FMO DATABASE

FMODB ID: J3M79

Calculation Name: 5CLV-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CLV

Chain ID: A

ChEMBL ID:

UniProt ID: P03052

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	96
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-590402.75345
FMO2-HF: Nuclear repulsion	554369.211352
FMO2-HF: Total energy	-36033.542097
FMO2-MP2: Total energy	-36141.83028

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:LYS )

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

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.
11.4	13.396	0.004	-0.827	-1.173	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.949 / q_NPA : 0.965

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	4	ARG	1	0.881	0.931	3.760	31.531	33.527	0.004	-0.827	-1.173	0.001
4	A	5	LEU	0	0.008	0.009	6.205	-0.795	-0.795	0.000	0.000	0.000	0.000
5	A	6	THR	0	0.006	0.001	9.984	1.498	1.498	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.787	-0.910	12.607	-15.490	-15.490	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.020	-0.020	15.694	0.546	0.546	0.000	0.000	0.000	0.000
8	A	9	GLN	0	0.073	0.043	11.498	-0.732	-0.732	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.006	0.001	12.668	0.184	0.184	0.000	0.000	0.000	0.000
10	A	11	GLN	0	-0.021	-0.035	14.864	0.837	0.837	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.909	-0.941	17.427	-15.860	-15.860	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.013	-0.014	15.147	0.572	0.572	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.060	-0.030	16.339	0.467	0.467	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.008	0.003	18.770	0.448	0.448	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.015	-0.014	22.178	0.053	0.053	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.039	-0.006	17.590	0.155	0.155	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.905	-0.955	21.887	-10.433	-10.433	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.058	-0.034	18.134	-0.366	-0.366	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.017	0.018	21.397	0.245	0.245	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.092	0.021	20.350	-0.363	-0.363	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.042	0.019	18.271	-0.580	-0.580	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.011	-0.010	15.437	-0.516	-0.516	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.034	0.028	15.095	-0.976	-0.976	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.943	-0.968	15.382	-13.794	-13.794	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.022	-0.016	11.835	-0.752	-0.752	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.002	-0.004	10.640	-1.081	-1.081	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.970	1.010	10.615	13.493	13.493	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.039	0.014	11.907	-0.696	-0.696	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.057	-0.022	6.099	-0.924	-0.924	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.049	-0.039	6.056	-2.084	-2.084	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.020	0.045	7.963	-1.956	-1.956	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.902	-0.942	10.658	-18.192	-18.192	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.092	-0.038	6.752	-0.237	-0.237	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.941	0.970	7.241	15.461	15.461	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.041	0.007	6.968	-0.783	-0.783	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.075	0.021	6.479	2.274	2.274	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.010	0.003	9.441	1.144	1.144	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.004	0.012	11.514	1.276	1.276	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.086	0.050	11.603	0.730	0.730	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.027	-0.004	13.985	0.595	0.595	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.044	-0.034	15.756	0.744	0.744	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.063	-0.044	16.923	0.600	0.600	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.001	0.003	17.221	0.474	0.474	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.014	0.029	19.982	0.378	0.378	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.030	-0.001	17.412	0.151	0.151	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.031	-0.002	17.762	-0.595	-0.595	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.991	0.965	13.111	15.170	15.170	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.005	0.007	13.217	-0.849	-0.849	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.049	0.032	14.609	-0.519	-0.519	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.049	0.022	10.810	-0.341	-0.341	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.006	0.003	10.110	-1.008	-1.008	0.000	0.000	0.000	0.000
52	A	53	GLN	0	-0.002	-0.015	11.119	-0.349	-0.349	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.038	-0.010	13.556	0.087	0.087	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.013	-0.003	7.191	-0.145	-0.145	0.000	0.000	0.000	0.000
55	A	56	HIS	0	-0.024	-0.009	10.510	-1.680	-1.680	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.949	0.979	11.350	14.284	14.284	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.052	0.033	12.335	0.172	0.172	0.000	0.000	0.000	0.000
58	A	59	TRP	0	0.014	-0.004	6.853	-1.971	-1.971	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.004	-0.012	11.180	-0.307	-0.307	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.051	0.029	13.999	0.446	0.446	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.016	-0.027	10.995	0.523	0.523	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.978	-0.989	11.382	-25.702	-25.702	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.972	-0.975	14.598	-15.457	-15.457	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.806	0.923	17.533	15.205	15.205	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.030	0.020	13.573	-0.524	-0.524	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.062	-0.027	16.716	-0.590	-0.590	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.026	-0.016	19.465	0.380	0.380	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.871	-0.941	22.274	-11.764	-11.764	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.030	-0.009	24.987	0.336	0.336	0.000	0.000	0.000	0.000
70	A	71	TYR	0	-0.088	-0.039	23.770	0.287	0.287	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.043	0.008	23.520	-0.052	-0.052	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.930	0.979	16.367	17.649	17.649	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.000	0.002	22.566	0.304	0.304	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.054	-0.031	22.419	-0.152	-0.152	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.044	0.013	25.023	0.319	0.319	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.014	0.008	28.128	-0.160	-0.160	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.006	-0.010	30.239	0.312	0.312	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.027	0.007	33.099	-0.049	-0.049	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.870	-0.934	34.492	-8.645	-8.645	0.000	0.000	0.000	0.000
80	A	81	HIS	0	0.041	0.022	34.831	-0.200	-0.200	0.000	0.000	0.000	0.000
81	A	82	GLN	0	0.036	-0.004	34.409	-0.274	-0.274	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.013	0.015	30.791	-0.293	-0.293	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.033	-0.014	30.584	-0.364	-0.364	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.003	0.000	31.920	-0.186	-0.186	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.014	0.012	27.238	-0.169	-0.169	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.914	0.947	26.985	10.670	10.670	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.885	0.950	27.685	9.182	9.182	0.000	0.000	0.000	0.000
88	A	89	TRP	0	-0.004	-0.012	29.297	-0.146	-0.146	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.892	-0.949	21.810	-14.563	-14.563	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.008	0.013	24.744	-0.410	-0.410	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.906	-0.970	26.533	-10.238	-10.238	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.008	0.009	24.982	0.052	0.052	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.913	0.970	17.731	16.047	16.047	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.896	0.957	23.820	10.476	10.476	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.894	0.956	25.990	10.431	10.431	0.000	0.000	0.000	0.000
96	A	1	NME	0	0.050	0.034	23.107	-0.476	-0.476	0.000	0.000	0.000	0.000

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