FMO DATABASE

FMODB ID: 3JLML

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	OptH
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	-791827.827492
FMO2-HF: Nuclear repulsion	750644.821167
FMO2-HF: Total energy	-41183.006325
FMO2-MP2: Total energy	-41302.53062

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.
-28.836	-23.542	6.902	-5.218	-6.978	0.035

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 : -0.966 / q_NPA : -0.991

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	-0.048	-0.005	2.710	-21.577	-14.500	0.405	-4.070	-3.412	0.028
4	A	4	ASN	0	0.087	0.058	2.505	22.959	20.985	6.499	-1.117	-3.408	0.007
5	A	5	ALA	0	-0.005	-0.013	4.268	-5.486	-5.387	-0.001	-0.026	-0.071	0.000
6	A	6	PRO	0	0.004	0.023	6.032	-2.611	-2.611	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.027	-0.025	9.533	-0.513	-0.513	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.829	0.885	12.191	-16.589	-16.589	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.011	-0.004	15.663	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.064	0.065	11.577	0.491	0.491	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.001	-0.001	16.218	-0.339	-0.339	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.011	-0.017	11.061	1.086	1.086	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.849	0.927	16.598	-15.448	-15.448	0.000	0.000	0.000	0.000
14	A	14	CYS	0	0.001	0.016	17.051	1.298	1.298	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.895	-0.950	18.919	12.162	12.162	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.082	0.065	19.320	0.423	0.423	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.035	0.009	22.321	-0.528	-0.528	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.121	-0.077	25.361	-0.567	-0.567	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.075	0.053	25.404	-0.454	-0.454	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.076	-0.044	22.145	0.117	0.117	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.910	0.948	22.814	-11.671	-11.671	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.015	0.000	20.833	0.619	0.619	0.000	0.000	0.000	0.000
23	A	23	TRP	0	0.031	0.019	18.716	-0.681	-0.681	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.017	-0.006	18.492	0.740	0.740	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.016	0.019	13.714	-0.530	-0.530	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.001	-0.017	16.992	-0.393	-0.393	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.002	0.000	14.343	-0.864	-0.864	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.011	0.006	14.596	1.651	1.651	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.136	0.043	11.350	1.088	1.088	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.026	0.009	10.123	2.319	2.319	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.862	0.917	10.158	-18.075	-18.075	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.045	0.050	10.200	0.196	0.196	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.948	0.987	4.768	-31.590	-31.498	-0.001	-0.005	-0.087	0.000
34	A	34	HIS	0	-0.014	-0.023	5.661	2.469	2.469	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.013	-0.001	7.731	-1.349	-1.349	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.064	0.010	9.019	2.922	2.922	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.816	-0.886	11.068	20.175	20.175	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.064	-0.026	11.828	1.025	1.025	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.002	-0.007	14.376	-1.089	-1.089	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.017	0.006	17.591	0.580	0.580	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.004	0.009	19.456	-0.712	-0.712	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.931	0.999	22.311	-10.732	-10.732	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.024	0.014	22.376	-0.399	-0.399	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.050	-0.022	25.559	-0.125	-0.125	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.031	0.006	28.959	0.033	0.033	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.048	-0.020	31.748	-0.223	-0.223	0.000	0.000	0.000	0.000
47	A	47	ARG	1	1.025	1.021	33.399	-7.919	-7.919	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.923	0.957	35.598	-8.777	-8.777	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.028	-0.039	36.271	0.133	0.133	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.006	0.024	35.459	-0.293	-0.293	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.053	0.017	35.583	0.216	0.216	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.009	-0.002	31.824	0.110	0.110	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.091	-0.045	30.932	0.325	0.325	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.003	0.004	28.727	-0.249	-0.249	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.044	-0.020	29.757	0.248	0.248	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.025	0.003	24.058	0.104	0.104	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.006	-0.012	29.176	-0.451	-0.451	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.021	-0.023	30.010	0.246	0.246	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.016	-0.010	28.241	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.729	-0.807	25.641	12.517	12.517	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.003	0.006	21.601	-0.356	-0.356	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.004	0.002	21.463	-0.055	-0.055	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.036	0.011	25.862	-0.333	-0.333	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.032	-0.010	28.030	0.313	0.313	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.004	-0.021	29.592	-0.217	-0.217	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.045	0.024	25.027	0.234	0.234	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.018	-0.022	27.349	-0.558	-0.558	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.034	-0.002	26.809	0.356	0.356	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.792	-0.889	27.890	9.856	9.856	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.161	-0.069	26.562	-0.121	-0.121	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.003	-0.008	22.825	0.509	0.509	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.851	-0.927	22.088	12.497	12.497	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.035	-0.031	17.578	0.631	0.631	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.017	0.011	16.023	-0.416	-0.416	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.053	0.030	14.176	1.151	1.151	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.776	0.860	6.266	-38.894	-38.894	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.926	-0.964	10.979	22.424	22.424	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.868	-0.925	12.444	16.018	16.018	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.097	-0.052	10.653	-1.054	-1.054	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.046	0.026	13.030	0.865	0.865	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.895	-0.954	13.865	18.298	18.298	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.016	-0.001	13.155	-0.367	-0.367	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.061	-0.042	15.228	-0.833	-0.833	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.007	0.011	17.416	-0.929	-0.929	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.973	-0.985	16.554	19.116	19.116	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.037	-0.023	18.987	-0.882	-0.882	0.000	0.000	0.000	0.000
87	A	87	THR	0	0.005	-0.013	21.292	0.206	0.206	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.054	0.005	22.005	-0.142	-0.142	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.016	-0.001	23.974	-0.220	-0.220	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.055	-0.074	25.930	-0.412	-0.412	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.036	0.023	20.490	-0.076	-0.076	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.009	0.003	24.441	0.216	0.216	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.948	0.975	27.080	-10.287	-10.287	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.040	0.020	23.810	-0.227	-0.227	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.010	0.008	23.796	0.433	0.433	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.008	0.007	26.330	-0.177	-0.177	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.007	0.008	28.792	-0.214	-0.214	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.006	-0.010	23.239	-0.121	-0.121	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.003	0.009	27.605	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.043	-0.020	29.650	-0.351	-0.351	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.006	-0.007	29.336	-0.233	-0.233	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.071	-0.028	25.919	-0.080	-0.080	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.007	0.009	30.532	-0.047	-0.047	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.033	-0.007	27.645	-0.075	-0.075	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.021	-0.001	32.300	-0.169	-0.169	0.000	0.000	0.000	0.000
106	A	106	TRP	0	-0.023	-0.032	29.003	0.038	0.038	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.021	0.021	31.974	0.030	0.030	0.000	0.000	0.000	0.000

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