FMO DATABASE

FMODB ID: Q1RKY

Calculation Name: 4LRK-A-Xray372

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: 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:

Apendix: None

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1555919.723146
FMO2-HF: Nuclear repulsion	1491351.31848
FMO2-HF: Total energy	-64568.404666
FMO2-MP2: Total energy	-64754.189978

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:142:SER)

Summations of interaction energy for fragment #1(A:142:SER)

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.
-2.932	-1.341	-0.005	-0.729	-0.857	0

Interaction energy analysis for fragmet #1(A:142:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.023

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].
3	A	144	VAL	0	0.023	0.014	3.543	-0.720	0.720	-0.003	-0.715	-0.722
4	A	145	PRO	0	-0.012	0.002	5.743	0.557	0.557	0.000	0.000	0.000
5	A	146	GLY	0	0.019	0.007	8.768	0.034	0.034	0.000	0.000	0.000
6	A	147	ASN	0	-0.028	-0.022	12.167	0.045	0.045	0.000	0.000	0.000
7	A	148	VAL	0	-0.043	-0.031	15.141	-0.013	-0.013	0.000	0.000	0.000
8	A	149	ILE	0	-0.027	-0.024	16.558	0.016	0.016	0.000	0.000	0.000
9	A	150	GLY	0	0.036	0.027	18.150	0.025	0.025	0.000	0.000	0.000
10	A	151	LYS	1	0.882	0.939	18.285	0.145	0.145	0.000	0.000	0.000
11	A	152	GLY	0	0.103	0.057	20.145	0.004	0.004	0.000	0.000	0.000
12	A	153	GLY	0	-0.029	-0.015	21.356	0.001	0.001	0.000	0.000	0.000
13	A	154	ASN	0	-0.001	0.003	19.377	-0.006	-0.006	0.000	0.000	0.000
14	A	155	ALA	0	0.016	0.004	15.982	0.017	0.017	0.000	0.000	0.000
15	A	156	VAL	0	-0.053	-0.014	14.427	-0.003	-0.003	0.000	0.000	0.000
16	A	157	VAL	0	0.028	0.015	14.066	-0.015	-0.015	0.000	0.000	0.000
17	A	158	TYR	0	-0.014	-0.010	11.303	0.026	0.026	0.000	0.000	0.000
18	A	159	GLU	-1	-0.849	-0.925	13.179	-0.441	-0.441	0.000	0.000	0.000
19	A	160	ASP	-1	-0.780	-0.891	8.858	-1.517	-1.517	0.000	0.000	0.000
20	A	161	MET	0	-0.071	-0.037	9.497	0.229	0.229	0.000	0.000	0.000
21	A	162	GLU	-1	-0.971	-0.984	5.509	-2.541	-2.541	0.000	0.000	0.000
22	A	163	ASP	-1	-0.850	-0.914	9.728	-0.153	-0.153	0.000	0.000	0.000
23	A	164	THR	0	0.011	0.005	12.752	-0.012	-0.012	0.000	0.000	0.000
24	A	165	THR	0	-0.101	-0.069	15.465	0.041	0.041	0.000	0.000	0.000
25	A	166	LYS	1	0.882	0.956	11.842	0.279	0.279	0.000	0.000	0.000
26	A	167	VAL	0	-0.021	-0.012	13.555	-0.034	-0.034	0.000	0.000	0.000
27	A	168	LEU	0	-0.048	-0.027	7.546	-0.006	-0.006	0.000	0.000	0.000
28	A	169	LYS	1	0.818	0.892	11.438	0.137	0.137	0.000	0.000	0.000
29	A	170	MET	0	-0.012	-0.012	7.356	-0.025	-0.025	0.000	0.000	0.000
30	A	171	PHE	0	0.021	-0.003	12.030	-0.013	-0.013	0.000	0.000	0.000
31	A	172	THR	0	-0.040	-0.022	13.688	0.031	0.031	0.000	0.000	0.000
32	A	173	ILE	0	0.009	-0.002	16.106	0.010	0.010	0.000	0.000	0.000
33	A	174	SER	0	-0.019	-0.008	15.958	0.003	0.003	0.000	0.000	0.000
34	A	175	GLN	0	0.012	0.014	16.480	-0.028	-0.028	0.000	0.000	0.000
35	A	176	SER	0	0.009	0.019	18.135	0.018	0.018	0.000	0.000	0.000
36	A	177	HIS	0	0.062	0.009	17.467	0.006	0.006	0.000	0.000	0.000
37	A	178	GLU	-1	-0.900	-0.959	19.417	0.065	0.065	0.000	0.000	0.000
38	A	179	GLU	-1	-0.878	-0.940	20.330	0.018	0.018	0.000	0.000	0.000
39	A	180	VAL	0	0.010	0.015	14.553	-0.008	-0.008	0.000	0.000	0.000
40	A	181	THR	0	-0.086	-0.056	17.640	-0.005	-0.005	0.000	0.000	0.000
41	A	182	SER	0	-0.069	-0.028	19.087	-0.010	-0.010	0.000	0.000	0.000
42	A	183	GLU	-1	-0.747	-0.840	18.136	-0.060	-0.060	0.000	0.000	0.000
43	A	184	VAL	0	-0.022	-0.021	15.066	-0.009	-0.009	0.000	0.000	0.000
44	A	185	ARG	1	0.920	0.958	18.004	-0.045	-0.045	0.000	0.000	0.000
45	A	186	CYS	0	0.001	0.000	21.171	-0.003	-0.003	0.000	0.000	0.000
46	A	187	PHE	0	0.067	0.039	18.416	-0.003	-0.003	0.000	0.000	0.000
47	A	188	ASN	0	0.000	-0.009	16.937	-0.020	-0.020	0.000	0.000	0.000
48	A	189	GLN	0	-0.066	-0.032	20.843	-0.001	-0.001	0.000	0.000	0.000
49	A	190	TYR	0	0.006	0.000	24.229	0.004	0.004	0.000	0.000	0.000
50	A	191	TYR	0	0.018	-0.014	21.433	0.000	0.000	0.000	0.000	0.000
51	A	192	GLY	0	-0.023	0.012	22.853	-0.003	-0.003	0.000	0.000	0.000
52	A	193	SER	0	-0.030	-0.030	20.251	-0.009	-0.009	0.000	0.000	0.000
53	A	194	GLY	0	0.028	0.013	16.114	-0.002	-0.002	0.000	0.000	0.000
54	A	195	SER	0	-0.020	-0.009	15.782	-0.035	-0.035	0.000	0.000	0.000
55	A	196	ALA	0	-0.023	-0.015	14.462	-0.038	-0.038	0.000	0.000	0.000
56	A	197	GLU	-1	-0.909	-0.944	8.700	-0.080	-0.080	0.000	0.000	0.000
57	A	198	LYS	1	0.912	0.958	10.999	-0.204	-0.204	0.000	0.000	0.000
58	A	199	ILE	0	0.015	0.013	5.053	0.014	0.014	0.000	0.000	0.000
59	A	200	TYR	0	-0.007	-0.013	5.990	0.005	0.005	0.000	0.000	0.000
60	A	201	ASN	0	-0.001	0.006	4.488	0.119	0.231	-0.001	-0.011	-0.100
61	A	202	ASP	-1	-0.856	-0.939	5.447	-0.252	-0.252	0.000	0.000	0.000
62	A	203	ASN	0	-0.119	-0.073	7.328	0.006	0.006	0.000	0.000	0.000
63	A	204	GLY	0	0.048	0.044	9.140	-0.031	-0.031	0.000	0.000	0.000
64	A	205	ASN	0	-0.077	-0.039	9.927	-0.067	-0.067	0.000	0.000	0.000
65	A	206	VAL	0	0.030	0.005	9.150	0.093	0.093	0.000	0.000	0.000
66	A	207	ILE	0	-0.008	-0.009	5.370	0.004	0.004	0.000	0.000	0.000
67	A	208	GLY	0	0.030	0.006	9.738	-0.059	-0.059	0.000	0.000	0.000
68	A	209	ILE	0	-0.029	0.003	10.503	0.051	0.051	0.000	0.000	0.000
69	A	210	ARG	1	0.903	0.968	4.605	1.514	1.553	-0.001	-0.003	-0.035
70	A	211	MET	0	-0.026	-0.020	10.760	0.090	0.090	0.000	0.000	0.000
71	A	212	ASN	0	0.051	0.029	14.400	-0.071	-0.071	0.000	0.000	0.000
72	A	213	LYS	1	0.911	0.968	16.934	0.343	0.343	0.000	0.000	0.000
73	A	214	ILE	0	-0.029	-0.007	18.662	0.017	0.017	0.000	0.000	0.000
74	A	215	ASN	0	-0.026	-0.009	22.224	-0.017	-0.017	0.000	0.000	0.000
75	A	216	GLY	0	0.024	0.002	25.362	0.009	0.009	0.000	0.000	0.000
76	A	217	GLU	-1	-0.947	-0.965	27.370	-0.131	-0.131	0.000	0.000	0.000
77	A	218	SER	0	0.035	0.011	28.412	0.009	0.009	0.000	0.000	0.000
78	A	219	LEU	0	0.010	0.001	29.943	0.003	0.003	0.000	0.000	0.000
79	A	220	LEU	0	-0.024	-0.002	30.354	0.004	0.004	0.000	0.000	0.000
80	A	221	ASP	-1	-0.937	-0.958	30.661	-0.087	-0.087	0.000	0.000	0.000
81	A	222	ILE	0	-0.072	-0.031	33.368	0.001	0.001	0.000	0.000	0.000
82	A	223	PRO	0	-0.049	-0.017	36.617	0.004	0.004	0.000	0.000	0.000
83	A	224	SER	0	-0.035	-0.030	40.076	0.004	0.004	0.000	0.000	0.000
84	A	225	LEU	0	0.022	0.019	37.040	-0.004	-0.004	0.000	0.000	0.000
85	A	226	PRO	0	0.000	0.010	39.778	0.003	0.003	0.000	0.000	0.000
86	A	227	ALA	0	0.080	0.015	42.473	0.000	0.000	0.000	0.000	0.000
87	A	228	GLN	0	-0.044	-0.028	40.419	-0.002	-0.002	0.000	0.000	0.000
88	A	229	ALA	0	0.023	0.023	38.543	0.000	0.000	0.000	0.000	0.000
89	A	230	GLU	-1	-0.845	-0.905	39.236	-0.026	-0.026	0.000	0.000	0.000
90	A	231	GLN	0	-0.068	-0.065	40.069	0.002	0.002	0.000	0.000	0.000
91	A	232	ALA	0	0.028	0.028	35.848	0.000	0.000	0.000	0.000	0.000
92	A	233	ILE	0	-0.002	-0.008	34.724	-0.001	-0.001	0.000	0.000	0.000
93	A	234	TYR	0	-0.086	-0.062	36.534	0.001	0.001	0.000	0.000	0.000
94	A	235	ASP	-1	-0.796	-0.866	35.543	-0.027	-0.027	0.000	0.000	0.000
95	A	236	MET	0	-0.052	-0.008	30.885	0.000	0.000	0.000	0.000	0.000
96	A	237	PHE	0	0.017	-0.011	32.781	0.002	0.002	0.000	0.000	0.000
97	A	238	ASP	-1	-0.872	-0.932	34.894	-0.015	-0.015	0.000	0.000	0.000
98	A	239	ARG	1	0.766	0.884	27.101	0.035	0.035	0.000	0.000	0.000
99	A	240	LEU	0	-0.009	-0.016	28.428	0.004	0.004	0.000	0.000	0.000
100	A	241	GLU	-1	-0.744	-0.830	31.488	-0.009	-0.009	0.000	0.000	0.000
101	A	242	LYS	1	0.874	0.955	33.469	0.013	0.013	0.000	0.000	0.000
102	A	243	LYS	1	0.828	0.911	28.380	0.013	0.013	0.000	0.000	0.000
103	A	244	GLY	0	-0.019	0.000	30.685	0.004	0.004	0.000	0.000	0.000
104	A	245	ILE	0	-0.058	-0.022	26.755	0.002	0.002	0.000	0.000	0.000
105	A	246	LEU	0	-0.015	-0.006	30.742	-0.003	-0.003	0.000	0.000	0.000
106	A	247	PHE	0	-0.001	-0.018	27.543	0.002	0.002	0.000	0.000	0.000
107	A	248	VAL	0	0.025	0.008	29.391	0.001	0.001	0.000	0.000	0.000
108	A	249	ASP	-1	-0.874	-0.925	28.168	-0.046	-0.046	0.000	0.000	0.000
109	A	250	THR	0	-0.015	0.002	30.370	-0.005	-0.005	0.000	0.000	0.000
110	A	251	THR	0	0.011	-0.005	30.820	-0.002	-0.002	0.000	0.000	0.000
111	A	252	GLU	-1	-0.820	-0.939	31.868	-0.055	-0.055	0.000	0.000	0.000
112	A	253	THR	0	-0.024	-0.022	27.740	-0.004	-0.004	0.000	0.000	0.000
113	A	254	ASN	0	-0.021	0.007	26.086	-0.017	-0.017	0.000	0.000	0.000
114	A	255	VAL	0	-0.013	-0.005	27.750	0.001	0.001	0.000	0.000	0.000
115	A	256	LEU	0	-0.007	0.002	24.464	-0.003	-0.003	0.000	0.000	0.000
116	A	257	TYR	0	-0.017	-0.030	29.043	0.006	0.006	0.000	0.000	0.000
117	A	258	ASP	-1	-0.773	-0.872	29.628	-0.091	-0.091	0.000	0.000	0.000
118	A	259	ARG	1	0.983	0.968	31.533	0.078	0.078	0.000	0.000	0.000
119	A	260	MET	0	-0.101	-0.035	31.161	0.004	0.004	0.000	0.000	0.000
120	A	261	ARG	1	0.838	0.897	28.231	0.090	0.090	0.000	0.000	0.000
121	A	262	ASN	0	-0.011	0.027	33.921	0.003	0.003	0.000	0.000	0.000
122	A	263	GLU	-1	-0.892	-0.953	29.765	-0.059	-0.059	0.000	0.000	0.000
123	A	264	PHE	0	-0.016	-0.017	31.601	-0.005	-0.005	0.000	0.000	0.000
124	A	265	ASN	0	-0.053	-0.039	26.148	0.010	0.010	0.000	0.000	0.000
125	A	266	PRO	0	0.015	0.024	26.302	-0.005	-0.005	0.000	0.000	0.000
126	A	267	ILE	0	-0.016	-0.003	22.067	-0.008	-0.008	0.000	0.000	0.000
127	A	268	ASP	-1	-0.850	-0.920	21.421	-0.094	-0.094	0.000	0.000	0.000
128	A	269	ILE	0	-0.053	-0.028	22.936	0.010	0.010	0.000	0.000	0.000
129	A	270	SER	0	0.017	0.001	23.766	0.006	0.006	0.000	0.000	0.000
130	A	271	SER	0	0.010	-0.013	26.068	-0.004	-0.004	0.000	0.000	0.000
131	A	272	TYR	0	0.008	0.014	29.257	0.004	0.004	0.000	0.000	0.000
132	A	273	ASN	0	-0.046	-0.026	28.211	0.003	0.003	0.000	0.000	0.000
133	A	274	VAL	0	0.003	0.011	32.198	0.000	0.000	0.000	0.000	0.000
134	A	275	SER	0	-0.040	-0.028	33.984	0.002	0.002	0.000	0.000	0.000
135	A	276	ASP	-1	-0.867	-0.944	35.974	0.022	0.022	0.000	0.000	0.000
136	A	277	ILE	0	-0.067	-0.027	38.227	0.000	0.000	0.000	0.000	0.000
137	A	278	SER	0	-0.070	-0.037	35.724	-0.001	-0.001	0.000	0.000	0.000
138	A	279	TRP	0	0.013	0.015	33.314	-0.003	-0.003	0.000	0.000	0.000
139	A	280	SER	0	0.027	0.012	37.482	0.001	0.001	0.000	0.000	0.000
140	A	281	GLU	-1	-0.815	-0.940	39.306	0.005	0.005	0.000	0.000	0.000
141	A	282	HIS	0	-0.008	-0.002	40.733	-0.001	-0.001	0.000	0.000	0.000
142	A	283	GLN	0	0.035	0.030	40.052	-0.001	-0.001	0.000	0.000	0.000
143	A	284	VAL	0	0.030	0.018	36.013	-0.002	-0.002	0.000	0.000	0.000
144	A	285	MET	0	-0.007	0.004	38.294	-0.003	-0.003	0.000	0.000	0.000
145	A	286	GLN	0	-0.030	-0.010	40.588	-0.001	-0.001	0.000	0.000	0.000
146	A	287	SER	0	-0.018	-0.018	37.273	-0.002	-0.002	0.000	0.000	0.000
147	A	288	TYR	0	-0.067	-0.070	34.484	-0.003	-0.003	0.000	0.000	0.000
148	A	289	HIS	0	-0.009	0.002	37.485	-0.002	-0.002	0.000	0.000	0.000
149	A	290	GLY	0	-0.011	-0.012	40.705	-0.002	-0.002	0.000	0.000	0.000
150	A	291	GLY	0	0.041	0.030	36.824	-0.002	-0.002	0.000	0.000	0.000
151	A	292	LYS	1	0.896	0.941	37.392	0.014	0.014	0.000	0.000	0.000
152	A	293	LEU	0	-0.054	-0.036	38.295	-0.002	-0.002	0.000	0.000	0.000
153	A	294	ASP	-1	-0.951	-0.963	38.962	-0.031	-0.031	0.000	0.000	0.000
154	A	295	LEU	0	0.039	0.023	33.645	-0.002	-0.002	0.000	0.000	0.000
155	A	296	ILE	0	-0.015	-0.017	37.823	-0.002	-0.002	0.000	0.000	0.000
156	A	297	SER	0	-0.033	-0.008	40.211	-0.001	-0.001	0.000	0.000	0.000
157	A	298	VAL	0	0.026	0.018	37.843	-0.001	-0.001	0.000	0.000	0.000
158	A	299	VAL	0	-0.008	-0.018	37.352	-0.002	-0.002	0.000	0.000	0.000
159	A	300	LEU	0	-0.002	-0.014	40.076	-0.001	-0.001	0.000	0.000	0.000
160	A	301	SER	0	-0.059	-0.022	43.326	0.001	0.001	0.000	0.000	0.000
161	A	302	LYS	1	0.802	0.912	37.539	0.052	0.052	0.000	0.000	0.000
162	A	303	ILE	0	-0.070	-0.002	42.221	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:142:SER)