FMO DATABASE

FMODB ID: 1766Z

Calculation Name: 3NJE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJE

Chain ID: A

ChEMBL ID:

UniProt ID: Q00517

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1647831.854726
FMO2-HF: Nuclear repulsion	1583522.96707
FMO2-HF: Total energy	-64308.887656
FMO2-MP2: Total energy	-64498.867834

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:35:ARG)

Summations of interaction energy for fragment #1(A:35: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.
-62.379	-54.101	7.876	-7.275	-8.88	-0.074

Interaction energy analysis for fragmet #1(A:35:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.993 / q_NPA : 0.987

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	37	GLN	0	0.024	0.002	2.781	-3.435	-0.221	0.124	-1.450	-1.889	-0.003
4	A	38	GLU	-1	-0.818	-0.892	1.977	-100.827	-96.176	7.754	-5.772	-6.633	-0.071
5	A	39	GLN	0	-0.094	-0.053	4.519	-0.727	-0.447	-0.001	-0.049	-0.230	0.000
6	A	40	ARG	1	1.015	1.007	6.192	28.136	28.136	0.000	0.000	0.000	0.000
7	A	41	MET	0	0.040	0.040	7.961	2.621	2.621	0.000	0.000	0.000	0.000
8	A	42	ARG	1	0.859	0.907	4.256	50.705	50.838	-0.001	-0.004	-0.128	0.000
9	A	43	GLU	-1	-0.887	-0.934	9.920	-24.913	-24.913	0.000	0.000	0.000	0.000
10	A	44	LEU	0	0.045	0.031	12.239	1.630	1.630	0.000	0.000	0.000	0.000
11	A	45	VAL	0	0.012	0.001	13.388	1.485	1.485	0.000	0.000	0.000	0.000
12	A	46	ARG	1	0.896	0.953	12.524	23.851	23.851	0.000	0.000	0.000	0.000
13	A	47	ALA	0	0.003	0.007	16.249	1.164	1.164	0.000	0.000	0.000	0.000
14	A	48	MET	0	0.011	0.001	17.965	1.198	1.198	0.000	0.000	0.000	0.000
15	A	49	GLY	0	0.045	0.018	18.990	0.784	0.784	0.000	0.000	0.000	0.000
16	A	50	ALA	0	-0.076	-0.045	20.486	0.628	0.628	0.000	0.000	0.000	0.000
17	A	51	LEU	0	0.054	0.034	22.363	0.578	0.578	0.000	0.000	0.000	0.000
18	A	52	GLU	-1	-0.796	-0.864	22.843	-13.344	-13.344	0.000	0.000	0.000	0.000
19	A	53	ARG	1	0.920	0.960	19.688	15.484	15.484	0.000	0.000	0.000	0.000
20	A	54	ASP	-1	-0.725	-0.813	26.146	-11.379	-11.379	0.000	0.000	0.000	0.000
21	A	55	LEU	0	0.038	0.019	27.400	0.435	0.435	0.000	0.000	0.000	0.000
22	A	56	THR	0	-0.042	-0.031	28.131	0.414	0.414	0.000	0.000	0.000	0.000
23	A	57	GLN	0	-0.111	-0.063	30.049	0.241	0.241	0.000	0.000	0.000	0.000
24	A	58	ALA	0	0.046	0.035	32.555	0.183	0.183	0.000	0.000	0.000	0.000
25	A	59	VAL	0	-0.041	-0.027	34.880	0.092	0.092	0.000	0.000	0.000	0.000
26	A	60	GLU	-1	-0.728	-0.847	38.609	-7.859	-7.859	0.000	0.000	0.000	0.000
27	A	61	ARG	1	0.907	0.955	40.910	7.510	7.510	0.000	0.000	0.000	0.000
28	A	62	PRO	0	0.046	0.059	41.029	-0.259	-0.259	0.000	0.000	0.000	0.000
29	A	63	VAL	0	-0.068	-0.048	39.706	0.003	0.003	0.000	0.000	0.000	0.000
30	A	64	ARG	1	0.820	0.901	42.921	6.727	6.727	0.000	0.000	0.000	0.000
31	A	65	ASP	-1	-0.814	-0.906	41.696	-7.383	-7.383	0.000	0.000	0.000	0.000
32	A	66	GLU	-1	-0.954	-0.997	42.917	-7.209	-7.209	0.000	0.000	0.000	0.000
33	A	67	LEU	0	-0.052	-0.023	44.548	0.172	0.172	0.000	0.000	0.000	0.000
34	A	68	GLY	0	-0.009	-0.007	46.314	0.183	0.183	0.000	0.000	0.000	0.000
35	A	69	ASP	-1	-0.883	-0.937	44.180	-6.970	-6.970	0.000	0.000	0.000	0.000
36	A	70	ASN	0	-0.003	0.000	45.502	-0.094	-0.094	0.000	0.000	0.000	0.000
37	A	71	ARG	1	0.834	0.896	37.200	8.075	8.075	0.000	0.000	0.000	0.000
38	A	72	GLY	0	0.099	0.043	41.896	-0.046	-0.046	0.000	0.000	0.000	0.000
39	A	73	ALA	0	-0.040	-0.004	39.894	-0.249	-0.249	0.000	0.000	0.000	0.000
40	A	74	PHE	0	-0.026	-0.035	32.621	-0.360	-0.360	0.000	0.000	0.000	0.000
41	A	75	LEU	0	-0.021	0.010	36.483	0.228	0.228	0.000	0.000	0.000	0.000
42	A	76	SER	0	-0.037	-0.049	34.514	-0.322	-0.322	0.000	0.000	0.000	0.000
43	A	77	GLU	-1	-0.731	-0.837	34.577	-8.269	-8.269	0.000	0.000	0.000	0.000
44	A	78	GLY	0	-0.020	-0.009	33.797	-0.312	-0.312	0.000	0.000	0.000	0.000
45	A	79	GLU	-1	-0.910	-0.957	32.233	-8.823	-8.823	0.000	0.000	0.000	0.000
46	A	80	ASN	0	-0.069	-0.055	31.734	-0.083	-0.083	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.798	-0.864	32.499	-8.577	-8.577	0.000	0.000	0.000	0.000
48	A	82	GLN	0	-0.041	-0.027	27.042	-0.315	-0.315	0.000	0.000	0.000	0.000
49	A	83	ILE	0	-0.067	-0.022	28.984	-0.484	-0.484	0.000	0.000	0.000	0.000
50	A	84	VAL	0	0.042	0.028	30.296	0.294	0.294	0.000	0.000	0.000	0.000
51	A	85	GLU	-1	-0.803	-0.881	31.295	-9.041	-9.041	0.000	0.000	0.000	0.000
52	A	86	PHE	0	0.008	0.009	29.839	0.144	0.144	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.015	-0.008	34.446	-0.248	-0.248	0.000	0.000	0.000	0.000
54	A	88	ARG	1	0.800	0.885	28.621	10.674	10.674	0.000	0.000	0.000	0.000
55	A	89	GLY	0	0.090	0.042	34.462	0.172	0.172	0.000	0.000	0.000	0.000
56	A	90	GLY	0	-0.036	-0.008	33.051	-0.242	-0.242	0.000	0.000	0.000	0.000
57	A	91	TRP	0	-0.017	0.002	26.448	-0.204	-0.204	0.000	0.000	0.000	0.000
58	A	102	LEU	0	0.026	0.022	36.632	0.061	0.061	0.000	0.000	0.000	0.000
59	A	103	GLN	0	-0.053	-0.045	29.393	-0.198	-0.198	0.000	0.000	0.000	0.000
60	A	104	ARG	1	0.798	0.886	34.577	8.618	8.618	0.000	0.000	0.000	0.000
61	A	105	VAL	0	-0.034	-0.032	29.513	-0.284	-0.284	0.000	0.000	0.000	0.000
62	A	106	ARG	1	0.821	0.885	29.801	9.494	9.494	0.000	0.000	0.000	0.000
63	A	107	TRP	0	-0.036	-0.025	21.874	-0.712	-0.712	0.000	0.000	0.000	0.000
64	A	108	SER	0	0.011	0.004	25.982	0.468	0.468	0.000	0.000	0.000	0.000
65	A	109	LEU	0	0.028	0.010	22.237	-0.652	-0.652	0.000	0.000	0.000	0.000
66	A	110	SER	0	-0.019	0.000	23.741	0.630	0.630	0.000	0.000	0.000	0.000
67	A	111	GLY	0	0.029	0.011	23.122	-0.490	-0.490	0.000	0.000	0.000	0.000
68	A	112	GLU	-1	-0.762	-0.845	18.025	-14.023	-14.023	0.000	0.000	0.000	0.000
69	A	113	THR	0	-0.046	-0.033	18.269	-0.676	-0.676	0.000	0.000	0.000	0.000
70	A	114	LEU	0	-0.027	-0.010	19.270	0.688	0.688	0.000	0.000	0.000	0.000
71	A	115	GLU	-1	-0.809	-0.899	20.408	-12.972	-12.972	0.000	0.000	0.000	0.000
72	A	116	ARG	1	0.784	0.891	23.003	12.578	12.578	0.000	0.000	0.000	0.000
73	A	117	ARG	1	0.836	0.884	24.897	11.077	11.077	0.000	0.000	0.000	0.000
74	A	118	TYR	0	0.028	0.014	26.276	0.193	0.193	0.000	0.000	0.000	0.000
75	A	119	TRP	0	0.025	0.006	30.182	-0.225	-0.225	0.000	0.000	0.000	0.000
76	A	120	LEU	0	-0.007	-0.002	33.489	-0.069	-0.069	0.000	0.000	0.000	0.000
77	A	121	VAL	0	0.011	0.011	36.137	0.112	0.112	0.000	0.000	0.000	0.000
78	A	122	LEU	0	-0.027	-0.022	39.477	0.032	0.032	0.000	0.000	0.000	0.000
79	A	123	ASP	-1	-0.898	-0.938	42.474	-6.950	-6.950	0.000	0.000	0.000	0.000
80	A	124	ARG	1	0.795	0.882	43.875	7.342	7.342	0.000	0.000	0.000	0.000
81	A	125	ALA	0	0.090	0.062	42.156	-0.170	-0.170	0.000	0.000	0.000	0.000
82	A	126	GLN	0	0.064	0.043	41.298	-0.176	-0.176	0.000	0.000	0.000	0.000
83	A	127	ASP	-1	-0.830	-0.890	40.967	-7.879	-7.879	0.000	0.000	0.000	0.000
84	A	128	SER	0	-0.040	-0.018	37.162	-0.218	-0.218	0.000	0.000	0.000	0.000
85	A	129	LYS	1	0.785	0.870	34.685	8.327	8.327	0.000	0.000	0.000	0.000
86	A	130	PRO	0	-0.007	0.004	31.785	-0.276	-0.276	0.000	0.000	0.000	0.000
87	A	131	ARG	1	0.886	0.946	27.347	10.770	10.770	0.000	0.000	0.000	0.000
88	A	132	VAL	0	0.030	0.016	24.203	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	133	GLN	0	-0.030	-0.022	21.633	0.047	0.047	0.000	0.000	0.000	0.000
90	A	134	GLN	0	0.011	0.003	18.923	-0.420	-0.420	0.000	0.000	0.000	0.000
91	A	135	VAL	0	-0.072	-0.041	17.294	-0.703	-0.703	0.000	0.000	0.000	0.000
92	A	136	LEU	0	-0.026	-0.015	13.487	-1.225	-1.225	0.000	0.000	0.000	0.000
93	A	137	ASP	-1	-0.809	-0.881	14.498	-15.423	-15.423	0.000	0.000	0.000	0.000
94	A	138	GLY	0	0.016	0.026	14.493	-1.217	-1.217	0.000	0.000	0.000	0.000
95	A	139	VAL	0	-0.061	-0.042	15.925	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	140	THR	0	-0.028	-0.024	18.522	0.442	0.442	0.000	0.000	0.000	0.000
97	A	141	ALA	0	0.006	0.013	20.675	0.582	0.582	0.000	0.000	0.000	0.000
98	A	142	LEU	0	0.002	-0.006	22.111	-0.655	-0.655	0.000	0.000	0.000	0.000
99	A	143	SER	0	0.024	0.020	24.729	0.341	0.341	0.000	0.000	0.000	0.000
100	A	144	TRP	0	-0.032	-0.037	26.773	-0.599	-0.599	0.000	0.000	0.000	0.000
101	A	145	ARG	1	0.841	0.898	29.844	9.438	9.438	0.000	0.000	0.000	0.000
102	A	146	PHE	0	-0.005	-0.004	32.320	-0.350	-0.350	0.000	0.000	0.000	0.000
103	A	147	LEU	0	-0.052	0.000	35.098	0.200	0.200	0.000	0.000	0.000	0.000
104	A	148	ASP	-1	-0.687	-0.846	37.033	-7.401	-7.401	0.000	0.000	0.000	0.000
105	A	149	LYS	1	0.927	0.951	40.721	6.717	6.717	0.000	0.000	0.000	0.000
106	A	150	GLU	-1	-0.971	-0.979	43.432	-6.508	-6.508	0.000	0.000	0.000	0.000
107	A	151	HIS	0	-0.064	-0.036	39.941	-0.136	-0.136	0.000	0.000	0.000	0.000
108	A	152	ASN	0	-0.012	-0.003	39.680	-0.089	-0.089	0.000	0.000	0.000	0.000
109	A	153	TRP	0	-0.058	-0.044	32.138	-0.165	-0.165	0.000	0.000	0.000	0.000
110	A	154	GLN	0	0.017	0.005	36.934	0.008	0.008	0.000	0.000	0.000	0.000
111	A	155	GLY	0	-0.003	-0.018	35.432	-0.278	-0.278	0.000	0.000	0.000	0.000
112	A	156	HIS	0	-0.030	-0.003	35.393	-0.121	-0.121	0.000	0.000	0.000	0.000
113	A	157	TRP	0	-0.044	-0.023	37.153	0.031	0.031	0.000	0.000	0.000	0.000
114	A	158	PRO	0	0.058	0.020	38.768	-0.130	-0.130	0.000	0.000	0.000	0.000
115	A	159	THR	0	-0.003	-0.008	41.589	-0.045	-0.045	0.000	0.000	0.000	0.000
116	A	160	ASP	-1	-0.866	-0.938	43.467	-6.545	-6.545	0.000	0.000	0.000	0.000
117	A	161	GLU	-1	-0.930	-0.955	46.704	-6.223	-6.223	0.000	0.000	0.000	0.000
118	A	162	GLY	0	-0.003	-0.003	47.738	-0.129	-0.129	0.000	0.000	0.000	0.000
119	A	163	SER	0	-0.043	-0.054	50.305	0.045	0.045	0.000	0.000	0.000	0.000
120	A	164	GLU	-1	-0.867	-0.949	49.850	-6.584	-6.584	0.000	0.000	0.000	0.000
121	A	165	GLU	-1	-0.950	-0.966	48.908	-6.291	-6.291	0.000	0.000	0.000	0.000
122	A	166	GLU	-1	-0.828	-0.899	47.801	-6.528	-6.528	0.000	0.000	0.000	0.000
123	A	167	ARG	1	0.773	0.897	45.397	6.398	6.398	0.000	0.000	0.000	0.000
124	A	168	LEU	0	-0.013	0.005	44.230	-0.210	-0.210	0.000	0.000	0.000	0.000
125	A	169	GLU	-1	-0.921	-0.970	43.781	-7.203	-7.203	0.000	0.000	0.000	0.000
126	A	170	SER	0	-0.068	-0.047	42.905	-0.220	-0.220	0.000	0.000	0.000	0.000
127	A	171	LEU	0	-0.026	-0.014	37.179	-0.164	-0.164	0.000	0.000	0.000	0.000
128	A	172	PRO	0	-0.006	0.017	35.216	0.163	0.163	0.000	0.000	0.000	0.000
129	A	173	LEU	0	0.034	0.010	36.875	-0.166	-0.166	0.000	0.000	0.000	0.000
130	A	174	ALA	0	-0.046	-0.034	32.615	-0.240	-0.240	0.000	0.000	0.000	0.000
131	A	175	VAL	0	0.020	0.026	29.409	0.190	0.190	0.000	0.000	0.000	0.000
132	A	176	GLU	-1	-0.857	-0.882	28.199	-10.216	-10.216	0.000	0.000	0.000	0.000
133	A	177	MET	0	-0.008	0.003	21.297	-0.056	-0.056	0.000	0.000	0.000	0.000
134	A	178	THR	0	-0.006	-0.008	23.762	-0.352	-0.352	0.000	0.000	0.000	0.000
135	A	179	LEU	0	0.003	0.003	17.803	0.107	0.107	0.000	0.000	0.000	0.000
136	A	180	GLU	-1	-0.814	-0.905	19.044	-11.960	-11.960	0.000	0.000	0.000	0.000
137	A	181	HIS	0	-0.006	-0.007	11.561	0.033	0.033	0.000	0.000	0.000	0.000
138	A	182	ARG	1	0.841	0.871	14.359	13.568	13.568	0.000	0.000	0.000	0.000
139	A	183	HIS	0	-0.068	-0.041	9.282	-0.820	-0.820	0.000	0.000	0.000	0.000
140	A	184	TYR	0	-0.050	-0.025	10.169	-1.724	-1.724	0.000	0.000	0.000	0.000
141	A	185	GLY	0	0.034	0.034	12.577	0.394	0.394	0.000	0.000	0.000	0.000
142	A	186	LYS	1	0.824	0.898	16.215	11.368	11.368	0.000	0.000	0.000	0.000
143	A	187	LEU	0	-0.037	-0.015	17.124	-0.461	-0.461	0.000	0.000	0.000	0.000
144	A	188	VAL	0	0.019	0.004	19.518	0.392	0.392	0.000	0.000	0.000	0.000
145	A	189	ARG	1	0.803	0.903	20.618	13.239	13.239	0.000	0.000	0.000	0.000
146	A	190	VAL	0	0.030	0.012	23.990	0.366	0.366	0.000	0.000	0.000	0.000
147	A	191	TRP	0	-0.065	-0.063	22.670	-0.322	-0.322	0.000	0.000	0.000	0.000
148	A	192	ARG	1	0.964	0.984	28.931	9.484	9.484	0.000	0.000	0.000	0.000
149	A	193	LEU	0	-0.006	0.008	31.867	-0.333	-0.333	0.000	0.000	0.000	0.000
150	A	194	LEU	0	-0.067	-0.036	32.915	0.033	0.033	0.000	0.000	0.000	0.000
151	A	195	ASP	-1	-0.920	-0.934	35.731	-7.743	-7.743	0.000	0.000	0.000	0.000
152	A	196	PRO	0	0.001	-0.016	39.308	0.083	0.083	0.000	0.000	0.000	0.000
153	A	197	PRO	0	0.020	0.007	37.665	-0.183	-0.183	0.000	0.000	0.000	0.000
154	A	198	LEU	0	-0.011	0.016	34.777	0.193	0.193	0.000	0.000	0.000	0.000
155	A	199	LYS	1	0.811	0.871	38.096	7.929	7.929	0.000	0.000	0.000	0.000
156	A	200	GLN	0	-0.005	0.002	37.322	-0.246	-0.246	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:35:ARG)