FMO DATABASE

FMODB ID: 72YQK

Calculation Name: 1B4A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B4A

Chain ID: A

ChEMBL ID:

UniProt ID: O31408

Base Structure: X-ray

Registration Date: 2023-06-22

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1246266.900268
FMO2-HF: Nuclear repulsion	1188095.455483
FMO2-HF: Total energy	-58171.444785
FMO2-MP2: Total energy	-58338.940949

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:4:GLY)

Summations of interaction energy for fragment #1(A:4: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.
-0.411	2.371	0.162	-1.166	-1.777	0

Interaction energy analysis for fragmet #1(A:4:GLY)

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 : 0.027

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	6	ARG	1	0.905	0.948	3.500	-1.066	0.338	-0.001	-0.639	-0.763	0.001
4	A	7	HIS	0	0.018	-0.013	2.848	-1.135	-0.292	0.147	-0.306	-0.683	-0.001
5	A	8	ILE	0	-0.020	-0.012	3.502	0.590	1.125	0.016	-0.221	-0.331	0.000
6	A	9	LYS	1	0.850	0.916	5.570	0.992	0.992	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.034	0.017	7.702	0.231	0.231	0.000	0.000	0.000	0.000
8	A	11	ARG	1	0.922	0.969	7.290	0.918	0.918	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.822	-0.888	10.001	-0.239	-0.239	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.019	0.013	11.892	0.087	0.087	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.028	-0.022	12.292	0.061	0.061	0.000	0.000	0.000	0.000
12	A	15	MET	0	-0.069	-0.031	14.151	0.031	0.031	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.012	-0.005	15.581	0.045	0.045	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.044	-0.017	17.774	0.044	0.044	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.851	-0.933	19.210	-0.191	-0.191	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.036	0.001	16.416	0.009	0.009	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.782	-0.883	19.501	-0.140	-0.140	0.000	0.000	0.000	0.000
18	A	21	THR	0	-0.045	-0.025	20.996	0.003	0.003	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.073	0.029	16.062	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.828	-0.918	17.152	-0.147	-0.147	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.768	-0.857	18.902	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.011	-0.010	12.292	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.056	-0.046	14.344	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.851	-0.922	15.420	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.840	0.889	15.981	0.195	0.195	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.070	-0.034	9.570	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.850	0.922	13.083	0.117	0.117	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.918	-0.947	15.253	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.088	-0.037	12.947	0.011	0.011	0.000	0.000	0.000	0.000
30	A	33	GLY	0	0.012	0.015	13.608	0.026	0.026	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.053	-0.038	6.487	0.051	0.051	0.000	0.000	0.000	0.000
32	A	35	ASN	0	0.009	0.009	11.512	-0.097	-0.097	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.010	-0.001	9.429	0.036	0.036	0.000	0.000	0.000	0.000
34	A	37	THR	0	0.055	0.026	12.417	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	38	GLN	0	0.100	0.017	13.798	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	39	ALA	0	-0.013	0.002	15.446	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.054	-0.035	9.005	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	41	VAL	0	0.061	0.033	10.572	-0.092	-0.092	0.000	0.000	0.000	0.000
39	A	42	SER	0	-0.020	-0.014	11.842	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.801	0.878	8.135	0.429	0.429	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.773	-0.877	7.411	-0.925	-0.925	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.010	0.001	9.493	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.950	0.978	12.610	0.264	0.264	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.848	-0.907	7.655	-0.781	-0.781	0.000	0.000	0.000	0.000
45	A	48	MET	0	-0.066	-0.025	7.055	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	49	GLN	0	-0.040	-0.021	9.807	0.087	0.087	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.021	-0.005	11.016	0.028	0.028	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.022	-0.013	14.380	0.042	0.042	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.854	0.942	18.091	0.196	0.196	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.013	0.001	20.691	0.016	0.016	0.000	0.000	0.000	0.000
51	A	54	PRO	0	0.018	0.017	22.924	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	55	MET	0	-0.026	-0.003	24.493	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.017	0.000	26.710	0.006	0.006	0.000	0.000	0.000	0.000
54	A	57	ASN	0	0.031	0.000	29.062	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.078	0.050	29.947	0.006	0.006	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.781	0.885	27.068	0.111	0.111	0.000	0.000	0.000	0.000
57	A	60	TYR	0	0.009	-0.010	24.022	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.968	0.984	18.965	0.246	0.246	0.000	0.000	0.000	0.000
59	A	62	TYR	0	-0.039	-0.027	16.145	0.006	0.006	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.021	-0.050	16.562	0.002	0.002	0.000	0.000	0.000	0.000
61	A	64	LEU	0	0.023	0.033	10.949	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	65	PRO	0	0.051	0.032	12.516	0.053	0.053	0.000	0.000	0.000	0.000
63	A	66	SER	0	-0.004	-0.014	14.317	0.018	0.018	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.811	-0.888	16.142	-0.203	-0.203	0.000	0.000	0.000	0.000
65	A	68	GLN	0	-0.011	-0.009	18.902	0.016	0.016	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.890	0.967	21.959	0.179	0.179	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.047	0.024	22.754	0.013	0.013	0.000	0.000	0.000	0.000
68	A	71	ASN	0	-0.063	-0.049	21.904	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.132	0.066	23.642	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.054	0.030	25.428	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.002	0.000	22.885	0.005	0.005	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.853	0.927	18.974	0.222	0.222	0.000	0.000	0.000	0.000
73	A	76	LEU	0	0.046	0.038	22.994	0.002	0.002	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.908	0.958	26.422	0.098	0.098	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.868	0.924	20.693	0.168	0.168	0.000	0.000	0.000	0.000
76	A	79	ALA	0	0.074	0.045	23.613	0.003	0.003	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.003	-0.003	24.563	0.008	0.008	0.000	0.000	0.000	0.000
78	A	81	VAL	0	-0.073	-0.038	25.465	0.007	0.007	0.000	0.000	0.000	0.000
79	A	82	ASP	-1	-0.919	-0.937	22.221	-0.120	-0.120	0.000	0.000	0.000	0.000
80	A	83	VAL	0	-0.063	-0.041	25.115	0.008	0.008	0.000	0.000	0.000	0.000
81	A	84	PHE	0	0.016	0.002	27.712	0.007	0.007	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.039	-0.007	31.154	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	LYS	1	0.798	0.877	34.094	0.043	0.043	0.000	0.000	0.000	0.000
84	A	87	LEU	0	0.011	0.017	36.759	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.829	-0.893	38.764	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	89	GLY	0	0.037	0.006	41.727	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.048	-0.012	44.323	0.002	0.002	0.000	0.000	0.000	0.000
88	A	91	GLY	0	0.033	0.024	47.221	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.059	-0.046	45.892	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	LEU	0	0.007	0.010	43.245	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	LEU	0	-0.002	-0.004	38.722	0.001	0.001	0.000	0.000	0.000	0.000
92	A	95	VAL	0	-0.011	-0.006	39.161	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.014	0.007	32.148	0.001	0.001	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.827	0.904	35.048	0.043	0.043	0.000	0.000	0.000	0.000
95	A	98	THR	0	0.028	-0.005	29.548	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.012	0.011	26.634	0.005	0.005	0.000	0.000	0.000	0.000
97	A	100	PRO	0	-0.004	-0.028	29.216	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	101	GLY	0	0.029	0.026	27.291	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	102	ASN	0	-0.044	-0.026	24.523	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	103	ALA	0	0.004	0.017	26.986	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	104	HIS	0	0.063	0.015	26.322	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	105	ALA	0	0.012	0.009	23.813	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	106	ILE	0	0.007	-0.007	25.540	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.062	0.019	28.030	0.000	0.000	0.000	0.000	0.000	0.000
105	A	108	VAL	0	0.009	0.021	25.024	0.000	0.000	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.063	-0.033	23.141	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.032	-0.030	27.166	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	ASP	-1	-0.866	-0.928	30.342	-0.078	-0.078	0.000	0.000	0.000	0.000
109	A	112	ASN	0	-0.069	-0.041	25.277	0.003	0.003	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.119	-0.059	29.118	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.931	-0.944	31.080	-0.079	-0.079	0.000	0.000	0.000	0.000
112	A	115	TRP	0	-0.023	-0.016	32.848	0.003	0.003	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.834	-0.916	36.639	-0.058	-0.058	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.881	-0.921	39.356	-0.056	-0.056	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.016	-0.018	35.514	0.003	0.003	0.000	0.000	0.000	0.000
116	A	119	VAL	0	-0.080	-0.029	38.798	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	120	GLY	0	0.057	0.025	37.195	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.061	-0.035	33.724	0.002	0.002	0.000	0.000	0.000	0.000
119	A	122	ILE	0	0.006	0.017	35.546	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	123	CYS	0	-0.043	-0.008	30.987	0.001	0.001	0.000	0.000	0.000	0.000
121	A	124	GLY	0	0.018	0.025	33.901	0.002	0.002	0.000	0.000	0.000	0.000
122	A	125	ASP	-1	-0.876	-0.941	31.167	-0.055	-0.055	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.847	-0.923	30.541	-0.052	-0.052	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.048	-0.032	32.617	0.001	0.001	0.000	0.000	0.000	0.000
125	A	128	CYS	0	-0.030	-0.016	32.878	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.013	0.002	35.016	0.002	0.002	0.000	0.000	0.000	0.000
127	A	130	ILE	0	0.068	0.017	35.029	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	131	ILE	0	-0.017	-0.003	38.357	0.003	0.003	0.000	0.000	0.000	0.000
129	A	132	CYS	0	0.014	0.017	40.761	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	133	ARG	1	0.879	0.937	41.296	0.056	0.056	0.000	0.000	0.000	0.000
131	A	134	THR	0	-0.005	-0.037	45.218	0.003	0.003	0.000	0.000	0.000	0.000
132	A	135	PRO	0	0.052	0.003	46.233	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.943	0.978	47.012	0.039	0.039	0.000	0.000	0.000	0.000
134	A	137	ASP	-1	-0.778	-0.873	43.326	-0.048	-0.048	0.000	0.000	0.000	0.000
135	A	138	ALA	0	0.048	0.039	42.508	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	139	LYS	1	0.941	0.961	42.295	0.039	0.039	0.000	0.000	0.000	0.000
137	A	140	LYS	1	0.751	0.857	41.910	0.051	0.051	0.000	0.000	0.000	0.000
138	A	141	VAL	0	0.075	0.037	37.015	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	142	SER	0	0.038	0.019	37.835	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	143	ASN	0	-0.061	-0.037	38.582	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	144	GLN	0	0.012	0.023	35.033	0.000	0.000	0.000	0.000	0.000	0.000
142	A	145	LEU	0	0.009	0.004	32.863	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	146	LEU	0	0.029	0.006	34.009	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	147	SER	0	-0.092	-0.032	35.737	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	148	MET	0	-0.096	-0.042	30.449	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	149	LEU	0	0.004	0.011	30.615	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)