# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:32:06 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (4S)-N~1~,N~1~-bis(2-chloroethyl)-N~4~-[(9Z)-6-chloro-2-methoxyacridin-9(10H)-ylidene]pentane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2Nc3cc(Cl)ccc3C(=N[C@@H](C)CCCN(CCCl)CCCl)c2c1
#
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
 QUM  QUM  (4S)-N~1~,N~1~-bis(2-chloroethyl)-N~4~-[(9Z)-6-chloro-2-methoxyacridin-9(10H)-ylidene]pentane-1,4-diamine  ligand  58  30  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QUM
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
 QUM  C2    C   CR6   0   0.405  -4.9767   2.0125  -0.6944
 QUM  C3    C   CR16  0  -0.384  -6.1383   1.3330  -1.0658
 QUM  C4    C   CR16  0  -0.325  -6.7216   0.4547  -0.1782
 QUM  C11   C   CR66  0   0.322  -6.1693   0.2208   1.0819
 QUM  C12   C   CR66  0   0.023  -4.9752   0.8651   1.4621
 QUM  C1    C   CR16  0  -0.415  -4.4202   1.7699   0.5502
 QUM  N10   N   NR16  0  -0.810  -6.8162  -0.6382   1.9325
 QUM  C14   C   CR66  0   0.354  -6.4303  -0.8244   3.2228
 QUM  C13   C   CR66  0  -0.031  -5.2434  -0.2404   3.6819
 QUM  C9    C   CR6   0   0.247  -4.3667   0.5433   2.7776
 QUM  C5    C   CR16  0  -0.293  -7.2227  -1.6049   4.0771
 QUM  C6    C   CR6   0  -0.049  -6.8260  -1.7789   5.3814
 QUM  C7    C   CR16  0  -0.225  -5.6593  -1.1984   5.8768
 QUM  C8    C   CR16  0  -0.309  -4.8884  -0.4450   5.0182
 QUM  N18   N   N     0  -0.391  -3.2145   0.8210   3.2506
 QUM  C19   C   CH1   0  -0.129  -2.1299   1.5350   2.6210
 QUM  C20   C   CH3   0  -0.650  -1.0946   1.8422   3.6983
 QUM  C21   C   CH2   0  -0.433  -1.5098   0.7107   1.4831
 QUM  C22   C   CH2   0  -0.452  -0.5349   1.5062   0.6224
 QUM  C23   C   CH2   0  -0.298  -0.1992   0.8057  -0.6878
 QUM  N24   N   NT    0  -0.418   0.2982  -0.5460  -0.5032
 QUM  C27   C   CH2   0  -0.285   1.6555  -0.6302  -0.0099
 QUM  C25   C   CH2   0  -0.287   0.0039  -1.4357  -1.6053
 QUM  C28   C   CH2   0  -0.450   1.7460  -1.7422   1.0190
 QUM  C26   C   CH2   0  -0.441  -1.3848  -2.0201  -1.4185
 QUM  CL1   CL  CL    0  -0.123  -7.8056  -2.7389   6.4388
 QUM  O15   O   O2    0  -0.473  -4.3321   2.9059  -1.4753
 QUM  C17   C   CH3   0  -0.438  -4.8538   3.1686  -2.7611
 QUM  CL2   CL  CL    0  -0.182  -1.8139  -3.0716  -2.8170
 QUM  CL3   CL  CL    0  -0.183   3.4367  -1.8986   1.6226
 QUM  H3    H   HCR6  0   0.289  -6.6007   1.4804  -2.0322
 QUM  H4    H   HCR6  0   0.277  -7.6334  -0.0579  -0.4602
 QUM  H1    H   HCR6  0   0.262  -3.5272   2.3190   0.7954
 QUM  H10   H   HNR6  0   0.413  -7.6789  -1.0550   1.6206
 QUM  H5    H   HCR6  0   0.289  -8.1340  -2.0570   3.7072
 QUM  H7    H   HCR6  0   0.275  -5.3667  -1.3369   6.9080
 QUM  H8    H   HCR6  0   0.263  -3.9739   0.0065   5.3762
 QUM  H19   H   HCH1  0   0.221  -2.4588   2.5038   2.2239
 QUM  H201  H   HCH3  0   0.215  -0.6961   0.9181   4.1215
 QUM  H202  H   HCH3  0   0.229  -1.5394   2.4215   4.5080
 QUM  H203  H   HCH3  0   0.221  -0.2603   2.4202   3.2988
 QUM  H211  H   HCH2  0   0.229  -2.3036   0.3127   0.8450
 QUM  H212  H   HCH2  0   0.232  -1.0107  -0.1611   1.9136
 QUM  H221  H   HCH2  0   0.229   0.3771   1.7311   1.1821
 QUM  H222  H   HCH2  0   0.229  -0.9697   2.4792   0.3695
 QUM  H231  H   HCH2  0   0.230  -1.1137   0.7508  -1.2846
 QUM  H232  H   HCH2  0   0.225   0.5038   1.4218  -1.2692
 QUM  H271  H   HCH2  0   0.233   2.3867  -0.7980  -0.8119
 QUM  H272  H   HCH2  0   0.253   1.9304   0.3107   0.4684
 QUM  H251  H   HCH2  0   0.230   0.0734  -0.9340  -2.5805
 QUM  H252  H   HCH2  0   0.255   0.7262  -2.2538  -1.6225
 QUM  H281  H   HCH2  0   0.281   1.4685  -2.7097   0.6039
 QUM  H282  H   HCH2  0   0.281   1.1121  -1.5295   1.8769
 QUM  H261  H   HCH2  0   0.270  -2.1492  -1.2475  -1.3601
 QUM  H262  H   HCH2  0   0.282  -1.4315  -2.6331  -0.5213
 QUM  H171  H   HCH3  0   0.227  -4.8692   2.2724  -3.3876
 QUM  H172  H   HCH3  0   0.260  -4.1952   3.9027  -3.2185
 QUM  H173  H   HCH3  0   0.227  -5.8645   3.5835  -2.7177

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
 QUM  C2   C3    aromatic  1.396  0.020  1.396
 QUM  C2   C1    aromatic  1.385  0.020  1.385
 QUM  C2   O15   single    1.350  0.020  1.350
 QUM  C3   C4    aromatic  1.378  0.020  1.378
 QUM  C3   H3    single    0.930  0.020  1.080
 QUM  C4   C11   aromatic  1.396  0.020  1.396
 QUM  C4   H4    single    0.930  0.020  1.080
 QUM  C11  C12   aromatic  1.409  0.020  1.409
 QUM  C11  N10   aromatic  1.371  0.020  1.371
 QUM  C12  C1    aromatic  1.399  0.020  1.399
 QUM  C12  C9    aromatic  1.485  0.020  1.485
 QUM  C1   H1    single    0.930  0.020  1.080
 QUM  N10  C14   aromatic  1.360  0.020  1.360
 QUM  N10  H10   single    0.860  0.020  1.020
 QUM  C14  C13   aromatic  1.400  0.020  1.400
 QUM  C14  C5    aromatic  1.402  0.020  1.402
 QUM  C13  C9    aromatic  1.483  0.020  1.483
 QUM  C13  C8    aromatic  1.398  0.020  1.398
 QUM  C9   N18   double    1.276  0.020  1.276
 QUM  C5   C6    aromatic  1.374  0.020  1.374
 QUM  C5   H5    single    0.930  0.020  1.080
 QUM  C6   C7    aromatic  1.394  0.020  1.394
 QUM  C6   CL1   single    1.732  0.020  1.732
 QUM  C7   C8    aromatic  1.378  0.020  1.378
 QUM  C7   H7    single    0.930  0.020  1.080
 QUM  C8   H8    single    0.930  0.020  1.080
 QUM  N18  C19   single    1.443  0.020  1.443
 QUM  C19  C20   single    1.525  0.020  1.525
 QUM  C19  C21   single    1.536  0.020  1.536
 QUM  C19  H19   single    0.970  0.020  1.090
 QUM  C20  H201  single    0.970  0.020  1.090
 QUM  C20  H202  single    0.970  0.020  1.090
 QUM  C20  H203  single    0.970  0.020  1.090
 QUM  C21  C22   single    1.524  0.020  1.524
 QUM  C21  H211  single    0.970  0.020  1.090
 QUM  C21  H212  single    0.970  0.020  1.090
 QUM  C22  C23   single    1.523  0.020  1.523
 QUM  C22  H221  single    0.970  0.020  1.090
 QUM  C22  H222  single    0.970  0.020  1.090
 QUM  C23  N24   single    1.452  0.020  1.452
 QUM  C23  H231  single    0.970  0.020  1.090
 QUM  C23  H232  single    0.970  0.020  1.090
 QUM  N24  C27   single    1.447  0.020  1.447
 QUM  N24  C25   single    1.447  0.020  1.447
 QUM  C27  C28   single    1.518  0.020  1.518
 QUM  C27  H271  single    0.970  0.020  1.090
 QUM  C27  H272  single    0.970  0.020  1.090
 QUM  C25  C26   single    1.518  0.020  1.518
 QUM  C25  H251  single    0.970  0.020  1.090
 QUM  C25  H252  single    0.970  0.020  1.090
 QUM  C28  CL3   single    1.802  0.020  1.802
 QUM  C28  H281  single    0.970  0.020  1.090
 QUM  C28  H282  single    0.970  0.020  1.090
 QUM  C26  CL2   single    1.802  0.020  1.802
 QUM  C26  H261  single    0.970  0.020  1.090
 QUM  C26  H262  single    0.970  0.020  1.090
 QUM  O15  C17   single    1.412  0.020  1.412
 QUM  C17  H171  single    0.970  0.020  1.090
 QUM  C17  H172  single    0.970  0.020  1.090
 QUM  C17  H173  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
 QUM  O15   C2   C1    116.35  3.000
 QUM  O15   C2   C3    124.42  3.000
 QUM  C1    C2   C3    119.22  3.000
 QUM  H3    C3   C4    118.78  3.000
 QUM  H3    C3   C2    121.82  3.000
 QUM  C4    C3   C2    119.40  3.000
 QUM  H4    C4   C11   119.27  3.000
 QUM  H4    C4   C3    119.35  3.000
 QUM  C11   C4   C3    121.39  3.000
 QUM  N10   C11  C12   121.26  3.000
 QUM  N10   C11  C4    118.58  3.000
 QUM  C12   C11  C4    120.16  3.000
 QUM  C9    C12  C1    123.71  3.000
 QUM  C9    C12  C11   119.16  3.000
 QUM  C1    C12  C11   117.12  3.000
 QUM  H1    C1   C12   120.69  3.000
 QUM  H1    C1   C2    116.66  3.000
 QUM  C12   C1   C2    122.65  3.000
 QUM  H10   N10  C14   118.70  3.000
 QUM  H10   N10  C11   118.10  3.000
 QUM  C14   N10  C11   122.73  3.000
 QUM  C5    C14  C13   120.75  3.000
 QUM  C5    C14  N10   119.60  3.000
 QUM  C13   C14  N10   119.65  3.000
 QUM  C8    C13  C9    120.67  3.000
 QUM  C8    C13  C14   117.89  3.000
 QUM  C9    C13  C14   121.43  3.000
 QUM  N18   C9   C13   115.01  3.000
 QUM  N18   C9   C12   130.64  3.000
 QUM  C13   C9   C12   114.36  3.000
 QUM  H5    C5   C6    120.96  3.000
 QUM  H5    C5   C14   120.00  3.000
 QUM  C6    C5   C14   119.04  3.000
 QUM  CL1   C6   C7    119.16  3.000
 QUM  CL1   C6   C5    119.10  3.000
 QUM  C7    C6   C5    121.74  3.000
 QUM  H7    C7   C8    120.87  3.000
 QUM  H7    C7   C6    120.81  3.000
 QUM  C8    C7   C6    118.32  3.000
 QUM  H8    C8   C7    119.69  3.000
 QUM  H8    C8   C13   118.06  3.000
 QUM  C7    C8   C13   122.25  3.000
 QUM  C19   N18  C9    128.65  3.000
 QUM  H19   C19  C21   109.07  3.000
 QUM  H19   C19  C20   106.33  3.000
 QUM  C21   C19  C20   110.94  3.000
 QUM  H19   C19  N18   111.68  3.000
 QUM  C21   C19  N18   111.17  3.000
 QUM  C20   C19  N18   107.56  3.000
 QUM  H203  C20  H202  107.61  3.000
 QUM  H203  C20  H201  108.14  3.000
 QUM  H202  C20  H201  108.10  3.000
 QUM  H203  C20  C19   111.54  3.000
 QUM  H202  C20  C19   110.77  3.000
 QUM  H201  C20  C19   110.55  3.000
 QUM  H212  C21  H211  105.73  3.000
 QUM  H212  C21  C22   110.28  3.000
 QUM  H211  C21  C22   108.95  3.000
 QUM  H212  C21  C19   108.70  3.000
 QUM  H211  C21  C19   109.55  3.000
 QUM  C22   C21  C19   113.35  3.000
 QUM  H222  C22  H221  105.46  3.000
 QUM  H222  C22  C23   107.30  3.000
 QUM  H221  C22  C23   110.55  3.000
 QUM  H222  C22  C21   109.88  3.000
 QUM  H221  C22  C21   110.59  3.000
 QUM  C23   C22  C21   112.74  3.000
 QUM  H232  C23  H231  105.90  3.000
 QUM  H232  C23  N24   111.67  3.000
 QUM  H231  C23  N24   108.01  3.000
 QUM  H232  C23  C22   109.73  3.000
 QUM  H231  C23  C22   107.95  3.000
 QUM  N24   C23  C22   113.22  3.000
 QUM  C25   N24  C27   114.52  3.000
 QUM  C25   N24  C23   113.95  3.000
 QUM  C27   N24  C23   114.77  3.000
 QUM  H272  C27  H271  106.51  3.000
 QUM  H272  C27  C28   108.65  3.000
 QUM  H271  C27  C28   110.09  3.000
 QUM  H272  C27  N24   109.62  3.000
 QUM  H271  C27  N24   112.61  3.000
 QUM  C28   C27  N24   109.26  3.000
 QUM  H252  C25  H251  106.64  3.000
 QUM  H252  C25  C26   108.59  3.000
 QUM  H251  C25  C26   110.05  3.000
 QUM  H252  C25  N24   109.77  3.000
 QUM  H251  C25  N24   112.49  3.000
 QUM  C26   C25  N24   109.21  3.000
 QUM  H282  C28  H281  109.02  3.000
 QUM  H282  C28  CL3   107.43  3.000
 QUM  H281  C28  CL3   106.84  3.000
 QUM  H282  C28  C27   110.90  3.000
 QUM  H281  C28  C27   112.17  3.000
 QUM  CL3   C28  C27   110.28  3.000
 QUM  H262  C26  H261  109.01  3.000
 QUM  H262  C26  CL2   107.53  3.000
 QUM  H261  C26  CL2   106.78  3.000
 QUM  H262  C26  C25   110.96  3.000
 QUM  H261  C26  C25   112.07  3.000
 QUM  CL2   C26  C25   110.31  3.000
 QUM  C17   O15  C2    118.24  3.000
 QUM  H173  C17  H172  108.69  3.000
 QUM  H173  C17  H171  108.71  3.000
 QUM  H172  C17  H171  108.72  3.000
 QUM  H173  C17  O15   112.08  3.000
 QUM  H172  C17  O15   106.55  3.000
 QUM  H171  C17  O15   111.99  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
 QUM  CONST_01  C11   C4   C3   C2      0.00   0.0  0
 QUM  CONST_02  C11   C12  C1   C2      0.00   0.0  0
 QUM  CONST_03  C9    C12  C1   C2    180.00   0.0  0
 QUM  CONST_04  C12   C1   C2   C3      0.00   0.0  0
 QUM  CONST_05  C12   C11  C4   C3      0.00   0.0  0
 QUM  CONST_06  N10   C11  C4   C3    180.00   0.0  0
 QUM  CONST_07  C1    C2   C3   C4      0.00   0.0  0
 QUM  CONST_08  C1    C12  C11  C4      0.00   0.0  0
 QUM  CONST_09  C9    C12  C11  C4    180.00   0.0  0
 QUM  CONST_10  C14   N10  C11  C4    180.00   0.0  0
 QUM  CONST_11  C13   C9   C12  C11     0.00   0.0  0
 QUM  CONST_12  C13   C14  N10  C11     0.00   0.0  0
 QUM  CONST_13  C5    C14  N10  C11   180.00   0.0  0
 QUM  CONST_14  C14   N10  C11  C12     0.00   0.0  0
 QUM  CONST_15  C14   C13  C9   C12     0.00   0.0  0
 QUM  CONST_16  C8    C13  C9   C12   180.00   0.0  0
 QUM  CONST_17  N10   C11  C12  C1    180.00   0.0  0
 QUM  CONST_18  C13   C9   C12  C1    180.00   0.0  0
 QUM  CONST_19  C9    C12  C11  N10     0.00   0.0  0
 QUM  CONST_20  C9    C13  C14  N10     0.00   0.0  0
 QUM  CONST_21  C8    C13  C14  N10   180.00   0.0  0
 QUM  CONST_22  C6    C5   C14  N10   180.00   0.0  0
 QUM  CONST_23  C7    C8   C13  C14     0.00   0.0  0
 QUM  CONST_24  C7    C6   C5   C14     0.00   0.0  0
 QUM  CONST_25  C6    C5   C14  C13     0.00   0.0  0
 QUM  CONST_26  C6    C7   C8   C13     0.00   0.0  0
 QUM  CONST_27  C5    C14  C13  C9    180.00   0.0  0
 QUM  CONST_28  C7    C8   C13  C9    180.00   0.0  0
 QUM  CONST_29  C8    C13  C14  C5      0.00   0.0  0
 QUM  CONST_30  C8    C7   C6   C5      0.00   0.0  0
 QUM  CONST_31  O15   C2   C3   C4    180.00   0.0  0
 QUM  CONST_32  N18   C9   C12  C11   180.00   0.0  0
 QUM  CONST_33  O15   C2   C1   C12   180.00   0.0  0
 QUM  CONST_34  N18   C9   C12  C1      0.00   0.0  0
 QUM  CONST_35  N18   C9   C13  C14   180.00   0.0  0
 QUM  CONST_36  CL1   C6   C5   C14   180.00   0.0  0
 QUM  CONST_37  N18   C9   C13  C8      0.00   0.0  0
 QUM  CONST_38  CL1   C6   C7   C8    180.00   0.0  0
 QUM  CONST_39  H4    C4   C3   C2    180.00   0.0  0
 QUM  CONST_40  H1    C1   C2   C3    180.00   0.0  0
 QUM  CONST_41  H10   N10  C11  C4      0.00   0.0  0
 QUM  CONST_42  H3    C3   C4   C11   180.00   0.0  0
 QUM  CONST_43  H5    C5   C14  N10     0.00   0.0  0
 QUM  CONST_44  H8    C8   C13  C14   180.00   0.0  0
 QUM  CONST_45  H7    C7   C8   C13   180.00   0.0  0
 QUM  Var_01    H171  C17  O15  C2    -61.10  30.0  3
 QUM  Var_02    C23   C22  C21  C19  -165.54  30.0  3
 QUM  Var_03    N24   C23  C22  C21   -54.61  30.0  3
 QUM  Var_04    C27   N24  C23  C22   -74.36  30.0  3
 QUM  Var_05    C28   C27  N24  C23   139.36  30.0  3
 QUM  Var_06    C26   C25  N24  C23   -85.15  30.0  3
 QUM  Var_07    CL3   C28  C27  N24   178.59  30.0  3
 QUM  Var_08    CL2   C26  C25  N24   177.26  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
 QUM  chir_01  C19  N18  C20  C21  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
 QUM  plan-1  C2   0.020
 QUM  plan-1  C3   0.020
 QUM  plan-1  C4   0.020
 QUM  plan-1  C11  0.020
 QUM  plan-1  C12  0.020
 QUM  plan-1  C1   0.020
 QUM  plan-1  N10  0.020
 QUM  plan-1  C14  0.020
 QUM  plan-1  C13  0.020
 QUM  plan-1  C9   0.020
 QUM  plan-1  C5   0.020
 QUM  plan-1  C6   0.020
 QUM  plan-1  C7   0.020
 QUM  plan-1  C8   0.020
 QUM  plan-1  N18  0.020
 QUM  plan-1  CL1  0.020
 QUM  plan-1  O15  0.020
 QUM  plan-1  H3   0.020
 QUM  plan-1  H4   0.020
 QUM  plan-1  H1   0.020
 QUM  plan-1  H10  0.020
 QUM  plan-1  H5   0.020
 QUM  plan-1  H7   0.020
 QUM  plan-1  H8   0.020

