FMO DATABASE

FMODB ID: 4JQRN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1685226.621064
FMO2-HF: Nuclear repulsion	1618993.070803
FMO2-HF: Total energy	-66233.550261
FMO2-MP2: Total energy	-66424.423642

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.
-7.236	-2.788	0.519	-1.709	-3.256	-0.001

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 : -0.020 / 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	0.871	0.927	3.290	-1.342	0.907	0.040	-1.070	-1.220	-0.002
4	A	18	ASN	0	0.035	0.004	5.519	0.754	0.754	0.000	0.000	0.000	0.000
5	A	19	HIS	0	0.023	0.007	7.290	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	20	VAL	0	0.017	0.005	11.978	0.067	0.067	0.000	0.000	0.000	0.000
7	A	21	VAL	0	0.004	-0.009	15.425	0.010	0.010	0.000	0.000	0.000	0.000
8	A	22	LEU	0	-0.006	-0.005	17.883	0.004	0.004	0.000	0.000	0.000	0.000
9	A	23	PHE	0	0.054	0.006	21.520	0.015	0.015	0.000	0.000	0.000	0.000
10	A	24	GLN	0	0.002	0.020	23.942	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	25	PRO	0	0.055	0.047	24.010	0.000	0.000	0.000	0.000	0.000	0.000
12	A	26	GLN	0	-0.032	-0.041	26.818	0.008	0.008	0.000	0.000	0.000	0.000
13	A	27	ILE	0	-0.032	-0.007	29.705	0.001	0.001	0.000	0.000	0.000	0.000
14	A	28	PRO	0	0.041	0.019	28.931	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	29	ALA	0	0.036	0.003	28.226	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	30	ASN	0	-0.006	0.002	26.566	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	31	THR	0	0.032	0.011	23.595	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	32	GLY	0	-0.014	-0.011	23.381	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	33	ASN	0	0.000	-0.015	23.763	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.034	0.022	19.319	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	35	ALA	0	0.015	0.016	19.100	-0.039	-0.039	0.000	0.000	0.000	0.000
22	A	36	ARG	1	0.882	0.927	18.797	0.195	0.195	0.000	0.000	0.000	0.000
23	A	37	THR	0	-0.012	-0.004	17.150	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.054	-0.022	14.946	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	39	ALA	0	-0.018	-0.007	14.155	-0.088	-0.088	0.000	0.000	0.000	0.000
26	A	40	ALA	0	-0.036	-0.016	15.000	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.010	-0.015	12.909	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	42	ASN	0	-0.011	0.021	8.681	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	43	THR	0	0.009	0.016	9.175	-0.250	-0.250	0.000	0.000	0.000	0.000
30	A	44	SER	0	-0.055	-0.044	9.943	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	45	LEU	0	-0.022	-0.016	12.112	0.057	0.057	0.000	0.000	0.000	0.000
32	A	46	HIS	0	-0.026	-0.001	11.228	0.083	0.083	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.012	-0.014	16.555	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.037	-0.001	19.505	0.019	0.019	0.000	0.000	0.000	0.000
35	A	49	ARG	1	0.867	0.932	22.423	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	50	PRO	0	-0.005	-0.014	25.476	0.010	0.010	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.005	-0.005	25.006	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	52	GLY	0	-0.011	-0.015	28.203	0.006	0.006	0.000	0.000	0.000	0.000
39	A	53	PHE	0	-0.036	-0.025	27.016	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	54	PRO	0	0.010	0.017	30.757	0.000	0.000	0.000	0.000	0.000	0.000
41	A	55	ILE	0	0.016	-0.006	26.966	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	56	ASP	-1	-0.842	-0.905	30.076	-0.067	-0.067	0.000	0.000	0.000	0.000
43	A	57	ASP	-1	-0.842	-0.926	30.394	-0.096	-0.096	0.000	0.000	0.000	0.000
44	A	58	LYS	1	0.998	0.995	30.969	0.067	0.067	0.000	0.000	0.000	0.000
45	A	59	LYS	1	0.842	0.894	32.930	0.062	0.062	0.000	0.000	0.000	0.000
46	A	60	MET	0	-0.011	0.018	28.006	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	61	LYS	1	0.804	0.890	21.465	0.219	0.219	0.000	0.000	0.000	0.000
48	A	62	ARG	1	0.924	0.945	27.093	0.102	0.102	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.075	-0.032	28.212	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.015	0.016	25.641	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.064	-0.017	25.386	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	66	ASP	-1	-0.745	-0.865	24.626	-0.188	-0.188	0.000	0.000	0.000	0.000
53	A	67	TYR	0	-0.039	-0.021	23.673	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	68	TRP	0	0.031	0.016	18.379	0.005	0.005	0.000	0.000	0.000	0.000
55	A	69	ASP	-1	-0.846	-0.906	18.659	-0.230	-0.230	0.000	0.000	0.000	0.000
56	A	70	LYS	1	0.977	0.944	14.327	0.376	0.376	0.000	0.000	0.000	0.000
57	A	71	LEU	0	-0.029	0.008	14.547	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	72	ASP	-1	-0.794	-0.842	10.658	-0.398	-0.398	0.000	0.000	0.000	0.000
59	A	73	VAL	0	-0.016	-0.003	13.671	0.001	0.001	0.000	0.000	0.000	0.000
60	A	74	HIS	1	0.818	0.906	11.400	0.226	0.226	0.000	0.000	0.000	0.000
61	A	75	PHE	0	-0.011	-0.017	16.293	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	76	TYR	0	0.056	0.010	13.997	0.029	0.029	0.000	0.000	0.000	0.000
63	A	77	ASP	-1	-0.848	-0.897	20.703	0.034	0.034	0.000	0.000	0.000	0.000
64	A	78	SER	0	-0.043	-0.030	22.774	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	79	LEU	0	0.034	0.008	20.868	0.007	0.007	0.000	0.000	0.000	0.000
66	A	80	ASN	0	0.010	-0.004	20.885	0.026	0.026	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.871	-0.935	20.781	0.162	0.162	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.026	0.005	14.243	0.029	0.029	0.000	0.000	0.000	0.000
69	A	83	MET	0	-0.033	-0.024	16.192	0.038	0.038	0.000	0.000	0.000	0.000
70	A	84	ASN	0	-0.040	0.001	17.238	0.049	0.049	0.000	0.000	0.000	0.000
71	A	85	ILE	0	-0.021	-0.011	12.925	0.050	0.050	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.114	-0.027	12.259	0.104	0.104	0.000	0.000	0.000	0.000
73	A	87	SER	0	0.034	0.016	9.255	0.069	0.069	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.025	0.002	9.185	0.191	0.191	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.795	0.891	10.631	-0.467	-0.467	0.000	0.000	0.000	0.000
76	A	90	LEU	0	-0.009	-0.007	13.170	-0.081	-0.081	0.000	0.000	0.000	0.000
77	A	91	HIS	0	0.050	0.038	14.660	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	92	LEU	0	-0.024	-0.005	18.377	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.000	0.002	19.579	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	94	THR	0	-0.031	-0.026	23.027	0.005	0.005	0.000	0.000	0.000	0.000
81	A	95	LYS	1	0.883	0.921	26.815	0.032	0.032	0.000	0.000	0.000	0.000
82	A	96	PHE	0	-0.012	-0.028	30.001	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	97	ALA	0	0.039	0.067	26.429	0.006	0.006	0.000	0.000	0.000	0.000
84	A	98	ASN	0	-0.017	-0.011	28.481	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.931	0.955	20.547	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	100	THR	0	-0.027	-0.015	24.996	0.000	0.000	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.010	-0.020	20.360	0.010	0.010	0.000	0.000	0.000	0.000
88	A	102	SER	0	0.034	0.017	20.117	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	103	ASP	-1	-0.881	-0.918	20.977	-0.065	-0.065	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.902	-0.938	16.658	0.067	0.067	0.000	0.000	0.000	0.000
91	A	105	ASN	0	0.009	0.012	14.371	-0.071	-0.071	0.000	0.000	0.000	0.000
92	A	106	TYR	0	-0.076	-0.074	12.278	0.052	0.052	0.000	0.000	0.000	0.000
93	A	107	ASP	-1	-0.903	-0.936	10.529	-0.434	-0.434	0.000	0.000	0.000	0.000
94	A	108	ASP	-1	-0.786	-0.865	8.984	0.225	0.225	0.000	0.000	0.000	0.000
95	A	109	SER	0	-0.025	-0.019	4.073	-0.314	-0.198	-0.001	-0.016	-0.099	0.000
96	A	110	GLU	-1	-0.883	-0.931	4.818	1.261	1.343	-0.001	-0.005	-0.075	0.000
97	A	111	HIS	0	0.018	0.018	3.561	-3.410	-2.614	0.011	-0.290	-0.516	0.002
98	A	112	HIS	1	0.810	0.892	7.638	0.331	0.331	0.000	0.000	0.000	0.000
99	A	113	TYR	0	-0.018	-0.021	8.934	-0.256	-0.256	0.000	0.000	0.000	0.000
100	A	114	PHE	0	0.034	0.024	12.541	0.050	0.050	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.005	0.002	16.626	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	116	PHE	0	0.008	-0.008	18.112	0.004	0.004	0.000	0.000	0.000	0.000
103	A	117	GLY	0	0.008	-0.004	22.792	0.008	0.008	0.000	0.000	0.000	0.000
104	A	118	ARG	1	0.793	0.881	26.217	0.004	0.004	0.000	0.000	0.000	0.000
105	A	119	GLU	-1	-0.748	-0.887	28.698	-0.071	-0.071	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.817	-0.880	30.574	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	121	LYS	1	0.871	0.926	32.166	0.013	0.013	0.000	0.000	0.000	0.000
108	A	122	GLY	0	0.013	0.029	29.172	0.006	0.006	0.000	0.000	0.000	0.000
109	A	123	LEU	0	0.012	-0.009	23.804	0.000	0.000	0.000	0.000	0.000	0.000
110	A	124	PRO	0	0.001	-0.003	26.846	0.000	0.000	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.788	-0.894	29.083	0.045	0.045	0.000	0.000	0.000	0.000
112	A	126	GLU	-1	-0.830	-0.888	30.062	0.086	0.086	0.000	0.000	0.000	0.000
113	A	127	PHE	0	0.029	-0.001	21.060	0.005	0.005	0.000	0.000	0.000	0.000
114	A	128	MET	0	-0.024	-0.020	26.173	0.004	0.004	0.000	0.000	0.000	0.000
115	A	129	ARG	1	0.809	0.894	27.705	-0.056	-0.056	0.000	0.000	0.000	0.000
116	A	130	GLN	0	-0.074	-0.054	26.153	0.016	0.016	0.000	0.000	0.000	0.000
117	A	131	HIS	0	0.014	0.014	22.033	0.021	0.021	0.000	0.000	0.000	0.000
118	A	132	SER	0	0.019	0.033	24.092	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	133	GLU	-1	-0.852	-0.915	22.440	0.148	0.148	0.000	0.000	0.000	0.000
120	A	134	LYS	1	0.827	0.891	19.043	-0.190	-0.190	0.000	0.000	0.000	0.000
121	A	135	ALA	0	-0.066	-0.020	21.240	-0.021	-0.021	0.000	0.000	0.000	0.000
122	A	136	LEU	0	0.004	0.004	19.122	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	137	ARG	1	0.886	0.937	23.689	0.022	0.022	0.000	0.000	0.000	0.000
124	A	138	ILE	0	0.023	-0.002	23.315	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	139	PRO	0	-0.040	-0.011	26.422	0.007	0.007	0.000	0.000	0.000	0.000
126	A	140	VAL	0	-0.002	-0.001	29.805	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	141	ASN	0	0.032	0.019	32.582	0.009	0.009	0.000	0.000	0.000	0.000
128	A	142	ASP	-1	-0.916	-0.965	36.280	-0.033	-0.033	0.000	0.000	0.000	0.000
129	A	143	GLN	0	0.057	0.037	37.722	0.000	0.000	0.000	0.000	0.000	0.000
130	A	144	HIS	0	-0.015	-0.014	39.719	0.003	0.003	0.000	0.000	0.000	0.000
131	A	145	VAL	0	-0.005	-0.004	35.397	0.001	0.001	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.911	0.946	35.802	0.036	0.036	0.000	0.000	0.000	0.000
133	A	147	SER	0	0.004	-0.002	31.456	0.005	0.005	0.000	0.000	0.000	0.000
134	A	148	LEU	0	0.038	0.046	27.399	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	149	ASN	0	0.012	-0.004	27.997	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	150	LEU	0	0.053	0.020	24.100	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	151	SER	0	-0.003	-0.012	23.623	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	152	ASN	0	0.008	0.002	23.170	-0.024	-0.024	0.000	0.000	0.000	0.000
139	A	153	THR	0	-0.020	-0.012	23.241	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	154	VAL	0	0.006	0.007	18.405	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	155	CYS	0	-0.018	0.005	18.681	-0.042	-0.042	0.000	0.000	0.000	0.000
142	A	156	MET	0	0.014	0.005	18.833	-0.026	-0.026	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.021	-0.004	17.056	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	158	VAL	0	0.001	0.010	13.435	-0.015	-0.015	0.000	0.000	0.000	0.000
145	A	159	TYR	0	0.021	-0.014	14.457	-0.072	-0.072	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.811	-0.843	16.490	-0.238	-0.238	0.000	0.000	0.000	0.000
147	A	161	ALA	0	-0.003	-0.007	12.305	0.006	0.006	0.000	0.000	0.000	0.000
148	A	162	LEU	0	-0.027	-0.016	10.454	-0.044	-0.044	0.000	0.000	0.000	0.000
149	A	163	ARG	1	0.827	0.888	12.831	0.215	0.215	0.000	0.000	0.000	0.000
150	A	164	GLN	0	-0.074	-0.052	14.109	0.010	0.010	0.000	0.000	0.000	0.000
151	A	165	GLN	0	-0.001	0.018	8.826	-0.095	-0.095	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.890	-0.940	9.769	-0.658	-0.658	0.000	0.000	0.000	0.000
153	A	167	PHE	0	-0.074	-0.055	11.937	-0.010	-0.010	0.000	0.000	0.000	0.000
154	A	168	ILE	0	0.092	0.059	5.272	-0.142	-0.142	0.000	0.000	0.000	0.000
155	A	169	GLY	0	0.001	-0.001	6.486	-0.234	-0.234	0.000	0.000	0.000	0.000
156	A	170	LEU	0	-0.034	-0.025	7.551	0.013	0.013	0.000	0.000	0.000	0.000
157	A	171	GLU	-1	-0.956	-0.967	7.785	-0.833	-0.833	0.000	0.000	0.000	0.000
158	A	172	LEU	0	-0.047	-0.015	2.473	-0.780	-0.165	0.434	-0.173	-0.875	-0.001
159	A	173	SER	0	-0.050	-0.039	5.501	-0.143	-0.143	0.000	0.000	0.000	0.000
160	A	174	HIS	0	-0.072	-0.027	7.818	-0.028	-0.028	0.000	0.000	0.000	0.000
161	A	175	THR	0	0.006	0.010	3.257	-0.744	-0.154	0.036	-0.155	-0.471	0.000

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