FMO DATABASE

FMODB ID: 94YM2

Calculation Name: 5LNL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LNL

Chain ID: A

ChEMBL ID:

UniProt ID: P71401

Base Structure: X-ray

Registration Date: 2023-06-21

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817156.845945
FMO2-HF: Nuclear repulsion	767481.799798
FMO2-HF: Total energy	-49675.046147
FMO2-MP2: Total energy	-49821.21583

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:1607:MET)

Summations of interaction energy for fragment #1(A:1607: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.
0.148	2.403	4.824	-2.302	-4.777	-0.002

Interaction energy analysis for fragmet #1(A:1607:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.010

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	1609	PHE	0	-0.039	-0.034	2.249	-0.807	1.448	4.824	-2.302	-4.777	-0.002
4	A	1610	VAL	0	0.018	0.015	5.701	0.217	0.217	0.000	0.000	0.000	0.000
5	A	1611	SER	0	-0.011	-0.006	9.288	0.170	0.170	0.000	0.000	0.000	0.000
6	A	1612	GLY	0	0.030	0.016	12.530	0.021	0.021	0.000	0.000	0.000	0.000
7	A	1613	ASP	-1	-0.885	-0.941	15.104	-0.316	-0.316	0.000	0.000	0.000	0.000
8	A	1614	LYS	1	0.835	0.906	15.030	0.600	0.600	0.000	0.000	0.000	0.000
9	A	1615	ASP	-1	-0.854	-0.928	18.047	-0.373	-0.373	0.000	0.000	0.000	0.000
10	A	1616	THR	0	0.045	0.020	19.147	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	1617	THR	0	-0.029	-0.020	13.861	0.005	0.005	0.000	0.000	0.000	0.000
12	A	1618	SER	0	-0.055	-0.032	15.331	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	1619	VAL	0	0.027	0.001	8.853	0.039	0.039	0.000	0.000	0.000	0.000
14	A	1620	THR	0	-0.044	-0.011	11.598	-0.063	-0.063	0.000	0.000	0.000	0.000
15	A	1621	VAL	0	0.034	0.008	6.379	0.060	0.060	0.000	0.000	0.000	0.000
16	A	1622	GLU	-1	-0.757	-0.862	9.686	-0.700	-0.700	0.000	0.000	0.000	0.000
17	A	1623	SER	0	-0.009	-0.033	11.533	-0.093	-0.093	0.000	0.000	0.000	0.000
18	A	1624	LYS	1	0.750	0.842	13.168	0.702	0.702	0.000	0.000	0.000	0.000
19	A	1625	ASP	-1	-0.848	-0.892	16.280	-0.333	-0.333	0.000	0.000	0.000	0.000
20	A	1626	ASN	0	-0.023	-0.004	18.247	0.001	0.001	0.000	0.000	0.000	0.000
21	A	1627	GLY	0	0.032	0.023	15.456	-0.054	-0.054	0.000	0.000	0.000	0.000
22	A	1628	LYS	1	0.917	0.950	12.836	0.191	0.191	0.000	0.000	0.000	0.000
23	A	1629	ARG	1	0.871	0.918	12.449	0.493	0.493	0.000	0.000	0.000	0.000
24	A	1630	THR	0	0.045	0.015	8.409	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	1631	GLU	-1	-0.835	-0.870	9.588	-0.650	-0.650	0.000	0.000	0.000	0.000
26	A	1632	VAL	0	0.023	-0.002	6.491	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	1633	LYS	1	0.806	0.903	9.915	0.901	0.901	0.000	0.000	0.000	0.000
28	A	1634	ILE	0	0.012	0.004	8.432	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	1635	GLY	0	0.018	0.020	12.942	0.092	0.092	0.000	0.000	0.000	0.000
30	A	1636	ALA	0	0.007	0.007	16.449	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	1637	LYS	1	0.874	0.956	18.846	0.396	0.396	0.000	0.000	0.000	0.000
32	A	1638	THR	0	-0.038	-0.027	21.358	0.016	0.016	0.000	0.000	0.000	0.000
33	A	1639	SER	0	0.010	0.018	24.719	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	1640	VAL	0	-0.078	-0.027	27.982	0.013	0.013	0.000	0.000	0.000	0.000
35	A	1641	ILE	0	-0.018	-0.011	31.459	0.002	0.002	0.000	0.000	0.000	0.000
36	A	1642	LYS	1	0.904	0.967	34.262	0.170	0.170	0.000	0.000	0.000	0.000
37	A	1643	ASP	-1	-0.890	-0.956	37.711	-0.116	-0.116	0.000	0.000	0.000	0.000
38	A	1644	HIS	0	0.035	0.021	41.195	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	1645	ASN	0	-0.037	-0.030	44.714	0.003	0.003	0.000	0.000	0.000	0.000
40	A	1646	GLY	0	0.028	0.014	45.864	0.004	0.004	0.000	0.000	0.000	0.000
41	A	1647	LYS	1	0.946	0.979	42.938	0.097	0.097	0.000	0.000	0.000	0.000
42	A	1648	LEU	0	0.001	-0.001	37.430	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	1649	PHE	0	-0.047	-0.022	38.843	0.005	0.005	0.000	0.000	0.000	0.000
44	A	1650	THR	0	0.056	0.025	33.715	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	1651	GLY	0	0.035	0.008	33.858	0.007	0.007	0.000	0.000	0.000	0.000
46	A	1652	LYS	1	0.919	0.963	33.514	0.177	0.177	0.000	0.000	0.000	0.000
47	A	1653	GLU	-1	-0.926	-0.972	35.538	-0.129	-0.129	0.000	0.000	0.000	0.000
48	A	1654	LEU	0	-0.028	-0.016	38.416	0.008	0.008	0.000	0.000	0.000	0.000
49	A	1655	LYS	1	0.826	0.914	37.414	0.174	0.174	0.000	0.000	0.000	0.000
50	A	1656	ASP	-1	-0.874	-0.933	37.914	-0.157	-0.157	0.000	0.000	0.000	0.000
51	A	1657	ALA	0	-0.064	-0.025	40.830	0.007	0.007	0.000	0.000	0.000	0.000
52	A	1658	ASN	0	-0.073	-0.029	43.110	0.012	0.012	0.000	0.000	0.000	0.000
53	A	1659	ASN	0	0.036	0.012	44.175	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	1660	ASN	0	-0.032	-0.020	46.742	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	1661	GLY	0	0.013	-0.002	48.118	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	1662	VAL	0	0.001	0.014	42.473	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	1663	THR	0	-0.012	-0.007	42.229	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1664	VAL	0	0.019	0.016	36.761	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	1665	THR	0	0.030	0.005	34.094	0.001	0.001	0.000	0.000	0.000	0.000
60	A	1666	GLU	-1	-0.774	-0.898	33.861	-0.193	-0.193	0.000	0.000	0.000	0.000
61	A	1667	THR	0	-0.031	-0.013	29.542	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	1668	ASP	-1	-0.840	-0.929	30.499	-0.223	-0.223	0.000	0.000	0.000	0.000
63	A	1669	GLY	0	-0.039	-0.020	32.802	0.006	0.006	0.000	0.000	0.000	0.000
64	A	1670	LYS	1	0.829	0.902	29.887	0.233	0.233	0.000	0.000	0.000	0.000
65	A	1671	ASP	-1	-0.815	-0.898	29.491	-0.253	-0.253	0.000	0.000	0.000	0.000
66	A	1672	GLU	-1	-0.911	-0.966	29.472	-0.205	-0.205	0.000	0.000	0.000	0.000
67	A	1673	GLY	0	-0.049	-0.027	29.743	0.010	0.010	0.000	0.000	0.000	0.000
68	A	1674	ASN	0	0.000	0.003	25.483	0.021	0.021	0.000	0.000	0.000	0.000
69	A	1675	GLY	0	-0.021	-0.002	23.709	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	1676	LEU	0	-0.029	-0.009	20.404	0.025	0.025	0.000	0.000	0.000	0.000
71	A	1677	VAL	0	0.033	0.015	24.674	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	1678	THR	0	0.002	-0.004	26.182	0.007	0.007	0.000	0.000	0.000	0.000
73	A	1679	ALA	0	0.051	0.010	28.198	0.008	0.008	0.000	0.000	0.000	0.000
74	A	1680	LYS	1	0.973	0.980	31.100	0.162	0.162	0.000	0.000	0.000	0.000
75	A	1681	ALA	0	0.021	0.025	31.123	0.006	0.006	0.000	0.000	0.000	0.000
76	A	1682	VAL	0	0.056	0.028	31.447	0.007	0.007	0.000	0.000	0.000	0.000
77	A	1683	ILE	0	-0.016	-0.009	34.123	0.008	0.008	0.000	0.000	0.000	0.000
78	A	1684	ASP	-1	-0.951	-0.987	36.442	-0.125	-0.125	0.000	0.000	0.000	0.000
79	A	1685	ALA	0	0.008	0.008	36.319	0.005	0.005	0.000	0.000	0.000	0.000
80	A	1686	VAL	0	0.010	-0.003	37.625	0.006	0.006	0.000	0.000	0.000	0.000
81	A	1687	ASN	0	-0.024	-0.020	40.098	0.007	0.007	0.000	0.000	0.000	0.000
82	A	1688	LYS	1	0.901	0.969	40.376	0.119	0.119	0.000	0.000	0.000	0.000
83	A	1689	ALA	0	0.002	0.013	41.977	0.000	0.000	0.000	0.000	0.000	0.000
84	A	1690	GLY	0	-0.032	-0.031	43.955	0.003	0.003	0.000	0.000	0.000	0.000
85	A	1691	TRP	0	-0.014	0.007	46.981	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	1692	ARG	1	0.901	0.957	50.216	0.076	0.076	0.000	0.000	0.000	0.000
87	A	1693	VAL	0	0.018	0.011	52.928	0.002	0.002	0.000	0.000	0.000	0.000
88	A	1694	LYS	1	0.892	0.956	56.622	0.054	0.054	0.000	0.000	0.000	0.000
89	A	1695	THR	0	-0.019	-0.013	58.758	0.002	0.002	0.000	0.000	0.000	0.000
90	A	1696	THR	0	0.026	0.005	61.149	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1697	GLY	0	-0.022	-0.010	64.183	0.001	0.001	0.000	0.000	0.000	0.000
92	A	1698	ALA	0	0.035	0.001	64.671	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	1699	ASN	0	-0.077	-0.036	68.006	0.000	0.000	0.000	0.000	0.000	0.000
94	A	1700	GLY	0	0.052	0.046	69.222	0.001	0.001	0.000	0.000	0.000	0.000
95	A	1701	GLN	0	-0.024	-0.016	67.952	0.000	0.000	0.000	0.000	0.000	0.000
96	A	1702	ASN	0	-0.072	-0.036	63.582	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	1703	ASP	-1	-0.880	-0.942	63.161	-0.049	-0.049	0.000	0.000	0.000	0.000
98	A	1704	ASP	-1	-0.858	-0.909	58.434	-0.062	-0.062	0.000	0.000	0.000	0.000
99	A	1705	PHE	0	-0.050	-0.046	55.025	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1706	ALA	0	0.016	0.015	54.810	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	1707	THR	0	-0.020	-0.029	48.177	0.002	0.002	0.000	0.000	0.000	0.000
102	A	1708	VAL	0	0.019	0.023	51.324	0.000	0.000	0.000	0.000	0.000	0.000
103	A	1709	ALA	0	0.017	0.020	46.099	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	1710	SER	0	0.027	-0.003	44.551	0.005	0.005	0.000	0.000	0.000	0.000
105	A	1711	GLY	0	-0.030	-0.013	46.676	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	1712	THR	0	-0.027	-0.001	48.572	0.001	0.001	0.000	0.000	0.000	0.000
107	A	1713	ASN	0	-0.039	-0.022	51.509	0.000	0.000	0.000	0.000	0.000	0.000
108	A	1714	VAL	0	0.028	0.013	54.683	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1715	THR	0	-0.016	-0.011	57.223	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1716	PHE	0	-0.008	-0.001	59.336	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1717	ALA	0	0.041	0.021	63.252	0.001	0.001	0.000	0.000	0.000	0.000
112	A	1718	ASP	-1	-0.905	-0.945	66.490	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	1719	GLY	0	0.029	0.016	70.080	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	1720	ASN	0	-0.045	-0.033	72.609	0.001	0.001	0.000	0.000	0.000	0.000
115	A	1721	GLY	0	0.005	0.001	76.138	0.000	0.000	0.000	0.000	0.000	0.000
116	A	1722	THR	0	0.012	0.019	72.128	0.001	0.001	0.000	0.000	0.000	0.000
117	A	1723	THR	0	-0.016	-0.018	72.085	0.000	0.000	0.000	0.000	0.000	0.000
118	A	1724	ALA	0	0.030	0.013	66.807	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1725	GLU	-1	-0.926	-0.955	67.291	-0.027	-0.027	0.000	0.000	0.000	0.000
120	A	1726	VAL	0	-0.022	-0.011	60.573	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1727	THR	0	0.001	0.006	62.832	0.000	0.000	0.000	0.000	0.000	0.000
122	A	1728	LYS	1	0.932	0.967	52.850	0.039	0.039	0.000	0.000	0.000	0.000
123	A	1729	ALA	0	0.023	0.022	58.768	0.001	0.001	0.000	0.000	0.000	0.000
124	A	1730	ASN	0	0.017	-0.018	57.652	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	1731	ASP	-1	-0.896	-0.934	54.785	-0.027	-0.027	0.000	0.000	0.000	0.000
126	A	1732	GLY	0	-0.080	-0.039	53.398	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	1733	SER	0	0.007	-0.009	54.485	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	1734	ILE	0	-0.009	-0.003	55.749	0.001	0.001	0.000	0.000	0.000	0.000
129	A	1735	THR	0	-0.008	0.002	58.214	0.000	0.000	0.000	0.000	0.000	0.000
130	A	1736	VAL	0	-0.022	-0.011	60.679	0.000	0.000	0.000	0.000	0.000	0.000
131	A	1737	LYS	1	0.946	0.969	63.456	0.027	0.027	0.000	0.000	0.000	0.000
132	A	1738	TYR	0	-0.031	-0.019	66.544	0.000	0.000	0.000	0.000	0.000	0.000
133	A	1739	ASN	0	-0.030	-0.001	69.883	0.001	0.001	0.000	0.000	0.000	0.000
134	A	1740	VAL	0	0.031	0.008	73.491	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	1741	LYS	1	0.923	0.969	76.665	0.029	0.029	0.000	0.000	0.000	0.000
136	A	1742	VAL	0	-0.002	-0.012	78.915	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1743	ALA	0	0.005	0.014	82.607	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1607:MET)