FMO DATABASE

FMODB ID: LNYV9

Calculation Name: 5XE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XE2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WII5

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-792377.874864
FMO2-HF: Nuclear repulsion	751194.590571
FMO2-HF: Total energy	-41183.284293
FMO2-MP2: Total energy	-41302.79726

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:GLU)

Summations of interaction energy for fragment #1(A:1: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.
-40.974	-35.233	8.088	-6.201	-7.629	0.059

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.954 / q_NPA : -0.980

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	MET	0	-0.044	0.007	1.996	-31.069	-25.882	5.788	-5.621	-5.355	0.057
4	A	4	ASN	0	0.066	0.045	2.778	16.433	16.894	2.301	-0.565	-2.197	0.002
5	A	5	ALA	0	-0.008	-0.016	4.154	-3.895	-3.802	-0.001	-0.015	-0.077	0.000
6	A	6	PRO	0	0.004	0.028	6.009	-2.270	-2.270	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.022	-0.021	9.381	-0.472	-0.472	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.812	0.872	12.159	-16.526	-16.526	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.002	-0.010	15.602	-0.044	-0.044	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.002	0.014	11.982	0.703	0.703	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.004	-0.005	16.641	-0.359	-0.359	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.016	-0.004	11.945	1.114	1.114	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.839	0.911	17.463	-15.505	-15.505	0.000	0.000	0.000	0.000
14	A	14	CYS	0	0.000	0.012	17.832	1.265	1.265	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.872	-0.939	19.548	12.104	12.104	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.073	0.059	19.645	0.415	0.415	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.029	0.008	22.709	-0.527	-0.527	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.134	-0.074	25.784	-0.513	-0.513	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.074	0.043	25.869	-0.479	-0.479	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.087	-0.044	22.852	0.089	0.089	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.909	0.951	23.476	-11.634	-11.634	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.021	-0.007	21.645	0.617	0.617	0.000	0.000	0.000	0.000
23	A	23	TRP	0	0.037	0.017	19.422	-0.727	-0.727	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.025	-0.007	19.245	0.734	0.734	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.021	0.018	13.750	-0.507	-0.507	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.002	-0.014	17.121	-0.385	-0.385	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.002	0.004	14.342	-0.810	-0.810	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.014	0.003	14.666	1.610	1.610	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.132	0.041	11.282	0.819	0.819	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.028	0.006	10.079	2.295	2.295	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.878	0.921	10.165	-17.984	-17.984	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.039	0.049	10.222	0.125	0.125	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.923	0.964	4.936	-31.052	-31.052	0.000	0.000	0.000	0.000
34	A	34	HIS	0	0.008	-0.002	5.734	3.214	3.214	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.016	-0.006	7.733	-1.327	-1.327	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.063	0.010	9.152	2.935	2.935	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.817	-0.884	11.126	20.273	20.273	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.044	-0.022	11.848	1.006	1.006	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.001	-0.003	14.446	-1.078	-1.078	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.016	0.003	17.619	0.565	0.565	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.002	0.010	19.679	-0.695	-0.695	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.944	0.998	22.829	-10.775	-10.775	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.003	0.005	23.197	-0.402	-0.402	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.043	-0.032	26.351	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.040	0.010	29.773	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.069	-0.020	32.609	-0.198	-0.198	0.000	0.000	0.000	0.000
47	A	47	ARG	1	1.028	1.021	34.149	-7.910	-7.910	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.919	0.961	35.989	-8.869	-8.869	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.018	-0.008	36.653	0.165	0.165	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.011	-0.003	35.656	-0.278	-0.278	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.047	0.015	35.622	0.211	0.211	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.011	-0.008	31.823	0.104	0.104	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.117	-0.064	30.988	0.304	0.304	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.012	0.011	28.869	-0.234	-0.234	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.032	-0.010	30.080	0.255	0.255	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.020	0.001	24.632	0.105	0.105	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.021	-0.021	29.349	-0.438	-0.438	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.013	-0.021	30.183	0.252	0.252	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.013	-0.006	28.297	-0.078	-0.078	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.740	-0.812	25.685	12.413	12.413	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.013	0.014	21.853	-0.351	-0.351	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.002	0.006	22.484	-0.056	-0.056	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.027	0.004	26.570	-0.327	-0.327	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.031	-0.009	28.931	0.307	0.307	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.008	-0.025	30.332	-0.250	-0.250	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.036	0.019	25.338	0.245	0.245	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.012	-0.016	27.835	-0.498	-0.498	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.032	-0.002	26.867	0.359	0.359	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.779	-0.875	27.920	9.821	9.821	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.132	-0.063	26.909	-0.154	-0.154	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.002	-0.009	22.998	0.499	0.499	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.840	-0.910	22.516	12.415	12.415	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.042	-0.032	17.712	0.603	0.603	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.020	0.015	16.465	-0.432	-0.432	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.035	0.018	14.316	1.152	1.152	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.777	0.856	6.397	-38.749	-38.749	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.930	-0.965	11.285	22.576	22.576	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.851	-0.915	12.652	15.990	15.990	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.103	-0.050	11.113	-1.042	-1.042	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.051	0.028	13.633	0.854	0.854	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.889	-0.940	14.672	18.076	18.076	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.007	-0.008	13.857	-0.647	-0.647	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.049	-0.039	15.969	-0.811	-0.811	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.009	0.015	18.087	-0.929	-0.929	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.879	-0.942	15.311	20.650	20.650	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.036	-0.017	19.075	-0.895	-0.895	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.006	-0.025	21.350	0.212	0.212	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.047	0.002	22.082	-0.103	-0.103	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.011	0.001	24.028	-0.213	-0.213	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.017	-0.046	26.207	-0.463	-0.463	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.044	0.036	20.121	-0.133	-0.133	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.011	-0.001	24.458	0.215	0.215	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.892	0.948	27.061	-10.721	-10.721	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.045	0.015	23.858	-0.222	-0.222	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.021	0.023	23.663	0.449	0.449	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.004	0.007	26.283	-0.174	-0.174	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.012	0.017	28.778	-0.216	-0.216	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.010	-0.007	23.265	-0.118	-0.118	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.004	0.004	27.597	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.047	-0.027	29.638	-0.346	-0.346	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.019	-0.014	29.339	-0.239	-0.239	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.053	-0.022	25.860	-0.085	-0.085	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.011	0.008	30.556	-0.046	-0.046	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.028	-0.005	27.613	-0.076	-0.076	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.022	-0.003	32.305	-0.168	-0.168	0.000	0.000	0.000	0.000
106	A	106	TRP	0	-0.032	-0.035	28.735	0.049	0.049	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.029	0.025	32.007	0.049	0.049	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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