MASS   300 CSP    12.01100 C ! for SPA
MASS   301 OSP    15.99900 O ! for SPA
MASS   302 OP     15.99900 O ! for SPA


RESI AOS         -2.00  ! ophosphoserine(SEP)-adenosine-5'-monophosphate, 
                        ! from analogy from Elijah Roberts's 3/11/2005 AMO
                        ! ER's notes:
                        ! This molecule was constructed by taking the ATP molecule up to O5'
                        ! and then appending P, O1P, O2P, and O3P from 5PHO (O3P was change
                        ! from type ON4 to ON2). ASP was then joined to O3P at C and the H5T charge
                        ! was added to C as per the CHARMM standard procedures.
                        
! This section is from SER.
GROUP   
ATOM N    NH1    -0.47  !                       
ATOM HN   H       0.31  !                  
ATOM CA   CT1     0.07  !                 
ATOM HA   HB      0.09  !                
!integer charge   -2    !             HN-N   HB1  (-)O3S
!Anaology with ER's AMP !                |   |        |
GROUP                   !             HA-CA--CB--OGS--PS==O1S
ATOM CB   CT2    -0.08  !                |   |        |
ATOM HB1  HA      0.09  !                |   HB2  (-)O2S 
ATOM HB2  HA      0.09  !              O=C           
ATOM OGS  ON2    -0.50  !                |
ATOM O1S  ON3    -0.90  !                
ATOM O2S  ON3    -0.90  !                
ATOM O3S  ON3    -0.90  !                
ATOM PS   P       1.10  !                
GROUP
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB   CA           
BOND N    HN        N    CA        C    CA
BOND CA   HA        CB   HB1       CB   HB2
BOND C    O3P
BOND CB   OGS       OGS  PS        PS   O2S       PS   O3S
DOUBLE  O   C       PS   O1S       
IMPR N    C    CA   HN


RESI SPA         -4.00  ! ophosphoserine(SEP) being attached to Cytosine from CCA end of tRNA, 
                        ! SEP (o-phospho serine) partial charges taken from AOS above. -AS
                        
GROUP                   !SEP and Adenine charges were used for this with NTER and 5TER charges for ends.
ATOM P    P       1.50  !
ATOM O1P  ON3    -0.78  !                      H61  H62!
ATOM O2P  ON3    -0.78  !                        \  /    
ATOM O5'  ON2    -0.57  !                         N6
ATOM C5'  CN8B   -0.08  !                         |
ATOM H5'  HN8     0.09  !                         C6
ATOM H5'' HN8     0.09  !                       //  \
GROUP                   !                       N1   C5--N7\\ 
ATOM N9   NN2    -0.05  !                       |    ||     C8-H8
ATOM C5   CN5     0.28  !                       C2   C4--N9/
ATOM N7   NN4    -0.71  !                      / \\ /     \
ATOM C8   CN4     0.34  !                    H2   N3       \
ATOM H8   HN3     0.12  !                                   \
ATOM N1   NN3A   -0.74  !                                    \
ATOM C2   CN4     0.50  !                                     \
ATOM H2   HN3     0.13  !                                      \ 
ATOM N3   NN3A   -0.75  !                                       \
ATOM C4   CN5     0.43  !                   O1P    H5' H4'  O4'  \
ATOM C6   CN2     0.46  !                    |      |    \ /   \  \
ATOM N6   NN1    -0.77  !                   -P-O5'-C5'---C4'    C1'
ATOM H61  HN1     0.38  !                    |      |     \     / \
ATOM H62  HN1     0.38  !                   O2P    H5''   C3'--C2' H1'
GROUP                   !                                / \   / \             
ATOM N    NH1    -0.47  !          |-------------------O3' H3' O2' H2''   
ATOM HN   H       0.31  !          |                            |
                        !          |                           H2'
                        !          |      
ATOM CA   CT1     0.08  !          |   
ATOM HA   HB      0.09  !          |   
!integer charge   -2    !          |  HN-N  HB1  (-)O3S
!Anaology with ER's AMP !          |     |   |        |
GROUP                   !          |  HA-CA--CB--OGS--PS==O1S
ATOM CB   CT2    -0.08  !          |     |   |        |
ATOM HB1  HA      0.09  !          |     |   HB2  (-)O2S 
ATOM HB2  HA      0.09  !          |   O=C           
ATOM OGS  ON2    -0.50  !          \-----/
ATOM O1S  ON3    -0.90  !                
ATOM O2S  ON3    -0.90  !                
ATOM O3S  ON3    -0.90  !                
ATOM PS   P       1.10  !                
GROUP
ATOM C    CSP     0.63  !   Analogy with ester bond in fatty acid
ATOM O    OSP    -0.52  !   Analogy with ester bond in fatty acid
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  OP     -0.34  !  Analogy with ester bond in fatty acid.
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43 
GROUP                   !
ATOM C4'  CN7     0.16  !
ATOM H4'  HN7     0.09  !
ATOM O4'  ON6B   -0.50  !
ATOM C1'  CN7B    0.16  !
ATOM H1'  HN7     0.09  !
BOND CB   CA           
BOND N    HN        N    CA        C    CA
BOND CA   HA        CB   HB1       CB   HB2
BOND C    O3'
BOND CB   OGS       OGS  PS        PS   O2S       PS   O3S
BOND P    O1P       P    O2P       P     O5'
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C3'  O3'      
BOND C2'  O2'       O2'  H2'       
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE  N1  C6      C2   N3        C4   C5        N7   C8
DOUBLE   O    C     PS   O1S          
IMPR N6   C6   H61  H62        C6   N1   C5   N6        
IMPR C    O3'  CA   O

END