FMO DATABASE

FMODB ID: K3YK3

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1557631.547608
FMO2-HF: Nuclear repulsion	1493062.520954
FMO2-HF: Total energy	-64569.026654
FMO2-MP2: Total energy	-64754.812936

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.
-2.906	-1.405	-0.005	-0.662	-0.832	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 : -0.004 / q_NPA : -0.027

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	0.016	0.002	3.580	-0.267	1.072	-0.003	-0.649	-0.687
4	A	145	PRO	0	-0.013	0.005	5.767	0.535	0.535	0.000	0.000	0.000
5	A	146	GLY	0	0.027	0.003	8.802	0.051	0.051	0.000	0.000	0.000
6	A	147	ASN	0	-0.086	-0.055	12.195	0.076	0.076	0.000	0.000	0.000
7	A	148	VAL	0	-0.044	-0.031	15.178	-0.020	-0.020	0.000	0.000	0.000
8	A	149	ILE	0	-0.017	-0.017	16.532	0.018	0.018	0.000	0.000	0.000
9	A	150	GLY	0	0.036	0.029	18.201	0.027	0.027	0.000	0.000	0.000
10	A	151	LYS	1	0.886	0.943	18.284	0.167	0.167	0.000	0.000	0.000
11	A	152	GLY	0	0.099	0.053	20.193	0.004	0.004	0.000	0.000	0.000
12	A	153	GLY	0	-0.032	-0.017	21.405	0.003	0.003	0.000	0.000	0.000
13	A	154	ASN	0	-0.010	-0.009	19.273	-0.004	-0.004	0.000	0.000	0.000
14	A	155	ALA	0	0.027	0.013	15.785	0.013	0.013	0.000	0.000	0.000
15	A	156	VAL	0	-0.062	-0.020	14.482	0.004	0.004	0.000	0.000	0.000
16	A	157	VAL	0	0.028	0.015	14.116	-0.024	-0.024	0.000	0.000	0.000
17	A	158	TYR	0	-0.007	-0.008	11.344	0.042	0.042	0.000	0.000	0.000
18	A	159	GLU	-1	-0.824	-0.906	13.221	-0.511	-0.511	0.000	0.000	0.000
19	A	160	ASP	-1	-0.749	-0.870	8.713	-1.908	-1.908	0.000	0.000	0.000
20	A	161	MET	0	-0.074	-0.031	9.534	0.251	0.251	0.000	0.000	0.000
21	A	162	GLU	-1	-0.952	-0.973	5.522	-3.296	-3.296	0.000	0.000	0.000
22	A	163	ASP	-1	-0.848	-0.909	9.757	-0.334	-0.334	0.000	0.000	0.000
23	A	164	THR	0	0.019	0.005	12.807	-0.004	-0.004	0.000	0.000	0.000
24	A	165	THR	0	-0.088	-0.059	15.503	0.057	0.057	0.000	0.000	0.000
25	A	166	LYS	1	0.890	0.958	12.094	0.438	0.438	0.000	0.000	0.000
26	A	167	VAL	0	-0.032	-0.022	13.564	-0.025	-0.025	0.000	0.000	0.000
27	A	168	LEU	0	-0.030	-0.017	7.685	0.000	0.000	0.000	0.000	0.000
28	A	169	LYS	1	0.788	0.879	11.336	0.227	0.227	0.000	0.000	0.000
29	A	170	MET	0	-0.017	-0.014	7.271	-0.051	-0.051	0.000	0.000	0.000
30	A	171	PHE	0	0.023	0.000	11.866	0.001	0.001	0.000	0.000	0.000
31	A	172	THR	0	-0.041	-0.023	13.626	0.030	0.030	0.000	0.000	0.000
32	A	173	ILE	0	0.001	-0.007	16.152	0.017	0.017	0.000	0.000	0.000
33	A	174	SER	0	-0.015	-0.010	15.900	-0.004	-0.004	0.000	0.000	0.000
34	A	175	GLN	0	0.001	0.020	16.376	-0.028	-0.028	0.000	0.000	0.000
35	A	176	SER	0	-0.030	-0.039	18.038	0.020	0.020	0.000	0.000	0.000
36	A	177	HIS	0	0.052	0.008	16.940	-0.005	-0.005	0.000	0.000	0.000
37	A	178	GLU	-1	-0.874	-0.942	19.275	0.043	0.043	0.000	0.000	0.000
38	A	179	GLU	-1	-0.810	-0.851	20.276	-0.005	-0.005	0.000	0.000	0.000
39	A	180	VAL	0	0.016	0.017	14.313	-0.014	-0.014	0.000	0.000	0.000
40	A	181	THR	0	-0.063	-0.053	17.402	-0.011	-0.011	0.000	0.000	0.000
41	A	182	SER	0	-0.058	-0.034	18.833	-0.013	-0.013	0.000	0.000	0.000
42	A	183	GLU	-1	-0.748	-0.852	18.001	-0.131	-0.131	0.000	0.000	0.000
43	A	184	VAL	0	-0.011	-0.014	14.778	-0.013	-0.013	0.000	0.000	0.000
44	A	185	ARG	1	0.926	0.965	17.822	-0.012	-0.012	0.000	0.000	0.000
45	A	186	CYS	0	0.011	0.000	21.081	-0.001	-0.001	0.000	0.000	0.000
46	A	187	PHE	0	0.066	0.037	18.706	-0.002	-0.002	0.000	0.000	0.000
47	A	188	ASN	0	-0.045	-0.044	17.047	-0.016	-0.016	0.000	0.000	0.000
48	A	189	GLN	0	-0.051	-0.021	21.086	0.003	0.003	0.000	0.000	0.000
49	A	190	TYR	0	0.036	0.020	24.365	0.009	0.009	0.000	0.000	0.000
50	A	191	TYR	0	0.002	-0.017	21.667	0.002	0.002	0.000	0.000	0.000
51	A	192	GLY	0	-0.016	0.015	23.052	-0.004	-0.004	0.000	0.000	0.000
52	A	193	SER	0	-0.023	-0.013	20.452	-0.007	-0.007	0.000	0.000	0.000
53	A	194	GLY	0	0.015	0.007	16.283	-0.003	-0.003	0.000	0.000	0.000
54	A	195	SER	0	-0.027	-0.024	15.960	-0.049	-0.049	0.000	0.000	0.000
55	A	196	ALA	0	-0.022	-0.011	14.694	-0.042	-0.042	0.000	0.000	0.000
56	A	197	GLU	-1	-0.880	-0.918	8.742	-0.441	-0.441	0.000	0.000	0.000
57	A	198	LYS	1	0.877	0.933	10.693	-0.139	-0.139	0.000	0.000	0.000
58	A	199	ILE	0	0.020	0.018	4.685	-0.049	0.000	-0.001	-0.003	-0.044
59	A	200	TYR	0	-0.008	-0.019	5.784	0.055	0.055	0.000	0.000	0.000
60	A	201	ASN	0	-0.004	0.003	4.461	0.057	0.170	-0.001	-0.010	-0.101
61	A	202	ASP	-1	-0.870	-0.944	5.381	0.578	0.578	0.000	0.000	0.000
62	A	203	ASN	0	-0.105	-0.058	6.925	-0.001	-0.001	0.000	0.000	0.000
63	A	204	GLY	0	0.046	0.043	9.040	-0.048	-0.048	0.000	0.000	0.000
64	A	205	ASN	0	-0.064	-0.039	10.064	-0.076	-0.076	0.000	0.000	0.000
65	A	206	VAL	0	0.021	0.002	9.143	0.074	0.074	0.000	0.000	0.000
66	A	207	ILE	0	-0.009	-0.008	5.156	0.007	0.007	0.000	0.000	0.000
67	A	208	GLY	0	0.033	0.006	9.547	-0.052	-0.052	0.000	0.000	0.000
68	A	209	ILE	0	-0.039	-0.001	10.242	0.047	0.047	0.000	0.000	0.000
69	A	210	ARG	1	0.845	0.931	5.483	1.857	1.857	0.000	0.000	0.000
70	A	211	MET	0	-0.039	-0.026	10.863	0.099	0.099	0.000	0.000	0.000
71	A	212	ASN	0	0.044	0.028	14.622	-0.089	-0.089	0.000	0.000	0.000
72	A	213	LYS	1	0.878	0.944	16.242	0.473	0.473	0.000	0.000	0.000
73	A	214	ILE	0	-0.033	-0.001	18.882	0.018	0.018	0.000	0.000	0.000
74	A	215	ASN	0	-0.037	-0.014	22.457	-0.014	-0.014	0.000	0.000	0.000
75	A	216	GLY	0	0.026	-0.005	25.572	0.010	0.010	0.000	0.000	0.000
76	A	217	GLU	-1	-0.950	-0.968	27.370	-0.166	-0.166	0.000	0.000	0.000
77	A	218	SER	0	-0.014	-0.032	28.452	0.010	0.010	0.000	0.000	0.000
78	A	219	LEU	0	0.016	0.000	29.988	0.005	0.005	0.000	0.000	0.000
79	A	220	LEU	0	-0.001	0.004	30.361	0.006	0.006	0.000	0.000	0.000
80	A	221	ASP	-1	-0.914	-0.927	30.980	-0.111	-0.111	0.000	0.000	0.000
81	A	222	ILE	0	-0.064	-0.024	33.194	0.002	0.002	0.000	0.000	0.000
82	A	223	PRO	0	-0.048	-0.028	36.660	0.004	0.004	0.000	0.000	0.000
83	A	224	SER	0	-0.052	-0.027	40.112	0.004	0.004	0.000	0.000	0.000
84	A	225	LEU	0	0.017	0.013	37.187	-0.005	-0.005	0.000	0.000	0.000
85	A	226	PRO	0	-0.004	0.005	40.066	0.004	0.004	0.000	0.000	0.000
86	A	227	ALA	0	0.083	0.016	42.708	0.000	0.000	0.000	0.000	0.000
87	A	228	GLN	0	-0.036	-0.023	40.496	-0.002	-0.002	0.000	0.000	0.000
88	A	229	ALA	0	0.024	0.023	38.777	-0.001	-0.001	0.000	0.000	0.000
89	A	230	GLU	-1	-0.832	-0.889	39.422	-0.043	-0.043	0.000	0.000	0.000
90	A	231	GLN	0	-0.075	-0.060	40.455	0.003	0.003	0.000	0.000	0.000
91	A	232	ALA	0	0.036	0.034	36.145	0.000	0.000	0.000	0.000	0.000
92	A	233	ILE	0	-0.008	-0.004	34.895	-0.002	-0.002	0.000	0.000	0.000
93	A	234	TYR	0	-0.088	-0.076	36.614	0.001	0.001	0.000	0.000	0.000
94	A	235	ASP	-1	-0.825	-0.897	35.868	-0.053	-0.053	0.000	0.000	0.000
95	A	236	MET	0	-0.047	-0.003	31.054	-0.002	-0.002	0.000	0.000	0.000
96	A	237	PHE	0	0.047	0.001	32.892	0.001	0.001	0.000	0.000	0.000
97	A	238	ASP	-1	-0.800	-0.881	34.935	-0.035	-0.035	0.000	0.000	0.000
98	A	239	ARG	1	0.818	0.908	27.155	0.079	0.079	0.000	0.000	0.000
99	A	240	LEU	0	-0.028	-0.020	28.384	0.002	0.002	0.000	0.000	0.000
100	A	241	GLU	-1	-0.734	-0.814	31.537	-0.032	-0.032	0.000	0.000	0.000
101	A	242	LYS	1	0.777	0.885	33.707	0.041	0.041	0.000	0.000	0.000
102	A	243	LYS	1	0.786	0.894	27.431	0.054	0.054	0.000	0.000	0.000
103	A	244	GLY	0	-0.025	-0.006	30.692	0.004	0.004	0.000	0.000	0.000
104	A	245	ILE	0	-0.078	-0.033	26.664	0.002	0.002	0.000	0.000	0.000
105	A	246	LEU	0	-0.009	-0.001	30.589	-0.002	-0.002	0.000	0.000	0.000
106	A	247	PHE	0	-0.003	-0.016	27.440	0.002	0.002	0.000	0.000	0.000
107	A	248	VAL	0	0.037	0.011	29.063	0.002	0.002	0.000	0.000	0.000
108	A	249	ASP	-1	-0.865	-0.907	27.993	-0.072	-0.072	0.000	0.000	0.000
109	A	250	THR	0	-0.018	0.001	30.028	-0.007	-0.007	0.000	0.000	0.000
110	A	251	THR	0	0.006	-0.020	30.581	-0.001	-0.001	0.000	0.000	0.000
111	A	252	GLU	-1	-0.814	-0.917	31.566	-0.078	-0.078	0.000	0.000	0.000
112	A	253	THR	0	-0.008	-0.020	27.707	-0.005	-0.005	0.000	0.000	0.000
113	A	254	ASN	0	-0.039	-0.009	25.835	-0.022	-0.022	0.000	0.000	0.000
114	A	255	VAL	0	-0.008	-0.005	27.572	-0.002	-0.002	0.000	0.000	0.000
115	A	256	LEU	0	-0.004	0.011	24.608	-0.002	-0.002	0.000	0.000	0.000
116	A	257	TYR	0	-0.025	-0.032	29.116	0.007	0.007	0.000	0.000	0.000
117	A	258	ASP	-1	-0.763	-0.868	29.701	-0.132	-0.132	0.000	0.000	0.000
118	A	259	ARG	1	0.976	0.968	31.751	0.106	0.106	0.000	0.000	0.000
119	A	260	MET	0	-0.097	-0.032	31.053	0.006	0.006	0.000	0.000	0.000
120	A	261	ARG	1	0.837	0.897	27.863	0.138	0.138	0.000	0.000	0.000
121	A	262	ASN	0	-0.022	0.012	34.107	0.004	0.004	0.000	0.000	0.000
122	A	263	GLU	-1	-0.847	-0.917	29.161	-0.107	-0.107	0.000	0.000	0.000
123	A	264	PHE	0	0.002	-0.014	31.797	-0.006	-0.006	0.000	0.000	0.000
124	A	265	ASN	0	-0.066	-0.051	26.390	0.007	0.007	0.000	0.000	0.000
125	A	266	PRO	0	0.021	0.025	26.456	-0.004	-0.004	0.000	0.000	0.000
126	A	267	ILE	0	-0.016	0.001	21.998	-0.012	-0.012	0.000	0.000	0.000
127	A	268	ASP	-1	-0.808	-0.898	21.086	-0.152	-0.152	0.000	0.000	0.000
128	A	269	ILE	0	-0.052	-0.023	22.686	0.015	0.015	0.000	0.000	0.000
129	A	270	SER	0	0.020	0.002	23.442	0.005	0.005	0.000	0.000	0.000
130	A	271	SER	0	0.015	-0.004	25.745	-0.003	-0.003	0.000	0.000	0.000
131	A	272	TYR	0	0.000	0.006	28.942	0.005	0.005	0.000	0.000	0.000
132	A	273	ASN	0	-0.055	-0.030	27.858	0.003	0.003	0.000	0.000	0.000
133	A	274	VAL	0	0.000	0.006	31.935	0.001	0.001	0.000	0.000	0.000
134	A	275	SER	0	-0.018	-0.018	33.783	0.002	0.002	0.000	0.000	0.000
135	A	276	ASP	-1	-0.888	-0.950	35.761	0.014	0.014	0.000	0.000	0.000
136	A	277	ILE	0	-0.061	-0.021	38.051	0.000	0.000	0.000	0.000	0.000
137	A	278	SER	0	-0.044	-0.027	35.349	-0.001	-0.001	0.000	0.000	0.000
138	A	279	TRP	0	-0.011	0.000	33.280	-0.004	-0.004	0.000	0.000	0.000
139	A	280	SER	0	0.040	0.001	37.253	0.001	0.001	0.000	0.000	0.000
140	A	281	GLU	-1	-0.840	-0.949	39.283	-0.010	-0.010	0.000	0.000	0.000
141	A	282	HIS	0	-0.006	0.000	40.460	-0.002	-0.002	0.000	0.000	0.000
142	A	283	GLN	0	0.036	0.047	39.717	-0.001	-0.001	0.000	0.000	0.000
143	A	284	VAL	0	0.019	0.022	35.721	-0.003	-0.003	0.000	0.000	0.000
144	A	285	MET	0	0.013	0.013	38.010	-0.004	-0.004	0.000	0.000	0.000
145	A	286	GLN	0	-0.026	-0.008	40.279	-0.001	-0.001	0.000	0.000	0.000
146	A	287	SER	0	-0.025	-0.033	37.150	-0.002	-0.002	0.000	0.000	0.000
147	A	288	TYR	0	-0.072	-0.074	34.004	-0.004	-0.004	0.000	0.000	0.000
148	A	289	HIS	0	-0.001	0.005	37.161	-0.004	-0.004	0.000	0.000	0.000
149	A	290	GLY	0	-0.005	-0.007	40.368	-0.002	-0.002	0.000	0.000	0.000
150	A	291	GLY	0	0.042	0.031	36.494	-0.002	-0.002	0.000	0.000	0.000
151	A	292	LYS	1	0.873	0.909	37.166	0.033	0.033	0.000	0.000	0.000
152	A	293	LEU	0	-0.061	-0.036	38.045	-0.002	-0.002	0.000	0.000	0.000
153	A	294	ASP	-1	-0.948	-0.961	38.482	-0.048	-0.048	0.000	0.000	0.000
154	A	295	LEU	0	0.029	0.019	33.477	-0.002	-0.002	0.000	0.000	0.000
155	A	296	ILE	0	-0.022	-0.022	37.597	-0.002	-0.002	0.000	0.000	0.000
156	A	297	SER	0	-0.019	-0.003	40.095	0.000	0.000	0.000	0.000	0.000
157	A	298	VAL	0	0.018	0.023	37.385	0.000	0.000	0.000	0.000	0.000
158	A	299	VAL	0	-0.019	-0.022	37.331	-0.002	-0.002	0.000	0.000	0.000
159	A	300	LEU	0	-0.003	-0.013	40.030	0.000	0.000	0.000	0.000	0.000
160	A	301	SER	0	-0.060	-0.028	43.152	0.002	0.002	0.000	0.000	0.000
161	A	302	LYS	1	0.801	0.911	37.315	0.074	0.074	0.000	0.000	0.000
162	A	303	ILE	0	-0.065	-0.005	41.999	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)