FMO DATABASE

FMODB ID: LJ129

Calculation Name: 2YY3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YY3

Chain ID: A

ChEMBL ID:

UniProt ID: P58748

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:

Apendix: None

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-644916.054558
FMO2-HF: Nuclear repulsion	608819.499039
FMO2-HF: Total energy	-36096.555519
FMO2-MP2: Total energy	-36202.681709

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-18.328	-24.136	30.711	-11.409	-13.494	0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : 0.013

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

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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	3	ASP	-1	-0.884	-0.923	2.300	-12.843	-8.237	2.862	-3.354	-4.113	-0.025
4	A	4	PHE	0	0.006	0.012	3.960	3.791	4.327	0.025	-0.120	-0.441	-0.001
5	A	5	ASN	0	-0.023	-0.028	2.400	-6.197	-8.014	7.543	-2.358	-3.368	0.012
6	A	6	LEU	0	0.000	-0.002	4.276	-0.324	-0.207	0.000	-0.038	-0.079	0.000
7	A	7	VAL	0	-0.016	-0.012	8.123	-0.153	-0.153	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.066	0.037	11.241	0.025	0.025	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.097	-0.042	14.922	-0.052	-0.052	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.040	0.025	17.609	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.746	0.841	20.682	-0.232	-0.232	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.026	0.012	24.203	0.019	0.019	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.013	-0.005	27.108	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.010	0.000	30.868	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.005	-0.015	33.333	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.890	-0.932	36.588	0.101	0.101	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.076	-0.065	37.336	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.936	-0.942	38.938	0.067	0.067	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.049	-0.009	34.554	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.045	-0.045	35.482	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.048	0.016	31.843	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.815	-0.892	30.560	0.058	0.058	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.876	-0.923	30.338	0.100	0.100	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.029	0.026	29.933	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.813	-0.893	25.356	0.094	0.094	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.847	-0.915	25.778	0.104	0.104	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.772	0.869	26.645	-0.115	-0.115	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.044	0.032	24.428	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.799	0.876	21.991	-0.053	-0.053	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.728	0.863	21.699	-0.126	-0.126	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.019	0.018	23.680	0.005	0.005	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.030	-0.003	17.115	0.045	0.045	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.034	-0.007	17.750	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.908	-0.975	17.045	0.690	0.690	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.763	0.888	12.392	-1.158	-1.158	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.006	-0.018	12.019	0.359	0.359	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.005	-0.002	12.422	-0.126	-0.126	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.037	-0.016	13.290	0.043	0.043	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.012	0.001	12.710	-0.089	-0.089	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.811	0.900	14.610	-0.089	-0.089	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.021	0.024	18.216	0.052	0.052	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.822	-0.878	21.553	0.038	0.038	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.802	0.880	24.163	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.828	-0.895	27.012	0.113	0.113	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.002	-0.004	29.732	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.001	-0.002	33.191	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.016	-0.022	35.786	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.050	-0.026	38.226	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.015	0.017	39.306	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.036	0.029	35.232	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.024	-0.028	31.092	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.035	0.043	28.556	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.023	-0.013	26.317	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.830	0.902	22.109	-0.106	-0.106	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.026	0.007	19.557	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.055	-0.060	15.402	0.037	0.037	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.035	0.024	14.322	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.049	-0.019	9.042	0.048	0.048	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.097	0.018	9.263	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.702	0.784	2.013	-12.787	-22.083	20.282	-5.537	-5.450	0.024
61	A	61	ASP	-1	-0.821	-0.873	6.654	1.772	1.772	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.851	-0.898	5.381	7.469	7.469	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.882	-0.950	9.193	0.973	0.973	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.010	0.009	11.243	0.269	0.269	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.087	-0.044	8.125	-0.307	-0.307	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.020	-0.025	13.516	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.001	-0.014	11.361	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.807	-0.897	17.179	0.656	0.656	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.724	-0.804	17.840	0.821	0.821	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.054	-0.041	17.429	-0.048	-0.048	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.004	0.010	20.576	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.897	-0.962	22.992	0.457	0.457	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.866	0.920	20.769	-0.612	-0.612	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.063	-0.053	20.732	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.838	-0.915	25.812	0.265	0.265	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.976	-0.977	27.566	0.322	0.322	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.107	-0.041	27.522	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.827	-0.909	30.521	0.130	0.130	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.047	-0.052	33.178	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.022	0.005	28.857	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.945	-0.974	32.107	0.164	0.164	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.012	-0.014	29.955	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.084	-0.052	24.901	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.861	-0.921	24.740	0.351	0.351	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.024	-0.022	18.497	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.843	-0.883	21.200	0.256	0.256	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.064	-0.041	18.134	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.035	0.011	13.096	0.024	0.024	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.058	-0.023	11.650	-0.060	-0.060	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.807	0.879	7.989	-1.866	-1.866	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.020	0.007	4.537	-0.265	-0.219	-0.001	-0.002	-0.043	0.000

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