FMO DATABASE

FMODB ID: 6NQRZ

Calculation Name: 3F13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F13

Chain ID: A

ChEMBL ID:

UniProt ID: Q7NWQ3

Base Structure: X-ray

Registration Date: 2023-09-20

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1371894.721895
FMO2-HF: Nuclear repulsion	1314777.311291
FMO2-HF: Total energy	-57117.410604
FMO2-MP2: Total energy	-57285.132825

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:11:ARG)

Summations of interaction energy for fragment #1(A:11:ARG)

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.
96.39	98.559	-0.014	-0.75	-1.404	0

Interaction energy analysis for fragmet #1(A:11:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.987 / q_NPA : 0.968

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	13	PRO	0	-0.076	-0.037	3.794	-4.564	-2.589	-0.012	-0.737	-1.226
4	A	14	SER	0	0.029	0.014	5.265	2.904	3.016	-0.001	-0.006	-0.105
5	A	15	ASP	-1	-0.890	-0.926	7.905	-20.685	-20.685	0.000	0.000	0.000
6	A	16	LEU	0	-0.032	-0.013	9.531	-1.648	-1.648	0.000	0.000	0.000
7	A	17	ALA	0	-0.010	-0.006	11.840	1.501	1.501	0.000	0.000	0.000
8	A	18	ARG	1	0.845	0.895	13.360	15.965	15.965	0.000	0.000	0.000
9	A	19	ARG	1	0.923	0.978	12.973	20.554	20.554	0.000	0.000	0.000
10	A	20	ALA	0	0.011	0.011	17.519	0.610	0.610	0.000	0.000	0.000
11	A	21	THR	0	-0.025	-0.012	19.623	-0.770	-0.770	0.000	0.000	0.000
12	A	22	ALA	0	0.057	0.026	21.971	0.433	0.433	0.000	0.000	0.000
13	A	23	ILE	0	0.002	0.005	25.179	-0.276	-0.276	0.000	0.000	0.000
14	A	24	ILE	0	0.030	0.003	27.290	0.254	0.254	0.000	0.000	0.000
15	A	25	GLU	-1	-0.821	-0.872	30.212	-9.602	-9.602	0.000	0.000	0.000
16	A	26	MET	0	-0.017	-0.005	31.784	0.246	0.246	0.000	0.000	0.000
17	A	27	PRO	0	0.012	0.000	34.703	-0.039	-0.039	0.000	0.000	0.000
18	A	28	ASP	-1	-0.866	-0.919	35.586	-8.136	-8.136	0.000	0.000	0.000
19	A	29	GLY	0	-0.019	-0.012	31.846	-0.183	-0.183	0.000	0.000	0.000
20	A	30	VAL	0	-0.044	-0.019	26.619	-0.025	-0.025	0.000	0.000	0.000
21	A	31	LEU	0	-0.002	0.011	27.129	-0.195	-0.195	0.000	0.000	0.000
22	A	32	VAL	0	-0.050	-0.020	23.142	-0.506	-0.506	0.000	0.000	0.000
23	A	33	THR	0	0.039	0.010	22.016	0.196	0.196	0.000	0.000	0.000
24	A	34	ALA	0	0.007	-0.026	20.247	-0.682	-0.682	0.000	0.000	0.000
25	A	35	SER	0	0.026	0.020	17.290	0.170	0.170	0.000	0.000	0.000
26	A	36	ARG	1	0.816	0.926	15.470	16.789	16.789	0.000	0.000	0.000
27	A	37	GLY	0	0.126	0.085	18.483	0.866	0.866	0.000	0.000	0.000
28	A	38	GLY	0	0.006	-0.008	17.276	-1.132	-1.132	0.000	0.000	0.000
29	A	39	ARG	1	0.897	0.957	13.383	18.982	18.982	0.000	0.000	0.000
30	A	40	TYR	0	0.078	0.043	18.515	-0.409	-0.409	0.000	0.000	0.000
31	A	41	ASN	0	-0.025	-0.027	15.887	0.058	0.058	0.000	0.000	0.000
32	A	42	LEU	0	-0.004	0.009	19.615	0.496	0.496	0.000	0.000	0.000
33	A	43	PRO	0	0.000	0.025	20.446	-0.806	-0.806	0.000	0.000	0.000
34	A	44	GLY	0	0.027	-0.009	20.827	0.206	0.206	0.000	0.000	0.000
35	A	45	GLY	0	-0.003	0.021	17.206	-0.472	-0.472	0.000	0.000	0.000
36	A	46	LYS	1	0.907	0.942	12.038	20.899	20.899	0.000	0.000	0.000
37	A	47	ALA	0	0.041	0.030	16.845	0.556	0.556	0.000	0.000	0.000
38	A	48	ASN	0	-0.013	-0.026	18.050	-1.753	-1.753	0.000	0.000	0.000
39	A	49	ARG	1	0.955	0.959	15.444	17.985	17.985	0.000	0.000	0.000
40	A	50	GLY	0	0.033	0.015	20.631	0.317	0.317	0.000	0.000	0.000
41	A	51	GLU	-1	-0.747	-0.804	21.764	-13.135	-13.135	0.000	0.000	0.000
42	A	52	LEU	0	0.030	0.018	23.073	-0.739	-0.739	0.000	0.000	0.000
43	A	53	ARG	1	0.857	0.908	18.858	15.162	15.162	0.000	0.000	0.000
44	A	54	SER	0	0.015	0.010	23.321	-0.155	-0.155	0.000	0.000	0.000
45	A	55	GLN	0	0.067	0.025	26.148	-0.029	-0.029	0.000	0.000	0.000
46	A	56	ALA	0	0.032	0.022	21.614	0.128	0.128	0.000	0.000	0.000
47	A	57	LEU	0	-0.011	0.003	23.018	-0.117	-0.117	0.000	0.000	0.000
48	A	58	ILE	0	0.006	0.002	24.598	0.047	0.047	0.000	0.000	0.000
49	A	59	ARG	1	0.873	0.936	20.876	13.781	13.781	0.000	0.000	0.000
50	A	60	GLU	-1	-0.860	-0.940	19.592	-15.319	-15.319	0.000	0.000	0.000
51	A	61	ILE	0	-0.007	-0.002	23.678	-0.057	-0.057	0.000	0.000	0.000
52	A	62	ARG	1	0.945	0.985	25.925	10.012	10.012	0.000	0.000	0.000
53	A	63	GLU	-1	-0.885	-0.951	23.939	-11.496	-11.496	0.000	0.000	0.000
54	A	64	GLH	0	-0.029	-0.034	20.259	0.213	0.213	0.000	0.000	0.000
55	A	65	THR	0	-0.038	-0.015	24.717	0.256	0.256	0.000	0.000	0.000
56	A	66	GLY	0	0.037	0.018	28.136	0.377	0.377	0.000	0.000	0.000
57	A	67	LEU	0	-0.060	-0.029	30.265	0.397	0.397	0.000	0.000	0.000
58	A	68	ARG	1	0.964	0.967	30.928	8.437	8.437	0.000	0.000	0.000
59	A	69	ILE	0	-0.002	-0.010	28.491	0.196	0.196	0.000	0.000	0.000
60	A	70	ASN	0	-0.010	0.008	32.719	0.087	0.087	0.000	0.000	0.000
61	A	71	SER	0	0.038	0.027	34.807	0.210	0.210	0.000	0.000	0.000
62	A	72	MET	0	-0.045	-0.035	28.187	-0.290	-0.290	0.000	0.000	0.000
63	A	73	LEU	0	0.018	0.025	31.917	0.173	0.173	0.000	0.000	0.000
64	A	74	TYR	0	-0.060	-0.079	25.141	-0.113	-0.113	0.000	0.000	0.000
65	A	75	LEU	0	-0.027	-0.013	27.041	0.309	0.309	0.000	0.000	0.000
66	A	76	PHE	0	0.009	-0.013	22.496	0.144	0.144	0.000	0.000	0.000
67	A	77	ASP	-1	-0.777	-0.838	21.123	-13.201	-13.201	0.000	0.000	0.000
68	A	78	HIS	0	-0.021	-0.013	16.158	0.871	0.871	0.000	0.000	0.000
69	A	79	ILE	0	0.035	0.018	14.879	-0.618	-0.618	0.000	0.000	0.000
70	A	80	THR	0	-0.042	-0.033	11.507	-0.140	-0.140	0.000	0.000	0.000
71	A	81	PRO	0	0.067	0.025	7.466	0.168	0.168	0.000	0.000	0.000
72	A	82	PHE	0	0.017	0.020	4.731	-1.463	-1.381	-0.001	-0.007	-0.073
73	A	83	ASN	0	-0.052	-0.055	9.528	0.240	0.240	0.000	0.000	0.000
74	A	84	ALA	0	0.070	0.046	13.290	0.809	0.809	0.000	0.000	0.000
75	A	85	HIS	1	0.773	0.879	14.851	18.097	18.097	0.000	0.000	0.000
76	A	86	LYS	1	0.926	0.981	18.864	12.987	12.987	0.000	0.000	0.000
77	A	87	VAL	0	0.011	0.005	21.669	-0.349	-0.349	0.000	0.000	0.000
78	A	88	TYR	0	0.019	-0.002	24.066	0.236	0.236	0.000	0.000	0.000
79	A	89	LEU	0	0.044	0.043	27.544	-0.263	-0.263	0.000	0.000	0.000
80	A	90	CYS	0	-0.075	-0.039	28.661	0.046	0.046	0.000	0.000	0.000
81	A	91	ILE	0	0.079	0.044	31.442	0.001	0.001	0.000	0.000	0.000
82	A	92	ALA	0	-0.007	-0.016	32.790	-0.087	-0.087	0.000	0.000	0.000
83	A	93	GLN	0	-0.034	-0.005	34.901	-0.084	-0.084	0.000	0.000	0.000
84	A	94	GLY	0	-0.001	-0.011	36.209	0.001	0.001	0.000	0.000	0.000
85	A	95	GLN	0	0.022	0.006	35.713	-0.125	-0.125	0.000	0.000	0.000
86	A	96	PRO	0	-0.018	0.003	30.418	-0.096	-0.096	0.000	0.000	0.000
87	A	97	LYS	1	0.943	0.956	30.743	9.262	9.262	0.000	0.000	0.000
88	A	98	PRO	0	-0.031	0.013	27.150	-0.214	-0.214	0.000	0.000	0.000
89	A	99	GLN	0	0.000	-0.005	26.247	0.678	0.678	0.000	0.000	0.000
90	A	100	ASN	0	-0.053	-0.031	23.680	-0.399	-0.399	0.000	0.000	0.000
91	A	101	GLU	-1	-0.868	-0.941	18.561	-14.884	-14.884	0.000	0.000	0.000
92	A	102	ILE	0	-0.125	-0.056	20.749	-0.565	-0.565	0.000	0.000	0.000
93	A	103	GLU	-1	-0.867	-0.942	22.684	-12.585	-12.585	0.000	0.000	0.000
94	A	104	ARG	1	0.853	0.923	21.543	13.756	13.756	0.000	0.000	0.000
95	A	105	ILE	0	-0.010	-0.019	24.866	-0.561	-0.561	0.000	0.000	0.000
96	A	106	ALA	0	-0.018	-0.001	26.883	0.264	0.264	0.000	0.000	0.000
97	A	107	LEU	0	0.039	0.015	28.459	-0.183	-0.183	0.000	0.000	0.000
98	A	108	VAL	0	-0.036	-0.019	24.946	0.008	0.008	0.000	0.000	0.000
99	A	109	SER	0	0.066	0.025	28.360	0.180	0.180	0.000	0.000	0.000
100	A	110	SER	0	-0.016	-0.001	28.937	0.111	0.111	0.000	0.000	0.000
101	A	111	PRO	0	0.005	-0.021	24.794	-0.314	-0.314	0.000	0.000	0.000
102	A	112	ASP	-1	-0.963	-0.985	24.046	-10.833	-10.833	0.000	0.000	0.000
103	A	113	THR	0	0.017	0.035	24.378	0.127	0.127	0.000	0.000	0.000
104	A	114	ASP	-1	-0.773	-0.886	24.975	-10.628	-10.628	0.000	0.000	0.000
105	A	115	MET	0	-0.101	-0.036	23.713	-0.448	-0.448	0.000	0.000	0.000
106	A	116	ASP	-1	-0.841	-0.935	18.720	-15.643	-15.643	0.000	0.000	0.000
107	A	117	LEU	0	-0.067	-0.033	19.571	-0.520	-0.520	0.000	0.000	0.000
108	A	118	PHE	0	0.011	-0.002	10.784	-0.348	-0.348	0.000	0.000	0.000
109	A	119	VAL	0	0.066	0.031	11.945	0.776	0.776	0.000	0.000	0.000
110	A	120	GLU	-1	-0.808	-0.897	12.876	-20.023	-20.023	0.000	0.000	0.000
111	A	121	GLY	0	0.040	0.029	15.640	0.695	0.695	0.000	0.000	0.000
112	A	122	ARG	1	0.874	0.935	18.502	13.501	13.501	0.000	0.000	0.000
113	A	123	ALA	0	-0.052	-0.028	17.804	0.671	0.671	0.000	0.000	0.000
114	A	124	ILE	0	-0.024	-0.013	18.318	0.571	0.571	0.000	0.000	0.000
115	A	125	LEU	0	0.064	0.021	21.319	0.553	0.553	0.000	0.000	0.000
116	A	126	ARG	1	0.955	0.983	20.041	12.921	12.921	0.000	0.000	0.000
117	A	127	ARG	1	0.818	0.902	20.995	13.107	13.107	0.000	0.000	0.000
118	A	128	TYR	0	-0.047	-0.092	25.144	0.275	0.275	0.000	0.000	0.000
119	A	129	ALA	0	0.014	0.005	27.379	0.347	0.347	0.000	0.000	0.000
120	A	130	ARG	1	0.966	0.974	23.481	11.256	11.256	0.000	0.000	0.000
121	A	131	LEU	0	0.052	0.043	29.000	0.213	0.213	0.000	0.000	0.000
122	A	132	ARG	1	0.888	0.937	31.022	9.302	9.302	0.000	0.000	0.000
123	A	133	ASN	0	-0.017	-0.003	33.476	0.349	0.349	0.000	0.000	0.000
124	A	134	GLU	-1	-0.930	-0.948	31.427	-9.182	-9.182	0.000	0.000	0.000
125	A	135	GLU	-1	-0.900	-0.939	35.336	-7.285	-7.285	0.000	0.000	0.000
126	A	136	THR	0	0.007	0.001	34.638	-0.019	-0.019	0.000	0.000	0.000
127	A	137	ALA	0	0.098	0.042	37.559	0.005	0.005	0.000	0.000	0.000
128	A	138	LYS	1	0.854	0.938	30.093	9.942	9.942	0.000	0.000	0.000
129	A	139	GLY	0	0.043	0.022	34.691	-0.105	-0.105	0.000	0.000	0.000
130	A	140	GLU	-1	-0.919	-0.962	35.556	-7.319	-7.319	0.000	0.000	0.000
131	A	141	ALA	0	0.002	0.002	36.288	0.069	0.069	0.000	0.000	0.000
132	A	142	LEU	0	-0.028	-0.011	31.627	-0.041	-0.041	0.000	0.000	0.000
133	A	143	ARG	1	0.867	0.909	35.374	7.968	7.968	0.000	0.000	0.000
134	A	144	ALA	0	0.011	0.015	38.070	0.112	0.112	0.000	0.000	0.000
135	A	145	LEU	0	-0.016	-0.015	35.245	0.063	0.063	0.000	0.000	0.000
136	A	146	LEU	0	-0.026	-0.016	33.749	0.034	0.034	0.000	0.000	0.000
137	A	147	GLY	0	-0.042	-0.011	37.674	0.096	0.096	0.000	0.000	0.000
138	A	148	LEU	0	0.025	0.012	40.334	0.124	0.124	0.000	0.000	0.000
139	A	149	ALA	0	0.018	-0.001	37.483	0.083	0.083	0.000	0.000	0.000
140	A	150	ARG	1	0.947	0.979	39.501	7.609	7.609	0.000	0.000	0.000
141	A	151	TYR	0	-0.015	-0.010	41.370	0.100	0.100	0.000	0.000	0.000
142	A	152	ILE	0	0.003	-0.004	41.403	0.114	0.114	0.000	0.000	0.000
143	A	153	ALA	0	0.011	0.004	40.429	0.061	0.061	0.000	0.000	0.000
144	A	154	LYS	1	0.897	0.960	42.520	6.542	6.542	0.000	0.000	0.000
145	A	155	VAL	0	-0.048	-0.020	45.760	0.152	0.152	0.000	0.000	0.000
146	A	156	ASP	-1	-0.937	-0.954	43.297	-7.121	-7.121	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:ARG)