FMO DATABASE

FMODB ID: 2JNLR

Calculation Name: 1BD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BD8

Chain ID: A

ChEMBL ID:

UniProt ID: P55273

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1357442.647706
FMO2-HF: Nuclear repulsion	1299554.321612
FMO2-HF: Total energy	-57888.326094
FMO2-MP2: Total energy	-58058.958932

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-13.291	-5.799	3.07	-3.416	-7.145	-0.008

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.042 / q_NPA : 1.008

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	9	GLY	0	0.122	0.060	3.317	-0.500	0.873	0.004	-0.551	-0.826	0.002
4	A	10	ASP	-1	-0.832	-0.919	2.591	-51.648	-48.689	0.920	-1.670	-2.210	-0.013
5	A	11	ARG	1	0.702	0.804	1.983	47.935	50.670	2.149	-1.174	-3.710	0.003
6	A	12	LEU	0	0.057	0.038	5.365	3.558	3.708	-0.001	-0.008	-0.140	0.000
7	A	13	SER	0	0.049	0.019	7.356	3.658	3.658	0.000	0.000	0.000	0.000
8	A	14	GLY	0	-0.009	0.003	7.246	2.322	2.322	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.050	-0.030	8.274	2.214	2.214	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.049	0.020	10.227	2.250	2.250	0.000	0.000	0.000	0.000
11	A	17	ALA	0	-0.006	0.004	11.509	1.689	1.689	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.791	0.877	8.672	29.317	29.317	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.050	0.034	13.505	1.038	1.038	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.846	-0.909	11.787	-22.956	-22.956	0.000	0.000	0.000	0.000
15	A	21	VAL	0	0.052	0.002	14.092	-0.889	-0.889	0.000	0.000	0.000	0.000
16	A	22	GLN	0	-0.021	-0.009	15.668	0.279	0.279	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.841	-0.904	8.574	-31.780	-31.780	0.000	0.000	0.000	0.000
18	A	24	VAL	0	0.013	0.005	11.843	-1.009	-1.009	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.866	0.913	13.202	15.115	15.115	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.862	0.936	10.964	25.111	25.111	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.017	-0.021	7.021	-0.429	-0.429	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.004	0.009	10.543	0.262	0.262	0.000	0.000	0.000	0.000
23	A	29	HIS	0	-0.016	-0.017	13.329	0.504	0.504	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.909	0.975	13.605	19.522	19.522	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.859	-0.894	6.484	-35.888	-35.888	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.013	0.010	11.227	0.311	0.311	0.000	0.000	0.000	0.000
27	A	33	VAL	0	-0.044	-0.016	7.430	-0.397	-0.397	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.042	0.026	10.039	0.157	0.157	0.000	0.000	0.000	0.000
29	A	35	PRO	0	0.027	0.000	10.278	-1.876	-1.876	0.000	0.000	0.000	0.000
30	A	36	ASP	-1	-0.839	-0.915	11.733	-17.202	-17.202	0.000	0.000	0.000	0.000
31	A	37	ALA	0	-0.090	-0.044	6.094	-0.510	-0.510	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.009	0.005	7.153	-0.987	-0.987	0.000	0.000	0.000	0.000
33	A	39	ASN	0	-0.065	-0.039	5.050	-3.466	-3.391	-0.001	-0.003	-0.071	0.000
34	A	40	ARG	1	0.876	0.912	4.272	45.632	45.832	-0.001	-0.010	-0.188	0.000
35	A	41	PHE	0	-0.052	-0.027	6.829	1.352	1.352	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.003	0.012	9.064	1.774	1.774	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.861	0.930	10.076	18.118	18.118	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.071	0.034	9.651	-2.016	-2.016	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.006	-0.017	10.615	0.272	0.272	0.000	0.000	0.000	0.000
40	A	46	LEU	0	0.043	0.015	11.984	0.316	0.316	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.047	0.023	14.359	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.049	-0.021	11.355	0.249	0.249	0.000	0.000	0.000	0.000
43	A	49	MET	0	-0.049	0.007	14.754	-0.700	-0.700	0.000	0.000	0.000	0.000
44	A	50	MET	0	0.013	0.010	15.992	1.037	1.037	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.040	0.014	18.152	0.298	0.298	0.000	0.000	0.000	0.000
46	A	52	GLY	0	0.040	0.043	21.518	0.526	0.526	0.000	0.000	0.000	0.000
47	A	53	SER	0	-0.043	-0.026	19.172	0.203	0.203	0.000	0.000	0.000	0.000
48	A	54	THR	0	0.033	0.008	20.992	-0.419	-0.419	0.000	0.000	0.000	0.000
49	A	55	ALA	0	-0.031	-0.018	21.498	-0.074	-0.074	0.000	0.000	0.000	0.000
50	A	56	ILE	0	-0.008	0.007	15.488	-0.252	-0.252	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.064	0.026	18.251	-0.416	-0.416	0.000	0.000	0.000	0.000
52	A	58	LEU	0	0.059	0.033	20.016	-0.035	-0.035	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.824	-0.906	17.955	-14.534	-14.534	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.018	-0.018	13.531	-0.393	-0.393	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.003	0.005	17.235	0.060	0.060	0.000	0.000	0.000	0.000
56	A	62	LYS	1	0.869	0.936	20.055	13.803	13.803	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.060	-0.023	16.442	0.907	0.907	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.025	-0.015	17.374	-0.324	-0.324	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.056	-0.018	15.805	-0.108	-0.108	0.000	0.000	0.000	0.000
60	A	66	SER	0	0.001	-0.002	16.394	0.995	0.995	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.004	-0.012	18.396	-0.519	-0.519	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.005	-0.005	20.992	0.035	0.035	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.032	0.009	15.529	0.148	0.148	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.010	0.010	18.976	0.191	0.191	0.000	0.000	0.000	0.000
65	A	71	ASP	-1	-0.817	-0.865	18.085	-14.429	-14.429	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.008	-0.014	19.366	0.380	0.380	0.000	0.000	0.000	0.000
67	A	73	SER	0	-0.085	-0.049	21.697	0.593	0.593	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.067	0.025	23.285	0.424	0.424	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.012	0.002	21.905	0.439	0.439	0.000	0.000	0.000	0.000
70	A	76	SER	0	0.010	-0.021	21.008	-0.462	-0.462	0.000	0.000	0.000	0.000
71	A	77	PRO	0	-0.024	-0.025	18.795	0.161	0.161	0.000	0.000	0.000	0.000
72	A	78	VAL	0	0.051	0.030	21.432	0.026	0.026	0.000	0.000	0.000	0.000
73	A	79	HIS	0	0.053	0.023	24.799	-0.097	-0.097	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.807	-0.890	21.248	-13.140	-13.140	0.000	0.000	0.000	0.000
75	A	81	ALA	0	-0.052	-0.016	24.069	0.110	0.110	0.000	0.000	0.000	0.000
76	A	82	ALA	0	-0.001	0.002	25.316	0.258	0.258	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.876	0.928	23.628	12.390	12.390	0.000	0.000	0.000	0.000
78	A	84	THR	0	-0.069	-0.063	24.399	0.074	0.074	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.031	0.035	27.646	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	PHE	0	-0.026	-0.016	24.056	0.099	0.099	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.028	0.008	27.709	-0.159	-0.159	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.845	-0.917	28.662	-10.118	-10.118	0.000	0.000	0.000	0.000
83	A	89	THR	0	-0.020	-0.035	22.576	-0.063	-0.063	0.000	0.000	0.000	0.000
84	A	90	LEU	0	0.013	0.017	25.621	-0.162	-0.162	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.882	0.935	27.454	9.634	9.634	0.000	0.000	0.000	0.000
86	A	92	VAL	0	0.003	0.010	24.232	0.015	0.015	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.033	-0.022	21.395	-0.163	-0.163	0.000	0.000	0.000	0.000
88	A	94	VAL	0	0.016	0.005	25.255	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	95	GLU	-1	-0.966	-0.972	28.474	-10.191	-10.191	0.000	0.000	0.000	0.000
90	A	96	HIS	0	-0.122	-0.069	24.210	-0.049	-0.049	0.000	0.000	0.000	0.000
91	A	97	GLY	0	0.014	0.009	25.080	-0.292	-0.292	0.000	0.000	0.000	0.000
92	A	98	ALA	0	-0.063	-0.032	24.687	-0.062	-0.062	0.000	0.000	0.000	0.000
93	A	99	ASP	-1	-0.859	-0.934	26.049	-9.108	-9.108	0.000	0.000	0.000	0.000
94	A	100	VAL	0	-0.001	-0.007	28.061	-0.320	-0.320	0.000	0.000	0.000	0.000
95	A	101	ASN	0	-0.024	-0.028	30.443	0.261	0.261	0.000	0.000	0.000	0.000
96	A	102	VAL	0	-0.020	0.000	26.873	0.210	0.210	0.000	0.000	0.000	0.000
97	A	103	PRO	0	-0.020	-0.005	29.314	-0.188	-0.188	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.758	-0.851	26.961	-10.367	-10.367	0.000	0.000	0.000	0.000
99	A	105	GLY	0	0.005	-0.014	27.418	0.330	0.330	0.000	0.000	0.000	0.000
100	A	106	THR	0	-0.155	-0.104	28.984	0.319	0.319	0.000	0.000	0.000	0.000
101	A	107	GLY	0	-0.004	-0.010	31.619	0.339	0.339	0.000	0.000	0.000	0.000
102	A	108	ALA	0	-0.039	-0.011	31.170	0.249	0.249	0.000	0.000	0.000	0.000
103	A	109	LEU	0	0.039	0.029	30.954	-0.267	-0.267	0.000	0.000	0.000	0.000
104	A	110	PRO	0	0.036	0.005	28.414	0.022	0.022	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.033	0.016	30.648	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	112	HIS	0	0.015	0.010	33.974	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	113	LEU	0	-0.026	-0.009	28.144	0.048	0.048	0.000	0.000	0.000	0.000
108	A	114	ALA	0	-0.003	0.005	32.245	-0.036	-0.036	0.000	0.000	0.000	0.000
109	A	115	VAL	0	-0.003	0.001	33.475	0.113	0.113	0.000	0.000	0.000	0.000
110	A	116	GLN	0	-0.066	-0.028	34.171	0.363	0.363	0.000	0.000	0.000	0.000
111	A	117	GLU	-1	-0.939	-0.980	31.077	-9.701	-9.701	0.000	0.000	0.000	0.000
112	A	118	GLY	0	-0.062	-0.013	34.529	0.041	0.041	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.013	-0.006	30.925	0.272	0.272	0.000	0.000	0.000	0.000
114	A	120	THR	0	0.044	0.007	35.467	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	121	ALA	0	0.011	0.009	35.629	0.073	0.073	0.000	0.000	0.000	0.000
116	A	122	VAL	0	0.000	-0.005	31.438	0.006	0.006	0.000	0.000	0.000	0.000
117	A	123	VAL	0	0.021	0.012	34.401	0.034	0.034	0.000	0.000	0.000	0.000
118	A	124	SER	0	-0.027	-0.017	37.080	0.148	0.148	0.000	0.000	0.000	0.000
119	A	125	PHE	0	-0.038	-0.024	31.817	0.077	0.077	0.000	0.000	0.000	0.000
120	A	126	LEU	0	0.038	0.013	31.528	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.026	0.000	35.690	0.070	0.070	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.012	0.021	39.272	0.162	0.162	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.881	-0.976	33.949	-9.078	-9.078	0.000	0.000	0.000	0.000
124	A	130	SER	0	-0.065	-0.023	35.746	-0.198	-0.198	0.000	0.000	0.000	0.000
125	A	131	ASP	-1	-0.824	-0.890	36.801	-7.617	-7.617	0.000	0.000	0.000	0.000
126	A	132	LEU	0	-0.004	-0.016	38.848	-0.074	-0.074	0.000	0.000	0.000	0.000
127	A	133	HIS	0	-0.007	-0.009	41.088	0.077	0.077	0.000	0.000	0.000	0.000
128	A	134	ARG	1	0.797	0.888	36.738	8.003	8.003	0.000	0.000	0.000	0.000
129	A	135	ARG	1	0.800	0.878	39.344	6.894	6.894	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.792	-0.887	35.619	-8.175	-8.175	0.000	0.000	0.000	0.000
131	A	137	ALA	0	0.017	0.011	35.334	0.224	0.224	0.000	0.000	0.000	0.000
132	A	138	ARG	1	0.844	0.920	37.300	7.842	7.842	0.000	0.000	0.000	0.000
133	A	139	GLY	0	-0.021	-0.007	40.097	0.207	0.207	0.000	0.000	0.000	0.000
134	A	140	LEU	0	-0.061	-0.033	40.512	0.218	0.218	0.000	0.000	0.000	0.000
135	A	141	THR	0	0.028	-0.006	39.982	-0.185	-0.185	0.000	0.000	0.000	0.000
136	A	142	PRO	0	0.014	0.000	37.962	0.022	0.022	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.021	0.003	40.126	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.781	-0.841	43.749	-6.727	-6.727	0.000	0.000	0.000	0.000
139	A	145	LEU	0	-0.003	0.007	37.210	0.031	0.031	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.046	0.033	41.718	-0.038	-0.038	0.000	0.000	0.000	0.000
141	A	147	LEU	0	-0.034	-0.024	43.003	0.129	0.129	0.000	0.000	0.000	0.000
142	A	148	GLN	0	-0.060	-0.029	43.016	-0.040	-0.040	0.000	0.000	0.000	0.000
143	A	149	ARG	1	0.853	0.926	38.896	8.172	8.172	0.000	0.000	0.000	0.000
144	A	150	GLY	0	0.012	0.015	43.698	0.007	0.007	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.039	-0.018	42.455	0.053	0.053	0.000	0.000	0.000	0.000
146	A	152	GLN	0	0.051	-0.001	44.414	-0.061	-0.061	0.000	0.000	0.000	0.000
147	A	153	ASP	-1	-0.856	-0.910	43.841	-7.003	-7.003	0.000	0.000	0.000	0.000
148	A	154	LEU	0	-0.046	-0.033	39.398	-0.068	-0.068	0.000	0.000	0.000	0.000
149	A	155	VAL	0	-0.046	-0.015	43.062	0.004	0.004	0.000	0.000	0.000	0.000
150	A	156	ASP	-1	-0.904	-0.954	46.008	-6.393	-6.393	0.000	0.000	0.000	0.000
151	A	157	ILE	0	-0.035	-0.014	41.532	0.033	0.033	0.000	0.000	0.000	0.000
152	A	158	LEU	0	-0.028	-0.025	40.270	0.021	0.021	0.000	0.000	0.000	0.000
153	A	159	GLN	0	-0.008	-0.004	44.364	0.106	0.106	0.000	0.000	0.000	0.000
154	A	160	GLY	0	-0.034	-0.003	47.325	0.115	0.115	0.000	0.000	0.000	0.000
155	A	161	HIS	0	-0.012	-0.005	43.187	0.082	0.082	0.000	0.000	0.000	0.000
156	A	162	MET	0	-0.089	-0.031	45.884	0.122	0.122	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)