FMO DATABASE

FMODB ID: 82Q7Y

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1399870.034065
FMO2-HF: Nuclear repulsion	1338319.515056
FMO2-HF: Total energy	-61550.519009
FMO2-MP2: Total energy	-61733.078649

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.
-13.75	-11.202	9.141	-5.461	-6.228	-0.029

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 : 0.058 / q_NPA : 0.023

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	-0.943	-0.978	1.870	-14.971	-14.084	8.948	-4.970	-4.865	-0.029
4	A	58	ASP	-1	-0.845	-0.926	2.538	-2.535	-1.187	0.195	-0.461	-1.082	0.000
5	A	59	ILE	0	0.042	0.015	4.376	1.275	1.467	-0.001	-0.026	-0.165	0.000
6	A	60	SER	0	-0.067	-0.016	6.897	0.707	0.707	0.000	0.000	0.000	0.000
7	A	61	LYS	1	0.945	0.962	6.577	1.904	1.904	0.000	0.000	0.000	0.000
8	A	62	GLY	0	0.055	0.017	8.680	0.327	0.327	0.000	0.000	0.000	0.000
9	A	63	TYR	0	-0.002	-0.010	10.553	0.244	0.244	0.000	0.000	0.000	0.000
10	A	64	ASN	0	-0.034	-0.010	12.314	0.206	0.206	0.000	0.000	0.000	0.000
11	A	65	ALA	0	-0.025	-0.011	13.318	0.115	0.115	0.000	0.000	0.000	0.000
12	A	66	ALA	0	0.012	0.007	14.841	0.096	0.096	0.000	0.000	0.000	0.000
13	A	67	LEU	0	0.055	0.011	16.783	0.068	0.068	0.000	0.000	0.000	0.000
14	A	68	ASN	0	-0.035	0.004	17.571	0.060	0.060	0.000	0.000	0.000	0.000
15	A	69	TYR	0	-0.057	-0.050	19.312	0.050	0.050	0.000	0.000	0.000	0.000
16	A	70	LEU	0	-0.006	-0.006	20.325	0.029	0.029	0.000	0.000	0.000	0.000
17	A	71	SER	0	-0.055	-0.003	22.713	0.030	0.030	0.000	0.000	0.000	0.000
18	A	72	TYR	0	-0.047	-0.014	23.382	0.020	0.020	0.000	0.000	0.000	0.000
19	A	73	GLN	0	-0.030	-0.020	26.461	0.008	0.008	0.000	0.000	0.000	0.000
20	A	74	LEU	0	0.065	0.046	26.252	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	75	ARG	1	0.813	0.902	23.135	0.234	0.234	0.000	0.000	0.000	0.000
22	A	76	THR	0	-0.014	-0.008	25.338	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	77	ARG	1	0.967	0.937	20.436	0.244	0.244	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.949	0.981	21.251	0.150	0.150	0.000	0.000	0.000	0.000
25	A	79	GLU	-1	-0.822	-0.909	21.544	-0.216	-0.216	0.000	0.000	0.000	0.000
26	A	80	VAL	0	-0.010	-0.009	17.419	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	81	GLU	-1	-0.826	-0.911	17.474	-0.341	-0.341	0.000	0.000	0.000	0.000
28	A	82	ASP	-1	-0.957	-0.999	17.007	-0.281	-0.281	0.000	0.000	0.000	0.000
29	A	83	LYS	1	0.913	1.001	17.179	0.398	0.398	0.000	0.000	0.000	0.000
30	A	84	LEU	0	0.000	-0.020	12.583	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	85	ARG	1	0.895	0.927	12.459	0.269	0.269	0.000	0.000	0.000	0.000
32	A	86	SER	0	-0.124	-0.051	14.561	0.038	0.038	0.000	0.000	0.000	0.000
33	A	87	LEU	0	-0.103	-0.068	11.460	0.055	0.055	0.000	0.000	0.000	0.000
34	A	88	ASP	-1	-0.986	-0.965	10.237	-0.426	-0.426	0.000	0.000	0.000	0.000
35	A	89	ILE	0	0.036	0.035	7.806	-0.116	-0.116	0.000	0.000	0.000	0.000
36	A	90	HIS	0	0.050	0.021	6.564	0.171	0.171	0.000	0.000	0.000	0.000
37	A	91	GLU	-1	-0.767	-0.885	10.049	-0.480	-0.480	0.000	0.000	0.000	0.000
38	A	92	ASP	-1	-0.943	-0.963	9.401	-0.379	-0.379	0.000	0.000	0.000	0.000
39	A	93	TYR	0	0.015	-0.004	4.883	-0.266	-0.145	-0.001	-0.004	-0.116	0.000
40	A	94	ILE	0	-0.039	-0.007	9.923	0.031	0.031	0.000	0.000	0.000	0.000
41	A	95	SER	0	0.014	0.002	12.731	0.059	0.059	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.914	-0.952	9.649	-0.858	-0.858	0.000	0.000	0.000	0.000
43	A	97	ILE	0	-0.022	-0.017	9.956	0.061	0.061	0.000	0.000	0.000	0.000
44	A	98	ILE	0	0.019	-0.003	14.057	0.074	0.074	0.000	0.000	0.000	0.000
45	A	99	ASN	0	-0.008	-0.008	16.920	0.077	0.077	0.000	0.000	0.000	0.000
46	A	100	LYS	1	0.914	0.986	15.134	0.477	0.477	0.000	0.000	0.000	0.000
47	A	101	LEU	0	-0.001	-0.017	16.905	0.032	0.032	0.000	0.000	0.000	0.000
48	A	102	ILE	0	-0.024	-0.005	19.752	0.034	0.034	0.000	0.000	0.000	0.000
49	A	103	ASP	-1	-0.967	-0.968	20.827	-0.215	-0.215	0.000	0.000	0.000	0.000
50	A	104	LEU	0	-0.095	-0.052	19.075	0.014	0.014	0.000	0.000	0.000	0.000
51	A	105	ASP	-1	-0.873	-0.921	23.271	-0.176	-0.176	0.000	0.000	0.000	0.000
52	A	106	LEU	0	-0.062	-0.027	20.539	0.001	0.001	0.000	0.000	0.000	0.000
53	A	107	ILE	0	-0.032	-0.007	19.734	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	108	ASN	0	-0.010	-0.036	23.948	0.016	0.016	0.000	0.000	0.000	0.000
55	A	109	ASP	-1	-0.753	-0.893	26.813	-0.193	-0.193	0.000	0.000	0.000	0.000
56	A	110	LYS	1	0.900	0.945	28.980	0.123	0.123	0.000	0.000	0.000	0.000
57	A	111	ASN	0	0.013	0.003	30.312	0.018	0.018	0.000	0.000	0.000	0.000
58	A	112	TYR	0	-0.021	-0.006	28.662	0.012	0.012	0.000	0.000	0.000	0.000
59	A	113	ALA	0	0.022	-0.001	31.197	0.008	0.008	0.000	0.000	0.000	0.000
60	A	114	GLU	-1	-0.816	-0.900	33.936	-0.101	-0.101	0.000	0.000	0.000	0.000
61	A	115	SER	0	-0.047	-0.015	33.578	0.006	0.006	0.000	0.000	0.000	0.000
62	A	116	TYR	0	0.029	0.019	34.162	0.008	0.008	0.000	0.000	0.000	0.000
63	A	117	VAL	0	0.026	0.007	36.077	0.006	0.006	0.000	0.000	0.000	0.000
64	A	118	ARG	1	0.945	0.971	38.506	0.104	0.104	0.000	0.000	0.000	0.000
65	A	119	THR	0	-0.007	-0.003	37.546	0.005	0.005	0.000	0.000	0.000	0.000
66	A	120	MET	0	-0.040	-0.007	38.880	0.004	0.004	0.000	0.000	0.000	0.000
67	A	121	MET	0	-0.025	0.034	41.521	0.004	0.004	0.000	0.000	0.000	0.000
68	A	122	ASN	0	-0.006	-0.007	43.079	0.007	0.007	0.000	0.000	0.000	0.000
69	A	123	THR	0	-0.087	-0.048	41.785	0.002	0.002	0.000	0.000	0.000	0.000
70	A	124	SER	0	-0.078	-0.055	42.778	0.001	0.001	0.000	0.000	0.000	0.000
71	A	125	ASP	-1	-0.810	-0.914	44.905	-0.063	-0.063	0.000	0.000	0.000	0.000
72	A	126	LYS	1	0.858	0.924	42.643	0.076	0.076	0.000	0.000	0.000	0.000
73	A	127	GLY	0	0.072	0.035	45.461	0.000	0.000	0.000	0.000	0.000	0.000
74	A	128	PRO	0	0.039	-0.002	43.570	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	129	LYS	1	0.962	0.986	42.245	0.053	0.053	0.000	0.000	0.000	0.000
76	A	130	VAL	0	0.000	0.005	41.219	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	131	ILE	0	0.001	0.006	39.086	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	132	LYS	1	0.917	0.943	37.418	0.083	0.083	0.000	0.000	0.000	0.000
79	A	133	LEU	0	0.008	0.020	36.660	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	134	ASN	0	-0.055	-0.042	35.580	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	135	LEU	0	0.016	0.011	33.367	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	136	SER	0	0.039	0.019	31.967	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	137	LYS	1	0.845	0.926	31.288	0.102	0.102	0.000	0.000	0.000	0.000
84	A	138	LYS	1	0.872	0.948	28.752	0.160	0.160	0.000	0.000	0.000	0.000
85	A	139	GLY	0	-0.020	0.000	27.071	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	140	ILE	0	-0.033	0.005	27.979	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	141	ASP	-1	-0.867	-0.933	29.447	-0.140	-0.140	0.000	0.000	0.000	0.000
88	A	142	ASP	-1	-0.861	-0.931	31.793	-0.093	-0.093	0.000	0.000	0.000	0.000
89	A	143	ASN	0	0.015	0.002	34.577	0.000	0.000	0.000	0.000	0.000	0.000
90	A	144	ILE	0	0.084	0.046	30.438	0.002	0.002	0.000	0.000	0.000	0.000
91	A	145	ALA	0	-0.058	-0.035	34.568	0.002	0.002	0.000	0.000	0.000	0.000
92	A	146	GLU	-1	-0.974	-1.002	36.348	-0.077	-0.077	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.873	-0.922	37.371	-0.090	-0.090	0.000	0.000	0.000	0.000
94	A	148	ALA	0	-0.036	-0.021	36.624	0.003	0.003	0.000	0.000	0.000	0.000
95	A	149	LEU	0	-0.054	-0.052	38.750	0.003	0.003	0.000	0.000	0.000	0.000
96	A	150	ILE	0	0.005	0.032	41.615	0.005	0.005	0.000	0.000	0.000	0.000
97	A	151	LEU	0	-0.054	-0.030	40.165	0.003	0.003	0.000	0.000	0.000	0.000
98	A	152	TYR	0	-0.044	-0.020	44.091	0.003	0.003	0.000	0.000	0.000	0.000
99	A	153	THR	0	0.034	0.013	45.884	0.003	0.003	0.000	0.000	0.000	0.000
100	A	154	ASP	-1	-0.820	-0.917	49.211	-0.055	-0.055	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.018	-0.005	52.132	0.000	0.000	0.000	0.000	0.000	0.000
102	A	156	LEU	0	0.026	0.018	48.389	0.000	0.000	0.000	0.000	0.000	0.000
103	A	157	GLN	0	-0.057	-0.051	48.065	0.001	0.001	0.000	0.000	0.000	0.000
104	A	158	VAL	0	0.027	0.009	50.954	0.001	0.001	0.000	0.000	0.000	0.000
105	A	159	GLU	-1	-0.884	-0.929	53.737	-0.051	-0.051	0.000	0.000	0.000	0.000
106	A	160	LYS	1	0.867	0.946	48.036	0.065	0.065	0.000	0.000	0.000	0.000
107	A	161	GLY	0	0.005	-0.031	52.521	0.000	0.000	0.000	0.000	0.000	0.000
108	A	162	VAL	0	0.051	0.026	54.070	0.001	0.001	0.000	0.000	0.000	0.000
109	A	163	THR	0	0.016	0.027	54.384	0.001	0.001	0.000	0.000	0.000	0.000
110	A	164	LEU	0	-0.128	-0.070	50.756	0.001	0.001	0.000	0.000	0.000	0.000
111	A	165	ALA	0	0.008	-0.005	55.159	0.001	0.001	0.000	0.000	0.000	0.000
112	A	166	GLU	-1	-0.843	-0.930	58.164	-0.040	-0.040	0.000	0.000	0.000	0.000
113	A	167	LYS	1	0.887	0.946	53.597	0.053	0.053	0.000	0.000	0.000	0.000
114	A	168	LEU	0	-0.055	-0.038	55.257	0.001	0.001	0.000	0.000	0.000	0.000
115	A	169	ALA	0	0.032	0.026	59.407	0.001	0.001	0.000	0.000	0.000	0.000
116	A	170	ASN	0	0.019	0.005	62.546	0.002	0.002	0.000	0.000	0.000	0.000
117	A	171	ARG	1	0.889	0.957	55.149	0.044	0.044	0.000	0.000	0.000	0.000
118	A	172	TYR	0	-0.014	-0.024	57.557	0.000	0.000	0.000	0.000	0.000	0.000
119	A	173	SER	0	0.003	0.017	64.150	0.001	0.001	0.000	0.000	0.000	0.000
120	A	174	HIS	0	-0.025	-0.013	67.318	0.001	0.001	0.000	0.000	0.000	0.000
121	A	175	ASP	-1	-0.919	-0.947	64.891	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	176	SER	0	-0.004	-0.010	68.334	0.000	0.000	0.000	0.000	0.000	0.000
123	A	177	TYR	0	-0.020	-0.059	67.269	0.000	0.000	0.000	0.000	0.000	0.000
124	A	178	ARG	1	0.983	0.994	66.802	0.027	0.027	0.000	0.000	0.000	0.000
125	A	179	ASN	0	0.010	-0.007	65.230	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	180	LYS	1	0.956	0.994	63.612	0.031	0.031	0.000	0.000	0.000	0.000
127	A	181	GLN	0	0.099	0.036	62.230	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	182	ASN	0	-0.064	-0.022	60.806	0.000	0.000	0.000	0.000	0.000	0.000
129	A	183	LYS	1	0.944	0.981	58.955	0.032	0.032	0.000	0.000	0.000	0.000
130	A	184	ILE	0	0.012	0.011	57.399	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	185	LYS	1	0.979	0.987	56.305	0.036	0.036	0.000	0.000	0.000	0.000
132	A	186	GLN	0	0.004	0.010	54.590	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	187	SER	0	-0.027	-0.018	53.006	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	188	LEU	0	0.040	0.016	51.465	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	189	LEU	0	-0.005	0.007	50.665	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.109	-0.048	48.649	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	191	LYS	1	0.860	0.929	46.913	0.056	0.056	0.000	0.000	0.000	0.000
138	A	192	GLY	0	-0.017	0.007	45.823	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	193	PHE	0	0.039	0.024	46.771	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	194	SER	0	-0.018	-0.017	49.737	0.002	0.002	0.000	0.000	0.000	0.000
141	A	195	TYR	0	0.056	0.004	51.310	0.000	0.000	0.000	0.000	0.000	0.000
142	A	196	ASP	-1	-0.825	-0.897	54.692	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	197	ILE	0	-0.013	0.005	51.435	0.001	0.001	0.000	0.000	0.000	0.000
144	A	198	ILE	0	-0.059	-0.041	52.944	0.001	0.001	0.000	0.000	0.000	0.000
145	A	199	ASP	-1	-0.932	-0.966	56.279	-0.038	-0.038	0.000	0.000	0.000	0.000
146	A	200	THR	0	0.005	0.003	57.625	0.001	0.001	0.000	0.000	0.000	0.000
147	A	201	ILE	0	-0.030	0.002	54.129	0.000	0.000	0.000	0.000	0.000	0.000
148	A	202	ILE	0	-0.122	-0.064	58.760	0.001	0.001	0.000	0.000	0.000	0.000
149	A	203	GLN	0	0.024	0.023	61.677	0.000	0.000	0.000	0.000	0.000	0.000
150	A	204	GLU	-1	-0.931	-0.975	60.426	-0.039	-0.039	0.000	0.000	0.000	0.000
151	A	205	LEU	0	-0.056	-0.041	61.271	0.001	0.001	0.000	0.000	0.000	0.000
152	A	206	ASP	-1	-0.867	-0.904	63.447	-0.033	-0.033	0.000	0.000	0.000	0.000
153	A	207	LEU	0	-0.045	-0.006	66.254	0.001	0.001	0.000	0.000	0.000	0.000
154	A	208	ILE	0	-0.102	-0.032	62.639	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)