FMO DATABASE

FMODB ID: YY6L2

Calculation Name: 3UAF-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UAF

Chain ID: A

ChEMBL ID:

UniProt ID: G5ED35

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-913850.807139
FMO2-HF: Nuclear repulsion	867366.032222
FMO2-HF: Total energy	-46484.774917
FMO2-MP2: Total energy	-46617.93534

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:21:LYS )

Summations of interaction energy for fragment #1(A:21:LYS )

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.
-121.812	-119.769	-0.015	-0.763	-1.266	0

Interaction energy analysis for fragmet #1(A:21:LYS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.960 / q_NPA : 0.961

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].
3	A	23	SER	0	-0.012	0.007	3.781	-4.755	-2.947	-0.015	-0.689	-1.104
4	A	77	CYS	0	-0.068	-0.020	5.085	2.448	2.496	-0.001	-0.003	-0.045
5	A	25	LEU	0	0.062	0.013	8.809	-1.054	-1.054	0.000	0.000	0.000
6	A	26	MET	0	-0.004	-0.001	11.710	1.398	1.398	0.000	0.000	0.000
7	A	27	ALA	0	0.050	0.042	15.281	-0.120	-0.120	0.000	0.000	0.000
8	A	28	THR	0	-0.060	-0.042	18.073	0.861	0.861	0.000	0.000	0.000
9	A	29	GLY	0	0.064	0.019	21.602	-0.213	-0.213	0.000	0.000	0.000
10	A	30	VAL	0	-0.061	-0.020	24.934	0.229	0.229	0.000	0.000	0.000
11	A	31	LEU	0	0.027	0.024	27.427	0.077	0.077	0.000	0.000	0.000
12	A	32	LYS	1	0.906	0.943	30.194	9.761	9.761	0.000	0.000	0.000
13	A	97	CYS	0	-0.015	0.023	33.487	0.187	0.187	0.000	0.000	0.000
14	A	34	PRO	0	-0.046	-0.031	36.013	0.201	0.201	0.000	0.000	0.000
15	A	35	THR	0	-0.003	-0.025	39.230	0.172	0.172	0.000	0.000	0.000
16	A	36	ASP	-1	-0.837	-0.931	39.710	-7.544	-7.544	0.000	0.000	0.000
17	A	37	PRO	0	-0.013	-0.002	38.536	-0.218	-0.218	0.000	0.000	0.000
18	A	38	GLU	-1	-0.825	-0.906	38.124	-7.923	-7.923	0.000	0.000	0.000
19	A	39	ALA	0	-0.023	-0.008	36.350	-0.193	-0.193	0.000	0.000	0.000
20	A	40	VAL	0	-0.031	-0.005	33.188	-0.311	-0.311	0.000	0.000	0.000
21	A	41	LYS	1	0.772	0.895	32.534	7.698	7.698	0.000	0.000	0.000
22	A	42	LYS	1	0.889	0.953	31.806	8.752	8.752	0.000	0.000	0.000
23	A	43	VAL	0	0.033	0.023	28.712	0.101	0.101	0.000	0.000	0.000
24	A	44	HIS	0	-0.048	-0.024	24.501	0.068	0.068	0.000	0.000	0.000
25	A	45	ILE	0	-0.026	-0.022	22.020	-0.022	-0.022	0.000	0.000	0.000
26	A	46	ASP	-1	-0.692	-0.826	20.644	-13.338	-13.338	0.000	0.000	0.000
27	A	47	LEU	0	-0.056	-0.032	14.074	-0.003	-0.003	0.000	0.000	0.000
28	A	48	TRP	0	0.008	0.002	16.172	-0.369	-0.369	0.000	0.000	0.000
29	A	49	ASP	-1	-0.708	-0.838	10.791	-27.211	-27.211	0.000	0.000	0.000
30	A	50	ALA	0	0.044	0.011	14.015	0.597	0.597	0.000	0.000	0.000
31	A	51	ALA	0	-0.037	-0.019	11.262	0.626	0.626	0.000	0.000	0.000
32	A	52	ALA	0	0.002	0.005	11.700	0.440	0.440	0.000	0.000	0.000
33	A	53	ALA	0	0.026	0.013	12.845	1.024	1.024	0.000	0.000	0.000
34	A	54	ALA	0	-0.051	-0.014	15.169	0.789	0.789	0.000	0.000	0.000
35	A	55	ALA	0	-0.071	-0.025	12.650	0.428	0.428	0.000	0.000	0.000
36	A	56	GLU	-1	-0.965	-0.982	14.572	-13.955	-13.955	0.000	0.000	0.000
37	A	57	SER	0	-0.113	-0.057	12.646	0.041	0.041	0.000	0.000	0.000
38	A	58	ASP	-1	-0.928	-0.973	14.324	-15.611	-15.611	0.000	0.000	0.000
39	A	59	ASP	-1	-0.879	-0.936	13.712	-17.139	-17.139	0.000	0.000	0.000
40	A	60	LEU	0	-0.023	-0.007	15.448	-0.392	-0.392	0.000	0.000	0.000
41	A	61	MET	0	-0.074	-0.013	10.467	-0.496	-0.496	0.000	0.000	0.000
42	A	62	GLY	0	-0.008	-0.018	14.455	-0.006	-0.006	0.000	0.000	0.000
43	A	63	ARG	1	0.831	0.905	17.253	12.947	12.947	0.000	0.000	0.000
44	A	64	THR	0	-0.065	-0.029	21.044	0.316	0.316	0.000	0.000	0.000
45	A	65	TRP	0	0.000	-0.001	23.608	0.318	0.318	0.000	0.000	0.000
46	A	66	SER	0	-0.061	-0.024	27.232	-0.029	-0.029	0.000	0.000	0.000
47	A	67	ASP	-1	-0.790	-0.908	28.821	-9.730	-9.730	0.000	0.000	0.000
48	A	68	ARG	1	0.911	0.935	31.412	8.877	8.877	0.000	0.000	0.000
49	A	69	ASN	0	-0.063	-0.045	33.239	0.470	0.470	0.000	0.000	0.000
50	A	70	GLY	0	0.059	0.046	31.682	0.008	0.008	0.000	0.000	0.000
51	A	71	ASN	0	-0.075	-0.023	28.056	-0.438	-0.438	0.000	0.000	0.000
52	A	72	PHE	0	0.046	0.023	21.835	0.169	0.169	0.000	0.000	0.000
53	A	73	GLN	0	-0.021	-0.020	20.839	-0.023	-0.023	0.000	0.000	0.000
54	A	74	VAL	0	0.015	0.017	17.763	0.393	0.393	0.000	0.000	0.000
55	A	75	THR	0	-0.013	-0.019	13.787	-0.688	-0.688	0.000	0.000	0.000
56	A	76	GLY	0	0.059	0.031	13.318	1.022	1.022	0.000	0.000	0.000
57	A	78	ALA	0	0.104	0.055	7.705	2.104	2.104	0.000	0.000	0.000
58	A	79	SER	0	-0.042	-0.045	3.940	-7.319	-7.132	0.001	-0.071	-0.117
59	A	80	ASH	0	-0.040	-0.034	5.548	4.135	4.135	0.000	0.000	0.000
60	A	81	PHE	0	-0.018	-0.014	5.489	-4.627	-4.627	0.000	0.000	0.000
61	A	82	GLY	0	0.016	0.012	7.647	2.025	2.025	0.000	0.000	0.000
62	A	83	PRO	0	-0.040	-0.037	10.269	-1.889	-1.889	0.000	0.000	0.000
63	A	84	ILE	0	0.036	0.025	11.671	-1.291	-1.291	0.000	0.000	0.000
64	A	85	ASN	0	0.007	0.002	6.075	-0.323	-0.323	0.000	0.000	0.000
65	A	86	THR	0	-0.069	-0.038	6.196	-7.661	-7.661	0.000	0.000	0.000
66	A	87	PRO	0	-0.043	-0.025	6.299	3.202	3.202	0.000	0.000	0.000
67	A	88	ASP	-1	-0.885	-0.950	9.210	-22.168	-22.168	0.000	0.000	0.000
68	A	89	PRO	0	-0.050	-0.007	11.335	1.412	1.412	0.000	0.000	0.000
69	A	90	TYR	0	0.084	0.044	14.119	1.184	1.184	0.000	0.000	0.000
70	A	91	LEU	0	-0.086	-0.049	17.891	-0.055	-0.055	0.000	0.000	0.000
71	A	92	TYR	0	0.012	0.022	20.605	0.667	0.667	0.000	0.000	0.000
72	A	93	ILE	0	0.009	-0.006	23.398	0.125	0.125	0.000	0.000	0.000
73	A	94	GLN	0	0.017	0.009	26.496	0.041	0.041	0.000	0.000	0.000
74	A	95	HIS	0	-0.019	-0.011	29.495	0.219	0.219	0.000	0.000	0.000
75	A	96	ASN	0	0.007	-0.009	32.528	0.153	0.153	0.000	0.000	0.000
76	A	98	PRO	0	0.026	0.025	36.715	-0.115	-0.115	0.000	0.000	0.000
77	A	99	HIS	0	-0.073	-0.044	35.875	0.210	0.210	0.000	0.000	0.000
78	A	100	ARG	1	0.914	0.950	37.519	8.624	8.624	0.000	0.000	0.000
79	A	101	ASP	-1	-0.927	-0.953	40.727	-7.552	-7.552	0.000	0.000	0.000
80	A	102	SER	0	-0.018	-0.019	39.823	0.158	0.158	0.000	0.000	0.000
81	A	103	ASN	0	-0.033	-0.022	41.464	0.022	0.022	0.000	0.000	0.000
82	A	104	ALA	0	-0.019	0.002	37.382	-0.030	-0.030	0.000	0.000	0.000
83	A	105	THR	0	0.033	0.018	36.045	0.049	0.049	0.000	0.000	0.000
84	A	106	ASN	0	-0.030	-0.004	33.074	-0.057	-0.057	0.000	0.000	0.000
85	A	107	PRO	0	0.011	-0.001	28.621	-0.120	-0.120	0.000	0.000	0.000
86	A	108	ILE	0	-0.009	0.012	26.385	0.014	0.014	0.000	0.000	0.000
87	A	109	GLN	0	0.054	0.018	22.755	-0.687	-0.687	0.000	0.000	0.000
88	A	110	ILE	0	-0.081	-0.045	20.883	0.304	0.304	0.000	0.000	0.000
89	A	111	ASP	-1	-0.848	-0.928	18.241	-17.440	-17.440	0.000	0.000	0.000
90	A	112	VAL	0	-0.099	-0.034	14.549	0.272	0.272	0.000	0.000	0.000
91	A	113	ILE	0	0.032	0.012	14.485	-1.061	-1.061	0.000	0.000	0.000
92	A	114	PRO	0	0.066	0.024	10.575	-0.493	-0.493	0.000	0.000	0.000
93	A	115	LEU	0	-0.054	-0.019	10.025	-2.591	-2.591	0.000	0.000	0.000
94	A	116	PHE	0	-0.003	-0.016	6.553	0.227	0.227	0.000	0.000	0.000
95	A	117	LEU	0	-0.011	0.003	9.062	0.835	0.835	0.000	0.000	0.000
96	A	118	PRO	0	-0.047	-0.042	8.447	-3.415	-3.415	0.000	0.000	0.000
97	A	119	SER	0	-0.069	-0.003	11.286	2.965	2.965	0.000	0.000	0.000
98	A	120	ILE	0	-0.005	-0.008	12.892	-0.398	-0.398	0.000	0.000	0.000
99	A	121	VAL	0	0.035	0.021	14.698	0.692	0.692	0.000	0.000	0.000
100	A	122	ARG	1	0.889	0.941	17.307	15.064	15.064	0.000	0.000	0.000
101	A	123	LEU	0	0.052	0.020	20.055	0.187	0.187	0.000	0.000	0.000
102	A	124	GLY	0	-0.018	0.008	22.899	0.457	0.457	0.000	0.000	0.000
103	A	125	ASN	0	-0.043	-0.038	26.347	-0.098	-0.098	0.000	0.000	0.000
104	A	126	VAL	0	0.040	0.019	25.277	-0.079	-0.079	0.000	0.000	0.000
105	A	127	TYR	0	-0.058	-0.041	28.437	0.267	0.267	0.000	0.000	0.000
106	A	128	LEU	0	0.028	0.009	29.263	-0.193	-0.193	0.000	0.000	0.000
107	A	129	ASP	-1	-0.727	-0.863	32.500	-8.713	-8.713	0.000	0.000	0.000
108	A	130	ARG	1	0.771	0.864	32.940	9.322	9.322	0.000	0.000	0.000
109	A	131	TYR	0	0.025	-0.003	31.471	-0.206	-0.206	0.000	0.000	0.000
110	A	132	LEU	0	0.000	0.004	26.246	0.133	0.133	0.000	0.000	0.000
111	A	133	GLU	-1	-0.885	-0.968	30.340	-10.170	-10.170	0.000	0.000	0.000
112	A	134	ASP	-1	-0.840	-0.879	32.880	-8.782	-8.782	0.000	0.000	0.000
113	A	135	TYR	0	-0.089	-0.043	32.912	0.294	0.294	0.000	0.000	0.000
114	A	136	HIS	0	-0.041	-0.030	27.539	0.280	0.280	0.000	0.000	0.000
115	A	137	HIS	-1	-0.948	-0.943	32.954	-8.559	-8.559	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:LYS )