FMO DATABASE

FMODB ID: JQGM9

Calculation Name: 3EY6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EY6

Chain ID: A

ChEMBL ID:

UniProt ID: Q14318

Base Structure: X-ray

Registration Date: 2023-09-23

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-904508.070538
FMO2-HF: Nuclear repulsion	859306.694671
FMO2-HF: Total energy	-45201.375867
FMO2-MP2: Total energy	-45330.700288

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:33:MET)

Summations of interaction energy for fragment #1(A:33:MET)

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.
-2.898	-1.261	-0.012	-0.585	-1.039	0.002

Interaction energy analysis for fragmet #1(A:33:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.014

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	35	GLU	-1	-0.912	-0.946	3.852	0.218	1.633	-0.010	-0.560	-0.845	0.002
4	A	36	TRP	0	-0.063	-0.038	6.659	0.256	0.256	0.000	0.000	0.000	0.000
5	A	37	LEU	0	0.027	0.020	9.868	-0.161	-0.161	0.000	0.000	0.000	0.000
6	A	38	ASP	-1	-0.855	-0.937	12.940	0.473	0.473	0.000	0.000	0.000	0.000
7	A	39	ILE	0	-0.032	-0.026	16.214	-0.041	-0.041	0.000	0.000	0.000	0.000
8	A	40	LEU	0	-0.010	-0.011	18.537	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	41	GLY	0	-0.015	0.015	20.051	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	42	ASN	0	-0.018	-0.024	21.171	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	43	GLY	0	0.020	0.006	18.643	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	44	LEU	0	-0.058	-0.027	19.350	0.033	0.033	0.000	0.000	0.000	0.000
13	A	45	LEU	0	0.005	0.015	19.241	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	46	ARG	1	0.917	0.980	12.405	-0.804	-0.804	0.000	0.000	0.000	0.000
15	A	47	LYS	1	0.892	0.944	11.679	-1.068	-1.068	0.000	0.000	0.000	0.000
16	A	48	LYS	1	0.895	0.942	4.563	-5.790	-5.684	-0.001	-0.018	-0.086	0.000
17	A	49	THR	0	-0.029	-0.019	6.860	-0.162	-0.162	0.000	0.000	0.000	0.000
18	A	50	LEU	0	-0.054	-0.036	5.968	1.411	1.411	0.000	0.000	0.000	0.000
19	A	51	VAL	0	0.007	0.003	6.139	0.133	0.133	0.000	0.000	0.000	0.000
20	A	52	PRO	0	-0.027	-0.031	4.508	-0.149	-0.033	-0.001	-0.007	-0.108	0.000
21	A	53	GLY	0	0.094	0.070	7.885	-0.196	-0.196	0.000	0.000	0.000	0.000
22	A	54	PRO	0	-0.030	-0.007	9.133	-0.073	-0.073	0.000	0.000	0.000	0.000
23	A	55	PRO	0	0.008	-0.020	9.366	0.045	0.045	0.000	0.000	0.000	0.000
24	A	56	GLY	0	-0.001	0.003	11.363	0.007	0.007	0.000	0.000	0.000	0.000
25	A	57	SER	0	-0.070	-0.014	11.843	0.049	0.049	0.000	0.000	0.000	0.000
26	A	58	SER	0	0.015	-0.001	14.112	0.000	0.000	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.957	0.989	13.599	-0.418	-0.418	0.000	0.000	0.000	0.000
28	A	60	PRO	0	-0.004	0.021	17.531	-0.041	-0.041	0.000	0.000	0.000	0.000
29	A	61	VAL	0	-0.029	-0.015	20.919	0.010	0.010	0.000	0.000	0.000	0.000
30	A	62	LYS	1	0.891	0.936	23.985	-0.240	-0.240	0.000	0.000	0.000	0.000
31	A	63	GLY	0	-0.002	-0.001	26.510	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	64	GLN	0	-0.029	-0.016	23.866	0.008	0.008	0.000	0.000	0.000	0.000
33	A	65	VAL	0	0.003	0.004	27.436	0.014	0.014	0.000	0.000	0.000	0.000
34	A	66	VAL	0	-0.017	-0.010	22.728	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	67	THR	0	0.007	0.003	23.756	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	68	VAL	0	-0.025	-0.024	20.275	0.019	0.019	0.000	0.000	0.000	0.000
37	A	69	HIS	0	-0.079	-0.029	19.002	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.007	-0.003	19.096	0.059	0.059	0.000	0.000	0.000	0.000
39	A	71	GLN	0	0.033	0.025	17.344	-0.075	-0.075	0.000	0.000	0.000	0.000
40	A	72	THR	0	0.005	-0.003	19.767	0.048	0.048	0.000	0.000	0.000	0.000
41	A	73	SER	0	-0.030	-0.014	19.629	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	74	LEU	0	0.036	0.012	21.827	0.021	0.021	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.922	-0.955	20.817	0.378	0.378	0.000	0.000	0.000	0.000
44	A	76	ASN	0	-0.032	-0.024	20.774	0.033	0.033	0.000	0.000	0.000	0.000
45	A	77	GLY	0	0.024	0.013	20.803	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	78	THR	0	-0.049	-0.020	21.714	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	79	ARG	1	0.871	0.930	21.330	-0.305	-0.305	0.000	0.000	0.000	0.000
48	A	80	VAL	0	-0.021	-0.020	24.381	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	81	GLN	0	-0.071	-0.034	25.158	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	82	GLU	-1	-0.858	-0.933	22.028	0.331	0.331	0.000	0.000	0.000	0.000
51	A	83	GLU	-1	-0.870	-0.924	23.843	0.186	0.186	0.000	0.000	0.000	0.000
52	A	84	PRO	0	0.000	-0.002	23.031	0.028	0.028	0.000	0.000	0.000	0.000
53	A	85	GLU	-1	-0.970	-0.999	23.627	0.157	0.157	0.000	0.000	0.000	0.000
54	A	86	LEU	0	0.002	0.016	24.502	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	87	VAL	0	0.003	-0.004	25.495	0.015	0.015	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.007	-0.010	23.317	0.000	0.000	0.000	0.000	0.000	0.000
57	A	89	THR	0	0.041	0.025	27.766	0.003	0.003	0.000	0.000	0.000	0.000
58	A	90	LEU	0	-0.008	0.005	22.527	0.010	0.010	0.000	0.000	0.000	0.000
59	A	91	GLY	0	-0.004	-0.022	26.684	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	92	ASP	-1	-0.895	-0.931	28.482	0.159	0.159	0.000	0.000	0.000	0.000
61	A	93	CYS	0	-0.075	-0.051	30.014	0.012	0.012	0.000	0.000	0.000	0.000
62	A	94	ASP	-1	-0.919	-0.959	32.049	0.179	0.179	0.000	0.000	0.000	0.000
63	A	95	VAL	0	-0.025	0.008	25.885	0.009	0.009	0.000	0.000	0.000	0.000
64	A	96	ILE	0	-0.020	0.000	24.309	0.006	0.006	0.000	0.000	0.000	0.000
65	A	97	GLN	0	0.074	0.010	25.406	0.023	0.023	0.000	0.000	0.000	0.000
66	A	98	ALA	0	0.005	0.002	21.146	0.021	0.021	0.000	0.000	0.000	0.000
67	A	99	LEU	0	-0.004	0.019	20.242	0.058	0.058	0.000	0.000	0.000	0.000
68	A	100	ASP	-1	-0.836	-0.922	21.732	0.283	0.283	0.000	0.000	0.000	0.000
69	A	101	LEU	0	-0.013	-0.019	21.992	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	102	SER	0	-0.058	-0.054	16.941	0.037	0.037	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.044	0.009	17.477	0.047	0.047	0.000	0.000	0.000	0.000
72	A	104	PRO	0	-0.006	0.000	18.548	0.004	0.004	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.062	-0.037	15.455	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	106	MET	0	-0.127	-0.048	13.847	0.083	0.083	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.849	-0.925	11.236	0.359	0.359	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.039	-0.039	14.205	0.043	0.043	0.000	0.000	0.000	0.000
77	A	109	GLY	0	-0.015	-0.017	14.544	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	110	GLU	-1	-0.803	-0.872	10.636	1.137	1.137	0.000	0.000	0.000	0.000
79	A	111	THR	0	-0.011	-0.017	10.982	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	112	ALA	0	-0.024	-0.023	10.139	0.352	0.352	0.000	0.000	0.000	0.000
81	A	113	MET	0	0.008	0.022	11.179	-0.186	-0.186	0.000	0.000	0.000	0.000
82	A	114	VAL	0	-0.013	-0.018	12.835	0.100	0.100	0.000	0.000	0.000	0.000
83	A	115	THR	0	-0.037	-0.014	14.747	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	116	ALA	0	-0.004	-0.012	17.189	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	117	ASP	-1	-0.777	-0.894	20.665	0.278	0.278	0.000	0.000	0.000	0.000
86	A	118	SER	0	0.046	0.035	23.808	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.913	0.960	26.822	-0.252	-0.252	0.000	0.000	0.000	0.000
88	A	120	TYR	0	-0.034	-0.019	23.835	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	121	CYS	0	-0.025	-0.005	24.016	0.022	0.022	0.000	0.000	0.000	0.000
90	A	122	TYR	0	0.045	0.010	26.548	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	123	GLY	0	0.003	0.014	29.359	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	124	PRO	0	0.014	-0.018	31.214	0.002	0.002	0.000	0.000	0.000	0.000
93	A	125	GLN	0	-0.016	0.002	33.877	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	126	GLY	0	0.016	0.029	31.891	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	127	ARG	1	0.922	0.952	28.238	-0.228	-0.228	0.000	0.000	0.000	0.000
96	A	128	SER	0	-0.037	0.011	32.708	0.004	0.004	0.000	0.000	0.000	0.000
97	A	129	PRO	0	0.021	-0.011	34.156	0.003	0.003	0.000	0.000	0.000	0.000
98	A	130	TYR	0	0.007	-0.019	30.668	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	131	ILE	0	-0.004	0.016	27.091	0.013	0.013	0.000	0.000	0.000	0.000
100	A	132	PRO	0	0.015	0.010	29.859	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	133	PRO	0	-0.009	-0.011	31.204	0.013	0.013	0.000	0.000	0.000	0.000
102	A	134	HIS	0	-0.007	-0.021	30.512	0.006	0.006	0.000	0.000	0.000	0.000
103	A	135	ALA	0	-0.012	0.010	27.078	0.011	0.011	0.000	0.000	0.000	0.000
104	A	136	ALA	0	0.029	0.022	22.543	0.008	0.008	0.000	0.000	0.000	0.000
105	A	137	LEU	0	-0.050	-0.039	22.081	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	138	CYS	0	-0.027	-0.016	16.974	0.052	0.052	0.000	0.000	0.000	0.000
107	A	139	LEU	0	-0.001	-0.007	17.662	-0.061	-0.061	0.000	0.000	0.000	0.000
108	A	140	GLU	-1	-0.894	-0.949	13.805	0.887	0.887	0.000	0.000	0.000	0.000
109	A	141	VAL	0	0.003	-0.010	15.113	-0.111	-0.111	0.000	0.000	0.000	0.000
110	A	142	THR	0	0.028	0.031	14.825	0.124	0.124	0.000	0.000	0.000	0.000
111	A	143	LEU	0	0.000	0.013	16.155	-0.068	-0.068	0.000	0.000	0.000	0.000
112	A	144	LYS	1	0.907	0.960	17.589	-0.236	-0.236	0.000	0.000	0.000	0.000
113	A	145	THR	0	-0.014	-0.015	20.007	-0.021	-0.021	0.000	0.000	0.000	0.000
114	A	146	ALA	0	0.043	0.018	21.678	0.023	0.023	0.000	0.000	0.000	0.000
115	A	147	VAL	0	-0.041	-0.006	23.443	-0.017	-0.017	0.000	0.000	0.000	0.000
116	A	148	ASP	-1	-0.860	-0.923	26.865	0.113	0.113	0.000	0.000	0.000	0.000
117	A	149	GLY	0	0.023	0.016	29.271	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	150	PRO	0	-0.040	-0.018	31.907	-0.008	-0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:33:MET)