FMO DATABASE

FMODB ID: 3JRNL

Calculation Name: 3EY6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EY6

Chain ID: A

ChEMBL ID:

UniProt ID: Q14318

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905718.160461
FMO2-HF: Nuclear repulsion	860516.478614
FMO2-HF: Total energy	-45201.681847
FMO2-MP2: Total energy	-45331.019419

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:33:MET)

Summations of interaction energy for fragment #1(A:33:MET)

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.
-3.682	-1.859	-0.004	-0.675	-1.144	0.002

Interaction energy analysis for fragmet #1(A:33:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : 0.000

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	35	GLU	-1	-0.897	-0.944	3.852	-1.026	0.480	-0.002	-0.580	-0.924	0.002
4	A	36	TRP	0	-0.058	-0.039	6.696	0.452	0.452	0.000	0.000	0.000	0.000
5	A	37	LEU	0	0.022	0.020	9.906	-0.258	-0.258	0.000	0.000	0.000	0.000
6	A	38	ASP	-1	-0.828	-0.923	12.959	0.395	0.395	0.000	0.000	0.000	0.000
7	A	39	ILE	0	-0.040	-0.028	16.251	-0.050	-0.050	0.000	0.000	0.000	0.000
8	A	40	LEU	0	-0.012	-0.011	18.537	-0.047	-0.047	0.000	0.000	0.000	0.000
9	A	41	GLY	0	-0.020	0.014	20.090	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	42	ASN	0	-0.027	-0.028	21.208	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	43	GLY	0	0.017	0.001	18.679	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	44	LEU	0	-0.043	-0.018	19.385	0.042	0.042	0.000	0.000	0.000	0.000
13	A	45	LEU	0	0.000	0.012	19.123	0.015	0.015	0.000	0.000	0.000	0.000
14	A	46	ARG	1	0.896	0.962	12.472	-0.757	-0.757	0.000	0.000	0.000	0.000
15	A	47	LYS	1	0.878	0.937	11.685	-1.320	-1.320	0.000	0.000	0.000	0.000
16	A	48	LYS	1	0.889	0.941	4.207	-7.022	-6.825	-0.001	-0.082	-0.114	0.000
17	A	49	THR	0	-0.041	-0.035	6.803	-0.164	-0.164	0.000	0.000	0.000	0.000
18	A	50	LEU	0	-0.065	-0.041	5.914	1.540	1.540	0.000	0.000	0.000	0.000
19	A	51	VAL	0	0.007	0.002	6.116	0.424	0.424	0.000	0.000	0.000	0.000
20	A	52	PRO	0	-0.023	-0.029	5.174	-0.269	-0.149	-0.001	-0.013	-0.106	0.000
21	A	53	GLY	0	0.077	0.062	8.184	-0.253	-0.253	0.000	0.000	0.000	0.000
22	A	54	PRO	0	-0.013	0.000	10.182	0.141	0.141	0.000	0.000	0.000	0.000
23	A	55	PRO	0	0.010	-0.012	10.691	-0.060	-0.060	0.000	0.000	0.000	0.000
24	A	56	GLY	0	-0.003	0.004	12.507	-0.042	-0.042	0.000	0.000	0.000	0.000
25	A	57	SER	0	-0.072	-0.026	12.833	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	58	SER	0	0.001	-0.006	14.693	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.949	0.989	12.694	-0.547	-0.547	0.000	0.000	0.000	0.000
28	A	60	PRO	0	-0.006	0.017	17.735	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	61	VAL	0	-0.034	-0.019	21.175	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	62	LYS	1	0.836	0.898	24.082	-0.290	-0.290	0.000	0.000	0.000	0.000
31	A	63	GLY	0	-0.007	-0.003	26.484	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	64	GLN	0	-0.033	-0.025	24.236	0.019	0.019	0.000	0.000	0.000	0.000
33	A	65	VAL	0	-0.004	-0.001	27.686	0.011	0.011	0.000	0.000	0.000	0.000
34	A	66	VAL	0	-0.016	-0.012	22.832	0.013	0.013	0.000	0.000	0.000	0.000
35	A	67	THR	0	0.006	0.007	23.789	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	68	VAL	0	-0.023	-0.023	20.222	0.048	0.048	0.000	0.000	0.000	0.000
37	A	69	HIS	0	-0.080	-0.025	19.052	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.010	-0.008	19.059	0.076	0.076	0.000	0.000	0.000	0.000
39	A	71	GLN	0	0.011	0.023	16.738	-0.114	-0.114	0.000	0.000	0.000	0.000
40	A	72	THR	0	-0.005	-0.008	19.728	0.040	0.040	0.000	0.000	0.000	0.000
41	A	73	SER	0	0.024	0.006	19.967	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	74	LEU	0	0.011	0.005	21.827	0.017	0.017	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.942	-0.965	20.810	0.369	0.369	0.000	0.000	0.000	0.000
44	A	76	ASN	0	-0.008	0.000	20.774	0.038	0.038	0.000	0.000	0.000	0.000
45	A	77	GLY	0	0.025	0.015	20.807	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	78	THR	0	-0.062	-0.040	21.739	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	79	ARG	1	0.813	0.875	20.495	-0.462	-0.462	0.000	0.000	0.000	0.000
48	A	80	VAL	0	-0.027	-0.025	24.381	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	81	GLN	0	-0.064	-0.043	25.129	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	82	GLU	-1	-0.804	-0.887	21.908	0.512	0.512	0.000	0.000	0.000	0.000
51	A	83	GLU	-1	-0.861	-0.908	23.812	0.286	0.286	0.000	0.000	0.000	0.000
52	A	84	PRO	0	0.007	-0.001	23.002	0.042	0.042	0.000	0.000	0.000	0.000
53	A	85	GLU	-1	-0.856	-0.922	23.598	0.393	0.393	0.000	0.000	0.000	0.000
54	A	86	LEU	0	0.000	0.013	24.497	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	87	VAL	0	0.004	-0.004	25.454	0.025	0.025	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.012	-0.012	23.207	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	89	THR	0	0.036	0.028	27.718	0.013	0.013	0.000	0.000	0.000	0.000
58	A	90	LEU	0	-0.016	0.001	22.371	0.003	0.003	0.000	0.000	0.000	0.000
59	A	91	GLY	0	0.004	-0.024	26.686	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	92	ASP	-1	-0.889	-0.928	28.342	0.219	0.219	0.000	0.000	0.000	0.000
61	A	93	CYS	0	-0.050	-0.044	29.957	0.009	0.009	0.000	0.000	0.000	0.000
62	A	94	ASP	-1	-0.950	-0.970	31.990	0.223	0.223	0.000	0.000	0.000	0.000
63	A	95	VAL	0	-0.016	0.010	25.853	0.011	0.011	0.000	0.000	0.000	0.000
64	A	96	ILE	0	-0.014	0.003	24.252	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	97	GLN	0	0.060	0.008	25.349	0.023	0.023	0.000	0.000	0.000	0.000
66	A	98	ALA	0	0.011	0.003	21.190	0.022	0.022	0.000	0.000	0.000	0.000
67	A	99	LEU	0	0.002	0.025	20.288	0.069	0.069	0.000	0.000	0.000	0.000
68	A	100	ASP	-1	-0.793	-0.886	21.675	0.340	0.340	0.000	0.000	0.000	0.000
69	A	101	LEU	0	-0.007	-0.012	22.043	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	102	SER	0	-0.050	-0.054	16.887	0.036	0.036	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.040	0.007	17.419	0.069	0.069	0.000	0.000	0.000	0.000
72	A	104	PRO	0	0.000	0.003	18.515	0.029	0.029	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.058	-0.032	14.967	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	106	MET	0	-0.102	-0.043	13.882	0.087	0.087	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.864	-0.933	11.839	0.726	0.726	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.029	-0.031	14.624	0.075	0.075	0.000	0.000	0.000	0.000
77	A	109	GLY	0	-0.010	-0.014	15.192	0.003	0.003	0.000	0.000	0.000	0.000
78	A	110	GLU	-1	-0.802	-0.854	10.351	1.818	1.818	0.000	0.000	0.000	0.000
79	A	111	THR	0	0.001	-0.007	10.893	-0.186	-0.186	0.000	0.000	0.000	0.000
80	A	112	ALA	0	-0.019	-0.019	10.096	0.471	0.471	0.000	0.000	0.000	0.000
81	A	113	MET	0	0.008	0.019	11.114	-0.234	-0.234	0.000	0.000	0.000	0.000
82	A	114	VAL	0	-0.009	-0.018	12.795	0.067	0.067	0.000	0.000	0.000	0.000
83	A	115	THR	0	-0.021	0.003	14.695	-0.038	-0.038	0.000	0.000	0.000	0.000
84	A	116	ALA	0	-0.008	-0.014	17.189	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	117	ASP	-1	-0.742	-0.886	20.665	0.264	0.264	0.000	0.000	0.000	0.000
86	A	118	SER	0	0.017	0.024	23.808	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.907	0.968	26.861	-0.218	-0.218	0.000	0.000	0.000	0.000
88	A	120	TYR	0	-0.022	-0.023	23.867	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	121	CYS	0	-0.034	-0.013	24.034	0.036	0.036	0.000	0.000	0.000	0.000
90	A	122	TYR	0	0.053	0.017	26.548	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	123	GLY	0	0.015	0.021	29.355	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	124	PRO	0	0.015	-0.017	31.214	0.004	0.004	0.000	0.000	0.000	0.000
93	A	125	GLN	0	-0.014	0.001	34.122	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	126	GLY	0	0.016	0.029	31.890	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	127	ARG	1	0.906	0.943	28.040	-0.301	-0.301	0.000	0.000	0.000	0.000
96	A	128	SER	0	-0.034	0.014	32.708	0.006	0.006	0.000	0.000	0.000	0.000
97	A	129	PRO	0	0.014	-0.014	34.061	0.005	0.005	0.000	0.000	0.000	0.000
98	A	130	TYR	0	0.008	-0.018	30.611	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	131	ILE	0	0.002	0.017	26.977	0.013	0.013	0.000	0.000	0.000	0.000
100	A	132	PRO	0	0.013	0.007	29.976	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	133	PRO	0	-0.011	-0.011	31.204	0.013	0.013	0.000	0.000	0.000	0.000
102	A	134	HIS	0	-0.019	-0.026	30.477	0.004	0.004	0.000	0.000	0.000	0.000
103	A	135	ALA	0	-0.005	0.014	27.178	0.007	0.007	0.000	0.000	0.000	0.000
104	A	136	ALA	0	0.031	0.024	22.607	0.012	0.012	0.000	0.000	0.000	0.000
105	A	137	LEU	0	-0.043	-0.034	22.081	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	138	CYS	0	-0.043	-0.020	17.020	0.047	0.047	0.000	0.000	0.000	0.000
107	A	139	LEU	0	-0.003	-0.007	17.659	-0.056	-0.056	0.000	0.000	0.000	0.000
108	A	140	GLU	-1	-0.891	-0.945	13.603	1.190	1.190	0.000	0.000	0.000	0.000
109	A	141	VAL	0	0.010	-0.008	15.067	-0.128	-0.128	0.000	0.000	0.000	0.000
110	A	142	THR	0	0.027	0.027	14.782	0.200	0.200	0.000	0.000	0.000	0.000
111	A	143	LEU	0	-0.001	0.012	16.115	-0.116	-0.116	0.000	0.000	0.000	0.000
112	A	144	LYS	1	0.800	0.885	17.836	-0.413	-0.413	0.000	0.000	0.000	0.000
113	A	145	THR	0	-0.014	-0.015	20.235	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	146	ALA	0	0.037	0.014	22.098	0.015	0.015	0.000	0.000	0.000	0.000
115	A	147	VAL	0	-0.035	-0.007	23.950	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	148	ASP	-1	-0.853	-0.909	27.507	0.219	0.219	0.000	0.000	0.000	0.000
117	A	149	GLY	0	0.030	0.019	29.776	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	PRO	0	-0.047	-0.021	32.325	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:MET)