FMO DATABASE

FMODB ID: N1LZQ

Calculation Name: 3DLV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLV

Chain ID: B

ChEMBL ID:

UniProt ID: Q8TZT9

Base Structure: X-ray

Registration Date: 2023-03-14

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-801291.856607
FMO2-HF: Nuclear repulsion	760223.671908
FMO2-HF: Total energy	-41068.184699
FMO2-MP2: Total energy	-41191.018201

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(B:2:GLY)

Summations of interaction energy for fragment #1(B:2:GLY)

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.
-5.84	-8.442	14.079	-6.595	-4.881	-0.033

Interaction energy analysis for fragmet #1(B:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.028

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	B	4	PHE	0	-0.037	-0.021	2.793	0.465	2.723	0.055	-1.090	-1.222	0.005
4	B	5	VAL	0	0.032	0.015	6.448	-0.089	-0.089	0.000	0.000	0.000	0.000
5	B	6	VAL	0	-0.038	-0.026	9.059	0.057	0.057	0.000	0.000	0.000	0.000
6	B	7	TRP	0	0.088	0.035	11.320	0.057	0.057	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.056	0.020	14.910	0.017	0.017	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.052	0.022	17.216	0.021	0.021	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.793	-0.884	12.448	-0.584	-0.584	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.034	-0.031	13.707	0.041	0.041	0.000	0.000	0.000	0.000
11	B	12	ASP	-1	-0.686	-0.848	16.814	-0.217	-0.217	0.000	0.000	0.000	0.000
12	B	13	SER	0	-0.082	-0.062	20.491	0.031	0.031	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.892	0.951	22.954	0.214	0.214	0.000	0.000	0.000	0.000
14	B	15	LEU	0	0.007	0.042	21.327	0.017	0.017	0.000	0.000	0.000	0.000
15	B	16	SER	0	0.010	0.009	23.783	0.007	0.007	0.000	0.000	0.000	0.000
16	B	17	ARG	1	0.916	0.936	17.168	0.039	0.039	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.953	0.984	21.299	0.033	0.033	0.000	0.000	0.000	0.000
18	B	19	TYR	0	-0.050	-0.056	23.397	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	GLY	0	0.071	0.041	19.344	-0.019	-0.019	0.000	0.000	0.000	0.000
20	B	21	ARG	1	0.792	0.910	17.665	0.105	0.105	0.000	0.000	0.000	0.000
21	B	22	ILE	0	-0.021	-0.016	12.698	0.048	0.048	0.000	0.000	0.000	0.000
22	B	23	VAL	0	-0.014	-0.015	13.892	0.062	0.062	0.000	0.000	0.000	0.000
23	B	24	PRO	0	-0.029	-0.021	16.245	0.018	0.018	0.000	0.000	0.000	0.000
24	B	25	ARG	1	1.023	0.993	19.314	0.021	0.021	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.025	0.020	22.424	-0.013	-0.013	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.021	-0.002	16.629	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.025	-0.003	18.733	-0.031	-0.031	0.000	0.000	0.000	0.000
28	B	29	VAL	0	0.046	0.019	19.171	0.026	0.026	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.920	-0.944	21.614	-0.170	-0.170	0.000	0.000	0.000	0.000
30	B	31	SER	0	0.027	0.002	23.524	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	32	PRO	0	-0.052	0.002	18.594	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.955	0.975	20.575	0.297	0.297	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.082	0.032	17.496	-0.041	-0.041	0.000	0.000	0.000	0.000
34	B	35	GLU	-1	-0.786	-0.896	17.814	-0.424	-0.424	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.784	-0.856	19.368	-0.335	-0.335	0.000	0.000	0.000	0.000
36	B	37	ILE	0	-0.011	-0.005	13.400	-0.027	-0.027	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.002	0.009	14.320	-0.119	-0.119	0.000	0.000	0.000	0.000
38	B	39	ARG	1	0.936	0.973	15.268	0.314	0.314	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.018	-0.010	14.950	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	41	ALA	0	-0.032	-0.025	10.930	-0.035	-0.035	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.872	-0.941	11.879	-0.721	-0.721	0.000	0.000	0.000	0.000
42	B	43	GLU	-1	-0.913	-0.969	14.237	-0.362	-0.362	0.000	0.000	0.000	0.000
43	B	44	LEU	0	-0.107	-0.058	11.048	0.081	0.081	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.871	0.949	10.884	0.488	0.488	0.000	0.000	0.000	0.000
45	B	46	PHE	0	-0.029	-0.014	7.713	-0.238	-0.238	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.978	0.998	7.636	1.511	1.511	0.000	0.000	0.000	0.000
47	B	48	VAL	0	0.035	-0.003	8.957	-0.426	-0.426	0.000	0.000	0.000	0.000
48	B	49	ILE	0	-0.109	-0.043	8.118	0.188	0.188	0.000	0.000	0.000	0.000
49	B	50	ARG	1	0.896	0.928	11.676	0.673	0.673	0.000	0.000	0.000	0.000
50	B	51	VAL	0	0.000	0.005	13.933	-0.123	-0.123	0.000	0.000	0.000	0.000
51	B	52	GLU	-1	-0.845	-0.907	16.596	-0.364	-0.364	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.957	-1.004	19.167	-0.371	-0.371	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.914	-0.940	21.919	-0.218	-0.218	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.864	0.925	25.058	0.266	0.266	0.000	0.000	0.000	0.000
55	B	56	LEU	0	0.068	0.010	28.012	0.009	0.009	0.000	0.000	0.000	0.000
56	B	57	ASN	0	0.015	0.009	30.907	0.003	0.003	0.000	0.000	0.000	0.000
57	B	58	PRO	0	-0.115	-0.015	32.010	0.006	0.006	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.944	0.915	30.902	0.123	0.123	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.008	0.008	35.567	0.005	0.005	0.000	0.000	0.000	0.000
60	B	61	SER	0	0.021	0.016	37.206	0.004	0.004	0.000	0.000	0.000	0.000
61	B	62	GLY	0	0.002	0.004	38.152	0.004	0.004	0.000	0.000	0.000	0.000
62	B	63	ILE	0	-0.044	-0.015	35.660	0.002	0.002	0.000	0.000	0.000	0.000
63	B	64	ASP	-1	-0.842	-0.917	31.554	-0.128	-0.128	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.854	-0.932	31.789	-0.108	-0.108	0.000	0.000	0.000	0.000
65	B	66	GLU	-1	-0.936	-0.945	27.345	-0.144	-0.144	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.000	0.007	25.794	-0.019	-0.019	0.000	0.000	0.000	0.000
67	B	68	ARG	1	0.926	0.993	27.883	0.172	0.172	0.000	0.000	0.000	0.000
68	B	69	THR	0	-0.047	-0.038	23.579	0.000	0.000	0.000	0.000	0.000	0.000
69	B	70	PHE	0	0.044	0.032	19.105	-0.010	-0.010	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.031	0.001	19.531	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.072	-0.028	14.832	0.002	0.002	0.000	0.000	0.000	0.000
72	B	73	ILE	0	0.029	0.022	11.531	0.013	0.013	0.000	0.000	0.000	0.000
73	B	74	VAL	0	-0.029	-0.009	8.874	-0.145	-0.145	0.000	0.000	0.000	0.000
74	B	75	LEU	0	0.006	0.005	7.149	0.182	0.182	0.000	0.000	0.000	0.000
75	B	76	GLU	-1	-0.845	-0.940	4.341	-3.232	-2.918	0.000	-0.092	-0.222	0.000
76	B	77	SER	0	-0.021	-0.003	2.993	1.658	2.719	0.029	-0.489	-0.601	0.001
77	B	78	PRO	0	0.052	0.031	1.768	-5.317	-12.414	13.905	-4.569	-2.239	-0.036
78	B	79	TYR	0	-0.024	-0.011	4.075	2.043	2.285	0.001	-0.034	-0.208	0.000
79	B	80	GLY	0	0.077	0.033	3.114	-1.659	-1.073	0.090	-0.318	-0.358	-0.003
80	B	81	LYS	1	0.869	0.936	4.836	-0.206	-0.172	-0.001	-0.003	-0.031	0.000
81	B	82	SER	0	0.000	-0.005	6.116	-0.080	-0.080	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.986	0.979	8.112	-0.414	-0.414	0.000	0.000	0.000	0.000
83	B	84	SER	0	0.045	0.020	5.328	-0.249	-0.249	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.022	0.014	8.052	0.049	0.049	0.000	0.000	0.000	0.000
85	B	86	LYS	1	0.900	0.955	10.827	0.096	0.096	0.000	0.000	0.000	0.000
86	B	87	LEU	0	0.022	0.018	9.655	0.043	0.043	0.000	0.000	0.000	0.000
87	B	88	ILE	0	0.040	0.024	9.718	0.041	0.041	0.000	0.000	0.000	0.000
88	B	89	ALA	0	-0.011	-0.008	13.388	0.062	0.062	0.000	0.000	0.000	0.000
89	B	90	GLN	0	-0.050	-0.037	16.041	0.023	0.023	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.898	0.973	15.875	0.406	0.406	0.000	0.000	0.000	0.000
91	B	92	ILE	0	0.047	0.028	16.785	0.033	0.033	0.000	0.000	0.000	0.000
92	B	93	ARG	1	0.846	0.927	19.490	0.239	0.239	0.000	0.000	0.000	0.000
93	B	94	GLU	-1	-0.885	-0.948	20.640	-0.249	-0.249	0.000	0.000	0.000	0.000
94	B	95	PHE	0	-0.027	-0.014	18.294	0.028	0.028	0.000	0.000	0.000	0.000
95	B	96	ARG	1	0.745	0.818	22.951	0.289	0.289	0.000	0.000	0.000	0.000
96	B	97	ARG	1	0.974	0.986	25.596	0.163	0.163	0.000	0.000	0.000	0.000
97	B	98	ARG	1	0.903	0.969	23.039	0.247	0.247	0.000	0.000	0.000	0.000
98	B	99	SER	0	-0.051	-0.024	27.002	0.008	0.008	0.000	0.000	0.000	0.000
99	B	100	ALA	0	-0.006	0.004	29.411	0.009	0.009	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.034	0.025	31.126	0.009	0.009	0.000	0.000	0.000	0.000
101	B	102	THR	0	-0.024	-0.020	32.607	0.012	0.012	0.000	0.000	0.000	0.000
102	B	103	LEU	0	-0.064	-0.020	32.258	-0.009	-0.009	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.004	-0.012	32.951	-0.004	-0.004	0.000	0.000	0.000	0.000
104	B	105	PRO	0	0.014	0.023	34.489	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLY)