FMO DATABASE

FMODB ID: Q1Q3Y

Calculation Name: 4L3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L3R

Chain ID: A

ChEMBL ID:

UniProt ID:

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1312890.675324
FMO2-HF: Nuclear repulsion	1257098.285837
FMO2-HF: Total energy	-55792.389487
FMO2-MP2: Total energy	-55956.485023

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:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-34.282	-31.247	2.961	-2.358	-3.639	0.012

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.928 / q_NPA : -0.974

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	32	VAL	0	-0.010	-0.011	3.140	-8.846	-6.290	0.045	-1.135	-1.467	0.006
4	A	33	MET	0	0.032	0.015	2.331	-10.714	-10.223	2.917	-1.220	-2.188	0.006
5	A	34	GLU	-1	-0.774	-0.863	5.090	23.026	23.026	0.000	0.000	0.000	0.000
6	A	35	ILE	0	-0.043	-0.023	6.998	-3.967	-3.967	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.010	-0.016	8.347	-2.481	-2.481	0.000	0.000	0.000	0.000
8	A	37	ASN	0	-0.123	-0.056	8.375	-2.516	-2.516	0.000	0.000	0.000	0.000
9	A	38	ASP	-1	-0.907	-0.947	10.352	16.394	16.394	0.000	0.000	0.000	0.000
10	A	39	LYS	1	0.747	0.879	10.817	-24.482	-24.482	0.000	0.000	0.000	0.000
11	A	40	THR	0	-0.006	0.003	15.549	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	41	TRP	0	-0.036	-0.024	11.936	-1.323	-1.323	0.000	0.000	0.000	0.000
13	A	42	LYS	1	0.775	0.884	18.189	-11.746	-11.746	0.000	0.000	0.000	0.000
14	A	43	LEU	0	-0.018	-0.005	21.613	0.221	0.221	0.000	0.000	0.000	0.000
15	A	44	SER	0	-0.029	-0.016	22.403	-0.328	-0.328	0.000	0.000	0.000	0.000
16	A	45	ARG	1	0.914	0.961	20.063	-13.797	-13.797	0.000	0.000	0.000	0.000
17	A	46	ILE	0	0.012	0.008	24.223	0.445	0.445	0.000	0.000	0.000	0.000
18	A	47	THR	0	-0.019	-0.015	24.984	-0.547	-0.547	0.000	0.000	0.000	0.000
19	A	48	THR	0	0.022	-0.012	26.003	0.325	0.325	0.000	0.000	0.000	0.000
20	A	49	GLU	-1	-0.863	-0.931	21.944	12.921	12.921	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.933	0.959	23.186	-11.440	-11.440	0.000	0.000	0.000	0.000
22	A	51	GLY	0	0.013	0.031	25.468	-0.234	-0.234	0.000	0.000	0.000	0.000
23	A	52	LYS	1	0.892	0.923	26.221	-10.485	-10.485	0.000	0.000	0.000	0.000
24	A	53	GLU	-1	-0.781	-0.858	28.751	9.887	9.887	0.000	0.000	0.000	0.000
25	A	54	GLN	0	-0.001	0.010	28.260	-0.049	-0.049	0.000	0.000	0.000	0.000
26	A	55	PHE	0	0.014	-0.016	28.078	0.343	0.343	0.000	0.000	0.000	0.000
27	A	56	TYR	0	0.011	0.019	28.791	-0.128	-0.128	0.000	0.000	0.000	0.000
28	A	57	GLN	0	0.020	0.002	31.716	-0.219	-0.219	0.000	0.000	0.000	0.000
29	A	58	GLY	0	0.043	0.013	35.281	0.059	0.059	0.000	0.000	0.000	0.000
30	A	59	LEU	0	-0.065	-0.005	30.155	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	60	TRP	0	-0.020	-0.028	32.385	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	61	SER	0	-0.017	-0.022	37.769	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	62	ASN	0	0.000	-0.001	41.450	-0.170	-0.170	0.000	0.000	0.000	0.000
34	A	63	GLU	-1	-0.860	-0.931	41.290	7.182	7.182	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.023	0.015	41.254	0.144	0.144	0.000	0.000	0.000	0.000
36	A	65	GLU	-1	-0.823	-0.896	39.287	7.627	7.627	0.000	0.000	0.000	0.000
37	A	66	GLU	-1	-0.777	-0.865	35.762	8.663	8.663	0.000	0.000	0.000	0.000
38	A	67	LYS	1	0.879	0.921	36.659	-7.258	-7.258	0.000	0.000	0.000	0.000
39	A	68	ALA	0	0.007	0.000	37.907	0.127	0.127	0.000	0.000	0.000	0.000
40	A	69	SER	0	0.006	-0.038	33.521	0.132	0.132	0.000	0.000	0.000	0.000
41	A	70	ARG	1	0.799	0.870	32.606	-8.675	-8.675	0.000	0.000	0.000	0.000
42	A	71	GLU	-1	-0.850	-0.874	34.317	8.155	8.155	0.000	0.000	0.000	0.000
43	A	72	LEU	0	-0.036	-0.016	33.625	0.165	0.165	0.000	0.000	0.000	0.000
44	A	73	LEU	0	0.009	0.004	27.241	0.212	0.212	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.802	0.875	29.614	-8.299	-8.299	0.000	0.000	0.000	0.000
46	A	75	ILE	0	-0.011	0.013	31.145	0.080	0.080	0.000	0.000	0.000	0.000
47	A	76	THR	0	0.029	0.013	26.475	0.246	0.246	0.000	0.000	0.000	0.000
48	A	77	GLU	-1	-0.803	-0.914	26.335	10.415	10.415	0.000	0.000	0.000	0.000
49	A	78	ASN	0	-0.032	0.005	26.721	0.286	0.286	0.000	0.000	0.000	0.000
50	A	79	PHE	0	-0.025	-0.018	25.942	0.202	0.202	0.000	0.000	0.000	0.000
51	A	80	THR	0	-0.025	-0.015	22.270	0.481	0.481	0.000	0.000	0.000	0.000
52	A	81	LEU	0	-0.019	-0.015	17.301	-0.353	-0.353	0.000	0.000	0.000	0.000
53	A	82	ASN	0	-0.009	0.009	16.624	0.527	0.527	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.052	0.036	11.996	-0.658	-0.658	0.000	0.000	0.000	0.000
55	A	84	ASN	0	-0.006	-0.016	13.360	-0.356	-0.356	0.000	0.000	0.000	0.000
56	A	85	CYS	0	0.013	-0.003	12.113	1.730	1.730	0.000	0.000	0.000	0.000
57	A	86	ALA	0	0.035	0.030	14.872	-0.651	-0.651	0.000	0.000	0.000	0.000
58	A	87	ASP	-1	-0.900	-0.945	18.379	14.047	14.047	0.000	0.000	0.000	0.000
59	A	88	VAL	0	-0.042	-0.020	19.984	-0.691	-0.691	0.000	0.000	0.000	0.000
60	A	89	ASN	0	-0.071	-0.048	22.122	-0.292	-0.292	0.000	0.000	0.000	0.000
61	A	90	GLY	0	0.013	0.014	23.748	-0.274	-0.274	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.942	-0.967	18.809	16.266	16.266	0.000	0.000	0.000	0.000
63	A	92	VAL	0	-0.031	-0.011	14.892	-0.168	-0.168	0.000	0.000	0.000	0.000
64	A	93	THR	0	0.001	0.011	15.025	1.207	1.207	0.000	0.000	0.000	0.000
65	A	94	GLY	0	0.018	-0.002	12.548	0.158	0.158	0.000	0.000	0.000	0.000
66	A	95	THR	0	-0.079	-0.059	13.569	-0.374	-0.374	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.012	-0.002	15.158	0.827	0.827	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.033	0.024	17.416	-1.020	-1.020	0.000	0.000	0.000	0.000
69	A	98	ALA	0	-0.020	-0.018	20.052	0.426	0.426	0.000	0.000	0.000	0.000
70	A	99	HIS	1	0.818	0.896	22.624	-11.026	-11.026	0.000	0.000	0.000	0.000
71	A	100	ALA	0	0.000	0.019	26.132	0.129	0.129	0.000	0.000	0.000	0.000
72	A	101	VAL	0	-0.011	-0.005	28.354	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.848	0.919	31.782	-8.357	-8.357	0.000	0.000	0.000	0.000
74	A	103	ALA	0	-0.064	-0.021	30.607	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	104	ASN	0	0.002	-0.013	27.090	0.380	0.380	0.000	0.000	0.000	0.000
76	A	105	ILE	0	0.007	0.006	22.295	-0.321	-0.321	0.000	0.000	0.000	0.000
77	A	106	SER	0	-0.021	-0.014	23.098	0.064	0.064	0.000	0.000	0.000	0.000
78	A	107	ASP	-1	-0.822	-0.895	19.676	14.383	14.383	0.000	0.000	0.000	0.000
79	A	108	ALA	0	-0.039	-0.005	20.115	-0.154	-0.154	0.000	0.000	0.000	0.000
80	A	109	ILE	0	0.038	0.007	18.293	0.847	0.847	0.000	0.000	0.000	0.000
81	A	110	LEU	0	0.004	0.015	11.564	-0.395	-0.395	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.899	0.947	13.638	-18.050	-18.050	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.036	0.005	8.572	-0.991	-0.991	0.000	0.000	0.000	0.000
84	A	113	ASP	-1	-0.829	-0.905	7.884	32.061	32.061	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.051	0.021	4.687	-1.460	-1.472	-0.001	-0.003	0.016	0.000
86	A	115	LYS	1	0.865	0.931	5.775	-35.938	-35.938	0.000	0.000	0.000	0.000
87	A	116	GLU	-1	-0.889	-0.916	7.943	18.447	18.447	0.000	0.000	0.000	0.000
88	A	117	HIS	0	-0.059	-0.019	6.902	-1.734	-1.734	0.000	0.000	0.000	0.000
89	A	118	THR	0	-0.027	-0.038	10.392	-1.291	-1.291	0.000	0.000	0.000	0.000
90	A	119	ILE	0	-0.023	-0.029	11.561	1.576	1.576	0.000	0.000	0.000	0.000
91	A	120	SER	0	-0.045	-0.012	13.932	-1.311	-1.311	0.000	0.000	0.000	0.000
92	A	121	ILE	0	0.045	0.018	16.363	0.835	0.835	0.000	0.000	0.000	0.000
93	A	122	SER	0	-0.008	0.002	18.831	-0.933	-0.933	0.000	0.000	0.000	0.000
94	A	123	GLY	0	0.028	-0.001	21.782	0.264	0.264	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.928	0.969	24.607	-9.966	-9.966	0.000	0.000	0.000	0.000
96	A	125	ALA	0	0.038	0.022	26.960	0.221	0.221	0.000	0.000	0.000	0.000
97	A	126	TYR	0	-0.017	0.003	28.465	-0.338	-0.338	0.000	0.000	0.000	0.000
98	A	127	GLY	0	0.058	0.019	30.787	0.076	0.076	0.000	0.000	0.000	0.000
99	A	128	SER	0	-0.014	-0.016	33.359	0.099	0.099	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.679	-0.846	31.870	9.178	9.178	0.000	0.000	0.000	0.000
101	A	130	SER	0	-0.049	-0.032	35.228	-0.152	-0.152	0.000	0.000	0.000	0.000
102	A	131	ASP	-1	-0.735	-0.840	33.753	8.742	8.742	0.000	0.000	0.000	0.000
103	A	132	LYS	1	0.839	0.904	34.838	-7.558	-7.558	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.048	0.039	29.040	0.177	0.177	0.000	0.000	0.000	0.000
105	A	134	ALA	0	-0.004	-0.013	29.902	0.359	0.359	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.859	0.935	29.778	-7.979	-7.979	0.000	0.000	0.000	0.000
107	A	136	VAL	0	0.030	0.031	28.010	0.201	0.201	0.000	0.000	0.000	0.000
108	A	137	PHE	0	0.010	0.003	23.357	0.290	0.290	0.000	0.000	0.000	0.000
109	A	138	ILE	0	-0.002	-0.009	25.092	0.396	0.396	0.000	0.000	0.000	0.000
110	A	139	SER	0	-0.040	-0.037	25.868	0.169	0.169	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.022	0.006	24.532	0.150	0.150	0.000	0.000	0.000	0.000
112	A	141	LEU	0	-0.020	-0.022	19.958	0.502	0.502	0.000	0.000	0.000	0.000
113	A	142	PHE	0	-0.026	-0.009	20.785	0.490	0.490	0.000	0.000	0.000	0.000
114	A	143	ASN	0	-0.036	-0.005	23.091	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	144	VAL	0	-0.048	-0.028	17.357	-0.098	-0.098	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.034	-0.019	17.942	-0.207	-0.207	0.000	0.000	0.000	0.000
117	A	146	LYS	1	0.873	0.943	14.529	-14.128	-14.128	0.000	0.000	0.000	0.000
118	A	147	TYR	0	-0.025	-0.016	7.060	-0.885	-0.885	0.000	0.000	0.000	0.000
119	A	148	GLU	-1	-0.823	-0.885	11.803	17.007	17.007	0.000	0.000	0.000	0.000
120	A	149	GLY	0	-0.017	-0.024	11.650	-1.114	-1.114	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.765	-0.852	10.206	20.401	20.401	0.000	0.000	0.000	0.000
122	A	151	VAL	0	0.036	0.015	9.730	-0.303	-0.303	0.000	0.000	0.000	0.000
123	A	152	HIS	1	0.818	0.899	11.545	-18.234	-18.234	0.000	0.000	0.000	0.000
124	A	153	ASN	0	-0.066	-0.042	14.591	-1.938	-1.938	0.000	0.000	0.000	0.000
125	A	154	LEU	0	0.052	0.035	12.382	1.196	1.196	0.000	0.000	0.000	0.000
126	A	155	THR	0	-0.053	-0.024	14.990	-1.774	-1.774	0.000	0.000	0.000	0.000
127	A	156	LEU	0	0.024	0.016	14.530	0.899	0.899	0.000	0.000	0.000	0.000
128	A	157	TYR	0	-0.049	-0.063	16.611	-1.392	-1.392	0.000	0.000	0.000	0.000
129	A	158	PHE	0	0.005	0.003	19.121	0.312	0.312	0.000	0.000	0.000	0.000
130	A	159	LYS	1	0.953	0.974	21.937	-12.072	-12.072	0.000	0.000	0.000	0.000
131	A	160	ASP	-1	-0.797	-0.883	25.227	9.666	9.666	0.000	0.000	0.000	0.000
132	A	161	GLY	0	0.055	0.043	28.767	-0.222	-0.222	0.000	0.000	0.000	0.000
133	A	162	ASN	0	-0.049	-0.031	29.580	0.268	0.268	0.000	0.000	0.000	0.000
134	A	163	THR	0	-0.048	-0.025	29.159	0.022	0.022	0.000	0.000	0.000	0.000
135	A	164	THR	0	0.001	0.006	22.632	0.126	0.126	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.782	0.873	24.474	-10.269	-10.269	0.000	0.000	0.000	0.000
137	A	166	VAL	0	0.007	0.011	20.118	0.492	0.492	0.000	0.000	0.000	0.000
138	A	167	MET	0	-0.029	0.010	20.403	-0.646	-0.646	0.000	0.000	0.000	0.000
139	A	168	GLY	0	-0.013	-0.007	19.618	0.703	0.703	0.000	0.000	0.000	0.000
140	A	169	PHE	0	0.027	-0.004	17.864	-0.774	-0.774	0.000	0.000	0.000	0.000
141	A	170	THR	0	0.006	0.005	18.467	0.355	0.355	0.000	0.000	0.000	0.000
142	A	171	ALA	0	0.046	0.025	15.406	-0.326	-0.326	0.000	0.000	0.000	0.000
143	A	172	ARG	1	0.874	0.945	17.352	-13.644	-13.644	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)