FMO DATABASE

FMODB ID: 2JLYR

Calculation Name: 4NEE-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NEE

Chain ID: E

ChEMBL ID:

UniProt ID: P18484

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1291610.027931
FMO2-HF: Nuclear repulsion	1236062.442989
FMO2-HF: Total energy	-55547.584942
FMO2-MP2: Total energy	-55712.065182

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(E:55:ALA)

Summations of interaction energy for fragment #1(E:55:ALA)

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.
-14.276	-7.593	8.431	-6.612	-8.498	-0.028

Interaction energy analysis for fragmet #1(E:55:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.007

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	E	57	ALA	0	0.050	0.021	3.891	1.215	2.330	-0.006	-0.489	-0.619	0.002
4	E	58	ALA	0	-0.022	-0.003	1.978	0.107	0.020	2.456	-0.828	-1.541	0.003
5	E	59	ALA	0	0.022	0.008	2.350	-2.841	-1.746	2.382	-1.431	-2.046	0.008
6	E	60	ALA	0	-0.050	-0.023	3.973	-1.244	-1.043	0.014	-0.059	-0.156	0.001
7	E	61	ALA	0	0.005	0.022	7.100	-0.352	-0.352	0.000	0.000	0.000	0.000
8	E	72	PRO	0	-0.019	-0.032	19.505	0.012	0.012	0.000	0.000	0.000	0.000
9	E	73	GLN	0	-0.039	-0.010	18.834	-0.034	-0.034	0.000	0.000	0.000	0.000
10	E	74	VAL	0	-0.012	0.014	18.716	-0.015	-0.015	0.000	0.000	0.000	0.000
11	E	75	PRO	0	-0.027	-0.010	21.374	-0.009	-0.009	0.000	0.000	0.000	0.000
12	E	76	LEU	0	0.008	0.000	23.293	0.007	0.007	0.000	0.000	0.000	0.000
13	E	77	ARG	1	0.880	0.930	18.430	-0.241	-0.241	0.000	0.000	0.000	0.000
14	E	78	PRO	0	-0.009	0.007	23.184	0.000	0.000	0.000	0.000	0.000	0.000
15	E	79	MET	0	0.044	0.029	17.832	0.001	0.001	0.000	0.000	0.000	0.000
16	E	80	THR	0	-0.041	-0.030	21.964	-0.013	-0.013	0.000	0.000	0.000	0.000
17	E	81	TYR	0	0.020	-0.010	21.725	0.007	0.007	0.000	0.000	0.000	0.000
18	E	82	LYS	1	0.875	0.911	20.532	-0.065	-0.065	0.000	0.000	0.000	0.000
19	E	83	ALA	0	-0.008	0.007	19.373	0.000	0.000	0.000	0.000	0.000	0.000
20	E	84	ALA	0	0.074	0.031	17.332	0.018	0.018	0.000	0.000	0.000	0.000
21	E	85	VAL	0	0.012	0.035	16.202	-0.025	-0.025	0.000	0.000	0.000	0.000
22	E	86	ASP	-1	-0.871	-0.914	15.712	0.041	0.041	0.000	0.000	0.000	0.000
23	E	87	LEU	0	-0.029	-0.009	12.122	0.024	0.024	0.000	0.000	0.000	0.000
24	E	88	SER	0	-0.004	-0.019	11.622	-0.021	-0.021	0.000	0.000	0.000	0.000
25	E	89	HIS	0	-0.008	-0.004	11.026	-0.129	-0.129	0.000	0.000	0.000	0.000
26	E	90	PHE	0	0.047	0.032	9.517	-0.008	-0.008	0.000	0.000	0.000	0.000
27	E	91	LEU	0	-0.009	-0.020	7.181	0.152	0.152	0.000	0.000	0.000	0.000
28	E	92	LYS	1	0.888	0.964	6.028	-0.047	-0.047	0.000	0.000	0.000	0.000
29	E	93	GLU	-1	-0.954	-0.982	7.059	-0.253	-0.253	0.000	0.000	0.000	0.000
30	E	94	LYS	1	0.714	0.874	3.854	-3.719	-3.390	0.002	-0.082	-0.248	0.000
31	E	95	GLY	0	0.045	0.023	2.610	-2.734	-0.731	0.960	-1.512	-1.450	-0.017
32	E	96	GLY	0	0.007	-0.026	2.547	-5.396	-3.518	2.622	-2.183	-2.317	-0.025
33	E	97	LEU	0	-0.018	-0.005	4.043	0.925	1.074	0.001	-0.028	-0.121	0.000
34	E	98	GLU	-1	-0.790	-0.882	6.893	-0.406	-0.406	0.000	0.000	0.000	0.000
35	E	99	GLY	0	0.005	0.015	7.681	-0.144	-0.144	0.000	0.000	0.000	0.000
36	E	100	LEU	0	-0.106	-0.037	5.704	0.016	0.016	0.000	0.000	0.000	0.000
37	E	101	ILE	0	0.030	0.007	8.525	0.106	0.106	0.000	0.000	0.000	0.000
38	E	102	HIS	0	-0.010	-0.019	11.348	-0.027	-0.027	0.000	0.000	0.000	0.000
39	E	103	SER	0	0.023	0.001	12.869	0.027	0.027	0.000	0.000	0.000	0.000
40	E	104	GLN	0	-0.030	-0.022	14.317	-0.023	-0.023	0.000	0.000	0.000	0.000
41	E	105	ARG	1	0.967	0.991	12.557	0.052	0.052	0.000	0.000	0.000	0.000
42	E	106	ARG	1	0.858	0.921	7.872	0.525	0.525	0.000	0.000	0.000	0.000
43	E	107	GLN	0	0.013	0.014	11.457	0.016	0.016	0.000	0.000	0.000	0.000
44	E	108	ASP	-1	-0.823	-0.903	13.689	0.114	0.114	0.000	0.000	0.000	0.000
45	E	109	ILE	0	-0.037	-0.022	9.455	0.053	0.053	0.000	0.000	0.000	0.000
46	E	110	LEU	0	-0.021	0.000	8.496	0.147	0.147	0.000	0.000	0.000	0.000
47	E	111	ASP	-1	-0.740	-0.880	11.156	0.154	0.154	0.000	0.000	0.000	0.000
48	E	112	LEU	0	-0.018	-0.009	14.672	0.019	0.019	0.000	0.000	0.000	0.000
49	E	113	TRP	0	0.026	0.028	9.321	0.203	0.203	0.000	0.000	0.000	0.000
50	E	114	ILE	0	-0.003	0.000	11.426	0.034	0.034	0.000	0.000	0.000	0.000
51	E	115	TYR	0	-0.010	0.005	13.858	-0.019	-0.019	0.000	0.000	0.000	0.000
52	E	116	HIS	0	-0.009	-0.023	15.527	-0.031	-0.031	0.000	0.000	0.000	0.000
53	E	117	THR	0	-0.012	-0.017	12.661	0.012	0.012	0.000	0.000	0.000	0.000
54	E	118	GLN	0	-0.030	-0.019	14.195	-0.079	-0.079	0.000	0.000	0.000	0.000
55	E	119	GLY	0	0.034	0.040	17.491	-0.042	-0.042	0.000	0.000	0.000	0.000
56	E	120	TYR	0	-0.015	-0.016	16.778	-0.034	-0.034	0.000	0.000	0.000	0.000
57	E	121	PHE	0	0.030	0.016	19.244	0.023	0.023	0.000	0.000	0.000	0.000
58	E	122	PRO	0	-0.013	0.003	18.485	-0.011	-0.011	0.000	0.000	0.000	0.000
59	E	123	ASP	-1	-0.876	-0.948	19.764	0.051	0.051	0.000	0.000	0.000	0.000
60	E	124	TRP	0	-0.026	-0.017	14.445	-0.031	-0.031	0.000	0.000	0.000	0.000
61	E	125	GLN	0	-0.013	0.022	13.342	-0.092	-0.092	0.000	0.000	0.000	0.000
62	E	126	ASN	0	0.027	0.004	18.546	-0.023	-0.023	0.000	0.000	0.000	0.000
63	E	127	TYR	0	-0.018	-0.030	15.113	-0.025	-0.025	0.000	0.000	0.000	0.000
64	E	128	THR	0	-0.031	-0.017	21.861	0.008	0.008	0.000	0.000	0.000	0.000
65	E	129	PRO	0	0.005	0.000	23.946	-0.010	-0.010	0.000	0.000	0.000	0.000
66	E	130	GLY	0	-0.028	0.012	25.521	-0.008	-0.008	0.000	0.000	0.000	0.000
67	E	131	PRO	0	-0.029	-0.028	25.854	0.010	0.010	0.000	0.000	0.000	0.000
68	E	132	GLY	0	-0.004	-0.013	24.539	0.006	0.006	0.000	0.000	0.000	0.000
69	E	133	VAL	0	-0.061	-0.048	19.838	-0.007	-0.007	0.000	0.000	0.000	0.000
70	E	134	ARG	1	0.782	0.875	19.935	0.141	0.141	0.000	0.000	0.000	0.000
71	E	135	TYR	0	0.023	0.005	19.780	-0.031	-0.031	0.000	0.000	0.000	0.000
72	E	136	PRO	0	0.013	0.014	18.758	0.016	0.016	0.000	0.000	0.000	0.000
73	E	137	LEU	0	-0.002	-0.015	20.877	0.006	0.006	0.000	0.000	0.000	0.000
74	E	138	THR	0	-0.042	-0.034	20.234	0.015	0.015	0.000	0.000	0.000	0.000
75	E	139	PHE	0	0.001	-0.003	20.973	-0.013	-0.013	0.000	0.000	0.000	0.000
76	E	140	GLY	0	0.026	-0.008	20.503	0.017	0.017	0.000	0.000	0.000	0.000
77	E	141	TRP	0	-0.007	-0.003	11.246	0.004	0.004	0.000	0.000	0.000	0.000
78	E	142	CYS	0	-0.082	-0.047	15.000	-0.004	-0.004	0.000	0.000	0.000	0.000
79	E	143	TYR	0	-0.020	-0.019	8.310	0.002	0.002	0.000	0.000	0.000	0.000
80	E	144	LYS	1	0.856	0.917	14.719	0.267	0.267	0.000	0.000	0.000	0.000
81	E	145	LEU	0	0.015	0.021	14.639	-0.060	-0.060	0.000	0.000	0.000	0.000
82	E	146	VAL	0	-0.003	-0.005	15.853	0.039	0.039	0.000	0.000	0.000	0.000
83	E	147	PRO	0	0.019	0.017	17.368	-0.024	-0.024	0.000	0.000	0.000	0.000
84	E	148	VAL	0	-0.025	-0.012	16.214	-0.009	-0.009	0.000	0.000	0.000	0.000
85	E	149	GLU	-1	-0.857	-0.921	19.019	-0.191	-0.191	0.000	0.000	0.000	0.000
86	E	150	PRO	0	0.024	-0.009	21.705	-0.008	-0.008	0.000	0.000	0.000	0.000
87	E	151	ASP	-1	-0.796	-0.881	23.769	-0.179	-0.179	0.000	0.000	0.000	0.000
88	E	152	LYS	1	0.816	0.882	18.698	0.204	0.204	0.000	0.000	0.000	0.000
89	E	153	VAL	0	-0.011	-0.001	19.274	-0.016	-0.016	0.000	0.000	0.000	0.000
90	E	154	GLU	-1	-0.847	-0.923	20.416	-0.122	-0.122	0.000	0.000	0.000	0.000
91	E	155	GLU	-1	-0.919	-0.948	21.150	-0.148	-0.148	0.000	0.000	0.000	0.000
92	E	156	ALA	0	-0.048	-0.018	16.597	-0.002	-0.002	0.000	0.000	0.000	0.000
93	E	157	ASN	0	-0.012	-0.033	18.046	0.003	0.003	0.000	0.000	0.000	0.000
94	E	158	LYS	1	0.765	0.892	20.529	0.157	0.157	0.000	0.000	0.000	0.000
95	E	159	GLY	0	-0.003	0.003	21.515	-0.011	-0.011	0.000	0.000	0.000	0.000
96	E	160	GLU	-1	-0.929	-0.964	23.727	-0.074	-0.074	0.000	0.000	0.000	0.000
97	E	161	ASN	0	-0.099	-0.066	20.752	0.009	0.009	0.000	0.000	0.000	0.000
98	E	162	THR	0	0.009	0.016	17.785	0.000	0.000	0.000	0.000	0.000	0.000
99	E	163	SER	0	0.008	-0.001	16.403	0.009	0.009	0.000	0.000	0.000	0.000
100	E	164	LEU	0	0.055	0.029	17.955	-0.014	-0.014	0.000	0.000	0.000	0.000
101	E	165	LEU	0	0.001	0.010	18.026	0.002	0.002	0.000	0.000	0.000	0.000
102	E	166	HIS	0	-0.012	-0.009	11.371	0.025	0.025	0.000	0.000	0.000	0.000
103	E	167	PRO	0	-0.021	-0.030	11.694	0.009	0.009	0.000	0.000	0.000	0.000
104	E	168	VAL	0	0.012	0.012	13.742	0.003	0.003	0.000	0.000	0.000	0.000
105	E	169	SER	0	0.025	0.002	16.192	0.007	0.007	0.000	0.000	0.000	0.000
106	E	170	LEU	0	-0.064	-0.009	16.846	0.019	0.019	0.000	0.000	0.000	0.000
107	E	171	HIS	0	-0.044	-0.023	19.897	0.007	0.007	0.000	0.000	0.000	0.000
108	E	172	GLY	0	0.059	0.035	20.524	0.011	0.011	0.000	0.000	0.000	0.000
109	E	173	MET	0	-0.071	-0.035	20.689	0.014	0.014	0.000	0.000	0.000	0.000
110	E	174	ASP	-1	-0.851	-0.937	17.781	-0.080	-0.080	0.000	0.000	0.000	0.000
111	E	175	ASP	-1	-0.766	-0.851	21.024	-0.113	-0.113	0.000	0.000	0.000	0.000
112	E	176	PRO	0	-0.012	-0.006	22.739	0.004	0.004	0.000	0.000	0.000	0.000
113	E	177	GLU	-1	-0.864	-0.935	25.457	-0.079	-0.079	0.000	0.000	0.000	0.000
114	E	178	ARG	1	0.831	0.931	24.333	0.082	0.082	0.000	0.000	0.000	0.000
115	E	179	GLU	-1	-0.797	-0.881	21.780	-0.147	-0.147	0.000	0.000	0.000	0.000
116	E	180	VAL	0	0.009	0.002	17.126	0.001	0.001	0.000	0.000	0.000	0.000
117	E	181	LEU	0	0.007	0.012	16.824	-0.011	-0.011	0.000	0.000	0.000	0.000
118	E	182	GLU	-1	-0.829	-0.910	12.485	-0.511	-0.511	0.000	0.000	0.000	0.000
119	E	183	TRP	0	-0.014	-0.008	10.122	0.014	0.014	0.000	0.000	0.000	0.000
120	E	184	ARG	1	0.773	0.862	11.092	0.442	0.442	0.000	0.000	0.000	0.000
121	E	185	PHE	0	0.028	-0.001	11.834	0.086	0.086	0.000	0.000	0.000	0.000
122	E	186	ASP	-1	-0.824	-0.911	13.629	-0.169	-0.169	0.000	0.000	0.000	0.000
123	E	187	SER	0	0.023	-0.006	17.390	0.014	0.014	0.000	0.000	0.000	0.000
124	E	188	ARG	1	0.931	0.978	19.122	0.124	0.124	0.000	0.000	0.000	0.000
125	E	189	LEU	0	0.038	0.018	18.048	0.021	0.021	0.000	0.000	0.000	0.000
126	E	190	ALA	0	0.017	0.018	19.804	0.017	0.017	0.000	0.000	0.000	0.000
127	E	191	PHE	0	-0.070	-0.033	21.666	0.017	0.017	0.000	0.000	0.000	0.000
128	E	192	HIS	0	-0.073	-0.046	24.906	0.010	0.010	0.000	0.000	0.000	0.000
129	E	193	HIS	0	-0.007	0.013	25.020	-0.017	-0.017	0.000	0.000	0.000	0.000
130	E	194	VAL	0	0.043	0.014	24.362	0.006	0.006	0.000	0.000	0.000	0.000
131	E	195	ALA	0	0.032	0.023	24.391	0.003	0.003	0.000	0.000	0.000	0.000
132	E	196	ARG	1	0.892	0.949	26.391	0.031	0.031	0.000	0.000	0.000	0.000
133	E	197	GLU	-1	-0.902	-0.939	29.392	-0.067	-0.067	0.000	0.000	0.000	0.000
134	E	198	LEU	0	-0.010	-0.013	26.868	0.003	0.003	0.000	0.000	0.000	0.000
135	E	199	HIS	1	0.843	0.900	28.641	0.059	0.059	0.000	0.000	0.000	0.000
136	E	200	PRO	0	0.044	0.026	31.307	0.004	0.004	0.000	0.000	0.000	0.000
137	E	201	GLU	-1	-0.844	-0.894	33.694	-0.036	-0.036	0.000	0.000	0.000	0.000
138	E	202	TYR	0	-0.015	-0.006	28.248	0.001	0.001	0.000	0.000	0.000	0.000
139	E	203	PHE	0	-0.077	-0.025	26.647	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:55:ALA)