FMO DATABASE

FMODB ID: R9N98

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	OptAll
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	-755874.174494
FMO2-HF: Nuclear repulsion	713919.653745
FMO2-HF: Total energy	-41954.520748
FMO2-MP2: Total energy	-42073.972037

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.
-26.173	-21.236	16.985	-5.652	-16.272	-0.059

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 : -0.012 / q_NPA : -0.003

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	THR	0	0.029	-0.021	3.122	0.425	-0.050	0.093	1.571	-1.190	-0.003
4	A	4	GLU	-1	-0.873	-0.914	5.892	1.903	1.903	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.819	-0.893	1.914	-13.026	-11.621	9.524	-5.190	-5.740	-0.056
6	A	6	LEU	0	0.023	0.012	3.060	-1.642	-0.917	2.914	-0.662	-2.977	0.004
7	A	7	GLN	0	-0.070	-0.039	4.867	-1.354	-1.318	0.004	-0.031	-0.009	0.000
8	A	8	VAL	0	-0.017	-0.010	7.540	-0.362	-0.362	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.068	0.034	4.777	-0.443	-0.370	-0.001	-0.009	-0.063	0.000
10	A	10	ALA	0	0.015	0.007	6.876	-0.361	-0.361	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.027	-0.030	9.595	-0.321	-0.321	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.939	-0.961	8.726	-0.069	-0.069	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.027	-0.007	8.449	-0.150	-0.150	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.015	-0.003	11.994	-0.112	-0.112	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.045	-0.016	14.712	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.019	-0.009	13.285	-0.084	-0.084	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.044	0.004	15.914	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.041	-0.029	17.670	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.025	-0.021	19.743	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.058	0.032	19.981	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.864	0.929	21.174	-0.205	-0.205	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.048	-0.032	23.577	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.018	0.021	23.684	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.010	-0.014	24.675	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.029	-0.019	27.427	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.822	-0.904	29.335	0.052	0.052	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.006	0.012	30.236	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.022	-0.004	29.551	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.850	-0.906	33.721	0.062	0.062	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.016	0.003	34.895	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	MET	0	-0.061	-0.023	34.549	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.798	0.881	34.900	-0.065	-0.065	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.944	-0.958	39.530	0.030	0.030	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.848	0.913	41.142	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.019	0.000	39.163	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.036	-0.022	37.593	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.001	0.015	36.443	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.039	0.027	34.302	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.016	0.007	33.288	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.868	-0.928	31.761	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.024	-0.014	30.758	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.799	0.880	29.026	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.000	-0.002	27.371	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.104	-0.047	26.028	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.818	-0.899	24.665	0.025	0.025	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.010	0.000	23.211	0.004	0.004	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.023	-0.005	21.607	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.844	-0.920	20.175	-0.047	-0.047	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.839	-0.894	18.886	0.052	0.052	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.011	-0.020	17.123	0.017	0.017	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.039	-0.008	15.871	0.011	0.011	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.821	0.908	13.732	-0.073	-0.073	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.028	0.017	11.820	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.041	-0.018	11.253	0.055	0.055	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.084	-0.017	9.562	0.076	0.076	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.076	0.041	7.263	-0.123	-0.123	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.006	-0.014	6.580	0.175	0.175	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.039	-0.035	8.483	0.024	0.024	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.846	-0.916	5.375	-1.116	-1.116	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.020	-0.011	2.878	-1.007	-0.437	0.913	-0.223	-1.260	0.000
61	A	61	LEU	0	-0.023	-0.019	4.964	-0.288	-0.244	-0.001	-0.002	-0.041	0.000
62	A	62	GLN	0	-0.054	-0.015	7.491	0.020	0.020	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.842	-0.909	2.382	-6.335	-5.609	0.593	-0.226	-1.094	-0.002
64	A	64	TYR	0	-0.023	0.009	5.153	0.091	0.182	-0.001	-0.004	-0.086	0.000
65	A	65	ALA	0	-0.063	-0.034	6.513	0.083	0.083	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.119	-0.064	7.301	0.097	0.097	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.017	-0.010	8.496	0.116	0.116	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.080	-0.052	2.586	-0.246	0.312	1.243	-0.407	-1.394	-0.003
69	A	69	GLU	-1	-0.835	-0.914	4.901	-0.410	-0.221	-0.001	-0.009	-0.179	0.000
70	A	70	ILE	0	0.030	0.020	2.309	-2.071	-1.252	1.707	-0.445	-2.081	0.001
71	A	71	LYS	1	0.758	0.859	4.511	0.304	0.410	-0.001	-0.010	-0.094	0.000
72	A	72	ILE	0	0.024	0.012	6.864	0.450	0.450	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.859	-0.928	8.763	0.666	0.666	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.001	-0.014	10.852	0.041	0.041	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.013	-0.001	10.755	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	76	MET	0	0.042	0.029	5.704	-0.320	-0.250	-0.001	-0.005	-0.064	0.000
77	A	77	VAL	0	-0.027	-0.003	10.558	-0.116	-0.116	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.032	0.014	13.531	-0.091	-0.091	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.013	-0.007	11.580	-0.083	-0.083	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.005	-0.013	10.640	0.033	0.033	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.862	-0.926	13.849	0.233	0.233	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.028	0.026	16.750	-0.081	-0.081	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.042	0.030	12.812	-0.055	-0.055	0.000	0.000	0.000	0.000
84	A	84	MET	0	0.025	0.026	16.002	-0.062	-0.062	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.050	-0.036	18.371	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.040	-0.030	19.546	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.051	-0.010	19.199	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.000	-0.012	21.243	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.054	-0.022	24.038	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.856	0.906	21.485	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.791	-0.888	23.741	0.015	0.015	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.016	-0.010	27.144	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.023	0.010	28.830	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.004	0.004	26.987	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.930	-0.962	30.956	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.052	-0.034	32.827	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.017	0.007	33.301	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.825	-0.895	35.237	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.013	-0.003	37.101	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.002	-0.012	38.032	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.787	0.897	36.368	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.739	0.873	39.979	0.002	0.002	0.000	0.000	0.000	0.000

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