Supporting information for Kirschner and Woods (August 28, 2001) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.191362798.
Table 1. Glycam 2000A parameters
GLYCAM PARAMETERS (FOR AMBER 5.0, RESP 0.010), COPYRIGHT R.J.WOODS, CCRC 2000
MASS
AC 12.01 0.00 CT ALPHA ANOMERIC CARBON (P94=PARM94)
EC 12.01 0.00 CT BETA ANOMERIC CARBON
OG 16.00 0.00 OS GLYCOSIDIC OXYGEN
OL 16.00 0.00 OS RING OXYGEN FOR L- AND 1C4(D) SUGARS
OH 16.00 0.00 OH HYDROXYL OXYGEN
OS 16.00 0.00 OS RING OXYGEN SUGARS
CL 35.45 0.00 Chlorine atom
I2 40.08 0.00 CALCIUM ION (2+)
BOND
AC-CT 310.00 1.527 P94 K CT-CT
EC-CT 310.00 1.519 P94 K CT-CT
AC-H2 340.00 1.090 P94 CT-H2
EC-H2 340.00 1.090 P94 CT-H2
C -HC 331.00 1.090 P91 CT-HC FOR FORMYL GROUPS
C -EC 317.00 1.570 P91 C-CT AB INITIO 6-31G*
EC-N 337.00 1.460 P94 K CT-N
AC-OS 320.00 1.416 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS
AC-OL 320.00 1.416 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS
EC-OS 320.00 1.425 AVG OF GAL GLU XYL,K P94 CT-OS
EC-OL 320.00 1.425 AVG OF GAL GLU XYL,K P94 CT-OS
CT-OL 320.00 1.410 P94 CT-OS
AC-OG 320.00 1.405 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS
EC-OG 320.00 1.389 AVG OF GAL GLU XYL,K P94 CT-OS
CT-OG 320.00 1.435 AVG OF MAN GLU GAL XYL,K P94 CT-OS
AC-OH 320.00 1.396 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS
EC-OH 320.00 1.387 AVG OF GAL GLU XYL,K P94 CT-OS
CT-CL 232.40 1.758 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070.
CT-H2 340.0 1.100 CT-H2 for CH2CL2 from J.Phys.Chem.(1998)8070.
ANGL
AC-CT-CT 40.00 111.80 P94 K CT-CT-CT
EC-CT-CT 40.00 109.40 P94 K CT-CT-CT
CT-AC-CT 40.00 109.50 P94 CT-CT-CT
CT-EC-CT 40.00 109.50 P94 CT-CT-CT
AC-CT-H1 50.00 109.50 P94 CT-CT-H1
AC-CT-HC 50.00 109.50 P94 CT-CT-H1
EC-CT-H1 50.00 109.50 P94 CT-CT-H1
EC-CT-HC 50.00 109.50 P94 CT-CT-H1
EC-CT-N 80.00 109.70 P91 ALA JACS 94, 2657
AC-CT-N 80.00 109.70 P91 ALA JACS 94, 2657
AC-CT-OH 50.00 109.50 P94 CT-CT-OH
EC-CT-OH 50.00 109.50 P94 CT-CT-OH
EC-C -O2 70.00 117.00 P94 CT-C -O2
AC-CT-OS 50.00 109.50 P94 CT-CT-OS
AC-CT-OL 50.00 109.50 P94 CT-CT-OS
EC-CT-OS 50.00 109.50 P94 CT-CT-OS
EC-CT-OL 50.00 109.50 P94 CT-CT-OS
AC-CT-OG 50.00 109.50 P94 CT-CT-OS
EC-CT-OG 50.00 109.50 P94 CT-CT-OS
C -AC-CT 63.00 111.10 P94 C -CT-CT
C -EC-CT 63.00 111.10 P94 C -CT-CT
C -AC-OL 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE
C -EC-OL 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE
C -AC-OG 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE
C -EC-OG 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE
CT-CT-OL 50.00 109.50 P94 CT-CT-OS
CT-CT-OG 50.00 109.50 P94 CT-CT-OS
CT-AC-H2 50.00 109.50 P94 CT-CT-H2
CT-EC-H2 50.00 109.50 P94 CT-CT-H2
CT-EC-N 80.00 109.70 P91 CT-CT-N ALA JAAC 94, 2657
CT-AC-OG 50.00 109.50 P94 CT-CT-OS
CT-EC-OG 50.00 109.50 P94 CT-CT-OS
CT-AC-OH 50.00 109.50 P94 CT-CT-OS
CT-EC-OH 50.00 109.50 P94 CT-CT-OS
CT-AC-OS 50.00 110.50 P94 CT-CT-OS
CT-AC-OL 50.00 110.50 P94 CT-CT-OS
CT-EC-OS 50.00 109.50 P94 CT-CT-OS
CT-EC-OL 50.00 109.50 P94 CT-CT-OS
H2-EC-N 35.00 109.50 P91 H-CT-N
H2-C -N 55.00 112.40 AVG K C-C=O, H-C-N FOR N-FORMYL
H2-C -O 55.00 122.20 AVG K C-C=O, H-C-N FOR FORMYL
H2-AC-OG 35.00 109.50 FROM FITTING TO DMM
H2-EC-OG 35.00 109.50 FROM FITTING TO DMM
H2-AC-OH 35.00 109.50 FROM FITTING TO DMM
H2-EC-OH 35.00 109.50 FROM FITTING TO DMM
H2-AC-OS 35.00 109.50 FROM FITTING TO DMM
H2-AC-OL 35.00 109.50 FROM FITTING TO DMM
H2-EC-OS 35.00 109.50 FROM FITTING TO DMM
H2-EC-OL 35.00 109.50 FROM FITTING TO DMM
H1-CT-OL 35.00 109.50 FROM FITTING TO DMM
H1-CT-OG 35.00 109.50 FROM FITTING TO DMM
C -N -EC 50.00 121.90 P94 C -N -CT
EC-N -H 30.00 118.04 P94 CT-N -H
AC-OS-CT 60.00 113.50 AVG OF GAL MAN GLU, K P94 CT-OS-CT
AC-OL-CT 60.00 113.50 AVG OF GAL MAN GLU, K P94 CT-OS-CT
EC-OS-CT 60.00 111.90 AVG OF GAL GLU XYL, K P94 CT-OS-CT
EC-OL-CT 60.00 111.90 AVG OF GAL GLU XYL, K P94 CT-OS-CT
AC-OG-CT 60.00 113.80 AVG OF GAL MAN GLU, K P94 CT-OS-CT
EC-OG-CT 60.00 114.70 AVG OF GAL GLU XYL, K P94 CT-OS-CT
N -EC-OS 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM
N -EC-OL 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM
OG-AC-OS 110.70 112.00 AVG OF GAL MAN GLU, K FROM DMM
OG-AC-OL 110.70 112.00 AVG OF GAL MAN GLU, K FROM DMM
OG-EC-OS 110.70 107.60 AVG OF GAL GLU XYL, K FROM DMM
OG-EC-OL 110.70 107.60 AVG OF GAL GLU XYL, K FROM DMM
OH-AC-OS 110.70 111.60 AVG OF GAL MAN GLU, K FROM DMM
OH-AC-OL 110.70 111.60 AVG OF GAL MAN GLU, K FROM DMM
OH-EC-OS 110.70 107.20 AVG OF GAL GLU XYL, K FROM DMM
OH-EC-OL 110.70 107.20 AVG OF GAL GLU XYL, K FROM DMM
AC-OH-HO 55.00 108.50 P94 CT-OH-HO
EC-OH-HO 55.00 108.50 P94 CT-OH-HO
OS-CT-C 63.00 112.36 (C -EC-OG) const., gaussian 94 angle (uronic H+) LCM
O -C -EC 70.00 117.00 from (EC-C -O2) LCM
OH-C -EC 70.00 117.00 from (EC-C -O2) LCM
O2-C -OH 80.0 126.00 copied from parm96.dat ( AA GLU ) LCM
CL-CT-CL 77.70 111.30 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070.
CL-CT-H2 38.10 107.70 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070.
DIHE
X -CT-AC-X 9 1.40 0.00 3. P94 X-CT-CT-X
X -CT-EC-X 9 1.40 0.00 3. P94 X-CT-CT-X
X -CT-CT-X 9 1.40 0.00 3. P94 X-CT-CT-X
X -CT-OG-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -AC-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -AC-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -EC-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -EC-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -CT-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -CT-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X
X -C -N -X 4 10.00 180.00 2. P94 X-C-N-X
X -N -CT-X 1 0.00 0.00 1. P94 X-N-CT-X
H2-AC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC ALPHA
H2-EC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC BETA
C -EC-OG-CT 1 5.45 0.00 -1. EXO-ANOMERIC
1 0.47 0.00 -2. EFFECT ALPHA SIALIC ACID
1 -0.65 0.00 3. C-C-O-C AB INITIO
CT-AC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC ALPHA
CT-EC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC BETA
CT-OG-AC-OS 1 1.39 265.77 -1. EXO-ANOMERIC
1 0.70 312.04 -2. EFFECT ALPHA
1 0.91 347.72 3. O-C-O-C
CT-OG-AC-OL 1 1.39 94.64 -1. EXO-ANOMERIC
1 0.70 48.01 -2. EFFECT ALPHA (L and 1C4(D))
1 0.91 12.07 3. O-C-O-C
CT-OG-EC-OS 1 0.85 144.06 -1. EXO-ANOMERIC
1 0.74 353.55 -2. EFFECT BETA
1 0.97 6.43 3. O-C-O-C
CT-OG-EC-OL 1 0.85 216.10 -1. EXO-ANOMERIC
1 0.74 6.72 -2. EFFECT (BETA 4C1(L) and ALPHA 1C4(D))
1 0.97 353.73 3. O-C-O-C
CT-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta)
1 0.00 0. -2. (psi alpha=beta)
1 1.35 0. 1. (psi alpha=beta)
H1-CT-OG-AC 1 0.00 0. 1. (psi alpha=beta)
CT-CT-OG-EC 1 0.00 0. -3. (psi beta=alpha)
1 0.00 0. -2. (psi beta=alpha)
1 1.35 0. 1. (psi beta=alpha)
H1-CT-OG-EC 1 0.00 0. 1. (psi beta=alpha)
AC-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta)
1 0.00 0. -2. (psi alpha=beta)
1 1.35 0. 1. (psi alpha=beta)
AC-CT-OG-EC 1 0.00 0. -3. (psi alpha=beta)
1 0.00 0. -2. (psi alpha=beta)
1 1.35 0. 1. (psi alpha=beta)
EC-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta)
1 0.00 0. -2. (psi alpha=beta)
1 1.35 0. 1. (psi alpha=beta)
EC-CT-OG-EC 1 0.00 0. -3. (psi alpha=beta)
1 0.00 0. -2. (psi alpha=beta)
1 1.35 0. 1. (psi alpha=beta)
OS-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X
OL-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X
CT-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X
H2-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X
CT-EC-N -C 1 0.0 0.0 1. N-LINKED
H2-EC-N -C 1 0.0 0.0 1. N-LINKED
OS-EC-N -C 1 0.64 341.97 -1. N-LINKED
1 1.91 3.37 -2. GLYCOSIDE
1 -0.87 173.13 3. REVISED '97
OL-EC-N -C 1 0.64 18.03 -1. N-LINKED
1 1.91 356.63 -2. GLYCOSIDE (L and 2C4(D))
1 -0.87 186.87 3. REVISED '97
C -N -CT-CT 1 0.50 180.0 -4. P94 2-N-Acetyl
1 0.15 180.0 -3. P94 CT-CT-N -C
1 0.00 0.00 -2.
1 0.53 0.0 1. P94
C -N -CT-AC 1 0.50 180.0 -4. P94 2-N-Acetyl
1 0.15 180.0 -3. P94 CT-CT-N -C
1 0.00 0.00 -2.
1 0.53 0.0 1. P94
C -N -CT-EC 1 0.50 180.0 -4. P94 2-N-Acetyl
1 0.15 180.0 -3. P94 CT-CT-N -C
1 0.00 0.00 -2.
1 0.53 0.0 1. P94
CT-EC-C -O2 1 0.00 0.00 2. AXIAL CO2-
CT-EC-C -OH 1 0.00 0.00 2. copied from (CT-EC-C -O2) LCM
OG-EC-C -O2 1 0.00 0.00 2. AXIAL CO2-
OG-EC-C -OH 1 0.00 0.00 2. copied from (OG-EC-C -O2) LCM
OL-EC-C -O2 2 2.80 180.00 2. AXIAL CO2-
OL-EC-C -OH 2 2.80 180.00 2. copied from (OL-EC-C -O2) LCM
CT-EC-C -O 1 0.00 0.00 2. copied from (CT-EC-C -O2) LCM
OG-EC-C -O 1 0.00 0.00 2. copied from (OG-EC-C -O2) LCM
OL-EC-C -O 2 2.80 180.00 2. copied from (OL-EC-C -O2) LCM
OG-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK
OH-CT-CT-CT 1 -0.40 0.00 1. SCEE=1.0, SCNB=1.0 Propanol KNK
OL-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK
OS-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK
OG-CT-CT-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OH-CT-CT-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2. An Approximate Parameter
OG-CT-CT-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-CT-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OG-CT-CT-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-CT-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OS-CT-CT-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OG-CT-AC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OH-CT-AC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2. An Approximate Parameter
OG-CT-AC-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-AC-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OG-CT-AC-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-AC-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OG-CT-EC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OH-CT-EC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2. An Approximate Parameter
OG-CT-EC-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-EC-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
OG-CT-EC-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK
OH-CT-EC-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK
1 0.50 0.00 2.
AC-CT-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
EC-CT-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
CT-AC-OH-HO 1 -0.90 0.00 -1. HO-OH-CT-CT Mannose
1 0.00 0.00 -2.
1 0.50 0.00 3.
CT-EC-OH-HO 1 -0.90 0.00 -1. HO-OH-CT-CT Mannose
1 0.00 0.00 -2.
1 0.50 0.00 3.
H2-AC-OH-HO 1 0.50 0.00 3. P94 X-CT-OH-X
H2-EC-OH-HO 1 0.50 0.00 3. P94 X-CT-OH-X
OS-AC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
OL-AC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
OS-EC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
OL-EC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X
CT-CT-C -O2 1 0.00 0.00 -1. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
CT-CT-C -O2 1 0.00 0.00 -2. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
CT-CT-C -O2 1 0.00 0.00 3. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
H1-CT-C -O2 1 0.00 0.00 -1. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
H1-CT-C -O2 1 0.00 0.00 -2. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
H1-CT-C -O2 1 0.00 0.00 3. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM
OS-CT-C -O2 2 0.00 0.00 -1. uronic H+ LCM
OS-CT-C -O2 2 1.40 190.00 -2. uronic H+ LCM
OS-CT-C -O2 2 0.09 160.00 -3. uronic H+ LCM
OS-CT-C -O2 2 0.13 161.00 4. uronic H+ LCM
IMPR
X -X -N -H 5.25 180. 2.
X -X -C -O 10.5 180. 2.
X -O2-C -O2 10.5 180. 2.
X -O2-C -OH 10.5 180. 2.
HBON
H OG 7557.00 2385.00
H OL 7557.00 2385.00
HW OG 7557.00 2385.00
HW OL 7557.00 2385.00
HO OG 7557.00 2385.00
HO OL 7557.00 2385.00
NONB
AC 1.9080 0.0860
EC 1.9080 0.0860
I2 1.6000 0.1000
OG 1.8310 0.1400
OH 1.9610 0.1400
OL 1.8310 0.1400
OS 1.8310 0.1400
CL 1.9480 0.2650
END
N.B. Correct rotational behavior for O-C-C-O fragments requires SCEE=SCNB=1.0. This is
in contrast to "standard" AMBER, in which it is normal to set SCEE=1.2 and SCNB=2.0. Unless
you are attempting to generate rotamer populations, it is OK to use the "standard" values.
Using non-standard values (SCEE=SCNB=1.0) may be unacceptable when a protein is also present.
GLYCAM contributors include:
Karl N. Kirschner
Laura C. Morris
Sompathana Sundara