FMO DATABASE

FMODB ID: GN1J1

Calculation Name: 1XE0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XE0

Chain ID: A

ChEMBL ID:

UniProt ID: P07222

Base Structure: X-ray

Registration Date: 2023-06-20

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	108
LigandCharge	DAR=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-762625.969922
FMO2-HF: Nuclear repulsion	722317.090698
FMO2-HF: Total energy	-40308.879224
FMO2-MP2: Total energy	-40428.710796

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:13:DAR)

Summations of interaction energy for fragment #1(A:13:DAR)

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.
-123.865	-124.929	25.542	-11.77	-12.708	-0.131

Interaction energy analysis for fragmet #1(A:13:DAR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.898

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	15	SER	0	0.025	0.026	2.902	-13.250	-8.870	0.650	-2.426	-2.604	-0.016
4	A	16	GLN	0	0.012	0.009	1.833	-41.847	-48.161	19.502	-7.441	-5.747	-0.079
5	A	17	ASN	0	0.017	0.009	1.948	-20.363	-19.720	5.392	-1.891	-4.144	-0.036
6	A	18	PHE	0	0.021	0.018	4.294	0.520	0.640	-0.001	-0.007	-0.111	0.000
7	A	19	LEU	0	-0.018	-0.014	7.460	0.566	0.566	0.000	0.000	0.000	0.000
8	A	20	PHE	0	0.043	0.025	10.264	1.018	1.018	0.000	0.000	0.000	0.000
9	A	21	GLY	0	0.001	-0.017	13.183	-0.084	-0.084	0.000	0.000	0.000	0.000
10	A	22	CYS	0	-0.072	-0.013	16.739	0.371	0.371	0.000	0.000	0.000	0.000
11	A	23	GLU	-1	-0.857	-0.927	20.368	-11.718	-11.718	0.000	0.000	0.000	0.000
12	A	24	LEU	0	-0.037	-0.007	23.604	0.179	0.179	0.000	0.000	0.000	0.000
13	A	25	LYS	1	0.968	0.970	26.599	10.162	10.162	0.000	0.000	0.000	0.000
14	A	26	ALA	0	0.007	0.005	30.213	0.017	0.017	0.000	0.000	0.000	0.000
15	A	27	ASP	-1	-0.930	-0.971	32.996	-9.244	-9.244	0.000	0.000	0.000	0.000
16	A	28	LYS	1	0.888	0.928	25.288	11.872	11.872	0.000	0.000	0.000	0.000
17	A	29	LYS	1	0.967	0.988	28.786	8.690	8.690	0.000	0.000	0.000	0.000
18	A	30	GLU	-1	-0.788	-0.859	26.887	-10.709	-10.709	0.000	0.000	0.000	0.000
19	A	31	TYR	0	-0.002	-0.008	18.970	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	32	SER	0	0.016	0.018	23.190	-0.092	-0.092	0.000	0.000	0.000	0.000
21	A	33	PHE	0	-0.003	0.001	13.478	0.042	0.042	0.000	0.000	0.000	0.000
22	A	34	LYS	1	0.955	0.957	19.174	13.211	13.211	0.000	0.000	0.000	0.000
23	A	35	VAL	0	-0.032	-0.019	14.501	-0.574	-0.574	0.000	0.000	0.000	0.000
24	A	36	GLU	-1	-0.947	-0.960	17.529	-14.202	-14.202	0.000	0.000	0.000	0.000
25	A	37	ASP	-1	-0.976	-0.989	17.760	-14.332	-14.332	0.000	0.000	0.000	0.000
26	A	38	ASP	-1	-0.836	-0.894	13.869	-21.385	-21.385	0.000	0.000	0.000	0.000
27	A	39	GLU	-1	-0.830	-0.906	14.839	-16.339	-16.339	0.000	0.000	0.000	0.000
28	A	40	ASN	0	-0.105	-0.081	10.750	-2.917	-2.917	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.933	-0.942	11.912	-19.135	-19.135	0.000	0.000	0.000	0.000
30	A	42	HIS	1	0.769	0.834	10.707	20.279	20.279	0.000	0.000	0.000	0.000
31	A	43	GLN	0	-0.026	-0.033	9.393	1.818	1.818	0.000	0.000	0.000	0.000
32	A	44	LEU	0	-0.006	0.007	10.560	-1.959	-1.959	0.000	0.000	0.000	0.000
33	A	45	SER	0	0.033	0.024	8.746	1.506	1.506	0.000	0.000	0.000	0.000
34	A	46	LEU	0	-0.002	-0.017	10.684	-0.682	-0.682	0.000	0.000	0.000	0.000
35	A	47	ARG	1	0.919	0.941	7.692	25.532	25.532	0.000	0.000	0.000	0.000
36	A	48	THR	0	-0.064	-0.041	13.323	1.008	1.008	0.000	0.000	0.000	0.000
37	A	49	VAL	0	0.051	0.038	16.634	-0.146	-0.146	0.000	0.000	0.000	0.000
38	A	50	SER	0	-0.024	-0.012	20.198	0.318	0.318	0.000	0.000	0.000	0.000
39	A	51	LEU	0	0.025	0.019	22.397	0.054	0.054	0.000	0.000	0.000	0.000
40	A	52	GLY	0	0.023	0.017	25.890	-0.118	-0.118	0.000	0.000	0.000	0.000
41	A	53	ALA	0	0.003	-0.001	27.058	0.292	0.292	0.000	0.000	0.000	0.000
42	A	54	SER	0	-0.040	-0.034	29.685	0.198	0.198	0.000	0.000	0.000	0.000
43	A	55	ALA	0	-0.026	0.020	29.883	0.274	0.274	0.000	0.000	0.000	0.000
44	A	56	LYS	1	1.019	1.001	31.969	8.309	8.309	0.000	0.000	0.000	0.000
45	A	57	ASP	-1	-0.800	-0.905	33.731	-8.864	-8.864	0.000	0.000	0.000	0.000
46	A	58	GLU	-1	-0.906	-0.967	34.224	-8.306	-8.306	0.000	0.000	0.000	0.000
47	A	59	LEU	0	-0.034	-0.027	30.808	-0.236	-0.236	0.000	0.000	0.000	0.000
48	A	60	HIS	0	-0.039	-0.006	28.850	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	61	VAL	0	-0.035	-0.017	27.912	-0.210	-0.210	0.000	0.000	0.000	0.000
50	A	62	VAL	0	0.007	0.008	22.720	0.103	0.103	0.000	0.000	0.000	0.000
51	A	63	GLU	-1	-0.862	-0.941	24.780	-10.415	-10.415	0.000	0.000	0.000	0.000
52	A	64	ALA	0	0.022	0.011	21.025	-0.316	-0.316	0.000	0.000	0.000	0.000
53	A	65	GLU	-1	-0.877	-0.935	23.006	-10.275	-10.275	0.000	0.000	0.000	0.000
54	A	66	GLY	0	0.064	0.015	22.311	-0.426	-0.426	0.000	0.000	0.000	0.000
55	A	67	ILE	0	-0.011	0.023	22.333	0.528	0.528	0.000	0.000	0.000	0.000
56	A	68	ASN	0	0.041	0.023	22.539	-0.519	-0.519	0.000	0.000	0.000	0.000
57	A	69	TYR	0	0.034	-0.008	23.678	-0.101	-0.101	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.948	-0.969	24.696	-9.530	-9.530	0.000	0.000	0.000	0.000
59	A	71	GLY	0	-0.022	-0.017	26.247	0.307	0.307	0.000	0.000	0.000	0.000
60	A	72	LYS	1	0.906	0.961	27.251	9.324	9.324	0.000	0.000	0.000	0.000
61	A	73	THR	0	0.015	0.009	26.854	-0.354	-0.354	0.000	0.000	0.000	0.000
62	A	74	ILE	0	-0.041	-0.018	24.736	0.485	0.485	0.000	0.000	0.000	0.000
63	A	75	LYS	1	0.952	0.979	26.203	9.177	9.177	0.000	0.000	0.000	0.000
64	A	76	ILE	0	0.002	0.012	20.969	0.349	0.349	0.000	0.000	0.000	0.000
65	A	77	ALA	0	-0.007	-0.012	24.796	-0.195	-0.195	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.037	-0.011	19.474	-0.138	-0.138	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.030	0.000	21.985	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	80	SER	0	-0.016	-0.009	23.985	0.383	0.383	0.000	0.000	0.000	0.000
69	A	81	LEU	0	-0.026	0.000	23.470	-0.085	-0.085	0.000	0.000	0.000	0.000
70	A	82	LYS	1	0.946	0.973	27.764	8.663	8.663	0.000	0.000	0.000	0.000
71	A	83	PRO	0	0.021	0.018	29.737	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.042	-0.027	30.781	-0.139	-0.139	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.073	-0.033	30.679	0.154	0.154	0.000	0.000	0.000	0.000
74	A	86	GLN	0	0.001	-0.010	24.841	-0.500	-0.500	0.000	0.000	0.000	0.000
75	A	87	PRO	0	0.061	0.028	25.941	-0.147	-0.147	0.000	0.000	0.000	0.000
76	A	88	THR	0	-0.011	-0.016	19.943	-0.413	-0.413	0.000	0.000	0.000	0.000
77	A	89	VAL	0	0.026	0.034	19.736	0.276	0.276	0.000	0.000	0.000	0.000
78	A	90	SER	0	-0.022	-0.027	14.892	-0.801	-0.801	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.007	-0.020	15.250	0.525	0.525	0.000	0.000	0.000	0.000
80	A	92	GLY	0	-0.044	-0.014	12.338	-0.066	-0.066	0.000	0.000	0.000	0.000
81	A	93	GLY	0	-0.077	-0.030	9.681	-1.002	-1.002	0.000	0.000	0.000	0.000
82	A	94	PHE	0	0.028	0.015	10.618	0.231	0.231	0.000	0.000	0.000	0.000
83	A	95	GLU	-1	-0.933	-0.961	7.761	-26.586	-26.586	0.000	0.000	0.000	0.000
84	A	96	ILE	0	-0.031	-0.013	12.332	1.521	1.521	0.000	0.000	0.000	0.000
85	A	97	THR	0	0.058	0.032	14.317	-1.613	-1.613	0.000	0.000	0.000	0.000
86	A	98	PRO	0	-0.068	0.020	15.040	0.987	0.987	0.000	0.000	0.000	0.000
87	A	99	PRO	0	-0.020	-0.038	17.980	0.194	0.194	0.000	0.000	0.000	0.000
88	A	100	VAL	0	0.035	0.011	17.930	0.320	0.320	0.000	0.000	0.000	0.000
89	A	101	ILE	0	-0.023	-0.008	21.012	-0.296	-0.296	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.041	-0.014	18.556	0.062	0.062	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.784	0.845	23.026	10.761	10.761	0.000	0.000	0.000	0.000
92	A	104	LEU	0	-0.031	0.001	26.529	-0.100	-0.100	0.000	0.000	0.000	0.000
93	A	105	LYS	1	0.948	0.974	28.498	10.050	10.050	0.000	0.000	0.000	0.000
94	A	106	SER	0	-0.045	-0.042	30.806	0.389	0.389	0.000	0.000	0.000	0.000
95	A	107	GLY	0	0.055	0.046	31.422	-0.291	-0.291	0.000	0.000	0.000	0.000
96	A	108	SER	0	-0.100	-0.066	33.058	-0.056	-0.056	0.000	0.000	0.000	0.000
97	A	109	GLY	0	0.027	0.028	29.443	-0.118	-0.118	0.000	0.000	0.000	0.000
98	A	110	PRO	0	0.018	0.007	27.083	0.431	0.431	0.000	0.000	0.000	0.000
99	A	111	VAL	0	-0.012	-0.012	23.611	0.040	0.040	0.000	0.000	0.000	0.000
100	A	112	TYR	0	-0.042	-0.026	20.576	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	113	VAL	0	0.014	0.003	17.210	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	114	SER	0	0.001	0.013	14.524	-0.404	-0.404	0.000	0.000	0.000	0.000
103	A	115	GLY	0	0.062	0.014	11.754	0.478	0.478	0.000	0.000	0.000	0.000
104	A	116	GLN	0	-0.027	0.001	5.361	0.465	0.465	0.000	0.000	0.000	0.000
105	A	117	HIS	0	0.053	0.049	8.943	1.904	1.904	0.000	0.000	0.000	0.000
106	A	118	LEU	0	-0.021	-0.017	4.741	-4.525	-4.418	-0.001	-0.005	-0.102	0.000
107	A	119	VAL	0	0.054	0.032	5.872	4.406	4.406	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.012	0.021	6.094	-6.117	-6.117	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:DAR)