FMO DATABASE

FMODB ID: VR721

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

Total energy (hartree)

FMO2-HF: Electronic energy	-795165.667041
FMO2-HF: Nuclear repulsion	754285.222292
FMO2-HF: Total energy	-40880.444749
FMO2-MP2: Total energy	-41000.067505

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.
-0.576	0.486	0.001	-0.668	-0.394	0.003

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 : -0.030 / q_NPA : -0.025

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	-0.065	-0.012	3.777	0.305	1.538	0.002	-0.649	-0.585	0.003
4	A	5	ALA	0	0.052	0.020	5.476	0.177	0.177	0.000	0.000	0.000	0.000
5	A	6	VAL	0	0.034	0.027	9.093	0.200	0.200	0.000	0.000	0.000	0.000
6	A	7	ALA	0	-0.004	0.003	11.561	0.008	0.008	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.068	-0.037	15.039	0.016	0.016	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.811	-0.900	17.969	-0.172	-0.172	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.064	-0.045	21.325	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.068	-0.032	23.820	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.015	0.000	26.222	0.003	0.003	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.060	-0.033	27.254	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.020	0.021	29.986	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.025	-0.032	33.140	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.759	-0.887	32.384	-0.158	-0.158	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.894	0.943	35.525	0.116	0.116	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.055	-0.035	37.817	0.007	0.007	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.038	-0.009	33.395	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.857	-0.930	36.603	-0.125	-0.125	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.934	-0.965	35.170	-0.122	-0.122	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.033	-0.008	33.775	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.006	-0.004	34.726	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.032	0.016	35.614	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.031	0.011	30.006	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.030	0.005	30.380	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.038	-0.018	31.257	0.006	0.006	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.146	-0.075	28.124	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.043	0.017	25.610	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.915	0.949	25.440	0.139	0.139	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.019	-0.010	24.617	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.004	0.003	21.466	0.010	0.010	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.053	0.008	20.038	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.000	0.004	17.020	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.016	-0.015	19.077	0.032	0.032	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.014	-0.011	18.634	-0.062	-0.062	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.010	-0.003	20.335	0.044	0.044	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.037	-0.011	21.749	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.824	0.886	24.144	0.309	0.309	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.740	-0.819	25.763	-0.217	-0.217	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.032	0.015	29.261	0.015	0.015	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.007	0.003	30.783	0.012	0.012	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.063	-0.038	32.982	0.022	0.022	0.000	0.000	0.000	0.000
43	A	44	GLN	0	0.040	0.016	34.801	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.059	-0.026	37.252	0.011	0.011	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.822	-0.914	32.974	-0.173	-0.173	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.801	-0.866	33.406	-0.191	-0.191	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.036	-0.032	29.747	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	49	ALA	0	-0.026	-0.001	28.845	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.025	-0.002	23.995	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.038	-0.035	27.376	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.007	-0.006	24.264	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	53	TRP	0	0.022	-0.011	24.450	0.035	0.035	0.000	0.000	0.000	0.000
53	A	54	THR	0	0.054	0.029	23.729	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.011	0.011	18.848	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.035	-0.028	22.169	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.031	-0.017	22.110	0.017	0.017	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.014	0.023	26.283	0.015	0.015	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.846	0.927	28.340	0.197	0.197	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.012	0.001	26.272	0.012	0.012	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.025	0.014	30.004	0.014	0.014	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.109	-0.078	29.510	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.011	0.031	24.720	0.008	0.008	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.021	0.010	28.510	0.010	0.010	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.914	0.922	30.569	0.140	0.140	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.057	-0.028	31.960	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	0.009	-0.004	27.451	0.002	0.002	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.021	-0.002	26.999	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.037	0.012	26.811	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.041	0.031	24.462	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	71	TYR	0	0.061	0.018	20.279	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.002	0.018	22.524	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.007	-0.013	24.234	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.031	-0.014	18.427	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.037	-0.024	19.692	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.834	-0.889	20.955	-0.319	-0.319	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.117	-0.054	19.865	0.021	0.021	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.008	0.000	18.182	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.029	-0.009	15.336	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.933	0.958	12.199	1.194	1.194	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.021	0.004	14.288	-0.088	-0.088	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.018	-0.004	12.395	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.054	0.028	17.741	0.008	0.008	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.025	-0.001	15.303	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	85	VAL	0	0.004	-0.008	19.800	0.025	0.025	0.000	0.000	0.000	0.000
85	A	86	THR	0	0.003	0.004	23.250	0.007	0.007	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.003	-0.004	24.604	0.021	0.021	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.007	-0.004	28.371	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.793	-0.887	30.453	-0.095	-0.095	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.027	0.003	33.233	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.008	-0.002	34.819	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.794	0.897	37.072	0.098	0.098	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.057	-0.030	35.197	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.050	-0.037	32.076	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.053	0.008	27.112	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.892	-0.900	27.404	-0.149	-0.149	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.025	-0.016	22.480	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.031	0.045	18.386	0.010	0.010	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.036	-0.034	18.973	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	100	TRP	0	-0.001	-0.004	11.855	0.019	0.019	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.833	0.906	11.914	0.843	0.843	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.035	-0.020	8.879	-0.026	-0.026	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.864	-0.924	7.129	-1.138	-1.138	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.018	-0.021	4.914	-0.972	-1.143	-0.001	-0.019	0.191	0.000

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