FMO DATABASE

FMODB ID: M3YVZ

Calculation Name: 1XOU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XOU

Chain ID: B

ChEMBL ID:

UniProt ID: Q47184

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptAll
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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-468740.983676
FMO2-HF: Nuclear repulsion	435893.666026
FMO2-HF: Total energy	-32847.31765
FMO2-MP2: Total energy	-32945.651869

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(B:2:GLY)

Summations of interaction energy for fragment #1(B:2:GLY)

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.
-1.876	2.07	1.615	-2.44	-3.12	-0.011

Interaction energy analysis for fragmet #1(B:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.022

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	B	4	VAL	0	0.045	0.031	3.782	0.687	1.622	0.001	-0.416	-0.520	0.000
4	B	5	SER	0	0.034	0.011	2.355	-3.710	-1.416	1.610	-1.807	-2.097	-0.011
5	B	6	GLN	0	0.037	0.015	3.783	-0.393	0.324	0.004	-0.217	-0.503	0.000
6	B	7	THR	0	-0.007	-0.008	5.767	0.445	0.445	0.000	0.000	0.000	0.000
7	B	8	ARG	1	1.014	1.014	7.391	0.705	0.705	0.000	0.000	0.000	0.000
8	B	9	ASN	0	0.008	-0.005	6.881	-0.086	-0.086	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.919	0.955	9.109	0.460	0.460	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.865	-0.916	11.580	-0.354	-0.354	0.000	0.000	0.000	0.000
11	B	12	LEU	0	-0.044	-0.027	12.329	0.031	0.031	0.000	0.000	0.000	0.000
12	B	13	LEU	0	0.010	0.001	12.905	0.019	0.019	0.000	0.000	0.000	0.000
13	B	14	ASP	-1	-0.836	-0.893	15.568	-0.081	-0.081	0.000	0.000	0.000	0.000
14	B	15	LYS	1	0.905	0.934	15.495	0.229	0.229	0.000	0.000	0.000	0.000
15	B	16	LYS	1	0.928	0.980	16.926	-0.013	-0.013	0.000	0.000	0.000	0.000
16	B	17	ILE	0	0.045	0.029	18.692	0.002	0.002	0.000	0.000	0.000	0.000
17	B	18	ARG	1	0.868	0.913	20.549	0.069	0.069	0.000	0.000	0.000	0.000
18	B	19	SER	0	-0.049	-0.037	22.353	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.892	-0.943	24.118	0.026	0.026	0.000	0.000	0.000	0.000
20	B	21	ILE	0	-0.023	-0.008	25.786	0.001	0.001	0.000	0.000	0.000	0.000
21	B	22	GLU	-1	-0.833	-0.916	27.399	-0.027	-0.027	0.000	0.000	0.000	0.000
22	B	23	ALA	0	-0.040	-0.009	28.612	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	24	ILE	0	0.033	0.012	28.854	0.001	0.001	0.000	0.000	0.000	0.000
24	B	25	LYS	1	0.807	0.873	30.850	0.022	0.022	0.000	0.000	0.000	0.000
25	B	26	LYS	1	0.893	0.972	30.411	0.023	0.023	0.000	0.000	0.000	0.000
26	B	27	ILE	0	0.067	0.035	34.005	0.001	0.001	0.000	0.000	0.000	0.000
27	B	28	ILE	0	-0.019	-0.017	35.139	0.001	0.001	0.000	0.000	0.000	0.000
28	B	29	ALA	0	-0.021	-0.005	37.982	0.000	0.000	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.914	-0.971	36.978	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	31	PHE	0	-0.003	-0.009	39.827	0.001	0.001	0.000	0.000	0.000	0.000
31	B	32	ASP	-1	-0.845	-0.899	42.539	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	33	VAL	0	0.059	0.041	44.063	0.000	0.000	0.000	0.000	0.000	0.000
33	B	34	VAL	0	-0.036	0.003	43.435	0.001	0.001	0.000	0.000	0.000	0.000
34	B	35	LYS	1	0.785	0.877	46.430	0.001	0.001	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.891	-0.952	48.697	-0.004	-0.004	0.000	0.000	0.000	0.000
36	B	37	SER	0	0.003	-0.008	48.671	0.000	0.000	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.012	-0.010	50.455	0.001	0.001	0.000	0.000	0.000	0.000
38	B	39	ASN	0	-0.040	-0.010	52.233	0.000	0.000	0.000	0.000	0.000	0.000
39	B	40	GLU	-1	-0.910	-0.958	53.749	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.058	-0.028	52.924	0.000	0.000	0.000	0.000	0.000	0.000
41	B	42	SER	0	-0.008	-0.031	56.007	0.001	0.001	0.000	0.000	0.000	0.000
42	B	43	GLU	-1	-0.845	-0.905	58.305	0.001	0.001	0.000	0.000	0.000	0.000
43	B	44	LYS	1	0.815	0.893	57.868	-0.004	-0.004	0.000	0.000	0.000	0.000
44	B	45	ALA	0	-0.001	-0.014	59.762	0.000	0.000	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.778	0.886	61.702	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	47	THR	0	-0.027	-0.017	64.776	0.000	0.000	0.000	0.000	0.000	0.000
47	B	48	ASP	-1	-0.828	-0.899	61.584	0.005	0.005	0.000	0.000	0.000	0.000
48	B	49	PRO	0	0.027	0.003	63.002	0.000	0.000	0.000	0.000	0.000	0.000
49	B	50	GLN	0	-0.016	-0.008	59.561	0.001	0.001	0.000	0.000	0.000	0.000
50	B	51	ALA	0	-0.008	-0.012	58.443	0.001	0.001	0.000	0.000	0.000	0.000
51	B	52	ALA	0	0.036	0.017	58.348	0.000	0.000	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.814	-0.892	58.461	0.012	0.012	0.000	0.000	0.000	0.000
53	B	54	LYN	0	0.005	0.016	54.920	0.000	0.000	0.000	0.000	0.000	0.000
54	B	55	LEU	0	-0.004	0.007	54.254	0.001	0.001	0.000	0.000	0.000	0.000
55	B	56	ASN	0	-0.042	-0.023	54.785	0.000	0.000	0.000	0.000	0.000	0.000
56	B	57	LYS	1	0.773	0.890	52.997	-0.012	-0.012	0.000	0.000	0.000	0.000
57	B	58	LEU	0	0.036	0.026	48.898	0.001	0.001	0.000	0.000	0.000	0.000
58	B	59	ILE	0	-0.004	0.001	50.462	0.001	0.001	0.000	0.000	0.000	0.000
59	B	60	GLU	-1	-0.851	-0.917	51.859	0.015	0.015	0.000	0.000	0.000	0.000
60	B	61	GLY	0	0.066	0.032	48.841	0.001	0.001	0.000	0.000	0.000	0.000
61	B	62	TYR	0	-0.011	-0.018	43.907	0.002	0.002	0.000	0.000	0.000	0.000
62	B	63	THR	0	-0.076	-0.055	47.551	0.001	0.001	0.000	0.000	0.000	0.000
63	B	64	TYR	0	-0.056	-0.034	48.549	0.001	0.001	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.009	0.021	48.266	0.001	0.001	0.000	0.000	0.000	0.000
65	B	66	GLU	-1	-0.798	-0.916	43.804	0.029	0.029	0.000	0.000	0.000	0.000
66	B	67	GLU	-1	-0.874	-0.936	42.838	0.020	0.020	0.000	0.000	0.000	0.000
67	B	68	ARG	1	0.802	0.900	42.553	-0.023	-0.023	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.829	0.915	41.642	-0.026	-0.026	0.000	0.000	0.000	0.000
69	B	70	LEU	0	-0.018	-0.015	38.143	0.003	0.003	0.000	0.000	0.000	0.000
70	B	71	TYR	0	0.006	0.012	37.808	0.001	0.001	0.000	0.000	0.000	0.000
71	B	72	ASP	-1	-0.808	-0.892	38.275	0.028	0.028	0.000	0.000	0.000	0.000
72	B	73	SER	0	-0.013	0.010	35.601	0.004	0.004	0.000	0.000	0.000	0.000
73	B	74	ALA	0	-0.028	-0.003	33.808	0.005	0.005	0.000	0.000	0.000	0.000
74	B	75	LEU	0	0.011	0.011	33.595	0.002	0.002	0.000	0.000	0.000	0.000
75	B	76	SER	0	0.037	-0.011	34.550	0.003	0.003	0.000	0.000	0.000	0.000
76	B	77	LYS	1	0.826	0.904	29.739	-0.047	-0.047	0.000	0.000	0.000	0.000
77	B	78	ILE	0	-0.003	0.001	29.797	0.003	0.003	0.000	0.000	0.000	0.000
78	B	79	GLU	-1	-0.891	-0.952	30.874	0.035	0.035	0.000	0.000	0.000	0.000
79	B	80	LYS	1	0.769	0.879	28.239	-0.072	-0.072	0.000	0.000	0.000	0.000
80	B	81	LEU	0	0.009	-0.005	25.209	0.006	0.006	0.000	0.000	0.000	0.000
81	B	82	ILE	0	0.010	0.015	27.049	0.000	0.000	0.000	0.000	0.000	0.000
82	B	83	GLU	-1	-0.844	-0.889	29.294	0.073	0.073	0.000	0.000	0.000	0.000
83	B	84	THR	0	-0.102	-0.049	24.088	0.005	0.005	0.000	0.000	0.000	0.000
84	B	85	LEU	0	-0.105	-0.059	23.226	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLY)