_fake_P1_conf_change
inputs:
- dir: dls/labxchem/data/2020/lb27995-1
type: model_building
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177 changes: 177 additions & 0 deletions test-data/inputs_1/Mpro-x0107_fake_P1/Mpro-x0107_fake_P1_conf_change.cif
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# electronic Ligand Builder and Optimisation Workbench (eLBOW)
# - a module of PHENIX version 1.17.1-3660-
# - file written: Thu Feb 27 14:50:10 2020
#
# Random seed: 3628800
# SMILES string: CC(=O)NC=1C=NC=CC1C
#
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
LIG LIG 'Unknown ' ligand 21 11 .
#
data_comp_LIG
#
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
LIG C01 C CH3 0 . -3.3281 -0.4226 1.1909
LIG C02 C C 0 . -1.8027 -0.4838 1.2161
LIG O03 O O 0 . -1.2417 -0.8701 2.1852
LIG N04 N NH1 0 . -1.0432 -0.1277 0.0320
LIG C05 C CR6 0 . 0.4031 -0.2451 0.0353
LIG C06 C CR16 0 . 1.0277 -1.1848 0.8385
LIG N07 N N 0 . 2.3372 -1.3431 0.8195
LIG C08 C CR16 0 . 3.0956 -0.6072 0.0308
LIG C09 C CR16 0 . 2.5475 0.3539 -0.8022
LIG C10 C CR6 0 . 1.1730 0.5451 -0.8058
LIG C11 C CH3 0 . 0.5240 1.5686 -1.7353
LIG H011 H HCH3 0 . -3.7199 -1.3367 0.7540
LIG H012 H HCH3 0 . -3.7030 -0.3162 2.2048
LIG H013 H HCH3 0 . -3.6465 0.4284 0.5960
LIG H041 H HNH1 0 . -1.5151 0.2179 -0.7798
LIG H061 H HCR6 0 . 0.4283 -1.8027 1.4959
LIG H081 H HCR6 0 . 4.1686 -0.7574 0.0345
LIG H091 H HCR6 0 . 3.1848 0.9498 -1.4439
LIG H111 H HCH3 0 . 1.2971 2.1255 -2.2569
LIG H112 H HCH3 0 . -0.1026 1.0547 -2.4586
LIG H113 H HCH3 0 . -0.0842 2.2536 -1.1513
#
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
LIG C02 C01 single 1.527 0.020 1.527
LIG O03 C02 double 1.184 0.020 1.184
LIG N04 C02 single 1.451 0.020 1.451
LIG C05 N04 single 1.451 0.020 1.451
LIG C06 C05 aromatic 1.385 0.020 1.385
LIG N07 C06 aromatic 1.319 0.020 1.319
LIG C08 N07 aromatic 1.319 0.020 1.319
LIG C09 C08 aromatic 1.385 0.020 1.385
LIG C10 C09 aromatic 1.388 0.020 1.388
LIG C11 C10 single 1.527 0.020 1.527
LIG C05 C10 aromatic 1.387 0.020 1.387
LIG H011 C01 single 0.970 0.020 1.090
LIG H012 C01 single 0.970 0.020 1.090
LIG H013 C01 single 0.970 0.020 1.090
LIG H041 N04 single 0.860 0.020 1.020
LIG H061 C06 single 0.930 0.020 1.080
LIG H081 C08 single 0.930 0.020 1.080
LIG H091 C09 single 0.930 0.020 1.080
LIG H111 C11 single 0.970 0.020 1.090
LIG H112 C11 single 0.970 0.020 1.090
LIG H113 C11 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
LIG H013 C01 H012 109.47 3.000
LIG H013 C01 H011 109.47 3.000
LIG H012 C01 H011 109.47 3.000
LIG H013 C01 C02 109.47 3.000
LIG H012 C01 C02 109.47 3.000
LIG H011 C01 C02 109.47 3.000
LIG N04 C02 O03 119.98 3.000
LIG N04 C02 C01 119.97 3.000
LIG O03 C02 C01 119.98 3.000
LIG H041 N04 C05 120.00 3.000
LIG H041 N04 C02 119.99 3.000
LIG C05 N04 C02 120.00 3.000
LIG C10 C05 C06 119.20 3.000
LIG C10 C05 N04 120.38 3.000
LIG C06 C05 N04 120.37 3.000
LIG H061 C06 N07 119.31 3.000
LIG H061 C06 C05 119.31 3.000
LIG N07 C06 C05 121.38 3.000
LIG C08 N07 C06 120.84 3.000
LIG H081 C08 C09 119.35 3.000
LIG H081 C08 N07 119.36 3.000
LIG C09 C08 N07 121.29 3.000
LIG H091 C09 C10 120.36 3.000
LIG H091 C09 C08 120.35 3.000
LIG C10 C09 C08 119.29 3.000
LIG C11 C10 C09 120.99 3.000
LIG C11 C10 C05 120.99 3.000
LIG C09 C10 C05 118.01 3.000
LIG H113 C11 H112 109.47 3.000
LIG H113 C11 H111 109.47 3.000
LIG H112 C11 H111 109.47 3.000
LIG H113 C11 C10 109.47 3.000
LIG H112 C11 C10 109.47 3.000
LIG H111 C11 C10 109.47 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
LIG CONST_01 C08 N07 C06 C05 -0.00 0.0 0
LIG CONST_02 C09 C08 N07 C06 -0.00 0.0 0
LIG CONST_03 C10 C09 C08 N07 0.00 0.0 0
LIG CONST_04 C05 C10 C09 C08 -0.00 0.0 0
LIG CONST_05 C06 C05 C10 C09 -0.00 0.0 0
LIG CONST_06 N07 C06 C05 C10 0.00 0.0 0
LIG CONST_07 N07 C06 C05 N04 177.40 0.0 0
LIG CONST_08 C09 C10 C05 N04 -177.40 0.0 0
LIG CONST_09 C11 C10 C05 C06 178.39 0.0 0
LIG CONST_10 C11 C10 C09 C08 -178.39 0.0 0
LIG CONST_11 H091 C09 C10 C05 -180.00 0.0 0
LIG CONST_12 H081 C08 N07 C06 -180.00 0.0 0
LIG CONST_13 H061 C06 N07 C08 180.00 0.0 0
LIG CONST_14 C06 C05 N04 C02 28.53 0.0 0
LIG CONST_15 C10 C05 N04 C02 -154.11 0.0 0
LIG CONST_16 H041 N04 C05 C06 -152.83 0.0 0
LIG CONST_17 C05 N04 C02 C01 -177.14 0.0 0
LIG CONST_18 C05 N04 C02 O03 0.00 0.0 0
LIG Var_01 H111 C11 C10 C05 176.24 30.0 2
LIG Var_02 H011 C01 C02 O03 -94.13 30.0 3
#
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
LIG plan-1 N04 0.020
LIG plan-1 C05 0.020
LIG plan-1 C06 0.020
LIG plan-1 N07 0.020
LIG plan-1 C08 0.020
LIG plan-1 C09 0.020
LIG plan-1 C10 0.020
LIG plan-1 C11 0.020
LIG plan-1 H061 0.020
LIG plan-1 H081 0.020
LIG plan-1 H091 0.020
LIG plan-2 C01 0.020
LIG plan-2 C02 0.020
LIG plan-2 O03 0.020
LIG plan-2 N04 0.020
LIG plan-2 C05 0.020
LIG plan-2 H041 0.020
Binary file added test-data/inputs_1/Mpro-x0107_fake_P1/Mpro-x0107_fake_P1_conf_change.mtz
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