FMO DATABASE

FMODB ID: JL959

Calculation Name: 3LF4-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n-[(2z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoyl]glycine

ligand 3-letter code: 0YG

PDB ID: 3LF4

Chain ID: B

ChEMBL ID:

UniProt ID: D1MPT3

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1578340.293407
FMO2-HF: Nuclear repulsion	1513912.681448
FMO2-HF: Total energy	-64427.611959
FMO2-MP2: Total energy	-64615.667337

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(B:67:0YG)

Summations of interaction energy for fragment #1(B:67:0YG)

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.
-689.024	-976.542	1367.741	-1044.951	-35.274	-1.085

Interaction energy analysis for fragmet #1(B:67:0YG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : -0.085 / q_NPA : -0.093

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].
2	B	69	SER	-1	0.096	0.070	1.520	-528.810	-839.694	1327.219	-1019.274	2.939	-0.952
3	B	70	ARG	1	0.767	0.855	2.106	18.121	21.812	5.444	-4.081	-5.055	0.054
4	B	71	ALA	0	0.027	0.022	5.684	-0.961	-0.961	0.000	0.000	0.000	0.000
5	B	72	TYR	0	-0.034	-0.011	7.385	1.355	1.355	0.000	0.000	0.000	0.000
6	B	73	VAL	0	-0.003	0.008	6.798	-3.110	-3.110	0.000	0.000	0.000	0.000
7	B	74	LYS	1	0.864	0.923	9.392	21.758	21.758	0.000	0.000	0.000	0.000
8	B	75	HIS	0	0.041	0.016	10.441	-1.982	-1.982	0.000	0.000	0.000	0.000
9	B	76	PRO	0	-0.005	0.004	14.585	0.735	0.735	0.000	0.000	0.000	0.000
10	B	77	ALA	0	0.010	-0.001	17.869	-0.064	-0.064	0.000	0.000	0.000	0.000
11	B	78	ASP	-1	-0.864	-0.914	20.866	-13.862	-13.862	0.000	0.000	0.000	0.000
12	B	79	ILE	0	-0.042	-0.016	15.340	-0.059	-0.059	0.000	0.000	0.000	0.000
13	B	80	PRO	0	-0.001	0.000	16.988	-0.435	-0.435	0.000	0.000	0.000	0.000
14	B	81	ASP	-1	-0.746	-0.846	12.179	-20.625	-20.625	0.000	0.000	0.000	0.000
15	B	82	TYR	0	0.036	-0.002	11.072	0.566	0.566	0.000	0.000	0.000	0.000
16	B	83	TRP	0	0.056	0.010	7.121	-0.064	-0.064	0.000	0.000	0.000	0.000
17	B	84	LYS	1	0.807	0.897	10.964	21.196	21.196	0.000	0.000	0.000	0.000
18	B	85	LEU	0	-0.004	-0.002	13.581	0.850	0.850	0.000	0.000	0.000	0.000
19	B	86	SER	0	-0.066	-0.040	12.438	0.720	0.720	0.000	0.000	0.000	0.000
20	B	87	PHE	0	-0.010	0.037	10.080	0.360	0.360	0.000	0.000	0.000	0.000
21	B	88	PRO	0	0.022	0.004	15.710	0.220	0.220	0.000	0.000	0.000	0.000
22	B	89	GLU	-1	-0.798	-0.894	16.357	-11.847	-11.847	0.000	0.000	0.000	0.000
23	B	90	GLY	0	0.015	-0.008	12.827	-0.188	-0.188	0.000	0.000	0.000	0.000
24	B	91	PHE	0	-0.038	-0.033	5.866	-0.009	-0.009	0.000	0.000	0.000	0.000
25	B	92	LYS	1	0.936	0.976	9.406	13.646	13.646	0.000	0.000	0.000	0.000
26	B	93	TRP	0	0.019	0.006	2.538	-5.515	-2.641	0.861	-0.747	-2.989	-0.022
27	B	94	GLU	-1	-0.919	-0.952	8.187	-16.451	-16.451	0.000	0.000	0.000	0.000
28	B	95	ARG	1	0.842	0.896	1.851	27.909	27.234	12.067	-4.229	-7.163	0.024
29	B	96	VAL	0	0.001	0.005	7.270	1.260	1.260	0.000	0.000	0.000	0.000
30	B	97	MET	0	-0.063	-0.034	3.032	-3.435	-2.542	0.168	-0.268	-0.792	0.003
31	B	98	ASN	0	0.029	0.018	7.457	2.090	2.090	0.000	0.000	0.000	0.000
32	B	99	PHE	0	0.033	-0.004	6.247	-2.567	-2.567	0.000	0.000	0.000	0.000
33	B	100	GLU	-1	-0.839	-0.912	10.275	-18.429	-18.429	0.000	0.000	0.000	0.000
34	B	101	ASP	-1	-0.827	-0.903	13.068	-18.099	-18.099	0.000	0.000	0.000	0.000
35	B	102	GLY	0	0.013	0.015	14.478	0.962	0.962	0.000	0.000	0.000	0.000
36	B	103	GLY	0	-0.003	0.018	12.999	0.425	0.425	0.000	0.000	0.000	0.000
37	B	104	VAL	0	-0.001	-0.002	11.384	-1.113	-1.113	0.000	0.000	0.000	0.000
38	B	105	VAL	0	0.005	-0.007	8.378	0.538	0.538	0.000	0.000	0.000	0.000
39	B	106	THR	0	-0.023	0.012	9.157	-0.361	-0.361	0.000	0.000	0.000	0.000
40	B	107	VAL	0	-0.007	-0.014	6.380	0.390	0.390	0.000	0.000	0.000	0.000
41	B	108	THR	0	-0.013	-0.002	8.984	0.649	0.649	0.000	0.000	0.000	0.000
42	B	109	GLN	0	0.031	0.025	4.971	-0.053	-0.053	0.000	0.000	0.000	0.000
43	B	110	ASP	-1	-0.822	-0.902	7.867	-13.608	-13.608	0.000	0.000	0.000	0.000
44	B	111	SER	0	0.028	-0.006	7.037	-0.071	-0.071	0.000	0.000	0.000	0.000
45	B	112	SER	0	-0.023	-0.013	9.494	0.147	0.147	0.000	0.000	0.000	0.000
46	B	113	LEU	0	0.015	0.010	12.556	-0.499	-0.499	0.000	0.000	0.000	0.000
47	B	114	GLN	0	-0.047	-0.033	15.095	0.250	0.250	0.000	0.000	0.000	0.000
48	B	115	ASP	-1	-0.887	-0.939	17.721	-11.156	-11.156	0.000	0.000	0.000	0.000
49	B	116	GLY	0	-0.036	-0.014	18.979	-0.075	-0.075	0.000	0.000	0.000	0.000
50	B	117	GLU	-1	-0.905	-0.932	14.653	-14.763	-14.763	0.000	0.000	0.000	0.000
51	B	118	PHE	0	-0.051	-0.038	10.205	0.263	0.263	0.000	0.000	0.000	0.000
52	B	119	ILE	0	-0.008	-0.001	11.725	-0.271	-0.271	0.000	0.000	0.000	0.000
53	B	120	TYR	0	-0.005	-0.022	6.363	1.288	1.288	0.000	0.000	0.000	0.000
54	B	121	LYS	1	0.912	0.963	8.820	14.120	14.120	0.000	0.000	0.000	0.000
55	B	122	VAL	0	0.031	0.005	5.777	0.046	0.046	0.000	0.000	0.000	0.000
56	B	123	LYS	1	0.930	0.976	8.643	15.647	15.647	0.000	0.000	0.000	0.000
57	B	124	LEU	0	0.039	0.016	8.388	-1.109	-1.109	0.000	0.000	0.000	0.000
58	B	125	ARG	1	0.927	0.959	11.286	17.933	17.933	0.000	0.000	0.000	0.000
59	B	126	GLY	0	0.021	0.017	13.150	-1.052	-1.052	0.000	0.000	0.000	0.000
60	B	127	THR	0	-0.034	-0.028	13.878	1.297	1.297	0.000	0.000	0.000	0.000
61	B	128	ASN	0	-0.037	-0.043	15.317	-0.138	-0.138	0.000	0.000	0.000	0.000
62	B	129	PHE	0	0.018	0.022	10.293	-0.239	-0.239	0.000	0.000	0.000	0.000
63	B	130	PRO	0	0.040	0.036	16.179	0.751	0.751	0.000	0.000	0.000	0.000
64	B	131	SER	0	-0.032	-0.026	18.546	-0.554	-0.554	0.000	0.000	0.000	0.000
65	B	132	ASP	-1	-0.868	-0.919	21.013	-12.429	-12.429	0.000	0.000	0.000	0.000
66	B	133	GLY	0	0.012	0.011	17.087	0.048	0.048	0.000	0.000	0.000	0.000
67	B	134	PRO	0	-0.006	-0.024	13.306	0.119	0.119	0.000	0.000	0.000	0.000
68	B	135	VAL	0	0.009	0.018	11.150	-0.642	-0.642	0.000	0.000	0.000	0.000
69	B	136	MET	0	-0.006	0.001	13.817	-0.373	-0.373	0.000	0.000	0.000	0.000
70	B	137	GLN	0	-0.040	-0.017	17.215	0.629	0.629	0.000	0.000	0.000	0.000
71	B	138	LYS	1	0.943	0.985	15.714	17.088	17.088	0.000	0.000	0.000	0.000
72	B	139	LYS	1	0.892	0.930	15.782	16.034	16.034	0.000	0.000	0.000	0.000
73	B	140	THR	0	0.016	0.014	10.834	0.560	0.560	0.000	0.000	0.000	0.000
74	B	141	MET	0	-0.015	0.003	11.801	1.240	1.240	0.000	0.000	0.000	0.000
75	B	142	GLY	0	0.026	0.024	8.673	0.148	0.148	0.000	0.000	0.000	0.000
76	B	143	TRP	0	-0.006	-0.005	3.953	-5.056	-3.792	0.014	-0.456	-0.823	-0.004
77	B	144	GLU	-1	-0.897	-0.952	6.179	-24.867	-24.867	0.000	0.000	0.000	0.000
78	B	145	ALA	0	-0.023	-0.011	6.056	-5.453	-5.453	0.000	0.000	0.000	0.000
79	B	146	ILE	0	-0.024	-0.006	2.628	-3.122	-1.030	0.782	-0.495	-2.379	0.000
80	B	147	SER	0	0.002	-0.004	6.046	2.165	2.165	0.000	0.000	0.000	0.000
81	B	148	GLU	-1	-0.802	-0.869	4.203	-46.082	-45.698	0.001	-0.045	-0.340	0.000
82	B	149	ARG	1	0.906	0.941	7.485	27.566	27.566	0.000	0.000	0.000	0.000
83	B	150	MET	0	-0.035	-0.004	8.119	-1.921	-1.921	0.000	0.000	0.000	0.000
84	B	151	TYR	0	-0.004	-0.016	11.060	1.470	1.470	0.000	0.000	0.000	0.000
85	B	152	PRO	0	-0.002	0.017	13.641	-0.516	-0.516	0.000	0.000	0.000	0.000
86	B	153	GLU	-1	-0.847	-0.926	15.497	-15.830	-15.830	0.000	0.000	0.000	0.000
87	B	154	ASP	-1	-0.911	-0.957	17.043	-13.145	-13.145	0.000	0.000	0.000	0.000
88	B	155	GLY	0	0.011	0.019	19.056	0.120	0.120	0.000	0.000	0.000	0.000
89	B	156	ALA	0	-0.057	-0.041	13.870	0.016	0.016	0.000	0.000	0.000	0.000
90	B	157	LEU	0	0.011	0.008	10.471	0.232	0.232	0.000	0.000	0.000	0.000
91	B	158	LYS	1	0.823	0.903	10.267	15.976	15.976	0.000	0.000	0.000	0.000
92	B	159	GLY	0	0.047	0.023	7.042	0.121	0.121	0.000	0.000	0.000	0.000
93	B	160	GLU	-1	-0.828	-0.912	7.079	-22.259	-22.259	0.000	0.000	0.000	0.000
94	B	161	ILE	0	-0.047	-0.013	2.600	-2.023	-1.104	2.183	-0.585	-2.517	0.000
95	B	162	LYS	1	0.843	0.917	6.388	25.771	25.771	0.000	0.000	0.000	0.000
96	B	163	GLN	0	-0.039	-0.031	3.551	-0.804	-0.461	0.005	-0.070	-0.278	0.000
97	B	164	ARG	1	0.872	0.930	5.832	23.623	23.623	0.000	0.000	0.000	0.000
98	B	165	LEU	0	-0.061	-0.019	6.887	-3.374	-3.374	0.000	0.000	0.000	0.000
99	B	166	LYS	1	0.908	0.934	8.252	31.047	31.047	0.000	0.000	0.000	0.000
100	B	167	LEU	0	0.036	0.021	11.689	-0.742	-0.742	0.000	0.000	0.000	0.000
101	B	168	LYS	1	0.884	0.905	14.563	18.558	18.558	0.000	0.000	0.000	0.000
102	B	169	ASP	-1	-0.902	-0.940	17.864	-15.791	-15.791	0.000	0.000	0.000	0.000
103	B	170	GLY	0	-0.021	0.017	18.487	0.586	0.586	0.000	0.000	0.000	0.000
104	B	171	GLY	0	0.055	0.012	16.481	0.716	0.716	0.000	0.000	0.000	0.000
105	B	172	HIS	0	-0.098	-0.052	11.869	-0.210	-0.210	0.000	0.000	0.000	0.000
106	B	173	TYR	0	-0.023	-0.034	9.576	0.412	0.412	0.000	0.000	0.000	0.000
107	B	174	ASP	-1	-0.793	-0.882	8.589	-26.973	-26.973	0.000	0.000	0.000	0.000
108	B	175	ALA	0	0.015	0.005	5.089	0.903	0.903	0.000	0.000	0.000	0.000
109	B	176	GLU	-1	-0.882	-0.922	6.985	-22.616	-22.616	0.000	0.000	0.000	0.000
110	B	177	VAL	0	-0.045	-0.040	2.599	-1.822	-0.469	0.550	-0.399	-1.504	0.002
111	B	178	LYS	1	0.916	0.965	5.749	20.024	20.024	0.000	0.000	0.000	0.000
112	B	179	THR	0	-0.022	0.003	4.482	-1.788	-1.416	-0.001	-0.008	-0.364	0.000
113	B	180	THR	0	0.016	0.015	6.991	1.029	1.029	0.000	0.000	0.000	0.000
114	B	181	TYR	0	-0.018	-0.047	4.287	0.051	0.860	0.000	-0.056	-0.753	0.000
115	B	182	LYS	1	0.895	0.946	9.726	13.997	13.997	0.000	0.000	0.000	0.000
116	B	183	ALA	0	0.028	0.017	12.248	0.030	0.030	0.000	0.000	0.000	0.000
117	B	184	LYS	1	0.755	0.859	12.738	14.223	14.223	0.000	0.000	0.000	0.000
118	B	185	LYS	1	0.821	0.924	16.342	12.691	12.691	0.000	0.000	0.000	0.000
119	B	186	PRO	0	-0.024	-0.030	17.960	-0.527	-0.527	0.000	0.000	0.000	0.000
120	B	187	VAL	0	-0.013	0.009	15.833	0.140	0.140	0.000	0.000	0.000	0.000
121	B	188	GLN	0	0.010	0.008	18.789	0.027	0.027	0.000	0.000	0.000	0.000
122	B	189	LEU	0	-0.025	-0.011	15.073	-0.620	-0.620	0.000	0.000	0.000	0.000
123	B	190	PRO	0	0.007	0.019	13.815	0.640	0.640	0.000	0.000	0.000	0.000
124	B	191	GLY	0	0.059	0.021	17.064	0.254	0.254	0.000	0.000	0.000	0.000
125	B	192	ALA	0	-0.016	-0.027	15.349	-0.823	-0.823	0.000	0.000	0.000	0.000
126	B	193	TYR	0	-0.082	-0.047	11.314	0.362	0.362	0.000	0.000	0.000	0.000
127	B	194	ASN	0	0.019	0.004	11.351	-0.982	-0.982	0.000	0.000	0.000	0.000
128	B	195	VAL	0	0.028	0.013	6.229	0.981	0.981	0.000	0.000	0.000	0.000
129	B	196	ASN	0	-0.016	0.002	7.483	-3.985	-3.985	0.000	0.000	0.000	0.000
130	B	197	ILE	0	0.001	-0.017	2.162	-4.878	-3.162	2.426	-1.177	-2.965	-0.016
131	B	198	LYS	1	0.822	0.909	5.381	36.472	36.868	-0.001	-0.007	-0.388	0.000
132	B	199	LEU	0	-0.001	-0.007	2.332	-6.376	-4.684	0.765	-0.594	-1.862	-0.003
133	B	200	ASP	-1	-0.842	-0.903	5.500	-30.048	-30.048	0.000	0.000	0.000	0.000
134	B	201	ILE	0	0.014	0.002	8.383	-1.050	-1.050	0.000	0.000	0.000	0.000
135	B	202	THR	0	-0.020	-0.025	10.614	0.902	0.902	0.000	0.000	0.000	0.000
136	B	203	SER	0	-0.065	-0.043	13.381	1.869	1.869	0.000	0.000	0.000	0.000
137	B	204	HIS	0	0.017	-0.003	14.562	-1.938	-1.938	0.000	0.000	0.000	0.000
138	B	205	ASN	0	0.026	0.019	16.638	0.106	0.106	0.000	0.000	0.000	0.000
139	B	206	GLU	-1	-0.926	-0.962	19.037	-13.545	-13.545	0.000	0.000	0.000	0.000
140	B	207	ASP	-1	-0.850	-0.914	20.481	-15.278	-15.278	0.000	0.000	0.000	0.000
141	B	208	TYR	0	-0.137	-0.070	13.841	-0.740	-0.740	0.000	0.000	0.000	0.000
142	B	209	THR	0	-0.033	-0.019	16.053	-0.721	-0.721	0.000	0.000	0.000	0.000
143	B	210	ILE	0	-0.048	-0.027	16.354	0.035	0.035	0.000	0.000	0.000	0.000
144	B	211	VAL	0	-0.032	-0.018	11.255	-0.190	-0.190	0.000	0.000	0.000	0.000
145	B	212	GLU	-1	-0.883	-0.901	12.079	-19.570	-19.570	0.000	0.000	0.000	0.000
146	B	213	GLN	0	0.001	-0.013	5.856	-6.920	-6.920	0.000	0.000	0.000	0.000
147	B	214	TYR	0	0.013	0.014	8.439	1.939	1.939	0.000	0.000	0.000	0.000
148	B	215	GLU	-1	-0.764	-0.847	1.735	-135.134	-129.891	15.258	-12.460	-8.041	-0.171
149	B	216	ARG	1	0.921	0.975	5.904	30.077	30.077	0.000	0.000	0.000	0.000
150	B	217	ALA	0	0.048	0.014	5.173	-3.773	-3.773	0.000	0.000	0.000	0.000
151	B	218	GLU	-1	-0.826	-0.896	7.104	-16.994	-16.994	0.000	0.000	0.000	0.000
152	B	219	GLY	0	0.014	0.020	10.116	-1.296	-1.296	0.000	0.000	0.000	0.000
153	B	220	ARG	1	0.795	0.871	11.664	21.407	21.407	0.000	0.000	0.000	0.000
154	B	221	HIS	0	0.074	0.027	14.511	-1.209	-1.209	0.000	0.000	0.000	0.000
155	B	222	SER	0	-0.033	-0.021	15.944	-0.123	-0.123	0.000	0.000	0.000	0.000
156	B	223	THR	0	-0.036	-0.021	17.912	0.687	0.687	0.000	0.000	0.000	0.000
157	B	224	GLY	0	0.073	0.026	21.535	-0.243	-0.243	0.000	0.000	0.000	0.000
158	B	225	GLY	0	-0.012	0.001	24.054	0.400	0.400	0.000	0.000	0.000	0.000
159	B	226	MET	0	-0.020	-0.021	23.926	-0.571	-0.571	0.000	0.000	0.000	0.000
160	B	227	ASP	-1	-0.992	-0.969	24.283	-11.061	-11.061	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:67:0YG)