FMO DATABASE

FMODB ID: ZYZ5N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-278655.578063
FMO2-HF: Nuclear repulsion	256840.662756
FMO2-HF: Total energy	-21814.915307
FMO2-MP2: Total energy	-21878.613756

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.
-10.85	-14.97	17.552	-7.532	-5.901	0.022

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 : 0.013 / q_NPA : 0.009

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

Sort

Graph Options

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	0.005	0.014	3.804	-0.286	1.827	-0.031	-1.130	-0.953	0.000
4	A	4	THR	0	0.001	0.014	6.391	-0.451	-0.451	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.016	-0.023	7.907	0.160	0.160	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.009	0.017	10.316	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.023	-0.013	14.412	0.010	0.010	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.083	0.036	18.044	0.013	0.013	0.000	0.000	0.000	0.000
9	A	9	MET	0	0.082	0.027	17.380	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.859	-0.925	17.758	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.848	-0.916	15.841	-0.301	-0.301	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.022	-0.010	12.564	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.055	-0.028	14.241	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.049	-0.013	16.761	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.841	0.912	12.026	0.290	0.290	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.077	0.035	11.231	-0.062	-0.062	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.015	-0.003	10.437	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.028	0.000	8.545	-0.109	-0.109	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.042	-0.012	5.835	-0.511	-0.511	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.009	0.008	2.684	-1.397	-0.044	0.284	-0.431	-1.206	0.001
21	A	21	GLU	-1	-0.904	-0.968	4.457	1.024	1.142	-0.001	-0.012	-0.105	0.000
22	A	22	GLY	0	-0.009	-0.021	4.212	-0.517	-0.281	-0.001	-0.039	-0.195	0.000
23	A	23	THR	0	-0.070	-0.027	1.839	-6.866	-15.159	17.286	-5.753	-3.241	0.020
24	A	24	PHE	0	-0.027	-0.015	3.779	-1.525	-1.172	0.015	-0.167	-0.201	0.001
25	A	25	ILE	0	-0.028	-0.030	7.118	0.106	0.106	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.025	0.023	9.893	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.035	-0.020	13.001	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.944	0.950	14.955	0.306	0.306	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.914	-0.952	18.071	-0.155	-0.155	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.030	-0.011	20.025	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.053	-0.022	18.692	0.009	0.009	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.806	-0.872	17.582	-0.070	-0.070	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.020	-0.014	10.148	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.011	0.008	12.120	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.017	0.008	8.538	0.051	0.051	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.865	0.919	6.692	-0.113	-0.113	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.036	-0.016	7.301	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.981	0.989	9.739	-0.166	-0.166	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.929	-0.966	12.082	0.073	0.073	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.000	0.004	12.767	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	TRP	0	0.025	0.007	10.903	0.036	0.036	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.933	0.970	12.362	-0.053	-0.053	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.884	0.925	13.158	0.071	0.071	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.024	-0.014	11.706	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.019	-0.011	15.305	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.020	-0.007	16.267	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.001	0.003	19.927	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.897	-0.948	23.219	-0.070	-0.070	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.010	-0.007	23.979	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.011	0.000	24.598	0.006	0.006	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.048	-0.031	26.545	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.008	0.006	25.045	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.027	-0.010	28.837	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.026	0.018	31.951	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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