FMO DATABASE

FMODB ID: 3JL4L

Calculation Name: 1ELK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ELK

Chain ID: A

ChEMBL ID:

UniProt ID: O60784

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	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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1500658.278796
FMO2-HF: Nuclear repulsion	1440259.238503
FMO2-HF: Total energy	-60399.040292
FMO2-MP2: Total energy	-60574.480906

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:SER)

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

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.
-5.021	0.27	0.397	-2.798	-2.89	0.016

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.010

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	PHE	0	-0.032	0.003	2.788	-4.711	0.317	0.397	-2.755	-2.670	0.016
4	A	4	LEU	0	-0.018	-0.021	4.378	-0.732	-0.469	0.000	-0.043	-0.220	0.000
5	A	5	LEU	0	0.006	-0.008	7.048	0.029	0.029	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.011	0.022	9.840	0.025	0.025	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.047	-0.003	12.064	-0.117	-0.117	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.039	0.021	13.287	0.002	0.002	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.030	0.012	15.359	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.019	0.021	17.278	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.002	0.025	15.837	0.020	0.020	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.049	0.015	17.818	0.030	0.030	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.068	0.048	18.330	0.032	0.032	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.020	0.006	19.083	0.023	0.023	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.067	-0.034	19.962	0.050	0.050	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.813	0.896	22.970	0.247	0.247	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.023	0.016	20.024	0.014	0.014	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.873	-0.912	22.569	-0.170	-0.170	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.830	0.899	24.000	0.196	0.196	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.033	0.013	26.704	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.044	-0.038	24.587	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.775	-0.866	27.407	-0.115	-0.115	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.005	-0.001	28.985	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.104	-0.064	31.457	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.030	0.003	31.105	0.006	0.006	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.028	-0.017	34.448	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.015	-0.015	35.486	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.837	-0.908	31.484	-0.137	-0.137	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.838	-0.904	31.547	-0.130	-0.130	0.000	0.000	0.000	0.000
30	A	30	TRP	0	0.028	-0.014	31.795	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.009	0.017	33.180	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.006	-0.006	28.537	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.040	-0.032	28.099	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	34	MET	0	0.001	0.015	28.006	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.734	-0.841	27.628	-0.207	-0.207	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.064	-0.040	22.719	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.029	-0.020	23.663	-0.030	-0.030	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.858	-0.925	25.090	-0.207	-0.207	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.006	-0.008	21.273	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.071	-0.024	19.864	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.020	-0.027	21.298	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.957	-0.966	23.829	-0.206	-0.206	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.076	-0.044	20.093	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.839	-0.914	15.610	-0.471	-0.471	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.940	-0.979	14.609	-0.538	-0.538	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.061	0.033	15.350	-0.065	-0.065	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.000	0.001	16.171	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.878	0.932	10.593	0.995	0.995	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.864	-0.951	12.979	-0.952	-0.952	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.010	0.007	14.592	0.042	0.042	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.011	0.016	14.119	0.037	0.037	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.850	0.926	9.870	1.039	1.039	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.022	-0.011	14.035	0.072	0.072	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.047	0.014	17.612	0.050	0.050	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.844	0.922	11.179	0.848	0.848	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.841	0.931	16.204	0.274	0.274	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.757	0.869	17.482	0.209	0.209	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.006	0.010	20.200	0.035	0.035	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.014	-0.010	15.834	0.030	0.030	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.027	-0.009	19.037	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.061	-0.036	21.200	0.042	0.042	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.869	0.923	23.989	0.082	0.082	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.010	0.004	27.639	0.010	0.010	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.016	-0.026	26.848	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	HIS	0	-0.006	0.010	29.723	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.733	-0.847	26.635	-0.133	-0.133	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.033	-0.013	24.845	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	68	MET	0	0.004	0.010	26.545	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.020	0.033	28.585	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.007	-0.009	23.325	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.026	-0.016	23.745	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.003	-0.022	25.970	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.018	0.037	23.786	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.008	0.007	20.627	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.813	-0.878	23.979	-0.172	-0.172	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.044	-0.036	27.101	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.003	-0.021	22.745	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.034	-0.023	23.243	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.838	0.898	25.233	0.176	0.176	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.046	-0.016	27.495	0.023	0.023	0.000	0.000	0.000	0.000
81	A	81	CYS	0	-0.029	0.029	23.282	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.045	0.024	24.531	0.013	0.013	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.007	-0.038	21.861	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.795	0.876	18.545	0.372	0.372	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.029	0.013	17.713	-0.064	-0.064	0.000	0.000	0.000	0.000
86	A	86	HIS	0	-0.010	-0.007	18.689	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.041	0.005	16.274	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.031	0.001	12.548	-0.059	-0.059	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.027	0.003	15.495	-0.034	-0.034	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.019	0.011	18.053	0.024	0.024	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.042	-0.030	13.831	0.012	0.012	0.000	0.000	0.000	0.000
92	A	92	GLN	0	0.038	0.000	13.912	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.829	-0.916	11.359	-0.783	-0.783	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.014	0.043	13.341	0.041	0.041	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.067	0.027	15.130	0.058	0.058	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.825	-0.907	15.877	-0.190	-0.190	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.102	-0.080	14.138	0.029	0.029	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.011	0.010	16.052	0.023	0.023	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.012	0.020	18.611	0.035	0.035	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.058	0.024	20.513	0.029	0.029	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.838	0.891	13.570	0.320	0.320	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.063	-0.032	20.976	0.023	0.023	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.026	0.013	23.166	0.018	0.018	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.011	0.015	21.722	0.016	0.016	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.050	0.011	25.593	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.920	0.964	22.095	0.033	0.033	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.030	-0.021	23.943	0.017	0.017	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.055	-0.026	25.818	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.051	0.039	27.716	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.004	0.010	29.883	0.006	0.006	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.037	-0.004	32.349	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.041	0.028	33.195	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.029	0.004	27.572	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	114	HIS	0	0.005	0.007	29.050	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.833	-0.929	30.165	-0.103	-0.103	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.806	0.903	28.491	0.155	0.155	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.011	-0.003	25.097	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.027	-0.006	27.208	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	119	ASN	0	-0.010	-0.029	29.647	0.000	0.000	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.029	0.017	25.167	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.009	0.000	23.740	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	122	GLN	0	0.041	0.034	26.023	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.034	-0.039	29.368	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	TRP	0	0.006	-0.008	20.638	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	125	ALA	0	-0.023	-0.002	26.094	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.816	-0.910	26.971	-0.128	-0.128	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.055	-0.022	28.711	0.005	0.005	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.003	-0.012	23.087	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.760	0.866	26.554	0.127	0.127	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.020	-0.005	28.662	0.007	0.007	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.002	-0.001	24.854	0.013	0.013	0.000	0.000	0.000	0.000
132	A	132	PRO	0	0.014	-0.003	24.029	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	133	ASP	-1	-0.844	-0.905	19.613	-0.278	-0.278	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.018	0.001	19.426	-0.041	-0.041	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.008	-0.016	21.235	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	136	GLY	0	-0.004	0.023	18.601	0.019	0.019	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.028	0.009	19.533	0.021	0.021	0.000	0.000	0.000	0.000
138	A	138	VAL	0	-0.003	0.009	21.883	0.023	0.023	0.000	0.000	0.000	0.000
139	A	139	THR	0	-0.039	-0.032	21.690	0.026	0.026	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.020	-0.007	18.535	0.017	0.017	0.000	0.000	0.000	0.000
141	A	141	TYR	0	0.001	-0.019	23.133	0.018	0.018	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.811	-0.876	26.557	-0.099	-0.099	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.888	-0.921	24.853	-0.098	-0.098	0.000	0.000	0.000	0.000
144	A	144	LEU	0	0.027	0.004	24.406	0.013	0.013	0.000	0.000	0.000	0.000
145	A	145	ARG	1	0.891	0.936	27.727	0.118	0.118	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.893	0.943	27.898	0.111	0.111	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.741	0.854	25.871	0.102	0.102	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.007	0.015	30.624	0.006	0.006	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.081	-0.029	28.311	0.003	0.003	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.877	-0.951	32.006	-0.076	-0.076	0.000	0.000	0.000	0.000
151	A	151	PHE	0	-0.029	-0.024	28.302	-0.010	-0.010	0.000	0.000	0.000	0.000
152	A	152	PRO	0	0.020	0.035	33.483	0.006	0.006	0.000	0.000	0.000	0.000
153	A	153	MET	0	-0.030	-0.012	35.959	-0.002	-0.002	0.000	0.000	0.000	0.000

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