FMO DATABASE

FMODB ID: YZNN2

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	OptH
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	-1645493.54872
FMO2-HF: Nuclear repulsion	1581185.873311
FMO2-HF: Total energy	-64307.675409
FMO2-MP2: Total energy	-64497.695004

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.
-19.114	-14.874	0.148	-1.549	-2.837	0.001

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 : 1.047 / q_NPA : 1.013

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	0.015	-0.003	3.056	-2.751	-0.358	0.034	-1.016	-1.410	0.003
4	A	38	GLU	-1	-0.907	-0.949	2.995	-46.866	-45.452	0.115	-0.418	-1.110	-0.002
5	A	39	GLN	0	-0.096	-0.052	4.104	-1.958	-1.525	-0.001	-0.115	-0.317	0.000
6	A	40	ARG	1	0.988	0.989	5.705	27.801	27.801	0.000	0.000	0.000	0.000
7	A	41	MET	0	0.044	0.044	7.905	2.256	2.256	0.000	0.000	0.000	0.000
8	A	42	ARG	1	0.953	0.963	6.803	39.598	39.598	0.000	0.000	0.000	0.000
9	A	43	GLU	-1	-0.900	-0.938	9.565	-25.044	-25.044	0.000	0.000	0.000	0.000
10	A	44	LEU	0	0.053	0.031	11.890	1.686	1.686	0.000	0.000	0.000	0.000
11	A	45	VAL	0	-0.020	-0.012	13.086	1.423	1.423	0.000	0.000	0.000	0.000
12	A	46	ARG	1	0.912	0.948	12.105	22.999	22.999	0.000	0.000	0.000	0.000
13	A	47	ALA	0	-0.005	0.012	15.884	1.092	1.092	0.000	0.000	0.000	0.000
14	A	48	MET	0	0.014	0.000	17.779	1.179	1.179	0.000	0.000	0.000	0.000
15	A	49	GLY	0	0.024	0.019	18.775	0.715	0.715	0.000	0.000	0.000	0.000
16	A	50	ALA	0	-0.074	-0.051	20.154	0.678	0.678	0.000	0.000	0.000	0.000
17	A	51	LEU	0	0.059	0.039	22.094	0.540	0.540	0.000	0.000	0.000	0.000
18	A	52	GLU	-1	-0.861	-0.917	23.471	-12.365	-12.365	0.000	0.000	0.000	0.000
19	A	53	ARG	1	0.921	0.953	19.991	14.908	14.908	0.000	0.000	0.000	0.000
20	A	54	ASP	-1	-0.746	-0.847	26.295	-11.422	-11.422	0.000	0.000	0.000	0.000
21	A	55	LEU	0	0.028	0.016	27.376	0.428	0.428	0.000	0.000	0.000	0.000
22	A	56	THR	0	-0.054	-0.032	28.628	0.385	0.385	0.000	0.000	0.000	0.000
23	A	57	GLN	0	-0.075	-0.037	29.933	0.493	0.493	0.000	0.000	0.000	0.000
24	A	58	ALA	0	0.036	0.030	32.428	0.208	0.208	0.000	0.000	0.000	0.000
25	A	59	VAL	0	-0.043	-0.031	34.452	0.141	0.141	0.000	0.000	0.000	0.000
26	A	60	GLU	-1	-0.878	-0.939	38.143	-7.586	-7.586	0.000	0.000	0.000	0.000
27	A	61	ARG	1	0.890	0.949	40.386	7.559	7.559	0.000	0.000	0.000	0.000
28	A	62	PRO	0	0.067	0.060	40.656	-0.252	-0.252	0.000	0.000	0.000	0.000
29	A	63	VAL	0	-0.059	-0.040	39.320	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	64	ARG	1	0.911	0.961	42.511	6.579	6.579	0.000	0.000	0.000	0.000
31	A	65	ASP	-1	-0.833	-0.922	41.653	-7.381	-7.381	0.000	0.000	0.000	0.000
32	A	66	GLU	-1	-0.957	-1.001	42.230	-7.270	-7.270	0.000	0.000	0.000	0.000
33	A	67	LEU	0	-0.038	-0.018	44.316	0.144	0.144	0.000	0.000	0.000	0.000
34	A	68	GLY	0	-0.048	-0.013	46.390	0.177	0.177	0.000	0.000	0.000	0.000
35	A	69	ASP	-1	-0.894	-0.934	44.871	-6.780	-6.780	0.000	0.000	0.000	0.000
36	A	70	ASN	0	-0.042	-0.031	45.018	-0.191	-0.191	0.000	0.000	0.000	0.000
37	A	71	ARG	1	0.845	0.911	37.071	8.049	8.049	0.000	0.000	0.000	0.000
38	A	72	GLY	0	0.079	0.031	41.544	0.004	0.004	0.000	0.000	0.000	0.000
39	A	73	ALA	0	-0.037	-0.016	39.604	-0.226	-0.226	0.000	0.000	0.000	0.000
40	A	74	PHE	0	-0.013	-0.027	32.490	-0.352	-0.352	0.000	0.000	0.000	0.000
41	A	75	LEU	0	-0.029	0.005	36.120	0.219	0.219	0.000	0.000	0.000	0.000
42	A	76	SER	0	-0.033	-0.055	34.550	-0.301	-0.301	0.000	0.000	0.000	0.000
43	A	77	GLU	-1	-0.732	-0.848	34.620	-8.180	-8.180	0.000	0.000	0.000	0.000
44	A	78	GLY	0	-0.027	-0.014	34.024	-0.301	-0.301	0.000	0.000	0.000	0.000
45	A	79	GLU	-1	-0.934	-0.970	32.651	-8.813	-8.813	0.000	0.000	0.000	0.000
46	A	80	ASN	0	-0.060	-0.050	32.387	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.784	-0.851	33.138	-8.402	-8.402	0.000	0.000	0.000	0.000
48	A	82	GLN	0	-0.023	-0.009	27.618	-0.252	-0.252	0.000	0.000	0.000	0.000
49	A	83	ILE	0	-0.064	-0.033	29.269	-0.492	-0.492	0.000	0.000	0.000	0.000
50	A	84	VAL	0	0.037	0.034	29.971	0.290	0.290	0.000	0.000	0.000	0.000
51	A	85	GLU	-1	-0.815	-0.911	30.931	-9.164	-9.164	0.000	0.000	0.000	0.000
52	A	86	PHE	0	0.000	0.000	29.294	0.144	0.144	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.025	-0.010	33.863	-0.273	-0.273	0.000	0.000	0.000	0.000
54	A	88	ARG	1	0.855	0.914	27.592	10.609	10.609	0.000	0.000	0.000	0.000
55	A	89	GLY	0	0.082	0.043	34.098	0.142	0.142	0.000	0.000	0.000	0.000
56	A	90	GLY	0	-0.019	0.004	32.358	-0.316	-0.316	0.000	0.000	0.000	0.000
57	A	91	TRP	0	-0.035	-0.007	26.075	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	102	LEU	0	-0.027	-0.020	35.967	-0.047	-0.047	0.000	0.000	0.000	0.000
59	A	103	GLN	0	-0.059	-0.039	29.513	-0.199	-0.199	0.000	0.000	0.000	0.000
60	A	104	ARG	1	0.844	0.925	33.735	8.611	8.611	0.000	0.000	0.000	0.000
61	A	105	VAL	0	-0.040	-0.026	28.724	-0.320	-0.320	0.000	0.000	0.000	0.000
62	A	106	ARG	1	0.841	0.904	29.232	9.576	9.576	0.000	0.000	0.000	0.000
63	A	107	TRP	0	-0.031	-0.015	21.528	-0.746	-0.746	0.000	0.000	0.000	0.000
64	A	108	SER	0	0.040	0.011	25.944	0.468	0.468	0.000	0.000	0.000	0.000
65	A	109	LEU	0	0.010	0.006	22.237	-0.619	-0.619	0.000	0.000	0.000	0.000
66	A	110	SER	0	-0.029	0.005	24.043	0.591	0.591	0.000	0.000	0.000	0.000
67	A	111	GLY	0	0.037	0.018	23.381	-0.490	-0.490	0.000	0.000	0.000	0.000
68	A	112	GLU	-1	-0.783	-0.868	18.591	-14.018	-14.018	0.000	0.000	0.000	0.000
69	A	113	THR	0	-0.052	-0.014	18.551	-0.719	-0.719	0.000	0.000	0.000	0.000
70	A	114	LEU	0	-0.014	-0.005	19.486	0.673	0.673	0.000	0.000	0.000	0.000
71	A	115	GLU	-1	-0.850	-0.921	20.543	-12.937	-12.937	0.000	0.000	0.000	0.000
72	A	116	ARG	1	0.783	0.882	23.102	12.642	12.642	0.000	0.000	0.000	0.000
73	A	117	ARG	1	0.887	0.920	24.709	10.839	10.839	0.000	0.000	0.000	0.000
74	A	118	TYR	0	0.031	0.005	24.845	0.103	0.103	0.000	0.000	0.000	0.000
75	A	119	TRP	0	0.006	0.006	29.569	-0.275	-0.275	0.000	0.000	0.000	0.000
76	A	120	LEU	0	-0.020	-0.009	32.633	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	121	VAL	0	0.028	0.022	35.109	0.092	0.092	0.000	0.000	0.000	0.000
78	A	122	LEU	0	-0.039	-0.029	38.339	0.029	0.029	0.000	0.000	0.000	0.000
79	A	123	ASP	-1	-0.897	-0.939	41.437	-6.872	-6.872	0.000	0.000	0.000	0.000
80	A	124	ARG	1	0.844	0.909	42.320	7.437	7.437	0.000	0.000	0.000	0.000
81	A	125	ALA	0	0.069	0.043	41.194	-0.162	-0.162	0.000	0.000	0.000	0.000
82	A	126	GLN	0	0.045	0.033	40.613	-0.245	-0.245	0.000	0.000	0.000	0.000
83	A	127	ASP	-1	-0.968	-0.991	39.400	-8.083	-8.083	0.000	0.000	0.000	0.000
84	A	128	SER	0	-0.007	0.023	36.359	-0.198	-0.198	0.000	0.000	0.000	0.000
85	A	129	LYS	1	0.916	0.943	33.300	8.713	8.713	0.000	0.000	0.000	0.000
86	A	130	PRO	0	-0.009	0.003	31.431	-0.297	-0.297	0.000	0.000	0.000	0.000
87	A	131	ARG	1	0.879	0.950	26.325	10.840	10.840	0.000	0.000	0.000	0.000
88	A	132	VAL	0	0.033	0.008	24.227	0.070	0.070	0.000	0.000	0.000	0.000
89	A	133	GLN	0	-0.034	-0.009	20.650	-0.169	-0.169	0.000	0.000	0.000	0.000
90	A	134	GLN	0	0.013	-0.015	18.928	-0.325	-0.325	0.000	0.000	0.000	0.000
91	A	135	VAL	0	-0.071	-0.037	17.367	-0.876	-0.876	0.000	0.000	0.000	0.000
92	A	136	LEU	0	-0.023	-0.011	13.876	-1.186	-1.186	0.000	0.000	0.000	0.000
93	A	137	ASP	-1	-0.804	-0.888	14.272	-16.277	-16.277	0.000	0.000	0.000	0.000
94	A	138	GLY	0	-0.026	-0.009	15.046	-0.825	-0.825	0.000	0.000	0.000	0.000
95	A	139	VAL	0	-0.034	-0.026	16.288	0.114	0.114	0.000	0.000	0.000	0.000
96	A	140	THR	0	0.012	-0.004	18.920	0.231	0.231	0.000	0.000	0.000	0.000
97	A	141	ALA	0	-0.007	0.007	21.282	0.576	0.576	0.000	0.000	0.000	0.000
98	A	142	LEU	0	-0.006	-0.006	22.686	-0.588	-0.588	0.000	0.000	0.000	0.000
99	A	143	SER	0	-0.013	-0.003	25.139	0.457	0.457	0.000	0.000	0.000	0.000
100	A	144	TRP	0	0.010	-0.019	26.141	-0.566	-0.566	0.000	0.000	0.000	0.000
101	A	145	ARG	1	0.842	0.914	30.023	9.296	9.296	0.000	0.000	0.000	0.000
102	A	146	PHE	0	0.000	-0.005	32.266	-0.345	-0.345	0.000	0.000	0.000	0.000
103	A	147	LEU	0	-0.042	0.001	35.023	0.175	0.175	0.000	0.000	0.000	0.000
104	A	148	ASP	-1	-0.687	-0.845	37.028	-7.286	-7.286	0.000	0.000	0.000	0.000
105	A	149	LYS	1	0.947	0.956	40.741	6.757	6.757	0.000	0.000	0.000	0.000
106	A	150	GLU	-1	-0.976	-0.978	43.309	-6.440	-6.440	0.000	0.000	0.000	0.000
107	A	151	HIS	0	-0.095	-0.050	40.274	-0.124	-0.124	0.000	0.000	0.000	0.000
108	A	152	ASN	0	0.020	0.016	40.087	-0.137	-0.137	0.000	0.000	0.000	0.000
109	A	153	TRP	0	-0.068	-0.046	32.190	-0.160	-0.160	0.000	0.000	0.000	0.000
110	A	154	GLN	0	0.001	-0.007	37.208	0.104	0.104	0.000	0.000	0.000	0.000
111	A	155	GLY	0	-0.023	-0.026	35.286	-0.273	-0.273	0.000	0.000	0.000	0.000
112	A	156	HIS	0	-0.008	0.007	35.408	-0.143	-0.143	0.000	0.000	0.000	0.000
113	A	157	TRP	0	-0.051	-0.013	37.091	0.057	0.057	0.000	0.000	0.000	0.000
114	A	158	PRO	0	0.024	-0.002	38.839	-0.125	-0.125	0.000	0.000	0.000	0.000
115	A	159	THR	0	0.012	-0.006	41.520	0.007	0.007	0.000	0.000	0.000	0.000
116	A	160	ASP	-1	-0.932	-0.982	43.649	-6.476	-6.476	0.000	0.000	0.000	0.000
117	A	161	GLU	-1	-0.986	-0.982	46.785	-6.218	-6.218	0.000	0.000	0.000	0.000
118	A	162	GLY	0	0.010	0.004	48.163	-0.095	-0.095	0.000	0.000	0.000	0.000
119	A	163	SER	0	-0.058	-0.033	50.662	0.003	0.003	0.000	0.000	0.000	0.000
120	A	164	GLU	-1	-0.906	-0.980	49.854	-6.460	-6.460	0.000	0.000	0.000	0.000
121	A	165	GLU	-1	-0.969	-0.977	48.565	-6.317	-6.317	0.000	0.000	0.000	0.000
122	A	166	GLU	-1	-0.847	-0.922	47.817	-6.347	-6.347	0.000	0.000	0.000	0.000
123	A	167	ARG	1	0.948	0.982	45.381	6.520	6.520	0.000	0.000	0.000	0.000
124	A	168	LEU	0	-0.057	-0.030	43.888	-0.239	-0.239	0.000	0.000	0.000	0.000
125	A	169	GLU	-1	-0.909	-0.957	43.339	-6.935	-6.935	0.000	0.000	0.000	0.000
126	A	170	SER	0	-0.061	-0.008	42.696	-0.176	-0.176	0.000	0.000	0.000	0.000
127	A	171	LEU	0	-0.025	-0.019	36.643	-0.186	-0.186	0.000	0.000	0.000	0.000
128	A	172	PRO	0	0.008	0.023	35.059	0.143	0.143	0.000	0.000	0.000	0.000
129	A	173	LEU	0	0.031	0.008	36.900	-0.121	-0.121	0.000	0.000	0.000	0.000
130	A	174	ALA	0	-0.059	-0.037	32.589	-0.215	-0.215	0.000	0.000	0.000	0.000
131	A	175	VAL	0	0.028	0.027	29.221	0.177	0.177	0.000	0.000	0.000	0.000
132	A	176	GLU	-1	-0.857	-0.903	27.900	-10.055	-10.055	0.000	0.000	0.000	0.000
133	A	177	MET	0	-0.014	0.009	20.991	-0.063	-0.063	0.000	0.000	0.000	0.000
134	A	178	THR	0	0.007	-0.005	23.914	-0.286	-0.286	0.000	0.000	0.000	0.000
135	A	179	LEU	0	-0.032	-0.018	17.728	0.082	0.082	0.000	0.000	0.000	0.000
136	A	180	GLU	-1	-0.937	-0.965	19.455	-11.805	-11.805	0.000	0.000	0.000	0.000
137	A	181	HIS	0	0.004	0.003	11.907	-0.100	-0.100	0.000	0.000	0.000	0.000
138	A	182	ARG	1	0.804	0.855	14.515	13.910	13.910	0.000	0.000	0.000	0.000
139	A	183	HIS	0	-0.068	-0.051	9.917	-0.327	-0.327	0.000	0.000	0.000	0.000
140	A	184	TYR	0	-0.030	-0.016	11.518	-0.709	-0.709	0.000	0.000	0.000	0.000
141	A	185	GLY	0	0.051	0.044	12.833	0.373	0.373	0.000	0.000	0.000	0.000
142	A	186	LYS	1	0.969	0.981	16.383	10.844	10.844	0.000	0.000	0.000	0.000
143	A	187	LEU	0	-0.045	-0.020	17.571	-0.281	-0.281	0.000	0.000	0.000	0.000
144	A	188	VAL	0	0.027	0.011	19.788	0.266	0.266	0.000	0.000	0.000	0.000
145	A	189	ARG	1	0.874	0.951	19.676	13.377	13.377	0.000	0.000	0.000	0.000
146	A	190	VAL	0	0.050	0.023	24.098	0.279	0.279	0.000	0.000	0.000	0.000
147	A	191	TRP	0	-0.078	-0.048	22.502	-0.261	-0.261	0.000	0.000	0.000	0.000
148	A	192	ARG	1	0.972	0.985	28.810	9.280	9.280	0.000	0.000	0.000	0.000
149	A	193	LEU	0	-0.020	-0.005	31.970	-0.295	-0.295	0.000	0.000	0.000	0.000
150	A	194	LEU	0	-0.060	-0.030	33.538	0.106	0.106	0.000	0.000	0.000	0.000
151	A	195	ASP	-1	-0.928	-0.929	35.801	-7.555	-7.555	0.000	0.000	0.000	0.000
152	A	196	PRO	0	-0.039	-0.034	39.200	0.091	0.091	0.000	0.000	0.000	0.000
153	A	197	PRO	0	0.062	0.017	37.878	-0.184	-0.184	0.000	0.000	0.000	0.000
154	A	198	LEU	0	-0.024	-0.005	34.927	0.222	0.222	0.000	0.000	0.000	0.000
155	A	199	LYS	1	0.988	0.998	38.434	7.378	7.378	0.000	0.000	0.000	0.000
156	A	200	GLN	0	-0.009	-0.008	37.031	-0.183	-0.183	0.000	0.000	0.000	0.000

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