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 SM1
. “Local” 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 energies are calculated in the rigid geometry model with ICFF (red
dashed lines) and MMFF94s (blue dotted lines) “local” energy functions at different
values of the torsion angle. For the Cartesian model calculations (solid lines), bond
lengths and bond angles for each value of the torsion angle are relaxed in Cartesian
coordinates with the MMFF94s local energy. Marked with circles are data points
included in the calculation of the energy RMSD (
E
MMFF94s(local)< 5 kcal). Torsion profiles
(1) am02(C-N-C-H): Rmsd=0.11 kcal (Rank 46)
(2) am04(C-N-C-C): Rmsd=0.29 kcal (Rank 84)
0 60 120 180 240 300 360
(3) am07(H-C-N-C): Rmsd=0.40 kcal (Rank 99)
0 60 120 180 240 300 360
(4) am09(N-C-C-N): Rmsd=0.08 kcal (Rank 30)
0 60 120 180 240 300 360
0 1 2 3
(5) am09(H-C-N-C): Rmsd=0.16 kcal (Rank 69)
2
(6) am10(N-C-C-N): Rmsd=0.12 kcal (Rank 51)
(7) am10(C-C-N-C): Rmsd=0.45 kcal (Rank 102)
(8) am13(C-C-N-C): Rmsd=0.05 kcal (Rank 15)
0 60 120 180 240 300 360
(9) am13(H-O-N-C): Rmsd=0.11 kcal (Rank 44)
0 60 120 180 240 300 360
0 1 2
(10) am14(H-O-N-C): Rmsd=0.02 kcal (Rank 5)
0 60 120 180 240 300 360
0 1 2
(11) am14(C-N-C-H): Rmsd=0.09 kcal (Rank 38)
1 2 3 4
(12) am14(C-C-N-C): Rmsd=0.04 kcal (Rank 8)
(13) am15(C-C-N-C): Rmsd=0.89 kcal (Rank 109)
(14) am15(C-C-C-N): Rmsd=0.21 kcal (Rank 78)
0 60 120 180 240 300 360
0 1 2
(15) am16(C-C-N-H): Rmsd=0.51 kcal (Rank 105)
0 60 120 180 240 300 360
(16) am16(N-C-C-N): Rmsd=0.09 kcal (Rank 39)
0 60 120 180 240 300 360
0 1 2 3
(17) am17(C-C-N-H): Rmsd=0.57 kcal (Rank 106)
2
(18) am17(N-C-C-N): Rmsd=0.13 kcal (Rank 58)
(19) ca01(H-O-C-H): Rmsd=0.00 kcal (Rank 1)
(20) ca02(H-O-C-C): Rmsd=0.04 kcal (Rank 13)
0 60 120 180 240 300 360
(21) ca03(O-C-C-H): Rmsd=0.08 kcal (Rank 31)
0 60 120 180 240 300 360
0 1 2
(22) ca04(H-O-C=O): Rmsd=0.15 kcal (Rank 67)
0 60 120 180 240 300 360
(23) ca05(O-C-C-O): Rmsd=0.05 kcal (Rank 14)
1 2 3 4 5
(24) ca07(H-C-C-O): Rmsd=0.09 kcal (Rank 34)
(25) ca08(H-O-C-C): Rmsd=0.09 kcal (Rank 40)
(26) ca09(H-O-C-C): Rmsd=0.13 kcal (Rank 56)
0 60 120 180 240 300 360
(27) ce01(C-O-C-H): Rmsd=0.07 kcal (Rank 20)
0 60 120 180 240 300 360
(28) ce01(H-C-O-C): Rmsd=0.10 kcal (Rank 42)
0 60 120 180 240 300 360
0 1
(29) ce02(O-C-C-H): Rmsd=0.01 kcal (Rank 3)
1
(30) ce02(C-O-C-C): Rmsd=0.37 kcal (Rank 97)
(31) ce05(C-O-C-H): Rmsd=1.35 kcal (Rank 110)
0 60 120 180 240 300 360
0 1 2 3 4 5
(32) ce06(C-C-O-C): Rmsd=0.31 kcal (Rank 86)
0 60 120 180 240 300 360
0 1 2 3
(33) ce07(C-C-O-C): Rmsd=0.42 kcal (Rank 100)
0 60 120 180 240 300 360
0 1 2 3
(34) ce10(H-C-C-O): Rmsd=0.03 kcal (Rank 6)
0 60 120 180 240 300 360
0 1 2 3 4 5
(35) cj01(C=C-C=C): Rmsd=0.36 kcal (Rank 94)
1 2 3 4 5 6 7
(36) cj02(C-C-C=C): Rmsd=0.58 kcal (Rank 107)
(37) cj03(C-C-C-C): Rmsd=0.21 kcal (Rank 79)
(38) cj04(C-C-C-N): Rmsd=0.14 kcal (Rank 61)
0 60 120 180 240 300 360
(39) cj05(N-C-C-H): Rmsd=0.33 kcal (Rank 89)
0 60 120 180 240 300 360
(40) cj06(C-C-C-H): Rmsd=0.43 kcal (Rank 101)
0 60 120 180 240 300 360
(41) cj07(H-C-C-H): Rmsd=0.48 kcal (Rank 103)
2
(42) cj08(C-C-C-H): Rmsd=0.01 kcal (Rank 4)
(43) cj09(C-C-C-O): Rmsd=0.09 kcal (Rank 35)
0 60 120 180 240 300 360
0 1 2 3 4 5
(44) cj13(C=C-C=C): Rmsd=0.60 kcal (Rank 108)
0 60 120 180 240 300 360
0 1 2 3 4 5 6 7
(45) cj13(C-C=C-C): Rmsd=0.24 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=0.13 kcal (Rank 55)
0 60 120 180 240 300 360
0 1 2 3
(47) co05(C-C-C-H): Rmsd=0.08 kcal (Rank 29)
1 2
(48) co06(C-C-C-C): Rmsd=0.07 kcal (Rank 22)
(49) co07(C-C-C-C): Rmsd=0.23 kcal (Rank 80)
0 60 120 180 240 300 360
0 1 2 3 4 5
(50) co08(C-C-C-H): Rmsd=0.09 kcal (Rank 32)
0 60 120 180 240 300 360
0 1 2 3 4
(51) co08(C=C-C-C): Rmsd=0.13 kcal (Rank 59)
0 60 120 180 240 300 360
0 1 2 3
(52) co09(C-C-C-H): Rmsd=0.14 kcal (Rank 64)
0 60 120 180 240 300 360
0 1 2 3 4
(53) co10(C-C-C-H): Rmsd=0.10 kcal (Rank 41)
1 2
(54) co12(C-C-C-O): Rmsd=0.12 kcal (Rank 50)
(55) co13(H-C-C-C): Rmsd=0.36 kcal (Rank 96)
(56) hl04(H-C-C-H): Rmsd=0.04 kcal (Rank 7)
0 60 120 180 240 300 360
(57) hl05(H-C-C-H): Rmsd=0.07 kcal (Rank 24)
0 60 120 180 240 300 360
(58) hl09(C-C-C-H): Rmsd=0.04 kcal (Rank 12)
0 60 120 180 240 300 360
(59) hl10(C-C-C-H): Rmsd=0.11 kcal (Rank 47)
1
(60) im01(H-N=C-N): Rmsd=0.00 kcal (Rank 2)
(61) im04(C-N=C-N): Rmsd=0.32 kcal (Rank 87)
(62) im07(H-C-C=C): Rmsd=0.19 kcal (Rank 75)
0 60 120 180 240 300 360
(63) kt03(O-C-O-C): Rmsd=0.24 kcal (Rank 81)
0 60 120 180 240 300 360
(64) kt04(H-C-C-C): Rmsd=0.12 kcal (Rank 48)
0 60 120 180 240 300 360
(65) kt05(H-O-C-H): Rmsd=0.14 kcal (Rank 60)
1 2 3 4
(66) nc05(N-C-C-C): Rmsd=0.13 kcal (Rank 57)
(67) nh02(N-C-C-C): Rmsd=0.15 kcal (Rank 66)
0 60 120 180 240 300 360
0 1 2 3 4 5 6
(68) nh03(H-N-C-C): Rmsd=0.13 kcal (Rank 52)
0 60 120 180 240 300 360
0 1 2 3
(69) nh11(H-N-C-H): Rmsd=0.08 kcal (Rank 28)
0 60 120 180 240 300 360
0 1 2 3
(70) nh16(C=C-C-H): Rmsd=0.13 kcal (Rank 53)
0 60 120 180 240 300 360
0 1 2 3
(71) nh17(C-C-C-N): Rmsd=0.04 kcal (Rank 11)
1 2 3 4
(72) nh18(N-C-C-H): Rmsd=0.05 kcal (Rank 16)
(73) nh20(C-C-N-H): Rmsd=0.15 kcal (Rank 65)
0 60 120 180 240 300 360
0 1 2 3 4 5 6 7
(74) nh21(C-C-N-C): Rmsd=0.38 kcal (Rank 98)
0 60 120 180 240 300 360
0 1 2 3 4 5 6 7 8
(75) nh22(C-C-N-O): Rmsd=0.10 kcal (Rank 43)
0 60 120 180 240 300 360
0 1 2 3 4 5 6
(76) nh23(O-N-C-H): Rmsd=0.20 kcal (Rank 76)
0 60 120 180 240 300 360
0 1 2 3 4 5 6
(77) oh02(H-O-C-C): Rmsd=0.06 kcal (Rank 18)
1 2
(78) oh03(H-O-C-C): Rmsd=0.08 kcal (Rank 25)
(79) oh03(O-C-C-C): Rmsd=0.11 kcal (Rank 45)
0 60 120 180 240 300 360
0 1 2 3 4 5
(80) oh04(H-O-C-C): Rmsd=0.07 kcal (Rank 19)
0 60 120 180 240 300 360
0 1 2
(81) oh06(H-O-C-C): Rmsd=0.09 kcal (Rank 37)
0 60 120 180 240 300 360
0 1 2
(82) oh07(H-O-C-C): Rmsd=0.09 kcal (Rank 33)
0 60 120 180 240 300 360
0 1 2
(83) oh10(H-O-C=C): Rmsd=0.34 kcal (Rank 91)
1 2 3 4 5 6
(84) oh11(H-O-C-H): Rmsd=0.18 kcal (Rank 73)
(85) oh12(C=C-C-H): Rmsd=0.09 kcal (Rank 36)
0 60 120 180 240 300 360
0 1 2 3
(86) oh13(C-C-C-H): Rmsd=0.04 kcal (Rank 10)
0 60 120 180 240 300 360
0 1 2 3 4
(87) oh14(H-O-C-H): Rmsd=0.07 kcal (Rank 21)
0 60 120 180 240 300 360
0 1 2
(88) oh14(C-C-C-H): Rmsd=0.12 kcal (Rank 49)
0 60 120 180 240 300 360
0 1 2 3 4 5 6
(89) oh15(H-O-C-H): Rmsd=0.08 kcal (Rank 27)
1 2
(90) oh15(O-C-C-H): Rmsd=0.06 kcal (Rank 17)
(91) or01(C-C-O-C): Rmsd=0.35 kcal (Rank 93)
0 60 120 180 240 300 360
0 1 2 3 4 5
(92) or02(C-O-C=C): Rmsd=0.50 kcal (Rank 104)
0 60 120 180 240 300 360
0 1 2 3 4 5 6 7 8
(93) or03(C-C-O-C): Rmsd=0.36 kcal (Rank 95)
0 60 120 180 240 300 360
0 1 2 3 4 5
(94) or13(C-O-C-C): Rmsd=0.33 kcal (Rank 90)
0 60 120 180 240 300 360
0 1 2 3 4 5
(95) ra04(C-C-C-C): Rmsd=0.17 kcal (Rank 72)
1 2 3 4 5
(96) ra12(C-C-C-C): Rmsd=0.34 kcal (Rank 92)
(97) re03(C-C-C=C): Rmsd=0.30 kcal (Rank 85)
(98) re04(C-C-C-C): Rmsd=0.14 kcal (Rank 62)
0 60 120 180 240 300 360
(99) re05(C-C-C=C): Rmsd=0.17 kcal (Rank 71)
0 60 120 180 240 300 360
(100) re07(C-C-C=C): Rmsd=0.18 kcal (Rank 74)
0 60 120 180 240 300 360
0 1 2 3
(101) re08(C-C=C-C): Rmsd=0.16 kcal (Rank 68)
3
(102) re10(C-C=C-C): Rmsd=0.16 kcal (Rank 70)
(103) sr02(H-S-C-H): Rmsd=0.07 kcal (Rank 23)
0 60 120 180 240 300 360
0 1 2
(104) sr04(C-C-S-S): Rmsd=0.33 kcal (Rank 88)
0 60 120 180 240 300 360
0 1 2 3 4
(105) sr09(C-C-C-H): Rmsd=0.14 kcal (Rank 63)
0 60 120 180 240 300 360
0 1 2 3 4 5
(106) sr09(H-S-C-H): Rmsd=0.08 kcal (Rank 26)
0 60 120 180 240 300 360
0 1 2
(107) sr11(H-S-C-H): Rmsd=0.13 kcal (Rank 54)
1 2
(108) sr11(H-C-C-H): Rmsd=0.04 kcal (Rank 9)
(109) sr12(C-C-C-H): Rmsd=0.21 kcal (Rank 77)
0 60 120 180 240 300 360
0 1 2 3 4 5
(110) sr12(C-S-C-H): Rmsd=0.29 kcal (Rank 83)
0 60 120 180 240 300 360
