FMO DATABASE

FMODB ID: MVM9Z

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	OptHSide
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	-818139.120334
FMO2-HF: Nuclear repulsion	768463.380281
FMO2-HF: Total energy	-49675.740052
FMO2-MP2: Total energy	-49821.905481

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.
-1.174	2.353	3.108	-2.1	-4.535	-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 : -0.028 / q_NPA : -0.006

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	-0.030	-0.028	2.640	-2.364	1.163	3.108	-2.100	-4.535	-0.002
4	A	1610	VAL	0	0.025	0.015	5.704	0.382	0.382	0.000	0.000	0.000	0.000
5	A	1611	SER	0	-0.033	-0.020	9.231	0.158	0.158	0.000	0.000	0.000	0.000
6	A	1612	GLY	0	0.038	0.022	11.923	0.030	0.030	0.000	0.000	0.000	0.000
7	A	1613	ASP	-1	-0.869	-0.940	14.478	-0.387	-0.387	0.000	0.000	0.000	0.000
8	A	1614	LYS	1	0.821	0.900	14.787	0.702	0.702	0.000	0.000	0.000	0.000
9	A	1615	ASP	-1	-0.793	-0.875	17.850	-0.418	-0.418	0.000	0.000	0.000	0.000
10	A	1616	THR	0	0.047	0.017	17.918	0.018	0.018	0.000	0.000	0.000	0.000
11	A	1617	THR	0	-0.058	-0.038	13.436	0.013	0.013	0.000	0.000	0.000	0.000
12	A	1618	SER	0	-0.022	-0.006	15.077	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	1619	VAL	0	0.011	-0.003	8.387	0.045	0.045	0.000	0.000	0.000	0.000
14	A	1620	THR	0	-0.040	-0.012	11.610	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	1621	VAL	0	0.030	0.007	6.476	0.056	0.056	0.000	0.000	0.000	0.000
16	A	1622	GLU	-1	-0.760	-0.867	9.706	-0.697	-0.697	0.000	0.000	0.000	0.000
17	A	1623	SER	0	-0.012	-0.035	11.576	-0.076	-0.076	0.000	0.000	0.000	0.000
18	A	1624	LYS	1	0.762	0.848	13.210	0.698	0.698	0.000	0.000	0.000	0.000
19	A	1625	ASP	-1	-0.845	-0.887	16.387	-0.321	-0.321	0.000	0.000	0.000	0.000
20	A	1626	ASN	0	-0.028	-0.007	18.286	0.000	0.000	0.000	0.000	0.000	0.000
21	A	1627	GLY	0	0.031	0.023	15.480	-0.052	-0.052	0.000	0.000	0.000	0.000
22	A	1628	LYS	1	0.918	0.948	12.800	0.110	0.110	0.000	0.000	0.000	0.000
23	A	1629	ARG	1	0.877	0.923	12.585	0.462	0.462	0.000	0.000	0.000	0.000
24	A	1630	THR	0	0.042	0.019	8.543	0.011	0.011	0.000	0.000	0.000	0.000
25	A	1631	GLU	-1	-0.834	-0.880	9.710	-0.635	-0.635	0.000	0.000	0.000	0.000
26	A	1632	VAL	0	0.023	0.003	6.513	-0.102	-0.102	0.000	0.000	0.000	0.000
27	A	1633	LYS	1	0.808	0.904	9.942	0.931	0.931	0.000	0.000	0.000	0.000
28	A	1634	ILE	0	0.006	0.003	8.099	-0.093	-0.093	0.000	0.000	0.000	0.000
29	A	1635	GLY	0	0.020	0.020	12.692	0.105	0.105	0.000	0.000	0.000	0.000
30	A	1636	ALA	0	-0.006	-0.004	16.077	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	1637	LYS	1	0.851	0.924	18.484	0.446	0.446	0.000	0.000	0.000	0.000
32	A	1638	THR	0	-0.022	-0.012	20.929	0.018	0.018	0.000	0.000	0.000	0.000
33	A	1639	SER	0	-0.042	-0.042	24.308	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	1640	VAL	0	-0.080	-0.042	27.528	0.014	0.014	0.000	0.000	0.000	0.000
35	A	1641	ILE	0	-0.019	-0.009	31.032	0.002	0.002	0.000	0.000	0.000	0.000
36	A	1642	LYS	1	0.830	0.919	33.823	0.197	0.197	0.000	0.000	0.000	0.000
37	A	1643	ASP	-1	-0.895	-0.954	37.264	-0.129	-0.129	0.000	0.000	0.000	0.000
38	A	1644	HIS	0	0.022	0.010	40.743	0.001	0.001	0.000	0.000	0.000	0.000
39	A	1645	ASN	0	-0.028	-0.024	44.248	0.005	0.005	0.000	0.000	0.000	0.000
40	A	1646	GLY	0	0.040	0.018	45.434	0.004	0.004	0.000	0.000	0.000	0.000
41	A	1647	LYS	1	0.947	0.982	42.146	0.115	0.115	0.000	0.000	0.000	0.000
42	A	1648	LEU	0	0.003	0.000	37.009	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	1649	PHE	0	-0.057	-0.032	38.327	0.006	0.006	0.000	0.000	0.000	0.000
44	A	1650	THR	0	0.014	-0.029	33.234	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	1651	GLY	0	0.020	-0.003	33.468	0.008	0.008	0.000	0.000	0.000	0.000
46	A	1652	LYS	1	0.888	0.935	33.294	0.202	0.202	0.000	0.000	0.000	0.000
47	A	1653	GLU	-1	-0.852	-0.896	35.447	-0.148	-0.148	0.000	0.000	0.000	0.000
48	A	1654	LEU	0	-0.036	-0.023	38.109	0.009	0.009	0.000	0.000	0.000	0.000
49	A	1655	LYS	1	0.804	0.896	37.276	0.186	0.186	0.000	0.000	0.000	0.000
50	A	1656	ASP	-1	-0.858	-0.909	38.002	-0.174	-0.174	0.000	0.000	0.000	0.000
51	A	1657	ALA	0	-0.049	-0.019	40.835	0.007	0.007	0.000	0.000	0.000	0.000
52	A	1658	ASN	0	-0.070	-0.033	42.983	0.013	0.013	0.000	0.000	0.000	0.000
53	A	1659	ASN	0	0.008	0.000	44.127	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	1660	ASN	0	-0.010	-0.007	46.739	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1661	GLY	0	0.023	0.005	47.897	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	1662	VAL	0	-0.008	0.008	42.276	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	1663	THR	0	-0.005	0.002	42.243	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1664	VAL	0	0.019	0.014	36.664	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	1665	THR	0	0.033	0.014	34.068	0.002	0.002	0.000	0.000	0.000	0.000
60	A	1666	GLU	-1	-0.759	-0.878	33.947	-0.205	-0.205	0.000	0.000	0.000	0.000
61	A	1667	THR	0	-0.008	-0.006	29.505	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	1668	ASP	-1	-0.801	-0.898	30.510	-0.240	-0.240	0.000	0.000	0.000	0.000
63	A	1669	GLY	0	-0.027	-0.012	32.737	0.006	0.006	0.000	0.000	0.000	0.000
64	A	1670	LYS	1	0.817	0.891	30.008	0.247	0.247	0.000	0.000	0.000	0.000
65	A	1671	ASP	-1	-0.789	-0.862	28.785	-0.287	-0.287	0.000	0.000	0.000	0.000
66	A	1672	GLU	-1	-0.892	-0.959	29.274	-0.226	-0.226	0.000	0.000	0.000	0.000
67	A	1673	GLY	0	-0.051	-0.022	29.228	0.011	0.011	0.000	0.000	0.000	0.000
68	A	1674	ASN	0	-0.003	0.006	25.108	0.023	0.023	0.000	0.000	0.000	0.000
69	A	1675	GLY	0	-0.015	0.002	23.196	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	1676	LEU	0	-0.024	-0.005	19.997	0.028	0.028	0.000	0.000	0.000	0.000
71	A	1677	VAL	0	0.027	0.008	24.238	0.001	0.001	0.000	0.000	0.000	0.000
72	A	1678	THR	0	0.009	0.002	25.905	0.008	0.008	0.000	0.000	0.000	0.000
73	A	1679	ALA	0	0.056	0.015	27.902	0.009	0.009	0.000	0.000	0.000	0.000
74	A	1680	LYS	1	0.957	0.980	30.842	0.171	0.171	0.000	0.000	0.000	0.000
75	A	1681	ALA	0	0.024	0.021	30.741	0.008	0.008	0.000	0.000	0.000	0.000
76	A	1682	VAL	0	0.064	0.028	31.083	0.008	0.008	0.000	0.000	0.000	0.000
77	A	1683	ILE	0	-0.014	-0.007	33.776	0.009	0.009	0.000	0.000	0.000	0.000
78	A	1684	ASP	-1	-0.872	-0.944	36.091	-0.136	-0.136	0.000	0.000	0.000	0.000
79	A	1685	ALA	0	0.016	0.015	35.930	0.006	0.006	0.000	0.000	0.000	0.000
80	A	1686	VAL	0	0.017	-0.001	37.281	0.006	0.006	0.000	0.000	0.000	0.000
81	A	1687	ASN	0	-0.023	-0.019	39.730	0.008	0.008	0.000	0.000	0.000	0.000
82	A	1688	LYS	1	0.804	0.914	39.493	0.137	0.137	0.000	0.000	0.000	0.000
83	A	1689	ALA	0	-0.005	0.009	41.554	0.000	0.000	0.000	0.000	0.000	0.000
84	A	1690	GLY	0	-0.032	-0.031	43.549	0.004	0.004	0.000	0.000	0.000	0.000
85	A	1691	TRP	0	-0.022	0.003	46.566	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	1692	ARG	1	0.899	0.947	49.777	0.087	0.087	0.000	0.000	0.000	0.000
87	A	1693	VAL	0	0.007	0.007	52.482	0.002	0.002	0.000	0.000	0.000	0.000
88	A	1694	LYS	1	0.786	0.888	56.184	0.058	0.058	0.000	0.000	0.000	0.000
89	A	1695	THR	0	-0.021	-0.014	58.354	0.002	0.002	0.000	0.000	0.000	0.000
90	A	1696	THR	0	0.018	0.003	60.723	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1697	GLY	0	-0.014	-0.014	63.749	0.002	0.002	0.000	0.000	0.000	0.000
92	A	1698	ALA	0	0.026	-0.001	64.248	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	1699	ASN	0	-0.076	-0.032	67.572	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	1700	GLY	0	0.068	0.040	69.012	0.001	0.001	0.000	0.000	0.000	0.000
95	A	1701	GLN	0	-0.034	-0.014	67.422	0.000	0.000	0.000	0.000	0.000	0.000
96	A	1702	ASN	0	-0.054	-0.024	63.065	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	1703	ASP	-1	-0.821	-0.912	62.508	-0.055	-0.055	0.000	0.000	0.000	0.000
98	A	1704	ASP	-1	-0.827	-0.886	58.025	-0.068	-0.068	0.000	0.000	0.000	0.000
99	A	1705	PHE	0	-0.028	-0.031	54.590	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1706	ALA	0	0.004	0.013	54.392	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	1707	THR	0	-0.009	-0.012	47.782	0.001	0.001	0.000	0.000	0.000	0.000
102	A	1708	VAL	0	0.014	0.019	51.003	0.000	0.000	0.000	0.000	0.000	0.000
103	A	1709	ALA	0	0.025	0.025	45.769	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	1710	SER	0	0.034	0.016	44.147	0.006	0.006	0.000	0.000	0.000	0.000
105	A	1711	GLY	0	-0.024	-0.011	46.340	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	1712	THR	0	-0.045	-0.026	48.280	0.002	0.002	0.000	0.000	0.000	0.000
107	A	1713	ASN	0	-0.043	-0.023	51.198	0.000	0.000	0.000	0.000	0.000	0.000
108	A	1714	VAL	0	0.026	0.012	54.285	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1715	THR	0	-0.015	-0.009	56.889	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1716	PHE	0	-0.003	0.000	58.730	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1717	ALA	0	0.038	0.024	62.907	0.002	0.002	0.000	0.000	0.000	0.000
112	A	1718	ASP	-1	-0.826	-0.914	66.157	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	1719	GLY	0	0.016	0.015	69.736	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	1720	ASN	0	-0.035	-0.033	72.254	0.001	0.001	0.000	0.000	0.000	0.000
115	A	1721	GLY	0	0.025	0.009	75.771	0.000	0.000	0.000	0.000	0.000	0.000
116	A	1722	THR	0	0.014	0.015	71.760	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1723	THR	0	-0.034	-0.026	72.005	0.000	0.000	0.000	0.000	0.000	0.000
118	A	1724	ALA	0	0.014	0.014	66.476	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1725	GLU	-1	-0.814	-0.885	67.075	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	1726	VAL	0	-0.003	-0.001	60.243	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1727	THR	0	0.006	0.003	62.526	0.000	0.000	0.000	0.000	0.000	0.000
122	A	1728	LYS	1	0.911	0.962	52.555	0.048	0.048	0.000	0.000	0.000	0.000
123	A	1729	ALA	0	0.036	0.033	58.415	0.001	0.001	0.000	0.000	0.000	0.000
124	A	1730	ASN	0	0.011	-0.017	57.401	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	1731	ASP	-1	-0.906	-0.945	54.505	-0.035	-0.035	0.000	0.000	0.000	0.000
126	A	1732	GLY	0	-0.065	-0.033	53.099	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	1733	SER	0	0.019	-0.003	54.186	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	1734	ILE	0	-0.020	-0.013	55.204	0.002	0.002	0.000	0.000	0.000	0.000
129	A	1735	THR	0	0.005	0.010	57.871	0.000	0.000	0.000	0.000	0.000	0.000
130	A	1736	VAL	0	-0.026	-0.010	60.325	0.001	0.001	0.000	0.000	0.000	0.000
131	A	1737	LYS	1	0.844	0.912	63.090	0.033	0.033	0.000	0.000	0.000	0.000
132	A	1738	TYR	0	-0.018	-0.023	65.494	0.000	0.000	0.000	0.000	0.000	0.000
133	A	1739	ASN	0	-0.077	-0.035	69.506	0.001	0.001	0.000	0.000	0.000	0.000
134	A	1740	VAL	0	0.029	0.006	73.123	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	1741	LYS	1	0.842	0.932	74.797	0.035	0.035	0.000	0.000	0.000	0.000
136	A	1742	VAL	0	0.008	-0.005	78.562	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1743	ALA	0	0.014	0.021	82.247	0.001	0.001	0.000	0.000	0.000	0.000

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