FMODB ID: 6N67Z
Calculation Name: 3DMW-A-Xray372
Preferred Name: Collagen
Target Type: PROTEIN COMPLEX GROUP
Ligand Name: 4-hydroxyproline
ligand 3-letter code: HYP
PDB ID: 3DMW
Chain ID: A
ChEMBL ID: CHEMBL2364188
UniProt ID: P02461
Base Structure: X-ray
Registration Date: 2023-06-21
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptHSide |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 37 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -71757.256967 |
---|---|
FMO2-HF: Nuclear repulsion | 58778.975307 |
FMO2-HF: Total energy | -12978.28166 |
FMO2-MP2: Total energy | -13014.320163 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:3:ILE)
Summations of interaction energy for
fragment #1(A:3:ILE)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-0.956 | 1.209 | 0.043 | -0.442 | -1.767 | 0.008 |
Interaction energy analysis for fragmet #1(A:3:ILE)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | A | 5 | PRO | 0 | -0.061 | -0.020 | 3.420 | -0.634 | 1.488 | 0.044 | -0.439 | -1.728 | 0.008 |
4 | A | 6 | HYP | 0 | 0.009 | 0.010 | 4.914 | -0.327 | -0.284 | -0.001 | -0.003 | -0.039 | 0.000 |
5 | A | 7 | GLY | 0 | 0.034 | 0.018 | 7.468 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | PRO | 0 | -0.008 | -0.009 | 10.569 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | ARG | 1 | 0.927 | 0.980 | 13.892 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | GLY | 0 | 0.046 | 0.011 | 16.296 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | ASN | 0 | 0.005 | 0.001 | 18.823 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | ARG | 1 | 0.931 | 0.971 | 22.411 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | GLY | 0 | 0.041 | 0.015 | 25.172 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | GLU | -1 | -0.971 | -0.973 | 27.193 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | ARG | 1 | 0.799 | 0.868 | 30.610 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | GLY | 0 | 0.040 | 0.006 | 33.446 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | SER | 0 | 0.004 | 0.015 | 35.819 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | GLU | -1 | -0.830 | -0.901 | 39.073 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | GLY | 0 | 0.005 | -0.002 | 41.968 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | SER | 0 | -0.013 | -0.003 | 44.595 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | HYP | 0 | -0.012 | -0.005 | 47.867 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | GLY | 0 | 0.010 | 0.001 | 51.180 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | HIS | 0 | -0.001 | 0.015 | 53.156 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | HYP | 0 | -0.002 | -0.007 | 55.980 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | GLY | 0 | 0.007 | -0.001 | 59.327 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | MET | 0 | -0.009 | -0.004 | 61.393 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | HYP | 0 | -0.005 | -0.007 | 64.453 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | GLY | 0 | 0.015 | 0.015 | 67.860 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | PRO | 0 | -0.005 | -0.013 | 69.992 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | HYP | 0 | -0.015 | 0.001 | 73.096 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | GLY | 0 | 0.016 | 0.006 | 76.426 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | PRO | 0 | -0.006 | 0.000 | 78.520 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | HYP | 0 | 0.000 | -0.004 | 81.642 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | GLY | 0 | 0.017 | 0.008 | 85.037 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | ALA | 0 | -0.023 | -0.001 | 87.391 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | HYP | 0 | 0.000 | -0.009 | 90.442 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | GLY | 0 | 0.009 | 0.002 | 93.284 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | PRO | 0 | -0.015 | 0.003 | 95.736 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | CYS | 0 | 0.019 | 0.005 | 99.147 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |