FMO DATABASE

FMODB ID: YNQL2

Calculation Name: 2EF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EF7

Chain ID: A

ChEMBL ID:

UniProt ID: Q96Y20

Base Structure: X-ray

Registration Date: 2023-09-26

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1029447.068042
FMO2-HF: Nuclear repulsion	979582.908328
FMO2-HF: Total energy	-49864.159714
FMO2-MP2: Total energy	-50007.636888

3D Structure Molmil

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-8.718	-2.445	1.783	-3.081	-4.977	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.016

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

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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	3	GLU	-1	-0.987	-0.998	3.648	-3.306	-1.074	0.001	-1.151	-1.082	0.003
4	A	4	GLU	-1	-0.786	-0.866	5.783	-0.312	-0.312	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.006	-0.017	7.814	-0.019	-0.019	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.032	-0.036	11.442	0.138	0.138	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.947	0.963	14.805	0.426	0.426	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.928	-0.954	11.703	-0.238	-0.238	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.056	-0.035	8.819	0.081	0.081	0.000	0.000	0.000	0.000
10	A	10	MET	0	-0.114	-0.034	14.949	0.033	0.033	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.973	0.996	18.386	0.183	0.183	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.060	0.011	21.152	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.046	-0.031	23.745	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.022	0.007	25.460	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.006	-0.002	28.272	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.026	-0.015	31.870	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.007	0.008	33.572	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.017	-0.011	36.668	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.917	0.938	38.710	0.134	0.134	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.892	-0.937	39.968	-0.096	-0.096	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.004	0.016	41.110	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.991	0.989	43.072	0.070	0.070	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.021	0.017	43.634	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.006	-0.014	43.960	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.889	-0.938	44.095	-0.068	-0.068	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.021	-0.016	38.709	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.004	-0.006	40.120	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.933	0.988	41.669	0.056	0.056	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.003	0.004	36.981	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.032	-0.023	36.043	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.007	0.001	37.665	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.947	-0.992	39.975	-0.053	-0.053	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.862	0.939	34.696	0.080	0.080	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.013	0.009	34.755	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.051	-0.016	31.821	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.074	0.028	32.393	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.086	-0.066	30.765	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.003	0.020	32.281	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.015	0.004	28.317	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.021	0.016	31.835	0.009	0.009	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.039	-0.025	32.025	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.854	-0.924	34.671	-0.131	-0.131	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.054	0.015	35.503	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.045	-0.035	31.753	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.929	0.985	30.836	0.188	0.188	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.009	0.011	27.814	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.001	0.001	31.056	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.054	0.009	32.674	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.061	-0.012	29.409	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.033	0.044	33.032	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.020	-0.016	32.596	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.854	-0.943	35.223	-0.079	-0.079	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.921	0.956	37.020	0.101	0.101	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.828	-0.911	36.162	-0.122	-0.122	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.045	0.025	39.313	0.003	0.003	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.001	-0.001	41.638	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.908	0.955	38.658	0.109	0.109	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.038	0.013	43.514	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.028	0.017	45.348	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.018	-0.001	46.955	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.832	0.915	45.964	0.081	0.081	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.014	0.006	49.404	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.879	0.962	47.100	0.080	0.080	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.053	0.027	50.077	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.049	0.022	48.909	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.908	-0.960	48.481	-0.062	-0.062	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.079	-0.048	45.890	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.949	0.985	44.549	0.094	0.094	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.042	0.015	39.355	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.908	-0.988	39.979	-0.117	-0.117	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.979	-0.987	41.032	-0.089	-0.089	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.083	-0.044	40.830	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.047	0.010	36.581	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.041	-0.004	33.236	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.010	-0.018	34.285	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.027	-0.036	29.014	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.052	0.027	30.600	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.049	0.000	24.597	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.033	-0.015	24.441	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.019	0.008	17.918	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.964	0.981	19.489	0.452	0.452	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.828	-0.948	18.140	-0.403	-0.403	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.908	-0.950	15.676	-0.578	-0.578	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.095	-0.043	14.590	-0.088	-0.088	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.104	0.063	10.380	0.081	0.081	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.017	0.011	9.469	0.182	0.182	0.000	0.000	0.000	0.000
87	A	87	THR	0	0.006	-0.014	9.354	0.203	0.203	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.042	0.030	12.097	0.125	0.125	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.015	0.003	14.886	0.108	0.108	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.006	-0.003	13.073	0.089	0.089	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.023	-0.021	15.939	0.079	0.079	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.018	0.015	17.799	0.064	0.064	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.022	-0.005	18.771	0.045	0.045	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.913	0.957	16.834	0.518	0.518	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.030	0.006	21.361	0.012	0.012	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.012	-0.015	23.714	0.031	0.031	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.043	-0.006	24.662	0.014	0.014	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.025	-0.009	23.583	0.027	0.027	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.932	0.948	22.061	0.172	0.172	0.000	0.000	0.000	0.000
100	A	100	HIS	0	0.023	0.001	21.644	-0.016	-0.016	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.009	0.013	19.794	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.016	0.003	22.447	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.002	0.008	19.725	-0.024	-0.024	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.013	-0.009	22.637	0.037	0.037	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.735	-0.878	22.344	-0.299	-0.299	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.872	-0.947	23.035	-0.311	-0.311	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.834	0.917	24.390	0.270	0.270	0.000	0.000	0.000	0.000
108	A	108	GLY	0	-0.018	-0.016	26.609	0.020	0.020	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.071	-0.041	27.746	0.022	0.022	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.000	-0.006	26.490	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.896	0.955	23.017	0.244	0.244	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.033	0.007	22.812	0.016	0.016	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.062	-0.004	22.661	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.040	0.046	15.156	0.009	0.009	0.000	0.000	0.000	0.000
115	A	115	SER	0	-0.034	-0.040	18.792	0.010	0.010	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.046	-0.006	16.516	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.898	0.945	16.233	0.194	0.194	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.743	-0.866	15.488	-0.277	-0.277	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.026	-0.007	12.011	-0.030	-0.030	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.002	-0.015	11.238	-0.088	-0.088	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.868	0.962	11.029	0.212	0.212	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.081	0.048	9.160	0.046	0.046	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.098	-0.045	6.811	-0.173	-0.173	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.921	-0.987	6.169	-0.513	-0.513	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.910	-0.953	7.505	0.046	0.046	0.000	0.000	0.000	0.000
126	A	126	MET	0	-0.090	-0.021	2.593	-0.710	0.393	0.435	-0.250	-1.289	0.000
127	A	127	PHE	0	-0.088	-0.042	2.501	-5.622	-2.684	1.347	-1.680	-2.606	-0.023

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