FMO DATABASE

FMODB ID: J3VY9

Calculation Name: 3E3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E3V

Chain ID: A

ChEMBL ID:

UniProt ID: Q1WV04

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1404759.783777
FMO2-HF: Nuclear repulsion	1343207.594344
FMO2-HF: Total energy	-61552.189433
FMO2-MP2: Total energy	-61734.695858

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:55:LEU)

Summations of interaction energy for fragment #1(A:55:LEU)

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.
-10.921	-8.757	9.597	-5.407	-6.356	-0.036

Interaction energy analysis for fragmet #1(A:55:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.022

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	57	ASP	-1	-0.860	-0.935	1.887	-14.553	-14.259	9.394	-4.838	-4.850	-0.035
4	A	58	ASP	-1	-0.857	-0.924	2.620	-1.871	-0.552	0.201	-0.463	-1.058	-0.001
5	A	59	ILE	0	0.083	0.030	4.305	1.178	1.417	-0.001	-0.037	-0.201	0.000
6	A	60	SER	0	-0.052	-0.019	6.881	0.736	0.736	0.000	0.000	0.000	0.000
7	A	61	LYS	1	0.841	0.910	4.932	3.424	3.424	0.000	0.000	0.000	0.000
8	A	62	GLY	0	0.066	0.022	8.728	0.332	0.332	0.000	0.000	0.000	0.000
9	A	63	TYR	0	-0.036	-0.047	10.646	0.275	0.275	0.000	0.000	0.000	0.000
10	A	64	ASN	0	-0.005	0.001	12.390	0.216	0.216	0.000	0.000	0.000	0.000
11	A	65	ALA	0	-0.010	0.004	13.207	0.127	0.127	0.000	0.000	0.000	0.000
12	A	66	ALA	0	0.015	0.008	14.658	0.098	0.098	0.000	0.000	0.000	0.000
13	A	67	LEU	0	0.037	0.007	16.623	0.070	0.070	0.000	0.000	0.000	0.000
14	A	68	ASN	0	-0.069	-0.033	17.365	0.095	0.095	0.000	0.000	0.000	0.000
15	A	69	TYR	0	-0.064	-0.046	18.992	0.054	0.054	0.000	0.000	0.000	0.000
16	A	70	LEU	0	0.016	0.010	19.788	0.032	0.032	0.000	0.000	0.000	0.000
17	A	71	SER	0	-0.087	-0.039	22.390	0.031	0.031	0.000	0.000	0.000	0.000
18	A	72	TYR	0	-0.028	-0.009	22.845	0.031	0.031	0.000	0.000	0.000	0.000
19	A	73	GLN	0	-0.044	-0.032	25.910	0.014	0.014	0.000	0.000	0.000	0.000
20	A	74	LEU	0	0.059	0.048	25.635	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	75	ARG	1	0.787	0.887	22.427	0.233	0.233	0.000	0.000	0.000	0.000
22	A	76	THR	0	0.001	0.000	25.209	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	77	ARG	1	0.884	0.897	19.228	0.231	0.231	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.866	0.924	20.916	0.147	0.147	0.000	0.000	0.000	0.000
25	A	79	GLU	-1	-0.738	-0.840	21.154	-0.206	-0.206	0.000	0.000	0.000	0.000
26	A	80	VAL	0	0.006	0.005	17.012	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	81	GLU	-1	-0.817	-0.885	16.833	-0.321	-0.321	0.000	0.000	0.000	0.000
28	A	82	ASP	-1	-0.793	-0.900	16.492	-0.225	-0.225	0.000	0.000	0.000	0.000
29	A	83	LYS	1	0.884	0.956	16.934	0.348	0.348	0.000	0.000	0.000	0.000
30	A	84	LEU	0	0.016	0.005	11.823	-0.031	-0.031	0.000	0.000	0.000	0.000
31	A	85	ARG	1	0.882	0.902	12.507	0.232	0.232	0.000	0.000	0.000	0.000
32	A	86	SER	0	-0.145	-0.065	14.359	0.047	0.047	0.000	0.000	0.000	0.000
33	A	87	LEU	0	-0.092	-0.056	11.171	0.033	0.033	0.000	0.000	0.000	0.000
34	A	88	ASP	-1	-0.943	-0.963	9.930	-0.214	-0.214	0.000	0.000	0.000	0.000
35	A	89	ILE	0	-0.034	0.022	7.670	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	90	HIS	0	0.013	0.012	6.251	0.314	0.314	0.000	0.000	0.000	0.000
37	A	91	GLU	-1	-0.762	-0.870	9.190	-0.433	-0.433	0.000	0.000	0.000	0.000
38	A	92	ASP	-1	-0.921	-0.955	9.160	-0.203	-0.203	0.000	0.000	0.000	0.000
39	A	93	TYR	0	-0.011	-0.016	3.523	-0.577	-0.265	0.003	-0.069	-0.247	0.000
40	A	94	ILE	0	-0.044	-0.004	9.651	0.008	0.008	0.000	0.000	0.000	0.000
41	A	95	SER	0	0.000	-0.001	12.561	0.048	0.048	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.882	-0.916	9.315	-0.879	-0.879	0.000	0.000	0.000	0.000
43	A	97	ILE	0	0.018	0.009	9.631	0.059	0.059	0.000	0.000	0.000	0.000
44	A	98	ILE	0	-0.001	-0.002	13.856	0.068	0.068	0.000	0.000	0.000	0.000
45	A	99	ASN	0	-0.016	-0.018	17.058	0.069	0.069	0.000	0.000	0.000	0.000
46	A	100	LYS	1	0.915	0.977	15.239	0.431	0.431	0.000	0.000	0.000	0.000
47	A	101	LEU	0	-0.008	-0.020	16.624	0.020	0.020	0.000	0.000	0.000	0.000
48	A	102	ILE	0	-0.027	-0.012	19.571	0.031	0.031	0.000	0.000	0.000	0.000
49	A	103	ASP	-1	-0.966	-0.980	19.989	-0.231	-0.231	0.000	0.000	0.000	0.000
50	A	104	LEU	0	-0.053	-0.026	18.961	0.013	0.013	0.000	0.000	0.000	0.000
51	A	105	ASP	-1	-0.876	-0.920	22.926	-0.169	-0.169	0.000	0.000	0.000	0.000
52	A	106	LEU	0	-0.053	-0.019	20.477	0.002	0.002	0.000	0.000	0.000	0.000
53	A	107	ILE	0	-0.032	-0.011	19.561	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	108	ASN	0	0.000	-0.016	23.755	0.017	0.017	0.000	0.000	0.000	0.000
55	A	109	ASP	-1	-0.745	-0.884	25.927	-0.182	-0.182	0.000	0.000	0.000	0.000
56	A	110	LYS	1	0.871	0.930	28.729	0.108	0.108	0.000	0.000	0.000	0.000
57	A	111	ASN	0	0.019	0.010	30.405	0.015	0.015	0.000	0.000	0.000	0.000
58	A	112	TYR	0	-0.041	-0.022	27.911	0.013	0.013	0.000	0.000	0.000	0.000
59	A	113	ALA	0	0.013	0.003	31.061	0.007	0.007	0.000	0.000	0.000	0.000
60	A	114	GLU	-1	-0.781	-0.887	33.731	-0.093	-0.093	0.000	0.000	0.000	0.000
61	A	115	SER	0	-0.050	-0.034	33.072	0.005	0.005	0.000	0.000	0.000	0.000
62	A	116	TYR	0	0.040	0.026	33.882	0.007	0.007	0.000	0.000	0.000	0.000
63	A	117	VAL	0	0.000	-0.003	35.817	0.006	0.006	0.000	0.000	0.000	0.000
64	A	118	ARG	1	0.895	0.930	37.618	0.101	0.101	0.000	0.000	0.000	0.000
65	A	119	THR	0	0.002	0.001	37.122	0.004	0.004	0.000	0.000	0.000	0.000
66	A	120	MET	0	-0.030	0.003	38.668	0.004	0.004	0.000	0.000	0.000	0.000
67	A	121	MET	0	-0.026	0.016	41.239	0.004	0.004	0.000	0.000	0.000	0.000
68	A	122	ASN	0	-0.042	-0.018	43.125	0.007	0.007	0.000	0.000	0.000	0.000
69	A	123	THR	0	-0.061	-0.037	41.469	0.001	0.001	0.000	0.000	0.000	0.000
70	A	124	SER	0	-0.044	-0.028	42.510	0.001	0.001	0.000	0.000	0.000	0.000
71	A	125	ASP	-1	-0.768	-0.874	44.626	-0.059	-0.059	0.000	0.000	0.000	0.000
72	A	126	LYS	1	0.845	0.913	42.736	0.067	0.067	0.000	0.000	0.000	0.000
73	A	127	GLY	0	0.073	0.042	45.461	0.000	0.000	0.000	0.000	0.000	0.000
74	A	128	PRO	0	0.042	0.004	43.099	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	129	LYS	1	0.876	0.956	41.842	0.045	0.045	0.000	0.000	0.000	0.000
76	A	130	VAL	0	0.011	0.000	40.941	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	131	ILE	0	-0.003	0.006	38.709	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	132	LYS	1	0.889	0.944	37.053	0.070	0.070	0.000	0.000	0.000	0.000
79	A	133	LEU	0	-0.012	0.002	36.247	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	134	ASN	0	-0.034	-0.035	34.986	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	135	LEU	0	0.009	0.024	32.854	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	136	SER	0	0.031	0.015	31.473	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	137	LYS	1	0.848	0.926	30.794	0.088	0.088	0.000	0.000	0.000	0.000
84	A	138	LYS	1	0.832	0.925	27.649	0.157	0.157	0.000	0.000	0.000	0.000
85	A	139	GLY	0	-0.020	-0.003	26.724	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	140	ILE	0	-0.058	-0.013	27.282	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	141	ASP	-1	-0.845	-0.926	28.768	-0.121	-0.121	0.000	0.000	0.000	0.000
88	A	142	ASP	-1	-0.850	-0.926	31.217	-0.081	-0.081	0.000	0.000	0.000	0.000
89	A	143	ASN	0	0.036	0.018	34.674	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	144	ILE	0	0.046	0.025	30.153	0.003	0.003	0.000	0.000	0.000	0.000
91	A	145	ALA	0	-0.028	-0.021	34.269	0.000	0.000	0.000	0.000	0.000	0.000
92	A	146	GLU	-1	-0.937	-0.992	35.841	-0.068	-0.068	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.883	-0.928	36.847	-0.085	-0.085	0.000	0.000	0.000	0.000
94	A	148	ALA	0	0.012	0.006	36.181	0.001	0.001	0.000	0.000	0.000	0.000
95	A	149	LEU	0	-0.050	-0.044	38.290	0.003	0.003	0.000	0.000	0.000	0.000
96	A	150	ILE	0	-0.002	0.019	41.215	0.004	0.004	0.000	0.000	0.000	0.000
97	A	151	LEU	0	-0.014	-0.004	39.688	0.003	0.003	0.000	0.000	0.000	0.000
98	A	152	TYR	0	-0.059	-0.049	43.691	0.003	0.003	0.000	0.000	0.000	0.000
99	A	153	THR	0	0.015	-0.004	45.437	0.003	0.003	0.000	0.000	0.000	0.000
100	A	154	ASP	-1	-0.849	-0.925	48.758	-0.049	-0.049	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.038	0.004	51.609	0.000	0.000	0.000	0.000	0.000	0.000
102	A	156	LEU	0	0.037	0.025	48.165	0.000	0.000	0.000	0.000	0.000	0.000
103	A	157	GLN	0	-0.043	-0.039	48.054	0.000	0.000	0.000	0.000	0.000	0.000
104	A	158	VAL	0	0.002	-0.002	50.568	0.001	0.001	0.000	0.000	0.000	0.000
105	A	159	GLU	-1	-0.889	-0.931	53.471	-0.048	-0.048	0.000	0.000	0.000	0.000
106	A	160	LYS	1	0.824	0.910	46.747	0.064	0.064	0.000	0.000	0.000	0.000
107	A	161	GLY	0	0.017	-0.013	52.273	0.001	0.001	0.000	0.000	0.000	0.000
108	A	162	VAL	0	0.040	0.013	53.740	0.001	0.001	0.000	0.000	0.000	0.000
109	A	163	THR	0	0.019	0.019	54.053	0.001	0.001	0.000	0.000	0.000	0.000
110	A	164	LEU	0	-0.118	-0.051	50.324	0.000	0.000	0.000	0.000	0.000	0.000
111	A	165	ALA	0	0.024	0.002	54.897	0.001	0.001	0.000	0.000	0.000	0.000
112	A	166	GLU	-1	-0.802	-0.908	57.900	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	167	LYS	1	0.872	0.939	54.485	0.047	0.047	0.000	0.000	0.000	0.000
114	A	168	LEU	0	-0.068	-0.031	54.938	0.001	0.001	0.000	0.000	0.000	0.000
115	A	169	ALA	0	0.033	0.018	59.062	0.001	0.001	0.000	0.000	0.000	0.000
116	A	170	ASN	0	-0.003	-0.016	62.164	0.002	0.002	0.000	0.000	0.000	0.000
117	A	171	ARG	1	0.910	0.967	54.479	0.041	0.041	0.000	0.000	0.000	0.000
118	A	172	TYR	0	0.005	-0.013	56.919	0.001	0.001	0.000	0.000	0.000	0.000
119	A	173	SER	0	0.052	0.031	63.596	0.001	0.001	0.000	0.000	0.000	0.000
120	A	174	HIS	0	0.002	-0.006	66.797	0.001	0.001	0.000	0.000	0.000	0.000
121	A	175	ASP	-1	-0.820	-0.874	64.621	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	176	SER	0	0.024	-0.003	67.811	0.000	0.000	0.000	0.000	0.000	0.000
123	A	177	TYR	0	-0.010	-0.039	67.444	0.000	0.000	0.000	0.000	0.000	0.000
124	A	178	ARG	1	0.936	0.961	65.953	0.024	0.024	0.000	0.000	0.000	0.000
125	A	179	ASN	0	-0.019	-0.011	64.900	0.000	0.000	0.000	0.000	0.000	0.000
126	A	180	LYS	1	0.804	0.918	63.237	0.027	0.027	0.000	0.000	0.000	0.000
127	A	181	GLN	0	0.043	0.014	61.969	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	182	ASN	0	-0.057	-0.027	60.660	0.000	0.000	0.000	0.000	0.000	0.000
129	A	183	LYS	1	0.870	0.918	58.610	0.028	0.028	0.000	0.000	0.000	0.000
130	A	184	ILE	0	0.002	0.012	57.105	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	185	LYS	1	0.852	0.912	56.068	0.031	0.031	0.000	0.000	0.000	0.000
132	A	186	GLN	0	-0.002	0.003	54.562	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	187	SER	0	-0.017	-0.010	52.590	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	188	LEU	0	0.046	0.025	51.220	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	189	LEU	0	-0.007	-0.002	50.402	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.114	-0.060	48.244	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	191	LYS	1	0.842	0.917	46.635	0.049	0.049	0.000	0.000	0.000	0.000
138	A	192	GLY	0	0.030	0.020	45.528	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	193	PHE	0	0.024	0.031	46.491	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	194	SER	0	-0.038	-0.042	49.347	0.001	0.001	0.000	0.000	0.000	0.000
141	A	195	TYR	0	0.048	0.000	51.175	0.000	0.000	0.000	0.000	0.000	0.000
142	A	196	ASP	-1	-0.777	-0.859	53.580	-0.039	-0.039	0.000	0.000	0.000	0.000
143	A	197	ILE	0	0.000	0.025	51.051	0.001	0.001	0.000	0.000	0.000	0.000
144	A	198	ILE	0	-0.031	-0.017	52.323	0.001	0.001	0.000	0.000	0.000	0.000
145	A	199	ASP	-1	-0.845	-0.925	55.918	-0.032	-0.032	0.000	0.000	0.000	0.000
146	A	200	THR	0	0.007	0.006	57.255	0.001	0.001	0.000	0.000	0.000	0.000
147	A	201	ILE	0	-0.041	-0.009	53.757	0.000	0.000	0.000	0.000	0.000	0.000
148	A	202	ILE	0	-0.074	-0.039	58.412	0.001	0.001	0.000	0.000	0.000	0.000
149	A	203	GLN	0	0.004	0.004	61.399	0.001	0.001	0.000	0.000	0.000	0.000
150	A	204	GLU	-1	-0.903	-0.955	60.484	-0.035	-0.035	0.000	0.000	0.000	0.000
151	A	205	LEU	0	-0.042	-0.025	61.165	0.000	0.000	0.000	0.000	0.000	0.000
152	A	206	ASP	-1	-0.802	-0.874	63.098	-0.029	-0.029	0.000	0.000	0.000	0.000
153	A	207	LEU	0	-0.055	-0.002	65.788	0.001	0.001	0.000	0.000	0.000	0.000
154	A	208	ILE	0	-0.127	-0.061	62.256	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:55:LEU)