FMO DATABASE

FMODB ID: J3Z99

Calculation Name: 5CLV-A-Xray372

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: 2023-06-20

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-589109.729778
FMO2-HF: Nuclear repulsion	553095.328868
FMO2-HF: Total energy	-36014.40091
FMO2-MP2: Total energy	-36122.582635

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.
11.086	13.12	0.001	-0.839	-1.196	0.002

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 : 0.948 / 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

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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	ARG	1	0.879	0.929	3.760	31.326	33.360	0.001	-0.839	-1.196	0.002
4	A	5	LEU	0	0.008	0.010	6.205	-0.895	-0.895	0.000	0.000	0.000	0.000
5	A	6	THR	0	0.009	0.003	9.984	1.438	1.438	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.788	-0.910	12.607	-15.544	-15.544	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.020	-0.020	15.694	0.528	0.528	0.000	0.000	0.000	0.000
8	A	9	GLN	0	0.071	0.042	11.498	-0.721	-0.721	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.006	0.001	12.683	0.177	0.177	0.000	0.000	0.000	0.000
10	A	11	GLN	0	-0.023	-0.036	14.878	0.796	0.796	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.908	-0.941	17.427	-15.866	-15.866	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.011	-0.014	15.160	0.577	0.577	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.058	-0.029	16.353	0.439	0.439	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.012	0.001	18.783	0.418	0.418	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.015	-0.014	22.191	0.038	0.038	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.039	-0.006	17.601	0.160	0.160	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.905	-0.956	21.899	-10.444	-10.444	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.058	-0.034	18.145	-0.357	-0.357	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.018	0.019	21.408	0.237	0.237	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.092	0.021	20.362	-0.356	-0.356	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.042	0.019	18.280	-0.567	-0.567	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.012	-0.011	15.446	-0.494	-0.494	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.035	0.028	15.107	-0.960	-0.960	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.942	-0.967	15.395	-13.789	-13.789	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.027	-0.018	11.844	-0.723	-0.723	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.009	0.000	10.652	-1.042	-1.042	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.965	1.009	10.629	13.503	13.503	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.036	0.012	11.920	-0.682	-0.682	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.054	-0.022	6.109	-0.883	-0.883	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.046	-0.037	6.070	-2.026	-2.026	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.019	0.044	7.977	-1.978	-1.978	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.904	-0.942	10.658	-18.214	-18.214	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.093	-0.039	6.752	-0.202	-0.202	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.946	0.973	7.231	15.429	15.429	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.034	0.005	6.963	-0.759	-0.759	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.078	0.022	6.485	2.244	2.244	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.010	0.003	9.445	1.103	1.103	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.004	0.012	11.508	1.244	1.244	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.084	0.050	11.613	0.708	0.708	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.026	-0.004	13.988	0.582	0.582	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.045	-0.034	15.759	0.722	0.722	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.061	-0.044	16.935	0.581	0.581	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.001	0.004	17.226	0.462	0.462	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.013	0.028	19.986	0.370	0.370	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.028	0.000	17.417	0.161	0.161	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.030	-0.001	17.765	-0.583	-0.583	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.993	0.966	13.109	15.203	15.203	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.007	0.006	13.218	-0.844	-0.844	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.046	0.031	14.612	-0.521	-0.521	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.051	0.023	10.815	-0.315	-0.315	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.008	0.003	10.113	-0.993	-0.993	0.000	0.000	0.000	0.000
52	A	53	GLN	0	-0.003	-0.015	11.123	-0.362	-0.362	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.035	-0.009	13.563	0.082	0.082	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.009	-0.004	7.202	-0.108	-0.108	0.000	0.000	0.000	0.000
55	A	56	HIS	0	-0.023	-0.008	10.517	-1.659	-1.659	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.950	0.979	11.357	14.246	14.246	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.053	0.034	12.345	0.182	0.182	0.000	0.000	0.000	0.000
58	A	59	TRP	0	0.015	-0.004	6.853	-1.928	-1.928	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.005	-0.013	11.190	-0.335	-0.335	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.053	0.029	13.999	0.411	0.411	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.022	-0.029	10.996	0.533	0.533	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.973	-0.988	11.382	-25.688	-25.688	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.972	-0.976	14.598	-15.505	-15.505	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.808	0.925	17.528	15.191	15.191	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.030	0.019	13.574	-0.504	-0.504	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.064	-0.027	16.716	-0.605	-0.605	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.027	-0.016	19.465	0.347	0.347	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.869	-0.941	22.274	-11.787	-11.787	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.030	-0.009	24.987	0.320	0.320	0.000	0.000	0.000	0.000
70	A	71	TYR	0	-0.087	-0.040	23.770	0.296	0.296	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.043	0.008	23.520	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.931	0.979	16.368	17.650	17.650	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.000	0.002	22.566	0.287	0.287	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.053	-0.031	22.421	-0.153	-0.153	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.043	0.013	25.023	0.299	0.299	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.013	0.008	28.128	-0.166	-0.166	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.006	-0.010	30.239	0.296	0.296	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.027	0.007	33.100	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.870	-0.934	34.493	-8.641	-8.641	0.000	0.000	0.000	0.000
80	A	81	HIS	0	0.042	0.023	34.831	-0.202	-0.202	0.000	0.000	0.000	0.000
81	A	82	GLN	0	0.036	-0.004	34.409	-0.267	-0.267	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.011	0.014	30.792	-0.280	-0.280	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.033	-0.014	30.585	-0.363	-0.363	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.006	0.001	31.921	-0.185	-0.185	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.012	0.011	27.239	-0.156	-0.156	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.913	0.947	26.986	10.678	10.678	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.888	0.952	27.686	9.175	9.175	0.000	0.000	0.000	0.000
88	A	89	TRP	0	-0.005	-0.012	29.298	-0.141	-0.141	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.893	-0.949	21.810	-14.544	-14.544	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.009	0.013	24.745	-0.410	-0.410	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.908	-0.970	26.534	-10.247	-10.247	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.011	0.011	24.980	0.058	0.058	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.908	0.966	17.732	16.052	16.052	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.900	0.960	23.821	10.452	10.452	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.945	0.990	24.014	10.179	10.179	0.000	0.000	0.000	0.000

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