FMO DATABASE

FMODB ID: 6NLNZ

Calculation Name: 3L8R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L8R

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DT03

Base Structure: X-ray

Registration Date: 2023-06-21

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-754762.640174
FMO2-HF: Nuclear repulsion	712809.978264
FMO2-HF: Total energy	-41952.66191
FMO2-MP2: Total energy	-42072.317031

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.
-26.579	-40.16	39.668	-5.894	-20.191	-0.067

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 : -0.014 / q_NPA : -0.001

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

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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	THR	0	0.041	0.009	2.734	1.659	-2.970	0.434	6.457	-2.261	0.010
4	A	4	GLU	-1	-0.878	-0.948	5.448	1.960	1.960	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.831	-0.911	1.667	-16.143	-22.755	18.786	-7.277	-4.897	-0.067
6	A	6	LEU	0	0.011	0.006	2.026	-0.287	-2.032	6.391	-1.051	-3.594	0.003
7	A	7	GLN	0	-0.036	-0.023	4.897	-0.418	-0.377	-0.001	-0.012	-0.028	0.000
8	A	8	VAL	0	-0.021	-0.002	7.755	-0.239	-0.239	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.069	0.036	5.929	-0.288	-0.288	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.006	0.003	7.971	-0.329	-0.329	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.043	-0.032	10.057	-0.276	-0.276	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.943	-0.962	10.292	0.481	0.481	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.026	-0.006	9.183	-0.162	-0.162	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.005	-0.002	13.126	-0.137	-0.137	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.047	-0.020	15.801	-0.087	-0.087	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.001	0.004	14.992	-0.108	-0.108	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.026	0.006	16.942	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.022	-0.006	18.722	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.014	0.004	20.964	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.054	0.036	21.351	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.869	0.912	22.693	-0.281	-0.281	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.091	-0.043	24.530	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.079	0.038	24.967	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.009	-0.012	25.919	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.066	-0.040	28.136	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.860	-0.914	30.652	0.117	0.117	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.013	-0.002	31.500	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.016	-0.022	30.433	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.911	-0.959	34.644	0.111	0.111	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.031	-0.021	36.224	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	MET	0	-0.062	-0.027	35.876	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.844	0.937	36.985	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.968	-0.973	40.830	0.059	0.059	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.907	0.953	42.476	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.003	0.000	40.607	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.030	-0.016	39.266	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.002	0.017	38.259	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.022	0.026	35.854	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.030	0.013	34.648	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.931	-0.967	33.244	0.051	0.051	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.005	-0.009	32.359	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.881	0.941	30.704	-0.104	-0.104	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.008	-0.013	28.883	0.013	0.013	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.033	-0.009	27.590	0.007	0.007	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.821	-0.908	26.247	0.108	0.108	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.016	0.002	24.793	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.021	-0.020	22.932	0.041	0.041	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.906	-0.942	21.582	0.087	0.087	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.906	-0.966	20.450	0.183	0.183	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.031	-0.032	18.522	0.044	0.044	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.030	-0.006	17.275	0.047	0.047	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.898	0.959	15.281	-0.172	-0.172	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.004	0.010	13.492	0.059	0.059	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.018	-0.037	12.662	0.140	0.140	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.056	-0.001	10.900	0.067	0.067	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.085	0.048	8.886	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.015	-0.015	7.903	0.467	0.467	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.067	-0.050	8.888	0.129	0.129	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.871	-0.930	5.578	-0.307	-0.307	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.009	-0.002	3.320	-0.789	-0.306	1.070	-0.278	-1.274	0.001
61	A	61	LEU	0	-0.031	-0.015	5.328	-0.318	-0.259	-0.001	-0.004	-0.054	0.000
62	A	62	GLN	0	-0.024	-0.013	7.652	-0.186	-0.186	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.841	-0.907	1.891	-9.216	-9.550	5.116	-1.704	-3.078	-0.016
64	A	64	TYR	0	-0.028	-0.008	4.982	-0.627	-0.527	-0.001	-0.007	-0.091	0.000
65	A	65	ALA	0	-0.079	-0.049	6.692	-0.261	-0.261	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.128	-0.052	6.352	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.017	-0.011	8.479	-0.084	-0.084	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.058	-0.042	2.517	-0.267	0.709	0.696	-0.389	-1.284	-0.002
69	A	69	GLU	-1	-0.927	-0.967	5.037	-0.129	-0.129	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.054	0.012	1.831	-1.852	-3.961	7.177	-1.592	-3.476	0.004
71	A	71	LYS	1	0.799	0.916	4.074	0.548	0.737	0.001	-0.037	-0.154	0.000
72	A	72	ILE	0	0.019	0.017	6.585	0.252	0.252	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.855	-0.928	8.171	0.586	0.586	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.005	-0.016	10.493	0.061	0.061	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.016	0.009	10.266	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	76	MET	0	0.039	0.022	6.045	-0.052	-0.052	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.006	0.003	10.421	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.014	0.007	13.380	-0.059	-0.059	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.021	-0.006	11.957	-0.067	-0.067	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.003	-0.001	10.850	0.028	0.028	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.896	-0.936	13.891	0.336	0.336	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.035	-0.023	16.950	-0.072	-0.072	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.011	0.007	13.469	-0.065	-0.065	0.000	0.000	0.000	0.000
84	A	84	MET	0	0.011	0.013	16.084	-0.065	-0.065	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.027	-0.009	18.657	-0.060	-0.060	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.006	0.021	20.297	-0.049	-0.049	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.025	0.011	20.007	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.009	-0.014	21.959	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.072	-0.041	24.552	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.981	0.992	22.914	-0.146	-0.146	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.918	-0.967	24.280	0.115	0.115	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.048	-0.013	27.836	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.018	-0.017	30.025	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.034	0.022	28.053	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.892	-0.950	32.013	0.053	0.053	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.088	-0.038	33.962	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.056	0.024	34.261	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.939	-0.969	36.494	0.039	0.039	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.056	-0.052	38.490	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.046	-0.020	38.896	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.862	0.957	38.478	-0.048	-0.048	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.920	0.975	41.750	-0.037	-0.037	0.000	0.000	0.000	0.000

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