FMO DATABASE

FMODB ID: GNVV1

Calculation Name: 3EQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EQ5

Chain ID: A

ChEMBL ID:

UniProt ID: P12757

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737319.888302
FMO2-HF: Nuclear repulsion	696401.258364
FMO2-HF: Total energy	-40918.629938
FMO2-MP2: Total energy	-41032.728363

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:135:SER)

Summations of interaction energy for fragment #1(A:135:SER)

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.
-4.843	1.191	1.061	-3.55	-3.546	-0.022

Interaction energy analysis for fragmet #1(A:135:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.008

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	137	PRO	0	0.039	0.004	3.599	-0.031	2.266	-0.001	-1.238	-1.059	0.006
4	A	138	SER	0	-0.049	-0.044	6.111	0.304	0.304	0.000	0.000	0.000	0.000
5	A	139	ASP	-1	-0.848	-0.911	2.589	-7.225	-3.612	1.064	-2.308	-2.369	-0.028
6	A	140	SER	0	0.030	0.023	4.925	-0.049	0.038	-0.001	-0.003	-0.083	0.000
7	A	141	SER	0	-0.023	-0.004	7.080	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	142	THR	0	-0.043	-0.040	9.770	-0.070	-0.070	0.000	0.000	0.000	0.000
9	A	143	GLU	-1	-0.899	-0.948	5.042	2.398	2.435	-0.001	-0.001	-0.035	0.000
10	A	144	LEU	0	-0.088	-0.028	9.252	-0.060	-0.060	0.000	0.000	0.000	0.000
11	A	145	THR	0	0.024	0.004	10.065	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	146	GLN	0	0.007	-0.006	11.972	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	147	THR	0	-0.036	-0.023	14.533	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	148	VAL	0	-0.013	-0.001	16.869	0.014	0.014	0.000	0.000	0.000	0.000
15	A	149	LEU	0	-0.046	-0.031	20.487	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	150	GLU	-1	-0.809	-0.917	23.242	-0.051	-0.051	0.000	0.000	0.000	0.000
17	A	151	GLY	0	-0.016	0.000	25.442	0.004	0.004	0.000	0.000	0.000	0.000
18	A	152	GLU	-1	-0.882	-0.935	24.532	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	153	SER	0	-0.049	-0.024	19.256	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	154	ILE	0	-0.003	0.002	19.561	0.012	0.012	0.000	0.000	0.000	0.000
21	A	155	SER	0	0.040	-0.002	16.646	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	156	CYS	0	-0.121	-0.058	13.921	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	157	PHE	0	0.066	0.050	12.020	0.032	0.032	0.000	0.000	0.000	0.000
24	A	158	GLN	0	0.023	0.019	9.309	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	159	VAL	0	0.024	-0.007	11.401	0.036	0.036	0.000	0.000	0.000	0.000
26	A	160	GLY	0	-0.009	-0.009	13.554	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	161	GLY	0	0.012	0.009	12.176	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	162	GLU	-1	-0.933	-0.962	13.210	-0.146	-0.146	0.000	0.000	0.000	0.000
29	A	163	LYS	1	0.966	0.989	11.991	0.231	0.231	0.000	0.000	0.000	0.000
30	A	164	ARG	1	0.905	0.944	14.453	0.029	0.029	0.000	0.000	0.000	0.000
31	A	165	LEU	0	0.041	0.014	16.589	0.022	0.022	0.000	0.000	0.000	0.000
32	A	166	CYS	0	-0.002	0.009	18.959	0.002	0.002	0.000	0.000	0.000	0.000
33	A	167	LEU	0	0.035	0.016	20.832	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	168	PRO	0	-0.003	-0.028	23.838	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	169	GLN	0	0.070	0.035	21.139	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	170	VAL	0	0.029	0.019	23.342	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	171	LEU	0	-0.013	-0.010	25.998	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	172	ASN	0	-0.046	-0.034	28.910	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	173	SER	0	-0.018	0.003	27.531	0.003	0.003	0.000	0.000	0.000	0.000
40	A	174	VAL	0	0.018	0.016	25.617	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	175	LEU	0	-0.033	-0.024	28.926	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	176	ARG	1	0.945	0.979	31.494	0.010	0.010	0.000	0.000	0.000	0.000
43	A	177	GLU	-1	-0.969	-0.983	33.836	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	178	PHE	0	0.022	0.016	33.797	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	179	THR	0	0.015	0.004	36.047	0.002	0.002	0.000	0.000	0.000	0.000
46	A	180	LEU	0	0.061	0.008	33.208	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	181	GLN	0	-0.003	0.009	36.273	0.000	0.000	0.000	0.000	0.000	0.000
48	A	182	GLN	0	0.023	0.023	37.814	0.000	0.000	0.000	0.000	0.000	0.000
49	A	183	ILE	0	0.027	0.009	31.700	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	184	ASN	0	-0.017	-0.023	33.585	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	185	THR	0	0.003	0.005	34.895	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	186	VAL	0	0.015	0.013	32.873	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	187	CYS	0	-0.065	-0.040	30.619	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	188	ASP	-1	-0.899	-0.942	32.367	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	189	GLU	-1	-0.968	-0.977	34.901	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	190	LEU	0	-0.109	-0.057	31.293	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	191	TYR	0	-0.003	0.002	30.808	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	192	ILE	0	-0.044	-0.013	26.443	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	193	TYR	0	0.005	0.014	22.640	0.007	0.007	0.000	0.000	0.000	0.000
60	A	194	CYS	0	-0.021	-0.014	24.438	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	195	SER	0	-0.023	0.001	21.728	0.002	0.002	0.000	0.000	0.000	0.000
62	A	196	ARG	1	0.930	0.949	23.343	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	197	CYS	0	-0.001	0.017	19.781	0.002	0.002	0.000	0.000	0.000	0.000
64	A	198	THR	0	0.043	0.022	16.895	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	199	SER	0	0.041	-0.003	19.951	0.002	0.002	0.000	0.000	0.000	0.000
66	A	200	ASP	-1	-0.889	-0.933	16.128	0.137	0.137	0.000	0.000	0.000	0.000
67	A	201	GLN	0	-0.013	-0.012	14.184	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	202	LEU	0	-0.067	-0.030	17.298	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	203	HIS	0	0.014	-0.002	19.710	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	204	ILE	0	0.024	0.016	13.505	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	205	LEU	0	0.018	-0.005	17.535	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	206	LYS	1	0.814	0.940	19.335	-0.065	-0.065	0.000	0.000	0.000	0.000
73	A	207	VAL	0	-0.023	-0.013	18.169	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	208	LEU	0	-0.049	-0.022	14.303	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	209	GLY	0	-0.010	0.007	18.858	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	210	ILE	0	-0.058	-0.012	19.022	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	211	LEU	0	-0.014	-0.023	22.225	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	212	PRO	0	0.036	0.021	24.585	0.004	0.004	0.000	0.000	0.000	0.000
79	A	213	PHE	0	0.113	0.020	23.842	0.001	0.001	0.000	0.000	0.000	0.000
80	A	214	ASN	0	-0.020	-0.010	27.570	0.004	0.004	0.000	0.000	0.000	0.000
81	A	215	ALA	0	-0.029	0.003	26.473	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	216	PRO	0	0.042	0.026	27.435	0.005	0.005	0.000	0.000	0.000	0.000
83	A	217	SER	0	-0.068	-0.041	25.810	0.000	0.000	0.000	0.000	0.000	0.000
84	A	218	CYS	0	0.044	0.016	22.480	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	219	GLY	0	-0.002	0.022	23.264	0.002	0.002	0.000	0.000	0.000	0.000
86	A	220	LEU	0	-0.017	-0.023	17.610	0.005	0.005	0.000	0.000	0.000	0.000
87	A	221	ILE	0	0.061	0.029	21.145	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	222	THR	0	0.060	0.043	19.043	0.005	0.005	0.000	0.000	0.000	0.000
89	A	223	LEU	0	0.028	-0.002	17.081	0.000	0.000	0.000	0.000	0.000	0.000
90	A	224	THR	0	0.000	-0.003	19.727	0.003	0.003	0.000	0.000	0.000	0.000
91	A	225	ASP	-1	-0.775	-0.909	22.014	-0.061	-0.061	0.000	0.000	0.000	0.000
92	A	226	ALA	0	-0.036	-0.020	22.660	0.006	0.006	0.000	0.000	0.000	0.000
93	A	227	GLN	0	0.030	0.009	21.431	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	228	ARG	1	0.829	0.924	25.327	0.067	0.067	0.000	0.000	0.000	0.000
95	A	229	LEU	0	0.011	0.015	27.550	0.004	0.004	0.000	0.000	0.000	0.000
96	A	230	CYS	0	-0.027	-0.022	26.975	0.004	0.004	0.000	0.000	0.000	0.000
97	A	231	ASN	0	-0.037	-0.014	28.479	0.003	0.003	0.000	0.000	0.000	0.000
98	A	232	ALA	0	0.004	0.016	31.397	0.002	0.002	0.000	0.000	0.000	0.000
99	A	233	LEU	0	-0.044	-0.012	32.180	0.003	0.003	0.000	0.000	0.000	0.000
100	A	234	LEU	0	-0.008	-0.009	30.810	0.002	0.002	0.000	0.000	0.000	0.000
101	A	235	ARG	1	0.756	0.882	29.451	0.057	0.057	0.000	0.000	0.000	0.000
102	A	236	PRO	0	0.003	0.021	35.885	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:135:SER)