Supplementary Material for
ICFF: A New Method to Incorporate Implicit Flexibility into an
Internal Coordinate Force Field
VSEVOLOD KATRITCH, MAXIM TOTROV and RUBEN ABAGYAN
Figure SM2
. Full conformational energy torsion profiles for all molecules in
MMFF94s evaluation suite. Full names of the molecules and definition of the torsion
angles can be found in Table SM1.
Conformational energy with soft empirical (red dashes lines) and MMFF94s van der
Waals (blue dotted lines) “1-5,1-6” repulsion potential is calculated at different values of
the torsion angle in the ICFF rigid geometry model. For the Cartesian MMFF94s model
calculations (black solid lines), bond lengths and bond angles for each value of the
torsion angle are relaxed in Cartesian coordinates. Marked with circles are data points
included in the calculation of the RMSD
(
E
MMFF94s< 5 kcal). Torsion profiles are ranked
(1) am02(C-N-C-H): Rmsd=0.74 kcal (Rank 102)
(2) am04(C-N-C-C): Rmsd=0.17 kcal (Rank 34)
0 60 120 180 240 300 360
(3) am07(H-C-N-C): Rmsd=0.18 kcal (Rank 35)
0 60 120 180 240 300 360
(4) am09(N-C-C-N): Rmsd=0.70 kcal (Rank 101)
0 60 120 180 240 300 360
(5) am09(H-C-N-C): Rmsd=0.55 kcal (Rank 93)
7
(6) am10(N-C-C-N): Rmsd=0.77 kcal (Rank 104)
(7) am10(C-C-N-C): Rmsd=0.44 kcal (Rank 83)
(8) am13(C-C-N-C): Rmsd=0.23 kcal (Rank 51)
0 60 120 180 240 300 360
(9) am13(H-O-N-C): Rmsd=0.21 kcal (Rank 46)
0 60 120 180 240 300 360
(10) am14(H-O-N-C): Rmsd=0.23 kcal (Rank 53)
0 60 120 180 240 300 360
(11) am14(C-N-C-H): Rmsd=0.56 kcal (Rank 96)
5
(12) am14(C-C-N-C): Rmsd=0.25 kcal (Rank 60)
(13) am15(C-C-N-C): Rmsd=0.97 kcal (Rank 108)
(14) am15(C-C-C-N): Rmsd=0.88 kcal (Rank 106)
0 60 120 180 240 300 360
(15) am16(C-C-N-H): Rmsd=0.22 kcal (Rank 49)
0 60 120 180 240 300 360
(16) am16(N-C-C-N): Rmsd=0.46 kcal (Rank 88)
0 60 120 180 240 300 360
(17) am17(C-C-N-H): Rmsd=0.56 kcal (Rank 95)
7
(18) am17(N-C-C-N): Rmsd=0.40 kcal (Rank 78)
(19) ca01(H-O-C-H): Rmsd=0.46 kcal (Rank 87)
(20) ca02(H-O-C-C): Rmsd=0.19 kcal (Rank 41)
0 60 120 180 240 300 360
(21) ca03(O-C-C-H): Rmsd=0.15 kcal (Rank 32)
0 60 120 180 240 300 360 0
1 2
(22) ca04(H-O-C=O): Rmsd=0.39 kcal (Rank 76)
0 60 120 180 240 300 360
(23) ca05(O-C-C-O): Rmsd=0.26 kcal (Rank 63)
2 3 4 5
(24) ca07(H-C-C-O): Rmsd=0.13 kcal (Rank 22)
(25) ca08(H-O-C-C): Rmsd=0.65 kcal (Rank 99)
(26) ca09(H-O-C-C): Rmsd=0.48 kcal (Rank 90)
0 60 120 180 240 300 360
(27) ce01(C-O-C-H): Rmsd=0.01 kcal (Rank 2)
0 60 120 180 240 300 360
(28) ce01(H-C-O-C): Rmsd=0.36 kcal (Rank 73)
0 60 120 180 240 300 360 0
1
(29) ce02(O-C-C-H): Rmsd=0.01 kcal (Rank 1)
1
(30) ce02(C-O-C-C): Rmsd=0.01 kcal (Rank 3)
(31) ce05(C-O-C-H): Rmsd=0.39 kcal (Rank 77)
0 60 120 180 240 300 360 0
1 2 3 4 5
(32) ce06(C-C-O-C): Rmsd=0.40 kcal (Rank 79)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9
(33) ce07(C-C-O-C): Rmsd=0.44 kcal (Rank 84)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9
(34) ce10(H-C-C-O): Rmsd=0.25 kcal (Rank 57)
0 60 120 180 240 300 360 0
1 2 3 4 5
(35) cj01(C=C-C=C): Rmsd=0.37 kcal (Rank 74)
3 4 5 6 7
(36) cj02(C-C-C=C): Rmsd=0.57 kcal (Rank 97)
(37) cj03(C-C-C-C): Rmsd=1.03 kcal (Rank 109)
0 60 120 180 240 300 360 0
1 2 3 4 5
(38) cj04(C-C-C-N): Rmsd=0.18 kcal (Rank 36)
0 60 120 180 240 300 360 0
1 2 3 4
(39) cj05(N-C-C-H): Rmsd=0.54 kcal (Rank 91)
0 60 120 180 240 300 360 0
1 2 3 4 5
(40) cj06(C-C-C-H): Rmsd=0.19 kcal (Rank 40)
0 60 120 180 240 300 360 0
1 2 3 4 5
(41) cj07(H-C-C-H): Rmsd=0.54 kcal (Rank 92)
5 6 7 8
(42) cj08(C-C-C-H): Rmsd=0.09 kcal (Rank 13)
(43) cj09(C-C-C-O): Rmsd=0.14 kcal (Rank 25)
0 60 120 180 240 300 360 0
1 2 3 4 5 6
(44) cj13(C=C-C=C): Rmsd=0.69 kcal (Rank 100)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(45) cj13(C-C=C-C): Rmsd=0.43 kcal (Rank 82)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
(46) co03(H-C-C-H): Rmsd=0.12 kcal (Rank 19)
0 60 120 180 240 300 360 0
1 2 3
(47) co05(C-C-C-H): Rmsd=0.14 kcal (Rank 27)
2 3
(48) co06(C-C-C-C): Rmsd=0.22 kcal (Rank 50)
(49) co07(C-C-C-C): Rmsd=0.20 kcal (Rank 44)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9 10
(50) co08(C-C-C-H): Rmsd=0.29 kcal (Rank 68)
0 60 120 180 240 300 360 0
1 2 3
(51) co08(C=C-C-C): Rmsd=0.46 kcal (Rank 86)
0 60 120 180 240 300 360 0
1 2 3 4
(52) co09(C-C-C-H): Rmsd=0.41 kcal (Rank 80)
0 60 120 180 240 300 360 0
1 2 3
(53) co10(C-C-C-H): Rmsd=0.09 kcal (Rank 15)
2
(54) co12(C-C-C-O): Rmsd=0.29 kcal (Rank 67)
(55) co13(H-C-C-C): Rmsd=1.14 kcal (Rank 110)
(56) hl04(H-C-C-H): Rmsd=0.18 kcal (Rank 38)
0 60 120 180 240 300 360
(57) hl05(H-C-C-H): Rmsd=0.28 kcal (Rank 65)
0 60 120 180 240 300 360
(58) hl09(C-C-C-H): Rmsd=0.06 kcal (Rank 4)
0 60 120 180 240 300 360
(59) hl10(C-C-C-H): Rmsd=0.12 kcal (Rank 21)
3 4 5 6 7
(60) im01(H-N=C-N): Rmsd=0.55 kcal (Rank 94)
(61) im04(C-N=C-N): Rmsd=0.85 kcal (Rank 105)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
(62) im07(H-C-C=C): Rmsd=0.15 kcal (Rank 31)
0 60 120 180 240 300 360 0
1 2 3 4 5 6
(63) kt03(O-C-O-C): Rmsd=0.21 kcal (Rank 47)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
(64) kt04(H-C-C-C): Rmsd=0.12 kcal (Rank 20)
0 60 120 180 240 300 360 0
1 2 3 4
(65) kt05(H-O-C-H): Rmsd=0.13 kcal (Rank 23)
3 4 5 6
(66) nc05(N-C-C-C): Rmsd=0.38 kcal (Rank 75)
(67) nh02(N-C-C-C): Rmsd=0.25 kcal (Rank 58)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8
(68) nh03(H-N-C-C): Rmsd=0.14 kcal (Rank 26)
0 60 120 180 240 300 360 0
1 2 3
(69) nh11(H-N-C-H): Rmsd=0.09 kcal (Rank 16)
0 60 120 180 240 300 360 0
1 2 3
(70) nh16(C=C-C-H): Rmsd=0.26 kcal (Rank 61)
0 60 120 180 240 300 360 0
1 2 3 4
(71) nh17(C-C-C-N): Rmsd=0.34 kcal (Rank 71)
2 3 4 5
(72) nh18(N-C-C-H): Rmsd=0.25 kcal (Rank 59)
(73) nh20(C-C-N-H): Rmsd=0.21 kcal (Rank 48)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9
(74) nh21(C-C-N-C): Rmsd=0.41 kcal (Rank 81)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9 10
(75) nh22(C-C-N-O): Rmsd=0.06 kcal (Rank 5)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(76) nh23(O-N-C-H): Rmsd=0.24 kcal (Rank 55)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(77) oh02(H-O-C-C): Rmsd=0.08 kcal (Rank 8)
2
(78) oh03(H-O-C-C): Rmsd=0.07 kcal (Rank 7)
(79) oh03(O-C-C-C): Rmsd=0.18 kcal (Rank 37)
0 60 120 180 240 300 360 0
1 2 3 4 5 6
(80) oh04(H-O-C-C): Rmsd=0.08 kcal (Rank 11)
0 60 120 180 240 300 360 0
1 2
(81) oh06(H-O-C-C): Rmsd=0.10 kcal (Rank 17)
0 60 120 180 240 300 360 0
1 2
(82) oh07(H-O-C-C): Rmsd=0.09 kcal (Rank 14)
0 60 120 180 240 300 360 0
1 2
(83) oh10(H-O-C=C): Rmsd=0.31 kcal (Rank 70)
2 3 4 5 6
(84) oh11(H-O-C-H): Rmsd=0.28 kcal (Rank 64)
(85) oh12(C=C-C-H): Rmsd=0.15 kcal (Rank 30)
0 60 120 180 240 300 360 0
1 2 3 4
(86) oh13(C-C-C-H): Rmsd=0.21 kcal (Rank 45)
0 60 120 180 240 300 360 0
1 2 3 4
(87) oh14(H-O-C-H): Rmsd=0.11 kcal (Rank 18)
0 60 120 180 240 300 360 0
1 2
(88) oh14(C-C-C-H): Rmsd=0.26 kcal (Rank 62)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(89) oh15(H-O-C-H): Rmsd=0.14 kcal (Rank 29)
4 5 6 7 8
(90) oh15(O-C-C-H): Rmsd=0.07 kcal (Rank 6)
(91) or01(C-C-O-C): Rmsd=0.24 kcal (Rank 56)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9
(92) or02(C-O-C=C): Rmsd=0.30 kcal (Rank 69)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(93) or03(C-C-O-C): Rmsd=0.24 kcal (Rank 54)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8 9
(94) or13(C-O-C-C): Rmsd=0.89 kcal (Rank 107)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7 8
(95) ra04(C-C-C-C): Rmsd=0.28 kcal (Rank 66)
3 4 5 6
(96) ra12(C-C-C-C): Rmsd=0.77 kcal (Rank 103)
(97) re03(C-C-C=C): Rmsd=0.20 kcal (Rank 42)
0 60 120 180 240 300 360 0
1 2 3
(98) re04(C-C-C-C): Rmsd=0.20 kcal (Rank 43)
0 60 120 180 240 300 360 0
1 2 3 4 5 6
(99) re05(C-C-C=C): Rmsd=0.15 kcal (Rank 33)
0 60 120 180 240 300 360 0
1 2 3 4
(100) re07(C-C-C=C): Rmsd=0.08 kcal (Rank 10)
0 60 120 180 240 300 360 0
1 2 3
(101) re08(C-C=C-C): Rmsd=0.19 kcal (Rank 39)
7 8 9 10 11 12 13 14 15
(102) re10(C-C=C-C): Rmsd=0.23 kcal (Rank 52)
(103) sr02(H-S-C-H): Rmsd=0.08 kcal (Rank 9)
0 60 120 180 240 300 360 0
1 2
(104) sr04(C-C-S-S): Rmsd=0.58 kcal (Rank 98)
0 60 120 180 240 300 360 0
1 2 3 4 5 6
(105) sr09(C-C-C-H): Rmsd=0.36 kcal (Rank 72)
0 60 120 180 240 300 360 0
1 2 3 4 5 6 7
(106) sr09(H-S-C-H): Rmsd=0.08 kcal (Rank 12)
0 60 120 180 240 300 360 0
1 2
(107) sr11(H-S-C-H): Rmsd=0.13 kcal (Rank 24)
2 3 4
(108) sr11(H-C-C-H): Rmsd=0.14 kcal (Rank 28)
(109) sr12(C-C-C-H): Rmsd=0.48 kcal (Rank 89)
7 8 9 10 11 12 13 14
(110) sr12(C-S-C-H): Rmsd=0.44 kcal (Rank 85)
