FMO DATABASE

FMODB ID: LZL59

Calculation Name: 2DP9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DP9

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM30

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1079934.651066
FMO2-HF: Nuclear repulsion	1030017.250898
FMO2-HF: Total energy	-49917.400167
FMO2-MP2: Total energy	-50065.057866

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:-2:MET)

Summations of interaction energy for fragment #1(A:-2: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.
-14.333	-6.836	10.687	-4.538	-13.648	-0.044

Interaction energy analysis for fragmet #1(A:-2:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.039

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	0	TYR	0	0.049	0.036	2.408	-7.700	-3.345	2.253	-2.059	-4.550	-0.018
4	A	1	MET	0	0.022	0.020	5.038	1.014	1.101	-0.001	-0.007	-0.079	0.000
5	A	2	GLU	-1	-0.914	-0.959	7.404	-1.395	-1.395	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.866	0.913	6.592	-0.896	-0.896	0.000	0.000	0.000	0.000
7	A	4	PRO	0	-0.007	0.005	8.650	-0.134	-0.134	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.954	0.968	11.523	0.399	0.399	0.000	0.000	0.000	0.000
9	A	6	LEU	0	-0.004	0.008	14.748	0.053	0.053	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.026	0.018	14.284	0.008	0.008	0.000	0.000	0.000	0.000
11	A	8	LEU	0	-0.007	0.000	14.938	-0.037	-0.037	0.000	0.000	0.000	0.000
12	A	9	ILE	0	-0.056	-0.034	16.096	0.069	0.069	0.000	0.000	0.000	0.000
13	A	10	VAL	0	0.009	0.006	14.780	-0.050	-0.050	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.938	0.976	17.874	-0.228	-0.228	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.734	-0.809	17.386	0.689	0.689	0.000	0.000	0.000	0.000
16	A	13	PRO	0	0.011	-0.016	19.031	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	14	TYR	0	0.045	-0.002	16.773	0.067	0.067	0.000	0.000	0.000	0.000
18	A	15	ALA	0	-0.001	-0.002	14.400	0.030	0.030	0.000	0.000	0.000	0.000
19	A	16	SER	0	0.002	-0.025	12.758	0.145	0.145	0.000	0.000	0.000	0.000
20	A	17	LEU	0	-0.024	0.001	12.351	0.150	0.150	0.000	0.000	0.000	0.000
21	A	18	ILE	0	-0.010	0.005	9.465	0.061	0.061	0.000	0.000	0.000	0.000
22	A	19	VAL	0	-0.033	-0.014	7.915	0.042	0.042	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.832	-0.879	7.615	2.232	2.232	0.000	0.000	0.000	0.000
24	A	21	GLY	0	0.002	-0.003	7.819	0.093	0.093	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.903	0.949	8.387	-0.971	-0.971	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.804	0.922	11.360	-0.367	-0.367	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.062	0.031	9.623	0.020	0.020	0.000	0.000	0.000	0.000
28	A	25	TRP	0	0.016	0.024	11.704	-0.090	-0.090	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.777	-0.889	14.351	0.268	0.268	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.013	0.008	16.012	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	28	ARG	1	0.783	0.880	18.090	-0.115	-0.115	0.000	0.000	0.000	0.000
32	A	29	ARG	1	0.894	0.942	21.777	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	30	ARG	1	0.923	0.967	23.588	0.029	0.029	0.000	0.000	0.000	0.000
34	A	31	LYS	1	0.948	1.001	21.657	0.102	0.102	0.000	0.000	0.000	0.000
35	A	32	THR	0	0.022	-0.017	17.847	0.001	0.001	0.000	0.000	0.000	0.000
36	A	33	ARG	1	0.821	0.887	19.752	0.145	0.145	0.000	0.000	0.000	0.000
37	A	34	HIS	0	-0.026	-0.001	13.295	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.872	0.925	14.147	0.365	0.365	0.000	0.000	0.000	0.000
39	A	36	GLY	0	0.036	0.033	10.983	0.019	0.019	0.000	0.000	0.000	0.000
40	A	37	PRO	0	0.026	0.020	8.088	0.155	0.155	0.000	0.000	0.000	0.000
41	A	38	LEU	0	-0.064	-0.024	9.348	0.182	0.182	0.000	0.000	0.000	0.000
42	A	39	GLY	0	0.028	0.012	10.161	0.097	0.097	0.000	0.000	0.000	0.000
43	A	40	ILE	0	0.006	0.006	10.231	-0.107	-0.107	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.043	-0.035	12.846	0.120	0.120	0.000	0.000	0.000	0.000
45	A	42	SER	0	0.004	-0.022	16.342	-0.101	-0.101	0.000	0.000	0.000	0.000
46	A	43	GLY	0	0.021	0.001	18.214	0.026	0.026	0.000	0.000	0.000	0.000
47	A	44	GLY	0	-0.123	-0.065	20.838	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	45	ARG	1	0.920	0.958	16.872	-0.521	-0.521	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.005	0.007	11.883	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	47	ILE	0	0.003	-0.011	12.075	0.092	0.092	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.095	0.044	8.398	0.400	0.400	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.016	0.027	5.758	0.134	0.134	0.000	0.000	0.000	0.000
53	A	50	ALA	0	0.055	0.025	5.595	0.289	0.289	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.815	-0.895	5.756	-2.619	-2.619	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.058	-0.027	7.785	0.159	0.159	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.030	0.000	9.578	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	54	GLY	0	-0.007	-0.005	12.400	0.026	0.026	0.000	0.000	0.000	0.000
58	A	55	VAL	0	-0.102	-0.052	15.633	0.033	0.033	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.875	-0.921	18.256	-0.202	-0.202	0.000	0.000	0.000	0.000
60	A	57	GLY	0	0.018	0.020	20.532	0.024	0.024	0.000	0.000	0.000	0.000
61	A	58	PRO	0	-0.097	-0.070	24.009	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	59	PHE	0	0.002	-0.003	21.180	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	60	SER	0	0.023	-0.014	26.647	0.009	0.009	0.000	0.000	0.000	0.000
64	A	61	VAL	0	0.018	-0.027	27.706	0.002	0.002	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.776	-0.882	27.846	0.039	0.039	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.849	-0.889	26.831	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.016	-0.009	21.995	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.013	0.015	23.642	0.011	0.011	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.027	0.002	25.615	0.009	0.009	0.000	0.000	0.000	0.000
70	A	67	HIS	0	-0.014	-0.017	20.166	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	68	GLN	0	0.020	0.003	20.217	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	69	GLU	-1	-0.823	-0.920	17.769	0.092	0.092	0.000	0.000	0.000	0.000
73	A	70	LYS	1	0.865	0.936	15.772	0.056	0.056	0.000	0.000	0.000	0.000
74	A	71	HIS	0	-0.027	-0.033	15.405	0.044	0.044	0.000	0.000	0.000	0.000
75	A	72	LEU	0	-0.050	-0.019	15.949	0.049	0.049	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.025	-0.011	19.462	0.024	0.024	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.889	-0.934	22.040	0.159	0.159	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.752	-0.868	25.649	0.070	0.070	0.000	0.000	0.000	0.000
79	A	76	ALA	0	-0.007	-0.003	28.237	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	77	PHE	0	-0.026	-0.031	25.231	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.027	0.020	23.188	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	79	ARG	1	0.786	0.866	27.049	-0.068	-0.068	0.000	0.000	0.000	0.000
83	A	80	ALA	0	-0.038	-0.006	30.512	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.015	-0.008	23.419	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.051	0.002	28.312	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	83	LYS	1	0.783	0.903	29.344	-0.085	-0.085	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.902	-0.946	32.942	0.020	0.020	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.905	-0.932	30.954	0.017	0.017	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.037	-0.035	29.103	0.004	0.004	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.049	-0.008	24.243	0.009	0.009	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.003	-0.009	21.691	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	89	ALA	0	0.033	0.014	18.116	0.029	0.029	0.000	0.000	0.000	0.000
93	A	90	TRP	0	-0.081	-0.052	15.112	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	91	VAL	0	0.042	0.010	12.194	0.060	0.060	0.000	0.000	0.000	0.000
95	A	92	LEU	0	-0.044	-0.037	8.876	-0.068	-0.068	0.000	0.000	0.000	0.000
96	A	93	GLU	-1	-0.857	-0.926	6.737	-1.317	-1.317	0.000	0.000	0.000	0.000
97	A	94	ASN	0	-0.055	-0.044	2.422	-0.295	-0.215	1.356	-0.091	-1.344	0.001
98	A	95	ALA	0	-0.026	-0.012	2.411	-2.070	-2.311	2.159	-0.306	-1.613	-0.021
99	A	96	PHE	0	0.010	0.008	2.618	-0.707	2.429	4.920	-2.029	-6.027	-0.006
100	A	97	ARG	1	0.794	0.860	5.049	-2.851	-2.771	0.000	-0.046	-0.035	0.000
101	A	98	TYR	0	-0.069	-0.062	6.202	0.486	0.486	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.882	-0.938	7.678	2.532	2.532	0.000	0.000	0.000	0.000
103	A	100	LYS	1	0.923	0.950	10.016	-1.397	-1.397	0.000	0.000	0.000	0.000
104	A	101	PRO	0	0.004	0.015	12.387	0.038	0.038	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.042	0.023	11.313	-0.164	-0.164	0.000	0.000	0.000	0.000
106	A	103	HIS	0	0.005	0.002	15.378	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	104	VAL	0	0.040	0.028	17.350	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	105	PRO	0	0.047	0.029	19.839	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	106	ARG	1	0.979	0.988	23.362	-0.255	-0.255	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.959	1.005	25.883	-0.161	-0.161	0.000	0.000	0.000	0.000
111	A	108	PRO	0	0.027	-0.008	28.513	0.009	0.009	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.065	0.023	28.932	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	110	ARG	1	0.789	0.884	22.549	-0.254	-0.254	0.000	0.000	0.000	0.000
114	A	111	VAL	0	0.059	0.037	23.942	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	112	MET	0	-0.054	-0.025	21.887	0.025	0.025	0.000	0.000	0.000	0.000
116	A	113	PHE	0	0.030	0.011	21.783	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	114	VAL	0	0.005	0.001	23.853	0.007	0.007	0.000	0.000	0.000	0.000
118	A	115	ASP	-1	-0.766	-0.824	21.641	-0.133	-0.133	0.000	0.000	0.000	0.000
119	A	116	LEU	0	0.017	-0.008	23.758	0.007	0.007	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.022	-0.025	22.273	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	118	GLU	-1	-0.842	-0.935	24.095	-0.139	-0.139	0.000	0.000	0.000	0.000
122	A	119	VAL	0	-0.056	-0.002	26.498	0.011	0.011	0.000	0.000	0.000	0.000
123	A	120	ARG	1	0.924	0.963	29.802	0.075	0.075	0.000	0.000	0.000	0.000
124	A	121	TRP	0	0.052	0.036	28.635	0.014	0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:MET)