# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:53:54 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-butyl-3-[[4-[[(4R)-2-imino-4-methyl-4-(2-methylpropyl)-5-oxo-imidazolidin-1-yl]methyl]phenyl]methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNC(=O)NCc1ccc(CN2C(=N)N[C@](C)(CC(C)C)C2=O)cc1
#
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
 BDV  BDV  1-butyl-3-[[4-[[(4R)-2-imino-4-methyl-4-(2-methylpropyl)-5-oxo-imidazolidin-1-yl]methyl]phenyl]methyl]urea  ligand  61  28  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BDV
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
 BDV  C1    C  CT    0  -0.041    5.1760   0.2181   0.1450
 BDV  N1    N  NH1   0  -0.661    4.8362   0.5762  -1.2175
 BDV  O1    O  O     0  -0.442    3.8770   0.9084   2.0992
 BDV  C2    C  C     0   0.613    3.8486   1.5084  -1.2963
 BDV  N2    N  NT    0  -0.526    3.3591   1.6730   0.0058
 BDV  O2    O  O     0  -0.549   -4.8631  -2.1162  -0.4615
 BDV  C3    C  C     0   0.585    4.0789   0.9515   0.9073
 BDV  N3    N  N     0  -0.684    3.4834   2.0782  -2.3700
 BDV  C4    C  CH3   0  -0.651    6.5372   0.7712   0.5679
 BDV  N4    N  NH1   0  -0.675   -3.6905  -0.3046   0.2544
 BDV  C5    C  CH2   0  -0.372    5.0374  -1.2854   0.4320
 BDV  N5    N  NH1   0  -0.683   -5.9363  -0.1361  -0.1574
 BDV  C6    C  CH1   0  -0.253    6.1362  -2.2119  -0.0942
 BDV  C7    C  CH3   0  -0.651    5.8395  -3.6350   0.3744
 BDV  C8    C  CH3   0  -0.657    6.2966  -2.1890  -1.6116
 BDV  C9    C  CH2   0  -0.455    2.1706   2.4264   0.3585
 BDV  C10   C  CR6   0   0.138    0.9475   1.5488   0.4101
 BDV  C11   C  CR16  0  -0.277    0.5144   1.0091   1.6143
 BDV  C12   C  CR16  0  -0.291   -0.5919   0.1694   1.6544
 BDV  C13   C  CR6   0   0.069   -1.2856  -0.1499   0.4944
 BDV  C14   C  CR16  0  -0.272   -0.8568   0.4010  -0.7119
 BDV  C15   C  CR16  0  -0.285    0.2469   1.2363  -0.7543
 BDV  C16   C  CH2   0  -0.322   -2.4869  -1.0552   0.5383
 BDV  C17   C  CH2   0  -0.242   -7.2253  -0.5820  -0.6349
 BDV  C18   C  CH2   0  -0.444   -8.3529   0.1555   0.0711
 BDV  C19   C  CH2   0  -0.425   -9.7267  -0.2899  -0.4134
 BDV  C20   C  C     0   0.732   -4.8375  -0.9316  -0.1423
 BDV  C21   C  CH3   0  -0.662  -10.8599   0.4463   0.2870
 BDV  HN1   H  HNH1  0   0.397    5.5253   0.5525  -1.9504
 BDV  HN3   H  H     0   0.341    2.7414   2.7509  -2.2312
 BDV  H4    H  HCH3  0   0.251    6.5762   1.8546   0.4496
 BDV  H4A   H  HCH3  0   0.245    6.7414   0.5292   1.6103
 BDV  H4B   H  HCH3  0   0.252    7.3342   0.3409  -0.0387
 BDV  HN4   H  HNH1  0   0.388   -3.7794   0.5784   0.7332
 BDV  H5    H  HCH2  0   0.239    4.9929  -1.4027   1.5186
 BDV  H5A   H  HCH2  0   0.231    4.0690  -1.6184   0.0421
 BDV  HN5   H  HNH1  0   0.388   -5.8116   0.8585  -0.0516
 BDV  H6    H  HCH1  0   0.229    7.0872  -1.9073   0.3554
 BDV  H7    H  HCH3  0   0.216    4.9039  -3.9997  -0.0561
 BDV  H7A   H  HCH3  0   0.228    6.6317  -4.3206   0.0701
 BDV  H7B   H  HCH3  0   0.226    5.7491  -3.6910   1.4606
 BDV  H8    H  HCH3  0   0.217    6.6825  -1.2407  -1.9859
 BDV  H8A   H  HCH3  0   0.232    7.0036  -2.9576  -1.9285
 BDV  H8B   H  HCH3  0   0.220    5.3463  -2.3869  -2.1122
 BDV  H9    H  HCH2  0   0.296    2.3476   2.9039   1.3212
 BDV  H9A   H  HCH2  0   0.286    2.0432   3.2295  -0.3670
 BDV  H11   H  HCR6  0   0.253    1.0408   1.2433   2.5307
 BDV  H12   H  HCR6  0   0.254   -0.9168  -0.2400   2.6035
 BDV  H14   H  HCR6  0   0.253   -1.3897   0.1726  -1.6273
 BDV  H15   H  HCR6  0   0.249    0.5654   1.6480  -1.7050
 BDV  H16   H  HCH2  0   0.241   -2.5364  -1.5516   1.5138
 BDV  H16A  H  HCH2  0   0.257   -2.3850  -1.8398  -0.2112
 BDV  H17   H  HCH2  0   0.218   -7.3169  -0.4430  -1.7189
 BDV  H17A  H  HCH2  0   0.235   -7.3128  -1.6522  -0.4474
 BDV  H18   H  HCH2  0   0.222   -8.2696  -0.0086   1.1497
 BDV  H18A  H  HCH2  0   0.219   -8.2456   1.2341  -0.0889
 BDV  H19   H  HCH2  0   0.216   -9.8002  -0.1338  -1.4939
 BDV  H19A  H  HCH2  0   0.216   -9.8345  -1.3670  -0.2541
 BDV  H21   H  HCH3  0   0.229  -11.8342   0.1104  -0.0684
 BDV  H21A  H  HCH3  0   0.218  -10.8271   0.2851   1.3660
 BDV  H21B  H  HCH3  0   0.218  -10.7970   1.5222   0.1140

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
 BDV  C1   N1    single    1.449  0.020  1.449
 BDV  C1   C3    single    1.524  0.020  1.524
 BDV  C1   C4    single    1.529  0.020  1.529
 BDV  C1   C5    single    1.537  0.020  1.537
 BDV  N1   C2    single    1.360  0.020  1.360
 BDV  O1   C3    double    1.210  0.020  1.210
 BDV  C2   N2    single    1.401  0.020  1.401
 BDV  C2   N3    double    1.269  0.020  1.269
 BDV  N2   C3    single    1.361  0.020  1.361
 BDV  N2   C9    single    1.451  0.020  1.451
 BDV  O2   C20   double    1.227  0.020  1.227
 BDV  N4   C16   single    1.447  0.020  1.447
 BDV  N4   C20   single    1.366  0.020  1.366
 BDV  C5   C6    single    1.531  0.020  1.531
 BDV  N5   C17   single    1.445  0.020  1.445
 BDV  N5   C20   single    1.357  0.020  1.357
 BDV  C6   C7    single    1.527  0.020  1.527
 BDV  C6   C8    single    1.526  0.020  1.526
 BDV  C9   C10   single    1.506  0.020  1.506
 BDV  C10  C11   aromatic  1.389  0.020  1.389
 BDV  C10  C15   aromatic  1.394  0.020  1.394
 BDV  C11  C12   aromatic  1.389  0.020  1.389
 BDV  C12  C13   aromatic  1.389  0.020  1.389
 BDV  C13  C14   aromatic  1.394  0.020  1.394
 BDV  C13  C16   single    1.505  0.020  1.505
 BDV  C14  C15   aromatic  1.385  0.020  1.385
 BDV  C17  C18   single    1.521  0.020  1.521
 BDV  C18  C19   single    1.523  0.020  1.523
 BDV  C19  C21   single    1.522  0.020  1.522
 BDV  N1   HN1   single    0.890  0.020  1.040
 BDV  N3   HN3   single    0.890  0.020  1.040
 BDV  C4   H4    single    0.970  0.020  1.090
 BDV  C4   H4A   single    0.970  0.020  1.090
 BDV  C4   H4B   single    0.970  0.020  1.090
 BDV  N4   HN4   single    0.890  0.020  1.040
 BDV  C5   H5    single    0.970  0.020  1.090
 BDV  C5   H5A   single    0.970  0.020  1.090
 BDV  N5   HN5   single    0.860  0.020  1.020
 BDV  C6   H6    single    0.970  0.020  1.090
 BDV  C7   H7    single    0.970  0.020  1.090
 BDV  C7   H7A   single    0.970  0.020  1.090
 BDV  C7   H7B   single    0.970  0.020  1.090
 BDV  C8   H8    single    0.970  0.020  1.090
 BDV  C8   H8A   single    0.970  0.020  1.090
 BDV  C8   H8B   single    0.970  0.020  1.090
 BDV  C9   H9    single    0.970  0.020  1.090
 BDV  C9   H9A   single    0.970  0.020  1.090
 BDV  C11  H11   single    0.930  0.020  1.080
 BDV  C12  H12   single    0.930  0.020  1.080
 BDV  C14  H14   single    0.930  0.020  1.080
 BDV  C15  H15   single    0.930  0.020  1.080
 BDV  C16  H16   single    0.970  0.020  1.090
 BDV  C16  H16A  single    0.970  0.020  1.090
 BDV  C17  H17   single    0.970  0.020  1.090
 BDV  C17  H17A  single    0.970  0.020  1.090
 BDV  C18  H18   single    0.970  0.020  1.090
 BDV  C18  H18A  single    0.970  0.020  1.090
 BDV  C19  H19   single    0.970  0.020  1.090
 BDV  C19  H19A  single    0.970  0.020  1.090
 BDV  C21  H21   single    0.970  0.020  1.090
 BDV  C21  H21A  single    0.970  0.020  1.090
 BDV  C21  H21B  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
 BDV  C5    C1   C4    112.49  3.000
 BDV  C5    C1   C3    108.21  3.000
 BDV  C4    C1   C3    109.17  3.000
 BDV  C5    C1   N1    113.34  3.000
 BDV  C4    C1   N1    112.30  3.000
 BDV  C3    C1   N1    100.52  3.000
 BDV  HN1   N1   C2    118.11  3.000
 BDV  HN1   N1   C1    121.22  3.000
 BDV  C2    N1   C1    113.21  3.000
 BDV  N3    C2   N2    129.28  3.000
 BDV  N3    C2   N1    124.44  3.000
 BDV  N2    C2   N1    106.28  3.000
 BDV  C9    N2   C3    123.21  3.000
 BDV  C9    N2   C2    124.98  3.000
 BDV  C3    N2   C2    111.64  3.000
 BDV  N2    C3   O1    125.69  3.000
 BDV  N2    C3   C1    107.73  3.000
 BDV  O1    C3   C1    126.57  3.000
 BDV  HN3   N3   C2    113.18  3.000
 BDV  H4B   C4   H4A   107.92  3.000
 BDV  H4B   C4   H4    107.79  3.000
 BDV  H4A   C4   H4    108.53  3.000
 BDV  H4B   C4   C1    110.74  3.000
 BDV  H4A   C4   C1    110.56  3.000
 BDV  H4    C4   C1    111.18  3.000
 BDV  HN4   N4   C20   117.76  3.000
 BDV  HN4   N4   C16   115.75  3.000
 BDV  C20   N4   C16   121.16  3.000
 BDV  H5A   C5   H5    106.56  3.000
 BDV  H5A   C5   C6    109.16  3.000
 BDV  H5    C5   C6    107.80  3.000
 BDV  H5A   C5   C1    108.09  3.000
 BDV  H5    C5   C1    107.10  3.000
 BDV  C6    C5   C1    117.60  3.000
 BDV  HN5   N5   C20   118.50  3.000
 BDV  HN5   N5   C17   116.72  3.000
 BDV  C20   N5   C17   123.04  3.000
 BDV  H6    C6   C8    108.23  3.000
 BDV  H6    C6   C7    107.57  3.000
 BDV  C8    C6   C7    109.84  3.000
 BDV  H6    C6   C5    108.30  3.000
 BDV  C8    C6   C5    114.09  3.000
 BDV  C7    C6   C5    108.61  3.000
 BDV  H7B   C7   H7A   107.79  3.000
 BDV  H7B   C7   H7    107.71  3.000
 BDV  H7A   C7   H7    107.58  3.000
 BDV  H7B   C7   C6    111.67  3.000
 BDV  H7A   C7   C6    111.03  3.000
 BDV  H7    C7   C6    110.88  3.000
 BDV  H8B   C8   H8A   107.63  3.000
 BDV  H8B   C8   H8    107.95  3.000
 BDV  H8A   C8   H8    106.48  3.000
 BDV  H8B   C8   C6    111.20  3.000
 BDV  H8A   C8   C6    110.26  3.000
 BDV  H8    C8   C6    113.06  3.000
 BDV  H9A   C9   H9    106.53  3.000
 BDV  H9A   C9   C10   110.93  3.000
 BDV  H9    C9   C10   110.93  3.000
 BDV  H9A   C9   N2    108.46  3.000
 BDV  H9    C9   N2    108.03  3.000
 BDV  C10   C9   N2    111.77  3.000
 BDV  C15   C10  C11   118.70  3.000
 BDV  C15   C10  C9    120.66  3.000
 BDV  C11   C10  C9    120.62  3.000
 BDV  H11   C11  C12   119.57  3.000
 BDV  H11   C11  C10   119.88  3.000
 BDV  C12   C11  C10   120.54  3.000
 BDV  H12   C12  C13   119.67  3.000
 BDV  H12   C12  C11   119.50  3.000
 BDV  C13   C12  C11   120.84  3.000
 BDV  C16   C13  C14   120.57  3.000
 BDV  C16   C13  C12   120.85  3.000
 BDV  C14   C13  C12   118.57  3.000
 BDV  H14   C14  C15   119.56  3.000
 BDV  H14   C14  C13   119.77  3.000
 BDV  C15   C14  C13   120.67  3.000
 BDV  H15   C15  C14   119.35  3.000
 BDV  H15   C15  C10   119.98  3.000
 BDV  C14   C15  C10   120.67  3.000
 BDV  H16A  C16  H16   106.88  3.000
 BDV  H16A  C16  C13   109.78  3.000
 BDV  H16   C16  C13   109.55  3.000
 BDV  H16A  C16  N4    108.44  3.000
 BDV  H16   C16  N4    111.86  3.000
 BDV  C13   C16  N4    110.26  3.000
 BDV  H17A  C17  H17   106.73  3.000
 BDV  H17A  C17  C18   109.68  3.000
 BDV  H17   C17  C18   109.59  3.000
 BDV  H17A  C17  N5    108.53  3.000
 BDV  H17   C17  N5    111.22  3.000
 BDV  C18   C17  N5    110.99  3.000
 BDV  H18A  C18  H18   106.51  3.000
 BDV  H18A  C18  C19   109.25  3.000
 BDV  H18   C18  C19   109.77  3.000
 BDV  H18A  C18  C17   109.69  3.000
 BDV  H18   C18  C17   109.16  3.000
 BDV  C19   C18  C17   112.28  3.000
 BDV  H19A  C19  H19   106.11  3.000
 BDV  H19A  C19  C21   109.63  3.000
 BDV  H19   C19  C21   109.60  3.000
 BDV  H19A  C19  C18   109.29  3.000
 BDV  H19   C19  C18   109.44  3.000
 BDV  C21   C19  C18   112.56  3.000
 BDV  N5    C20  N4    114.47  3.000
 BDV  N5    C20  O2    123.11  3.000
 BDV  N4    C20  O2    122.42  3.000
 BDV  H21B  C21  H21A  107.49  3.000
 BDV  H21B  C21  H21   107.66  3.000
 BDV  H21A  C21  H21   107.68  3.000
 BDV  H21B  C21  C19   111.16  3.000
 BDV  H21A  C21  C19   111.17  3.000
 BDV  H21   C21  C19   111.49  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
 BDV  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 BDV  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 BDV  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 BDV  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 BDV  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 BDV  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 BDV  CONST_07  N2   C2   N1   C1      0.00   0.0  0
 BDV  CONST_08  C2   N2   C3   C1      0.00   0.0  0
 BDV  CONST_09  C3   N2   C2   N1      0.00   0.0  0
 BDV  CONST_10  C12  C11  C10  C9    180.00   0.0  0
 BDV  CONST_11  C14  C15  C10  C9    180.00   0.0  0
 BDV  CONST_12  C16  C13  C12  C11   180.00   0.0  0
 BDV  CONST_13  C16  C13  C14  C15   180.00   0.0  0
 BDV  CONST_14  N3   C2   N1   C1    180.00   0.0  0
 BDV  CONST_15  C9   N2   C3   C1    180.00   0.0  0
 BDV  CONST_16  C9   N2   C2   N1    180.00   0.0  0
 BDV  CONST_17  C2   N2   C3   O1    180.00   0.0  0
 BDV  CONST_18  N3   C2   N2   C3    180.00   0.0  0
 BDV  CONST_19  H12  C12  C11  C10   180.00   0.0  0
 BDV  CONST_20  H14  C14  C15  C10   180.00   0.0  0
 BDV  CONST_21  H15  C15  C10  C11   180.00   0.0  0
 BDV  CONST_22  H11  C11  C12  C13   180.00   0.0  0
 BDV  CONST_24  C9   N2   C3   O1      0.00   0.0  0
 BDV  CONST_25  C9   N2   C2   N3      0.00   0.0  0
 BDV  CONST_26  HN3  N3   C2   N1    180.00   0.0  0
 BDV  CONST_27  C16  N4   C20  O2      0.00   0.0  0
 BDV  CONST_28  C17  N5   C20  O2      0.00   0.0  0
 BDV  CONST_29  C17  N5   C20  N4    180.00   0.0  0
 BDV  CONST_30  C16  N4   C20  N5    180.00   0.0  0
 BDV  CONST_32  HN5  N5   C20  O2    180.00   0.0  0
 BDV  Var_01    C10  C9   N2   C2     92.59  30.0  3
 BDV  Var_02    C11  C10  C9   N2     95.43  30.0  2
 BDV  Var_03    C12  C13  C16  N4    110.55  30.0  2
 BDV  Var_04    C7   C6   C5   C1    176.66  30.0  3
 BDV  Var_05    C20  N4   C16  C13   160.94  30.0  1
 BDV  Var_06    C19  C18  C17  N5    179.85  30.0  3
 BDV  Var_07    C21  C19  C18  C17  -179.89  30.0  3
 BDV  Var_08    C20  N5   C17  C18   150.96  30.0  2
 BDV  Var_09    H7   C7   C6   C5     63.80  30.0  3
 BDV  Var_10    H8   C8   C6   C5     68.03  30.0  3
 BDV  Var_11    H21  C21  C19  C18  -179.68  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
 BDV  chir_01  C1  C3  N1  C5  positiv

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
 BDV  plan-1  C9   0.020
 BDV  plan-1  C10  0.020
 BDV  plan-1  C11  0.020
 BDV  plan-1  C12  0.020
 BDV  plan-1  C13  0.020
 BDV  plan-1  C14  0.020
 BDV  plan-1  C15  0.020
 BDV  plan-1  C16  0.020
 BDV  plan-1  H11  0.020
 BDV  plan-1  H12  0.020
 BDV  plan-1  H14  0.020
 BDV  plan-1  H15  0.020
 BDV  plan-2  O2   0.020
 BDV  plan-2  N4   0.020
 BDV  plan-2  N5   0.020
 BDV  plan-2  C16  0.020
 BDV  plan-2  C17  0.020
 BDV  plan-2  C20  0.020
 BDV  plan-2  HN4  0.020
 BDV  plan-2  HN5  0.020
 BDV  plan-3  C1   0.020
 BDV  plan-3  N1   0.020
 BDV  plan-3  O1   0.020
 BDV  plan-3  C2   0.020
 BDV  plan-3  N2   0.020
 BDV  plan-3  C3   0.020
 BDV  plan-3  N3   0.020
 BDV  plan-3  C9   0.020
 BDV  plan-3  HN1  0.020
 BDV  plan-3  HN3  0.020

