FMO DATABASE

FMODB ID: LNJY9

Calculation Name: 1VJX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1L2

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1523302.247257
FMO2-HF: Nuclear repulsion	1462051.190302
FMO2-HF: Total energy	-61251.056955
FMO2-MP2: Total energy	-61431.850702

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:HIS)

Summations of interaction energy for fragment #1(A:-2:HIS)

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.
-244.64	-230.042	21.454	-14.505	-21.544	-0.154

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.908

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	0	HIS	0	-0.033	-0.018	3.287	-2.380	-0.375	0.010	-0.991	-1.024	-0.001
4	A	1	MET	0	0.022	0.031	2.532	-2.235	-1.251	1.170	-0.657	-1.496	-0.003
5	A	2	LYS	1	0.854	0.910	5.276	23.147	23.170	-0.001	-0.002	-0.019	0.000
6	A	3	VAL	0	0.064	0.035	8.553	-2.536	-2.536	0.000	0.000	0.000	0.000
7	A	4	SER	0	0.018	0.009	11.044	-0.358	-0.358	0.000	0.000	0.000	0.000
8	A	5	ASP	-1	-0.889	-0.931	7.226	-29.517	-29.517	0.000	0.000	0.000	0.000
9	A	6	ILE	0	-0.019	-0.019	5.555	-1.976	-1.976	0.000	0.000	0.000	0.000
10	A	7	LEU	0	0.026	0.017	8.957	0.516	0.516	0.000	0.000	0.000	0.000
11	A	8	THR	0	-0.040	-0.014	11.004	1.480	1.480	0.000	0.000	0.000	0.000
12	A	9	VAL	0	-0.034	-0.013	6.456	0.713	0.713	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.012	-0.006	9.390	0.890	0.890	0.000	0.000	0.000	0.000
14	A	11	ILE	0	-0.042	-0.025	11.729	1.611	1.611	0.000	0.000	0.000	0.000
15	A	12	ARG	1	0.968	0.984	11.252	24.112	24.112	0.000	0.000	0.000	0.000
16	A	13	LEU	0	-0.016	0.009	8.058	1.212	1.212	0.000	0.000	0.000	0.000
17	A	14	GLH	0	-0.038	-0.053	12.222	1.599	1.599	0.000	0.000	0.000	0.000
18	A	15	GLU	-1	-0.864	-0.942	15.812	-16.567	-16.567	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.930	-0.974	13.470	-17.815	-17.815	0.000	0.000	0.000	0.000
20	A	17	GLY	0	0.035	0.023	15.664	0.761	0.761	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.902	-0.967	16.981	-12.671	-12.671	0.000	0.000	0.000	0.000
22	A	19	ARG	1	0.854	0.922	17.839	16.767	16.767	0.000	0.000	0.000	0.000
23	A	20	PHE	0	0.047	0.038	17.728	0.658	0.658	0.000	0.000	0.000	0.000
24	A	21	TYR	0	0.001	-0.002	18.015	0.860	0.860	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.936	0.960	22.318	12.655	12.655	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.827	-0.880	21.527	-13.462	-13.462	0.000	0.000	0.000	0.000
27	A	24	LEU	0	-0.014	-0.014	21.390	0.555	0.555	0.000	0.000	0.000	0.000
28	A	25	SER	0	-0.112	-0.071	24.909	0.665	0.665	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.937	-0.982	27.827	-10.596	-10.596	0.000	0.000	0.000	0.000
30	A	27	HIS	1	0.791	0.911	26.323	11.716	11.716	0.000	0.000	0.000	0.000
31	A	28	PHE	0	-0.014	-0.005	26.393	0.256	0.256	0.000	0.000	0.000	0.000
32	A	29	ASN	0	0.039	-0.013	31.296	0.152	0.152	0.000	0.000	0.000	0.000
33	A	30	GLY	0	-0.021	0.008	33.987	0.174	0.174	0.000	0.000	0.000	0.000
34	A	31	GLU	-1	-0.884	-0.950	33.947	-8.948	-8.948	0.000	0.000	0.000	0.000
35	A	32	ILE	0	-0.007	-0.001	28.926	-0.209	-0.209	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.892	0.962	29.342	9.290	9.290	0.000	0.000	0.000	0.000
37	A	34	LYS	1	0.978	0.984	29.657	8.648	8.648	0.000	0.000	0.000	0.000
38	A	35	THR	0	0.013	0.013	26.647	-0.226	-0.226	0.000	0.000	0.000	0.000
39	A	36	PHE	0	-0.008	-0.006	23.679	-0.311	-0.311	0.000	0.000	0.000	0.000
40	A	37	LEU	0	0.018	0.000	25.233	-0.399	-0.399	0.000	0.000	0.000	0.000
41	A	38	GLU	-1	-0.933	-0.958	27.008	-10.367	-10.367	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.047	-0.023	22.342	-0.278	-0.278	0.000	0.000	0.000	0.000
43	A	40	ALA	0	0.012	0.005	22.413	-0.578	-0.578	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.867	-0.932	23.179	-11.513	-11.513	0.000	0.000	0.000	0.000
45	A	42	GLN	0	-0.048	-0.059	23.314	0.419	0.419	0.000	0.000	0.000	0.000
46	A	43	GLH	0	-0.050	-0.046	17.249	-0.586	-0.586	0.000	0.000	0.000	0.000
47	A	44	ARG	1	0.861	0.953	19.981	11.253	11.253	0.000	0.000	0.000	0.000
48	A	45	ILE	0	-0.032	-0.021	22.050	-0.260	-0.260	0.000	0.000	0.000	0.000
49	A	46	HIS	0	-0.013	-0.006	18.651	0.629	0.629	0.000	0.000	0.000	0.000
50	A	47	ALA	0	0.048	0.030	18.117	-0.519	-0.519	0.000	0.000	0.000	0.000
51	A	48	GLU	-1	-0.947	-0.979	19.122	-12.383	-12.383	0.000	0.000	0.000	0.000
52	A	49	ILE	0	-0.069	-0.023	20.521	0.309	0.309	0.000	0.000	0.000	0.000
53	A	50	PHE	0	0.031	-0.005	15.340	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	51	ARG	1	0.909	0.952	18.351	14.672	14.672	0.000	0.000	0.000	0.000
55	A	52	LYS	1	0.914	0.966	20.048	11.888	11.888	0.000	0.000	0.000	0.000
56	A	53	MET	0	0.000	0.009	18.402	-0.088	-0.088	0.000	0.000	0.000	0.000
57	A	54	SER	0	-0.042	-0.027	16.365	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	55	ASP	-1	-0.960	-0.975	18.137	-13.092	-13.092	0.000	0.000	0.000	0.000
59	A	56	GLN	0	-0.046	-0.033	21.473	0.389	0.389	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.872	-0.922	18.785	-13.959	-13.959	0.000	0.000	0.000	0.000
61	A	58	ASN	0	-0.020	-0.014	20.893	-0.310	-0.310	0.000	0.000	0.000	0.000
62	A	59	TRP	0	0.018	-0.004	16.662	-0.743	-0.743	0.000	0.000	0.000	0.000
63	A	60	ASP	-1	-0.880	-0.945	18.047	-14.061	-14.061	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.819	-0.886	16.742	-16.672	-16.672	0.000	0.000	0.000	0.000
65	A	62	VAL	0	0.036	-0.011	14.961	-1.401	-1.401	0.000	0.000	0.000	0.000
66	A	63	ASP	-1	-0.844	-0.907	13.485	-19.888	-19.888	0.000	0.000	0.000	0.000
67	A	64	SER	0	-0.011	0.004	13.691	-0.176	-0.176	0.000	0.000	0.000	0.000
68	A	65	TYR	0	-0.080	-0.041	8.627	-1.502	-1.502	0.000	0.000	0.000	0.000
69	A	66	LEU	0	0.022	0.030	7.180	1.897	1.897	0.000	0.000	0.000	0.000
70	A	67	ALA	0	-0.041	-0.026	7.998	-1.927	-1.927	0.000	0.000	0.000	0.000
71	A	68	GLY	0	-0.019	-0.010	7.548	-0.773	-0.773	0.000	0.000	0.000	0.000
72	A	69	TYR	0	-0.054	-0.026	2.342	-7.724	-6.814	5.169	-1.696	-4.382	-0.004
73	A	70	ALA	0	0.064	0.038	2.946	3.653	5.207	0.074	-0.747	-0.881	-0.004
74	A	71	PHE	0	-0.048	-0.022	1.850	-45.365	-43.661	9.534	-5.781	-5.457	-0.082
75	A	72	TYR	0	-0.010	-0.025	2.658	-5.355	-0.756	3.876	-2.342	-6.134	-0.025
76	A	73	GLU	-1	-0.910	-0.946	2.325	-65.426	-62.645	1.623	-2.285	-2.119	-0.035
77	A	74	VAL	0	-0.062	-0.033	4.888	4.356	4.394	-0.001	-0.004	-0.032	0.000
78	A	75	PHE	0	0.022	0.001	7.295	1.160	1.160	0.000	0.000	0.000	0.000
79	A	76	PRO	0	0.015	0.008	10.788	0.109	0.109	0.000	0.000	0.000	0.000
80	A	77	ASP	-1	-0.842	-0.912	12.497	-16.216	-16.216	0.000	0.000	0.000	0.000
81	A	78	THR	0	-0.010	-0.017	15.414	0.720	0.720	0.000	0.000	0.000	0.000
82	A	79	SER	0	-0.015	-0.007	18.355	1.205	1.205	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.928	-0.958	21.019	-12.212	-12.212	0.000	0.000	0.000	0.000
84	A	81	ILE	0	0.021	-0.009	20.407	0.713	0.713	0.000	0.000	0.000	0.000
85	A	82	LEU	0	0.000	0.007	21.031	0.707	0.707	0.000	0.000	0.000	0.000
86	A	83	ARG	1	0.962	0.980	23.851	12.795	12.795	0.000	0.000	0.000	0.000
87	A	84	ARG	1	0.834	0.930	25.735	11.937	11.937	0.000	0.000	0.000	0.000
88	A	85	LYS	1	0.945	0.950	28.556	9.108	9.108	0.000	0.000	0.000	0.000
89	A	86	ASP	-1	-0.937	-0.960	30.412	-9.945	-9.945	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.035	0.001	24.748	-0.078	-0.078	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.006	-0.003	27.499	0.225	0.225	0.000	0.000	0.000	0.000
92	A	89	LEU	0	0.030	-0.003	26.624	-0.373	-0.373	0.000	0.000	0.000	0.000
93	A	90	LYS	1	0.919	0.962	24.891	11.746	11.746	0.000	0.000	0.000	0.000
94	A	91	GLU	-1	-0.853	-0.933	23.250	-12.588	-12.588	0.000	0.000	0.000	0.000
95	A	92	VAL	0	0.049	0.029	21.462	-0.711	-0.711	0.000	0.000	0.000	0.000
96	A	93	LEU	0	0.005	-0.004	20.672	-0.721	-0.721	0.000	0.000	0.000	0.000
97	A	94	ASP	-1	-0.852	-0.912	19.970	-14.276	-14.276	0.000	0.000	0.000	0.000
98	A	95	ILE	0	0.010	0.004	15.915	-0.906	-0.906	0.000	0.000	0.000	0.000
99	A	96	ALA	0	0.020	0.013	15.858	-1.156	-1.156	0.000	0.000	0.000	0.000
100	A	97	ILE	0	-0.042	-0.029	16.555	-0.699	-0.699	0.000	0.000	0.000	0.000
101	A	98	SER	0	-0.034	-0.023	12.688	-0.510	-0.510	0.000	0.000	0.000	0.000
102	A	99	VAL	0	0.082	0.047	11.457	-1.325	-1.325	0.000	0.000	0.000	0.000
103	A	100	GLH	0	-0.046	-0.038	11.794	-1.663	-1.663	0.000	0.000	0.000	0.000
104	A	101	LYS	1	0.893	0.929	13.380	17.842	17.842	0.000	0.000	0.000	0.000
105	A	102	ASP	-1	-0.840	-0.910	8.046	-31.351	-31.351	0.000	0.000	0.000	0.000
106	A	103	SER	0	0.004	-0.025	8.823	-3.084	-3.084	0.000	0.000	0.000	0.000
107	A	104	ILE	0	-0.076	-0.035	10.586	0.351	0.351	0.000	0.000	0.000	0.000
108	A	105	ILE	0	-0.034	-0.001	7.950	1.346	1.346	0.000	0.000	0.000	0.000
109	A	106	LEU	0	0.049	0.036	6.198	0.063	0.063	0.000	0.000	0.000	0.000
110	A	107	TYR	0	0.002	-0.012	8.550	1.212	1.212	0.000	0.000	0.000	0.000
111	A	108	TYR	0	-0.045	-0.042	11.942	2.582	2.582	0.000	0.000	0.000	0.000
112	A	109	GLU	-1	-0.829	-0.906	6.018	-44.873	-44.873	0.000	0.000	0.000	0.000
113	A	110	LEU	0	0.019	0.012	9.960	1.102	1.102	0.000	0.000	0.000	0.000
114	A	111	LYS	1	0.876	0.934	11.639	18.848	18.848	0.000	0.000	0.000	0.000
115	A	112	ASP	-1	-0.945	-0.979	12.722	-19.082	-19.082	0.000	0.000	0.000	0.000
116	A	113	GLY	0	-0.020	-0.007	12.572	0.415	0.415	0.000	0.000	0.000	0.000
117	A	114	LEU	0	-0.091	-0.030	13.479	0.760	0.760	0.000	0.000	0.000	0.000
118	A	115	VAL	0	-0.020	-0.022	16.603	0.337	0.337	0.000	0.000	0.000	0.000
119	A	116	ASN	0	-0.018	0.002	19.570	1.228	1.228	0.000	0.000	0.000	0.000
120	A	117	SER	0	0.026	-0.008	21.566	-0.419	-0.419	0.000	0.000	0.000	0.000
121	A	118	ASP	-1	-0.868	-0.949	23.988	-11.389	-11.389	0.000	0.000	0.000	0.000
122	A	119	ALA	0	0.025	0.029	19.681	-0.051	-0.051	0.000	0.000	0.000	0.000
123	A	120	GLN	0	0.005	-0.004	18.043	0.405	0.405	0.000	0.000	0.000	0.000
124	A	121	LYS	1	0.815	0.914	20.170	11.643	11.643	0.000	0.000	0.000	0.000
125	A	122	THR	0	-0.057	-0.033	21.355	0.256	0.256	0.000	0.000	0.000	0.000
126	A	123	VAL	0	0.057	0.020	15.436	0.061	0.061	0.000	0.000	0.000	0.000
127	A	124	LYS	1	0.913	0.957	18.459	13.082	13.082	0.000	0.000	0.000	0.000
128	A	125	LYS	1	0.944	0.983	20.211	12.040	12.040	0.000	0.000	0.000	0.000
129	A	126	ILE	0	0.021	0.018	17.532	0.322	0.322	0.000	0.000	0.000	0.000
130	A	127	ILE	0	0.015	0.015	15.303	0.051	0.051	0.000	0.000	0.000	0.000
131	A	128	ASP	-1	-0.934	-0.978	18.311	-13.772	-13.772	0.000	0.000	0.000	0.000
132	A	129	GLN	0	-0.046	-0.038	21.832	0.976	0.976	0.000	0.000	0.000	0.000
133	A	130	GLU	-1	-0.738	-0.778	16.554	-17.534	-17.534	0.000	0.000	0.000	0.000
134	A	131	LYS	1	0.897	0.948	18.756	14.863	14.863	0.000	0.000	0.000	0.000
135	A	132	GLU	-1	-0.889	-0.948	20.369	-11.621	-11.621	0.000	0.000	0.000	0.000
136	A	133	HIS	0	-0.003	0.036	19.694	1.069	1.069	0.000	0.000	0.000	0.000
137	A	134	LEU	0	0.004	0.004	17.594	0.336	0.336	0.000	0.000	0.000	0.000
138	A	135	ARG	1	0.878	0.947	20.570	11.653	11.653	0.000	0.000	0.000	0.000
139	A	136	LYS	1	0.870	0.940	24.036	11.126	11.126	0.000	0.000	0.000	0.000
140	A	137	LEU	0	0.026	0.001	19.448	0.448	0.448	0.000	0.000	0.000	0.000
141	A	138	LEU	0	-0.022	-0.017	21.173	0.268	0.268	0.000	0.000	0.000	0.000
142	A	139	GLU	-1	-0.871	-0.922	24.443	-10.029	-10.029	0.000	0.000	0.000	0.000
143	A	140	MET	0	0.027	0.017	26.354	0.298	0.298	0.000	0.000	0.000	0.000
144	A	141	LYS	1	0.828	0.911	23.350	13.168	13.168	0.000	0.000	0.000	0.000
145	A	142	ARG	1	0.864	0.928	26.842	10.239	10.239	0.000	0.000	0.000	0.000
146	A	143	GLU	-1	-0.940	-0.966	29.385	-9.376	-9.376	0.000	0.000	0.000	0.000
147	A	144	SER	0	-0.015	-0.008	30.916	0.217	0.217	0.000	0.000	0.000	0.000
148	A	145	THR	0	-0.059	-0.014	27.121	-0.236	-0.236	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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