FMO DATABASE

FMODB ID: 5JRZZ

Calculation Name: 3L8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DSR4

Base Structure: X-ray

Registration Date: 2023-09-22

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1688923.804133
FMO2-HF: Nuclear repulsion	1622689.678027
FMO2-HF: Total energy	-66234.126106
FMO2-MP2: Total energy	-66424.95665

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:15:LEU)

Summations of interaction energy for fragment #1(A:15:LEU)

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.
-7.793	-2.433	1.753	-2.294	-4.819	-0.011

Interaction energy analysis for fragmet #1(A:15:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.021

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	17	ARG	1	0.860	0.915	2.914	-1.795	0.769	0.247	-1.266	-1.545	-0.006
4	A	18	ASN	0	0.056	0.017	5.256	0.705	0.763	-0.001	-0.004	-0.053	0.000
5	A	19	HIS	0	0.018	0.005	7.400	-0.013	-0.013	0.000	0.000	0.000	0.000
6	A	20	VAL	0	0.014	0.007	11.724	0.091	0.091	0.000	0.000	0.000	0.000
7	A	21	VAL	0	0.014	-0.005	15.449	0.010	0.010	0.000	0.000	0.000	0.000
8	A	22	LEU	0	-0.007	0.001	17.928	0.013	0.013	0.000	0.000	0.000	0.000
9	A	23	PHE	0	0.051	0.002	21.571	0.016	0.016	0.000	0.000	0.000	0.000
10	A	24	GLN	0	-0.022	0.014	24.045	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	25	PRO	0	0.037	0.036	23.982	0.003	0.003	0.000	0.000	0.000	0.000
12	A	26	GLN	0	-0.018	-0.044	26.866	0.011	0.011	0.000	0.000	0.000	0.000
13	A	27	ILE	0	-0.037	-0.007	29.342	0.004	0.004	0.000	0.000	0.000	0.000
14	A	28	PRO	0	0.018	0.009	28.473	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	29	ALA	0	0.037	0.001	27.788	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	30	ASN	0	0.002	0.002	26.094	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	31	THR	0	0.047	0.014	23.456	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	32	GLY	0	-0.006	0.002	22.925	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	33	ASN	0	0.000	-0.015	23.030	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.021	0.030	18.957	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	35	ALA	0	0.029	0.013	18.690	-0.044	-0.044	0.000	0.000	0.000	0.000
22	A	36	ARG	1	0.862	0.919	18.311	0.221	0.221	0.000	0.000	0.000	0.000
23	A	37	THR	0	-0.011	-0.019	16.711	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.062	-0.015	14.490	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	39	ALA	0	0.011	0.004	13.559	-0.092	-0.092	0.000	0.000	0.000	0.000
26	A	40	ALA	0	-0.041	-0.021	14.227	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.011	-0.020	12.371	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	42	ASN	0	-0.013	0.025	8.279	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	43	THR	0	0.012	0.013	9.201	-0.237	-0.237	0.000	0.000	0.000	0.000
30	A	44	SER	0	-0.030	-0.035	9.574	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	45	LEU	0	-0.046	-0.032	11.628	0.064	0.064	0.000	0.000	0.000	0.000
32	A	46	HIS	0	-0.016	0.007	11.293	0.106	0.106	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.019	-0.015	16.600	0.002	0.002	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.039	-0.004	19.975	0.020	0.020	0.000	0.000	0.000	0.000
35	A	49	ARG	1	0.857	0.922	22.642	0.002	0.002	0.000	0.000	0.000	0.000
36	A	50	PRO	0	0.000	-0.008	25.664	0.009	0.009	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.026	0.008	25.295	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	52	GLY	0	-0.015	-0.017	28.220	0.007	0.007	0.000	0.000	0.000	0.000
39	A	53	PHE	0	-0.030	-0.020	27.124	0.001	0.001	0.000	0.000	0.000	0.000
40	A	54	PRO	0	-0.005	0.011	30.684	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	55	ILE	0	0.032	0.003	26.548	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	56	ASP	-1	-0.820	-0.902	29.959	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	57	ASP	-1	-0.835	-0.926	30.224	-0.108	-0.108	0.000	0.000	0.000	0.000
44	A	58	LYS	1	0.930	0.970	31.108	0.084	0.084	0.000	0.000	0.000	0.000
45	A	59	LYS	1	0.853	0.899	32.558	0.078	0.078	0.000	0.000	0.000	0.000
46	A	60	MET	0	-0.018	0.020	27.863	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	61	LYS	1	0.822	0.882	21.146	0.244	0.244	0.000	0.000	0.000	0.000
48	A	62	ARG	1	0.882	0.922	26.964	0.116	0.116	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.054	-0.013	27.892	0.000	0.000	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.043	0.022	25.438	0.000	0.000	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.066	-0.020	25.109	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	66	ASP	-1	-0.767	-0.871	24.281	-0.199	-0.199	0.000	0.000	0.000	0.000
53	A	67	TYR	0	-0.008	-0.008	22.891	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	68	TRP	0	-0.013	0.010	17.766	0.012	0.012	0.000	0.000	0.000	0.000
55	A	69	ASP	-1	-0.855	-0.925	18.128	-0.277	-0.277	0.000	0.000	0.000	0.000
56	A	70	LYS	1	1.000	0.998	14.416	0.392	0.392	0.000	0.000	0.000	0.000
57	A	71	LEU	0	-0.020	0.014	13.745	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	72	ASP	-1	-0.763	-0.857	10.325	-0.535	-0.535	0.000	0.000	0.000	0.000
59	A	73	VAL	0	-0.012	0.001	13.021	0.001	0.001	0.000	0.000	0.000	0.000
60	A	74	HIS	1	0.805	0.900	11.232	0.343	0.343	0.000	0.000	0.000	0.000
61	A	75	PHE	0	-0.020	-0.018	16.321	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	76	TYR	0	0.046	0.007	14.004	0.025	0.025	0.000	0.000	0.000	0.000
63	A	77	ASP	-1	-0.819	-0.898	20.690	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	78	SER	0	-0.035	-0.020	23.098	0.001	0.001	0.000	0.000	0.000	0.000
65	A	79	LEU	0	0.019	0.000	21.031	0.001	0.001	0.000	0.000	0.000	0.000
66	A	80	ASN	0	0.014	-0.001	21.283	0.013	0.013	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.882	-0.939	20.996	0.101	0.101	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.032	0.012	14.469	0.026	0.026	0.000	0.000	0.000	0.000
69	A	83	MET	0	-0.014	-0.007	16.579	0.021	0.021	0.000	0.000	0.000	0.000
70	A	84	ASN	0	-0.045	-0.004	17.730	0.043	0.043	0.000	0.000	0.000	0.000
71	A	85	ILE	0	-0.033	-0.020	12.961	0.043	0.043	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.099	-0.024	12.269	0.075	0.075	0.000	0.000	0.000	0.000
73	A	87	SER	0	0.032	0.015	9.568	0.067	0.067	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.032	0.008	9.270	0.143	0.143	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.819	0.897	10.963	-0.259	-0.259	0.000	0.000	0.000	0.000
76	A	90	LEU	0	-0.018	-0.004	13.390	-0.102	-0.102	0.000	0.000	0.000	0.000
77	A	91	HIS	0	0.050	0.038	14.602	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	92	LEU	0	-0.028	-0.016	18.229	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	93	ILE	0	-0.011	-0.001	19.360	0.000	0.000	0.000	0.000	0.000	0.000
80	A	94	THR	0	-0.047	-0.035	22.827	0.011	0.011	0.000	0.000	0.000	0.000
81	A	95	LYS	1	0.859	0.902	26.649	0.058	0.058	0.000	0.000	0.000	0.000
82	A	96	PHE	0	0.000	-0.015	29.669	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	97	ALA	0	0.052	0.067	26.599	0.007	0.007	0.000	0.000	0.000	0.000
84	A	98	ASN	0	-0.013	-0.010	28.520	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.861	0.935	20.529	0.042	0.042	0.000	0.000	0.000	0.000
86	A	100	THR	0	-0.055	-0.042	25.267	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.019	-0.010	20.152	0.010	0.010	0.000	0.000	0.000	0.000
88	A	102	SER	0	0.021	0.010	19.945	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	103	ASP	-1	-0.819	-0.882	21.065	-0.093	-0.093	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.883	-0.944	16.814	0.000	0.000	0.000	0.000	0.000	0.000
91	A	105	ASN	0	-0.019	-0.002	13.571	-0.070	-0.070	0.000	0.000	0.000	0.000
92	A	106	TYR	0	-0.067	-0.067	12.227	0.031	0.031	0.000	0.000	0.000	0.000
93	A	107	ASP	-1	-0.898	-0.929	10.502	-0.484	-0.484	0.000	0.000	0.000	0.000
94	A	108	ASP	-1	-0.779	-0.869	9.190	0.114	0.114	0.000	0.000	0.000	0.000
95	A	109	SER	0	-0.002	-0.008	4.480	-0.259	-0.188	-0.001	-0.005	-0.064	0.000
96	A	110	GLU	-1	-0.873	-0.918	4.695	0.795	0.881	-0.001	-0.007	-0.078	0.000
97	A	111	HIS	0	-0.010	0.008	3.885	-2.196	-1.754	0.000	-0.090	-0.352	0.000
98	A	112	HIS	1	0.803	0.893	7.768	0.545	0.545	0.000	0.000	0.000	0.000
99	A	113	TYR	0	-0.026	-0.033	9.157	-0.225	-0.225	0.000	0.000	0.000	0.000
100	A	114	PHE	0	0.018	0.011	12.245	0.061	0.061	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.011	-0.003	16.484	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	116	PHE	0	0.033	0.009	17.843	0.012	0.012	0.000	0.000	0.000	0.000
103	A	117	GLY	0	0.013	-0.005	22.491	0.010	0.010	0.000	0.000	0.000	0.000
104	A	118	ARG	1	0.789	0.879	26.044	0.035	0.035	0.000	0.000	0.000	0.000
105	A	119	GLU	-1	-0.735	-0.876	28.626	-0.104	-0.104	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.815	-0.880	30.537	-0.047	-0.047	0.000	0.000	0.000	0.000
107	A	121	LYS	1	0.851	0.915	32.018	0.041	0.041	0.000	0.000	0.000	0.000
108	A	122	GLY	0	0.014	0.032	28.910	0.005	0.005	0.000	0.000	0.000	0.000
109	A	123	LEU	0	0.023	-0.001	23.890	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	124	PRO	0	0.005	-0.003	26.925	0.002	0.002	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.794	-0.880	29.239	0.014	0.014	0.000	0.000	0.000	0.000
112	A	126	GLU	-1	-0.811	-0.886	30.129	0.052	0.052	0.000	0.000	0.000	0.000
113	A	127	PHE	0	0.016	-0.002	21.287	0.006	0.006	0.000	0.000	0.000	0.000
114	A	128	MET	0	-0.023	-0.025	26.398	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	129	ARG	1	0.801	0.885	27.967	-0.028	-0.028	0.000	0.000	0.000	0.000
116	A	130	GLN	0	-0.066	-0.047	26.182	0.011	0.011	0.000	0.000	0.000	0.000
117	A	131	HIS	0	-0.021	0.007	22.532	0.019	0.019	0.000	0.000	0.000	0.000
118	A	132	SER	0	0.008	0.000	24.250	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	133	GLU	-1	-0.832	-0.906	22.919	0.082	0.082	0.000	0.000	0.000	0.000
120	A	134	LYS	1	0.815	0.896	19.067	-0.118	-0.118	0.000	0.000	0.000	0.000
121	A	135	ALA	0	-0.035	0.001	21.279	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	136	LEU	0	0.014	0.007	19.216	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	137	ARG	1	0.886	0.942	23.709	0.058	0.058	0.000	0.000	0.000	0.000
124	A	138	ILE	0	0.020	0.004	23.208	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	139	PRO	0	-0.029	-0.009	26.514	0.010	0.010	0.000	0.000	0.000	0.000
126	A	140	VAL	0	0.005	-0.003	29.951	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	141	ASN	0	0.005	-0.006	32.665	0.009	0.009	0.000	0.000	0.000	0.000
128	A	142	ASP	-1	-0.831	-0.924	36.421	-0.050	-0.050	0.000	0.000	0.000	0.000
129	A	143	GLN	0	0.018	0.026	37.361	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	144	HIS	0	-0.004	0.008	39.327	0.003	0.003	0.000	0.000	0.000	0.000
131	A	145	VAL	0	0.017	0.002	35.236	0.001	0.001	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.850	0.921	35.665	0.050	0.050	0.000	0.000	0.000	0.000
133	A	147	SER	0	0.014	0.004	30.737	0.005	0.005	0.000	0.000	0.000	0.000
134	A	148	LEU	0	0.037	0.042	27.123	0.002	0.002	0.000	0.000	0.000	0.000
135	A	149	ASN	0	0.016	0.005	27.586	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	150	LEU	0	0.043	0.026	23.980	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	151	SER	0	-0.009	-0.011	23.251	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	152	ASN	0	0.004	-0.003	22.769	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	153	THR	0	0.005	-0.012	23.215	-0.011	-0.011	0.000	0.000	0.000	0.000
140	A	154	VAL	0	-0.007	-0.001	18.216	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	155	CYS	0	-0.032	-0.008	18.541	-0.044	-0.044	0.000	0.000	0.000	0.000
142	A	156	MET	0	0.007	0.003	18.708	-0.026	-0.026	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.013	0.006	16.773	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	158	VAL	0	0.006	0.003	13.088	-0.022	-0.022	0.000	0.000	0.000	0.000
145	A	159	TYR	0	0.015	-0.005	14.219	-0.066	-0.066	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.814	-0.849	16.383	-0.271	-0.271	0.000	0.000	0.000	0.000
147	A	161	ALA	0	-0.011	-0.013	12.297	0.001	0.001	0.000	0.000	0.000	0.000
148	A	162	LEU	0	-0.026	-0.013	10.218	-0.049	-0.049	0.000	0.000	0.000	0.000
149	A	163	ARG	1	0.813	0.876	12.692	0.257	0.257	0.000	0.000	0.000	0.000
150	A	164	GLN	0	-0.055	-0.037	13.986	0.031	0.031	0.000	0.000	0.000	0.000
151	A	165	GLN	0	-0.023	0.003	8.764	-0.094	-0.094	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.893	-0.955	9.796	-0.614	-0.614	0.000	0.000	0.000	0.000
153	A	167	PHE	0	-0.034	-0.027	11.843	-0.009	-0.009	0.000	0.000	0.000	0.000
154	A	168	ILE	0	0.066	0.052	5.537	-0.138	-0.138	0.000	0.000	0.000	0.000
155	A	169	GLY	0	-0.003	-0.005	6.421	-0.249	-0.249	0.000	0.000	0.000	0.000
156	A	170	LEU	0	-0.020	-0.016	7.449	-0.047	-0.047	0.000	0.000	0.000	0.000
157	A	171	GLU	-1	-0.926	-0.955	7.591	-0.778	-0.778	0.000	0.000	0.000	0.000
158	A	172	LEU	0	-0.038	-0.011	2.371	-0.834	-0.244	1.082	-0.290	-1.382	-0.002
159	A	173	SER	0	-0.041	-0.040	4.935	-0.233	-0.178	-0.001	-0.001	-0.053	0.000
160	A	174	HIS	0	-0.076	-0.030	7.461	0.036	0.036	0.000	0.000	0.000	0.000
161	A	175	THR	0	-0.026	-0.007	2.766	-1.814	-0.320	0.428	-0.631	-1.292	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:LEU)