FMO DATABASE

FMODB ID: LJY29

Calculation Name: 3LRX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LRX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZS3

Base Structure: X-ray

Registration Date: 2023-06-19

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1186911.036774
FMO2-HF: Nuclear repulsion	1134913.896163
FMO2-HF: Total energy	-51997.140611
FMO2-MP2: Total energy	-52148.953266

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:88:GLY)

Summations of interaction energy for fragment #1(A:88:GLY)

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.
-1.039	0.213	-0.007	-0.635	-0.61	0.002

Interaction energy analysis for fragmet #1(A:88:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.014

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	90	LEU	0	-0.006	-0.003	3.859	-0.205	1.047	-0.007	-0.635	-0.610	0.002
4	A	91	GLY	0	0.015	0.015	6.356	0.533	0.533	0.000	0.000	0.000	0.000
5	A	92	THR	0	-0.031	-0.036	9.995	-0.113	-0.113	0.000	0.000	0.000	0.000
6	A	93	PRO	0	-0.051	-0.004	10.884	0.117	0.117	0.000	0.000	0.000	0.000
7	A	94	VAL	0	-0.014	-0.027	12.865	0.109	0.109	0.000	0.000	0.000	0.000
8	A	95	PRO	0	0.017	0.025	16.510	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	96	MET	0	-0.016	-0.016	17.889	0.028	0.028	0.000	0.000	0.000	0.000
10	A	97	GLU	-1	-0.923	-0.952	20.942	-0.291	-0.291	0.000	0.000	0.000	0.000
11	A	98	LYS	1	0.907	0.956	24.541	0.197	0.197	0.000	0.000	0.000	0.000
12	A	99	PHE	0	-0.010	-0.014	22.871	0.009	0.009	0.000	0.000	0.000	0.000
13	A	100	GLY	0	0.033	0.028	28.308	0.016	0.016	0.000	0.000	0.000	0.000
14	A	101	LYS	1	0.870	0.939	29.807	0.160	0.160	0.000	0.000	0.000	0.000
15	A	102	ILE	0	-0.029	-0.016	24.632	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	103	LEU	0	0.004	0.020	27.829	0.004	0.004	0.000	0.000	0.000	0.000
17	A	104	ALA	0	-0.029	-0.017	22.672	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	105	ILE	0	0.027	0.002	23.983	0.019	0.019	0.000	0.000	0.000	0.000
19	A	106	GLY	0	0.039	0.003	21.542	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	107	ALA	0	-0.020	-0.003	21.908	0.034	0.034	0.000	0.000	0.000	0.000
21	A	108	TYR	0	-0.019	-0.027	21.263	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	109	THR	0	0.038	0.002	17.409	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	110	GLY	0	0.021	0.030	17.234	-0.040	-0.040	0.000	0.000	0.000	0.000
24	A	111	ILE	0	-0.004	-0.003	18.020	-0.051	-0.051	0.000	0.000	0.000	0.000
25	A	112	VAL	0	-0.037	-0.021	15.184	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	113	GLU	-1	-0.826	-0.895	12.963	-1.120	-1.120	0.000	0.000	0.000	0.000
27	A	114	VAL	0	0.028	0.011	15.266	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	115	TYR	0	0.036	0.033	18.239	0.022	0.022	0.000	0.000	0.000	0.000
29	A	116	PRO	0	-0.028	-0.013	14.481	0.037	0.037	0.000	0.000	0.000	0.000
30	A	117	ILE	0	0.019	0.019	14.662	0.024	0.024	0.000	0.000	0.000	0.000
31	A	118	ALA	0	0.038	0.011	17.905	0.040	0.040	0.000	0.000	0.000	0.000
32	A	119	LYS	1	0.909	0.953	19.771	0.335	0.335	0.000	0.000	0.000	0.000
33	A	120	ALA	0	-0.014	-0.002	18.570	0.031	0.031	0.000	0.000	0.000	0.000
34	A	121	TRP	0	0.031	-0.017	20.674	0.023	0.023	0.000	0.000	0.000	0.000
35	A	122	GLN	0	0.061	0.041	22.948	0.018	0.018	0.000	0.000	0.000	0.000
36	A	123	GLU	-1	-0.994	-0.988	23.179	-0.206	-0.206	0.000	0.000	0.000	0.000
37	A	124	ILE	0	-0.073	-0.034	21.930	0.016	0.016	0.000	0.000	0.000	0.000
38	A	125	GLY	0	-0.054	-0.039	25.392	0.016	0.016	0.000	0.000	0.000	0.000
39	A	126	ASN	0	-0.072	-0.029	25.116	0.020	0.020	0.000	0.000	0.000	0.000
40	A	127	ASP	-1	-0.874	-0.939	28.237	-0.179	-0.179	0.000	0.000	0.000	0.000
41	A	128	VAL	0	-0.004	-0.013	24.526	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	129	THR	0	-0.026	-0.014	27.934	0.018	0.018	0.000	0.000	0.000	0.000
43	A	130	THR	0	0.030	0.009	23.741	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	131	LEU	0	0.010	0.014	26.162	0.022	0.022	0.000	0.000	0.000	0.000
45	A	132	HIS	0	-0.005	-0.001	23.578	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	133	VAL	0	0.016	0.013	25.972	0.021	0.021	0.000	0.000	0.000	0.000
47	A	134	THR	0	0.010	0.000	25.015	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	135	PHE	0	0.028	0.011	26.956	0.011	0.011	0.000	0.000	0.000	0.000
49	A	136	GLU	-1	-0.869	-0.956	28.826	-0.104	-0.104	0.000	0.000	0.000	0.000
50	A	137	PRO	0	-0.053	-0.021	29.455	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	138	MET	0	-0.085	-0.049	23.983	0.004	0.004	0.000	0.000	0.000	0.000
52	A	139	VAL	0	0.008	0.030	24.976	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	140	ILE	0	-0.019	-0.027	21.389	0.010	0.010	0.000	0.000	0.000	0.000
54	A	141	LEU	0	-0.018	-0.021	19.304	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	142	LYS	1	0.820	0.893	23.892	0.134	0.134	0.000	0.000	0.000	0.000
56	A	143	GLU	-1	-0.804	-0.904	27.322	-0.136	-0.136	0.000	0.000	0.000	0.000
57	A	144	GLU	-1	-0.946	-0.972	22.405	-0.193	-0.193	0.000	0.000	0.000	0.000
58	A	145	LEU	0	-0.040	-0.032	22.834	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	146	GLU	-1	-0.834	-0.895	24.988	-0.153	-0.153	0.000	0.000	0.000	0.000
60	A	147	LYS	1	0.903	0.962	27.641	0.159	0.159	0.000	0.000	0.000	0.000
61	A	148	ALA	0	-0.091	-0.036	23.878	0.000	0.000	0.000	0.000	0.000	0.000
62	A	149	VAL	0	-0.019	-0.013	24.986	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	150	THR	0	-0.040	0.012	27.612	0.018	0.018	0.000	0.000	0.000	0.000
64	A	151	ARG	1	0.824	0.868	30.420	0.181	0.181	0.000	0.000	0.000	0.000
65	A	152	HIS	0	-0.013	-0.012	26.406	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	153	ILE	0	0.014	0.008	29.672	0.015	0.015	0.000	0.000	0.000	0.000
67	A	154	VAL	0	0.010	0.001	28.627	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	155	GLU	-1	-0.825	-0.904	30.088	-0.129	-0.129	0.000	0.000	0.000	0.000
69	A	156	PRO	0	-0.038	-0.009	30.844	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	157	VAL	0	-0.012	-0.017	31.134	0.010	0.010	0.000	0.000	0.000	0.000
71	A	158	PRO	0	0.053	0.033	32.394	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	159	LEU	0	-0.036	-0.014	29.953	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	160	ASN	0	0.049	0.005	32.941	0.011	0.011	0.000	0.000	0.000	0.000
74	A	161	PRO	0	-0.020	-0.011	33.274	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	162	ASN	0	-0.064	-0.034	34.441	0.009	0.009	0.000	0.000	0.000	0.000
76	A	163	GLN	0	-0.007	0.013	35.761	0.002	0.002	0.000	0.000	0.000	0.000
77	A	164	ASP	-1	-0.815	-0.914	33.024	-0.087	-0.087	0.000	0.000	0.000	0.000
78	A	165	PHE	0	0.039	0.000	25.234	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	166	LEU	0	-0.003	0.004	30.557	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	167	ALA	0	-0.035	-0.010	31.609	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	168	ASN	0	0.014	0.001	31.263	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	169	MET	0	-0.005	-0.005	24.892	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	170	LYS	1	0.947	0.990	29.807	0.121	0.121	0.000	0.000	0.000	0.000
84	A	171	ASN	0	-0.014	-0.012	32.728	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	172	VAL	0	0.049	0.039	27.052	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	173	SER	0	-0.042	-0.037	29.014	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	174	GLN	0	-0.130	-0.080	30.617	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	175	ARG	1	0.909	0.961	32.236	0.129	0.129	0.000	0.000	0.000	0.000
89	A	176	LEU	0	0.007	-0.001	26.499	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	177	LYS	1	0.892	0.946	30.874	0.152	0.152	0.000	0.000	0.000	0.000
91	A	178	GLU	-1	-0.868	-0.931	33.174	-0.122	-0.122	0.000	0.000	0.000	0.000
92	A	179	LYS	1	0.840	0.899	32.568	0.144	0.144	0.000	0.000	0.000	0.000
93	A	180	VAL	0	-0.008	-0.002	29.538	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	181	ARG	1	0.803	0.890	32.714	0.136	0.136	0.000	0.000	0.000	0.000
95	A	182	GLU	-1	-0.844	-0.919	36.072	-0.130	-0.130	0.000	0.000	0.000	0.000
96	A	183	LEU	0	-0.027	-0.027	32.005	0.004	0.004	0.000	0.000	0.000	0.000
97	A	184	LEU	0	-0.072	-0.034	31.886	0.000	0.000	0.000	0.000	0.000	0.000
98	A	185	GLU	-1	-0.903	-0.914	35.937	-0.116	-0.116	0.000	0.000	0.000	0.000
99	A	186	SER	0	-0.074	-0.022	39.111	0.008	0.008	0.000	0.000	0.000	0.000
100	A	187	GLU	-1	-0.852	-0.894	35.642	-0.153	-0.153	0.000	0.000	0.000	0.000
101	A	188	ASP	-1	-0.912	-0.944	37.178	-0.154	-0.154	0.000	0.000	0.000	0.000
102	A	189	TRP	0	-0.014	-0.045	30.908	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	190	ASP	-1	-0.819	-0.881	30.823	-0.190	-0.190	0.000	0.000	0.000	0.000
104	A	191	LEU	0	-0.076	-0.046	23.977	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	192	VAL	0	0.026	0.018	26.393	0.003	0.003	0.000	0.000	0.000	0.000
106	A	193	PHE	0	-0.024	-0.010	16.922	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	194	MET	0	-0.038	0.002	21.643	0.034	0.034	0.000	0.000	0.000	0.000
108	A	195	VAL	0	0.070	0.044	15.874	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	196	GLY	0	0.033	0.009	19.040	0.036	0.036	0.000	0.000	0.000	0.000
110	A	197	PRO	0	-0.011	-0.002	19.537	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	198	VAL	0	0.073	0.026	20.110	0.016	0.016	0.000	0.000	0.000	0.000
112	A	199	GLY	0	-0.025	-0.015	21.745	0.015	0.015	0.000	0.000	0.000	0.000
113	A	200	ASP	-1	-0.768	-0.898	24.545	-0.201	-0.201	0.000	0.000	0.000	0.000
114	A	201	GLN	0	-0.033	-0.037	18.810	0.015	0.015	0.000	0.000	0.000	0.000
115	A	202	LYS	1	0.919	0.968	24.347	0.231	0.231	0.000	0.000	0.000	0.000
116	A	203	GLN	0	-0.071	-0.042	26.935	0.025	0.025	0.000	0.000	0.000	0.000
117	A	204	VAL	0	0.077	0.035	27.017	0.010	0.010	0.000	0.000	0.000	0.000
118	A	205	PHE	0	0.025	0.021	26.370	0.010	0.010	0.000	0.000	0.000	0.000
119	A	206	GLU	-1	-0.859	-0.923	28.484	-0.173	-0.173	0.000	0.000	0.000	0.000
120	A	207	VAL	0	-0.041	-0.013	31.669	0.012	0.012	0.000	0.000	0.000	0.000
121	A	208	VAL	0	0.068	0.020	28.806	0.007	0.007	0.000	0.000	0.000	0.000
122	A	209	LYS	1	0.750	0.863	31.306	0.187	0.187	0.000	0.000	0.000	0.000
123	A	210	GLU	-1	-0.897	-0.930	32.803	-0.124	-0.124	0.000	0.000	0.000	0.000
124	A	211	TYR	0	-0.064	-0.063	35.052	0.008	0.008	0.000	0.000	0.000	0.000
125	A	212	GLY	0	-0.038	-0.012	35.113	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	213	VAL	0	0.016	0.029	30.476	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	214	PRO	0	-0.035	-0.009	27.800	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	215	MET	0	0.019	0.009	24.298	0.005	0.005	0.000	0.000	0.000	0.000
129	A	216	LYS	1	0.836	0.940	16.191	0.701	0.701	0.000	0.000	0.000	0.000
130	A	217	VAL	0	0.007	-0.001	18.799	0.017	0.017	0.000	0.000	0.000	0.000
131	A	218	ASP	-1	-0.787	-0.904	14.502	-0.684	-0.684	0.000	0.000	0.000	0.000
132	A	219	LEU	0	-0.054	-0.023	10.740	0.014	0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:88:GLY)