FMO DATABASE

FMODB ID: 85Y6Y

Calculation Name: 3E1E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E1E

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LMG0

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1148423.800701
FMO2-HF: Nuclear repulsion	1096036.96756
FMO2-HF: Total energy	-52386.833141
FMO2-MP2: Total energy	-52537.05051

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:6:GLY)

Summations of interaction energy for fragment #1(A:6: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.
1.226	3.325	0.148	-0.922	-1.326	0.002

Interaction energy analysis for fragmet #1(A:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.009

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	8	ALA	0	0.011	-0.002	3.436	-0.776	0.511	0.013	-0.613	-0.687	0.002
4	A	9	GLN	0	-0.037	-0.027	3.044	0.399	0.992	0.136	-0.217	-0.513	0.000
5	A	10	LYS	1	0.910	0.993	4.133	1.707	1.926	-0.001	-0.092	-0.126	0.000
6	A	11	VAL	0	-0.013	-0.012	6.130	0.742	0.742	0.000	0.000	0.000	0.000
7	A	12	ARG	1	0.942	0.957	7.557	0.722	0.722	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.860	-0.908	8.147	-1.106	-1.106	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.029	-0.018	9.830	0.220	0.220	0.000	0.000	0.000	0.000
10	A	15	PHE	0	0.012	0.004	11.917	0.112	0.112	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.028	-0.014	12.916	0.079	0.079	0.000	0.000	0.000	0.000
12	A	17	ARG	1	0.869	0.934	13.755	0.547	0.547	0.000	0.000	0.000	0.000
13	A	18	GLN	0	0.024	0.018	16.257	0.072	0.072	0.000	0.000	0.000	0.000
14	A	19	PRO	0	0.016	-0.001	18.743	0.014	0.014	0.000	0.000	0.000	0.000
15	A	20	VAL	0	0.047	0.017	21.727	0.012	0.012	0.000	0.000	0.000	0.000
16	A	21	MET	0	0.012	0.019	17.624	0.019	0.019	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.010	0.005	20.795	0.014	0.014	0.000	0.000	0.000	0.000
18	A	23	THR	0	-0.076	-0.033	22.073	0.018	0.018	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.025	-0.015	23.674	0.013	0.013	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.028	0.028	23.459	0.010	0.010	0.000	0.000	0.000	0.000
21	A	26	ALA	0	-0.028	-0.015	20.428	0.009	0.009	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.898	0.942	17.808	0.108	0.108	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.006	-0.005	11.821	0.010	0.010	0.000	0.000	0.000	0.000
24	A	29	ASP	-1	-0.919	-0.953	15.438	-0.075	-0.075	0.000	0.000	0.000	0.000
25	A	30	THR	0	0.014	0.008	13.947	0.020	0.020	0.000	0.000	0.000	0.000
26	A	31	LEU	0	-0.041	-0.034	8.822	-0.070	-0.070	0.000	0.000	0.000	0.000
27	A	32	LEU	0	-0.015	-0.008	9.454	0.085	0.085	0.000	0.000	0.000	0.000
28	A	33	PRO	0	0.002	-0.002	7.853	-0.105	-0.105	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.048	0.037	10.057	0.027	0.027	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.944	0.975	12.496	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	36	VAL	0	-0.037	-0.007	11.989	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	37	GLU	-1	-0.935	-0.969	14.460	0.006	0.006	0.000	0.000	0.000	0.000
33	A	38	LEU	0	-0.004	0.009	15.648	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	39	CYS	0	-0.069	-0.043	18.721	0.022	0.022	0.000	0.000	0.000	0.000
35	A	40	MET	0	0.012	0.010	21.551	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	41	PRO	0	-0.022	0.003	24.320	0.012	0.012	0.000	0.000	0.000	0.000
37	A	42	TYR	0	0.006	0.003	27.567	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	43	ASP	-1	-0.808	-0.911	30.116	-0.088	-0.088	0.000	0.000	0.000	0.000
39	A	44	ARG	1	0.972	0.987	32.148	0.053	0.053	0.000	0.000	0.000	0.000
40	A	45	ALA	0	-0.056	-0.011	32.852	0.003	0.003	0.000	0.000	0.000	0.000
41	A	46	LEU	0	-0.012	-0.001	28.620	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	47	THR	0	-0.088	-0.046	32.918	0.002	0.002	0.000	0.000	0.000	0.000
43	A	48	GLN	0	-0.011	-0.004	35.735	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	49	GLN	0	-0.023	-0.034	38.626	0.002	0.002	0.000	0.000	0.000	0.000
45	A	50	HIS	0	-0.021	-0.009	41.168	0.000	0.000	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.024	0.036	38.819	0.002	0.002	0.000	0.000	0.000	0.000
47	A	52	PHE	0	0.011	-0.002	36.246	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	LEU	0	0.028	0.013	29.314	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	54	HIS	0	0.036	0.020	33.238	0.002	0.002	0.000	0.000	0.000	0.000
50	A	55	ALA	0	0.049	0.017	32.056	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	56	GLY	0	0.017	-0.001	31.006	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	57	ILE	0	0.022	0.018	27.829	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	58	VAL	0	0.004	-0.003	27.042	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	59	SER	0	-0.012	-0.024	26.347	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	60	THR	0	0.001	0.008	23.909	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	61	VAL	0	0.022	0.012	21.188	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	62	LEU	0	0.001	0.004	21.142	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.848	-0.932	21.288	-0.156	-0.156	0.000	0.000	0.000	0.000
59	A	64	SER	0	0.003	0.004	18.354	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	65	ALA	0	-0.029	-0.012	17.029	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	66	CYS	0	-0.003	-0.014	16.660	0.001	0.001	0.000	0.000	0.000	0.000
62	A	67	GLY	0	0.029	0.012	16.936	0.006	0.006	0.000	0.000	0.000	0.000
63	A	68	TYR	0	0.019	-0.012	12.495	-0.054	-0.054	0.000	0.000	0.000	0.000
64	A	69	ALA	0	0.003	0.014	12.074	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	70	ALA	0	0.031	0.013	13.219	0.042	0.042	0.000	0.000	0.000	0.000
66	A	71	PHE	0	-0.048	-0.029	10.221	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	72	SER	0	-0.105	-0.060	8.301	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.024	-0.024	8.289	0.161	0.161	0.000	0.000	0.000	0.000
69	A	74	MET	0	-0.081	-0.005	10.741	0.100	0.100	0.000	0.000	0.000	0.000
70	A	75	GLU	-1	-0.894	-0.945	8.745	0.158	0.158	0.000	0.000	0.000	0.000
71	A	76	GLU	-1	-0.944	-0.998	5.620	-1.030	-1.030	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.949	-0.973	7.368	-0.398	-0.398	0.000	0.000	0.000	0.000
73	A	78	ALA	0	-0.055	-0.012	10.709	0.041	0.041	0.000	0.000	0.000	0.000
74	A	79	ALA	0	0.010	-0.006	11.607	-0.132	-0.132	0.000	0.000	0.000	0.000
75	A	80	VAL	0	-0.013	-0.001	14.228	0.056	0.056	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.016	-0.001	16.016	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.027	-0.012	19.776	0.023	0.023	0.000	0.000	0.000	0.000
78	A	83	VAL	0	-0.045	-0.027	22.182	0.004	0.004	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.874	-0.927	24.995	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.040	0.025	24.934	0.000	0.000	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.893	0.957	27.357	0.031	0.031	0.000	0.000	0.000	0.000
82	A	87	VAL	0	0.005	-0.005	28.999	0.001	0.001	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.037	-0.008	30.563	0.002	0.002	0.000	0.000	0.000	0.000
84	A	89	PHE	0	0.030	-0.002	31.194	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.057	0.006	32.029	0.003	0.003	0.000	0.000	0.000	0.000
86	A	91	ASN	0	-0.018	-0.006	34.983	0.004	0.004	0.000	0.000	0.000	0.000
87	A	92	PRO	0	0.002	0.018	35.365	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.026	0.011	32.284	0.001	0.001	0.000	0.000	0.000	0.000
89	A	94	GLU	-1	-0.913	-0.965	34.088	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.022	0.006	33.298	0.003	0.003	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.861	-0.933	32.511	-0.040	-0.040	0.000	0.000	0.000	0.000
92	A	97	ARG	1	0.890	0.952	25.349	0.038	0.038	0.000	0.000	0.000	0.000
93	A	98	PHE	0	0.004	-0.003	26.712	0.007	0.007	0.000	0.000	0.000	0.000
94	A	99	ALA	0	-0.025	-0.006	22.856	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	100	PHE	0	-0.002	-0.010	21.322	0.009	0.009	0.000	0.000	0.000	0.000
96	A	101	ARG	1	0.836	0.910	19.571	0.009	0.009	0.000	0.000	0.000	0.000
97	A	102	ALA	0	0.042	0.024	17.815	0.010	0.010	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.917	-0.970	17.037	0.033	0.033	0.000	0.000	0.000	0.000
99	A	104	VAL	0	-0.030	-0.016	15.371	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	105	VAL	0	-0.036	-0.011	18.144	0.020	0.020	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.926	0.947	20.780	-0.046	-0.046	0.000	0.000	0.000	0.000
102	A	107	PRO	0	0.055	0.045	16.277	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	108	GLY	0	-0.026	-0.035	17.897	0.015	0.015	0.000	0.000	0.000	0.000
104	A	109	ARG	1	0.914	0.952	17.834	-0.086	-0.086	0.000	0.000	0.000	0.000
105	A	110	THR	0	0.049	0.063	17.721	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.068	0.006	19.624	-0.020	-0.020	0.000	0.000	0.000	0.000
107	A	112	THR	0	-0.032	0.001	16.910	0.029	0.029	0.000	0.000	0.000	0.000
108	A	113	VAL	0	0.009	0.018	19.844	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	114	ALA	0	0.013	0.011	18.967	0.014	0.014	0.000	0.000	0.000	0.000
110	A	115	THR	0	0.014	0.016	20.940	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.057	0.011	21.423	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	117	THR	0	-0.038	-0.005	23.088	0.006	0.006	0.000	0.000	0.000	0.000
113	A	118	ALA	0	-0.020	-0.005	24.313	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	119	TYR	0	0.009	-0.015	24.600	0.009	0.009	0.000	0.000	0.000	0.000
115	A	120	ALA	0	0.019	0.011	27.954	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	121	PHE	0	-0.059	-0.049	25.973	0.006	0.006	0.000	0.000	0.000	0.000
117	A	122	ARG	1	0.942	0.979	31.439	0.021	0.021	0.000	0.000	0.000	0.000
118	A	123	ASP	-1	-0.840	-0.897	34.676	-0.022	-0.022	0.000	0.000	0.000	0.000
119	A	124	GLY	0	-0.072	-0.049	33.067	0.003	0.003	0.000	0.000	0.000	0.000
120	A	125	GLU	-1	-0.910	-0.951	32.557	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	126	GLU	-1	-0.845	-0.908	26.961	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	127	ARG	1	0.863	0.912	31.316	0.017	0.017	0.000	0.000	0.000	0.000
123	A	128	ALA	0	0.029	0.026	29.887	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	129	ILE	0	-0.016	-0.015	29.625	0.002	0.002	0.000	0.000	0.000	0.000
125	A	130	ALA	0	0.000	-0.041	29.275	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	131	THR	0	-0.009	0.011	27.816	0.001	0.001	0.000	0.000	0.000	0.000
127	A	132	MET	0	0.017	0.008	24.542	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	133	THR	0	-0.042	-0.006	25.246	0.008	0.008	0.000	0.000	0.000	0.000
129	A	134	ALA	0	0.027	0.003	22.448	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	135	THR	0	-0.038	-0.039	23.216	0.013	0.013	0.000	0.000	0.000	0.000
131	A	136	LEU	0	0.001	-0.001	17.841	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	137	MET	0	-0.011	-0.023	19.963	0.030	0.030	0.000	0.000	0.000	0.000
133	A	138	ALA	0	-0.019	-0.010	15.465	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	139	LEU	0	-0.055	-0.040	16.461	0.030	0.030	0.000	0.000	0.000	0.000
135	A	140	ILE	0	0.045	0.016	14.886	-0.043	-0.043	0.000	0.000	0.000	0.000
136	A	141	GLY	0	0.009	0.022	15.274	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)