FMO DATABASE

FMODB ID: R9GY8

Calculation Name: 1YCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZN2

Base Structure: X-ray

Registration Date: 2023-09-19

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-378285.084809
FMO2-HF: Nuclear repulsion	352506.699811
FMO2-HF: Total energy	-25778.384998
FMO2-MP2: Total energy	-25853.931326

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-18.619	-16.222	8.791	-4.17	-7.016	0.011

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.016

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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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	7	LEU	0	0.049	0.029	2.166	-6.412	-5.344	5.285	-2.351	-4.001	0.023
4	A	8	GLU	-1	-0.730	-0.868	1.852	-6.181	-5.465	3.495	-1.748	-2.463	-0.012
5	A	9	LYS	1	0.855	0.915	3.498	0.375	0.879	0.012	-0.067	-0.448	0.000
6	A	10	VAL	0	0.029	0.015	5.418	0.221	0.221	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.033	0.029	6.323	0.059	0.059	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.776	0.866	5.879	1.703	1.703	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.953	-0.966	9.125	0.489	0.489	0.000	0.000	0.000	0.000
10	A	14	TRP	0	0.015	0.000	11.138	0.066	0.066	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.834	0.930	12.182	0.701	0.701	0.000	0.000	0.000	0.000
12	A	16	GLY	0	-0.040	-0.010	14.052	0.044	0.044	0.000	0.000	0.000	0.000
13	A	17	HIS	0	-0.043	-0.019	15.907	0.044	0.044	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.945	0.974	17.581	0.025	0.025	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.020	0.005	14.582	0.031	0.031	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.026	0.000	17.908	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.043	0.011	14.664	0.014	0.014	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.056	-0.016	16.533	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.064	0.021	16.362	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	24	GLY	0	0.013	0.012	17.975	0.016	0.016	0.000	0.000	0.000	0.000
21	A	25	GLY	0	-0.074	-0.052	19.683	0.018	0.018	0.000	0.000	0.000	0.000
22	A	26	ASP	-1	-0.828	-0.893	20.207	0.052	0.052	0.000	0.000	0.000	0.000
23	A	27	HIS	0	-0.024	0.008	20.943	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.024	-0.027	22.036	0.016	0.016	0.000	0.000	0.000	0.000
25	A	29	PHE	0	-0.037	-0.006	21.346	0.007	0.007	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.010	-0.023	20.608	0.010	0.010	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.021	-0.003	20.266	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.024	-0.001	19.165	0.011	0.011	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.033	0.022	11.332	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.802	-0.885	15.756	-0.306	-0.306	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.836	-0.925	12.948	-0.748	-0.748	0.000	0.000	0.000	0.000
32	A	36	PHE	0	-0.033	-0.020	6.757	0.134	0.134	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.868	-0.943	8.569	-1.376	-1.376	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.955	-0.973	4.915	-6.318	-6.209	-0.001	-0.004	-0.104	0.000
35	A	39	GLU	-1	-0.929	-0.937	7.786	-0.923	-0.923	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.049	-0.019	10.756	0.212	0.212	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.017	-0.017	10.741	-0.115	-0.115	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.050	-0.023	13.261	0.090	0.090	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.001	-0.007	16.011	0.014	0.014	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.794	0.872	18.640	0.260	0.260	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.871	-0.929	21.689	-0.147	-0.147	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.029	0.029	22.065	0.011	0.011	0.000	0.000	0.000	0.000
43	A	47	VAL	0	-0.039	-0.038	24.534	0.010	0.010	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.740	-0.859	25.378	-0.080	-0.080	0.000	0.000	0.000	0.000
45	A	49	VAL	0	0.002	-0.011	27.808	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.057	-0.017	30.102	0.006	0.006	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.006	0.001	31.018	0.002	0.002	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.025	-0.014	29.496	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.838	0.901	26.755	0.100	0.100	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.023	0.013	26.902	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.751	0.868	25.605	0.179	0.179	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.040	-0.042	21.636	0.001	0.001	0.000	0.000	0.000	0.000
53	A	57	MET	0	-0.006	0.012	19.825	0.030	0.030	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.018	0.020	17.070	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.018	-0.014	15.111	0.058	0.058	0.000	0.000	0.000	0.000
56	A	60	GLY	0	0.083	0.055	13.544	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	61	LEU	0	0.005	-0.023	6.769	0.128	0.128	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.938	-0.969	10.739	-0.844	-0.844	0.000	0.000	0.000	0.000
59	A	63	ASP	-1	-0.988	-0.983	12.493	-0.284	-0.284	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.009	-0.015	11.770	0.080	0.080	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.079	-0.028	12.777	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	66	TRP	0	-0.042	-0.044	12.596	0.076	0.076	0.000	0.000	0.000	0.000
63	A	67	ILE	0	0.033	0.025	9.912	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	68	MET	0	-0.037	-0.021	13.185	0.107	0.107	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.019	0.014	15.086	-0.054	-0.054	0.000	0.000	0.000	0.000
66	A	70	LEU	0	-0.038	-0.015	16.768	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)