FMO DATABASE

FMODB ID: VRJV1

Calculation Name: 1L3A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L3A

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LL85

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1535827.110168
FMO2-HF: Nuclear repulsion	1471637.80216
FMO2-HF: Total energy	-64189.308008
FMO2-MP2: Total energy	-64378.513777

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:89:THR)

Summations of interaction energy for fragment #1(A:89:THR)

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.
-0.605	2.027	0.012	-1.551	-1.093	0.004

Interaction energy analysis for fragmet #1(A:89:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.026

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	91	LYS	1	0.898	0.955	3.425	-1.891	0.741	0.012	-1.551	-1.093	0.004
4	A	92	VAL	0	0.039	0.009	5.103	0.809	0.809	0.000	0.000	0.000	0.000
5	A	93	PHE	0	-0.023	-0.018	7.686	0.054	0.054	0.000	0.000	0.000	0.000
6	A	94	VAL	0	0.037	0.029	10.027	0.113	0.113	0.000	0.000	0.000	0.000
7	A	95	GLY	0	0.061	0.002	12.710	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	96	TYR	0	-0.047	0.002	16.235	0.018	0.018	0.000	0.000	0.000	0.000
9	A	97	SER	0	0.015	-0.017	19.075	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	98	ILE	0	-0.027	0.007	22.253	0.019	0.019	0.000	0.000	0.000	0.000
11	A	99	TYR	0	0.026	0.004	22.602	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	100	LYS	1	0.819	0.894	28.474	0.117	0.117	0.000	0.000	0.000	0.000
13	A	101	GLY	0	-0.031	-0.010	32.157	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	102	LYS	1	0.982	0.987	35.477	0.092	0.092	0.000	0.000	0.000	0.000
15	A	103	ALA	0	0.033	0.020	31.109	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	104	ALA	0	-0.014	0.005	26.719	0.008	0.008	0.000	0.000	0.000	0.000
17	A	105	LEU	0	-0.016	-0.013	24.565	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	106	THR	0	0.009	0.015	19.162	0.018	0.018	0.000	0.000	0.000	0.000
19	A	107	VAL	0	0.002	0.008	19.097	0.002	0.002	0.000	0.000	0.000	0.000
20	A	108	GLU	-1	-0.851	-0.911	14.852	-0.559	-0.559	0.000	0.000	0.000	0.000
21	A	109	PRO	0	-0.005	0.012	11.956	0.035	0.035	0.000	0.000	0.000	0.000
22	A	110	ARG	1	0.878	0.919	13.066	0.264	0.264	0.000	0.000	0.000	0.000
23	A	111	SER	0	0.008	-0.007	10.002	0.082	0.082	0.000	0.000	0.000	0.000
24	A	112	PRO	0	0.025	0.023	11.749	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	113	GLU	-1	-0.847	-0.885	13.120	-0.319	-0.319	0.000	0.000	0.000	0.000
26	A	114	PHE	0	0.051	0.011	12.056	0.080	0.080	0.000	0.000	0.000	0.000
27	A	115	SER	0	0.008	0.002	15.989	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	116	PRO	0	0.011	0.002	17.744	0.039	0.039	0.000	0.000	0.000	0.000
29	A	117	LEU	0	-0.032	-0.028	18.886	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	118	ASP	-1	-0.867	-0.925	21.638	0.056	0.056	0.000	0.000	0.000	0.000
31	A	119	SER	0	-0.023	-0.025	21.572	0.001	0.001	0.000	0.000	0.000	0.000
32	A	120	GLY	0	-0.012	0.005	18.170	0.022	0.022	0.000	0.000	0.000	0.000
33	A	121	ALA	0	0.003	0.022	17.795	0.048	0.048	0.000	0.000	0.000	0.000
34	A	122	PHE	0	-0.007	-0.018	14.655	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	123	LYS	1	0.924	0.970	17.907	0.057	0.057	0.000	0.000	0.000	0.000
36	A	124	LEU	0	-0.024	-0.001	15.940	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	125	SER	0	-0.063	-0.063	18.312	0.012	0.012	0.000	0.000	0.000	0.000
38	A	126	ARG	1	0.815	0.891	18.473	0.221	0.221	0.000	0.000	0.000	0.000
39	A	127	GLU	-1	-0.872	-0.918	17.432	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	128	GLY	0	-0.012	-0.008	15.497	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	129	MET	0	-0.050	-0.025	16.295	0.017	0.017	0.000	0.000	0.000	0.000
42	A	130	VAL	0	0.020	0.021	16.633	-0.042	-0.042	0.000	0.000	0.000	0.000
43	A	131	MET	0	-0.075	-0.025	17.519	0.016	0.016	0.000	0.000	0.000	0.000
44	A	132	LEU	0	0.026	0.021	19.735	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	133	GLN	0	-0.013	-0.018	18.973	0.019	0.019	0.000	0.000	0.000	0.000
46	A	134	PHE	0	0.049	0.018	23.774	0.006	0.006	0.000	0.000	0.000	0.000
47	A	135	ALA	0	0.014	0.008	27.118	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	136	PRO	0	0.072	0.035	28.934	0.010	0.010	0.000	0.000	0.000	0.000
49	A	137	ALA	0	-0.023	-0.027	32.066	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	138	ALA	0	-0.030	-0.006	33.362	0.007	0.007	0.000	0.000	0.000	0.000
51	A	139	GLY	0	0.064	0.026	35.245	0.010	0.010	0.000	0.000	0.000	0.000
52	A	140	VAL	0	-0.042	-0.036	34.615	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	141	ARG	1	0.928	0.960	33.348	0.100	0.100	0.000	0.000	0.000	0.000
54	A	142	GLN	0	0.051	0.060	30.069	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	143	TYR	0	-0.025	-0.050	28.270	0.006	0.006	0.000	0.000	0.000	0.000
56	A	144	ASP	-1	-0.743	-0.854	29.175	-0.220	-0.220	0.000	0.000	0.000	0.000
57	A	145	TRP	0	-0.044	-0.037	24.166	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	146	SER	0	-0.009	0.001	26.702	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	147	ARG	1	0.839	0.907	29.146	0.177	0.177	0.000	0.000	0.000	0.000
60	A	148	LYS	1	0.884	0.961	21.862	0.391	0.391	0.000	0.000	0.000	0.000
61	A	149	GLN	0	0.039	0.014	27.896	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	150	VAL	0	0.002	-0.003	22.627	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	151	PHE	0	0.010	-0.007	24.402	0.012	0.012	0.000	0.000	0.000	0.000
64	A	152	SER	0	0.001	-0.010	21.741	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	153	LEU	0	-0.011	0.003	21.964	0.020	0.020	0.000	0.000	0.000	0.000
66	A	154	SER	0	-0.011	-0.038	21.515	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	155	VAL	0	0.107	0.032	20.234	0.004	0.004	0.000	0.000	0.000	0.000
68	A	156	THR	0	0.028	0.008	22.686	0.015	0.015	0.000	0.000	0.000	0.000
69	A	157	GLU	-1	-0.792	-0.863	25.759	-0.105	-0.105	0.000	0.000	0.000	0.000
70	A	158	ILE	0	-0.006	-0.004	20.230	0.001	0.001	0.000	0.000	0.000	0.000
71	A	159	GLY	0	0.032	0.013	24.590	0.009	0.009	0.000	0.000	0.000	0.000
72	A	160	SER	0	-0.025	-0.003	26.876	0.006	0.006	0.000	0.000	0.000	0.000
73	A	161	ILE	0	-0.032	-0.012	26.251	0.000	0.000	0.000	0.000	0.000	0.000
74	A	162	ILE	0	-0.058	-0.035	24.039	0.002	0.002	0.000	0.000	0.000	0.000
75	A	163	SER	0	-0.065	-0.027	27.461	0.008	0.008	0.000	0.000	0.000	0.000
76	A	164	LEU	0	-0.010	0.015	30.817	0.000	0.000	0.000	0.000	0.000	0.000
77	A	165	GLY	0	0.055	0.031	32.866	0.003	0.003	0.000	0.000	0.000	0.000
78	A	166	THR	0	-0.085	-0.074	35.543	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	167	LYS	1	0.946	0.953	37.275	0.014	0.014	0.000	0.000	0.000	0.000
80	A	168	ASP	-1	-0.870	-0.895	36.307	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	169	SER	0	0.064	0.011	36.130	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	170	CYS	0	-0.068	-0.014	32.262	0.002	0.002	0.000	0.000	0.000	0.000
83	A	171	GLU	-1	-0.825	-0.914	34.123	-0.072	-0.072	0.000	0.000	0.000	0.000
84	A	172	PHE	0	-0.010	-0.002	29.710	0.002	0.002	0.000	0.000	0.000	0.000
85	A	173	PHE	0	0.025	0.010	32.252	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	174	HIS	1	0.762	0.857	26.851	0.129	0.129	0.000	0.000	0.000	0.000
87	A	175	ASP	-1	-0.791	-0.912	31.497	-0.114	-0.114	0.000	0.000	0.000	0.000
88	A	176	PRO	0	-0.059	-0.028	30.537	0.001	0.001	0.000	0.000	0.000	0.000
89	A	177	ASN	0	-0.100	-0.045	31.995	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	178	LYS	1	0.976	0.982	31.584	0.101	0.101	0.000	0.000	0.000	0.000
91	A	179	GLY	0	0.111	0.064	35.428	0.006	0.006	0.000	0.000	0.000	0.000
92	A	180	ARG	1	0.830	0.924	35.362	0.082	0.082	0.000	0.000	0.000	0.000
93	A	181	SER	0	-0.015	-0.012	35.821	0.003	0.003	0.000	0.000	0.000	0.000
94	A	182	ASP	-1	-0.798	-0.907	38.618	-0.097	-0.097	0.000	0.000	0.000	0.000
95	A	183	GLU	-1	-0.921	-0.959	39.613	-0.070	-0.070	0.000	0.000	0.000	0.000
96	A	184	GLY	0	-0.028	0.001	38.263	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	185	ARG	1	0.951	0.963	39.135	0.093	0.093	0.000	0.000	0.000	0.000
98	A	186	VAL	0	-0.058	-0.038	33.540	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	187	ARG	1	0.945	0.977	34.448	0.088	0.088	0.000	0.000	0.000	0.000
100	A	188	LYS	1	0.847	0.918	27.867	0.195	0.195	0.000	0.000	0.000	0.000
101	A	189	VAL	0	-0.004	-0.002	32.722	0.004	0.004	0.000	0.000	0.000	0.000
102	A	190	LEU	0	-0.008	0.019	27.735	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	191	LYS	1	0.789	0.887	31.840	0.071	0.071	0.000	0.000	0.000	0.000
104	A	192	VAL	0	0.003	-0.002	30.116	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	193	GLU	-1	-0.816	-0.914	33.528	-0.050	-0.050	0.000	0.000	0.000	0.000
106	A	194	PRO	0	0.005	0.016	36.416	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	195	LEU	0	-0.045	-0.025	35.536	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	196	PRO	0	0.013	-0.003	39.197	0.004	0.004	0.000	0.000	0.000	0.000
109	A	197	ASP	-1	-0.870	-0.905	40.465	-0.043	-0.043	0.000	0.000	0.000	0.000
110	A	198	GLY	0	-0.030	-0.007	40.215	0.003	0.003	0.000	0.000	0.000	0.000
111	A	199	SER	0	-0.076	-0.064	37.458	0.003	0.003	0.000	0.000	0.000	0.000
112	A	200	GLY	0	-0.027	-0.037	34.470	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	201	HIS	0	0.000	0.024	32.680	0.001	0.001	0.000	0.000	0.000	0.000
114	A	202	PHE	0	-0.030	-0.009	33.550	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	203	PHE	0	0.012	-0.007	27.193	0.001	0.001	0.000	0.000	0.000	0.000
116	A	204	ASN	0	0.001	-0.016	31.845	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	205	LEU	0	-0.021	0.001	28.569	0.001	0.001	0.000	0.000	0.000	0.000
118	A	206	SER	0	0.002	0.002	32.513	0.001	0.001	0.000	0.000	0.000	0.000
119	A	207	VAL	0	-0.049	-0.028	31.284	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	208	GLN	0	0.033	0.026	34.392	0.007	0.007	0.000	0.000	0.000	0.000
121	A	209	ASN	0	0.006	0.001	35.090	0.001	0.001	0.000	0.000	0.000	0.000
122	A	210	LYS	1	0.957	0.982	37.810	0.098	0.098	0.000	0.000	0.000	0.000
123	A	211	LEU	0	-0.002	0.000	36.515	0.003	0.003	0.000	0.000	0.000	0.000
124	A	212	ILE	0	-0.007	0.004	36.451	0.000	0.000	0.000	0.000	0.000	0.000
125	A	213	ASN	0	-0.063	-0.028	39.728	0.003	0.003	0.000	0.000	0.000	0.000
126	A	214	LEU	0	-0.012	0.009	34.234	0.000	0.000	0.000	0.000	0.000	0.000
127	A	215	ASP	-1	-0.883	-0.968	38.765	-0.097	-0.097	0.000	0.000	0.000	0.000
128	A	216	GLU	-1	-0.878	-0.925	34.951	-0.136	-0.136	0.000	0.000	0.000	0.000
129	A	217	ASN	0	-0.018	-0.023	35.820	0.004	0.004	0.000	0.000	0.000	0.000
130	A	218	ILE	0	-0.018	0.014	31.374	0.001	0.001	0.000	0.000	0.000	0.000
131	A	219	TYR	0	0.007	0.008	33.368	0.000	0.000	0.000	0.000	0.000	0.000
132	A	220	ILE	0	-0.032	-0.025	28.915	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	221	PRO	0	-0.006	0.021	32.674	0.003	0.003	0.000	0.000	0.000	0.000
134	A	222	VAL	0	-0.038	-0.029	28.518	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	223	THR	0	0.037	-0.016	30.697	0.011	0.011	0.000	0.000	0.000	0.000
136	A	224	LYS	1	1.038	0.999	30.841	0.007	0.007	0.000	0.000	0.000	0.000
137	A	225	ALA	0	-0.013	-0.004	29.497	0.005	0.005	0.000	0.000	0.000	0.000
138	A	226	GLU	-1	-0.748	-0.834	26.562	-0.094	-0.094	0.000	0.000	0.000	0.000
139	A	227	PHE	0	0.015	0.013	26.015	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	228	ALA	0	0.015	0.009	26.462	0.003	0.003	0.000	0.000	0.000	0.000
141	A	229	VAL	0	-0.005	0.007	21.418	0.012	0.012	0.000	0.000	0.000	0.000
142	A	230	LEU	0	0.013	0.009	21.767	0.000	0.000	0.000	0.000	0.000	0.000
143	A	231	VAL	0	0.037	0.025	22.166	0.007	0.007	0.000	0.000	0.000	0.000
144	A	232	SER	0	-0.004	0.008	21.234	0.020	0.020	0.000	0.000	0.000	0.000
145	A	233	ALA	0	0.009	-0.002	18.106	0.021	0.021	0.000	0.000	0.000	0.000
146	A	234	PHE	0	-0.027	-0.037	17.843	0.002	0.002	0.000	0.000	0.000	0.000
147	A	235	ASN	0	-0.009	-0.023	19.806	0.019	0.019	0.000	0.000	0.000	0.000
148	A	236	PHE	0	-0.015	0.010	11.338	0.023	0.023	0.000	0.000	0.000	0.000
149	A	237	VAL	0	0.001	-0.018	13.673	0.038	0.038	0.000	0.000	0.000	0.000
150	A	238	MET	0	0.014	0.017	15.838	0.007	0.007	0.000	0.000	0.000	0.000
151	A	239	PRO	0	0.040	0.026	16.128	-0.009	-0.009	0.000	0.000	0.000	0.000
152	A	240	TYR	0	-0.015	-0.012	10.002	0.078	0.078	0.000	0.000	0.000	0.000
153	A	241	LEU	0	-0.105	-0.038	13.864	-0.035	-0.035	0.000	0.000	0.000	0.000
154	A	242	LEU	0	0.051	0.019	15.804	-0.031	-0.031	0.000	0.000	0.000	0.000
155	A	243	GLY	0	0.004	0.004	14.197	0.000	0.000	0.000	0.000	0.000	0.000
156	A	244	TRP	0	0.017	0.005	15.274	0.060	0.060	0.000	0.000	0.000	0.000
157	A	245	HIS	0	0.039	0.030	9.657	-0.046	-0.046	0.000	0.000	0.000	0.000
158	A	246	THR	0	-0.064	-0.042	11.086	0.083	0.083	0.000	0.000	0.000	0.000
159	A	247	ALA	0	0.032	0.024	13.393	0.021	0.021	0.000	0.000	0.000	0.000
160	A	248	VAL	0	0.031	0.017	15.053	0.015	0.015	0.000	0.000	0.000	0.000
161	A	249	ASN	0	-0.040	-0.007	10.250	-0.005	-0.005	0.000	0.000	0.000	0.000
162	A	250	SER	0	-0.057	-0.040	14.325	0.033	0.033	0.000	0.000	0.000	0.000
163	A	251	PHE	0	-0.040	-0.012	17.098	-0.049	-0.049	0.000	0.000	0.000	0.000
164	A	252	LYS	1	0.900	0.946	14.052	-0.782	-0.782	0.000	0.000	0.000	0.000
165	A	253	PRO	0	-0.008	-0.001	19.997	-0.016	-0.016	0.000	0.000	0.000	0.000
166	A	254	GLU	-1	-0.922	-0.949	20.967	0.433	0.433	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:89:THR)