FMO DATABASE

FMODB ID: 1NY2Z

Calculation Name: 3EJF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJF

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6Y1

Base Structure: X-ray

Registration Date: 2023-09-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1685978.72313
FMO2-HF: Nuclear repulsion	1620199.974074
FMO2-HF: Total energy	-65778.749056
FMO2-MP2: Total energy	-65966.598484

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:6:LYS)

Summations of interaction energy for fragment #1(A:6:LYS)

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.
-145.904	-139.947	13.625	-8.976	-10.605	-0.079

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.917 / q_NPA : 0.940

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	8	LYS	1	0.921	0.941	2.875	17.133	19.584	0.284	-1.303	-1.432	-0.007
4	A	9	PHE	0	0.003	-0.001	5.428	0.264	0.264	0.000	0.000	0.000	0.000
5	A	10	LEU	0	0.021	0.028	6.486	-2.388	-2.388	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.831	-0.892	6.911	-26.088	-26.088	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.050	0.010	9.353	-0.353	-0.353	0.000	0.000	0.000	0.000
8	A	13	LYS	1	0.809	0.897	10.827	19.472	19.472	0.000	0.000	0.000	0.000
9	A	14	THR	0	0.029	0.029	14.476	-0.273	-0.273	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.018	-0.024	17.998	0.294	0.294	0.000	0.000	0.000	0.000
11	A	16	VAL	0	0.031	0.025	20.559	-0.100	-0.100	0.000	0.000	0.000	0.000
12	A	17	GLY	0	-0.010	-0.008	24.292	0.333	0.333	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.800	-0.887	24.922	-11.028	-11.028	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.002	0.007	21.213	-0.367	-0.367	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.041	-0.046	22.197	-0.450	-0.450	0.000	0.000	0.000	0.000
16	A	21	VAL	0	-0.009	0.000	22.602	-0.260	-0.260	0.000	0.000	0.000	0.000
17	A	22	VAL	0	0.007	0.004	18.312	-0.441	-0.441	0.000	0.000	0.000	0.000
18	A	23	ILE	0	0.018	0.012	18.011	-0.821	-0.821	0.000	0.000	0.000	0.000
19	A	24	ALA	0	-0.011	-0.001	17.967	-0.453	-0.453	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.842	0.904	16.491	14.414	14.414	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.006	0.006	13.951	-0.548	-0.548	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.021	-0.016	13.539	-0.840	-0.840	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.900	-0.936	15.358	-14.218	-14.218	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.794	-0.871	12.982	-16.271	-16.271	0.000	0.000	0.000	0.000
25	A	30	PHE	0	-0.035	-0.028	8.981	-1.470	-1.470	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.758	0.896	9.729	14.669	14.669	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.918	-0.959	8.575	-22.299	-22.299	0.000	0.000	0.000	0.000
28	A	33	PHE	0	0.002	-0.007	9.451	-1.499	-1.499	0.000	0.000	0.000	0.000
29	A	34	CYS	0	-0.027	0.016	10.879	1.360	1.360	0.000	0.000	0.000	0.000
30	A	35	ILE	0	-0.024	-0.015	12.944	-0.230	-0.230	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.027	0.008	14.799	0.155	0.155	0.000	0.000	0.000	0.000
32	A	37	ASN	0	-0.018	-0.030	17.186	0.888	0.888	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.000	0.001	20.837	-0.222	-0.222	0.000	0.000	0.000	0.000
34	A	39	ALA	0	0.017	0.020	22.847	0.657	0.657	0.000	0.000	0.000	0.000
35	A	40	ASN	0	-0.025	-0.026	24.877	0.185	0.185	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.754	-0.855	26.665	-10.778	-10.778	0.000	0.000	0.000	0.000
37	A	42	HIS	0	-0.019	-0.010	27.730	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	43	MET	0	-0.053	-0.018	23.129	0.032	0.032	0.000	0.000	0.000	0.000
39	A	44	THR	0	0.032	0.021	27.623	-0.077	-0.077	0.000	0.000	0.000	0.000
40	A	45	HIS	0	-0.029	-0.037	24.822	0.356	0.356	0.000	0.000	0.000	0.000
41	A	46	GLY	0	0.050	0.033	29.050	0.071	0.071	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.049	-0.032	30.977	0.197	0.197	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.034	0.015	29.213	-0.314	-0.314	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.021	-0.003	23.095	0.135	0.135	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.049	0.038	25.295	-0.137	-0.137	0.000	0.000	0.000	0.000
46	A	51	LYS	1	0.813	0.903	26.287	9.385	9.385	0.000	0.000	0.000	0.000
47	A	52	ALA	0	0.023	0.014	26.266	0.083	0.083	0.000	0.000	0.000	0.000
48	A	53	ILE	0	-0.012	-0.013	21.276	-0.089	-0.089	0.000	0.000	0.000	0.000
49	A	54	ALA	0	0.024	0.006	24.606	-0.105	-0.105	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.840	-0.895	27.496	-9.498	-9.498	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.062	-0.036	22.050	0.091	0.091	0.000	0.000	0.000	0.000
52	A	57	CYS	0	-0.069	-0.041	22.546	-0.345	-0.345	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.025	0.028	24.814	0.015	0.015	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.005	-0.009	28.469	-0.188	-0.188	0.000	0.000	0.000	0.000
55	A	60	ASP	-1	-0.862	-0.926	27.471	-10.435	-10.435	0.000	0.000	0.000	0.000
56	A	61	PHE	0	-0.014	-0.006	22.165	-0.275	-0.275	0.000	0.000	0.000	0.000
57	A	62	VAL	0	0.018	0.011	25.912	-0.204	-0.204	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.879	-0.947	28.631	-9.376	-9.376	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.016	-0.016	21.887	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	65	CYS	0	-0.052	-0.005	24.872	-0.328	-0.328	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.849	-0.923	26.607	-9.154	-9.154	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.826	-0.905	29.772	-9.557	-9.557	0.000	0.000	0.000	0.000
63	A	68	TYR	0	0.011	0.011	23.060	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.015	-0.009	27.586	0.065	0.065	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.749	0.858	29.507	9.553	9.553	0.000	0.000	0.000	0.000
66	A	71	LYS	1	0.809	0.907	29.872	10.308	10.308	0.000	0.000	0.000	0.000
67	A	72	HIS	0	-0.061	-0.027	26.512	0.144	0.144	0.000	0.000	0.000	0.000
68	A	73	GLY	0	0.022	0.029	28.900	-0.089	-0.089	0.000	0.000	0.000	0.000
69	A	74	PRO	0	-0.010	-0.019	28.685	-0.343	-0.343	0.000	0.000	0.000	0.000
70	A	75	GLN	0	-0.059	-0.033	23.563	-0.682	-0.682	0.000	0.000	0.000	0.000
71	A	76	GLN	0	0.001	-0.031	22.526	0.024	0.024	0.000	0.000	0.000	0.000
72	A	77	ARG	1	0.822	0.896	12.431	21.619	21.619	0.000	0.000	0.000	0.000
73	A	78	LEU	0	-0.007	0.007	19.842	0.126	0.126	0.000	0.000	0.000	0.000
74	A	79	VAL	0	0.029	0.019	14.601	0.015	0.015	0.000	0.000	0.000	0.000
75	A	80	THR	0	-0.017	-0.012	17.662	0.550	0.550	0.000	0.000	0.000	0.000
76	A	81	PRO	0	-0.007	-0.001	18.460	-0.824	-0.824	0.000	0.000	0.000	0.000
77	A	82	SER	0	0.010	-0.029	18.289	0.625	0.625	0.000	0.000	0.000	0.000
78	A	83	PHE	0	0.014	0.008	20.681	0.398	0.398	0.000	0.000	0.000	0.000
79	A	84	VAL	0	0.032	0.028	19.842	0.473	0.473	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.944	0.963	17.927	12.974	12.974	0.000	0.000	0.000	0.000
81	A	86	GLY	0	0.030	0.015	14.947	0.350	0.350	0.000	0.000	0.000	0.000
82	A	87	ILE	0	0.013	0.014	13.979	-1.156	-1.156	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.059	-0.019	8.739	-0.279	-0.279	0.000	0.000	0.000	0.000
84	A	89	CYS	0	-0.026	-0.020	13.616	-0.122	-0.122	0.000	0.000	0.000	0.000
85	A	90	VAL	0	0.030	0.030	15.787	-0.530	-0.530	0.000	0.000	0.000	0.000
86	A	91	ASN	0	-0.048	-0.028	13.638	1.121	1.121	0.000	0.000	0.000	0.000
87	A	92	ASN	0	-0.008	-0.010	16.745	0.668	0.668	0.000	0.000	0.000	0.000
88	A	93	VAL	0	0.007	0.005	16.740	0.047	0.047	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.023	0.002	20.137	0.581	0.581	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.026	0.008	22.051	-0.633	-0.633	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.044	-0.018	23.799	0.329	0.329	0.000	0.000	0.000	0.000
92	A	97	ARG	1	0.879	0.911	26.832	10.688	10.688	0.000	0.000	0.000	0.000
93	A	98	HIS	0	0.041	0.002	30.148	-0.150	-0.150	0.000	0.000	0.000	0.000
94	A	99	GLY	0	-0.031	-0.014	33.528	0.102	0.102	0.000	0.000	0.000	0.000
95	A	100	ASP	-1	-0.830	-0.907	28.617	-10.982	-10.982	0.000	0.000	0.000	0.000
96	A	101	ASN	0	-0.027	-0.027	30.740	0.268	0.268	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.044	-0.027	27.512	0.001	0.001	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.035	0.020	26.670	-0.535	-0.535	0.000	0.000	0.000	0.000
99	A	104	HIS	0	-0.006	-0.006	21.860	0.068	0.068	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.772	-0.874	22.560	-12.822	-12.822	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.824	0.899	21.672	10.980	10.980	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.002	0.002	21.972	-0.442	-0.442	0.000	0.000	0.000	0.000
103	A	108	VAL	0	-0.014	0.008	17.397	-0.859	-0.859	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.002	-0.002	17.299	-1.235	-1.235	0.000	0.000	0.000	0.000
105	A	110	ALA	0	0.006	0.017	17.520	-0.835	-0.835	0.000	0.000	0.000	0.000
106	A	111	TYR	0	0.014	-0.017	15.701	-0.876	-0.876	0.000	0.000	0.000	0.000
107	A	112	LYS	1	0.823	0.906	13.094	21.300	21.300	0.000	0.000	0.000	0.000
108	A	113	ASN	0	-0.058	-0.034	12.845	-1.533	-1.533	0.000	0.000	0.000	0.000
109	A	114	VAL	0	-0.011	0.007	12.003	0.044	0.044	0.000	0.000	0.000	0.000
110	A	115	LEU	0	0.001	0.013	7.141	-0.788	-0.788	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.045	0.012	8.918	2.773	2.773	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.873	-0.927	8.031	-30.853	-30.853	0.000	0.000	0.000	0.000
113	A	118	GLY	0	-0.006	-0.005	5.860	1.917	1.917	0.000	0.000	0.000	0.000
114	A	119	VAL	0	-0.047	-0.008	5.820	-2.425	-2.425	0.000	0.000	0.000	0.000
115	A	120	VAL	0	-0.014	0.005	2.130	-7.536	-7.281	5.236	-2.481	-3.010	-0.010
116	A	121	ASN	0	-0.006	-0.021	4.652	-2.081	-2.012	-0.001	-0.009	-0.058	0.000
117	A	122	TYR	0	0.027	0.010	6.525	2.682	2.682	0.000	0.000	0.000	0.000
118	A	123	VAL	0	0.004	0.007	10.862	0.556	0.556	0.000	0.000	0.000	0.000
119	A	124	VAL	0	0.007	-0.004	13.882	0.105	0.105	0.000	0.000	0.000	0.000
120	A	125	PRO	0	0.019	0.030	16.691	0.425	0.425	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.027	-0.003	20.020	-0.447	-0.447	0.000	0.000	0.000	0.000
122	A	127	LEU	0	-0.002	0.004	18.495	0.716	0.716	0.000	0.000	0.000	0.000
123	A	128	SER	0	0.037	-0.003	22.727	0.089	0.089	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.004	0.012	26.099	0.395	0.395	0.000	0.000	0.000	0.000
125	A	130	GLY	0	-0.011	0.011	28.453	0.346	0.346	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.060	-0.016	28.311	0.335	0.335	0.000	0.000	0.000	0.000
127	A	132	PHE	0	-0.010	-0.016	31.259	0.029	0.029	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.024	0.008	33.161	-0.057	-0.057	0.000	0.000	0.000	0.000
129	A	134	VAL	0	-0.026	-0.009	26.883	-0.267	-0.267	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.816	-0.902	29.009	-10.552	-10.552	0.000	0.000	0.000	0.000
131	A	136	PHE	0	0.016	-0.024	26.000	-0.421	-0.421	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.821	0.924	25.054	9.873	9.873	0.000	0.000	0.000	0.000
133	A	138	MET	0	0.006	0.008	24.868	-0.438	-0.438	0.000	0.000	0.000	0.000
134	A	139	SER	0	-0.012	-0.003	23.109	-0.870	-0.870	0.000	0.000	0.000	0.000
135	A	140	ILE	0	0.011	0.005	20.665	-0.809	-0.809	0.000	0.000	0.000	0.000
136	A	141	ASP	-1	-0.813	-0.887	20.005	-14.307	-14.307	0.000	0.000	0.000	0.000
137	A	142	ALA	0	-0.016	-0.015	19.892	-0.721	-0.721	0.000	0.000	0.000	0.000
138	A	143	MET	0	-0.025	-0.004	15.858	-1.008	-1.008	0.000	0.000	0.000	0.000
139	A	144	ARG	1	0.823	0.908	15.544	14.646	14.646	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.833	-0.905	15.120	-17.114	-17.114	0.000	0.000	0.000	0.000
141	A	146	ALA	0	-0.046	-0.029	14.746	-1.132	-1.132	0.000	0.000	0.000	0.000
142	A	147	PHE	0	0.034	-0.007	11.019	-1.694	-1.694	0.000	0.000	0.000	0.000
143	A	148	GLU	-1	-0.843	-0.912	10.206	-27.375	-27.375	0.000	0.000	0.000	0.000
144	A	149	GLY	0	-0.037	-0.013	9.075	-0.871	-0.871	0.000	0.000	0.000	0.000
145	A	150	CYS	0	-0.088	-0.025	5.952	-6.188	-6.188	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.011	-0.021	1.892	-21.932	-21.173	8.001	-4.095	-4.665	-0.055
147	A	152	ILE	0	-0.022	0.002	3.243	-15.986	-14.041	0.098	-0.925	-1.118	-0.007
148	A	153	ARG	1	0.794	0.883	3.673	32.949	33.427	0.007	-0.163	-0.322	0.000
149	A	154	VAL	0	0.019	0.008	7.437	0.351	0.351	0.000	0.000	0.000	0.000
150	A	155	LEU	0	-0.032	-0.013	11.178	1.017	1.017	0.000	0.000	0.000	0.000
151	A	156	LEU	0	0.038	0.027	13.961	0.265	0.265	0.000	0.000	0.000	0.000
152	A	157	PHE	0	-0.026	-0.027	17.055	0.716	0.716	0.000	0.000	0.000	0.000
153	A	158	SER	0	0.007	-0.026	20.272	0.163	0.163	0.000	0.000	0.000	0.000
154	A	159	LEU	0	-0.003	0.004	24.053	0.083	0.083	0.000	0.000	0.000	0.000
155	A	160	SER	0	-0.034	-0.012	27.011	0.440	0.440	0.000	0.000	0.000	0.000
156	A	161	GLN	0	0.020	-0.017	25.947	-0.371	-0.371	0.000	0.000	0.000	0.000
157	A	162	GLU	-1	-0.804	-0.894	26.898	-10.289	-10.289	0.000	0.000	0.000	0.000
158	A	163	HIS	0	-0.016	-0.003	24.638	-0.500	-0.500	0.000	0.000	0.000	0.000
159	A	164	ILE	0	0.020	0.008	20.538	-0.555	-0.555	0.000	0.000	0.000	0.000
160	A	165	ASP	-1	-0.824	-0.897	23.461	-10.945	-10.945	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.063	-0.069	24.724	0.179	0.179	0.000	0.000	0.000	0.000
162	A	167	PHE	0	0.023	0.021	16.103	-0.424	-0.424	0.000	0.000	0.000	0.000
163	A	168	ASP	-1	-0.827	-0.933	20.942	-14.007	-14.007	0.000	0.000	0.000	0.000
164	A	169	VAL	0	-0.078	-0.040	22.334	-0.102	-0.102	0.000	0.000	0.000	0.000
165	A	170	THR	0	-0.023	-0.013	22.695	-0.126	-0.126	0.000	0.000	0.000	0.000
166	A	171	CYS	0	-0.118	-0.028	18.984	-0.874	-0.874	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)