FMO DATABASE

FMODB ID: 14ZJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-795200.582083
FMO2-HF: Nuclear repulsion	754319.441173
FMO2-HF: Total energy	-40881.140911
FMO2-MP2: Total energy	-41000.7647

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.
-0.221	0.92	-0.008	-0.676	-0.459	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 : -0.015 / q_NPA : -0.009

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	-0.015	0.002	3.837	0.411	1.656	-0.007	-0.659	-0.580	0.002
4	A	5	ALA	0	0.011	0.001	5.592	0.313	0.313	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.031	-0.005	9.337	0.189	0.189	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.008	0.007	12.157	0.014	0.014	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.057	-0.033	15.590	0.009	0.009	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.807	-0.896	18.642	-0.184	-0.184	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.072	-0.049	22.025	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.051	-0.027	24.225	0.004	0.004	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.005	0.009	26.586	0.002	0.002	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.059	-0.026	27.465	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.000	-0.005	30.138	0.016	0.016	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.005	-0.014	33.415	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.774	-0.895	32.983	-0.157	-0.157	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.867	0.919	36.139	0.120	0.120	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.047	-0.021	38.451	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.003	0.013	34.243	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.905	-0.945	37.459	-0.123	-0.123	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.902	-0.958	35.960	-0.121	-0.121	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.009	0.015	34.362	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.040	0.016	35.110	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.022	0.016	35.844	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.001	-0.010	30.526	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.002	0.004	30.882	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.043	-0.015	31.390	0.002	0.002	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.104	-0.063	28.728	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.029	0.019	26.245	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.865	0.916	26.241	0.151	0.151	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.035	0.009	25.437	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.004	0.003	21.776	0.013	0.013	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.069	-0.009	20.499	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.019	0.008	17.467	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.019	-0.019	19.514	0.034	0.034	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.002	0.003	19.093	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.020	0.000	20.743	0.043	0.043	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.023	-0.006	22.164	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.818	0.888	24.551	0.294	0.294	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.752	-0.816	26.415	-0.211	-0.211	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.012	-0.001	29.123	0.017	0.017	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.015	0.013	30.910	0.010	0.010	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.060	-0.036	33.550	0.020	0.020	0.000	0.000	0.000	0.000
43	A	44	GLN	0	0.028	0.005	35.379	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.042	-0.012	37.632	0.011	0.011	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.815	-0.902	33.207	-0.172	-0.172	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.791	-0.865	33.801	-0.189	-0.189	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.036	-0.035	30.221	-0.027	-0.027	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.010	0.015	29.261	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.015	0.004	24.129	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.031	-0.034	27.568	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.006	-0.007	24.672	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	53	TRP	0	0.030	0.000	24.931	0.035	0.035	0.000	0.000	0.000	0.000
53	A	54	THR	0	0.043	0.020	24.146	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.007	-0.005	18.958	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.028	-0.023	22.274	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.002	-0.001	22.286	0.022	0.022	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.029	0.036	26.498	0.013	0.013	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.823	0.914	28.436	0.189	0.189	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.017	-0.016	26.703	0.013	0.013	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.020	0.007	30.269	0.017	0.017	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.096	-0.071	29.670	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.019	0.019	24.755	0.006	0.006	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.039	0.029	28.733	0.012	0.012	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.882	0.906	30.995	0.140	0.140	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.059	-0.037	32.003	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	0.002	-0.012	27.726	0.004	0.004	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.019	-0.004	27.521	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.049	0.026	27.176	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.028	0.022	24.844	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	TYR	0	0.044	0.013	21.149	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.002	0.007	23.046	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.001	-0.009	24.336	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.032	-0.017	19.079	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.036	-0.021	19.973	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.834	-0.888	21.538	-0.302	-0.302	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.108	-0.055	19.847	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.006	0.008	18.764	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.018	0.000	15.639	-0.123	-0.123	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.907	0.934	12.360	1.121	1.121	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.011	0.005	14.717	-0.087	-0.087	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.040	-0.018	12.655	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.051	0.023	17.963	0.019	0.019	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.035	-0.011	15.630	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	85	VAL	0	0.001	0.012	20.160	0.023	0.023	0.000	0.000	0.000	0.000
85	A	86	THR	0	-0.018	-0.016	23.449	0.004	0.004	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.000	0.006	25.059	0.019	0.019	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.010	-0.002	28.876	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.797	-0.887	30.945	-0.104	-0.104	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.017	0.004	34.201	0.005	0.005	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.012	-0.012	35.496	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.758	0.872	36.393	0.111	0.111	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.047	-0.025	35.996	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.029	-0.019	32.098	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.023	-0.004	27.651	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.873	-0.906	27.701	-0.153	-0.153	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.009	-0.005	22.587	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.021	0.029	18.703	0.015	0.015	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.020	-0.017	19.483	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	100	TRP	0	-0.018	-0.017	12.055	0.010	0.010	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.818	0.892	12.677	0.844	0.844	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.034	-0.011	9.398	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.839	-0.915	7.850	-1.018	-1.018	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.001	0.002	5.010	-0.866	-0.970	-0.001	-0.017	0.121	0.000

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