FMO DATABASE

FMODB ID: YZYZ2

Calculation Name: 2XLI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XLI

Chain ID: A

ChEMBL ID:

UniProt ID: Q02MM2

Base Structure: X-ray

Registration Date: 2023-06-21

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	170
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1764433.108939
FMO2-HF: Nuclear repulsion	1696898.133444
FMO2-HF: Total energy	-67534.975495
FMO2-MP2: Total energy	-67734.638578

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:-1:PHE)

Summations of interaction energy for fragment #1(A:-1:PHE)

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.
-19.686	-8.416	14.301	-7.772	-17.799	0.018

Interaction energy analysis for fragmet #1(A:-1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.019

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	1	MET	0	-0.108	-0.027	2.647	-7.174	-2.080	2.031	-2.564	-4.561	0.016
4	A	2	ASP	-1	-0.818	-0.890	2.307	-5.689	-5.564	5.749	-1.822	-4.052	-0.019
5	A	3	HIS	0	-0.026	-0.016	3.852	0.159	0.390	0.007	-0.001	-0.237	0.000
6	A	4	TYR	0	-0.013	-0.027	6.102	0.057	0.057	0.000	0.000	0.000	0.000
7	A	5	LEU	0	0.019	0.014	8.217	0.069	0.069	0.000	0.000	0.000	0.000
8	A	6	ASP	-1	-0.761	-0.858	11.868	-0.409	-0.409	0.000	0.000	0.000	0.000
9	A	7	ILE	0	0.002	0.003	13.906	0.026	0.026	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.933	0.953	17.102	0.187	0.187	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.004	0.006	19.883	0.008	0.008	0.000	0.000	0.000	0.000
12	A	10	ARG	1	0.891	0.951	22.902	0.113	0.113	0.000	0.000	0.000	0.000
13	A	11	PRO	0	-0.005	-0.009	26.069	0.005	0.005	0.000	0.000	0.000	0.000
14	A	12	ASP	-1	-0.824	-0.941	28.770	-0.059	-0.059	0.000	0.000	0.000	0.000
15	A	13	PRO	0	-0.046	-0.019	31.543	0.001	0.001	0.000	0.000	0.000	0.000
16	A	14	DGL	-1	-0.952	-0.954	34.479	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	15	PHE	0	-0.061	-0.030	30.167	0.004	0.004	0.000	0.000	0.000	0.000
18	A	16	PRO	0	0.016	0.023	29.382	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	17	PRO	0	0.088	0.027	24.786	0.002	0.002	0.000	0.000	0.000	0.000
20	A	18	ALA	0	0.001	0.000	24.233	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	19	GLN	0	0.038	0.032	24.633	0.000	0.000	0.000	0.000	0.000	0.000
22	A	20	LEU	0	0.084	0.039	24.751	0.002	0.002	0.000	0.000	0.000	0.000
23	A	21	MET	0	-0.008	0.018	18.822	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	22	SER	0	-0.051	-0.044	20.930	0.002	0.002	0.000	0.000	0.000	0.000
25	A	23	VAL	0	-0.006	0.005	22.542	0.005	0.005	0.000	0.000	0.000	0.000
26	A	24	LEU	0	0.035	0.022	18.237	0.005	0.005	0.000	0.000	0.000	0.000
27	A	25	PHE	0	0.017	-0.008	14.626	0.006	0.006	0.000	0.000	0.000	0.000
28	A	26	GLY	0	-0.005	-0.014	18.928	0.009	0.009	0.000	0.000	0.000	0.000
29	A	27	LYS	1	0.933	0.968	21.506	0.048	0.048	0.000	0.000	0.000	0.000
30	A	28	LEU	0	0.045	0.018	13.416	0.007	0.007	0.000	0.000	0.000	0.000
31	A	29	HIS	0	-0.069	-0.047	17.364	0.015	0.015	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.027	-0.020	18.668	0.012	0.012	0.000	0.000	0.000	0.000
33	A	31	ALA	0	0.038	0.015	18.043	0.011	0.011	0.000	0.000	0.000	0.000
34	A	32	LEU	0	-0.005	-0.001	13.108	0.012	0.012	0.000	0.000	0.000	0.000
35	A	33	VAL	0	-0.074	-0.034	16.937	0.024	0.024	0.000	0.000	0.000	0.000
36	A	34	ALA	0	-0.041	-0.008	19.817	0.011	0.011	0.000	0.000	0.000	0.000
37	A	35	GLN	0	-0.021	0.007	15.131	0.012	0.012	0.000	0.000	0.000	0.000
38	A	36	GLY	0	0.001	0.004	18.027	0.017	0.017	0.000	0.000	0.000	0.000
39	A	37	GLY	0	-0.017	0.002	14.430	0.022	0.022	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.850	-0.931	12.064	0.386	0.386	0.000	0.000	0.000	0.000
41	A	39	ARG	1	0.977	0.978	8.024	-0.744	-0.744	0.000	0.000	0.000	0.000
42	A	40	ILE	0	0.010	0.021	7.915	0.023	0.023	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.013	0.013	7.020	0.018	0.018	0.000	0.000	0.000	0.000
44	A	42	VAL	0	-0.050	-0.013	7.927	-0.054	-0.054	0.000	0.000	0.000	0.000
45	A	43	SER	0	-0.011	-0.005	8.578	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	44	PHE	0	0.013	-0.014	10.558	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	45	PRO	0	-0.009	-0.012	12.320	0.024	0.024	0.000	0.000	0.000	0.000
48	A	46	ASP	-1	-0.829	-0.910	14.036	-0.194	-0.194	0.000	0.000	0.000	0.000
49	A	47	LEU	0	-0.101	-0.042	15.180	0.019	0.019	0.000	0.000	0.000	0.000
50	A	48	ASP	-1	-0.823	-0.913	18.128	-0.083	-0.083	0.000	0.000	0.000	0.000
51	A	49	GLU	-1	-0.922	-0.984	17.495	-0.051	-0.051	0.000	0.000	0.000	0.000
52	A	50	SER	0	-0.035	-0.007	21.256	0.008	0.008	0.000	0.000	0.000	0.000
53	A	51	ARG	1	0.874	0.938	24.514	0.076	0.076	0.000	0.000	0.000	0.000
54	A	52	SER	0	0.008	0.009	22.767	0.000	0.000	0.000	0.000	0.000	0.000
55	A	53	ARG	1	0.963	0.972	22.697	0.069	0.069	0.000	0.000	0.000	0.000
56	A	54	LEU	0	-0.015	-0.006	17.001	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	55	GLY	0	0.031	0.030	18.078	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	56	GLU	-1	-0.907	-0.970	20.364	-0.103	-0.103	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.801	0.897	14.661	0.268	0.268	0.000	0.000	0.000	0.000
60	A	58	LEU	0	-0.010	-0.001	13.401	0.008	0.008	0.000	0.000	0.000	0.000
61	A	59	ARG	1	0.790	0.876	8.089	0.511	0.511	0.000	0.000	0.000	0.000
62	A	60	ILE	0	-0.044	-0.023	10.108	0.021	0.021	0.000	0.000	0.000	0.000
63	A	61	HIS	0	0.013	-0.015	4.612	-0.473	-0.367	-0.001	-0.005	-0.100	0.000
64	A	62	ALA	0	0.035	-0.002	6.274	0.258	0.258	0.000	0.000	0.000	0.000
65	A	63	SER	0	0.094	0.068	6.614	-0.268	-0.268	0.000	0.000	0.000	0.000
66	A	64	ALA	0	0.040	0.009	8.160	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	65	ASP	-1	-0.896	-0.949	10.799	0.013	0.013	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.903	-0.956	10.481	0.339	0.339	0.000	0.000	0.000	0.000
69	A	67	LEU	0	-0.041	-0.024	9.680	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	68	ARG	1	0.977	0.975	12.080	0.212	0.212	0.000	0.000	0.000	0.000
71	A	69	ALA	0	0.015	0.013	15.281	0.007	0.007	0.000	0.000	0.000	0.000
72	A	70	LEU	0	-0.080	-0.042	13.894	0.006	0.006	0.000	0.000	0.000	0.000
73	A	71	LEU	0	-0.055	-0.037	14.310	0.000	0.000	0.000	0.000	0.000	0.000
74	A	72	ALA	0	-0.003	0.019	17.698	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	ARG	1	0.880	0.945	18.991	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	74	PRO	0	0.053	0.037	21.998	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	75	TRP	0	-0.002	-0.016	16.982	0.010	0.010	0.000	0.000	0.000	0.000
78	A	76	LEU	0	-0.014	-0.020	19.423	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	77	GLU	-1	-0.938	-0.962	23.217	-0.056	-0.056	0.000	0.000	0.000	0.000
80	A	78	GLY	0	-0.026	-0.014	26.918	0.003	0.003	0.000	0.000	0.000	0.000
81	A	79	LEU	0	-0.009	-0.009	22.774	0.002	0.002	0.000	0.000	0.000	0.000
82	A	80	ARG	1	0.976	0.980	22.456	0.093	0.093	0.000	0.000	0.000	0.000
83	A	81	ASP	-1	-0.858	-0.902	25.583	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	82	HIS	0	-0.019	-0.007	26.433	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	83	LEU	0	-0.063	-0.040	21.131	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	84	GLN	0	-0.040	-0.020	21.874	0.007	0.007	0.000	0.000	0.000	0.000
87	A	85	PHE	0	-0.030	-0.020	17.940	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	86	GLY	0	0.001	0.014	16.171	0.005	0.005	0.000	0.000	0.000	0.000
89	A	87	GLU	-1	-0.920	-0.974	16.156	-0.275	-0.275	0.000	0.000	0.000	0.000
90	A	88	PRO	0	-0.061	-0.038	12.624	-0.046	-0.046	0.000	0.000	0.000	0.000
91	A	89	ALA	0	0.011	0.020	11.007	0.024	0.024	0.000	0.000	0.000	0.000
92	A	90	VAL	0	0.028	0.016	6.937	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	91	VAL	0	-0.069	-0.043	3.714	-0.129	0.155	0.003	-0.045	-0.242	0.000
94	A	92	PRO	0	0.000	0.006	6.910	-0.044	-0.044	0.000	0.000	0.000	0.000
95	A	93	HIS	0	-0.036	0.008	6.774	-0.190	-0.190	0.000	0.000	0.000	0.000
96	A	94	PRO	0	0.049	0.008	8.215	0.069	0.069	0.000	0.000	0.000	0.000
97	A	95	THR	0	-0.016	-0.028	6.425	-0.053	-0.053	0.000	0.000	0.000	0.000
98	A	96	PRO	0	-0.019	0.004	8.187	0.137	0.137	0.000	0.000	0.000	0.000
99	A	97	TYR	0	0.007	0.014	2.940	-2.770	-0.410	0.943	-0.851	-2.453	0.011
100	A	98	ARG	1	0.866	0.940	6.809	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	99	GLN	0	0.081	0.050	7.162	-0.062	-0.062	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.009	-0.001	8.945	0.015	0.015	0.000	0.000	0.000	0.000
103	A	101	SER	0	0.017	0.016	11.088	0.010	0.010	0.000	0.000	0.000	0.000
104	A	102	ARG	1	0.977	0.997	13.842	-0.031	-0.031	0.000	0.000	0.000	0.000
105	A	103	VAL	0	-0.024	-0.007	17.238	0.013	0.013	0.000	0.000	0.000	0.000
106	A	104	GLN	0	-0.043	-0.037	20.000	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.073	0.034	23.491	0.004	0.004	0.000	0.000	0.000	0.000
108	A	106	LYS	1	0.930	0.963	26.799	-0.036	-0.036	0.000	0.000	0.000	0.000
109	A	107	SER	0	0.038	0.009	29.615	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	108	ASN	0	-0.003	0.012	31.356	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	109	PRO	0	0.095	0.050	33.995	0.003	0.003	0.000	0.000	0.000	0.000
112	A	110	GLU	-1	-0.748	-0.878	36.704	0.015	0.015	0.000	0.000	0.000	0.000
113	A	111	ARG	1	0.943	0.977	30.804	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	112	LEU	0	-0.030	-0.024	32.985	0.003	0.003	0.000	0.000	0.000	0.000
115	A	113	ARG	1	0.994	0.989	35.521	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	114	ARG	1	0.889	0.915	38.028	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	115	ARG	1	0.919	0.948	31.862	-0.049	-0.049	0.000	0.000	0.000	0.000
118	A	116	LEU	0	0.005	0.009	37.037	0.002	0.002	0.000	0.000	0.000	0.000
119	A	117	MET	0	0.004	0.028	38.699	0.000	0.000	0.000	0.000	0.000	0.000
120	A	118	ARG	1	0.923	0.969	37.289	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	119	ARG	1	0.974	1.010	34.122	-0.050	-0.050	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.077	-0.058	23.093	0.002	0.002	0.000	0.000	0.000	0.000
123	A	140	ASP	-1	-0.913	-0.935	26.073	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	141	LEU	0	-0.011	-0.011	19.889	0.000	0.000	0.000	0.000	0.000	0.000
125	A	142	PRO	0	0.076	0.050	19.174	0.002	0.002	0.000	0.000	0.000	0.000
126	A	143	PHE	0	-0.076	-0.046	20.932	0.006	0.006	0.000	0.000	0.000	0.000
127	A	144	VAL	0	0.043	0.049	19.605	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	145	THR	0	-0.021	-0.026	22.264	0.010	0.010	0.000	0.000	0.000	0.000
129	A	146	LEU	0	0.014	0.006	20.745	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	147	ARG	1	1.015	0.995	25.337	0.007	0.007	0.000	0.000	0.000	0.000
131	A	148	SER	0	-0.042	-0.009	27.116	0.002	0.002	0.000	0.000	0.000	0.000
132	A	149	GLN	0	0.023	0.008	27.406	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	150	SER	0	0.036	0.013	29.310	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	151	THR	0	-0.070	-0.034	31.123	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	152	GLY	0	0.060	0.035	32.050	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	153	GLN	0	-0.029	-0.010	31.823	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	154	HIS	0	0.035	0.011	29.137	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	155	PHE	0	-0.076	-0.030	23.005	0.002	0.002	0.000	0.000	0.000	0.000
139	A	156	ARG	1	0.969	0.997	25.448	0.015	0.015	0.000	0.000	0.000	0.000
140	A	157	LEU	0	-0.039	-0.018	18.344	0.009	0.009	0.000	0.000	0.000	0.000
141	A	158	PHE	0	-0.005	-0.015	20.717	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	159	ILE	0	0.009	0.003	14.939	0.009	0.009	0.000	0.000	0.000	0.000
143	A	160	ARG	1	0.983	0.989	15.898	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	161	HIS	0	0.051	0.027	11.569	-0.023	-0.023	0.000	0.000	0.000	0.000
145	A	162	GLY	0	-0.015	0.000	12.569	0.004	0.004	0.000	0.000	0.000	0.000
146	A	163	PRO	0	0.032	0.013	13.117	-0.015	-0.015	0.000	0.000	0.000	0.000
147	A	164	LEU	0	-0.009	-0.005	11.418	0.022	0.022	0.000	0.000	0.000	0.000
148	A	165	GLN	0	-0.018	0.002	8.295	-0.098	-0.098	0.000	0.000	0.000	0.000
149	A	166	VAL	0	0.027	0.007	9.550	0.071	0.071	0.000	0.000	0.000	0.000
150	A	167	THR	0	0.049	0.023	6.284	-0.055	-0.055	0.000	0.000	0.000	0.000
151	A	168	ALA	0	-0.033	-0.012	2.698	-0.928	-0.013	1.040	-0.545	-1.410	0.003
152	A	169	GLU	-1	-0.897	-0.952	4.800	-0.020	0.141	-0.001	-0.011	-0.148	0.000
153	A	170	GLU	-1	-0.955	-0.971	4.755	1.119	1.267	-0.001	-0.004	-0.143	0.000
154	A	171	GLY	0	-0.020	-0.019	6.489	-0.188	-0.188	0.000	0.000	0.000	0.000
155	A	172	GLY	0	0.008	0.012	6.553	0.070	0.070	0.000	0.000	0.000	0.000
156	A	173	PHE	0	-0.044	-0.044	4.643	-0.168	-0.069	-0.001	-0.002	-0.096	0.000
157	A	174	THR	0	-0.016	-0.018	10.521	0.031	0.031	0.000	0.000	0.000	0.000
158	A	175	CYS	0	0.051	0.038	13.329	-0.012	-0.012	0.000	0.000	0.000	0.000
159	A	176	TYR	0	-0.024	-0.026	15.222	-0.009	-0.009	0.000	0.000	0.000	0.000
160	A	177	GLY	0	0.060	0.038	11.333	-0.024	-0.024	0.000	0.000	0.000	0.000
161	A	178	LEU	0	-0.063	-0.033	10.231	-0.033	-0.033	0.000	0.000	0.000	0.000
162	A	179	SER	0	-0.010	-0.022	8.690	0.048	0.048	0.000	0.000	0.000	0.000
163	A	180	LYS	1	0.757	0.874	10.002	-0.256	-0.256	0.000	0.000	0.000	0.000
164	A	181	GLY	0	0.029	0.009	9.885	0.043	0.043	0.000	0.000	0.000	0.000
165	A	182	GLY	0	0.025	0.045	5.845	0.042	0.042	0.000	0.000	0.000	0.000
166	A	183	PHE	0	-0.013	0.000	4.038	-0.122	0.147	-0.001	-0.036	-0.232	0.000
167	A	184	VAL	0	-0.012	-0.010	2.637	-2.602	-0.975	0.355	-0.802	-1.181	-0.005
168	A	185	PRO	0	0.034	0.028	2.184	-0.109	-0.312	4.179	-1.074	-2.902	0.012
169	A	186	TRP	0	-0.032	-0.032	4.810	-0.381	-0.327	-0.001	-0.010	-0.042	0.000
170	A	187	PHE	0	0.053	0.033	6.234	0.014	0.014	0.000	0.000	0.000	0.000

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