FMO DATABASE

FMODB ID: 2J2RR

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	-71832.833516
FMO2-HF: Nuclear repulsion	58854.723336
FMO2-HF: Total energy	-12978.110181
FMO2-MP2: Total energy	-13014.168014

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.
-0.311	0.845	0.245	0.829	-2.231	0.007

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 : 0.010 / q_NPA : 0.012

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	-0.055	-0.020	3.128	0.000	1.091	0.246	0.833	-2.171	0.007
4	A	6	HYP	0	0.011	0.012	4.526	-0.280	-0.215	-0.001	-0.004	-0.060	0.000
5	A	7	GLY	0	0.032	0.016	7.186	-0.083	-0.083	0.000	0.000	0.000	0.000
6	A	8	PRO	0	-0.011	-0.011	10.198	0.090	0.090	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.931	0.983	13.535	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.047	0.011	16.012	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	11	ASN	0	0.003	0.000	18.545	0.007	0.007	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.931	0.967	22.091	0.034	0.034	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.034	0.014	24.890	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.960	-0.968	27.015	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.907	0.951	30.459	0.017	0.017	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.023	0.000	33.185	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.028	0.025	35.688	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.936	-0.985	39.013	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.005	-0.004	41.751	0.000	0.000	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.014	-0.006	44.406	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	21	HYP	0	-0.019	-0.005	47.781	0.000	0.000	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.016	0.002	51.012	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	HIS	0	0.004	0.017	52.946	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	24	HYP	0	-0.005	-0.008	55.853	0.000	0.000	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.006	-0.001	59.163	0.001	0.001	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.009	-0.005	61.197	0.000	0.000	0.000	0.000	0.000	0.000
25	A	27	HYP	0	-0.007	-0.006	64.265	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.012	0.012	67.669	0.000	0.000	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.003	-0.014	69.793	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	HYP	0	-0.017	0.000	72.911	0.000	0.000	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.018	0.008	76.237	0.000	0.000	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.005	0.000	78.315	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	HYP	0	-0.001	-0.005	81.441	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.021	0.012	84.841	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.018	0.000	87.181	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	HYP	0	-0.012	-0.014	90.225	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.012	0.003	93.079	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	PRO	0	-0.013	0.002	95.529	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	CYS	0	0.019	0.008	98.932	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)