FMO DATABASE

FMODB ID: R5RJ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1309894.209636
FMO2-HF: Nuclear repulsion	1254101.910324
FMO2-HF: Total energy	-55792.299311
FMO2-MP2: Total energy	-55956.333618

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.
-34.244	-32.002	3.457	-2.052	-3.648	0.014

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 : -0.951 / q_NPA : -0.981

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	-0.003	3.128	-8.132	-5.715	0.033	-1.059	-1.391	0.006
4	A	33	MET	0	0.036	0.012	2.605	-11.316	-11.491	3.424	-0.993	-2.257	0.008
5	A	34	GLU	-1	-0.760	-0.851	5.128	22.792	22.792	0.000	0.000	0.000	0.000
6	A	35	ILE	0	-0.052	-0.034	6.902	-3.951	-3.951	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.023	-0.021	8.485	-2.613	-2.613	0.000	0.000	0.000	0.000
8	A	37	ASN	0	-0.107	-0.047	8.480	-2.350	-2.350	0.000	0.000	0.000	0.000
9	A	38	ASP	-1	-0.923	-0.950	10.485	16.179	16.179	0.000	0.000	0.000	0.000
10	A	39	LYS	1	0.763	0.884	10.605	-24.415	-24.415	0.000	0.000	0.000	0.000
11	A	40	THR	0	-0.019	-0.008	15.559	-0.137	-0.137	0.000	0.000	0.000	0.000
12	A	41	TRP	0	-0.044	-0.023	11.888	-1.057	-1.057	0.000	0.000	0.000	0.000
13	A	42	LYS	1	0.799	0.888	18.291	-11.648	-11.648	0.000	0.000	0.000	0.000
14	A	43	LEU	0	-0.009	0.004	21.703	0.205	0.205	0.000	0.000	0.000	0.000
15	A	44	SER	0	-0.018	-0.017	22.415	-0.391	-0.391	0.000	0.000	0.000	0.000
16	A	45	ARG	1	0.924	0.974	20.531	-13.590	-13.590	0.000	0.000	0.000	0.000
17	A	46	ILE	0	0.022	0.019	24.477	0.444	0.444	0.000	0.000	0.000	0.000
18	A	47	THR	0	-0.007	0.005	25.532	-0.545	-0.545	0.000	0.000	0.000	0.000
19	A	48	THR	0	0.020	0.007	26.363	0.308	0.308	0.000	0.000	0.000	0.000
20	A	49	GLU	-1	-0.868	-0.933	22.369	12.756	12.756	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.937	0.959	23.922	-11.343	-11.343	0.000	0.000	0.000	0.000
22	A	51	GLY	0	0.007	0.032	26.221	-0.255	-0.255	0.000	0.000	0.000	0.000
23	A	52	LYS	1	0.921	0.940	26.625	-10.444	-10.444	0.000	0.000	0.000	0.000
24	A	53	GLU	-1	-0.847	-0.912	29.222	9.797	9.797	0.000	0.000	0.000	0.000
25	A	54	GLN	0	-0.015	-0.007	28.301	-0.057	-0.057	0.000	0.000	0.000	0.000
26	A	55	PHE	0	0.019	-0.017	28.400	0.322	0.322	0.000	0.000	0.000	0.000
27	A	56	TYR	0	0.016	0.017	29.200	-0.116	-0.116	0.000	0.000	0.000	0.000
28	A	57	GLN	0	0.005	-0.003	31.968	-0.232	-0.232	0.000	0.000	0.000	0.000
29	A	58	GLY	0	0.044	0.011	35.566	0.057	0.057	0.000	0.000	0.000	0.000
30	A	59	LEU	0	-0.066	-0.001	30.745	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	60	TRP	0	-0.006	-0.024	32.842	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	61	SER	0	-0.023	-0.028	38.108	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	62	ASN	0	-0.012	-0.006	41.653	-0.145	-0.145	0.000	0.000	0.000	0.000
34	A	63	GLU	-1	-0.852	-0.929	41.559	7.121	7.121	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.007	0.006	41.805	0.127	0.127	0.000	0.000	0.000	0.000
36	A	65	GLU	-1	-0.834	-0.903	39.614	7.606	7.606	0.000	0.000	0.000	0.000
37	A	66	GLU	-1	-0.769	-0.859	36.237	8.560	8.560	0.000	0.000	0.000	0.000
38	A	67	LYS	1	0.879	0.929	37.120	-7.233	-7.233	0.000	0.000	0.000	0.000
39	A	68	ALA	0	0.002	-0.007	38.344	0.120	0.120	0.000	0.000	0.000	0.000
40	A	69	SER	0	0.007	-0.027	34.044	0.115	0.115	0.000	0.000	0.000	0.000
41	A	70	ARG	1	0.798	0.869	32.761	-8.610	-8.610	0.000	0.000	0.000	0.000
42	A	71	GLU	-1	-0.845	-0.888	34.074	8.191	8.191	0.000	0.000	0.000	0.000
43	A	72	LEU	0	-0.025	-0.005	33.666	0.127	0.127	0.000	0.000	0.000	0.000
44	A	73	LEU	0	0.002	-0.002	27.446	0.223	0.223	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.833	0.902	29.743	-8.197	-8.197	0.000	0.000	0.000	0.000
46	A	75	ILE	0	-0.029	0.012	31.123	0.068	0.068	0.000	0.000	0.000	0.000
47	A	76	THR	0	0.007	-0.008	26.592	0.244	0.244	0.000	0.000	0.000	0.000
48	A	77	GLU	-1	-0.834	-0.924	26.602	10.292	10.292	0.000	0.000	0.000	0.000
49	A	78	ASN	0	-0.036	-0.002	27.111	0.248	0.248	0.000	0.000	0.000	0.000
50	A	79	PHE	0	-0.026	-0.015	26.058	0.151	0.151	0.000	0.000	0.000	0.000
51	A	80	THR	0	-0.025	-0.005	22.246	0.425	0.425	0.000	0.000	0.000	0.000
52	A	81	LEU	0	-0.011	-0.010	17.012	-0.312	-0.312	0.000	0.000	0.000	0.000
53	A	82	ASN	0	0.000	0.003	16.843	0.622	0.622	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.058	0.039	12.192	-0.640	-0.640	0.000	0.000	0.000	0.000
55	A	84	ASN	0	0.000	-0.012	13.705	-0.244	-0.244	0.000	0.000	0.000	0.000
56	A	85	CYS	0	0.016	0.014	12.231	1.038	1.038	0.000	0.000	0.000	0.000
57	A	86	ALA	0	0.040	0.017	14.944	-0.746	-0.746	0.000	0.000	0.000	0.000
58	A	87	ASP	-1	-0.926	-0.964	18.381	14.157	14.157	0.000	0.000	0.000	0.000
59	A	88	VAL	0	-0.030	-0.008	20.000	-0.839	-0.839	0.000	0.000	0.000	0.000
60	A	89	ASN	0	-0.076	-0.058	22.026	-0.303	-0.303	0.000	0.000	0.000	0.000
61	A	90	GLY	0	0.022	0.012	24.058	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.933	-0.949	18.931	15.880	15.880	0.000	0.000	0.000	0.000
63	A	92	VAL	0	-0.029	-0.011	15.106	-0.099	-0.099	0.000	0.000	0.000	0.000
64	A	93	THR	0	-0.011	-0.003	14.779	0.978	0.978	0.000	0.000	0.000	0.000
65	A	94	GLY	0	0.014	0.007	12.379	-0.109	-0.109	0.000	0.000	0.000	0.000
66	A	95	THR	0	-0.075	-0.055	13.405	-0.271	-0.271	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.010	-0.003	15.352	0.706	0.706	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.035	0.028	17.404	-1.114	-1.114	0.000	0.000	0.000	0.000
69	A	98	ALA	0	-0.019	-0.014	19.958	0.462	0.462	0.000	0.000	0.000	0.000
70	A	99	HIS	1	0.822	0.903	22.554	-11.026	-11.026	0.000	0.000	0.000	0.000
71	A	100	ALA	0	0.006	0.022	25.983	0.160	0.160	0.000	0.000	0.000	0.000
72	A	101	VAL	0	-0.007	-0.010	28.245	-0.065	-0.065	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.871	0.933	31.812	-8.209	-8.209	0.000	0.000	0.000	0.000
74	A	103	ALA	0	-0.050	-0.009	30.531	-0.073	-0.073	0.000	0.000	0.000	0.000
75	A	104	ASN	0	-0.005	-0.020	27.065	0.444	0.444	0.000	0.000	0.000	0.000
76	A	105	ILE	0	-0.002	0.009	22.293	-0.335	-0.335	0.000	0.000	0.000	0.000
77	A	106	SER	0	-0.008	-0.014	23.378	0.118	0.118	0.000	0.000	0.000	0.000
78	A	107	ASP	-1	-0.832	-0.891	19.948	14.223	14.223	0.000	0.000	0.000	0.000
79	A	108	ALA	0	-0.030	-0.014	20.192	-0.298	-0.298	0.000	0.000	0.000	0.000
80	A	109	ILE	0	0.019	-0.004	18.596	0.773	0.773	0.000	0.000	0.000	0.000
81	A	110	LEU	0	-0.007	0.006	11.873	-0.336	-0.336	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.905	0.957	13.707	-17.083	-17.083	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.032	-0.001	8.653	-0.886	-0.886	0.000	0.000	0.000	0.000
84	A	113	ASP	-1	-0.837	-0.912	8.443	29.254	29.254	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.045	0.000	4.917	-0.892	-0.892	0.000	0.000	0.000	0.000
86	A	115	LYS	1	0.884	0.948	5.985	-34.073	-34.073	0.000	0.000	0.000	0.000
87	A	116	GLU	-1	-0.893	-0.920	7.962	18.148	18.148	0.000	0.000	0.000	0.000
88	A	117	HIS	0	-0.062	-0.016	7.743	-1.394	-1.394	0.000	0.000	0.000	0.000
89	A	118	THR	0	-0.039	-0.048	10.585	-1.466	-1.466	0.000	0.000	0.000	0.000
90	A	119	ILE	0	-0.018	-0.029	11.667	1.512	1.512	0.000	0.000	0.000	0.000
91	A	120	SER	0	-0.045	-0.010	14.023	-1.178	-1.178	0.000	0.000	0.000	0.000
92	A	121	ILE	0	0.044	0.021	16.641	0.652	0.652	0.000	0.000	0.000	0.000
93	A	122	SER	0	-0.003	0.001	18.997	-0.875	-0.875	0.000	0.000	0.000	0.000
94	A	123	GLY	0	0.023	0.002	22.037	0.242	0.242	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.937	0.966	24.989	-9.842	-9.842	0.000	0.000	0.000	0.000
96	A	125	ALA	0	0.033	0.022	27.442	0.182	0.182	0.000	0.000	0.000	0.000
97	A	126	TYR	0	-0.023	0.001	28.540	-0.386	-0.386	0.000	0.000	0.000	0.000
98	A	127	GLY	0	0.050	0.017	30.973	0.052	0.052	0.000	0.000	0.000	0.000
99	A	128	SER	0	-0.015	-0.015	33.082	0.165	0.165	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.682	-0.849	31.745	9.277	9.277	0.000	0.000	0.000	0.000
101	A	130	SER	0	-0.035	-0.027	35.109	-0.138	-0.138	0.000	0.000	0.000	0.000
102	A	131	ASP	-1	-0.762	-0.858	34.066	8.659	8.659	0.000	0.000	0.000	0.000
103	A	132	LYS	1	0.868	0.908	34.537	-7.467	-7.467	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.046	0.039	29.414	0.181	0.181	0.000	0.000	0.000	0.000
105	A	134	ALA	0	-0.003	-0.011	30.049	0.369	0.369	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.855	0.929	29.929	-7.943	-7.943	0.000	0.000	0.000	0.000
107	A	136	VAL	0	0.014	0.018	28.219	0.192	0.192	0.000	0.000	0.000	0.000
108	A	137	PHE	0	0.005	-0.001	23.185	0.266	0.266	0.000	0.000	0.000	0.000
109	A	138	ILE	0	0.009	0.000	25.190	0.396	0.396	0.000	0.000	0.000	0.000
110	A	139	SER	0	-0.039	-0.036	25.931	0.170	0.170	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.025	0.009	25.018	0.130	0.130	0.000	0.000	0.000	0.000
112	A	141	LEU	0	-0.025	-0.018	19.954	0.487	0.487	0.000	0.000	0.000	0.000
113	A	142	PHE	0	-0.013	-0.009	20.946	0.481	0.481	0.000	0.000	0.000	0.000
114	A	143	ASN	0	-0.034	0.003	23.072	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	144	VAL	0	-0.046	-0.026	17.414	-0.062	-0.062	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.032	-0.018	18.260	-0.146	-0.146	0.000	0.000	0.000	0.000
117	A	146	LYS	1	0.882	0.951	14.822	-13.932	-13.932	0.000	0.000	0.000	0.000
118	A	147	TYR	0	-0.026	-0.016	7.479	-0.984	-0.984	0.000	0.000	0.000	0.000
119	A	148	GLU	-1	-0.815	-0.876	12.008	17.095	17.095	0.000	0.000	0.000	0.000
120	A	149	GLY	0	-0.012	-0.019	11.683	-1.230	-1.230	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.782	-0.858	10.244	20.555	20.555	0.000	0.000	0.000	0.000
122	A	151	VAL	0	0.029	0.017	9.786	-0.174	-0.174	0.000	0.000	0.000	0.000
123	A	152	HIS	1	0.834	0.897	11.639	-17.953	-17.953	0.000	0.000	0.000	0.000
124	A	153	ASN	0	-0.074	-0.050	14.567	-1.923	-1.923	0.000	0.000	0.000	0.000
125	A	154	LEU	0	0.050	0.034	12.395	1.183	1.183	0.000	0.000	0.000	0.000
126	A	155	THR	0	-0.041	-0.025	15.143	-1.648	-1.648	0.000	0.000	0.000	0.000
127	A	156	LEU	0	0.024	0.015	14.946	0.775	0.775	0.000	0.000	0.000	0.000
128	A	157	TYR	0	-0.054	-0.066	17.058	-1.350	-1.350	0.000	0.000	0.000	0.000
129	A	158	PHE	0	0.020	0.011	19.507	0.223	0.223	0.000	0.000	0.000	0.000
130	A	159	LYS	1	0.963	0.986	22.266	-11.884	-11.884	0.000	0.000	0.000	0.000
131	A	160	ASP	-1	-0.845	-0.899	25.392	9.654	9.654	0.000	0.000	0.000	0.000
132	A	161	GLY	0	0.044	0.028	28.768	-0.296	-0.296	0.000	0.000	0.000	0.000
133	A	162	ASN	0	-0.017	-0.022	29.797	0.264	0.264	0.000	0.000	0.000	0.000
134	A	163	THR	0	-0.062	-0.024	29.552	0.077	0.077	0.000	0.000	0.000	0.000
135	A	164	THR	0	0.025	0.007	23.180	0.146	0.146	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.800	0.887	25.048	-10.004	-10.004	0.000	0.000	0.000	0.000
137	A	166	VAL	0	-0.003	-0.002	20.996	0.482	0.482	0.000	0.000	0.000	0.000
138	A	167	MET	0	-0.027	-0.001	20.729	-0.698	-0.698	0.000	0.000	0.000	0.000
139	A	168	GLY	0	-0.025	-0.008	19.943	0.721	0.721	0.000	0.000	0.000	0.000
140	A	169	PHE	0	0.036	-0.004	17.841	-0.675	-0.675	0.000	0.000	0.000	0.000
141	A	170	THR	0	0.004	0.002	18.520	0.277	0.277	0.000	0.000	0.000	0.000
142	A	171	ALA	0	0.045	0.035	15.669	-0.420	-0.420	0.000	0.000	0.000	0.000
143	A	172	ARG	1	0.888	0.953	17.784	-13.685	-13.685	0.000	0.000	0.000	0.000

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