FMO DATABASE

FMODB ID: Z6R6N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-755358.499133
FMO2-HF: Nuclear repulsion	713404.57591
FMO2-HF: Total energy	-41953.923223
FMO2-MP2: Total energy	-42073.490935

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.
-21.808	-20.791	16.661	0.168	-17.845	-0.051

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 : -0.022 / q_NPA : 0.005

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	0.040	-0.014	2.768	3.949	-1.647	0.425	6.954	-1.783	-0.007
4	A	4	GLU	-1	-0.886	-0.934	5.489	2.219	2.219	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.836	-0.911	2.189	-10.135	-6.558	3.854	-3.434	-3.997	-0.041
6	A	6	LEU	0	0.011	0.006	2.544	-1.795	-1.366	3.878	-0.866	-3.442	0.005
7	A	7	GLN	0	-0.039	-0.022	5.091	-1.052	-1.024	0.000	-0.024	-0.004	0.000
8	A	8	VAL	0	-0.009	-0.004	7.752	-0.383	-0.383	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.067	0.035	5.640	-0.404	-0.404	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.012	0.006	7.631	-0.456	-0.456	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.046	-0.033	9.786	-0.381	-0.381	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.939	-0.958	9.454	0.305	0.305	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.016	0.001	8.780	-0.195	-0.195	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.004	0.003	12.735	-0.155	-0.155	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.054	-0.024	15.473	-0.103	-0.103	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.014	-0.009	14.069	-0.128	-0.128	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.029	0.004	16.567	-0.038	-0.038	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.028	-0.018	18.204	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.014	-0.005	20.441	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.049	0.029	20.509	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.859	0.906	21.997	-0.304	-0.304	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.051	-0.025	24.068	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.014	0.015	24.079	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.003	-0.004	25.204	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.042	-0.027	27.826	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.796	-0.882	29.881	0.112	0.112	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.001	0.005	30.750	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.011	-0.018	30.048	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.908	-0.932	34.059	0.111	0.111	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.046	-0.027	35.475	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	MET	0	-0.049	-0.026	34.847	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.835	0.911	36.149	-0.110	-0.110	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.960	-0.962	40.151	0.059	0.059	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.873	0.925	41.740	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.003	0.005	39.771	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.007	-0.026	38.299	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.007	0.011	37.189	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.048	0.038	34.679	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.026	0.017	33.680	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.867	-0.930	32.246	0.034	0.034	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.002	-0.007	31.262	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.802	0.872	29.627	-0.104	-0.104	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.015	-0.017	27.845	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.075	-0.028	26.452	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.821	-0.891	25.168	0.093	0.093	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.001	0.005	23.663	0.012	0.012	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.008	-0.005	21.890	0.028	0.028	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.871	-0.927	20.495	0.042	0.042	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.830	-0.906	19.342	0.175	0.175	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.011	-0.021	17.516	0.035	0.035	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.044	-0.011	16.219	0.034	0.034	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.837	0.912	14.241	-0.183	-0.183	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.002	0.005	12.356	0.033	0.033	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.043	-0.019	11.758	0.107	0.107	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.078	-0.017	9.703	0.081	0.081	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.081	0.048	7.784	-0.112	-0.112	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.015	-0.015	6.876	0.306	0.306	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.062	-0.051	8.223	0.051	0.051	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.857	-0.914	5.064	-0.871	-0.871	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.007	0.000	2.929	-0.959	-0.573	1.412	-0.309	-1.489	0.001
61	A	61	LEU	0	-0.020	-0.011	4.786	-0.493	-0.442	-0.001	-0.003	-0.046	0.000
62	A	62	GLN	0	-0.033	-0.010	7.380	-0.108	-0.108	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.846	-0.925	2.346	-8.796	-7.921	2.125	-0.881	-2.118	-0.008
64	A	64	TYR	0	-0.035	-0.006	4.609	-0.210	-0.097	-0.001	-0.007	-0.105	0.000
65	A	65	ALA	0	-0.075	-0.042	6.281	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.123	-0.058	6.505	0.060	0.060	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.021	-0.014	8.513	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.061	-0.032	2.569	-0.212	0.550	0.975	-0.392	-1.345	-0.003
69	A	69	GLU	-1	-0.874	-0.930	4.923	-0.452	-0.200	-0.001	-0.015	-0.237	0.000
70	A	70	ILE	0	0.034	0.006	2.164	-2.354	-2.379	3.994	-0.840	-3.129	0.002
71	A	71	LYS	1	0.767	0.884	4.047	0.602	0.767	0.001	-0.015	-0.150	0.000
72	A	72	ILE	0	0.029	0.020	6.623	0.412	0.412	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.849	-0.926	8.379	0.737	0.737	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.012	-0.026	10.759	0.060	0.060	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.022	0.016	10.869	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	76	MET	0	0.034	0.024	5.948	-0.204	-0.204	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.006	0.009	10.761	-0.107	-0.107	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.016	0.001	13.634	-0.104	-0.104	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.027	-0.004	11.707	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.021	-0.019	10.760	0.018	0.018	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.872	-0.925	13.709	0.330	0.330	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.034	0.007	16.687	-0.093	-0.093	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.020	0.016	13.048	-0.075	-0.075	0.000	0.000	0.000	0.000
84	A	84	MET	0	0.032	0.032	16.056	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.038	-0.028	18.526	-0.060	-0.060	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.007	0.000	19.922	-0.046	-0.046	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.054	-0.009	19.360	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.009	-0.009	21.427	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.074	-0.041	24.219	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.860	0.912	22.433	-0.099	-0.099	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.827	-0.904	23.429	0.079	0.079	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.057	-0.021	27.197	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.049	0.014	29.568	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.007	0.006	27.080	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.898	-0.954	31.188	0.032	0.032	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.081	-0.041	33.488	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.017	0.014	33.539	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.832	-0.900	35.670	0.021	0.021	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.037	-0.039	37.642	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.023	-0.009	38.421	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.788	0.909	36.813	-0.034	-0.034	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.830	0.919	40.212	-0.024	-0.024	0.000	0.000	0.000	0.000

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