FMO DATABASE

FMODB ID: Z6YZN

Calculation Name: 3EJC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9G096

Base Structure: X-ray

Registration Date: 2023-06-21

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1170664.978642
FMO2-HF: Nuclear repulsion	1110115.64571
FMO2-HF: Total energy	-60549.332932
FMO2-MP2: Total energy	-60724.88244

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-19.271	-15.808	16.335	-9.301	-10.495	-0.085

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.002

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	4	ILE	0	0.005	0.017	2.796	-1.128	0.888	0.141	-0.867	-1.290	0.004
4	A	5	LYS	1	0.907	0.940	5.371	-0.314	-0.297	-0.001	-0.003	-0.012	0.000
5	A	6	LYS	1	0.944	0.970	9.112	-0.352	-0.352	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.090	0.047	11.088	-0.071	-0.071	0.000	0.000	0.000	0.000
7	A	8	TYR	0	-0.048	-0.033	13.443	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	9	ARG	1	1.010	0.977	17.146	-0.176	-0.176	0.000	0.000	0.000	0.000
9	A	10	GLY	0	-0.009	0.005	20.694	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.007	0.041	14.970	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.944	0.972	19.289	-0.076	-0.076	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.029	0.002	16.824	0.016	0.016	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.037	0.014	15.997	0.013	0.013	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.023	0.004	14.734	0.034	0.034	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.896	-0.936	13.555	0.098	0.098	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.002	-0.009	10.772	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.038	-0.022	9.934	0.077	0.077	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.053	-0.023	9.885	0.103	0.103	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.853	-0.926	8.255	0.153	0.153	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.859	-0.936	5.618	0.765	0.765	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.051	-0.036	4.996	0.291	0.362	-0.001	-0.001	-0.069	0.000
22	A	23	GLU	-1	-0.894	-0.949	6.984	0.075	0.075	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.019	-0.003	2.217	-0.301	-0.454	1.297	-0.368	-0.776	-0.001
24	A	25	ILE	0	-0.038	-0.035	2.640	-2.587	-1.070	2.011	-1.256	-2.271	-0.010
25	A	26	ASN	0	-0.014	-0.014	3.590	-0.583	-0.741	0.015	0.280	-0.137	0.000
26	A	27	SER	0	-0.018	0.000	4.817	-0.131	-0.131	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.797	-0.902	1.856	-16.627	-16.520	12.875	-7.076	-5.907	-0.078
28	A	29	LEU	0	-0.039	0.003	5.110	0.225	0.232	-0.001	-0.002	-0.004	0.000
29	A	30	THR	0	-0.084	-0.040	8.029	0.082	0.082	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.055	-0.028	8.554	0.079	0.079	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.056	0.034	7.621	-0.158	-0.158	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.077	0.036	4.712	-0.173	-0.134	-0.001	-0.008	-0.029	0.000
33	A	34	ASN	0	-0.068	-0.042	4.928	0.586	0.586	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.039	-0.007	5.840	0.335	0.335	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.018	-0.003	8.325	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	37	HIS	1	0.740	0.849	8.460	0.753	0.753	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.924	0.954	13.294	0.088	0.088	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.008	0.003	15.506	0.032	0.032	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.005	0.005	15.490	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.904	-0.933	16.895	-0.197	-0.197	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.801	-0.904	12.077	-0.510	-0.510	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.054	-0.024	14.960	0.057	0.057	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.011	0.006	14.356	-0.046	-0.046	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.027	0.023	15.024	0.038	0.038	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.006	-0.013	16.079	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.951	0.972	18.138	0.043	0.043	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.937	0.974	14.299	0.177	0.177	0.000	0.000	0.000	0.000
48	A	49	THR	0	0.003	-0.002	20.483	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.009	0.006	20.251	0.006	0.006	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.004	-0.015	24.218	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.019	0.024	25.802	0.004	0.004	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.003	-0.001	27.430	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.024	-0.012	24.707	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.940	-0.962	26.847	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.066	-0.034	26.742	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	ASN	0	0.059	0.022	28.045	0.006	0.006	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.006	0.010	28.175	0.001	0.001	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.015	-0.011	28.333	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.050	0.028	27.528	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.024	-0.014	27.817	0.007	0.007	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.008	0.005	28.014	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.013	-0.014	29.021	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.003	-0.010	31.269	0.007	0.007	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.844	0.926	34.566	0.059	0.059	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.025	0.004	37.434	0.002	0.002	0.000	0.000	0.000	0.000
66	A	67	TRP	0	0.012	0.006	41.057	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	SER	0	0.001	-0.011	44.295	0.001	0.001	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.016	0.020	48.000	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.911	-0.954	51.067	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.052	0.016	51.478	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.078	0.026	54.973	0.000	0.000	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.018	0.009	58.711	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	GLY	0	0.046	0.043	59.970	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.019	-0.004	55.729	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.012	-0.019	52.180	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.034	-0.004	48.948	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	SER	0	0.012	0.007	47.389	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.022	-0.016	43.845	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.866	0.912	38.422	0.052	0.052	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.918	0.989	33.649	0.067	0.067	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.963	0.960	35.052	0.058	0.058	0.000	0.000	0.000	0.000
82	A	83	GLY	0	-0.010	0.007	32.782	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.022	-0.022	33.661	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	THR	0	0.027	0.024	36.138	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.033	-0.005	38.729	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.809	-0.893	39.924	-0.047	-0.047	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.002	-0.009	43.333	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.014	-0.016	46.797	0.001	0.001	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.010	0.010	49.722	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	GLY	0	0.011	-0.007	53.161	0.000	0.000	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.017	0.023	55.382	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.891	-0.959	58.013	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.057	-0.012	61.661	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	SER	0	0.008	-0.009	63.163	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.028	-0.016	65.069	0.000	0.000	0.000	0.000	0.000	0.000
96	A	97	SER	0	0.005	-0.020	66.507	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.001	0.030	61.654	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.002	-0.009	65.495	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	ALA	0	0.032	0.023	65.035	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.001	-0.004	62.432	0.000	0.000	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.024	0.000	62.720	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	ASN	0	0.018	-0.008	58.343	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.041	-0.019	56.384	0.000	0.000	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.027	-0.028	56.498	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.040	0.008	56.105	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.866	0.916	50.986	0.033	0.033	0.000	0.000	0.000	0.000
107	A	108	SER	0	0.013	0.018	50.289	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.012	-0.015	45.645	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.020	0.011	43.253	0.000	0.000	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.077	0.021	41.925	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.829	-0.904	38.120	-0.053	-0.053	0.000	0.000	0.000	0.000
112	A	113	PHE	0	-0.068	-0.047	39.527	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	CYS	0	-0.039	0.031	42.098	0.003	0.003	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.012	0.021	42.464	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.910	0.955	38.795	0.032	0.032	0.000	0.000	0.000	0.000
116	A	117	ASN	0	-0.036	-0.039	44.050	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.857	0.918	47.564	0.020	0.020	0.000	0.000	0.000	0.000
118	A	119	CYS	0	-0.036	0.004	47.254	0.000	0.000	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.014	-0.018	49.955	0.000	0.000	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.050	-0.029	48.978	0.000	0.000	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.022	0.002	52.750	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.012	-0.005	54.723	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	124	HIS	0	-0.067	-0.048	57.097	0.000	0.000	0.000	0.000	0.000	0.000
124	A	125	MET	0	-0.018	-0.002	59.939	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	126	VAL	0	0.026	-0.005	61.182	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	GLY	0	-0.010	-0.003	63.464	0.000	0.000	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.024	0.020	66.184	0.001	0.001	0.000	0.000	0.000	0.000
128	A	129	TRP	0	0.007	0.015	65.230	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	130	ASN	0	-0.015	0.000	65.621	0.000	0.000	0.000	0.000	0.000	0.000
130	A	131	ALA	0	0.034	0.017	60.815	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	PHE	0	-0.045	-0.010	56.988	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.026	0.004	56.168	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	ILE	0	-0.007	0.007	53.949	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	ASP	-1	-0.733	-0.843	53.528	-0.022	-0.022	0.000	0.000	0.000	0.000
135	A	136	ILE	0	0.002	-0.007	47.855	0.000	0.000	0.000	0.000	0.000	0.000
136	A	137	PRO	0	-0.016	-0.001	49.751	0.000	0.000	0.000	0.000	0.000	0.000
137	A	138	SER	0	0.039	0.009	45.879	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	139	SER	0	0.010	-0.002	46.548	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	140	GLY	0	0.069	0.031	48.660	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	VAL	0	-0.062	-0.028	49.303	0.000	0.000	0.000	0.000	0.000	0.000
141	A	142	CYS	0	-0.013	0.002	51.720	0.001	0.001	0.000	0.000	0.000	0.000
142	A	143	GLN	0	-0.006	-0.006	54.144	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	TRP	0	-0.037	-0.025	57.377	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	145	PHE	0	-0.009	-0.012	57.479	0.001	0.001	0.000	0.000	0.000	0.000
145	A	146	GLY	0	0.023	0.030	61.293	0.001	0.001	0.000	0.000	0.000	0.000
146	A	147	PRO	0	0.007	0.005	63.613	0.000	0.000	0.000	0.000	0.000	0.000
147	A	148	THR	0	0.009	-0.014	66.332	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	149	ALA	0	-0.004	0.011	65.672	0.000	0.000	0.000	0.000	0.000	0.000
149	A	150	SER	0	-0.006	-0.006	67.223	0.000	0.000	0.000	0.000	0.000	0.000
150	A	151	SER	0	-0.002	0.014	67.117	0.000	0.000	0.000	0.000	0.000	0.000
151	A	152	GLY	0	0.072	0.035	65.682	0.000	0.000	0.000	0.000	0.000	0.000
152	A	153	THR	0	-0.012	-0.011	60.553	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	154	PRO	0	0.006	0.017	58.366	0.000	0.000	0.000	0.000	0.000	0.000
154	A	155	ARG	1	0.844	0.918	55.986	0.025	0.025	0.000	0.000	0.000	0.000
155	A	156	GLY	0	0.080	0.028	53.917	0.001	0.001	0.000	0.000	0.000	0.000
156	A	157	THR	0	-0.023	-0.012	47.973	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	158	GLY	0	0.022	0.021	47.665	0.002	0.002	0.000	0.000	0.000	0.000
158	A	159	THR	0	-0.048	-0.025	42.591	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	TYR	0	0.010	-0.022	43.982	0.002	0.002	0.000	0.000	0.000	0.000
160	A	161	PRO	0	0.023	0.009	41.113	-0.003	-0.003	0.000	0.000	0.000	0.000
161	A	162	ILE	0	-0.017	0.004	37.384	0.001	0.001	0.000	0.000	0.000	0.000
162	A	163	ASP	-1	-0.901	-0.958	36.724	-0.037	-0.037	0.000	0.000	0.000	0.000
163	A	164	HIS	0	0.002	0.009	31.697	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)