FMO DATABASE

FMODB ID: 2JJ1R

Calculation Name: 5LCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LCY

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-523551.795419
FMO2-HF: Nuclear repulsion	488762.486665
FMO2-HF: Total energy	-34789.308754
FMO2-MP2: Total energy	-34889.468476

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-9.943	-0.488	8.29	-6.469	-11.276	-0.005

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : 0.042

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	4	SER	0	0.051	0.025	3.813	-0.890	1.233	-0.020	-1.046	-1.058	0.005
4	A	5	PRO	0	0.065	0.020	3.866	-0.374	-0.160	0.002	-0.073	-0.142	0.000
5	A	6	GLU	-1	-0.791	-0.887	5.960	0.167	0.167	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.808	-0.914	2.804	-0.032	0.518	0.202	-0.216	-0.536	0.000
7	A	8	LYS	1	0.802	0.884	2.298	0.247	3.554	2.069	-2.052	-3.324	0.000
8	A	9	LYS	1	0.798	0.887	3.214	0.461	0.232	0.047	0.400	-0.218	0.000
9	A	10	ARG	1	0.909	0.976	5.640	-0.650	-0.650	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.057	0.038	2.913	-0.940	-0.088	0.134	-0.174	-0.812	-0.001
11	A	12	LEU	0	0.003	0.004	5.422	-0.141	-0.141	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.041	-0.038	7.188	-0.094	-0.094	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.855	0.918	8.263	-0.607	-0.607	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.035	0.022	7.260	-0.055	-0.055	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.931	0.968	9.954	-0.161	-0.161	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.955	0.981	12.716	-0.202	-0.202	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.046	0.027	11.445	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.831	0.898	13.952	-0.128	-0.128	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.005	0.000	15.750	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.061	-0.032	17.068	0.005	0.005	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.045	0.017	17.353	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.801	-0.880	19.680	0.079	0.079	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.070	-0.033	21.815	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.008	-0.003	22.274	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.962	-0.984	23.689	0.075	0.075	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.980	0.989	23.801	-0.087	-0.087	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.007	-0.003	27.640	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.038	-0.025	26.820	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.933	-0.958	28.439	0.058	0.058	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.064	-0.034	31.721	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.038	0.000	33.593	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.947	-0.978	32.184	0.069	0.069	0.000	0.000	0.000	0.000
33	A	34	PRO	0	-0.026	-0.024	34.132	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	CYS	0	0.039	0.005	33.181	0.004	0.004	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.015	0.005	31.985	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.070	0.041	30.645	0.007	0.007	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.071	0.031	28.003	0.010	0.010	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.011	0.005	27.065	0.010	0.010	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.010	-0.008	26.706	0.010	0.010	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.004	-0.001	24.132	0.020	0.020	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.018	0.012	22.531	0.017	0.017	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.033	-0.015	22.043	0.020	0.020	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.011	-0.008	21.061	0.019	0.019	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.044	0.026	17.322	0.028	0.028	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.934	0.980	17.188	-0.193	-0.193	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.015	0.005	17.452	0.032	0.032	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.009	-0.010	14.614	0.037	0.037	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.012	-0.019	13.117	0.068	0.068	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.038	-0.025	12.723	0.043	0.043	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.026	0.015	13.430	0.051	0.051	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.017	-0.011	6.853	0.064	0.064	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.014	0.004	8.479	0.279	0.279	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.006	-0.002	9.926	0.200	0.200	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.782	-0.895	7.193	0.740	0.740	0.000	0.000	0.000	0.000
55	A	56	MET	0	-0.001	-0.002	2.321	-3.599	-3.004	3.045	-1.080	-2.560	0.000
56	A	57	VAL	0	-0.008	-0.003	6.367	0.665	0.665	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.873	-0.911	8.608	0.519	0.519	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.027	-0.022	2.170	-1.309	-0.488	2.769	-1.710	-1.880	-0.005
59	A	60	HIS	0	0.029	0.017	4.943	-0.165	0.011	-0.001	-0.011	-0.164	0.000
60	A	61	LEU	0	-0.018	-0.016	5.888	-0.716	-0.716	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.882	0.918	7.324	-0.702	-0.702	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.854	-0.927	3.310	-2.237	-1.243	0.044	-0.505	-0.533	-0.004
63	A	64	HIS	0	-0.070	-0.039	4.451	-0.728	-0.676	-0.001	-0.002	-0.049	0.000
64	A	65	LEU	0	-0.046	-0.031	9.035	-0.039	-0.039	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.066	-0.014	10.926	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.025	-0.015	9.456	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.016	-0.004	11.629	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.922	-0.951	13.753	-0.071	-0.071	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.026	-0.009	13.754	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.048	0.013	17.105	0.023	0.023	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.032	-0.017	18.349	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.865	-0.918	19.440	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.017	-0.011	15.490	0.010	0.010	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.906	0.949	14.653	0.023	0.023	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.015	0.015	15.444	0.039	0.039	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.002	-0.001	14.771	0.026	0.026	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.926	0.969	10.585	0.223	0.223	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.001	0.004	12.209	0.089	0.089	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.015	-0.016	14.417	0.047	0.047	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.962	-0.975	11.273	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.035	-0.012	9.306	0.067	0.067	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.021	0.012	12.701	0.031	0.031	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.021	-0.020	15.644	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.014	0.001	10.620	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.018	-0.006	13.695	0.016	0.016	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.931	0.966	15.974	-0.197	-0.197	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.024	0.001	17.320	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.030	-0.001	14.856	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)