FMO DATABASE

FMODB ID: 2NMVR

Calculation Name: 3ERS-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ERS

Chain ID: X

ChEMBL ID:

UniProt ID: P42589

Base Structure: X-ray

Registration Date: 2023-09-23

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-847104.023214
FMO2-HF: Nuclear repulsion	801235.657637
FMO2-HF: Total energy	-45868.365577
FMO2-MP2: Total energy	-45995.21264

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(X:1:MET)

Summations of interaction energy for fragment #1(X: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.
-3.592	-0.244	0.37	-1.883	-1.834	-0.005

Interaction energy analysis for fragmet #1(X:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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	X	3	THR	0	0.008	0.004	2.773	-4.284	-1.037	0.371	-1.867	-1.750	-0.005
4	X	4	VAL	0	-0.056	-0.027	4.431	0.374	0.475	-0.001	-0.016	-0.084	0.000
5	X	5	ALA	0	0.035	0.020	6.737	-0.090	-0.090	0.000	0.000	0.000	0.000
6	X	6	TYR	0	0.053	0.005	10.333	0.145	0.145	0.000	0.000	0.000	0.000
7	X	7	ALA	0	-0.001	-0.013	12.805	0.096	0.096	0.000	0.000	0.000	0.000
8	X	8	ASP	-1	-0.800	-0.894	8.894	0.064	0.064	0.000	0.000	0.000	0.000
9	X	9	PHE	0	0.041	0.022	10.818	0.174	0.174	0.000	0.000	0.000	0.000
10	X	10	ALA	0	-0.029	-0.022	11.749	0.041	0.041	0.000	0.000	0.000	0.000
11	X	11	ARG	1	0.833	0.914	11.717	-0.296	-0.296	0.000	0.000	0.000	0.000
12	X	12	LEU	0	0.027	0.033	10.035	0.033	0.033	0.000	0.000	0.000	0.000
13	X	13	GLU	-1	-0.881	-0.938	14.674	0.084	0.084	0.000	0.000	0.000	0.000
14	X	14	MET	0	0.005	0.009	12.601	0.035	0.035	0.000	0.000	0.000	0.000
15	X	15	ARG	1	0.804	0.875	17.404	-0.145	-0.145	0.000	0.000	0.000	0.000
16	X	16	VAL	0	0.030	0.024	20.207	0.017	0.017	0.000	0.000	0.000	0.000
17	X	17	GLY	0	0.015	0.012	22.324	0.001	0.001	0.000	0.000	0.000	0.000
18	X	18	LYS	1	0.835	0.901	24.154	-0.063	-0.063	0.000	0.000	0.000	0.000
19	X	19	ILE	0	0.012	0.012	23.518	0.006	0.006	0.000	0.000	0.000	0.000
20	X	20	VAL	0	-0.019	-0.023	27.247	-0.009	-0.009	0.000	0.000	0.000	0.000
21	X	21	GLU	-1	-0.895	-0.949	29.545	0.104	0.104	0.000	0.000	0.000	0.000
22	X	22	VAL	0	0.022	0.010	27.859	0.011	0.011	0.000	0.000	0.000	0.000
23	X	23	LYS	1	0.905	0.954	29.394	-0.128	-0.128	0.000	0.000	0.000	0.000
24	X	24	ARG	1	0.890	0.974	28.844	-0.126	-0.126	0.000	0.000	0.000	0.000
25	X	25	HIS	0	-0.041	-0.048	30.809	-0.012	-0.012	0.000	0.000	0.000	0.000
26	X	26	GLU	-1	-0.853	-0.928	33.337	0.095	0.095	0.000	0.000	0.000	0.000
27	X	27	ASN	0	-0.075	-0.052	35.334	-0.003	-0.003	0.000	0.000	0.000	0.000
28	X	28	ALA	0	0.000	0.007	32.143	0.007	0.007	0.000	0.000	0.000	0.000
29	X	29	ASP	-1	-0.876	-0.941	29.063	0.150	0.150	0.000	0.000	0.000	0.000
30	X	30	LYS	1	0.918	0.982	22.011	-0.229	-0.229	0.000	0.000	0.000	0.000
31	X	31	LEU	0	-0.043	-0.046	22.476	0.004	0.004	0.000	0.000	0.000	0.000
32	X	32	TYR	0	-0.071	-0.041	24.905	-0.012	-0.012	0.000	0.000	0.000	0.000
33	X	33	ILE	0	-0.050	-0.016	25.034	0.017	0.017	0.000	0.000	0.000	0.000
34	X	34	VAL	0	0.019	0.008	24.244	-0.013	-0.013	0.000	0.000	0.000	0.000
35	X	35	GLN	0	-0.013	-0.001	25.679	0.018	0.018	0.000	0.000	0.000	0.000
36	X	36	VAL	0	-0.008	-0.007	22.651	-0.009	-0.009	0.000	0.000	0.000	0.000
37	X	37	ASP	-1	-0.844	-0.918	25.908	0.083	0.083	0.000	0.000	0.000	0.000
38	X	38	VAL	0	-0.017	-0.032	23.178	0.001	0.001	0.000	0.000	0.000	0.000
39	X	39	GLY	0	-0.013	-0.004	26.299	-0.003	-0.003	0.000	0.000	0.000	0.000
40	X	40	GLN	0	-0.048	-0.035	29.485	-0.003	-0.003	0.000	0.000	0.000	0.000
41	X	41	LYS	1	0.946	0.992	24.253	-0.145	-0.145	0.000	0.000	0.000	0.000
42	X	42	THR	0	0.016	0.005	28.265	-0.002	-0.002	0.000	0.000	0.000	0.000
43	X	43	LEU	0	-0.046	-0.011	22.770	0.002	0.002	0.000	0.000	0.000	0.000
44	X	44	GLN	0	0.058	0.039	25.393	-0.013	-0.013	0.000	0.000	0.000	0.000
45	X	45	THR	0	-0.039	-0.049	19.734	0.023	0.023	0.000	0.000	0.000	0.000
46	X	46	VAL	0	-0.016	-0.015	21.306	-0.021	-0.021	0.000	0.000	0.000	0.000
47	X	47	THR	0	0.018	0.019	20.460	0.030	0.030	0.000	0.000	0.000	0.000
48	X	48	SER	0	-0.008	-0.016	17.846	-0.017	-0.017	0.000	0.000	0.000	0.000
49	X	49	LEU	0	0.044	-0.007	18.076	-0.005	-0.005	0.000	0.000	0.000	0.000
50	X	50	VAL	0	-0.049	-0.008	21.869	-0.010	-0.010	0.000	0.000	0.000	0.000
51	X	51	PRO	0	0.045	0.052	24.783	-0.009	-0.009	0.000	0.000	0.000	0.000
52	X	52	TYR	0	-0.098	-0.075	21.709	-0.006	-0.006	0.000	0.000	0.000	0.000
53	X	53	TYR	0	0.020	0.012	20.749	-0.006	-0.006	0.000	0.000	0.000	0.000
54	X	54	SER	0	0.083	0.025	25.992	0.005	0.005	0.000	0.000	0.000	0.000
55	X	55	GLU	-1	-0.804	-0.922	28.415	0.110	0.110	0.000	0.000	0.000	0.000
56	X	56	GLU	-1	-0.965	-0.987	30.262	0.064	0.064	0.000	0.000	0.000	0.000
57	X	57	GLU	-1	-0.821	-0.899	27.285	0.079	0.079	0.000	0.000	0.000	0.000
58	X	58	LEU	0	-0.023	-0.016	23.828	-0.001	-0.001	0.000	0.000	0.000	0.000
59	X	59	MET	0	-0.032	0.001	27.530	0.003	0.003	0.000	0.000	0.000	0.000
60	X	60	GLY	0	-0.008	0.007	30.089	-0.006	-0.006	0.000	0.000	0.000	0.000
61	X	61	LYS	1	0.746	0.871	24.043	-0.091	-0.091	0.000	0.000	0.000	0.000
62	X	62	THR	0	-0.025	-0.013	24.008	0.004	0.004	0.000	0.000	0.000	0.000
63	X	63	VAL	0	0.029	0.023	20.583	0.000	0.000	0.000	0.000	0.000	0.000
64	X	64	VAL	0	0.041	0.019	16.437	-0.013	-0.013	0.000	0.000	0.000	0.000
65	X	65	VAL	0	0.014	0.001	17.448	0.026	0.026	0.000	0.000	0.000	0.000
66	X	66	LEU	0	0.010	0.009	12.371	-0.020	-0.020	0.000	0.000	0.000	0.000
67	X	67	CYS	0	-0.065	-0.046	16.209	-0.006	-0.006	0.000	0.000	0.000	0.000
68	X	68	ASN	0	0.005	0.000	16.845	0.013	0.013	0.000	0.000	0.000	0.000
69	X	69	LEU	0	0.011	0.020	13.565	0.028	0.028	0.000	0.000	0.000	0.000
70	X	70	GLN	0	-0.012	-0.013	16.893	-0.041	-0.041	0.000	0.000	0.000	0.000
71	X	71	LYS	1	0.870	0.921	18.924	-0.199	-0.199	0.000	0.000	0.000	0.000
72	X	72	ALA	0	0.066	0.048	18.846	0.013	0.013	0.000	0.000	0.000	0.000
73	X	73	LYS	1	0.816	0.906	20.990	-0.229	-0.229	0.000	0.000	0.000	0.000
74	X	74	MET	0	0.049	0.017	19.869	0.011	0.011	0.000	0.000	0.000	0.000
75	X	75	ARG	1	0.970	0.987	23.411	-0.200	-0.200	0.000	0.000	0.000	0.000
76	X	76	GLY	0	0.016	0.010	26.549	-0.013	-0.013	0.000	0.000	0.000	0.000
77	X	77	GLU	-1	-0.850	-0.907	25.972	0.152	0.152	0.000	0.000	0.000	0.000
78	X	78	THR	0	-0.024	-0.025	24.787	0.020	0.020	0.000	0.000	0.000	0.000
79	X	79	SER	0	0.035	0.024	19.416	-0.023	-0.023	0.000	0.000	0.000	0.000
80	X	80	GLU	-1	-0.871	-0.949	21.100	0.200	0.200	0.000	0.000	0.000	0.000
81	X	81	CYS	0	-0.039	0.015	18.907	-0.008	-0.008	0.000	0.000	0.000	0.000
82	X	82	MET	0	0.000	0.014	14.893	-0.007	-0.007	0.000	0.000	0.000	0.000
83	X	83	LEU	0	0.034	0.016	16.402	-0.003	-0.003	0.000	0.000	0.000	0.000
84	X	84	LEU	0	-0.006	-0.004	12.373	0.038	0.038	0.000	0.000	0.000	0.000
85	X	85	CYS	0	-0.050	-0.022	13.005	-0.047	-0.047	0.000	0.000	0.000	0.000
86	X	86	ALA	0	-0.011	0.007	12.215	0.017	0.017	0.000	0.000	0.000	0.000
87	X	87	GLU	-1	-0.949	-0.981	10.788	0.399	0.399	0.000	0.000	0.000	0.000
88	X	88	THR	0	-0.009	-0.002	12.589	-0.010	-0.010	0.000	0.000	0.000	0.000
89	X	89	ASP	-1	-0.917	-0.963	11.734	0.208	0.208	0.000	0.000	0.000	0.000
90	X	90	ASP	-1	-0.896	-0.927	13.038	0.265	0.265	0.000	0.000	0.000	0.000
91	X	91	GLY	0	-0.032	-0.013	14.378	0.009	0.009	0.000	0.000	0.000	0.000
92	X	92	SER	0	-0.113	-0.067	15.155	-0.016	-0.016	0.000	0.000	0.000	0.000
93	X	93	GLU	-1	-0.887	-0.921	17.433	0.093	0.093	0.000	0.000	0.000	0.000
94	X	94	SER	0	0.024	0.003	14.621	0.006	0.006	0.000	0.000	0.000	0.000
95	X	95	VAL	0	-0.020	-0.003	16.457	-0.013	-0.013	0.000	0.000	0.000	0.000
96	X	96	LEU	0	-0.024	-0.024	16.736	0.009	0.009	0.000	0.000	0.000	0.000
97	X	97	LEU	0	0.003	0.010	13.080	-0.025	-0.025	0.000	0.000	0.000	0.000
98	X	98	THR	0	-0.010	-0.027	17.682	0.015	0.015	0.000	0.000	0.000	0.000
99	X	99	PRO	0	-0.055	-0.014	20.405	-0.015	-0.015	0.000	0.000	0.000	0.000
100	X	100	GLU	-1	-0.895	-0.944	22.333	-0.060	-0.060	0.000	0.000	0.000	0.000
101	X	101	ARG	1	0.944	0.975	23.883	0.033	0.033	0.000	0.000	0.000	0.000
102	X	102	MET	0	0.020	-0.002	26.423	0.006	0.006	0.000	0.000	0.000	0.000
103	X	103	MET	0	0.000	0.000	25.362	-0.010	-0.010	0.000	0.000	0.000	0.000
104	X	104	PRO	0	0.009	0.001	28.061	0.009	0.009	0.000	0.000	0.000	0.000
105	X	105	ALA	0	0.011	0.014	26.674	0.002	0.002	0.000	0.000	0.000	0.000
106	X	106	GLY	0	0.044	0.010	25.379	-0.006	-0.006	0.000	0.000	0.000	0.000
107	X	107	VAL	0	-0.057	-0.016	23.982	0.001	0.001	0.000	0.000	0.000	0.000
108	X	108	ARG	1	0.892	0.954	17.615	-0.101	-0.101	0.000	0.000	0.000	0.000
109	X	109	VAL	0	0.020	0.012	16.038	-0.019	-0.019	0.000	0.000	0.000	0.000
110	X	110	VAL	0	-0.056	-0.035	17.908	0.025	0.025	0.000	0.000	0.000	0.000
111	X	111	LEU	0	-0.009	-0.002	12.487	-0.012	-0.012	0.000	0.000	0.000	0.000
112	X	112	ASP	-1	-0.942	-0.960	16.743	-0.217	-0.217	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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