FMO DATABASE

FMODB ID: VQQ11

Calculation Name: 3ELI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ELI

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LN61

Base Structure: X-ray

Registration Date: 2023-09-21

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1412937.814442
FMO2-HF: Nuclear repulsion	1355036.638045
FMO2-HF: Total energy	-57901.176397
FMO2-MP2: Total energy	-58071.719997

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:2:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-9.819	-1.19	9.842	-7.86	-10.611	-0.042

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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	4	LEU	0	-0.003	0.014	3.821	0.094	1.889	-0.026	-0.961	-0.807	0.000
4	A	5	ARG	1	0.838	0.894	6.865	-0.982	-0.982	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.021	-0.013	10.492	0.008	0.008	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.886	-0.957	13.669	0.225	0.225	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.883	0.938	16.527	-0.310	-0.310	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.907	-0.939	20.796	0.108	0.108	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.000	-0.013	21.958	0.001	0.001	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.011	0.008	27.017	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.003	-0.012	28.248	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.018	0.007	30.178	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.024	0.006	27.555	0.001	0.001	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.875	-0.944	27.718	0.036	0.036	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.028	-0.015	29.313	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.007	-0.001	23.162	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	18	PHE	0	0.046	0.025	23.426	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.041	0.025	25.042	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	20	TRP	0	-0.031	-0.032	25.321	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.031	0.002	20.637	0.005	0.005	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.032	-0.026	21.466	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.868	-0.937	23.911	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.082	0.045	25.829	0.006	0.006	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.070	-0.036	26.873	0.004	0.004	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.912	0.968	26.981	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.026	0.008	21.352	0.008	0.008	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.086	-0.054	23.861	0.006	0.006	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.035	0.002	25.890	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	TRP	0	-0.070	-0.047	18.448	0.009	0.009	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.032	-0.017	16.661	0.018	0.018	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.057	0.023	18.185	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.046	-0.028	16.428	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.809	-0.894	19.070	0.137	0.137	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.015	-0.012	22.216	0.005	0.005	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.078	-0.045	19.061	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	37	HIS	0	0.019	0.024	23.275	0.004	0.004	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.067	0.033	23.180	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.062	-0.017	25.052	0.001	0.001	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.030	-0.006	28.037	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.940	-0.964	30.291	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.106	-0.060	26.947	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	43	HIS	0	0.034	0.002	24.336	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.916	-0.952	24.148	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.017	-0.018	20.350	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.832	-0.930	23.203	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	47	PHE	0	-0.050	-0.017	18.249	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.033	0.021	22.807	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.807	0.908	23.821	0.054	0.054	0.000	0.000	0.000	0.000
49	A	50	LEU	0	0.006	-0.008	22.809	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.002	0.001	22.569	0.006	0.006	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.011	-0.008	21.399	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	53	TRP	0	0.000	0.051	15.294	0.023	0.023	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.001	0.002	19.891	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.019	-0.022	19.602	0.017	0.017	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.004	0.030	19.931	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	57	MET	0	-0.015	-0.007	16.621	0.013	0.013	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.017	-0.024	21.748	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	59	ASN	0	0.071	0.048	21.863	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.014	-0.026	24.554	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.950	-0.967	26.497	0.024	0.024	0.000	0.000	0.000	0.000
61	A	62	GLY	0	-0.029	-0.008	27.571	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.055	-0.020	22.662	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.974	0.979	23.200	0.034	0.034	0.000	0.000	0.000	0.000
64	A	65	TYR	0	0.014	0.017	17.151	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.895	0.963	19.096	0.098	0.098	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.002	0.010	13.929	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.038	-0.058	16.332	0.025	0.025	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.045	-0.026	15.556	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.000	0.000	16.505	0.024	0.024	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.026	0.044	17.202	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.029	-0.027	15.559	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.078	-0.041	17.582	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.047	0.029	20.718	0.004	0.004	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.839	0.951	23.195	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.040	-0.010	24.990	0.008	0.008	0.000	0.000	0.000	0.000
76	A	77	PRO	0	-0.012	0.006	27.458	0.002	0.002	0.000	0.000	0.000	0.000
77	A	78	GLN	0	0.010	-0.011	23.554	0.012	0.012	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.081	0.005	19.617	0.007	0.007	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.037	0.023	18.786	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.026	0.024	16.129	0.010	0.010	0.000	0.000	0.000	0.000
81	A	82	PHE	0	-0.015	-0.012	14.899	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.005	0.027	12.832	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	84	TRP	0	-0.006	-0.006	10.123	0.085	0.085	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.094	0.022	11.054	-0.097	-0.097	0.000	0.000	0.000	0.000
85	A	86	TRP	0	-0.018	-0.007	10.552	0.067	0.067	0.000	0.000	0.000	0.000
86	A	87	HIS	0	-0.032	-0.003	14.419	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.909	-0.931	17.762	-0.132	-0.132	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.922	-0.965	19.260	-0.072	-0.072	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.949	-0.991	22.372	-0.069	-0.069	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.992	-0.984	21.976	-0.097	-0.097	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.987	0.997	16.104	0.205	0.205	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.811	0.926	14.091	0.253	0.253	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.030	-0.019	13.569	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.025	-0.020	8.037	0.008	0.008	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.871	-0.942	9.726	-0.308	-0.308	0.000	0.000	0.000	0.000
96	A	97	SER	0	0.019	0.028	6.527	-0.071	-0.071	0.000	0.000	0.000	0.000
97	A	98	HIS	0	-0.014	-0.025	8.044	0.199	0.199	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.018	0.014	9.506	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	100	MET	0	-0.058	-0.023	11.937	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.002	0.014	14.457	0.050	0.050	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.022	-0.021	16.763	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.016	-0.003	19.329	0.021	0.021	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.874	-0.935	22.091	0.129	0.129	0.000	0.000	0.000	0.000
104	A	105	PRO	0	-0.021	-0.031	24.646	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	CYS	0	0.050	0.023	27.006	0.006	0.006	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.040	-0.023	29.028	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.921	0.962	32.232	-0.058	-0.058	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.022	0.013	30.323	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	ALA	0	0.011	0.005	26.977	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.884	0.981	20.513	-0.169	-0.169	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.008	-0.003	18.407	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.034	-0.008	14.933	0.031	0.031	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.001	-0.006	11.645	-0.050	-0.050	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.757	-0.871	9.712	0.325	0.325	0.000	0.000	0.000	0.000
115	A	116	HIS	0	-0.001	-0.003	7.412	-0.026	-0.026	0.000	0.000	0.000	0.000
116	A	117	ARG	1	0.885	0.957	5.295	0.420	0.428	-0.001	-0.015	0.009	0.000
117	A	118	GLU	-1	-0.931	-0.976	3.312	-1.230	-0.865	0.023	-0.086	-0.302	0.000
118	A	119	LEU	0	-0.044	-0.023	2.235	-0.107	0.776	1.932	-1.099	-1.716	0.000
119	A	120	GLY	0	-0.044	-0.025	2.470	-1.453	-0.920	2.504	-1.240	-1.798	-0.016
120	A	121	ASP	-1	-0.812	-0.927	2.384	-1.565	-0.731	0.778	-0.705	-0.907	-0.001
121	A	122	ASP	-1	-0.910	-0.956	2.486	-3.286	-0.082	3.544	-2.863	-3.885	-0.029
122	A	123	GLU	-1	-0.968	-0.983	3.207	1.375	1.270	0.025	0.177	-0.097	0.000
123	A	124	MET	0	0.003	-0.010	4.974	0.176	0.176	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.024	-0.011	2.453	-3.562	-2.475	1.063	-1.046	-1.105	0.004
125	A	126	LEU	0	0.026	0.034	4.368	-0.165	-0.140	0.000	-0.022	-0.003	0.000
126	A	127	ARG	1	0.963	0.986	7.874	-0.273	-0.273	0.000	0.000	0.000	0.000
127	A	128	HIS	0	0.001	-0.009	7.062	-0.247	-0.247	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.889	-0.913	8.557	0.960	0.960	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.894	-0.951	10.110	0.301	0.301	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.004	0.004	12.150	-0.086	-0.086	0.000	0.000	0.000	0.000
131	A	132	TRP	0	0.029	-0.011	9.950	-0.074	-0.074	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.096	-0.052	13.729	-0.050	-0.050	0.000	0.000	0.000	0.000
133	A	134	SER	0	-0.058	-0.033	15.853	-0.050	-0.050	0.000	0.000	0.000	0.000
134	A	135	SER	0	-0.018	-0.007	16.997	-0.029	-0.029	0.000	0.000	0.000	0.000
135	A	136	LEU	0	0.035	0.000	15.899	-0.022	-0.022	0.000	0.000	0.000	0.000
136	A	137	ARG	1	0.811	0.905	19.467	-0.229	-0.229	0.000	0.000	0.000	0.000
137	A	138	LYS	1	0.879	0.943	22.038	-0.119	-0.119	0.000	0.000	0.000	0.000
138	A	139	LEU	0	0.109	0.079	21.249	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	140	ALA	0	-0.009	-0.007	23.471	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	141	ALA	0	-0.062	-0.035	25.313	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.871	-0.953	26.789	0.051	0.051	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.023	-0.004	25.620	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	144	ALA	0	-0.037	-0.017	29.241	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.050	-0.031	31.137	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.923	-0.953	32.326	0.033	0.033	0.000	0.000	0.000	0.000
146	A	147	HIS	1	0.772	0.905	33.435	-0.056	-0.056	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)