Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering)

Category Paths

  • Solution-based/Formulation

  • Role-based/Formulation Scientist

  • Product-based/Crystal Structure Prediction

  • Task-based/Crystal Structure Prediction

Description

This Floe is the second part of the Crystal Structure Prediction (CSP) protocol developed by OpenEye. The goal of it is to predict, starting from a conformational ensemble, the most stable crystal geometries. The energy function used is the combination of OpenEye’s proprietary Intermolecular Energy Force Field (IEFF) and the conformer strain energy on incoming records.

For each conformer in the ensemble, the electrostatic multipoles, needed for IEFF, are calculated. Crystal structures are then generated by randomly packing each conformer in a set list of space groups. By default, conformers are packed in the top 10 space groups by frequency. Alternative, a list of space groups can be specified instead. All crystal structures are then optimized with IEFF. The final results of the Floe are the deduplicated lowest energy crystal structures (5 kcal/mol default window).

We below list top 20 most frequent space groups with their respective frequencies ([Allen-1993], [Wilson-1988]). Data is provided for general and for chiral space groups.

Space group

Frequency

Chiral space group

Frequency

14

35.1

19

47.9

2

19.3

4

30.1

19

9.01

1

5.16

15

7.16

5

4.32

4

5.66

18

2.50

61

3.78

92

1.40

62

1.54

20

1.06

33

1.53

146

0.787

9

0.999

96

0.675

1

0.970

76

0.627

60

0.897

152

0.590

5

0.813

144

0.431

29

0.725

173

0.399

11

0.675

198

0.367

12

0.515

169

0.324

13

0.507

145

0.324

148

0.485

154

0.282

18

0.470

78

0.271

7

0.367

170

0.229

56

0.354

155

0.229

Promoted Parameters

Title in user interface (promoted name)

  • Dataset with Failed Calculations (failure) type: dataset_out: Dataset containing records with failed jobs from three stages of computation: qm multipoles, IEFF, or crystal visualization.
    Default: failure
  • Input Molecules (in) type: data_source: Dataset with input molecules on which crystal polymorph predictions need to be performed.
  • Predicted Crystal Structures (out) type: dataset_out: Resulting dataset with lowest in energy, deduplicated crystal structures (in the CIF format) predicted with IEFF Crystal Force Field.
    Default: top_structures
  • Dataset with computed QM multipoles (qm_mults) type: dataset_out: Resulting dataset with computed QM Multipoles, useful to store in case random packing stage needs to be re-done without recomputing QM Multipoles.
    Default: qm_mults
  • Dataset with unique conformers in top packings (unique_confs) type: dataset_out: Resulting dataset with all unique conformers in top IEFF crystal structures after rigid packing.
    Default: unique_confs

Parameter title in user interface (promoted name)

  • Collection Name (collection_name) type: collection_sink: Name for the created collections.
    Default: IEFF Crystal Packings Collection

Parameter title in user interface (promoted name)

  • Temp Collection Name (collection_name) type: collection_sink: Name for the created collections.
    Default: IEFF Temp Crystal Packings Collection

Parameter title in user interface (promoted name)

  • QM Multipoles Switch (switch) type: boolean: Controls if QM Multipoles are computed or this step is skipped.
    Default: True

Parameter title in user interface (promoted name)

  • Random Packing Switch (switch) type: boolean: Controls if Random Packing of monomer in crystal is performed or skipped.
    Default: True