FMO DATABASE

FMODB ID: N1LVQ

Calculation Name: 2ZV3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZV3

Chain ID: A

ChEMBL ID:

UniProt ID: Q60363

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-844207.243345
FMO2-HF: Nuclear repulsion	802142.001428
FMO2-HF: Total energy	-42065.241917
FMO2-MP2: Total energy	-42186.790785

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.
-26.662	-18.186	23.523	-7.655	-24.345	-0.082

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 : 0.016 / q_NPA : 0.050

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	MET	0	-0.001	0.013	3.762	-4.157	1.652	-0.050	-3.265	-2.494	0.019
4	A	4	VAL	0	-0.046	-0.017	6.611	-0.294	-0.294	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.009	-0.014	9.927	0.208	0.208	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.003	-0.009	13.145	-0.045	-0.045	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.009	-0.006	16.295	0.059	0.059	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.788	0.872	19.572	0.097	0.097	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.023	-0.028	23.046	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.792	-0.875	25.106	-0.125	-0.125	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.038	-0.020	25.522	0.011	0.011	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.022	0.030	28.829	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.057	-0.020	23.059	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.081	0.041	27.543	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.993	0.971	25.171	0.228	0.228	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.039	0.021	24.236	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.902	0.953	24.658	0.097	0.097	0.000	0.000	0.000	0.000
18	A	18	MET	0	0.029	0.017	21.594	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.002	0.008	19.734	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.009	0.010	19.745	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.024	0.041	20.662	0.022	0.022	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.064	0.022	17.397	0.011	0.011	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.016	0.005	16.019	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.014	-0.002	16.573	0.031	0.031	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.008	0.003	15.138	0.040	0.040	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.007	-0.016	11.307	0.031	0.031	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.004	0.007	11.773	0.076	0.076	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.876	-0.952	13.215	0.218	0.218	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.048	0.000	9.606	0.071	0.071	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.040	0.012	8.187	0.154	0.154	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.031	-0.019	9.033	0.182	0.182	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.808	-0.910	10.527	0.505	0.505	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.029	-0.003	5.293	0.082	0.082	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.926	0.963	7.433	-0.525	-0.525	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.914	0.948	8.683	-0.333	-0.333	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.860	0.950	8.584	-0.598	-0.598	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.015	0.004	5.485	0.083	0.083	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.041	0.016	5.874	0.350	0.350	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.994	0.994	7.548	-1.307	-1.307	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.024	0.018	2.229	-0.449	-0.135	1.413	-0.399	-1.328	0.002
41	A	41	VAL	0	-0.019	-0.004	3.415	1.150	2.359	1.065	-0.673	-1.600	-0.011
42	A	42	ASP	-1	-0.905	-0.960	4.775	1.035	1.040	-0.001	-0.007	0.003	0.000
43	A	43	GLU	-1	-0.985	-1.009	3.314	0.140	2.503	0.322	-0.921	-1.764	-0.007
44	A	44	TRP	0	-0.010	0.007	2.750	-4.355	-1.640	0.891	-1.062	-2.544	0.004
45	A	45	LEU	0	-0.053	-0.035	3.589	-2.020	-1.958	0.029	0.071	-0.162	0.001
46	A	46	ARG	1	0.894	0.968	6.953	-1.645	-1.645	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.944	-0.962	2.747	-8.460	-6.039	0.293	-1.297	-1.418	-0.014
48	A	48	GLY	0	0.011	0.012	6.415	-0.508	-0.508	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.018	-0.011	5.796	0.088	0.088	0.000	0.000	0.000	0.000
50	A	50	LYS	1	1.015	1.011	5.156	3.900	3.900	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.870	0.924	6.488	0.817	0.817	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.006	0.001	8.709	-0.026	-0.026	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.003	0.004	11.021	0.122	0.122	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.027	0.022	13.455	0.008	0.008	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.912	0.963	16.100	0.341	0.341	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.011	0.010	19.100	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.057	-0.055	21.548	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.056	0.031	24.769	0.018	0.018	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.840	-0.929	24.647	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.990	0.994	24.472	0.053	0.053	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.856	-0.925	21.421	-0.183	-0.183	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.030	-0.005	19.035	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.016	-0.006	19.593	0.009	0.009	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.918	-0.950	20.589	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.046	-0.019	15.564	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.042	0.026	15.816	0.036	0.036	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.026	0.006	16.434	0.053	0.053	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.946	0.983	16.383	0.071	0.071	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.046	0.026	12.153	0.035	0.035	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.877	0.925	13.036	-0.166	-0.166	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.092	-0.043	15.253	0.034	0.034	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.859	-0.925	12.058	0.254	0.254	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.030	0.001	12.051	0.078	0.078	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.053	-0.025	7.479	0.136	0.136	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.034	-0.007	5.869	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.046	-0.023	8.999	-0.116	-0.116	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.031	-0.008	11.569	0.024	0.024	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.044	0.006	14.774	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.012	0.011	17.494	0.021	0.021	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.964	0.975	20.424	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.872	-0.934	24.223	-0.061	-0.061	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.014	-0.005	26.455	0.008	0.008	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.020	0.006	30.463	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	91	THR	0	-0.046	-0.020	27.114	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	92	LEU	0	0.021	0.020	22.832	0.002	0.002	0.000	0.000	0.000	0.000
86	A	93	THR	0	-0.010	-0.056	22.464	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.013	-0.005	17.989	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.003	0.015	14.239	0.044	0.044	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.022	0.011	11.281	-0.083	-0.083	0.000	0.000	0.000	0.000
90	A	97	ILE	0	0.003	-0.003	8.338	0.118	0.118	0.000	0.000	0.000	0.000
91	A	98	GLY	0	0.027	0.042	5.508	-0.295	-0.295	0.000	0.000	0.000	0.000
92	A	99	PRO	0	-0.058	-0.056	2.488	-0.953	-0.176	0.429	-0.231	-0.975	0.001
93	A	100	GLU	-1	-0.869	-0.969	2.052	3.810	0.737	8.143	-1.553	-3.518	-0.008
94	A	101	LYS	1	0.962	0.975	2.331	-1.593	-5.187	4.344	3.889	-4.639	-0.027
95	A	102	ASP	-1	-0.856	-0.933	2.168	-11.455	-12.168	6.644	-2.171	-3.760	-0.042
96	A	103	GLU	-1	-0.801	-0.913	4.198	0.631	0.812	0.001	-0.036	-0.146	0.000
97	A	104	LYS	1	0.905	0.954	6.389	-1.007	-1.007	0.000	0.000	0.000	0.000
98	A	105	ILE	0	-0.009	0.002	5.157	0.007	0.007	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.815	-0.894	7.988	-1.331	-1.331	0.000	0.000	0.000	0.000
100	A	107	LYS	1	0.834	0.927	9.961	-0.088	-0.088	0.000	0.000	0.000	0.000
101	A	108	ILE	0	-0.077	-0.040	11.702	0.024	0.024	0.000	0.000	0.000	0.000
102	A	109	THR	0	-0.017	-0.034	11.053	-0.044	-0.044	0.000	0.000	0.000	0.000
103	A	110	GLY	0	0.041	0.038	12.670	-0.054	-0.054	0.000	0.000	0.000	0.000
104	A	111	HIS	0	-0.029	-0.008	13.398	-0.043	-0.043	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.051	-0.013	15.415	0.028	0.028	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.940	0.967	16.759	0.284	0.284	0.000	0.000	0.000	0.000
107	A	114	LEU	0	0.055	0.017	14.307	0.003	0.003	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.031	-0.018	17.831	0.045	0.045	0.000	0.000	0.000	0.000

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