FMO DATABASE

FMODB ID: LZVY9

Calculation Name: 5LFJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LFJ

Chain ID: A

ChEMBL ID:

UniProt ID: P9WKX3

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:

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-803633.915867
FMO2-HF: Nuclear repulsion	760804.986519
FMO2-HF: Total energy	-42828.929349
FMO2-MP2: Total energy	-42954.351373

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:37:LEU)

Summations of interaction energy for fragment #1(A:37:LEU)

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.
-10.164	-5.53	1.288	-1.698	-4.224	-0.001

Interaction energy analysis for fragmet #1(A:37:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / 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	39	ASP	-1	-0.954	-0.980	2.429	-3.555	-0.767	0.637	-1.205	-2.221	0.002
4	A	40	LEU	0	0.038	0.043	2.407	-1.662	-0.158	0.652	-0.436	-1.720	-0.003
5	A	41	VAL	0	-0.026	-0.015	4.787	0.520	0.630	-0.001	-0.008	-0.100	0.000
6	A	42	GLU	-1	-0.861	-0.921	8.170	-0.494	-0.494	0.000	0.000	0.000	0.000
7	A	43	GLN	0	-0.054	-0.027	9.872	0.257	0.257	0.000	0.000	0.000	0.000
8	A	44	PRO	0	0.039	0.003	10.243	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	45	ALA	0	-0.007	-0.006	12.938	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	46	LYS	1	0.852	0.945	16.342	0.215	0.215	0.000	0.000	0.000	0.000
11	A	47	VAL	0	0.092	0.044	12.630	0.015	0.015	0.000	0.000	0.000	0.000
12	A	48	MET	0	0.027	0.021	15.479	0.012	0.012	0.000	0.000	0.000	0.000
13	A	49	ARG	1	0.918	0.979	17.403	0.065	0.065	0.000	0.000	0.000	0.000
14	A	50	ILE	0	-0.004	0.004	18.933	0.011	0.011	0.000	0.000	0.000	0.000
15	A	51	GLY	0	0.066	0.031	19.016	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	52	THR	0	-0.063	-0.051	19.866	0.016	0.016	0.000	0.000	0.000	0.000
17	A	53	MET	0	-0.031	-0.006	22.809	0.013	0.013	0.000	0.000	0.000	0.000
18	A	54	ILE	0	0.026	0.013	20.921	0.009	0.009	0.000	0.000	0.000	0.000
19	A	55	LYS	1	0.916	0.958	22.808	0.095	0.095	0.000	0.000	0.000	0.000
20	A	56	GLN	0	0.010	0.004	24.971	0.010	0.010	0.000	0.000	0.000	0.000
21	A	57	LEU	0	0.007	0.000	27.395	0.005	0.005	0.000	0.000	0.000	0.000
22	A	58	LEU	0	-0.023	-0.002	26.013	0.005	0.005	0.000	0.000	0.000	0.000
23	A	59	GLU	-1	-1.019	-1.022	28.776	-0.057	-0.057	0.000	0.000	0.000	0.000
24	A	60	GLU	-1	-0.898	-0.951	31.118	-0.051	-0.051	0.000	0.000	0.000	0.000
25	A	61	VAL	0	-0.043	-0.010	31.813	0.003	0.003	0.000	0.000	0.000	0.000
26	A	62	ARG	1	0.839	0.903	28.100	0.099	0.099	0.000	0.000	0.000	0.000
27	A	63	ALA	0	-0.006	0.026	34.542	0.005	0.005	0.000	0.000	0.000	0.000
28	A	64	ALA	0	-0.038	-0.027	37.024	0.006	0.006	0.000	0.000	0.000	0.000
29	A	65	PRO	0	-0.038	-0.016	38.428	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	66	LEU	0	0.012	0.028	35.356	0.002	0.002	0.000	0.000	0.000	0.000
31	A	67	ASP	-1	-0.892	-0.922	39.877	-0.065	-0.065	0.000	0.000	0.000	0.000
32	A	68	GLU	-1	-0.910	-0.975	40.022	-0.079	-0.079	0.000	0.000	0.000	0.000
33	A	69	ALA	0	-0.008	0.002	39.348	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	70	SER	0	-0.035	-0.057	37.456	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	71	ARG	1	0.920	0.977	35.471	0.080	0.080	0.000	0.000	0.000	0.000
36	A	72	ASN	0	0.036	0.008	34.546	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	73	ARG	1	0.948	0.985	34.090	0.069	0.069	0.000	0.000	0.000	0.000
38	A	74	LEU	0	-0.013	-0.004	29.554	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	75	ARG	1	0.922	0.970	29.913	0.111	0.111	0.000	0.000	0.000	0.000
40	A	76	ASP	-1	-0.908	-0.950	29.400	-0.133	-0.133	0.000	0.000	0.000	0.000
41	A	77	ILE	0	-0.072	-0.045	27.212	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	78	HIS	0	0.037	0.020	24.005	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	79	ALA	0	0.036	0.021	24.405	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	80	THR	0	-0.064	-0.046	24.138	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	81	SER	0	-0.032	-0.014	22.519	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	82	ILE	0	0.082	0.031	19.542	-0.021	-0.021	0.000	0.000	0.000	0.000
47	A	83	ARG	1	0.962	0.993	19.135	0.169	0.169	0.000	0.000	0.000	0.000
48	A	84	GLU	-1	-0.957	-0.987	19.313	-0.204	-0.204	0.000	0.000	0.000	0.000
49	A	85	LEU	0	-0.044	-0.034	15.816	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	86	GLU	-1	-0.919	-0.960	14.831	-0.478	-0.478	0.000	0.000	0.000	0.000
51	A	87	ASP	-1	-0.957	-0.990	14.557	-0.332	-0.332	0.000	0.000	0.000	0.000
52	A	88	GLY	0	-0.055	-0.019	13.883	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	89	LEU	0	-0.045	-0.029	10.177	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	90	ALA	0	0.074	0.040	6.686	0.084	0.084	0.000	0.000	0.000	0.000
55	A	91	PRO	0	0.008	-0.021	8.497	0.075	0.075	0.000	0.000	0.000	0.000
56	A	92	GLU	-1	-0.866	-0.937	4.093	-3.686	-3.454	0.000	-0.049	-0.183	0.000
57	A	93	LEU	0	-0.007	-0.004	7.101	0.141	0.141	0.000	0.000	0.000	0.000
58	A	94	ARG	1	0.863	0.957	9.910	0.831	0.831	0.000	0.000	0.000	0.000
59	A	95	GLU	-1	-0.913	-0.957	12.297	-0.689	-0.689	0.000	0.000	0.000	0.000
60	A	96	GLU	-1	-0.976	-1.000	10.318	-0.985	-0.985	0.000	0.000	0.000	0.000
61	A	97	LEU	0	-0.024	-0.017	13.319	0.097	0.097	0.000	0.000	0.000	0.000
62	A	98	ASP	-1	-0.913	-0.963	15.570	-0.343	-0.343	0.000	0.000	0.000	0.000
63	A	99	ARG	1	0.903	0.959	12.026	0.775	0.775	0.000	0.000	0.000	0.000
64	A	100	LEU	0	-0.091	-0.031	15.371	0.050	0.050	0.000	0.000	0.000	0.000
65	A	101	THR	0	-0.080	-0.013	19.083	0.052	0.052	0.000	0.000	0.000	0.000
66	A	102	LEU	0	0.042	0.028	21.579	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	103	PRO	0	-0.029	-0.020	24.429	0.013	0.013	0.000	0.000	0.000	0.000
68	A	104	PHE	0	0.005	-0.007	26.603	0.009	0.009	0.000	0.000	0.000	0.000
69	A	105	ASN	0	0.027	0.006	30.079	0.001	0.001	0.000	0.000	0.000	0.000
70	A	106	GLU	-1	-0.950	-0.984	33.226	-0.126	-0.126	0.000	0.000	0.000	0.000
71	A	107	ASP	-1	-0.921	-0.946	34.961	-0.109	-0.109	0.000	0.000	0.000	0.000
72	A	108	ALA	0	-0.075	-0.038	37.048	0.008	0.008	0.000	0.000	0.000	0.000
73	A	109	VAL	0	-0.005	0.008	36.790	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	110	PRO	0	0.019	0.022	32.959	0.003	0.003	0.000	0.000	0.000	0.000
75	A	111	SER	0	0.013	-0.005	35.649	0.007	0.007	0.000	0.000	0.000	0.000
76	A	112	ASP	-1	-0.731	-0.904	34.770	-0.093	-0.093	0.000	0.000	0.000	0.000
77	A	113	ALA	0	-0.090	-0.048	33.690	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	114	GLU	-1	-0.874	-0.943	31.447	-0.146	-0.146	0.000	0.000	0.000	0.000
79	A	115	LEU	0	0.038	0.020	30.050	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	116	ARG	1	0.932	0.971	28.840	0.097	0.097	0.000	0.000	0.000	0.000
81	A	117	ILE	0	-0.031	-0.012	27.331	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	118	ALA	0	0.051	0.037	25.567	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	119	GLN	0	0.025	-0.005	23.994	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	120	ALA	0	-0.031	-0.015	23.543	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	121	GLN	0	-0.051	-0.032	20.620	0.003	0.003	0.000	0.000	0.000	0.000
86	A	122	LEU	0	0.027	0.012	18.747	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	123	VAL	0	-0.010	-0.009	18.686	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	124	GLY	0	0.015	0.009	18.954	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	125	TRP	0	-0.010	-0.004	11.907	0.027	0.027	0.000	0.000	0.000	0.000
90	A	126	LEU	0	-0.003	-0.005	14.450	-0.063	-0.063	0.000	0.000	0.000	0.000
91	A	127	GLU	-1	-0.913	-0.960	14.416	-0.148	-0.148	0.000	0.000	0.000	0.000
92	A	128	GLY	0	-0.012	-0.003	14.209	0.030	0.030	0.000	0.000	0.000	0.000
93	A	129	LEU	0	0.016	0.019	8.427	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	130	PHE	0	-0.036	-0.037	9.987	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	131	HIS	0	0.042	0.015	12.066	0.139	0.139	0.000	0.000	0.000	0.000
96	A	132	GLY	0	0.031	0.022	8.948	0.096	0.096	0.000	0.000	0.000	0.000
97	A	133	ILE	0	-0.011	-0.009	6.708	0.198	0.198	0.000	0.000	0.000	0.000
98	A	134	GLN	0	-0.003	0.008	7.979	0.408	0.408	0.000	0.000	0.000	0.000
99	A	135	THR	0	-0.019	-0.014	10.229	0.158	0.158	0.000	0.000	0.000	0.000
100	A	136	ALA	0	-0.012	0.001	5.133	0.141	0.141	0.000	0.000	0.000	0.000
101	A	137	LEU	0	0.036	0.014	7.236	0.306	0.306	0.000	0.000	0.000	0.000
102	A	138	PHE	0	-0.038	-0.019	8.978	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	139	ALA	0	0.033	0.013	8.780	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	140	GLN	0	0.008	0.001	5.681	-0.725	-0.725	0.000	0.000	0.000	0.000
105	A	141	GLN	0	-0.014	-0.008	10.145	-0.225	-0.225	0.000	0.000	0.000	0.000
106	A	142	MET	0	-0.052	-0.018	13.249	-0.131	-0.131	0.000	0.000	0.000	0.000
107	A	143	ALA	0	-0.025	-0.005	11.648	-0.069	-0.069	0.000	0.000	0.000	0.000
108	A	144	ALA	0	-0.046	-0.015	13.657	-0.064	-0.064	0.000	0.000	0.000	0.000
109	A	145	ARG	1	0.850	0.930	15.613	-0.546	-0.546	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:37:LEU)