FMO DATABASE

FMODB ID: 72YLK

Calculation Name: 1LN4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LN4

Chain ID: A

ChEMBL ID:

UniProt ID: P0AGK4

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-713749.845927
FMO2-HF: Nuclear repulsion	676144.480344
FMO2-HF: Total energy	-37605.365583
FMO2-MP2: Total energy	-37716.555921

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.
-19.11	-7.426	16.21	-9.088	-18.806	-0.062

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 : 0.012 / 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	A	3	LEU	0	-0.013	-0.012	2.668	-2.944	1.537	1.079	-2.021	-3.539	0.004
4	A	4	SER	0	0.010	-0.018	4.903	-0.509	-0.482	-0.001	-0.004	-0.022	0.000
5	A	5	THR	0	0.037	0.000	8.744	0.097	0.097	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.867	0.925	11.420	-0.493	-0.493	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.019	0.002	7.095	-0.070	-0.070	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.839	0.911	6.337	1.118	1.118	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.040	0.014	9.558	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.027	-0.008	10.773	-0.130	-0.130	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.023	0.014	6.315	-0.096	-0.096	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.881	0.932	10.875	-0.229	-0.229	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.031	-0.009	13.501	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.002	-0.004	12.344	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.041	0.020	12.951	-0.055	-0.055	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.055	-0.021	14.951	-0.083	-0.083	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.002	-0.010	18.148	-0.042	-0.042	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.017	0.034	13.762	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.971	0.983	18.088	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.049	-0.050	17.470	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.030	0.027	14.454	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.046	0.040	14.859	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.060	-0.033	17.502	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.025	0.036	14.545	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.030	-0.003	18.299	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.012	-0.013	20.621	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.027	-0.013	22.453	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.050	0.037	18.402	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.014	-0.012	11.754	0.018	0.018	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.005	0.002	16.081	0.012	0.012	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.866	-0.939	16.906	-0.182	-0.182	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.025	0.018	17.354	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.034	-0.025	16.021	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.022	0.008	10.821	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.041	0.020	13.299	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.857	-0.924	14.910	-0.091	-0.091	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.061	-0.038	9.971	0.015	0.015	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.790	-0.864	9.213	-0.481	-0.481	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.056	-0.031	11.205	0.050	0.050	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.022	-0.011	12.763	0.050	0.050	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.015	-0.011	6.255	0.086	0.086	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.813	-0.905	8.181	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.053	-0.024	10.400	0.073	0.073	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.060	-0.040	11.200	0.034	0.034	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.710	-0.805	6.883	1.108	1.108	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.072	-0.034	6.946	0.121	0.121	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.001	0.006	9.373	-0.111	-0.111	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.791	0.893	11.739	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.061	0.029	12.234	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.889	0.951	14.946	0.097	0.097	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.043	0.014	13.045	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.000	-0.006	17.713	0.013	0.013	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.028	0.023	19.114	0.030	0.030	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.821	-0.902	21.127	-0.165	-0.165	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.774	-0.850	21.596	-0.298	-0.298	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.894	0.923	14.215	0.482	0.482	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.891	-0.932	17.773	-0.392	-0.392	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.021	-0.023	16.980	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.804	0.893	15.839	0.260	0.260	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.029	-0.015	12.960	-0.075	-0.075	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.038	0.032	12.116	-0.148	-0.148	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.020	-0.008	12.386	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.014	-0.012	8.972	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.842	-0.913	7.790	-1.297	-1.297	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.028	-0.003	7.577	-0.175	-0.175	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.034	0.012	7.486	0.079	0.079	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.067	-0.011	2.472	-0.339	0.243	0.354	-0.286	-0.651	0.001
68	A	68	ARG	1	0.810	0.887	3.832	1.114	1.482	0.003	-0.097	-0.274	-0.001
69	A	69	GLU	-1	-0.927	-0.959	6.095	0.170	0.170	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.035	-0.033	6.361	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.016	0.028	3.678	-0.849	-0.408	0.039	-0.194	-0.287	0.001
72	A	72	ALA	0	-0.004	0.005	2.176	-8.171	-4.958	3.867	-3.096	-3.984	-0.035
73	A	73	CYS	0	-0.066	-0.038	2.475	-7.324	-4.802	5.115	-2.498	-5.139	-0.019
74	A	74	ASN	0	0.040	0.006	3.123	1.865	1.813	0.095	0.494	-0.536	0.001
75	A	75	VAL	0	-0.034	-0.006	6.774	0.125	0.125	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.004	-0.033	8.702	0.031	0.031	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.023	0.026	11.741	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.000	-0.002	13.980	0.041	0.041	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.043	0.025	17.628	0.018	0.018	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.778	0.861	18.797	0.146	0.146	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.023	-0.008	15.852	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.017	0.031	8.911	0.028	0.028	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.028	-0.012	10.742	0.082	0.082	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.002	-0.002	5.793	-0.090	-0.090	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.006	-0.026	3.664	-0.707	0.015	0.106	-0.197	-0.631	0.001
86	A	86	ARG	1	0.793	0.831	2.162	-0.261	0.937	1.886	-1.174	-1.910	-0.009
87	A	87	PRO	0	-0.066	-0.005	2.062	1.074	-0.781	3.668	-0.010	-1.803	-0.006
88	A	88	THR	0	0.041	0.003	4.915	-0.456	-0.419	-0.001	-0.005	-0.030	0.000
89	A	89	LYS	1	0.930	0.927	8.097	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.830	-0.891	11.066	0.287	0.287	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.835	0.922	7.401	-1.588	-1.588	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.826	0.914	10.512	-0.261	-0.261	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.040	-0.002	9.125	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	94	SER	0	0.020	0.011	9.938	0.204	0.204	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.013	-0.005	6.014	0.115	0.115	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.009	0.002	10.269	-0.117	-0.117	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.017	0.012	10.086	0.318	0.318	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.769	-0.832	9.492	0.487	0.487	0.000	0.000	0.000	0.000

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