FMO DATABASE

FMODB ID: KGK73

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1685160.154794
FMO2-HF: Nuclear repulsion	1618927.551831
FMO2-HF: Total energy	-66232.602963
FMO2-MP2: Total energy	-66423.480935

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.
-7.127	-2.607	1.676	-2.114	-4.081	-0.006

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 : -0.018 / q_NPA : -0.020

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	0.948	0.960	3.248	-1.416	0.950	0.064	-1.106	-1.324	-0.002
4	A	18	ASN	0	0.034	0.000	5.354	0.759	0.817	-0.001	-0.003	-0.053	0.000
5	A	19	HIS	0	0.009	0.006	7.182	-0.075	-0.075	0.000	0.000	0.000	0.000
6	A	20	VAL	0	0.020	0.005	11.756	0.073	0.073	0.000	0.000	0.000	0.000
7	A	21	VAL	0	0.008	-0.007	15.401	0.009	0.009	0.000	0.000	0.000	0.000
8	A	22	LEU	0	-0.014	-0.007	17.845	0.006	0.006	0.000	0.000	0.000	0.000
9	A	23	PHE	0	0.056	0.008	21.484	0.016	0.016	0.000	0.000	0.000	0.000
10	A	24	GLN	0	-0.010	0.010	23.903	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	25	PRO	0	0.048	0.053	24.216	0.001	0.001	0.000	0.000	0.000	0.000
12	A	26	GLN	0	-0.026	-0.057	26.784	0.006	0.006	0.000	0.000	0.000	0.000
13	A	27	ILE	0	-0.041	-0.012	29.450	0.002	0.002	0.000	0.000	0.000	0.000
14	A	28	PRO	0	0.039	0.016	28.682	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	29	ALA	0	0.040	0.002	27.970	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	30	ASN	0	0.002	0.012	26.245	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	31	THR	0	0.037	0.013	23.142	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	32	GLY	0	-0.006	-0.013	23.125	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	33	ASN	0	0.022	0.001	23.521	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.025	0.018	19.045	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	35	ALA	0	0.006	0.013	18.866	-0.042	-0.042	0.000	0.000	0.000	0.000
22	A	36	ARG	1	0.905	0.931	18.497	0.213	0.213	0.000	0.000	0.000	0.000
23	A	37	THR	0	0.000	0.005	16.881	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.050	-0.019	14.729	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	39	ALA	0	-0.022	-0.006	13.911	-0.094	-0.094	0.000	0.000	0.000	0.000
26	A	40	ALA	0	-0.040	-0.018	14.739	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.015	-0.013	12.836	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	42	ASN	0	-0.034	-0.003	8.386	0.028	0.028	0.000	0.000	0.000	0.000
29	A	43	THR	0	-0.027	-0.014	8.943	-0.236	-0.236	0.000	0.000	0.000	0.000
30	A	44	SER	0	-0.091	-0.067	10.051	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	45	LEU	0	-0.018	-0.011	11.833	0.060	0.060	0.000	0.000	0.000	0.000
32	A	46	HIS	0	-0.031	0.001	11.243	0.091	0.091	0.000	0.000	0.000	0.000
33	A	47	ILE	0	-0.001	-0.004	16.523	0.000	0.000	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.035	0.000	19.606	0.019	0.019	0.000	0.000	0.000	0.000
35	A	49	ARG	1	0.948	0.987	22.388	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	50	PRO	0	0.006	-0.015	25.444	0.010	0.010	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.005	-0.006	24.693	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	52	GLY	0	-0.014	-0.009	28.172	0.007	0.007	0.000	0.000	0.000	0.000
39	A	53	PHE	0	-0.052	-0.036	26.786	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	54	PRO	0	0.003	0.014	30.732	0.000	0.000	0.000	0.000	0.000	0.000
41	A	55	ILE	0	0.022	0.000	26.643	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	56	ASP	-1	-0.905	-0.952	30.058	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	57	ASP	-1	-0.835	-0.923	30.033	-0.109	-0.109	0.000	0.000	0.000	0.000
44	A	58	LYS	1	0.976	0.983	30.613	0.076	0.076	0.000	0.000	0.000	0.000
45	A	59	LYS	1	0.934	0.951	32.565	0.072	0.072	0.000	0.000	0.000	0.000
46	A	60	MET	0	-0.013	0.034	27.707	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	61	LYS	1	0.846	0.911	20.926	0.247	0.247	0.000	0.000	0.000	0.000
48	A	62	ARG	1	0.912	0.938	26.737	0.115	0.115	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.084	-0.027	27.846	0.001	0.001	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.042	0.030	25.714	0.000	0.000	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.088	-0.029	26.003	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	66	ASP	-1	-0.782	-0.902	24.427	-0.207	-0.207	0.000	0.000	0.000	0.000
53	A	67	TYR	0	-0.036	-0.023	23.383	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	68	TRP	0	0.028	0.016	17.949	0.009	0.009	0.000	0.000	0.000	0.000
55	A	69	ASP	-1	-0.813	-0.901	18.324	-0.246	-0.246	0.000	0.000	0.000	0.000
56	A	70	LYS	1	0.933	0.931	13.807	0.431	0.431	0.000	0.000	0.000	0.000
57	A	71	LEU	0	-0.039	0.014	14.203	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	72	ASP	-1	-0.821	-0.847	10.443	-0.459	-0.459	0.000	0.000	0.000	0.000
59	A	73	VAL	0	-0.018	-0.006	13.522	0.002	0.002	0.000	0.000	0.000	0.000
60	A	74	HIS	1	0.853	0.931	11.369	0.245	0.245	0.000	0.000	0.000	0.000
61	A	75	PHE	0	-0.010	-0.016	16.270	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	76	TYR	0	0.038	-0.006	14.068	0.032	0.032	0.000	0.000	0.000	0.000
63	A	77	ASP	-1	-0.903	-0.936	20.670	0.035	0.035	0.000	0.000	0.000	0.000
64	A	78	SER	0	-0.027	-0.030	22.751	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	79	LEU	0	0.028	-0.004	21.079	0.005	0.005	0.000	0.000	0.000	0.000
66	A	80	ASN	0	0.010	-0.003	20.842	0.030	0.030	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.898	-0.934	20.739	0.150	0.150	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.005	-0.009	14.274	0.029	0.029	0.000	0.000	0.000	0.000
69	A	83	MET	0	-0.041	-0.029	16.150	0.037	0.037	0.000	0.000	0.000	0.000
70	A	84	ASN	0	-0.018	0.011	17.195	0.047	0.047	0.000	0.000	0.000	0.000
71	A	85	ILE	0	-0.030	-0.014	12.693	0.051	0.051	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.111	-0.028	12.219	0.095	0.095	0.000	0.000	0.000	0.000
73	A	87	SER	0	0.041	0.014	9.045	0.045	0.045	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.032	0.012	9.137	0.173	0.173	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.891	0.962	10.631	-0.460	-0.460	0.000	0.000	0.000	0.000
76	A	90	LEU	0	0.001	0.002	13.137	-0.083	-0.083	0.000	0.000	0.000	0.000
77	A	91	HIS	0	0.058	0.041	14.574	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	92	LEU	0	-0.031	-0.011	18.371	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.008	0.007	19.338	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	94	THR	0	-0.032	-0.023	22.902	0.005	0.005	0.000	0.000	0.000	0.000
81	A	95	LYS	1	0.935	0.944	26.693	0.033	0.033	0.000	0.000	0.000	0.000
82	A	96	PHE	0	-0.020	-0.031	29.891	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	97	ALA	0	0.035	0.065	26.238	0.007	0.007	0.000	0.000	0.000	0.000
84	A	98	ASN	0	-0.006	-0.009	28.279	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.927	0.953	20.532	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	100	THR	0	-0.025	-0.008	24.497	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.029	-0.007	20.370	0.001	0.001	0.000	0.000	0.000	0.000
88	A	102	SER	0	0.050	0.012	19.843	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	103	ASP	-1	-0.929	-0.943	20.711	-0.067	-0.067	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.926	-0.942	16.488	0.075	0.075	0.000	0.000	0.000	0.000
91	A	105	ASN	0	0.004	0.013	14.568	-0.071	-0.071	0.000	0.000	0.000	0.000
92	A	106	TYR	0	-0.068	-0.068	11.946	0.055	0.055	0.000	0.000	0.000	0.000
93	A	107	ASP	-1	-0.903	-0.935	10.287	-0.398	-0.398	0.000	0.000	0.000	0.000
94	A	108	ASP	-1	-0.785	-0.875	8.895	0.215	0.215	0.000	0.000	0.000	0.000
95	A	109	SER	0	-0.009	-0.016	4.616	-0.286	-0.198	-0.001	-0.010	-0.077	0.000
96	A	110	GLU	-1	-0.985	-0.986	4.867	1.652	1.726	-0.001	-0.005	-0.068	0.000
97	A	111	HIS	0	0.038	0.028	3.634	-3.051	-2.480	0.005	-0.181	-0.395	0.001
98	A	112	HIS	1	0.777	0.865	7.638	0.314	0.314	0.000	0.000	0.000	0.000
99	A	113	TYR	0	-0.002	-0.013	9.660	-0.132	-0.132	0.000	0.000	0.000	0.000
100	A	114	PHE	0	0.032	0.023	12.451	0.057	0.057	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.005	0.002	16.471	-0.021	-0.021	0.000	0.000	0.000	0.000
102	A	116	PHE	0	0.003	-0.006	17.998	0.006	0.006	0.000	0.000	0.000	0.000
103	A	117	GLY	0	0.002	-0.010	22.605	0.008	0.008	0.000	0.000	0.000	0.000
104	A	118	ARG	1	0.782	0.892	26.131	0.011	0.011	0.000	0.000	0.000	0.000
105	A	119	GLU	-1	-0.774	-0.907	28.428	-0.082	-0.082	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.823	-0.897	30.365	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	121	LYS	1	0.929	0.960	32.144	0.013	0.013	0.000	0.000	0.000	0.000
108	A	122	GLY	0	0.006	0.023	28.988	0.006	0.006	0.000	0.000	0.000	0.000
109	A	123	LEU	0	0.009	-0.008	23.891	0.000	0.000	0.000	0.000	0.000	0.000
110	A	124	PRO	0	-0.007	-0.006	26.774	0.000	0.000	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.792	-0.892	29.036	0.043	0.043	0.000	0.000	0.000	0.000
112	A	126	GLU	-1	-0.832	-0.884	29.995	0.084	0.084	0.000	0.000	0.000	0.000
113	A	127	PHE	0	0.022	-0.006	20.990	0.006	0.006	0.000	0.000	0.000	0.000
114	A	128	MET	0	-0.013	-0.023	26.125	0.004	0.004	0.000	0.000	0.000	0.000
115	A	129	ARG	1	0.813	0.899	27.657	-0.054	-0.054	0.000	0.000	0.000	0.000
116	A	130	GLN	0	-0.079	-0.058	26.220	0.016	0.016	0.000	0.000	0.000	0.000
117	A	131	HIS	0	0.050	0.036	21.782	0.024	0.024	0.000	0.000	0.000	0.000
118	A	132	SER	0	0.011	0.027	24.073	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	133	GLU	-1	-0.908	-0.958	22.175	0.166	0.166	0.000	0.000	0.000	0.000
120	A	134	LYS	1	0.845	0.914	18.951	-0.205	-0.205	0.000	0.000	0.000	0.000
121	A	135	ALA	0	-0.062	-0.019	21.162	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	136	LEU	0	-0.003	0.002	18.903	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	137	ARG	1	0.914	0.956	23.514	0.026	0.026	0.000	0.000	0.000	0.000
124	A	138	ILE	0	0.023	-0.004	23.105	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	139	PRO	0	-0.048	-0.018	26.349	0.007	0.007	0.000	0.000	0.000	0.000
126	A	140	VAL	0	0.007	0.006	29.750	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	141	ASN	0	0.039	0.013	32.509	0.010	0.010	0.000	0.000	0.000	0.000
128	A	142	ASP	-1	-0.930	-0.961	36.212	-0.037	-0.037	0.000	0.000	0.000	0.000
129	A	143	GLN	0	0.063	0.036	37.629	0.000	0.000	0.000	0.000	0.000	0.000
130	A	144	HIS	0	-0.025	-0.022	39.629	0.003	0.003	0.000	0.000	0.000	0.000
131	A	145	VAL	0	0.000	0.003	35.118	0.001	0.001	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.886	0.931	35.606	0.041	0.041	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.032	-0.019	31.085	0.004	0.004	0.000	0.000	0.000	0.000
134	A	148	LEU	0	0.049	0.046	27.444	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	149	ASN	0	0.002	-0.012	27.933	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	150	LEU	0	0.062	0.019	23.697	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	151	SER	0	-0.006	-0.013	23.426	-0.014	-0.014	0.000	0.000	0.000	0.000
138	A	152	ASN	0	0.020	0.012	22.995	-0.028	-0.028	0.000	0.000	0.000	0.000
139	A	153	THR	0	-0.030	-0.013	23.308	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	154	VAL	0	0.005	0.012	18.226	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	155	CYS	0	-0.014	0.003	18.531	-0.045	-0.045	0.000	0.000	0.000	0.000
142	A	156	MET	0	0.010	0.005	18.716	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.018	0.002	16.801	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	158	VAL	0	-0.004	0.006	13.304	-0.012	-0.012	0.000	0.000	0.000	0.000
145	A	159	TYR	0	0.015	-0.015	14.378	-0.076	-0.076	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.801	-0.847	16.167	-0.247	-0.247	0.000	0.000	0.000	0.000
147	A	161	ALA	0	-0.003	-0.008	12.234	0.010	0.010	0.000	0.000	0.000	0.000
148	A	162	LEU	0	-0.022	-0.011	10.206	-0.041	-0.041	0.000	0.000	0.000	0.000
149	A	163	ARG	1	0.821	0.890	12.341	0.224	0.224	0.000	0.000	0.000	0.000
150	A	164	GLN	0	-0.078	-0.058	13.607	0.014	0.014	0.000	0.000	0.000	0.000
151	A	165	GLN	0	0.001	0.020	8.329	-0.119	-0.119	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.896	-0.943	9.360	-0.698	-0.698	0.000	0.000	0.000	0.000
153	A	167	PHE	0	-0.065	-0.050	11.408	-0.011	-0.011	0.000	0.000	0.000	0.000
154	A	168	ILE	0	0.107	0.066	4.863	-0.172	-0.172	0.000	0.000	0.000	0.000
155	A	169	GLY	0	-0.008	-0.008	6.255	-0.281	-0.281	0.000	0.000	0.000	0.000
156	A	170	LEU	0	-0.018	-0.016	7.329	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	171	GLU	-1	-0.970	-0.972	7.757	-0.892	-0.892	0.000	0.000	0.000	0.000
158	A	172	LEU	0	-0.052	-0.019	2.136	-0.636	-0.426	1.460	-0.329	-1.340	-0.002
159	A	173	SER	0	-0.014	-0.014	5.339	-0.164	-0.164	0.000	0.000	0.000	0.000
160	A	174	HIS	0	-0.077	-0.030	7.587	-0.040	-0.040	0.000	0.000	0.000	0.000
161	A	175	THR	0	0.005	0.012	3.275	-1.440	-0.287	0.150	-0.480	-0.824	-0.003

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