FMO DATABASE

FMODB ID: LJ239

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	OptAll
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	-590232.882614
FMO2-HF: Nuclear repulsion	554217.764023
FMO2-HF: Total energy	-36015.118591
FMO2-MP2: Total energy	-36123.292573

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.
9.226	10.774	0	-0.615	-0.933	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 : 0.976 / q_NPA : 0.973

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].	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	0.853	0.926	3.769	33.662	35.210	-0.615	-0.933	0.001
4	A	5	LEU	0	-0.012	0.006	5.994	-0.733	-0.733	0.000	0.000	0.000
5	A	6	THR	0	0.008	-0.016	9.691	1.168	1.168	0.000	0.000	0.000
6	A	7	GLU	-1	-0.730	-0.862	12.561	-15.894	-15.894	0.000	0.000	0.000
7	A	8	SER	0	0.002	0.000	15.340	0.903	0.903	0.000	0.000	0.000
8	A	9	GLN	0	0.060	0.055	11.283	-0.284	-0.284	0.000	0.000	0.000
9	A	10	PHE	0	-0.008	0.003	11.620	0.080	0.080	0.000	0.000	0.000
10	A	11	GLN	0	0.020	-0.009	14.447	0.603	0.603	0.000	0.000	0.000
11	A	12	GLU	-1	-0.834	-0.917	16.530	-16.792	-16.792	0.000	0.000	0.000
12	A	13	ALA	0	-0.009	-0.004	14.480	0.614	0.614	0.000	0.000	0.000
13	A	14	ILE	0	-0.008	-0.016	16.002	0.594	0.594	0.000	0.000	0.000
14	A	15	GLN	0	0.007	0.023	18.387	0.602	0.602	0.000	0.000	0.000
15	A	16	GLY	0	-0.009	-0.008	21.763	-0.072	-0.072	0.000	0.000	0.000
16	A	17	LEU	0	-0.057	-0.017	17.043	0.099	0.099	0.000	0.000	0.000
17	A	18	GLU	-1	-0.895	-0.949	21.454	-10.458	-10.458	0.000	0.000	0.000
18	A	19	VAL	0	-0.078	-0.036	17.875	-0.246	-0.246	0.000	0.000	0.000
19	A	20	GLY	0	0.042	0.027	20.910	0.229	0.229	0.000	0.000	0.000
20	A	21	GLN	0	0.077	0.020	19.543	-0.452	-0.452	0.000	0.000	0.000
21	A	22	GLN	0	0.059	0.020	17.820	-0.494	-0.494	0.000	0.000	0.000
22	A	23	THR	0	-0.041	-0.014	14.986	-0.425	-0.425	0.000	0.000	0.000
23	A	24	ILE	0	0.047	0.028	14.540	-1.044	-1.044	0.000	0.000	0.000
24	A	25	GLU	-1	-0.948	-0.967	14.826	-13.910	-13.910	0.000	0.000	0.000
25	A	26	ILE	0	-0.014	-0.016	11.406	-0.831	-0.831	0.000	0.000	0.000
26	A	27	ALA	0	-0.004	-0.001	10.222	-1.296	-1.296	0.000	0.000	0.000
27	A	28	ARG	1	0.855	0.918	9.997	14.203	14.203	0.000	0.000	0.000
28	A	29	GLY	0	0.024	0.009	10.808	-1.088	-1.088	0.000	0.000	0.000
29	A	30	VAL	0	-0.057	-0.025	5.305	-1.043	-1.043	0.000	0.000	0.000
30	A	31	LEU	0	-0.041	-0.022	5.702	-3.360	-3.360	0.000	0.000	0.000
31	A	32	VAL	0	0.013	0.022	7.288	-2.194	-2.194	0.000	0.000	0.000
32	A	33	ASP	-1	-0.807	-0.893	10.093	-19.066	-19.066	0.000	0.000	0.000
33	A	34	GLY	0	-0.056	-0.029	6.293	-0.734	-0.734	0.000	0.000	0.000
34	A	35	LYS	1	0.842	0.919	6.894	16.326	16.326	0.000	0.000	0.000
35	A	36	PRO	0	0.039	0.003	6.751	-0.865	-0.865	0.000	0.000	0.000
36	A	37	GLN	0	0.068	0.025	6.795	2.342	2.342	0.000	0.000	0.000
37	A	38	ALA	0	0.012	0.004	9.212	1.224	1.224	0.000	0.000	0.000
38	A	39	THR	0	0.047	0.030	11.476	0.684	0.684	0.000	0.000	0.000
39	A	40	PHE	0	0.033	0.041	10.941	0.764	0.764	0.000	0.000	0.000
40	A	41	ALA	0	-0.031	-0.012	13.648	0.671	0.671	0.000	0.000	0.000
41	A	42	THR	0	-0.046	-0.036	15.573	0.739	0.739	0.000	0.000	0.000
42	A	43	SER	0	-0.048	-0.048	16.429	0.540	0.540	0.000	0.000	0.000
43	A	44	LEU	0	-0.009	0.000	16.389	0.406	0.406	0.000	0.000	0.000
44	A	45	GLY	0	0.019	0.023	19.646	0.339	0.339	0.000	0.000	0.000
45	A	46	LEU	0	-0.021	0.013	16.613	0.125	0.125	0.000	0.000	0.000
46	A	47	THR	0	0.038	0.001	17.428	-0.592	-0.592	0.000	0.000	0.000
47	A	48	ARG	1	1.008	0.978	13.279	14.982	14.982	0.000	0.000	0.000
48	A	49	GLY	0	0.010	0.015	13.069	-0.792	-0.792	0.000	0.000	0.000
49	A	50	ALA	0	0.030	0.021	14.806	-0.340	-0.340	0.000	0.000	0.000
50	A	51	VAL	0	0.020	0.011	10.816	-0.265	-0.265	0.000	0.000	0.000
51	A	52	SER	0	-0.014	-0.005	9.974	-0.910	-0.910	0.000	0.000	0.000
52	A	53	GLN	0	0.025	0.010	11.009	-0.305	-0.305	0.000	0.000	0.000
53	A	54	ALA	0	-0.010	0.004	13.315	0.035	0.035	0.000	0.000	0.000
54	A	55	VAL	0	0.020	0.002	6.759	-0.189	-0.189	0.000	0.000	0.000
55	A	56	HIS	0	-0.008	-0.005	10.237	-1.447	-1.447	0.000	0.000	0.000
56	A	57	ARG	1	0.912	0.951	11.276	13.764	13.764	0.000	0.000	0.000
57	A	58	VAL	0	0.040	0.024	12.259	0.266	0.266	0.000	0.000	0.000
58	A	59	TRP	0	-0.036	-0.045	6.844	-1.502	-1.502	0.000	0.000	0.000
59	A	60	ALA	0	-0.018	-0.015	11.219	-0.344	-0.344	0.000	0.000	0.000
60	A	61	ALA	0	0.044	0.021	14.320	0.318	0.318	0.000	0.000	0.000
61	A	62	PHE	0	-0.019	-0.008	10.519	0.172	0.172	0.000	0.000	0.000
62	A	63	GLU	-1	-0.798	-0.890	10.399	-26.051	-26.051	0.000	0.000	0.000
63	A	64	ASP	-1	-0.933	-0.942	14.175	-15.195	-15.195	0.000	0.000	0.000
64	A	65	LYS	1	0.779	0.898	16.829	15.485	15.485	0.000	0.000	0.000
65	A	66	ASN	0	-0.019	-0.012	12.515	-0.247	-0.247	0.000	0.000	0.000
66	A	67	LEU	0	-0.024	-0.004	16.263	-0.493	-0.493	0.000	0.000	0.000
67	A	68	PRO	0	-0.039	-0.017	19.122	0.393	0.393	0.000	0.000	0.000
68	A	69	GLU	-1	-0.873	-0.941	21.981	-11.749	-11.749	0.000	0.000	0.000
69	A	70	GLY	0	-0.032	-0.016	24.987	0.261	0.261	0.000	0.000	0.000
70	A	71	TYR	0	-0.085	-0.038	23.569	0.373	0.373	0.000	0.000	0.000
71	A	72	ALA	0	0.038	0.012	23.093	-0.144	-0.144	0.000	0.000	0.000
72	A	73	ARG	1	0.806	0.878	16.063	17.224	17.224	0.000	0.000	0.000
73	A	74	VAL	0	0.010	0.002	22.164	0.426	0.426	0.000	0.000	0.000
74	A	75	THR	0	-0.043	-0.032	22.598	-0.219	-0.219	0.000	0.000	0.000
75	A	76	ALA	0	0.031	0.016	25.100	0.256	0.256	0.000	0.000	0.000
76	A	77	VAL	0	-0.011	0.010	28.228	-0.140	-0.140	0.000	0.000	0.000
77	A	78	LEU	0	0.000	-0.011	30.285	0.240	0.240	0.000	0.000	0.000
78	A	79	PRO	0	0.032	0.012	33.071	-0.052	-0.052	0.000	0.000	0.000
79	A	80	GLU	-1	-0.903	-0.945	34.691	-8.560	-8.560	0.000	0.000	0.000
80	A	81	HIS	0	0.068	0.027	34.835	-0.315	-0.315	0.000	0.000	0.000
81	A	82	GLN	0	0.032	0.005	34.526	-0.139	-0.139	0.000	0.000	0.000
82	A	83	ALA	0	0.043	0.025	30.739	-0.271	-0.271	0.000	0.000	0.000
83	A	84	TYR	0	-0.032	-0.003	30.717	-0.382	-0.382	0.000	0.000	0.000
84	A	85	ILE	0	0.002	0.005	32.222	-0.214	-0.214	0.000	0.000	0.000
85	A	86	VAL	0	0.012	0.005	27.641	-0.189	-0.189	0.000	0.000	0.000
86	A	87	ARG	1	0.911	0.939	26.753	10.603	10.603	0.000	0.000	0.000
87	A	88	LYS	1	0.867	0.929	28.090	9.041	9.041	0.000	0.000	0.000
88	A	89	TRP	0	0.014	-0.008	29.521	-0.128	-0.128	0.000	0.000	0.000
89	A	90	GLU	-1	-0.813	-0.876	21.699	-14.406	-14.406	0.000	0.000	0.000
90	A	91	ALA	0	0.025	0.009	24.891	-0.369	-0.369	0.000	0.000	0.000
91	A	92	ASP	-1	-0.838	-0.907	26.620	-9.923	-9.923	0.000	0.000	0.000
92	A	93	ALA	0	-0.013	0.001	24.832	0.064	0.064	0.000	0.000	0.000
93	A	94	LYS	1	0.816	0.883	19.514	14.800	14.800	0.000	0.000	0.000
94	A	95	LYS	1	0.819	0.915	23.647	10.374	10.374	0.000	0.000	0.000
95	A	96	LYS	1	0.943	0.989	23.160	10.385	10.385	0.000	0.000	0.000

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