FMO DATABASE

FMODB ID: R5LG8

Calculation Name: 3N3F-A-Xray372

Preferred Name: Collagen

Target Type: PROTEIN COMPLEX GROUP

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3F

Chain ID: A

ChEMBL ID: CHEMBL2364188

UniProt ID: P39059

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278700.74566
FMO2-HF: Nuclear repulsion	256885.566905
FMO2-HF: Total energy	-21815.178755
FMO2-MP2: Total energy	-21878.854104

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:1:ASN)

Summations of interaction energy for fragment #1(A:1:ASN)

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.
-11.351	-13.473	15.04	-6.817	-6.099	0.018

Interaction energy analysis for fragmet #1(A:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.002

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	3	VAL	0	-0.009	0.010	3.804	-0.497	1.635	-0.031	-1.132	-0.969	-0.001
4	A	4	THR	0	0.010	0.013	6.291	-0.260	-0.260	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.013	-0.016	7.918	0.103	0.103	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.003	0.013	10.197	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.008	0.005	14.389	0.009	0.009	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.005	-0.002	17.995	0.007	0.007	0.000	0.000	0.000	0.000
9	A	9	MET	0	0.071	0.025	17.378	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.859	-0.925	17.702	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.845	-0.916	16.238	-0.309	-0.309	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.004	-0.001	12.493	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.042	-0.024	13.974	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.032	-0.005	16.569	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.830	0.904	11.892	0.299	0.299	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.066	0.032	10.979	-0.086	-0.086	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.023	-0.014	10.192	-0.075	-0.075	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.026	0.000	8.386	-0.107	-0.107	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.028	-0.009	5.524	-0.456	-0.456	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.000	0.005	2.321	-1.498	-0.136	0.858	-0.591	-1.628	0.001
21	A	21	GLU	-1	-0.862	-0.950	4.461	0.603	0.728	-0.001	-0.012	-0.111	0.000
22	A	22	GLY	0	-0.009	-0.017	4.246	-0.643	-0.419	-0.001	-0.037	-0.186	0.000
23	A	23	THR	0	-0.081	-0.033	1.879	-7.381	-13.656	14.200	-4.920	-3.006	0.017
24	A	24	PHE	0	-0.006	-0.008	3.738	-1.217	-0.907	0.015	-0.125	-0.199	0.001
25	A	25	ILE	0	-0.033	-0.033	7.062	0.135	0.135	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.024	0.024	9.842	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.028	-0.018	13.001	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.932	0.935	14.472	0.300	0.300	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.860	-0.925	18.085	-0.165	-0.165	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.043	-0.042	20.043	0.006	0.006	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.066	-0.027	18.635	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.810	-0.858	17.527	-0.141	-0.141	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.017	-0.013	10.467	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.012	0.001	12.070	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.010	0.013	8.390	0.026	0.026	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.861	0.923	6.493	0.297	0.297	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.029	-0.020	7.298	-0.083	-0.083	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.888	0.941	9.745	0.037	0.037	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.882	-0.935	12.104	-0.067	-0.067	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.006	0.010	12.773	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	TRP	0	0.026	0.012	10.809	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.933	0.969	12.339	0.140	0.140	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.906	0.951	13.126	0.128	0.128	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.024	-0.011	12.030	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.010	-0.012	15.260	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.014	-0.003	16.001	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.007	-0.003	19.874	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.908	-0.951	23.161	-0.104	-0.104	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.011	-0.009	23.756	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.002	0.003	24.841	0.009	0.009	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.036	-0.022	26.482	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.002	-0.002	25.042	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.020	-0.007	28.874	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.018	0.016	31.990	-0.002	-0.002	0.000	0.000	0.000	0.000

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