FMO DATABASE

FMODB ID: 8J18Y

Calculation Name: 3EMF-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMF

Chain ID: A

ChEMBL ID:

UniProt ID: Q48152

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-733346.864386
FMO2-HF: Nuclear repulsion	690778.424585
FMO2-HF: Total energy	-42568.439801
FMO2-MP2: Total energy	-42695.283431

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:52:ACE )

Summations of interaction energy for fragment #1(A:52:ACE )

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.
1.027	2.005	-0.007	-0.43	-0.541	-0.001

Interaction energy analysis for fragmet #1(A:52:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.013

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	54	PRO	0	-0.005	0.005	3.819	0.719	1.697	-0.007	-0.430	-0.541	-0.001
4	A	55	VAL	0	0.035	0.032	6.886	0.110	0.110	0.000	0.000	0.000	0.000
5	A	56	THR	0	-0.069	-0.034	9.381	0.161	0.161	0.000	0.000	0.000	0.000
6	A	57	ASN	0	0.007	-0.023	13.046	0.003	0.003	0.000	0.000	0.000	0.000
7	A	58	LYS	1	0.974	0.972	16.498	0.175	0.175	0.000	0.000	0.000	0.000
8	A	59	LEU	0	-0.004	0.022	19.068	0.016	0.016	0.000	0.000	0.000	0.000
9	A	60	LYS	1	0.948	0.991	21.077	0.090	0.090	0.000	0.000	0.000	0.000
10	A	61	ALA	0	-0.026	-0.009	23.784	0.004	0.004	0.000	0.000	0.000	0.000
11	A	62	TYR	0	0.042	0.012	25.502	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	63	GLY	0	0.013	-0.002	28.896	0.004	0.004	0.000	0.000	0.000	0.000
13	A	64	ASP	-1	-0.961	-0.970	25.579	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	65	ALA	0	0.042	0.019	28.749	0.001	0.001	0.000	0.000	0.000	0.000
15	A	66	ASN	0	-0.060	-0.033	26.980	0.000	0.000	0.000	0.000	0.000	0.000
16	A	67	PHE	0	0.029	0.036	30.402	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	68	ASN	0	-0.005	-0.004	31.297	0.006	0.006	0.000	0.000	0.000	0.000
18	A	69	PHE	0	0.039	-0.011	34.130	0.000	0.000	0.000	0.000	0.000	0.000
19	A	70	THR	0	-0.034	0.002	37.128	0.002	0.002	0.000	0.000	0.000	0.000
20	A	71	ASN	0	-0.028	-0.022	33.313	0.003	0.003	0.000	0.000	0.000	0.000
21	A	72	ASN	0	-0.007	0.010	32.087	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	73	SER	0	0.018	-0.008	35.518	0.004	0.004	0.000	0.000	0.000	0.000
23	A	74	ILE	0	0.067	0.008	37.561	0.000	0.000	0.000	0.000	0.000	0.000
24	A	75	ALA	0	0.028	0.023	37.059	0.001	0.001	0.000	0.000	0.000	0.000
25	A	76	ASP	-1	-0.841	-0.904	32.940	-0.041	-0.041	0.000	0.000	0.000	0.000
26	A	77	ALA	0	-0.003	-0.008	34.698	0.000	0.000	0.000	0.000	0.000	0.000
27	A	78	GLU	-1	-0.907	-0.962	36.930	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	79	LYS	1	0.911	0.980	32.692	0.029	0.029	0.000	0.000	0.000	0.000
29	A	80	GLN	0	-0.030	-0.017	31.447	0.001	0.001	0.000	0.000	0.000	0.000
30	A	81	VAL	0	-0.033	-0.016	33.865	0.000	0.000	0.000	0.000	0.000	0.000
31	A	82	GLN	0	-0.056	-0.033	35.962	0.005	0.005	0.000	0.000	0.000	0.000
32	A	83	GLU	-1	-0.884	-0.953	34.633	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	84	ALA	0	-0.032	-0.016	33.652	0.001	0.001	0.000	0.000	0.000	0.000
34	A	85	TYR	0	0.047	0.018	31.578	0.002	0.002	0.000	0.000	0.000	0.000
35	A	86	LYS	1	0.983	1.016	29.601	0.013	0.013	0.000	0.000	0.000	0.000
36	A	87	GLY	0	-0.048	-0.016	26.199	0.004	0.004	0.000	0.000	0.000	0.000
37	A	88	LEU	0	-0.044	-0.019	25.095	0.000	0.000	0.000	0.000	0.000	0.000
38	A	89	LEU	0	-0.066	-0.040	20.493	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	90	ASN	0	0.000	0.001	24.335	0.006	0.006	0.000	0.000	0.000	0.000
40	A	91	LEU	0	-0.018	-0.029	22.218	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	92	ASN	0	-0.010	-0.004	25.614	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	93	GLU	-1	-0.891	-0.933	27.013	-0.072	-0.072	0.000	0.000	0.000	0.000
43	A	94	LYS	1	0.922	0.973	28.264	0.049	0.049	0.000	0.000	0.000	0.000
44	A	95	ASN	0	0.020	-0.009	29.172	0.006	0.006	0.000	0.000	0.000	0.000
45	A	96	ALA	0	0.030	-0.002	31.680	0.004	0.004	0.000	0.000	0.000	0.000
46	A	97	SER	0	-0.099	-0.048	33.230	0.002	0.002	0.000	0.000	0.000	0.000
47	A	98	ASP	-1	-0.858	-0.920	34.471	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	99	LYS	1	0.913	0.970	29.368	0.086	0.086	0.000	0.000	0.000	0.000
49	A	100	LEU	0	0.000	-0.009	26.559	0.000	0.000	0.000	0.000	0.000	0.000
50	A	101	LEU	0	-0.060	-0.028	25.131	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	102	VAL	0	-0.048	-0.027	20.058	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	103	GLU	-1	-0.900	-0.949	22.423	-0.121	-0.121	0.000	0.000	0.000	0.000
53	A	104	ASP	-1	-0.851	-0.914	21.515	-0.091	-0.091	0.000	0.000	0.000	0.000
54	A	105	ASN	0	-0.095	-0.030	20.018	0.002	0.002	0.000	0.000	0.000	0.000
55	A	106	THR	0	-0.045	-0.039	16.740	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	107	ALA	0	-0.013	-0.007	12.255	0.017	0.017	0.000	0.000	0.000	0.000
57	A	108	ALA	0	0.066	0.040	14.377	0.004	0.004	0.000	0.000	0.000	0.000
58	A	109	THR	0	-0.007	-0.012	12.158	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	110	VAL	0	0.065	0.007	10.959	0.029	0.029	0.000	0.000	0.000	0.000
60	A	111	GLY	0	-0.017	-0.014	13.494	0.017	0.017	0.000	0.000	0.000	0.000
61	A	112	ASN	0	0.037	0.025	15.645	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	113	LEU	0	0.090	0.043	15.343	0.009	0.009	0.000	0.000	0.000	0.000
63	A	114	ARG	1	0.922	0.976	13.626	-0.082	-0.082	0.000	0.000	0.000	0.000
64	A	115	LYS	1	0.923	0.968	19.130	0.049	0.049	0.000	0.000	0.000	0.000
65	A	116	LEU	0	0.019	0.029	20.703	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	117	GLY	0	0.047	0.013	23.659	0.008	0.008	0.000	0.000	0.000	0.000
67	A	118	TRP	0	-0.027	0.004	27.196	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	119	VAL	0	0.013	0.004	30.849	0.003	0.003	0.000	0.000	0.000	0.000
69	A	120	LEU	0	0.005	0.022	33.869	0.000	0.000	0.000	0.000	0.000	0.000
70	A	121	SER	0	0.070	0.024	36.514	0.000	0.000	0.000	0.000	0.000	0.000
71	A	122	SER	0	-0.038	0.004	39.971	0.001	0.001	0.000	0.000	0.000	0.000
72	A	123	LYS	1	0.975	0.972	43.429	0.003	0.003	0.000	0.000	0.000	0.000
73	A	124	ASN	0	0.019	0.015	46.661	0.000	0.000	0.000	0.000	0.000	0.000
74	A	125	GLY	0	0.011	-0.007	50.016	0.000	0.000	0.000	0.000	0.000	0.000
75	A	126	THR	0	0.032	-0.002	51.862	0.000	0.000	0.000	0.000	0.000	0.000
76	A	127	ARG	1	0.900	0.967	49.880	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	128	ASN	0	0.037	0.008	46.269	0.000	0.000	0.000	0.000	0.000	0.000
78	A	129	GLU	-1	-0.935	-0.958	42.060	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	130	LYS	1	0.890	0.974	38.259	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	131	SER	0	0.006	-0.021	37.135	0.000	0.000	0.000	0.000	0.000	0.000
81	A	132	GLN	0	-0.040	-0.039	34.551	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	133	GLN	0	-0.063	-0.050	28.902	0.001	0.001	0.000	0.000	0.000	0.000
83	A	134	VAL	0	0.018	0.028	29.884	0.003	0.003	0.000	0.000	0.000	0.000
84	A	135	LYS	1	0.869	0.914	23.414	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	136	HIS	0	0.006	-0.011	21.683	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	137	ALA	0	-0.082	-0.043	24.087	0.004	0.004	0.000	0.000	0.000	0.000
87	A	138	ASP	-1	-0.819	-0.884	25.988	0.029	0.029	0.000	0.000	0.000	0.000
88	A	139	GLU	-1	-0.964	-0.986	29.045	0.035	0.035	0.000	0.000	0.000	0.000
89	A	140	VAL	0	-0.063	-0.032	32.483	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	141	LEU	0	0.015	0.019	35.592	0.001	0.001	0.000	0.000	0.000	0.000
91	A	142	PHE	0	-0.042	-0.031	38.088	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	143	GLU	-1	-0.884	-0.947	42.018	0.019	0.019	0.000	0.000	0.000	0.000
93	A	144	GLY	0	-0.036	-0.011	44.882	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	145	LYS	1	0.995	0.982	48.203	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	146	GLY	0	-0.035	-0.022	51.240	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	147	GLY	0	0.028	0.013	54.609	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	148	VAL	0	-0.027	0.009	50.434	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	149	GLN	0	-0.015	-0.012	51.002	0.001	0.001	0.000	0.000	0.000	0.000
99	A	150	VAL	0	0.030	0.012	44.653	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	151	THR	0	-0.005	0.004	46.090	0.001	0.001	0.000	0.000	0.000	0.000
101	A	152	SER	0	0.001	-0.011	41.370	0.000	0.000	0.000	0.000	0.000	0.000
102	A	153	THR	0	-0.003	0.011	42.598	0.001	0.001	0.000	0.000	0.000	0.000
103	A	154	SER	0	0.013	-0.008	37.629	0.000	0.000	0.000	0.000	0.000	0.000
104	A	155	GLU	-1	-0.898	-0.956	39.058	0.017	0.017	0.000	0.000	0.000	0.000
105	A	156	ASN	0	0.026	0.033	35.947	0.001	0.001	0.000	0.000	0.000	0.000
106	A	157	GLY	0	-0.023	-0.004	34.017	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	158	LYS	1	0.936	0.983	34.658	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	159	HIS	0	-0.026	-0.033	34.201	0.001	0.001	0.000	0.000	0.000	0.000
109	A	160	THR	0	-0.027	-0.017	38.792	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	161	ILE	0	0.004	0.003	39.945	0.001	0.001	0.000	0.000	0.000	0.000
111	A	162	THR	0	-0.014	-0.007	43.489	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	163	PHE	0	-0.012	-0.011	44.279	0.001	0.001	0.000	0.000	0.000	0.000
113	A	164	ALA	0	0.014	0.008	49.618	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	165	LEU	0	-0.001	-0.002	53.207	0.000	0.000	0.000	0.000	0.000	0.000
115	A	166	NME	0	-0.020	-0.006	55.133	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:52:ACE )