FMO DATABASE

FMODB ID: 2J49R

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	OptAll
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	-1247890.751678
FMO2-HF: Nuclear repulsion	1189718.799257
FMO2-HF: Total energy	-58171.952421
FMO2-MP2: Total energy	-58339.404439

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.
-6.757	-2.791	2.234	-2.682	-3.518	-0.024

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 : 0.044 / q_NPA : 0.018

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	0.922	0.964	3.556	-2.701	-1.133	0.015	-0.754	-0.829	0.003
4	A	7	HIS	0	0.055	-0.002	2.430	-6.560	-4.535	2.217	-1.791	-2.451	-0.027
5	A	8	ILE	0	-0.021	-0.012	3.831	0.848	1.221	0.002	-0.137	-0.238	0.000
6	A	9	LYS	1	0.849	0.906	6.048	0.872	0.872	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.029	0.018	6.823	0.185	0.185	0.000	0.000	0.000	0.000
8	A	11	ARG	1	0.919	0.960	7.694	1.117	1.117	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.803	-0.874	10.230	-0.239	-0.239	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.021	0.017	11.605	0.100	0.100	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.017	-0.009	12.397	0.060	0.060	0.000	0.000	0.000	0.000
12	A	15	MET	0	-0.067	-0.035	13.987	0.015	0.015	0.000	0.000	0.000	0.000
13	A	16	SER	0	0.004	0.003	15.788	0.048	0.048	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.021	-0.012	18.104	0.058	0.058	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.872	-0.941	19.144	-0.206	-0.206	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.025	0.007	16.334	0.014	0.014	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.800	-0.879	19.351	-0.136	-0.136	0.000	0.000	0.000	0.000
18	A	21	THR	0	-0.029	-0.012	20.609	0.002	0.002	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.056	0.020	15.676	-0.038	-0.038	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.829	-0.928	16.453	-0.069	-0.069	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.752	-0.846	18.004	-0.130	-0.130	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.006	-0.002	11.302	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.064	-0.038	13.672	0.005	0.005	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.810	-0.892	14.733	0.041	0.041	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.839	0.896	15.570	0.162	0.162	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.078	-0.036	9.268	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.783	0.872	12.861	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.899	-0.942	15.384	0.053	0.053	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.074	-0.026	13.199	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	33	GLY	0	0.014	0.009	13.491	0.023	0.023	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.045	-0.037	6.685	0.148	0.148	0.000	0.000	0.000	0.000
32	A	35	ASN	0	0.015	0.007	11.547	-0.117	-0.117	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.011	0.007	9.523	0.097	0.097	0.000	0.000	0.000	0.000
34	A	37	THR	0	0.052	0.027	12.641	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	38	GLN	0	0.088	0.024	13.492	0.007	0.007	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.012	0.007	14.712	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.074	-0.039	8.859	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	41	VAL	0	0.070	0.029	10.129	-0.089	-0.089	0.000	0.000	0.000	0.000
39	A	42	SER	0	-0.021	-0.013	11.177	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.747	0.854	7.255	0.244	0.244	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.761	-0.875	6.888	-0.379	-0.379	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.004	-0.005	8.505	-0.177	-0.177	0.000	0.000	0.000	0.000
43	A	46	LYS	1	0.955	0.982	11.484	0.208	0.208	0.000	0.000	0.000	0.000
44	A	47	GLU	-1	-0.829	-0.887	6.556	-0.817	-0.817	0.000	0.000	0.000	0.000
45	A	48	MET	0	-0.069	-0.019	6.997	-0.147	-0.147	0.000	0.000	0.000	0.000
46	A	49	GLN	0	-0.038	-0.020	9.444	0.120	0.120	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.023	-0.004	11.223	0.032	0.032	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.008	0.003	14.235	0.053	0.053	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.792	0.901	18.022	0.195	0.195	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.013	-0.006	20.873	0.008	0.008	0.000	0.000	0.000	0.000
51	A	54	PRO	0	0.021	0.019	23.280	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	MET	0	-0.011	0.002	24.865	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.009	-0.009	27.050	0.007	0.007	0.000	0.000	0.000	0.000
54	A	57	ASN	0	0.006	0.002	29.462	0.002	0.002	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.014	0.017	30.539	0.006	0.006	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.836	0.900	26.839	0.100	0.100	0.000	0.000	0.000	0.000
57	A	60	TYR	0	0.030	-0.004	23.844	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.930	0.984	18.702	0.270	0.270	0.000	0.000	0.000	0.000
59	A	62	TYR	0	-0.038	-0.029	16.094	0.007	0.007	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.009	-0.039	17.023	0.005	0.005	0.000	0.000	0.000	0.000
61	A	64	LEU	0	0.016	0.016	11.537	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	65	PRO	0	0.066	0.039	12.906	0.064	0.064	0.000	0.000	0.000	0.000
63	A	66	SER	0	0.003	-0.010	14.632	0.020	0.020	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.815	-0.883	16.361	-0.230	-0.230	0.000	0.000	0.000	0.000
65	A	68	GLN	0	0.012	-0.017	19.048	0.024	0.024	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.871	0.945	22.198	0.213	0.213	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.008	0.005	22.973	0.017	0.017	0.000	0.000	0.000	0.000
68	A	71	ASN	0	-0.035	-0.027	22.286	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.117	0.058	24.077	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.075	0.042	25.311	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.003	0.003	23.110	0.000	0.000	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.831	0.931	19.347	0.270	0.270	0.000	0.000	0.000	0.000
73	A	76	LEU	0	0.057	0.033	22.904	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.860	0.936	26.215	0.120	0.120	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.829	0.934	20.419	0.212	0.212	0.000	0.000	0.000	0.000
76	A	79	ALA	0	0.091	0.038	23.108	0.009	0.009	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.009	-0.003	24.180	0.009	0.009	0.000	0.000	0.000	0.000
78	A	81	VAL	0	-0.051	-0.032	25.397	0.009	0.009	0.000	0.000	0.000	0.000
79	A	82	ASP	-1	-0.924	-0.946	22.138	-0.174	-0.174	0.000	0.000	0.000	0.000
80	A	83	VAL	0	-0.061	-0.032	24.713	0.007	0.007	0.000	0.000	0.000	0.000
81	A	84	PHE	0	0.019	0.008	27.297	0.008	0.008	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.044	-0.009	30.929	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	LYS	1	0.799	0.872	33.823	0.062	0.062	0.000	0.000	0.000	0.000
84	A	87	LEU	0	0.004	0.005	36.186	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.833	-0.884	38.468	-0.053	-0.053	0.000	0.000	0.000	0.000
86	A	89	GLY	0	0.040	-0.001	41.362	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.043	-0.014	43.992	0.003	0.003	0.000	0.000	0.000	0.000
88	A	91	GLY	0	0.036	0.026	46.906	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.058	-0.040	45.663	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	LEU	0	0.011	0.012	43.040	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	94	LEU	0	0.003	0.001	38.428	0.002	0.002	0.000	0.000	0.000	0.000
92	A	95	VAL	0	-0.013	-0.016	38.852	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.031	0.021	31.604	0.002	0.002	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.819	0.900	34.708	0.067	0.067	0.000	0.000	0.000	0.000
95	A	98	THR	0	0.030	-0.005	29.278	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.028	0.017	26.244	0.006	0.006	0.000	0.000	0.000	0.000
97	A	100	PRO	0	-0.012	-0.020	28.847	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	101	GLY	0	0.007	0.014	26.369	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	102	ASN	0	-0.039	-0.028	24.144	-0.021	-0.021	0.000	0.000	0.000	0.000
100	A	103	ALA	0	0.015	0.021	26.571	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	104	HIS	0	0.061	0.018	26.013	0.003	0.003	0.000	0.000	0.000	0.000
102	A	105	ALA	0	0.005	0.008	23.718	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.009	-0.011	25.624	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.070	0.027	28.121	0.002	0.002	0.000	0.000	0.000	0.000
105	A	108	VAL	0	0.010	0.013	25.112	0.001	0.001	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.076	-0.043	23.286	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.027	-0.019	27.278	0.002	0.002	0.000	0.000	0.000	0.000
108	A	111	ASP	-1	-0.836	-0.900	30.724	-0.100	-0.100	0.000	0.000	0.000	0.000
109	A	112	ASN	0	-0.063	-0.045	25.284	0.006	0.006	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.102	-0.057	29.118	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.948	-0.962	31.133	-0.094	-0.094	0.000	0.000	0.000	0.000
112	A	115	TRP	0	-0.018	-0.007	32.839	0.005	0.005	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.839	-0.916	36.722	-0.070	-0.070	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.853	-0.907	39.320	-0.070	-0.070	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.010	-0.009	35.581	0.004	0.004	0.000	0.000	0.000	0.000
116	A	119	VAL	0	-0.089	-0.051	39.256	0.000	0.000	0.000	0.000	0.000	0.000
117	A	120	GLY	0	0.053	0.030	36.861	0.000	0.000	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.073	-0.053	33.419	0.002	0.002	0.000	0.000	0.000	0.000
119	A	122	ILE	0	0.008	0.004	35.609	0.001	0.001	0.000	0.000	0.000	0.000
120	A	123	CYS	0	-0.072	-0.020	31.041	0.002	0.002	0.000	0.000	0.000	0.000
121	A	124	GLY	0	0.052	0.037	33.736	0.003	0.003	0.000	0.000	0.000	0.000
122	A	125	ASP	-1	-0.894	-0.951	30.493	-0.089	-0.089	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.818	-0.887	30.034	-0.079	-0.079	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.031	-0.025	32.303	0.002	0.002	0.000	0.000	0.000	0.000
125	A	128	CYS	0	-0.052	-0.035	32.562	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.007	0.009	34.694	0.003	0.003	0.000	0.000	0.000	0.000
127	A	130	ILE	0	0.046	0.004	34.889	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	131	ILE	0	-0.002	0.007	38.189	0.005	0.005	0.000	0.000	0.000	0.000
129	A	132	CYS	0	0.005	0.019	40.502	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	133	ARG	1	0.863	0.925	40.784	0.071	0.071	0.000	0.000	0.000	0.000
131	A	134	THR	0	0.003	-0.030	44.989	0.004	0.004	0.000	0.000	0.000	0.000
132	A	135	PRO	0	0.047	0.001	46.204	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.933	0.975	47.103	0.048	0.048	0.000	0.000	0.000	0.000
134	A	137	ASP	-1	-0.819	-0.879	43.108	-0.060	-0.060	0.000	0.000	0.000	0.000
135	A	138	ALA	0	0.057	0.036	42.384	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	139	LYS	1	0.939	0.964	42.256	0.050	0.050	0.000	0.000	0.000	0.000
137	A	140	LYS	1	0.768	0.870	41.743	0.063	0.063	0.000	0.000	0.000	0.000
138	A	141	VAL	0	0.090	0.039	36.921	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	142	SER	0	0.008	0.006	37.816	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	143	ASN	0	-0.057	-0.040	38.825	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	144	GLN	0	0.011	0.020	35.079	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	145	LEU	0	0.020	0.010	32.634	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	146	LEU	0	0.012	0.003	34.020	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	147	SER	0	-0.074	-0.034	35.499	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	148	MET	0	-0.059	-0.039	30.212	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	149	LEU	0	0.000	0.012	30.536	-0.005	-0.005	0.000	0.000	0.000	0.000

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