FMO DATABASE

FMODB ID: Z63GN

Calculation Name: 1YRN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YRN

Chain ID: A

ChEMBL ID:

UniProt ID: P0CY10

Base Structure: X-ray

Registration Date: 2023-09-20

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-266329.937227
FMO2-HF: Nuclear repulsion	245951.819129
FMO2-HF: Total energy	-20378.118098
FMO2-MP2: Total energy	-20437.602014

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:77:ILE)

Summations of interaction energy for fragment #1(A:77: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.
-18.312	-10.819	11.526	-5.598	-13.419	-0.013

Interaction energy analysis for fragmet #1(A:77:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.003

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	79	PRO	0	0.084	0.032	2.748	-2.943	-0.233	0.477	-1.461	-1.726	-0.010
4	A	80	GLN	0	0.080	0.034	5.319	-0.073	0.047	-0.001	-0.010	-0.108	0.000
5	A	81	ALA	0	0.014	0.007	2.250	0.912	-0.720	3.981	-0.786	-1.563	-0.002
6	A	82	ARG	1	0.890	0.917	2.225	-12.895	-10.003	4.029	-2.164	-4.756	0.006
7	A	83	ALA	0	0.038	0.037	3.599	0.047	0.101	0.040	0.070	-0.163	0.000
8	A	84	PHE	0	0.038	0.006	6.323	0.067	0.067	0.000	0.000	0.000	0.000
9	A	85	LEU	0	0.013	0.006	2.359	-0.508	-0.285	1.198	-0.294	-1.127	-0.002
10	A	86	GLU	-1	-0.785	-0.879	6.394	0.165	0.165	0.000	0.000	0.000	0.000
11	A	87	GLN	0	0.023	0.033	8.681	0.039	0.039	0.000	0.000	0.000	0.000
12	A	88	VAL	0	-0.009	0.007	9.659	0.031	0.031	0.000	0.000	0.000	0.000
13	A	89	PHE	0	0.024	-0.001	9.813	0.039	0.039	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.874	0.928	11.650	0.070	0.070	0.000	0.000	0.000	0.000
15	A	91	ARG	1	0.852	0.911	14.176	0.129	0.129	0.000	0.000	0.000	0.000
16	A	92	LYS	1	0.828	0.893	14.549	0.139	0.139	0.000	0.000	0.000	0.000
17	A	93	GLN	0	0.078	0.048	13.750	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	94	SER	0	-0.023	-0.009	13.862	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	95	LEU	0	0.004	0.007	10.987	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	96	ASN	0	0.055	0.029	15.222	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	97	SER	0	0.040	-0.005	15.665	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	98	LYS	1	1.003	1.013	15.793	0.121	0.121	0.000	0.000	0.000	0.000
23	A	99	GLU	-1	-0.721	-0.838	14.561	-0.171	-0.171	0.000	0.000	0.000	0.000
24	A	100	LYS	1	0.860	0.926	10.953	0.198	0.198	0.000	0.000	0.000	0.000
25	A	101	GLU	-1	-0.851	-0.916	11.130	-0.385	-0.385	0.000	0.000	0.000	0.000
26	A	102	GLU	-1	-0.888	-0.946	12.096	-0.241	-0.241	0.000	0.000	0.000	0.000
27	A	103	VAL	0	-0.017	-0.023	7.703	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	104	ALA	0	-0.011	-0.003	7.473	-0.093	-0.093	0.000	0.000	0.000	0.000
29	A	105	LYS	1	0.897	0.940	7.857	0.217	0.217	0.000	0.000	0.000	0.000
30	A	106	LYS	1	0.929	0.973	9.368	0.321	0.321	0.000	0.000	0.000	0.000
31	A	107	CYS	0	-0.104	-0.039	3.743	-0.143	0.015	0.001	-0.032	-0.127	0.000
32	A	108	GLY	0	0.021	0.019	4.639	-0.367	-0.271	-0.001	-0.007	-0.088	0.000
33	A	109	ILE	0	-0.063	-0.021	2.291	-1.721	-0.548	1.690	-0.529	-2.334	-0.004
34	A	110	THR	0	0.041	-0.002	5.550	0.181	0.181	0.000	0.000	0.000	0.000
35	A	111	PRO	0	0.118	0.020	6.833	-0.102	-0.102	0.000	0.000	0.000	0.000
36	A	112	LEU	0	-0.012	0.008	8.398	0.012	0.012	0.000	0.000	0.000	0.000
37	A	113	GLN	0	0.081	0.051	3.152	-0.537	0.121	0.032	-0.151	-0.539	0.000
38	A	114	VAL	0	0.032	0.031	4.860	-0.187	-0.064	-0.001	-0.004	-0.118	0.000
39	A	115	ARG	1	0.933	0.968	6.325	0.269	0.269	0.000	0.000	0.000	0.000
40	A	116	VAL	0	0.017	-0.008	5.058	0.069	0.069	0.000	0.000	0.000	0.000
41	A	117	TRP	0	0.002	0.030	2.940	-0.962	-0.044	0.081	-0.230	-0.770	-0.001
42	A	118	PHE	0	0.012	-0.010	6.053	0.136	0.136	0.000	0.000	0.000	0.000
43	A	119	ILE	0	-0.024	0.005	9.339	0.056	0.056	0.000	0.000	0.000	0.000
44	A	120	ASN	0	-0.012	-0.026	7.680	0.119	0.119	0.000	0.000	0.000	0.000
45	A	121	LYS	1	0.812	0.916	8.715	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	122	ARG	1	0.904	0.933	10.443	0.098	0.098	0.000	0.000	0.000	0.000
47	A	123	MET	0	-0.023	-0.016	13.055	0.005	0.005	0.000	0.000	0.000	0.000
48	A	124	ARG	1	0.876	0.938	9.264	-0.307	-0.307	0.000	0.000	0.000	0.000
49	A	125	SER	0	-0.021	0.018	13.790	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:77:ILE)