FMO DATABASE

FMODB ID: Z6YLN

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.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-71436.162036
FMO2-HF: Nuclear repulsion	58457.629951
FMO2-HF: Total energy	-12978.532084
FMO2-MP2: Total energy	-13014.546592

3D Structure

Snapshot

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.
-0.71	1.659	-0.011	-0.892	-1.466	0.006

Interaction energy analysis for fragmet #1(A:3:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.010

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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	-0.018	-0.011	3.325	-0.751	1.618	-0.011	-0.892	-1.466	0.006
4	A	6	HYP	0	-0.010	-0.005	5.600	-0.073	-0.073	0.000	0.000	0.000	0.000
5	A	7	GLY	0	0.026	0.026	7.970	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.008	-0.007	11.114	0.085	0.085	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.930	0.973	14.378	0.067	0.067	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.038	0.022	16.841	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	11	ASN	0	0.010	-0.005	19.225	0.012	0.012	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.905	0.953	22.846	0.069	0.069	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.024	0.014	25.379	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.935	-0.960	27.602	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.796	0.863	31.250	0.035	0.035	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.036	0.014	34.145	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.004	-0.003	36.284	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.810	-0.876	39.655	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.013	0.003	42.502	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.007	-0.007	45.172	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	21	HYP	0	-0.019	-0.011	48.146	0.000	0.000	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.008	0.015	51.608	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	HIS	0	0.009	0.003	53.511	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	24	HYP	0	-0.019	-0.014	56.248	0.000	0.000	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.013	0.013	59.763	0.001	0.001	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.018	-0.008	61.846	0.000	0.000	0.000	0.000	0.000	0.000
25	A	27	HYP	0	-0.004	-0.012	64.916	0.000	0.000	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.019	0.020	68.328	0.000	0.000	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.002	-0.014	70.374	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	HYP	0	-0.011	-0.005	73.424	0.000	0.000	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.017	0.021	76.754	0.000	0.000	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.005	-0.002	79.064	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	HYP	0	-0.008	-0.016	81.963	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.018	0.020	85.491	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.007	-0.008	87.746	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	HYP	0	-0.014	-0.015	90.904	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.015	0.021	93.885	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.000	-0.007	96.333	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	CYS	0	-0.007	0.009	99.599	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ILE)