FMO DATABASE

FMODB ID: YYLQ2

Calculation Name: 3K2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2Y

Chain ID: A

ChEMBL ID:

UniProt ID: F9USU1

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-795105.883649
FMO2-HF: Nuclear repulsion	754226.555034
FMO2-HF: Total energy	-40879.328614
FMO2-MP2: Total energy	-40999.050791

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:GLY)

Summations of interaction energy for fragment #1(A:2: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.
2.394	2.826	0.001	-0.272	-0.161	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.063

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	4	ALA	0	-0.041	-0.033	3.777	2.462	3.048	0.002	-0.253	-0.336	0.002
4	A	5	ALA	0	0.058	0.020	6.195	-0.313	-0.313	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.012	0.032	9.722	0.165	0.165	0.000	0.000	0.000	0.000
6	A	7	ALA	0	-0.010	-0.001	12.320	-0.098	-0.098	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.077	-0.040	15.900	0.002	0.002	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.812	-0.913	18.665	0.077	0.077	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.071	-0.042	21.972	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.060	-0.023	24.390	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.010	-0.011	26.700	0.004	0.004	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.048	-0.031	27.253	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.033	0.028	30.057	0.005	0.005	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.050	-0.049	33.149	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.746	-0.879	32.797	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.894	0.948	35.533	0.026	0.026	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.057	-0.041	37.823	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.067	-0.016	33.524	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.843	-0.926	36.610	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.953	-0.976	35.076	-0.051	-0.051	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.018	-0.012	34.007	0.001	0.001	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.007	0.003	34.733	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.040	0.020	35.561	0.003	0.003	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.020	0.001	29.918	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.062	-0.006	30.386	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.001	0.009	31.264	0.007	0.007	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.150	-0.080	28.171	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.057	0.030	25.463	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.888	0.930	25.447	0.028	0.028	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.021	-0.008	24.624	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.006	0.001	21.474	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.049	0.011	20.045	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.002	0.003	17.024	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.017	-0.014	19.084	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.021	-0.016	18.504	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.002	-0.002	20.073	0.027	0.027	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.043	-0.010	21.749	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.794	0.869	23.994	0.143	0.143	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.775	-0.875	25.717	-0.109	-0.109	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.026	0.013	28.910	0.010	0.010	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.017	0.009	30.602	0.006	0.006	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.052	-0.014	33.011	0.011	0.011	0.000	0.000	0.000	0.000
43	A	44	GLN	0	0.033	0.007	34.741	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.079	-0.045	37.314	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.856	-0.940	33.569	-0.053	-0.053	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.840	-0.893	33.327	-0.075	-0.075	0.000	0.000	0.000	0.000
47	A	48	ASN	0	0.021	0.000	29.745	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	49	ALA	0	-0.058	-0.021	28.945	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.032	0.003	24.243	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.027	-0.013	27.504	0.007	0.007	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.001	-0.006	24.259	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	53	TRP	0	0.015	-0.016	24.457	0.011	0.011	0.000	0.000	0.000	0.000
53	A	54	THR	0	0.060	0.040	23.736	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.017	0.006	18.506	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.064	-0.036	22.174	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.022	-0.011	22.233	0.010	0.010	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.024	0.030	26.288	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.891	0.924	28.346	0.084	0.084	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.002	-0.005	26.402	0.007	0.007	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.016	0.012	30.004	0.009	0.009	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.102	-0.050	29.567	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.025	0.043	24.927	0.009	0.009	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.019	0.008	28.841	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.999	0.989	30.985	0.041	0.041	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.067	-0.031	32.514	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	67	GLN	0	0.033	0.009	28.023	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.011	0.002	27.390	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.034	0.006	27.033	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.008	0.017	24.830	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	71	TYR	0	0.063	0.017	20.972	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.012	0.021	22.598	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	73	THR	0	0.009	0.004	23.888	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.052	-0.025	18.622	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.035	-0.026	19.523	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.815	-0.877	20.824	-0.165	-0.165	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.120	-0.054	19.337	0.012	0.012	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.001	0.001	17.938	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.026	-0.010	15.074	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.953	0.984	11.985	0.838	0.838	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.023	0.005	14.400	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.021	-0.008	12.427	-0.031	-0.031	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.054	0.027	17.750	0.031	0.031	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.021	0.002	15.446	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.004	-0.012	19.809	0.015	0.015	0.000	0.000	0.000	0.000
85	A	86	THR	0	0.010	0.009	23.258	0.016	0.016	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.011	0.004	24.613	0.008	0.008	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.009	-0.007	28.380	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.863	-0.936	30.461	0.011	0.011	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.037	-0.006	33.398	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.020	-0.010	34.827	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.883	0.952	37.397	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.061	-0.033	35.232	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.047	-0.023	32.089	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.053	0.008	26.945	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.896	-0.902	27.630	0.015	0.015	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.023	-0.021	22.524	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.026	0.051	18.719	0.005	0.005	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.031	-0.033	19.301	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	100	TRP	0	0.007	-0.001	12.388	0.060	0.060	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.918	0.966	12.264	0.010	0.010	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.028	-0.020	8.795	0.118	0.118	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.970	-0.991	7.013	0.056	0.056	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.016	-0.026	4.759	-0.549	-0.703	-0.001	-0.019	0.175	0.000

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