FMO DATABASE

FMODB ID: 6YR3Z

Calculation Name: 1JX7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JX7

Chain ID: A

ChEMBL ID:

UniProt ID: P0AB52

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	OptHSide
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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-926129.938091
FMO2-HF: Nuclear repulsion	881313.508153
FMO2-HF: Total energy	-44816.429939
FMO2-MP2: Total energy	-44945.919467

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:MET)

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

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.
-6.878	-1.061	3.13	-3.157	-5.789	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.002

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	LYS	1	0.861	0.934	2.428	-1.200	2.692	1.650	-2.389	-3.153	-0.004
4	A	4	ILE	0	-0.011	-0.005	4.176	0.243	0.375	0.001	-0.033	-0.100	0.000
5	A	5	VAL	0	-0.004	0.001	7.589	0.267	0.267	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.003	0.003	10.184	-0.009	-0.009	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.004	0.001	13.498	0.069	0.069	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.007	-0.016	16.669	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	9	ASN	0	0.033	0.012	20.044	0.000	0.000	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.005	0.002	23.599	0.018	0.018	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.074	0.045	25.266	0.004	0.004	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.045	0.021	26.017	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.046	-0.037	27.601	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.029	0.008	30.189	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.075	-0.048	27.550	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.755	-0.884	27.362	-0.141	-0.141	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.005	-0.001	23.963	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.016	0.029	21.136	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.035	0.012	21.754	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.042	-0.040	22.301	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.026	-0.017	18.116	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.020	0.005	17.342	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.910	0.957	18.132	0.179	0.179	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.014	-0.008	15.100	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.005	-0.003	13.867	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.004	-0.005	13.489	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.027	0.024	15.123	0.025	0.025	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.035	-0.026	10.553	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.822	0.910	7.291	-0.518	-0.518	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.967	-0.981	11.288	0.016	0.016	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.088	-0.023	11.626	0.084	0.084	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.936	-0.972	5.512	-1.667	-1.667	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.045	0.027	8.280	0.026	0.026	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.025	-0.031	4.663	0.159	0.306	-0.001	-0.006	-0.140	0.000
35	A	35	LEU	0	-0.040	-0.005	4.328	0.067	0.398	-0.001	-0.029	-0.301	0.000
36	A	36	ASP	-1	-0.813	-0.899	2.351	-1.570	-0.382	1.483	-0.673	-1.997	-0.003
37	A	37	LEU	0	0.000	0.007	4.297	-0.872	-0.819	-0.001	-0.027	-0.025	0.000
38	A	38	ARG	1	0.846	0.920	4.690	0.487	0.561	-0.001	0.000	-0.073	0.000
39	A	39	LEU	0	0.016	0.004	9.647	-0.113	-0.113	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.006	-0.005	13.377	0.059	0.059	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.021	-0.004	15.876	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.001	-0.012	19.566	0.021	0.021	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.030	-0.046	22.195	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.744	-0.872	25.979	-0.101	-0.101	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.012	0.015	22.395	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.009	-0.018	22.967	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.011	-0.009	24.546	0.015	0.015	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.013	-0.001	23.216	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.023	0.012	23.494	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.017	0.004	24.250	0.016	0.016	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.880	0.936	25.868	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.002	-0.004	28.767	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.030	-0.002	25.940	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.940	0.962	30.998	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.022	0.002	31.244	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.016	-0.019	34.421	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.941	-0.967	34.661	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.026	0.015	32.701	0.004	0.004	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.008	0.005	27.145	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.051	0.000	27.578	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.018	-0.003	23.379	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.002	-0.002	23.394	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.030	0.018	23.448	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	MET	0	-0.035	-0.013	20.944	0.004	0.004	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.032	0.015	18.698	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.838	-0.890	18.704	0.075	0.075	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.000	0.001	17.647	0.034	0.034	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.001	0.001	13.865	0.026	0.026	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.022	-0.027	14.504	0.055	0.055	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.013	0.011	16.185	0.058	0.058	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.056	-0.032	12.538	0.078	0.078	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.046	-0.030	11.600	0.089	0.089	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.012	0.018	10.258	0.076	0.076	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.021	-0.018	9.340	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.035	0.012	12.332	-0.101	-0.101	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.799	0.897	14.520	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.022	-0.012	16.941	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.034	-0.015	20.546	0.011	0.011	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.905	0.926	21.788	0.037	0.037	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.010	0.003	24.100	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	CYS	0	-0.058	-0.011	25.007	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.065	0.014	24.559	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.814	-0.861	27.314	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.019	0.004	29.906	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.799	0.868	28.836	0.095	0.095	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.008	0.023	32.119	0.004	0.004	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.007	-0.020	27.203	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.047	-0.055	27.256	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.005	-0.005	27.895	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.022	0.018	29.918	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.008	-0.008	28.569	0.004	0.004	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.007	0.003	23.834	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.039	-0.024	22.144	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.810	-0.922	21.867	0.116	0.116	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.003	0.012	17.903	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.084	-0.024	17.656	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.819	-0.893	17.339	0.140	0.140	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.012	0.003	19.500	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.036	0.035	17.847	0.014	0.014	0.000	0.000	0.000	0.000
100	A	100	THR	0	0.002	-0.025	18.068	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.053	0.026	18.128	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.001	-0.007	17.982	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.834	-0.917	13.652	-0.091	-0.091	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.033	0.019	13.842	-0.058	-0.058	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.035	-0.012	14.458	-0.088	-0.088	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.017	-0.008	11.722	0.050	0.050	0.000	0.000	0.000	0.000
107	A	107	TRP	0	-0.032	-0.012	9.720	-0.138	-0.138	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.028	-0.031	9.956	-0.166	-0.166	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.017	-0.005	12.147	-0.080	-0.080	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.070	-0.022	7.788	-0.065	-0.065	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.030	0.020	6.936	-0.276	-0.276	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.840	-0.896	5.876	-4.195	-4.195	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.863	0.915	8.631	2.226	2.226	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.022	0.003	10.046	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.025	0.011	12.515	0.063	0.063	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.001	-0.010	15.121	0.031	0.031	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.015	0.019	16.846	0.048	0.048	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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