FMO DATABASE

FMODB ID: M37VZ

Calculation Name: 4Q28-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Q28

Chain ID: A

ChEMBL ID:

UniProt ID: O60437

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	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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-795413.019534
FMO2-HF: Nuclear repulsion	751057.820976
FMO2-HF: Total energy	-44355.198558
FMO2-MP2: Total energy	-44484.093792

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:1645:GLY)

Summations of interaction energy for fragment #1(A:1645:GLY)

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.
0.878	2.049	-0.017	-0.583	-0.571	0

Interaction energy analysis for fragmet #1(A:1645:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.007

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].
3	A	1647	HIS	0	0.014	0.004	3.821	0.414	1.585	-0.017	-0.583	-0.571
4	A	1648	HIS	0	-0.063	-0.016	5.126	0.595	0.595	0.000	0.000	0.000
5	A	1649	HIS	0	0.050	0.026	9.095	-0.051	-0.051	0.000	0.000	0.000
6	A	1650	HIS	0	-0.026	-0.013	10.891	0.085	0.085	0.000	0.000	0.000
7	A	1651	HIS	0	-0.021	-0.008	14.993	-0.047	-0.047	0.000	0.000	0.000
8	A	1652	SER	0	0.010	0.026	18.509	0.037	0.037	0.000	0.000	0.000
9	A	1653	HIS	0	0.015	0.003	21.487	-0.019	-0.019	0.000	0.000	0.000
10	A	1654	MET	0	-0.047	-0.020	24.469	0.012	0.012	0.000	0.000	0.000
11	A	1655	ARG	1	1.004	0.999	28.078	0.031	0.031	0.000	0.000	0.000
12	A	1656	ARG	1	0.868	0.934	31.212	0.030	0.030	0.000	0.000	0.000
13	A	1657	SER	0	-0.038	-0.028	34.914	-0.003	-0.003	0.000	0.000	0.000
14	A	1658	ILE	0	-0.010	-0.009	37.100	0.003	0.003	0.000	0.000	0.000
15	A	1659	VAL	0	0.010	0.015	40.401	-0.002	-0.002	0.000	0.000	0.000
16	A	1660	VAL	0	-0.040	-0.036	42.370	0.001	0.001	0.000	0.000	0.000
17	A	1661	ILE	0	-0.003	0.003	44.561	0.000	0.000	0.000	0.000	0.000
18	A	1662	HIS	0	-0.043	-0.017	47.728	0.000	0.000	0.000	0.000	0.000
19	A	1663	PRO	0	0.006	-0.003	50.533	0.001	0.001	0.000	0.000	0.000
20	A	1664	ASP	-1	-0.851	-0.920	53.766	-0.002	-0.002	0.000	0.000	0.000
21	A	1665	THR	0	-0.079	-0.044	50.075	0.001	0.001	0.000	0.000	0.000
22	A	1666	GLY	0	0.052	0.024	49.635	0.001	0.001	0.000	0.000	0.000
23	A	1667	ARG	1	0.911	0.953	45.226	0.008	0.008	0.000	0.000	0.000
24	A	1668	GLU	-1	-0.908	-0.958	40.205	-0.001	-0.001	0.000	0.000	0.000
25	A	1669	LEU	0	-0.032	-0.004	43.522	-0.001	-0.001	0.000	0.000	0.000
26	A	1670	SER	0	0.025	0.027	41.146	-0.001	-0.001	0.000	0.000	0.000
27	A	1671	PRO	0	0.035	-0.002	41.841	0.000	0.000	0.000	0.000	0.000
28	A	1672	GLU	-1	-0.878	-0.944	42.235	-0.034	-0.034	0.000	0.000	0.000
29	A	1673	GLU	-1	-0.880	-0.953	43.366	-0.018	-0.018	0.000	0.000	0.000
30	A	1674	ALA	0	0.014	0.008	46.517	0.001	0.001	0.000	0.000	0.000
31	A	1675	HIS	0	0.003	0.001	48.379	0.001	0.001	0.000	0.000	0.000
32	A	1676	ARG	1	0.813	0.906	44.722	0.027	0.027	0.000	0.000	0.000
33	A	1677	ALA	0	-0.047	-0.005	50.871	0.001	0.001	0.000	0.000	0.000
34	A	1678	GLY	0	-0.005	-0.003	52.501	0.001	0.001	0.000	0.000	0.000
35	A	1679	LEU	0	-0.025	-0.010	50.431	0.001	0.001	0.000	0.000	0.000
36	A	1680	ILE	0	-0.057	-0.022	48.425	0.001	0.001	0.000	0.000	0.000
37	A	1681	ASP	-1	-0.837	-0.922	52.741	-0.018	-0.018	0.000	0.000	0.000
38	A	1682	TRP	0	0.040	0.001	48.712	-0.001	-0.001	0.000	0.000	0.000
39	A	1683	ASN	0	0.017	-0.004	50.739	-0.003	-0.003	0.000	0.000	0.000
40	A	1684	MET	0	0.036	0.039	48.954	-0.001	-0.001	0.000	0.000	0.000
41	A	1685	PHE	0	0.007	0.009	44.498	-0.001	-0.001	0.000	0.000	0.000
42	A	1686	VAL	0	0.021	0.009	46.222	-0.002	-0.002	0.000	0.000	0.000
43	A	1687	LYS	1	0.912	0.956	45.681	0.018	0.018	0.000	0.000	0.000
44	A	1688	LEU	0	0.027	0.027	44.529	-0.001	-0.001	0.000	0.000	0.000
45	A	1689	ARG	1	0.975	0.995	38.478	0.039	0.039	0.000	0.000	0.000
46	A	1690	SER	0	-0.182	-0.098	40.817	-0.002	-0.002	0.000	0.000	0.000
47	A	1691	GLN	0	0.037	0.005	41.059	-0.001	-0.001	0.000	0.000	0.000
48	A	1692	GLU	-1	-0.886	-0.932	37.356	-0.028	-0.028	0.000	0.000	0.000
49	A	1693	CYS	0	-0.057	-0.041	33.246	-0.002	-0.002	0.000	0.000	0.000
50	A	1694	ASP	-1	-0.891	-0.948	29.503	-0.054	-0.054	0.000	0.000	0.000
51	A	1695	TRP	0	0.029	0.026	28.099	-0.009	-0.009	0.000	0.000	0.000
52	A	1696	GLU	-1	-0.793	-0.889	22.259	-0.105	-0.105	0.000	0.000	0.000
53	A	1697	GLU	-1	-0.785	-0.860	19.482	-0.166	-0.166	0.000	0.000	0.000
54	A	1698	ILE	0	-0.029	-0.021	16.990	0.006	0.006	0.000	0.000	0.000
55	A	1699	SER	0	0.011	-0.002	15.008	-0.023	-0.023	0.000	0.000	0.000
56	A	1700	VAL	0	-0.039	-0.015	11.816	-0.011	-0.011	0.000	0.000	0.000
57	A	1701	LYS	1	0.947	0.972	9.616	0.189	0.189	0.000	0.000	0.000
58	A	1702	GLY	0	0.001	-0.006	7.436	-0.187	-0.187	0.000	0.000	0.000
59	A	1703	PRO	0	-0.021	-0.012	6.537	0.085	0.085	0.000	0.000	0.000
60	A	1704	ASN	0	-0.017	-0.015	7.740	0.115	0.115	0.000	0.000	0.000
61	A	1705	GLY	0	0.060	0.041	10.846	0.109	0.109	0.000	0.000	0.000
62	A	1706	GLU	-1	-0.984	-1.003	11.391	-0.403	-0.403	0.000	0.000	0.000
63	A	1707	SER	0	-0.027	0.016	13.612	0.048	0.048	0.000	0.000	0.000
64	A	1708	SER	0	-0.011	-0.013	16.091	0.003	0.003	0.000	0.000	0.000
65	A	1709	VAL	0	0.000	0.005	18.736	0.016	0.016	0.000	0.000	0.000
66	A	1710	ILE	0	0.013	0.023	21.771	0.005	0.005	0.000	0.000	0.000
67	A	1711	HIS	0	-0.032	-0.043	21.915	0.011	0.011	0.000	0.000	0.000
68	A	1712	ASP	-1	-0.799	-0.906	26.730	-0.065	-0.065	0.000	0.000	0.000
69	A	1713	ARG	1	0.830	0.875	23.587	0.122	0.122	0.000	0.000	0.000
70	A	1714	LYS	1	0.841	0.949	30.412	0.048	0.048	0.000	0.000	0.000
71	A	1715	SER	0	-0.079	-0.044	33.822	0.000	0.000	0.000	0.000	0.000
72	A	1716	GLY	0	0.023	0.017	31.571	0.000	0.000	0.000	0.000	0.000
73	A	1717	LYS	1	0.888	0.954	31.493	0.077	0.077	0.000	0.000	0.000
74	A	1718	LYS	1	0.972	0.988	26.148	0.152	0.152	0.000	0.000	0.000
75	A	1719	PHE	0	-0.004	-0.018	26.547	0.005	0.005	0.000	0.000	0.000
76	A	1720	SER	0	0.045	0.040	23.288	-0.002	-0.002	0.000	0.000	0.000
77	A	1721	ILE	0	0.077	0.027	21.507	0.019	0.019	0.000	0.000	0.000
78	A	1722	GLU	-1	-0.830	-0.920	19.299	-0.243	-0.243	0.000	0.000	0.000
79	A	1723	GLU	-1	-0.955	-0.981	23.021	-0.146	-0.146	0.000	0.000	0.000
80	A	1724	ALA	0	-0.109	-0.051	25.923	0.015	0.015	0.000	0.000	0.000
81	A	1725	LEU	0	-0.011	-0.006	22.817	0.011	0.011	0.000	0.000	0.000
82	A	1726	GLN	0	-0.031	-0.006	26.545	0.007	0.007	0.000	0.000	0.000
83	A	1727	SER	0	-0.077	-0.050	28.120	0.012	0.012	0.000	0.000	0.000
84	A	1728	GLY	0	0.043	0.021	30.241	0.008	0.008	0.000	0.000	0.000
85	A	1729	ARG	1	0.877	0.944	29.090	0.118	0.118	0.000	0.000	0.000
86	A	1730	LEU	0	0.006	0.016	25.545	0.006	0.006	0.000	0.000	0.000
87	A	1731	THR	0	0.047	0.010	28.923	-0.003	-0.003	0.000	0.000	0.000
88	A	1732	PRO	0	0.035	-0.002	25.749	0.002	0.002	0.000	0.000	0.000
89	A	1733	ALA	0	0.061	0.038	26.065	0.004	0.004	0.000	0.000	0.000
90	A	1734	GLN	0	-0.035	-0.035	27.986	0.003	0.003	0.000	0.000	0.000
91	A	1735	TYR	0	0.032	0.025	18.385	0.009	0.009	0.000	0.000	0.000
92	A	1736	ASP	-1	-0.829	-0.923	22.845	-0.075	-0.075	0.000	0.000	0.000
93	A	1737	ARG	1	0.928	0.976	23.591	0.046	0.046	0.000	0.000	0.000
94	A	1738	TYR	0	-0.086	-0.067	20.862	0.014	0.014	0.000	0.000	0.000
95	A	1739	VAL	0	-0.005	0.000	18.040	0.008	0.008	0.000	0.000	0.000
96	A	1740	ASN	0	-0.080	-0.045	19.835	0.021	0.021	0.000	0.000	0.000
97	A	1741	LYS	1	0.854	0.930	18.449	0.053	0.053	0.000	0.000	0.000
98	A	1742	ASP	-1	-0.866	-0.937	23.330	0.016	0.016	0.000	0.000	0.000
99	A	1743	MET	0	-0.108	-0.040	26.128	-0.007	-0.007	0.000	0.000	0.000
100	A	1744	SER	0	-0.035	-0.010	26.190	-0.004	-0.004	0.000	0.000	0.000
101	A	1745	ILE	0	0.073	0.013	24.708	-0.005	-0.005	0.000	0.000	0.000
102	A	1746	GLN	0	0.073	0.035	27.088	-0.003	-0.003	0.000	0.000	0.000
103	A	1747	GLU	-1	-0.898	-0.948	30.244	-0.030	-0.030	0.000	0.000	0.000
104	A	1748	LEU	0	0.045	0.023	24.191	-0.002	-0.002	0.000	0.000	0.000
105	A	1749	ALA	0	0.007	0.005	28.585	-0.007	-0.007	0.000	0.000	0.000
106	A	1750	VAL	0	-0.041	-0.004	29.990	-0.004	-0.004	0.000	0.000	0.000
107	A	1751	LEU	0	-0.026	-0.007	29.578	0.000	0.000	0.000	0.000	0.000
108	A	1752	VAL	0	-0.013	-0.001	27.169	-0.003	-0.003	0.000	0.000	0.000
109	A	1753	SER	0	-0.124	-0.069	30.594	0.000	0.000	0.000	0.000	0.000
110	A	1754	GLY	0	-0.030	-0.011	32.977	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1645:GLY)