FMO DATABASE

FMODB ID: K3RK3

Calculation Name: 4LRK-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LRK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XAL6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	163
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1560793.737649
FMO2-HF: Nuclear repulsion	1496074.460905
FMO2-HF: Total energy	-64719.276745
FMO2-MP2: Total energy	-64905.493537

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:141:ACE )

Summations of interaction energy for fragment #1(A:141:ACE )

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.
-1.349	0.427	0.014	-0.863	-0.927	-0.003

Interaction energy analysis for fragmet #1(A:141:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.007

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	143	PRO	0	0.000	0.027	3.426	-0.397	1.326	0.014	-0.857	-0.880	-0.003
4	A	144	VAL	0	0.028	0.018	4.929	0.342	0.395	0.000	-0.006	-0.047	0.000
5	A	145	PRO	0	-0.014	0.002	6.774	0.005	0.005	0.000	0.000	0.000	0.000
6	A	146	GLY	0	0.021	0.007	9.789	0.027	0.027	0.000	0.000	0.000	0.000
7	A	147	ASN	0	-0.032	-0.024	13.076	0.065	0.065	0.000	0.000	0.000	0.000
8	A	148	VAL	0	-0.041	-0.030	16.059	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	149	ILE	0	-0.027	-0.023	17.223	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	150	GLY	0	0.039	0.029	19.021	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	151	LYS	1	0.880	0.938	18.408	-0.111	-0.111	0.000	0.000	0.000	0.000
12	A	152	GLY	0	0.108	0.059	20.289	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	153	GLY	0	-0.030	-0.015	21.212	0.013	0.013	0.000	0.000	0.000	0.000
14	A	154	ASN	0	-0.002	0.003	19.355	0.012	0.012	0.000	0.000	0.000	0.000
15	A	155	ALA	0	0.013	0.003	16.145	0.016	0.016	0.000	0.000	0.000	0.000
16	A	156	VAL	0	-0.050	-0.013	14.589	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	157	VAL	0	0.030	0.016	14.568	0.005	0.005	0.000	0.000	0.000	0.000
18	A	158	TYR	0	-0.016	-0.011	12.375	0.028	0.028	0.000	0.000	0.000	0.000
19	A	159	GLU	-1	-0.850	-0.925	14.522	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	160	ASP	-1	-0.772	-0.888	11.332	-0.331	-0.331	0.000	0.000	0.000	0.000
21	A	161	MET	0	-0.077	-0.038	10.738	0.013	0.013	0.000	0.000	0.000	0.000
22	A	162	GLU	-1	-0.972	-0.984	8.987	-0.943	-0.943	0.000	0.000	0.000	0.000
23	A	163	ASP	-1	-0.851	-0.915	12.608	-0.192	-0.192	0.000	0.000	0.000	0.000
24	A	164	THR	0	0.012	0.005	15.791	0.022	0.022	0.000	0.000	0.000	0.000
25	A	165	THR	0	-0.100	-0.068	18.657	0.026	0.026	0.000	0.000	0.000	0.000
26	A	166	LYS	1	0.883	0.956	15.441	0.182	0.182	0.000	0.000	0.000	0.000
27	A	167	VAL	0	-0.019	-0.012	15.503	0.013	0.013	0.000	0.000	0.000	0.000
28	A	168	LEU	0	-0.051	-0.029	9.128	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	169	LYS	1	0.819	0.893	12.994	0.038	0.038	0.000	0.000	0.000	0.000
30	A	170	MET	0	-0.015	-0.014	7.629	-0.049	-0.049	0.000	0.000	0.000	0.000
31	A	171	PHE	0	0.021	-0.003	12.128	0.004	0.004	0.000	0.000	0.000	0.000
32	A	172	THR	0	-0.040	-0.022	12.816	0.051	0.051	0.000	0.000	0.000	0.000
33	A	173	ILE	0	0.008	-0.003	15.175	0.020	0.020	0.000	0.000	0.000	0.000
34	A	174	SER	0	-0.020	-0.008	15.716	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	175	GLN	0	0.010	0.013	16.637	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	176	SER	0	0.009	0.019	18.748	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	177	HIS	0	0.062	0.009	18.531	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	178	GLU	-1	-0.900	-0.958	20.939	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	179	GLU	-1	-0.874	-0.939	21.510	0.036	0.036	0.000	0.000	0.000	0.000
40	A	180	VAL	0	0.007	0.014	16.560	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	181	THR	0	-0.086	-0.056	19.456	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	182	SER	0	-0.069	-0.028	21.500	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	183	GLU	-1	-0.743	-0.838	20.240	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	184	VAL	0	-0.023	-0.022	17.899	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	185	ARG	1	0.918	0.956	20.921	0.032	0.032	0.000	0.000	0.000	0.000
46	A	186	CYS	0	0.001	0.001	24.398	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	187	PHE	0	0.070	0.040	21.804	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	188	ASN	0	-0.004	-0.010	20.978	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	189	GLN	0	-0.063	-0.032	24.749	0.002	0.002	0.000	0.000	0.000	0.000
50	A	190	TYR	0	0.004	0.001	27.754	0.001	0.001	0.000	0.000	0.000	0.000
51	A	191	TYR	0	0.014	-0.016	25.164	0.000	0.000	0.000	0.000	0.000	0.000
52	A	192	GLY	0	-0.016	0.014	26.972	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	193	SER	0	-0.032	-0.030	24.801	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	194	GLY	0	0.028	0.013	20.969	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	195	SER	0	-0.021	-0.008	20.465	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	196	ALA	0	-0.022	-0.014	18.209	0.002	0.002	0.000	0.000	0.000	0.000
57	A	197	GLU	-1	-0.907	-0.945	13.569	-0.343	-0.343	0.000	0.000	0.000	0.000
58	A	198	LYS	1	0.911	0.958	13.762	0.095	0.095	0.000	0.000	0.000	0.000
59	A	199	ILE	0	0.014	0.012	7.492	-0.073	-0.073	0.000	0.000	0.000	0.000
60	A	200	TYR	0	-0.005	-0.013	9.063	0.149	0.149	0.000	0.000	0.000	0.000
61	A	201	ASN	0	-0.003	0.005	5.651	-0.281	-0.281	0.000	0.000	0.000	0.000
62	A	202	ASP	-1	-0.853	-0.937	5.808	-0.300	-0.300	0.000	0.000	0.000	0.000
63	A	203	ASN	0	-0.122	-0.075	7.835	-0.059	-0.059	0.000	0.000	0.000	0.000
64	A	204	GLY	0	0.049	0.045	9.965	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	205	ASN	0	-0.079	-0.040	10.567	0.059	0.059	0.000	0.000	0.000	0.000
66	A	206	VAL	0	0.031	0.006	10.298	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	207	ILE	0	-0.013	-0.011	5.921	0.068	0.068	0.000	0.000	0.000	0.000
68	A	208	GLY	0	0.032	0.008	10.171	0.054	0.054	0.000	0.000	0.000	0.000
69	A	209	ILE	0	-0.031	0.001	11.747	-0.054	-0.054	0.000	0.000	0.000	0.000
70	A	210	ARG	1	0.898	0.966	8.794	0.575	0.575	0.000	0.000	0.000	0.000
71	A	211	MET	0	-0.020	-0.017	13.928	0.003	0.003	0.000	0.000	0.000	0.000
72	A	212	ASN	0	0.051	0.028	17.659	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	213	LYS	1	0.912	0.968	18.850	0.077	0.077	0.000	0.000	0.000	0.000
74	A	214	ILE	0	-0.032	-0.007	21.399	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	215	ASN	0	-0.024	-0.009	24.981	0.003	0.003	0.000	0.000	0.000	0.000
76	A	216	GLY	0	0.026	0.004	27.969	0.001	0.001	0.000	0.000	0.000	0.000
77	A	217	GLU	-1	-0.953	-0.968	29.092	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	218	SER	0	0.034	0.009	29.635	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	219	LEU	0	0.017	0.006	31.260	0.000	0.000	0.000	0.000	0.000	0.000
80	A	220	LEU	0	-0.027	-0.003	31.316	0.001	0.001	0.000	0.000	0.000	0.000
81	A	221	ASP	-1	-0.944	-0.962	31.740	0.018	0.018	0.000	0.000	0.000	0.000
82	A	222	ILE	0	-0.073	-0.033	34.881	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	223	PRO	0	-0.056	-0.021	37.900	0.000	0.000	0.000	0.000	0.000	0.000
84	A	224	SER	0	-0.046	-0.026	41.382	0.000	0.000	0.000	0.000	0.000	0.000
85	A	225	LEU	0	0.006	0.003	38.938	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	226	PRO	0	0.011	0.018	41.948	0.000	0.000	0.000	0.000	0.000	0.000
87	A	227	ALA	0	0.107	0.032	44.834	0.000	0.000	0.000	0.000	0.000	0.000
88	A	228	GLN	0	-0.064	-0.037	43.223	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	229	ALA	0	0.022	0.021	40.942	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	230	GLU	-1	-0.838	-0.899	41.818	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	231	GLN	0	-0.068	-0.067	43.420	0.001	0.001	0.000	0.000	0.000	0.000
92	A	232	ALA	0	0.024	0.027	38.784	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	233	ILE	0	0.005	-0.005	37.050	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	234	TYR	0	-0.089	-0.063	39.209	0.000	0.000	0.000	0.000	0.000	0.000
95	A	235	ASP	-1	-0.800	-0.868	38.971	-0.020	-0.020	0.000	0.000	0.000	0.000
96	A	236	MET	0	-0.053	-0.008	33.749	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	237	PHE	0	0.019	-0.011	35.807	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	238	ASP	-1	-0.874	-0.933	37.819	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	239	ARG	1	0.765	0.883	31.145	0.040	0.040	0.000	0.000	0.000	0.000
100	A	240	LEU	0	-0.011	-0.018	31.220	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	241	GLU	-1	-0.744	-0.830	34.586	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	242	LYS	1	0.872	0.954	37.144	0.025	0.025	0.000	0.000	0.000	0.000
103	A	243	LYS	1	0.826	0.910	32.276	0.041	0.041	0.000	0.000	0.000	0.000
104	A	244	GLY	0	-0.020	-0.001	34.033	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	245	ILE	0	-0.058	-0.023	29.769	0.001	0.001	0.000	0.000	0.000	0.000
106	A	246	LEU	0	-0.017	-0.007	33.472	0.001	0.001	0.000	0.000	0.000	0.000
107	A	247	PHE	0	-0.002	-0.018	29.390	0.002	0.002	0.000	0.000	0.000	0.000
108	A	248	VAL	0	0.025	0.008	30.855	0.002	0.002	0.000	0.000	0.000	0.000
109	A	249	ASP	-1	-0.875	-0.926	29.065	0.020	0.020	0.000	0.000	0.000	0.000
110	A	250	THR	0	-0.012	0.003	31.655	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	251	THR	0	0.008	-0.007	31.641	0.000	0.000	0.000	0.000	0.000	0.000
112	A	252	GLU	-1	-0.814	-0.936	32.975	0.009	0.009	0.000	0.000	0.000	0.000
113	A	253	THR	0	-0.031	-0.023	28.446	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	254	ASN	0	-0.019	0.007	27.362	0.000	0.000	0.000	0.000	0.000	0.000
115	A	255	VAL	0	-0.009	-0.003	29.371	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	256	LEU	0	-0.011	0.000	26.373	0.003	0.003	0.000	0.000	0.000	0.000
117	A	257	TYR	0	-0.011	-0.025	31.005	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	258	ASP	-1	-0.777	-0.874	32.292	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	259	ARG	1	0.989	0.972	34.004	0.009	0.009	0.000	0.000	0.000	0.000
120	A	260	MET	0	-0.103	-0.035	34.091	0.000	0.000	0.000	0.000	0.000	0.000
121	A	261	ARG	1	0.831	0.894	31.370	0.038	0.038	0.000	0.000	0.000	0.000
122	A	262	ASN	0	-0.007	0.030	37.082	0.001	0.001	0.000	0.000	0.000	0.000
123	A	263	GLU	-1	-0.898	-0.956	33.304	-0.035	-0.035	0.000	0.000	0.000	0.000
124	A	264	PHE	0	-0.008	-0.013	34.151	0.002	0.002	0.000	0.000	0.000	0.000
125	A	265	ASN	0	-0.061	-0.043	28.942	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	266	PRO	0	0.017	0.024	28.983	0.004	0.004	0.000	0.000	0.000	0.000
127	A	267	ILE	0	-0.013	-0.002	23.744	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	268	ASP	-1	-0.854	-0.922	22.682	0.010	0.010	0.000	0.000	0.000	0.000
129	A	269	ILE	0	-0.052	-0.026	24.966	0.001	0.001	0.000	0.000	0.000	0.000
130	A	270	SER	0	0.013	-0.002	25.808	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	271	SER	0	0.010	-0.013	27.949	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	272	TYR	0	0.004	0.013	31.085	0.003	0.003	0.000	0.000	0.000	0.000
133	A	273	ASN	0	-0.042	-0.025	30.021	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	274	VAL	0	-0.001	0.010	34.081	0.003	0.003	0.000	0.000	0.000	0.000
135	A	275	SER	0	-0.034	-0.026	35.581	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	276	ASP	-1	-0.871	-0.946	37.640	0.003	0.003	0.000	0.000	0.000	0.000
137	A	277	ILE	0	-0.069	-0.028	39.494	0.002	0.002	0.000	0.000	0.000	0.000
138	A	278	SER	0	-0.070	-0.037	36.858	0.001	0.001	0.000	0.000	0.000	0.000
139	A	279	TRP	0	0.014	0.016	34.348	0.000	0.000	0.000	0.000	0.000	0.000
140	A	280	SER	0	0.025	0.010	38.874	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	281	GLU	-1	-0.813	-0.940	41.401	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	282	HIS	0	-0.010	-0.002	42.651	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	283	GLN	0	0.033	0.030	41.464	0.000	0.000	0.000	0.000	0.000	0.000
144	A	284	VAL	0	0.030	0.018	37.658	0.001	0.001	0.000	0.000	0.000	0.000
145	A	285	MET	0	-0.002	0.006	39.968	0.000	0.000	0.000	0.000	0.000	0.000
146	A	286	GLN	0	-0.034	-0.011	42.447	0.000	0.000	0.000	0.000	0.000	0.000
147	A	287	SER	0	-0.019	-0.019	38.571	0.001	0.001	0.000	0.000	0.000	0.000
148	A	288	TYR	0	-0.067	-0.070	36.623	0.000	0.000	0.000	0.000	0.000	0.000
149	A	289	HIS	0	-0.010	0.002	39.181	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	290	GLY	0	-0.007	-0.011	42.427	0.000	0.000	0.000	0.000	0.000	0.000
151	A	291	GLY	0	0.037	0.028	38.213	0.001	0.001	0.000	0.000	0.000	0.000
152	A	292	LYS	1	0.895	0.941	39.002	0.008	0.008	0.000	0.000	0.000	0.000
153	A	293	LEU	0	-0.054	-0.036	40.104	0.000	0.000	0.000	0.000	0.000	0.000
154	A	294	ASP	-1	-0.951	-0.963	39.923	0.009	0.009	0.000	0.000	0.000	0.000
155	A	295	LEU	0	0.037	0.021	35.294	0.000	0.000	0.000	0.000	0.000	0.000
156	A	296	ILE	0	-0.016	-0.018	39.341	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	297	SER	0	-0.036	-0.009	42.096	0.000	0.000	0.000	0.000	0.000	0.000
158	A	298	VAL	0	0.021	0.015	38.932	0.000	0.000	0.000	0.000	0.000	0.000
159	A	299	VAL	0	-0.018	-0.025	39.393	0.000	0.000	0.000	0.000	0.000	0.000
160	A	300	LEU	0	0.002	-0.012	41.832	0.000	0.000	0.000	0.000	0.000	0.000
161	A	301	SER	0	-0.063	-0.023	44.550	0.000	0.000	0.000	0.000	0.000	0.000
162	A	302	LYS	1	0.778	0.897	38.777	-0.006	-0.006	0.000	0.000	0.000	0.000
163	A	303	ILE	-1	-0.970	-0.957	44.451	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:141:ACE )