FMO DATABASE

FMODB ID: 72JMK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-820020.168211
FMO2-HF: Nuclear repulsion	770343.913359
FMO2-HF: Total energy	-49676.254851
FMO2-MP2: Total energy	-49822.458658

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.
-2.34	1.458	2.705	-2.086	-4.417	-0.005

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 : -0.014 / q_NPA : -0.003

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	-0.020	-0.021	2.454	-3.969	-0.221	2.706	-2.083	-4.372	-0.005
4	A	1610	VAL	0	0.009	0.002	5.295	0.651	0.701	-0.001	-0.003	-0.045	0.000
5	A	1611	SER	0	-0.008	-0.012	8.677	0.078	0.078	0.000	0.000	0.000	0.000
6	A	1612	GLY	0	0.033	0.023	11.493	0.040	0.040	0.000	0.000	0.000	0.000
7	A	1613	ASP	-1	-0.884	-0.945	14.344	-0.479	-0.479	0.000	0.000	0.000	0.000
8	A	1614	LYS	1	0.852	0.906	13.867	0.882	0.882	0.000	0.000	0.000	0.000
9	A	1615	ASP	-1	-0.785	-0.879	17.201	-0.472	-0.472	0.000	0.000	0.000	0.000
10	A	1616	THR	0	0.027	0.025	18.563	0.007	0.007	0.000	0.000	0.000	0.000
11	A	1617	THR	0	-0.031	-0.012	13.296	0.007	0.007	0.000	0.000	0.000	0.000
12	A	1618	SER	0	-0.034	-0.005	14.857	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	1619	VAL	0	0.028	-0.006	8.194	0.011	0.011	0.000	0.000	0.000	0.000
14	A	1620	THR	0	-0.043	-0.011	11.168	0.039	0.039	0.000	0.000	0.000	0.000
15	A	1621	VAL	0	0.042	0.007	6.732	-0.126	-0.126	0.000	0.000	0.000	0.000
16	A	1622	GLU	-1	-0.764	-0.847	10.005	-0.713	-0.713	0.000	0.000	0.000	0.000
17	A	1623	SER	0	0.017	-0.017	11.345	-0.127	-0.127	0.000	0.000	0.000	0.000
18	A	1624	LYS	1	0.773	0.875	13.148	0.782	0.782	0.000	0.000	0.000	0.000
19	A	1625	ASP	-1	-0.845	-0.910	16.341	-0.351	-0.351	0.000	0.000	0.000	0.000
20	A	1626	ASN	0	-0.059	-0.013	18.445	0.018	0.018	0.000	0.000	0.000	0.000
21	A	1627	GLY	0	0.065	0.014	14.771	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	1628	LYS	1	0.930	0.969	12.289	0.062	0.062	0.000	0.000	0.000	0.000
23	A	1629	ARG	1	0.851	0.911	12.063	0.497	0.497	0.000	0.000	0.000	0.000
24	A	1630	THR	0	0.021	0.015	7.971	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	1631	GLU	-1	-0.835	-0.902	10.128	-0.674	-0.674	0.000	0.000	0.000	0.000
26	A	1632	VAL	0	0.022	0.013	6.125	0.006	0.006	0.000	0.000	0.000	0.000
27	A	1633	LYS	1	0.786	0.882	9.444	1.211	1.211	0.000	0.000	0.000	0.000
28	A	1634	ILE	0	0.000	-0.003	8.088	-0.136	-0.136	0.000	0.000	0.000	0.000
29	A	1635	GLY	0	0.020	0.015	12.641	0.120	0.120	0.000	0.000	0.000	0.000
30	A	1636	ALA	0	-0.001	0.017	16.145	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	1637	LYS	1	0.812	0.897	18.508	0.491	0.491	0.000	0.000	0.000	0.000
32	A	1638	THR	0	-0.034	-0.024	20.562	0.022	0.022	0.000	0.000	0.000	0.000
33	A	1639	SER	0	-0.046	-0.045	24.039	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	1640	VAL	0	-0.087	-0.056	27.094	0.011	0.011	0.000	0.000	0.000	0.000
35	A	1641	ILE	0	0.006	0.000	30.680	0.008	0.008	0.000	0.000	0.000	0.000
36	A	1642	LYS	1	0.832	0.921	33.432	0.228	0.228	0.000	0.000	0.000	0.000
37	A	1643	ASP	-1	-0.881	-0.948	36.960	-0.152	-0.152	0.000	0.000	0.000	0.000
38	A	1644	HIS	0	0.020	-0.001	40.519	0.001	0.001	0.000	0.000	0.000	0.000
39	A	1645	ASN	0	-0.031	-0.027	43.859	0.007	0.007	0.000	0.000	0.000	0.000
40	A	1646	GLY	0	0.055	0.053	45.086	0.006	0.006	0.000	0.000	0.000	0.000
41	A	1647	LYS	1	0.857	0.948	40.077	0.150	0.150	0.000	0.000	0.000	0.000
42	A	1648	LEU	0	0.004	-0.003	36.726	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	1649	PHE	0	-0.057	-0.043	37.791	0.006	0.006	0.000	0.000	0.000	0.000
44	A	1650	THR	0	0.011	-0.013	32.596	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	1651	GLY	0	0.030	0.002	33.096	0.011	0.011	0.000	0.000	0.000	0.000
46	A	1652	LYS	1	0.869	0.926	32.663	0.228	0.228	0.000	0.000	0.000	0.000
47	A	1653	GLU	-1	-0.780	-0.870	35.034	-0.166	-0.166	0.000	0.000	0.000	0.000
48	A	1654	LEU	0	-0.044	-0.023	37.818	0.010	0.010	0.000	0.000	0.000	0.000
49	A	1655	LYS	1	0.806	0.908	37.034	0.203	0.203	0.000	0.000	0.000	0.000
50	A	1656	ASP	-1	-0.844	-0.904	37.691	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	1657	ALA	0	-0.039	-0.021	40.498	0.009	0.009	0.000	0.000	0.000	0.000
52	A	1658	ASN	0	-0.061	-0.032	42.804	0.015	0.015	0.000	0.000	0.000	0.000
53	A	1659	ASN	0	0.008	0.006	43.731	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	1660	ASN	0	0.012	0.002	46.311	0.003	0.003	0.000	0.000	0.000	0.000
55	A	1661	GLY	0	0.017	0.009	47.202	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	1662	VAL	0	-0.006	0.006	41.761	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	1663	THR	0	-0.006	-0.001	41.730	0.002	0.002	0.000	0.000	0.000	0.000
58	A	1664	VAL	0	-0.001	0.013	36.421	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	1665	THR	0	0.032	0.008	34.047	0.005	0.005	0.000	0.000	0.000	0.000
60	A	1666	GLU	-1	-0.808	-0.903	34.272	-0.222	-0.222	0.000	0.000	0.000	0.000
61	A	1667	THR	0	0.018	0.000	29.446	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	1668	ASP	-1	-0.783	-0.869	30.727	-0.272	-0.272	0.000	0.000	0.000	0.000
63	A	1669	GLY	0	0.004	-0.004	32.447	0.003	0.003	0.000	0.000	0.000	0.000
64	A	1670	LYS	1	0.793	0.886	30.068	0.268	0.268	0.000	0.000	0.000	0.000
65	A	1671	ASP	-1	-0.779	-0.851	28.213	-0.337	-0.337	0.000	0.000	0.000	0.000
66	A	1672	GLU	-1	-0.905	-0.974	29.041	-0.250	-0.250	0.000	0.000	0.000	0.000
67	A	1673	GLY	0	-0.034	-0.021	29.160	0.013	0.013	0.000	0.000	0.000	0.000
68	A	1674	ASN	0	-0.025	-0.004	24.763	0.020	0.020	0.000	0.000	0.000	0.000
69	A	1675	GLY	0	0.019	0.015	22.923	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	1676	LEU	0	-0.027	-0.008	19.725	0.032	0.032	0.000	0.000	0.000	0.000
71	A	1677	VAL	0	0.019	0.009	23.944	0.005	0.005	0.000	0.000	0.000	0.000
72	A	1678	THR	0	0.017	0.006	26.032	0.008	0.008	0.000	0.000	0.000	0.000
73	A	1679	ALA	0	0.056	0.016	27.946	0.013	0.013	0.000	0.000	0.000	0.000
74	A	1680	LYS	1	0.951	0.984	30.711	0.204	0.204	0.000	0.000	0.000	0.000
75	A	1681	ALA	0	0.025	0.015	30.471	0.011	0.011	0.000	0.000	0.000	0.000
76	A	1682	VAL	0	0.042	0.021	30.920	0.009	0.009	0.000	0.000	0.000	0.000
77	A	1683	ILE	0	-0.004	0.000	33.636	0.011	0.011	0.000	0.000	0.000	0.000
78	A	1684	ASP	-1	-0.851	-0.938	35.955	-0.163	-0.163	0.000	0.000	0.000	0.000
79	A	1685	ALA	0	0.016	0.035	35.916	0.007	0.007	0.000	0.000	0.000	0.000
80	A	1686	VAL	0	0.030	0.002	37.127	0.009	0.009	0.000	0.000	0.000	0.000
81	A	1687	ASN	0	-0.031	-0.018	39.536	0.011	0.011	0.000	0.000	0.000	0.000
82	A	1688	LYS	1	0.792	0.893	39.454	0.163	0.163	0.000	0.000	0.000	0.000
83	A	1689	ALA	0	-0.013	0.003	40.889	0.004	0.004	0.000	0.000	0.000	0.000
84	A	1690	GLY	0	-0.007	-0.018	42.957	0.004	0.004	0.000	0.000	0.000	0.000
85	A	1691	TRP	0	-0.013	0.014	46.413	0.000	0.000	0.000	0.000	0.000	0.000
86	A	1692	ARG	1	0.844	0.892	49.365	0.100	0.100	0.000	0.000	0.000	0.000
87	A	1693	VAL	0	0.007	0.010	52.462	0.003	0.003	0.000	0.000	0.000	0.000
88	A	1694	LYS	1	0.793	0.906	56.179	0.068	0.068	0.000	0.000	0.000	0.000
89	A	1695	THR	0	-0.037	-0.034	58.114	0.002	0.002	0.000	0.000	0.000	0.000
90	A	1696	THR	0	0.031	0.017	60.537	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1697	GLY	0	-0.052	-0.030	63.360	0.002	0.002	0.000	0.000	0.000	0.000
92	A	1698	ALA	0	0.030	0.000	63.833	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	1699	ASN	0	-0.075	-0.034	67.135	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	1700	GLY	0	0.066	0.038	68.689	0.001	0.001	0.000	0.000	0.000	0.000
95	A	1701	GLN	0	-0.036	-0.014	66.700	0.000	0.000	0.000	0.000	0.000	0.000
96	A	1702	ASN	0	-0.047	-0.020	62.470	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	1703	ASP	-1	-0.814	-0.908	62.054	-0.064	-0.064	0.000	0.000	0.000	0.000
98	A	1704	ASP	-1	-0.824	-0.893	57.538	-0.079	-0.079	0.000	0.000	0.000	0.000
99	A	1705	PHE	0	-0.009	-0.021	54.442	0.002	0.002	0.000	0.000	0.000	0.000
100	A	1706	ALA	0	0.029	0.039	54.210	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	1707	THR	0	0.014	-0.007	47.429	0.001	0.001	0.000	0.000	0.000	0.000
102	A	1708	VAL	0	-0.016	-0.002	50.402	0.001	0.001	0.000	0.000	0.000	0.000
103	A	1709	ALA	0	0.031	0.024	45.573	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	1710	SER	0	-0.001	-0.011	43.068	0.007	0.007	0.000	0.000	0.000	0.000
105	A	1711	GLY	0	-0.019	-0.004	45.780	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	1712	THR	0	-0.063	-0.035	48.116	0.003	0.003	0.000	0.000	0.000	0.000
107	A	1713	ASN	0	-0.031	-0.017	51.056	0.001	0.001	0.000	0.000	0.000	0.000
108	A	1714	VAL	0	0.016	0.006	54.241	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1715	THR	0	-0.018	-0.012	56.859	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1716	PHE	0	0.012	0.007	58.222	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1717	ALA	0	0.046	0.031	62.907	0.002	0.002	0.000	0.000	0.000	0.000
112	A	1718	ASP	-1	-0.835	-0.918	66.135	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	1719	GLY	0	0.060	0.027	69.694	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	1720	ASN	0	-0.005	-0.012	72.634	0.001	0.001	0.000	0.000	0.000	0.000
115	A	1721	GLY	0	0.023	0.022	75.068	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	1722	THR	0	-0.004	0.004	71.843	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1723	THR	0	-0.010	-0.014	71.876	0.001	0.001	0.000	0.000	0.000	0.000
118	A	1724	ALA	0	0.007	0.005	66.511	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1725	GLU	-1	-0.804	-0.878	66.861	-0.041	-0.041	0.000	0.000	0.000	0.000
120	A	1726	VAL	0	-0.008	0.005	60.075	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	1727	THR	0	-0.022	-0.010	62.256	0.001	0.001	0.000	0.000	0.000	0.000
122	A	1728	LYS	1	0.909	0.947	52.721	0.062	0.062	0.000	0.000	0.000	0.000
123	A	1729	ALA	0	0.041	0.040	58.194	0.002	0.002	0.000	0.000	0.000	0.000
124	A	1730	ASN	0	-0.012	-0.025	57.026	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	1731	ASP	-1	-0.899	-0.943	54.174	-0.050	-0.050	0.000	0.000	0.000	0.000
126	A	1732	GLY	0	-0.052	-0.024	52.671	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	1733	SER	0	0.021	-0.005	53.742	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	1734	ILE	0	0.012	0.012	54.832	0.002	0.002	0.000	0.000	0.000	0.000
129	A	1735	THR	0	-0.022	-0.016	57.505	0.001	0.001	0.000	0.000	0.000	0.000
130	A	1736	VAL	0	-0.012	0.007	60.136	0.001	0.001	0.000	0.000	0.000	0.000
131	A	1737	LYS	1	0.825	0.904	62.849	0.043	0.043	0.000	0.000	0.000	0.000
132	A	1738	TYR	0	-0.024	-0.035	64.968	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	1739	ASN	0	-0.078	-0.040	69.309	0.002	0.002	0.000	0.000	0.000	0.000
134	A	1740	VAL	0	0.017	0.006	73.036	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	1741	LYS	1	0.811	0.917	74.145	0.043	0.043	0.000	0.000	0.000	0.000
136	A	1742	VAL	0	0.002	-0.012	78.120	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1743	ALA	0	0.011	0.016	81.911	0.000	0.000	0.000	0.000	0.000	0.000

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