CONFLEX Manual

Conformation Clustering Keyword

Keyword	Options	Description
CLUSTER		Conformation clustering will be performed by using a single linkage algorithm. This keyword should be used with “CONFLEX” keyword.
CCLUS_DISTANCE=		Definition of conformation distance (similarity) to be used for conformation clustering.
	TORSION	RMS difference of torsion angles.
	ATOM	RMS difference of atomic position after superimposing.
CCLUS_REFALL=		Automatically defines the reference atoms or torsion angles to determine the conformation distance. When “CCLUS_DISTANCE=TORSION” is selected to the conformation distance
	TORSION	All torsion angles to be used.
	COMPAR	All torsion angles to be used for comparison with conformers.
	PHIPSI	All φ/ψ torsion angles of peptide. (only for peptide)
		When “CCLUS_DISTANCE=ATOM” is specified to the conformation distance, the following options can be specified:
	ALPHA	All α carbons of peptide (only for peptide)
	HEAVY	All heavy atoms
	NOHYD	All atoms except for hydrogen
CCLUS_IREF=	I (I,J)	The atom number of the referenced atom, or atom numbers of the central bond of the reference torsion angle. This keyword uses one line to specify one reference.
CCLUS_XREF=	I (I,J)	The atom number of the atom to be excluded from reference atoms, the atom numbers of the central bond to be excluded from reference torsion angles. This keyword uses one line to specify one reference.
CCLUS_LIMIT=	f.ff AUTO	Threshold of conformation distance for conformation clustering AUTO prepares the threshold automatically
CCLUS_LIMIT_MAX=	f.ff	Maximum value of threshold for conformation clustering
CCLUS_EGFUNC=		Sort index is specified.
	STERIC	sorted by the “STERIC” energy order
	FREE	sorted by the Gibbs' “FREE” energy order
CCLUS_MAXCONF=	n	Maximum number of conformers referenced in conformation clustering.

UV/Vis/CD Spectrum and PPP/SCF-MO keyword

Keyword	Options	Description
UVCD		UV/Vis/CD Spectrum calculation will be performed.
CDUV		Same with “UVCD”
PIA_OPT=		In PPP/SCF-MO calculation, all π-atoms are automatically selected. However, SCF Instability is often caused by including some types of π-atoms, carbonyl and peptide bonds in widely distributed aromatic system.
	NOPEP	exclude all peptide bonds (CONH)
	NOATE	exclude all carboxyl groups (COO)
PIA_DEL=	I	Exclude I-atom from π-atoms
SCF=		Selection of SCF methods
	PPP	General PPP/SCF-MO calculation
	VESCF	Variable electronegativity calculation (Allinger's approach)
PPP= Example: PPP=(VB,VG)		Extensions of SCF-PPP calculation.
	VB	Variable beta method
	VG	Variable gamma method
	NEWG	New gamma method
SCF_ITER=	N	Maximum number of SCF iterations.
SCF_CONV=	f.ff	Threshold of SCF convergence.
PPPATOM=	(I,J,Z,IP,G,H)	Parameters of one-center term for atom type I bonded to atom type J (I and J are atom type number of MM2 force field): Z: The number of π-electrons on atom type I (-J) IP: Ionization potential for atom type I (-J) G: One-center repulsion integral H: Coulomb integral of Hückel Molecular Orbital (HMO) method
PPPBOND=	(I,J,B,K,A_0,A_1)	Parameters for bond between atom types I and J: B: Resonance integral (β) for bond I-J K: Resonance integral of (HMO) method for bond I-J A_0, A_1: A0 and A1 parameters for variable β method
PPPGAMM=	(I,J,D_0,D_1)	Parameters for bond between atom types I and J: D_0, D_1: D0 and D1 parameters for variable γ method
CIS= Example: CIS=(10,10)	(Nomo,Numo)	Specifies the number of electrons on the occupied and unoccupied molecular orbitals consid- ered in Single-CI calculation.
CURVE_PLOT=	(f1,f2,f3)	Range of spectrum, and incremental width for curve-fitting based on the gauss approximation. f1: Starting point in wave number (cm^-1) f2: Terminal point in wave number (cm^-1) f3: Incremental step width in wave number (cm^-1) Default: CURVE_PLOT=(10000.0,70000.0,200.0) In this case, the spectrum values at total 301 points are reported.
CURVE_DSIGMA=	f.ff	Standard deviation of the Gaussian distribution. Default value is 2000.0 cm^-1

NMR Analysis Keyword

Keyword	Options	Description
NMR		NMR ³J coupling constant calculation is performed. When the keyword “NMR_3JATYPE=” and /or “NMR_3J_ NUNBER=” are included, NMR ³J coupling constants are calculated by Karplus equation with setting constants and coefficients. Otherwise, all combinations of vicinal proton-proton coupling pairs around C_sp3-C_sp3 are automatically listed and the ³J_HH calculation is performed by Karplus-Imai equation.
NMR_3J_ATYPE=	(W,X,Y,Z)(A)(COS,P_ COS,m,B1,B2,...) (SIN,P_ SIN,n,C1,C2,...)	Parameters of Karplus equation for ³J_WZ coupling constants around X-Y bond are set. The general formula of Karplus equation is as follows: where W, X, Y, and Z are the serial number of atom types, and θ is W-X-Y-Z dihedral angle. Atom types, constants, and coefficients are separated by parentheses. Example: When the equation as below is applied to calculate ³J_CH for atom types 1-6-1-5 (C-O-C-H), the corresponding keyword is below: NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0) If the equation including only cosine as below is applied, the corresponding keyword is: NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,5.0,3,2.0,3.0,4.0)
NMR_3J_NUNBER=	(I,J,K,L)(A)(COS,P_COS,m,B1,B2,...)(SIN,P_SIN,n,C1,C2,...)	Parameters of Karplus equation for NMR ³J_IL coupling constants around J-K bond are set. The general formula of Karplus equation is same as above, I, J, K, and L are serial num- bers of input data, and θ is I-J-K-L dihedral angle. Serial numbers, constants, and coefficients are separated by parentheses. Example: When the equation as below is applied to calculate ³J₁₄ around 1-2-3-4 dihedral angle, the corresponding keyword is below: NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0) If the equation including only cosine as below is applied, the corresponding keyword is below: NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,5.0,3,2.0,3.0,4.0) Note: When the parameters for I-J-K-L are already set by the keyword “NMR_3J_ATYPE=”, the setting based on the atom types is overridden by this keyword.

Keyword

Options

Description

NMR

NMR ³J coupling constant calculation is performed.
When the keyword “NMR_3JATYPE=” and /or “NMR_3J_ NUNBER=” are included, NMR ³J coupling constants are calculated by Karplus equation with setting constants and coefficients. Otherwise, all combinations of vicinal proton-proton coupling pairs around C_sp3-C_sp3 are automatically listed and the ³J_HH calculation is performed by Karplus-Imai equation.

NMR_3J_ATYPE=

(W,X,Y,Z)(A)(COS,P_ COS,m,B1,B2,...) (SIN,P_ SIN,n,C1,C2,...)

Parameters of Karplus equation for ³J_WZ coupling constants around X-Y bond are set. The general formula of Karplus equation is as follows:

where W, X, Y, and Z are the serial number of atom types, and θ is W-X-Y-Z dihedral angle. Atom types, constants, and coefficients are separated by parentheses.
Example:
When the equation as below is applied to calculate ³J_CH for atom types 1-6-1-5 (C-O-C-H),

the corresponding keyword is below:

NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0)

If the equation including only cosine as below is applied,

the corresponding keyword is:

NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,5.0,3,2.0,3.0,4.0)

NMR_3J_NUNBER=

(I,J,K,L)(A)(COS,P_COS,m,B1,B2,...)(SIN,P_SIN,n,C1,C2,...)

Parameters of Karplus equation for NMR ³J_IL coupling constants around J-K bond are set. The general formula of Karplus equation is same as above, I, J, K, and L are serial num- bers of input data, and θ is I-J-K-L dihedral angle. Serial numbers, constants, and coefficients are separated by parentheses.

Example:
When the equation as below is applied to calculate ³J₁₄ around 1-2-3-4 dihedral angle,

the corresponding keyword is below:

NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0)

If the equation including only cosine as below is applied,

the corresponding keyword is below:

NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,5.0,3,2.0,3.0,4.0)

Note: When the parameters for I-J-K-L are already set by the keyword “NMR_3J_ATYPE=”, the setting based on the atom types is overridden by this keyword.

Solvent Effect Analysis Related Keywords using Generalized Born (GB/SA)

Keyword	Options	Description
GBSA		GB/SA calculation will be performed.
GBSA_ANALYZER= Example: GBSA_ANALYZER=FREE	SINGLE OPTIMZ FREE	Solvation energy analysis based on GB/SA calculation will be performed. In all options, GB/SA calculation will be performed after geometry optimization in gas phase. These options are set to the type of GB/SA calculation: -single-point (SINGLE) -geometry optimization (OPTIMZ or FREE) Solvation energy is defined by the total energy difference between gas phase and in solvent (SINGLE and OPTIMZ) or defined by the free energy difference between gas phase and in solvent (FREE).
GBSA_SOLVENT=	WATER OCTANOL	Solvent type is specified. If no solvent name, water environment will be applied as default.
MOL_DIELEC=	f.ff	Define the dielectric constant of molecule. By default, this value is set to 1.0.
SA=	NUM	The calculation of solvent accessible surface area will be performed numerically.
SA=	IGNORE	Do not calculate the non-electrostatic term.
NLR=	ON OFF	Neighbor-List Reduction will be performed. Default: ON
INIT_GEOM=	SAME	Initial geometry for the calculation that is including solvent effect is set to same as input geometry.