FMO DATABASE

FMODB ID: GNKN1

Calculation Name: 4PTA-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PTA

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0H2

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1089799.97583
FMO2-HF: Nuclear repulsion	1038629.107828
FMO2-HF: Total energy	-51170.868002
FMO2-MP2: Total energy	-51323.962243

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(D:4:GLN)

Summations of interaction energy for fragment #1(D:4:GLN)

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.
-0.289	1.193	-0.013	-0.66	-0.809	0.003

Interaction energy analysis for fragmet #1(D:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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

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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	D	6	PHE	0	0.035	0.021	3.808	-1.320	0.162	-0.013	-0.660	-0.809	0.003
4	D	7	THR	0	0.028	0.012	5.659	0.142	0.142	0.000	0.000	0.000	0.000
5	D	8	VAL	0	0.029	-0.002	8.231	-0.062	-0.062	0.000	0.000	0.000	0.000
6	D	9	GLU	-1	-0.875	-0.933	10.693	0.822	0.822	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.809	-0.900	7.771	1.200	1.200	0.000	0.000	0.000	0.000
8	D	11	ASN	0	0.016	0.016	10.306	-0.088	-0.088	0.000	0.000	0.000	0.000
9	D	12	TYR	0	-0.050	-0.050	12.335	-0.080	-0.080	0.000	0.000	0.000	0.000
10	D	13	LYS	1	0.774	0.883	10.674	-1.036	-1.036	0.000	0.000	0.000	0.000
11	D	14	GLU	-1	-0.957	-0.964	10.700	0.452	0.452	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.821	0.928	14.789	-0.232	-0.232	0.000	0.000	0.000	0.000
13	D	16	PHE	0	0.015	0.007	16.243	0.010	0.010	0.000	0.000	0.000	0.000
14	D	17	TYR	0	-0.003	0.008	21.088	-0.021	-0.021	0.000	0.000	0.000	0.000
15	D	18	GLN	0	0.025	0.002	22.705	-0.004	-0.004	0.000	0.000	0.000	0.000
16	D	19	LEU	0	0.038	0.008	26.015	-0.009	-0.009	0.000	0.000	0.000	0.000
17	D	20	PRO	0	-0.043	-0.007	28.589	-0.003	-0.003	0.000	0.000	0.000	0.000
18	D	21	LYS	1	0.919	0.944	24.677	-0.014	-0.014	0.000	0.000	0.000	0.000
19	D	22	VAL	0	0.046	0.035	30.744	0.003	0.003	0.000	0.000	0.000	0.000
20	D	23	PHE	0	-0.051	-0.040	33.682	0.000	0.000	0.000	0.000	0.000	0.000
21	D	24	PHE	0	-0.010	-0.021	31.419	0.006	0.006	0.000	0.000	0.000	0.000
22	D	25	THR	0	0.026	0.012	34.198	0.002	0.002	0.000	0.000	0.000	0.000
23	D	26	ASN	0	0.023	0.008	37.030	0.000	0.000	0.000	0.000	0.000	0.000
24	D	27	PRO	0	-0.031	-0.020	39.657	0.005	0.005	0.000	0.000	0.000	0.000
25	D	28	ASN	0	-0.019	-0.015	42.507	0.003	0.003	0.000	0.000	0.000	0.000
26	D	29	TYR	0	0.008	0.009	37.883	0.000	0.000	0.000	0.000	0.000	0.000
27	D	30	LYS	1	0.872	0.949	38.144	-0.026	-0.026	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.906	-0.938	39.746	0.044	0.044	0.000	0.000	0.000	0.000
29	D	32	LEU	0	-0.003	0.016	38.660	0.004	0.004	0.000	0.000	0.000	0.000
30	D	33	SER	0	-0.033	-0.051	39.666	0.008	0.008	0.000	0.000	0.000	0.000
31	D	34	ASN	0	0.057	0.001	34.749	-0.006	-0.006	0.000	0.000	0.000	0.000
32	D	35	ASP	-1	-0.807	-0.878	34.996	0.086	0.086	0.000	0.000	0.000	0.000
33	D	36	ALA	0	0.023	0.009	36.136	0.000	0.000	0.000	0.000	0.000	0.000
34	D	37	LYS	1	0.790	0.900	33.941	-0.062	-0.062	0.000	0.000	0.000	0.000
35	D	38	ILE	0	0.025	-0.004	30.219	-0.002	-0.002	0.000	0.000	0.000	0.000
36	D	39	ALA	0	0.008	0.008	31.671	0.000	0.000	0.000	0.000	0.000	0.000
37	D	40	TYR	0	-0.033	-0.043	32.544	-0.004	-0.004	0.000	0.000	0.000	0.000
38	D	41	ALA	0	-0.006	-0.005	28.499	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	42	ILE	0	-0.020	-0.001	28.956	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	43	LEU	0	0.002	-0.018	29.930	-0.005	-0.005	0.000	0.000	0.000	0.000
41	D	44	ARG	1	0.896	0.946	26.645	-0.009	-0.009	0.000	0.000	0.000	0.000
42	D	45	ASP	-1	-0.923	-0.961	24.790	0.048	0.048	0.000	0.000	0.000	0.000
43	D	46	ARG	1	0.879	0.943	27.489	-0.061	-0.061	0.000	0.000	0.000	0.000
44	D	47	LEU	0	0.001	0.001	30.036	-0.006	-0.006	0.000	0.000	0.000	0.000
45	D	48	GLN	0	0.071	0.025	25.052	-0.001	-0.001	0.000	0.000	0.000	0.000
46	D	49	LEU	0	-0.025	-0.014	28.081	-0.003	-0.003	0.000	0.000	0.000	0.000
47	D	50	SER	0	0.026	0.005	30.644	-0.001	-0.001	0.000	0.000	0.000	0.000
48	D	51	ILE	0	0.016	0.017	30.651	-0.002	-0.002	0.000	0.000	0.000	0.000
49	D	52	LYS	1	0.959	0.998	30.052	-0.008	-0.008	0.000	0.000	0.000	0.000
50	D	53	ASN	0	-0.129	-0.064	32.805	-0.001	-0.001	0.000	0.000	0.000	0.000
51	D	54	ASN	0	0.012	-0.009	35.616	-0.002	-0.002	0.000	0.000	0.000	0.000
52	D	55	TRP	0	-0.058	-0.015	36.572	0.003	0.003	0.000	0.000	0.000	0.000
53	D	56	ILE	0	-0.003	-0.006	35.478	0.000	0.000	0.000	0.000	0.000	0.000
54	D	57	ASP	-1	-0.793	-0.867	39.518	-0.021	-0.021	0.000	0.000	0.000	0.000
55	D	58	THR	0	0.008	-0.021	42.593	-0.003	-0.003	0.000	0.000	0.000	0.000
56	D	59	GLU	-1	-0.960	-0.974	44.030	-0.033	-0.033	0.000	0.000	0.000	0.000
57	D	60	GLY	0	-0.018	0.004	40.062	-0.004	-0.004	0.000	0.000	0.000	0.000
58	D	61	ASN	0	-0.089	-0.040	38.371	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	62	ILE	0	-0.002	-0.002	33.219	0.002	0.002	0.000	0.000	0.000	0.000
60	D	63	TYR	0	-0.017	0.003	37.437	0.005	0.005	0.000	0.000	0.000	0.000
61	D	64	PHE	0	-0.036	-0.026	33.395	0.002	0.002	0.000	0.000	0.000	0.000
62	D	65	ILE	0	0.021	0.022	38.718	0.000	0.000	0.000	0.000	0.000	0.000
63	D	66	TYR	0	0.004	0.005	33.921	0.006	0.006	0.000	0.000	0.000	0.000
64	D	67	THR	0	-0.075	-0.079	40.412	0.000	0.000	0.000	0.000	0.000	0.000
65	D	68	VAL	0	-0.014	-0.032	41.681	0.001	0.001	0.000	0.000	0.000	0.000
66	D	69	ALA	0	0.066	0.035	41.665	0.003	0.003	0.000	0.000	0.000	0.000
67	D	70	ASP	-1	-0.817	-0.866	37.830	0.048	0.048	0.000	0.000	0.000	0.000
68	D	71	LEU	0	0.030	0.001	36.963	0.005	0.005	0.000	0.000	0.000	0.000
69	D	72	GLU	-1	-0.814	-0.886	37.193	0.065	0.065	0.000	0.000	0.000	0.000
70	D	73	VAL	0	-0.003	-0.005	33.745	0.007	0.007	0.000	0.000	0.000	0.000
71	D	74	ILE	0	-0.078	-0.036	32.206	0.007	0.007	0.000	0.000	0.000	0.000
72	D	75	LEU	0	-0.027	-0.016	32.304	0.005	0.005	0.000	0.000	0.000	0.000
73	D	76	ASN	0	-0.033	-0.002	33.019	0.007	0.007	0.000	0.000	0.000	0.000
74	D	77	CYS	0	-0.080	-0.034	35.016	0.001	0.001	0.000	0.000	0.000	0.000
75	D	78	GLY	0	0.084	0.047	38.442	-0.003	-0.003	0.000	0.000	0.000	0.000
76	D	79	ASN	0	-0.010	-0.029	42.134	-0.003	-0.003	0.000	0.000	0.000	0.000
77	D	80	LYS	1	0.965	0.982	44.532	-0.052	-0.052	0.000	0.000	0.000	0.000
78	D	81	LYS	1	0.866	0.920	38.327	-0.089	-0.089	0.000	0.000	0.000	0.000
79	D	82	ILE	0	0.075	0.029	40.089	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	83	THR	0	-0.082	-0.036	42.021	-0.005	-0.005	0.000	0.000	0.000	0.000
81	D	84	LYS	1	0.835	0.916	41.427	-0.067	-0.067	0.000	0.000	0.000	0.000
82	D	85	ILE	0	0.005	0.009	37.963	-0.002	-0.002	0.000	0.000	0.000	0.000
83	D	86	LYS	1	0.874	0.936	41.701	-0.035	-0.035	0.000	0.000	0.000	0.000
84	D	87	LYS	1	0.979	0.989	43.137	-0.035	-0.035	0.000	0.000	0.000	0.000
85	D	88	GLU	-1	-0.768	-0.849	42.156	0.050	0.050	0.000	0.000	0.000	0.000
86	D	89	LEU	0	-0.012	-0.008	37.830	-0.002	-0.002	0.000	0.000	0.000	0.000
87	D	90	GLU	-1	-0.864	-0.930	41.871	0.018	0.018	0.000	0.000	0.000	0.000
88	D	91	ASN	0	-0.076	-0.017	44.926	-0.002	-0.002	0.000	0.000	0.000	0.000
89	D	92	VAL	0	0.017	0.011	41.457	-0.001	-0.001	0.000	0.000	0.000	0.000
90	D	93	ASP	-1	-0.910	-0.948	43.117	0.002	0.002	0.000	0.000	0.000	0.000
91	D	94	LEU	0	-0.041	-0.025	37.750	-0.002	-0.002	0.000	0.000	0.000	0.000
92	D	95	LEU	0	-0.083	-0.050	39.238	0.001	0.001	0.000	0.000	0.000	0.000
93	D	96	ILE	0	0.062	0.028	41.549	-0.001	-0.001	0.000	0.000	0.000	0.000
94	D	97	GLN	0	0.007	-0.007	43.835	0.002	0.002	0.000	0.000	0.000	0.000
95	D	98	LYS	1	0.955	0.997	45.292	0.008	0.008	0.000	0.000	0.000	0.000
96	D	99	ARG	1	0.921	0.970	47.890	-0.011	-0.011	0.000	0.000	0.000	0.000
97	D	100	GLN	0	-0.011	0.002	48.498	0.001	0.001	0.000	0.000	0.000	0.000
98	D	101	GLY	0	0.066	0.045	47.754	0.001	0.001	0.000	0.000	0.000	0.000
99	D	102	LEU	0	-0.025	-0.049	49.583	0.000	0.000	0.000	0.000	0.000	0.000
100	D	103	ASN	0	0.016	0.008	49.246	0.000	0.000	0.000	0.000	0.000	0.000
101	D	104	LYS	1	0.982	1.000	45.573	-0.029	-0.029	0.000	0.000	0.000	0.000
102	D	105	PRO	0	-0.024	-0.021	45.637	0.002	0.002	0.000	0.000	0.000	0.000
103	D	106	ASN	0	-0.008	-0.013	44.942	-0.005	-0.005	0.000	0.000	0.000	0.000
104	D	107	LEU	0	0.052	0.043	42.809	0.000	0.000	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.084	-0.046	40.044	0.001	0.001	0.000	0.000	0.000	0.000
106	D	109	TYR	0	-0.023	-0.047	39.982	-0.001	-0.001	0.000	0.000	0.000	0.000
107	D	110	LEU	0	0.016	0.014	33.999	0.003	0.003	0.000	0.000	0.000	0.000
108	D	111	LEU	0	0.004	0.019	37.932	-0.007	-0.007	0.000	0.000	0.000	0.000
109	D	112	LYS	1	0.939	0.986	34.126	0.045	0.045	0.000	0.000	0.000	0.000
110	D	113	PRO	0	0.025	0.011	34.388	0.000	0.000	0.000	0.000	0.000	0.000
111	D	114	ALA	0	0.018	0.017	37.399	-0.006	-0.006	0.000	0.000	0.000	0.000
112	D	115	ILE	0	0.013	-0.010	34.269	0.004	0.004	0.000	0.000	0.000	0.000
113	D	116	THR	0	-0.017	-0.027	38.150	-0.004	-0.004	0.000	0.000	0.000	0.000
114	D	117	LYS	1	1.006	0.973	38.761	0.031	0.031	0.000	0.000	0.000	0.000
115	D	118	ASN	0	-0.002	0.013	39.151	0.001	0.001	0.000	0.000	0.000	0.000
116	D	119	ASP	-1	-0.704	-0.813	36.290	0.006	0.006	0.000	0.000	0.000	0.000
117	D	120	ILE	0	-0.002	0.003	33.992	0.002	0.002	0.000	0.000	0.000	0.000
118	D	121	TYR	0	0.011	0.015	34.351	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	122	GLU	-1	-0.921	-0.981	35.349	0.021	0.021	0.000	0.000	0.000	0.000
120	D	123	ILE	0	-0.067	-0.044	30.219	0.006	0.006	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.879	-0.928	30.614	-0.027	-0.027	0.000	0.000	0.000	0.000
122	D	125	LYS	1	0.826	0.913	30.852	-0.017	-0.017	0.000	0.000	0.000	0.000
123	D	126	ALA	0	-0.028	-0.016	31.112	0.007	0.007	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.860	-0.919	25.677	0.016	0.016	0.000	0.000	0.000	0.000
125	D	128	ASN	0	-0.079	-0.035	26.473	-0.008	-0.008	0.000	0.000	0.000	0.000
126	D	129	GLU	-1	-0.963	-0.977	26.903	0.041	0.041	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:4:GLN)