FMO DATABASE

FMODB ID: 6Y5LZ

Calculation Name: 3ON1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ON1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KA76

Base Structure: X-ray

Registration Date: 2023-09-23

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-704206.725969
FMO2-HF: Nuclear repulsion	667221.529314
FMO2-HF: Total energy	-36985.196655
FMO2-MP2: Total energy	-37094.683429

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:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-158.093	-155.26	0.198	-1.4	-1.632	0.011

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.938 / q_NPA : -0.977

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	5	LYS	1	1.023	0.990	3.820	-31.530	-29.965	0.006	-0.771	-0.801	0.005
4	A	6	TRP	0	0.073	0.020	6.376	-1.093	-1.093	0.000	0.000	0.000	0.000
5	A	7	LEU	0	-0.001	0.011	3.289	-3.532	-2.337	0.193	-0.616	-0.772	0.006
6	A	8	SER	0	0.008	0.005	4.280	-3.448	-3.375	-0.001	-0.013	-0.059	0.000
7	A	9	LEU	0	0.000	-0.001	5.784	-2.597	-2.597	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.025	0.007	8.816	-2.093	-2.093	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.079	0.042	8.636	-1.705	-1.705	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.066	-0.035	9.944	-1.824	-1.824	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.039	0.025	12.203	-1.377	-1.377	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.019	-0.012	13.231	-1.220	-1.220	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.926	0.970	10.939	-20.959	-20.959	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.004	0.009	15.728	-0.858	-0.858	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.944	0.972	17.995	-13.075	-13.075	0.000	0.000	0.000	0.000
16	A	18	GLN	0	0.019	0.001	17.890	-0.882	-0.882	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.026	-0.001	13.765	0.136	0.136	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.017	0.008	18.515	-0.493	-0.493	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.001	-0.010	17.193	0.631	0.631	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.027	0.025	20.210	-0.567	-0.567	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.789	-0.883	22.519	10.809	10.809	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.773	-0.880	24.378	9.642	9.642	0.000	0.000	0.000	0.000
23	A	25	GLN	0	-0.071	-0.040	23.742	-0.417	-0.417	0.000	0.000	0.000	0.000
24	A	26	VAL	0	-0.003	-0.010	21.071	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.041	0.022	24.466	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.965	0.986	27.431	-9.284	-9.284	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.028	0.018	25.631	-0.234	-0.234	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.009	-0.003	25.104	-0.068	-0.068	0.000	0.000	0.000	0.000
29	A	31	GLN	0	0.016	0.012	27.624	-0.274	-0.274	0.000	0.000	0.000	0.000
30	A	32	ASN	0	-0.094	-0.052	30.558	-0.445	-0.445	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.040	0.034	29.563	-0.095	-0.095	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.054	-0.031	26.778	0.199	0.199	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.054	-0.032	21.925	0.448	0.448	0.000	0.000	0.000	0.000
34	A	36	THR	0	0.022	-0.009	21.620	-0.388	-0.388	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.036	-0.011	15.946	0.212	0.212	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.018	0.001	19.367	0.106	0.106	0.000	0.000	0.000	0.000
37	A	39	ILE	0	-0.005	0.003	12.763	0.307	0.307	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.007	-0.011	16.302	-0.304	-0.304	0.000	0.000	0.000	0.000
39	A	41	SER	0	0.014	-0.005	14.205	0.708	0.708	0.000	0.000	0.000	0.000
40	A	42	SER	0	0.041	-0.010	13.351	-1.286	-1.286	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.790	-0.870	15.333	17.017	17.017	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.076	-0.024	17.555	-0.750	-0.750	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.069	0.030	19.963	-0.123	-0.123	0.000	0.000	0.000	0.000
44	A	46	ILE	0	0.063	0.014	23.580	0.070	0.070	0.000	0.000	0.000	0.000
45	A	47	HIS	0	0.077	0.037	25.376	0.016	0.016	0.000	0.000	0.000	0.000
46	A	48	THR	0	-0.001	-0.001	22.353	-0.097	-0.097	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.829	0.892	19.597	-13.862	-13.862	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.888	0.940	23.729	-10.031	-10.031	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.861	0.930	27.212	-10.032	-10.032	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.008	-0.019	22.543	-0.129	-0.129	0.000	0.000	0.000	0.000
51	A	53	LEU	0	0.009	0.007	22.474	0.004	0.004	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.874	-0.924	25.802	9.476	9.476	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.842	0.911	27.979	-9.210	-9.210	0.000	0.000	0.000	0.000
54	A	56	CYS	0	-0.050	-0.041	24.885	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.047	0.040	27.015	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	SER	0	-0.058	-0.032	28.951	-0.268	-0.268	0.000	0.000	0.000	0.000
57	A	59	TYR	0	-0.041	-0.021	29.205	-0.225	-0.225	0.000	0.000	0.000	0.000
58	A	60	GLN	0	-0.023	0.005	28.592	0.068	0.068	0.000	0.000	0.000	0.000
59	A	61	ILE	0	-0.039	-0.007	23.294	0.248	0.248	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.005	0.005	20.756	0.117	0.117	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.041	-0.005	20.122	0.252	0.252	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.762	0.867	15.483	-15.251	-15.251	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.006	-0.003	16.547	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.038	0.019	11.039	0.520	0.520	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.009	0.006	9.603	-0.068	-0.068	0.000	0.000	0.000	0.000
66	A	68	ASN	0	0.098	0.060	10.334	-0.576	-0.576	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.900	0.937	11.425	-14.178	-14.178	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.037	0.009	10.965	0.710	0.710	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.032	-0.010	5.341	0.150	0.150	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.005	0.004	7.907	1.262	1.262	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.008	-0.008	10.387	-0.414	-0.414	0.000	0.000	0.000	0.000
72	A	74	ARG	1	1.017	1.011	5.329	-33.175	-33.175	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.032	-0.001	7.200	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.023	-0.007	8.309	-0.974	-0.974	0.000	0.000	0.000	0.000
75	A	77	GLY	0	-0.004	0.004	11.167	-1.617	-1.617	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.790	0.890	12.810	-17.935	-17.935	0.000	0.000	0.000	0.000
77	A	79	HIS	0	0.066	0.034	12.949	1.654	1.654	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.828	-0.915	13.199	17.305	17.305	0.000	0.000	0.000	0.000
79	A	81	ARG	1	0.835	0.911	14.231	-15.961	-15.961	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.028	0.008	14.966	0.697	0.697	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.027	0.020	17.334	0.157	0.157	0.000	0.000	0.000	0.000
82	A	84	ILE	0	0.005	-0.003	13.355	-0.261	-0.261	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.031	0.025	17.585	-0.100	-0.100	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.040	-0.030	16.312	0.204	0.204	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.933	0.962	19.033	-12.652	-12.652	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.796	-0.875	19.387	12.911	12.911	0.000	0.000	0.000	0.000
87	A	89	ALA	0	0.056	0.029	19.965	0.601	0.601	0.000	0.000	0.000	0.000
88	A	90	GLY	0	-0.011	-0.005	20.213	0.182	0.182	0.000	0.000	0.000	0.000
89	A	91	PHE	0	-0.006	-0.027	13.354	0.736	0.736	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.027	-0.009	16.001	0.786	0.786	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.988	0.997	17.779	-12.133	-12.133	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.967	0.991	13.537	-18.107	-18.107	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.010	-0.018	11.188	1.091	1.091	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.000	0.004	13.745	0.834	0.834	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.025	0.012	16.193	0.219	0.219	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.051	-0.035	9.866	0.676	0.676	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.062	-0.034	11.494	0.981	0.981	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.811	-0.876	12.979	15.666	15.666	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-1.014	-0.980	11.595	22.639	22.639	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)