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1) Molekul aspirin/asetil salisilat (C9H8O4)
Compute properties
Stretch :0.8943
Bend : 21.7533
Stretch-Bend :0.1600
Torsion :-7.7430
Non-1,4 VDW :2.2354
1,4 VDW :6.5155
Dipole/Dipole :6.4368
Total : 30.2522
The steric energy for frame 1: 30.252 kcal/mole
25 cartesian coordinates
Atom X Y ZC(1) 0.48 -0.386 -0.019C(2) 0.625 -1.781 -0.038C(3) 1.87 -2.418 -0.04C(4) 3.039 -1.664 -0.03C(5) 2.94 -0.274 -0.02C(6) 1.687 0.356 -0.015C(7) 1.66 1.849 -0.006O(8) 2.71 2.482 -0.006O(9) 0.524 2.581 0.001O(11) -0.711 0.295 -0.014C(12) -1.941 -0.287 0.028O(13) -2.199 -1.467 0.082C(14) -3.006 0.794 0.009H(21) -0.239 -2.458 -0.056H(20) 1.93 -3.518 -0.053H(19) 4.024 -2.159 -0.034H(18) 3.875 0.31 -0.017H(10) 0.781 3.518 0.003H(15) -4.024 0.341 0.016H(16) -2.914 1.42 -0.907H(17) -2.912 1.445 0.907Lp(22) -0.703 0.716 -0.442Lp(23) -0.686 0.74 0.389Lp(24) 0.209 2.459 0.497Lp(25) 0.206 2.462 -0.494
21 internal coordinates
Atom Bond Atom
Bond Length
Angle atom
first angle
third atom
second angle Angle type
C(1) ― ― ― ― ― ― ―C(2) C(1) 1.403 ― ― ― ― ―C(6) C(1) 1.417 C(2) 115.668 ― ― ―C(3) C(2) 1.399 C(1) 123.006 C(6) 0.608 DihedralC(5) C(6) 1.403 C(1) 121.725 C(2) -0.466 Dihedral
O(11) C(1) 1.372 C(2) 125.712 C(6) 118.618 Pro-SC(4) C(3) 1.391 C(2) 120.116 C(1) -0.345 DihedralC(7) C(6) 1.493 C(1) 120.574 C(5) 117.701 Pro-RC(12) O(11) 1.362 C(1) 124.872 C(2) 2.814 DihedralH(21) C(2) 1.098 C(1) 122.147 C(3) 114.847 Pro-RO(9) C(7) 1.352 C(6) 123.829 C(1) 0.07 DihedralC(14) C(12) 1.518 O(11) 109.212 C(1) -179.618 DihedralH(20) C(3) 1.103 C(2) 120.2 C(4) 119.684 Pro-RH(19) C(4) 1.102 C(3) 120.518 C(5) 120.731 Pro-RH(18) C(5) 1.102 C(4) 117.912 C(6) 121.356 Pro-RLp(22) O(11) 0.6 C(1) 109.5 C(12) 109.5 Pro-RLp(23) O(11) 0.6 C(1) 109.5 C(12) 109.5 Pro-SO(8) C(7) 1.227 C(6) 120.025 O(9) 116.146 Pro-RO(13) C(12) 1.209 O(11) 127.71 C(14) 123.076 Pro-RH(10) O(9) 0.972 C(7) 107.455 C(6) -179.818 DihedralH(15) C(14) 1.114 C(12) 110.612 O(11) 178.553 DihedralH(16) C(14) 1.114 C(12) 110.62 H(15) 108.043 Pro-RH(17) C(14) 1.114 C(12) 110.333 H(15) 108.043 Pro-SLp(24) O(9) 0.6 C(7) 109.5 H(10) 109.5 Pro-RLp(25) O(9) 0.6 C(7) 109.5 H(10) 109.5 Pro-S
2) Molekul asam palmitat / asam heksadekanoat ((CH3(CH2)14COOH)
Compute properties
Adding lone pairs to O O(17)
Note: Some parameters are not finalized (Quality = 3).
Stretch : 0.0000
Bend :8.1253
Stretch-Bend : -0.0000
Torsion : -1.5816
Non-1,4 VDW: -2.0468
1,4 VDW : 9.6872
Dipole/Dipole : 1.7836
Total : 25.9677
The steric energy for frame 1: 25.968 kcal/mole
52 cartesian coordinates
Atom X Y ZC(1) -9.807 0.332 0C(2) -8.495 1.105 0C(3) -7.328 0.126 0C(4) -6.016 0.899 0C(5) -4.849 -0.08 0C(6) -3.537 0.693 0C(7) -2.37 -0.286 0C(8) -1.058 0.487 0C(9) 0.109 -0.492 0C(10) 1.421 0.281 0C(11) 2.588 -0.698 0C(12) 3.9 0.075 0C(13) 5.067 -0.904 0C(14) 6.379 -0.131 0C(15) 7.546 -1.11 0C(16) 8.852 -0.356 0O(17) 9.833 -1.266 0O(19) 8.98 0.722 0.531H(20) -10.666 1.04 0H(21) -9.869 -0.313 0.905H(22) -9.869 -0.313 -0.905H(23) -8.442 1.743 0.91H(24) -8.442 1.743 -0.91H(25) -7.381 -0.513 -0.91H(26) -7.381 -0.513 0.91H(27) -5.963 1.537 0.91
H(28) -5.963 1.537 -0.91H(29) -4.902 -0.719 -0.91H(30) -4.902 -0.719 0.91H(31) -3.484 1.331 0.91H(32) -3.484 1.331 -0.91H(33) -2.423 -0.925 -0.91H(34) -2.423 -0.925 0.91H(35) -1.005 1.125 0.91H(36) -1.005 1.125 -0.91H(37) 0.056 -1.131 -0.91H(38) 0.056 -1.131 0.91H(39) 1.474 0.919 0.91H(40) 1.474 0.919 -0.91H(41) 2.535 -1.337 -0.91H(42) 2.535 -1.337 0.91H(43) 3.953 0.713 0.91H(44) 3.953 0.713 -0.91H(45) 5.014 -1.543 -0.91H(46) 5.014 -1.543 0.91H(47) 6.432 0.508 0.91H(48) 6.432 0.508 -0.91H(49) 7.497 -1.743 -0.914H(50) 7.497 -1.743 0.914H(18) 10.666 -0.766 0Lp(51) 9.798 -1.598 -0.499Lp(52) 9.798 -1.598 0.499
51 internal coordinates
Atom Bond Atom
Bond Length
Angle atom
first angle
third atom
second angle
Angle type
C(16) ― ― ― ― ― ― ―C(15) C(16) 1.509 ― ― ― ― ―C(14) C(15) 1.523 C(16) 110 ― ―C(13) C(14) 1.523 C(15) 109.5 C(16) 180 DihedralC(12) C(13) 1.523 C(14) 109.5 C(15) 180 DihedralC(11) C(12) 1.523 C(13) 109.5 C(14) 180 DihedralC(10) C(11) 1.523 C(12) 109.5 C(13) 180 DihedralC(9) C(10) 1.523 C(11) 109.5 C(12) 180 DihedralC(8) C(9) 1.523 C(10) 109.5 C(11) 180 DihedralC(7) C(8) 1.523 C(9) 109.5 C(10) 180 DihedralC(6) C(7) 1.523 C(8) 109.5 C(9) 180 DihedralC(5) C(6) 1.523 C(7) 109.5 C(8) 180 DihedralC(4) C(5) 1.523 C(6) 109.5 C(7) 180 DihedralC(3) C(4) 1.523 C(5) 109.5 C(6) 180 DihedralC(2) C(3) 1.523 C(4) 109.5 C(5) 180 DihedralC(1) C(2) 1.523 C(3) 109.5 C(4) 180 Dihedral
O(17) C(16) 1.338 C(15) 107.1 C(14) 180 DihedralO(19) C(16) 1.208 C(15) 122.5 O(17) 122 Pro-RH(18) O(17) 0.972 C(16) 106.1 C(15) 180 DihedralH(20) C(1) 1.113 C(2) 110 C(3) 180 DihedralH(21) C(1) 1.113 C(2) 110 H(20) 109 Pro-RH(22) C(1) 1.113 C(2) 110 H(20) 109 Pro-SH(23) C(2) 1.113 C(1) 109.41 C(3) 109.41 Pro-RH(24) C(2) 1.113 C(1) 109.41 C(3) 109.41 Pro-SH(25) C(3) 1.113 C(2) 109.41 C(4) 109.41 Pro-RH(26) C(3) 1.113 C(2) 109.41 C(4) 109.41 Pro-SH(27) C(4) 1.113 C(3) 109.41 C(5) 109.41 Pro-RH(28) C(4) 1.113 C(3) 109.41 C(5) 109.41 Pro-SH(29) C(5) 1.113 C(4) 109.41 C(6) 109.41 Pro-RH(30) C(5) 1.113 C(4) 109.41 C(6) 109.41 Pro-SH(31) C(6) 1.113 C(5) 109.41 C(7) 109.41 Pro-RH(32) C(6) 1.113 C(5) 109.41 C(7) 109.41 Pro-SH(33) C(7) 1.113 C(6) 109.41 C(8) 109.41 Pro-RH(34) C(7) 1.113 C(6) 109.41 C(8) 109.41 Pro-SH(35) C(8) 1.113 C(7) 109.41 C(9) 109.41 Pro-RH(36) C(8) 1.113 C(7) 109.41 C(9) 109.41 Pro-SH(37) C(9) 1.113 C(8) 109.41 C(10) 109.41 Pro-R
H(38) C(9) 1.113 C(8) 109.41 C(10) 109.41 Pro-SH(39) C(10) 1.113 C(9) 109.41 C(11) 109.41 Pro-RH(40) C(10) 1.113 C(9) 109.41 C(11) 109.41 Pro-SH(41) C(11) 1.113 C(10) 109.41 C(12) 109.41 Pro-RH(42) C(11) 1.113 C(10) 109.41 C(12) 109.41 Pro-SH(43) C(12) 1.113 C(11) 109.41 C(13) 109.41 Pro-RH(44) C(12) 1.113 C(11) 109.41 C(13) 109.41 Pro-SH(45) C(13) 1.113 C(12) 109.41 C(14) 109.41 Pro-RH(46) C(13) 1.113 C(12) 109.41 C(14) 109.41 Pro-SH(47) C(14) 1.113 C(13) 109.41 C(15) 109.41 Pro-RH(48) C(14) 1.113 C(13) 109.41 C(15) 109.41 Pro-SH(49) C(15) 1.113 C(14) 109.41 C(16) 108.8 Pro-RH(50) C(15) 1.113 C(14) 109.41 C(16) 108.8 Pro-S
3) Molekul asam amino arginin (C6H14N4O2)
Compute propertiesAdding lone pairs to N N(5)Adding lone pairs to N N(24)Adding lone pairs to O O(21)Pi System : 1 5 4 7Warning : Some parameters are guessed (Quality = 1).Stretch : 2.6331 Bend : 6.2556 Stretch-Bend :0.0491 Torsion :12.3694 Non-1,4 VDW :6.5212 1,4 VDW :7.7286 Dipole/Dipole :-2.6431 Total :32.9139 The steric energy for frame 1: 32.914 kcal/mole
30 cartesian coordinate
Atom X Y ZN(1) -4.827 -1.241 0.571C(4) -3.644 -0.382 0.571N(5) -3.644 0.878 0.571N(7) -2.309 -0.976 0.559C(9) -1.24 0.032 0.561C(12) 0.13 -0.634 0.549C(15) 1.215 0.435 0.551C(18) 2.585 -0.231 0.538C(20) 3.667 0.821 0.54O(21) 4.87 0.236 0.529O(23) 3.481 2.014 0.562N(24) 2.687 -1.08 -0.655H(2) -4.981 -1.916 -0.218H(3) -5.521 -1.172 1.356H(6) -2.684 1.228 0.571H(8) -2.151 -2.014 0.541H(10) -1.349 0.635 1.491H(11) -1.36 0.649 -0.358H(13) 0.229 -1.259 -0.367H(14) 0.239 -1.273 1.453H(16) 1.116 1.061 1.466H(17) 1.106 1.075 -0.354H(19) 2.705 -0.847 1.457H(22) 5.521 0.958 0.531H(25) 3.601 -1.531 -0.674H(26) 2.674 -0.495 -1.491Lp(27) -4.073 1.178 0.865Lp(28) 2.257 -1.498 -0.64Lp(29) 4.931 -0.087 0.027Lp(30) 4.937 -0.095 1.025
30 internal coordinates
Atom Bond Atom
Bond Length
Angle atom
first angle
third atom
second angle
Angle type
C(4) ― ― ― ― ― ― ―N(5) C(4) 1.26 ― ― ― ― ―N(1) C(4) 1.462 N(5) 126 ― ― ―N(7) C(4) 1.462 N(1) 119.999 N(5) 113.999 Pro-RH(2) N(1) 1.05 C(4) 119.733 N(5) 120 DihedralH(6) N(5) 1.022 C(4) 110 N(1) 180 DihedralC(9) N(7) 1.47 C(4) 112.667 N(1) 180 DihedralH(3) N(1) 1.05 C(4) 119.732 H(2) 120.532 Pro-R
Lp(27) N(5) 0.6 C(4) 120 H(6) 120 Pro-RC(12) C(9) 1.523 N(7) 110.74 C(4) 180 DihedralH(8) N(7) 1.05 C(4) 122.665 C(9) 124.665 Pro-RC(15) C(12) 1.523 C(9) 109.5 N(7) 180 DihedralH(10) C(9) 1.113 N(7) 107.5 C(12) 109.41 Pro-RH(11) C(9) 1.113 N(7) 107.5 C(12) 109.41 Pro-SC(18) C(15) 1.523 C(12) 109.5 C(9) 180 DihedralH(13) C(12) 1.113 C(9) 109.41 C(15) 109.41 Pro-RH(14) C(12) 1.113 C(9) 109.41 C(15) 109.41 Pro-SC(20) C(18) 1.509 C(15) 109.9 C(12) 180 DihedralH(16) C(15) 1.113 C(12) 109.41 C(18) 109.41 Pro-RH(17) C(15) 1.113 C(12) 109.41 C(18) 109.41 Pro-SO(21) C(20) 1.338 C(18) 109.9 C(15) 180 DihedralN(24) C(18) 1.468 C(15) 108.8 C(20) 110.74 Pro-RH(19) C(18) 1.113 C(15) 109.39 C(20) 107.9 Pro-SO(23) C(20) 1.208 C(18) 125.298 O(21) 124.798 Pro-RH(22) O(21) 0.972 C(20) 106.1 C(18) 180 DihedralH(25) N(24) 1.02 C(18) 109.47 C(15) 180 DihedralH(26) N(24) 1.02 C(18) 109.47 H(25) 104.5 Pro-RLp(28) N(24) 0.6 C(18) 109.5 H(25) 109.5 Pro-SLp(29) O(21) 0.6 C(20) 109.5 H(22) 109.5 Pro-RLp(30) O(21) 0.6 C(20) 109.5 H(22) 109.5 Pro-S
A. Dihedral Angle
Dihedral angle: The angle between two planes, where each plane is defined by three atoms. In
most common use, the angle between two bonds. In the Newman projection shown, the dihedral
angle between the Cl–C and H–C bonds is 60o (they are gauche), where as the dihedral angle
between the two C–Cl bonds is 180o (they are anti–periplanar).
Sudut dihedral: Sudut antara dua pesawat, di mana setiap pesawat ditetapkan oleh tiga atom.
Dalam penggunaan yang paling umum, sudut antara dua ikatan. Dalam proyeksi Newman
ditampilkan, sudut dihedral antara ikatan Cl-C dan H-C adalah 60o (mereka adalah gauche),
sedangkan sudut dihedral antara dua ikatan C-Cl adalah 180o (mereka anti-periplanar).
(Sumber: http://www.chem.ucla.edu/harding/IGOC/D/dihedral_angle.html)
Dihedral angels of four atom
The structure of a molecule can be defined with high precision by the dihedral angles between three successive chemical bond vectors (Figure 2). The dihedral angle varies only the distance between the first and fourth atoms; the other interatomic distances are constrained by the chemical bond lengths and bond angles.
Struktur molekul dapat didefinisikan dengan keakuratan yang tinggi dengan sudut dihedral antara tiga vektor ikatan kimia yang berurutan (Gambar 2). Sudut dihedral bervariasi hanya jarak antara pertama dan keempat atom; jarak interatomik lainnya dibatasi oleh panjang ikatan kimia dan sudut ikatan.
To visualize the dihedral angle of four atoms, it's helpful to look down the second bond vector (Figure 3), which is equivalent to the Newman projection in chemistry. The first atom is at 6 o'clock, the fourth atom is at roughly 2 o'clock and the second and third atoms are located in the center. The second bond vector is coming out of the page. The dihedral angle is the counterclockwise angle made by the vectors (red) and (blue). When the fourth atom eclipses the first atom, the dihedral angle is zero; when the atoms are exactly opposite (as in Figure 2), the dihedral angle is 180°.
Untuk memvisualisasikan sudut dihedral dari empat atom, sangat membantu bila kita melihat ke bawah vektor obligasi kedua (Gambar 3), yang setara dengan proyeksi Newman dalam kimia. Atom pertama
adalah pukul 6, atom keempat adalah pada sekitar 02:00 dan atom kedua dan ketiga berada di tengah. Vektor obligasi kedua yang keluar dari halaman. Sudut dihedral adalah sudut berlawanan yang dibuat oleh vektor (merah) dan (biru). Ketika atom keempat eclipses atom pertama, sudut dihedral adalah nol; ketika atom yang persis berlawanan (seperti pada Gambar 2), sudut dihedral adalah 180 °.
(Sumber: http://en.wikipedia.org/wiki/Dihedral_angle#Alternative_definitions)
Gambar 2
Gambar 4Gambar 3
B. Pro –S Angle