FMO DATABASE

FMODB ID: R5V68

Calculation Name: 1XKO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9X1V3

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptAll
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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1451870.982233
FMO2-HF: Nuclear repulsion	1392228.804407
FMO2-HF: Total energy	-59642.177825
FMO2-MP2: Total energy	-59814.106622

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(B:-3:GLY)

Summations of interaction energy for fragment #1(B:-3:GLY)

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.
-3.909	-1.416	5.075	-3.948	-3.617	-0.021

Interaction energy analysis for fragmet #1(B:-3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.004

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	B	-1	HIS	0	0.031	0.015	3.859	0.249	1.618	-0.009	-0.719	-0.640	0.002
4	B	0	MET	0	-0.019	-0.006	6.756	0.752	0.752	0.000	0.000	0.000	0.000
5	B	1	MET	0	0.021	-0.005	8.091	-0.451	-0.451	0.000	0.000	0.000	0.000
6	B	2	ASP	-1	-0.783	-0.869	10.464	-0.593	-0.593	0.000	0.000	0.000	0.000
7	B	3	ALA	0	0.064	0.025	13.079	0.087	0.087	0.000	0.000	0.000	0.000
8	B	4	ARG	1	0.818	0.888	15.222	0.665	0.665	0.000	0.000	0.000	0.000
9	B	5	ILE	0	0.037	0.019	11.124	0.050	0.050	0.000	0.000	0.000	0.000
10	B	6	VAL	0	-0.016	-0.003	15.238	0.067	0.067	0.000	0.000	0.000	0.000
11	B	7	ASN	0	-0.039	-0.036	17.073	0.085	0.085	0.000	0.000	0.000	0.000
12	B	8	ALA	0	0.027	0.032	17.632	0.040	0.040	0.000	0.000	0.000	0.000
13	B	9	LEU	0	0.020	0.023	16.706	0.040	0.040	0.000	0.000	0.000	0.000
14	B	10	ILE	0	0.011	-0.002	19.286	0.035	0.035	0.000	0.000	0.000	0.000
15	B	11	GLY	0	0.005	0.001	22.396	0.025	0.025	0.000	0.000	0.000	0.000
16	B	12	SER	0	0.009	-0.020	21.348	0.025	0.025	0.000	0.000	0.000	0.000
17	B	13	VAL	0	-0.012	0.012	22.173	0.022	0.022	0.000	0.000	0.000	0.000
18	B	14	TYR	0	-0.024	-0.016	24.740	0.015	0.015	0.000	0.000	0.000	0.000
19	B	15	GLU	-1	-0.794	-0.876	26.961	-0.125	-0.125	0.000	0.000	0.000	0.000
20	B	16	THR	0	-0.005	-0.018	25.296	0.013	0.013	0.000	0.000	0.000	0.000
21	B	17	ILE	0	0.009	-0.004	27.075	0.011	0.011	0.000	0.000	0.000	0.000
22	B	18	ARG	1	0.826	0.904	29.686	0.098	0.098	0.000	0.000	0.000	0.000
23	B	19	ASP	-1	-0.854	-0.925	30.976	-0.076	-0.076	0.000	0.000	0.000	0.000
24	B	20	VAL	0	-0.048	-0.019	29.673	0.007	0.007	0.000	0.000	0.000	0.000
25	B	21	LEU	0	-0.033	-0.018	30.864	0.007	0.007	0.000	0.000	0.000	0.000
26	B	22	GLY	0	0.012	0.018	34.420	0.002	0.002	0.000	0.000	0.000	0.000
27	B	23	ILE	0	-0.056	-0.026	34.310	0.000	0.000	0.000	0.000	0.000	0.000
28	B	24	GLU	-1	-0.823	-0.922	31.810	-0.107	-0.107	0.000	0.000	0.000	0.000
29	B	25	PRO	0	-0.046	0.004	28.714	0.003	0.003	0.000	0.000	0.000	0.000
30	B	26	LYS	1	0.815	0.881	30.834	0.099	0.099	0.000	0.000	0.000	0.000
31	B	27	THR	0	-0.013	-0.014	24.285	0.006	0.006	0.000	0.000	0.000	0.000
32	B	28	GLY	0	0.028	0.026	25.812	0.001	0.001	0.000	0.000	0.000	0.000
33	B	29	LYS	1	0.910	0.942	23.201	0.198	0.198	0.000	0.000	0.000	0.000
34	B	30	PRO	0	0.025	0.009	18.794	0.004	0.004	0.000	0.000	0.000	0.000
35	B	31	SER	0	-0.028	-0.015	18.941	0.000	0.000	0.000	0.000	0.000	0.000
36	B	32	THR	0	-0.010	0.001	12.858	0.010	0.010	0.000	0.000	0.000	0.000
37	B	33	VAL	0	-0.030	-0.006	14.693	0.039	0.039	0.000	0.000	0.000	0.000
38	B	34	SER	0	-0.024	-0.022	13.988	-0.041	-0.041	0.000	0.000	0.000	0.000
39	B	35	HIS	0	-0.083	-0.051	13.846	0.029	0.029	0.000	0.000	0.000	0.000
40	B	36	ILE	0	0.026	0.020	15.167	-0.034	-0.034	0.000	0.000	0.000	0.000
41	B	37	GLU	-1	-0.823	-0.894	18.061	0.044	0.044	0.000	0.000	0.000	0.000
42	B	38	ILE	0	-0.016	-0.010	21.077	-0.017	-0.017	0.000	0.000	0.000	0.000
43	B	39	PRO	0	-0.026	-0.013	24.337	0.011	0.011	0.000	0.000	0.000	0.000
44	B	40	HIS	0	-0.037	-0.010	25.522	0.010	0.010	0.000	0.000	0.000	0.000
45	B	41	SER	0	0.008	-0.009	28.197	0.006	0.006	0.000	0.000	0.000	0.000
46	B	42	LEU	0	0.010	-0.008	27.881	0.011	0.011	0.000	0.000	0.000	0.000
47	B	43	VAL	0	-0.030	-0.008	21.392	-0.012	-0.012	0.000	0.000	0.000	0.000
48	B	44	THR	0	0.007	0.015	22.369	0.017	0.017	0.000	0.000	0.000	0.000
49	B	45	VAL	0	-0.033	-0.017	16.826	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	46	ILE	0	0.048	0.035	16.956	0.011	0.011	0.000	0.000	0.000	0.000
51	B	47	GLY	0	0.008	0.005	14.098	-0.015	-0.015	0.000	0.000	0.000	0.000
52	B	48	ILE	0	-0.025	-0.022	12.039	-0.041	-0.041	0.000	0.000	0.000	0.000
53	B	49	THR	0	-0.038	-0.044	10.668	0.108	0.108	0.000	0.000	0.000	0.000
54	B	50	GLY	0	0.091	0.055	11.199	-0.103	-0.103	0.000	0.000	0.000	0.000
55	B	51	GLY	0	-0.011	-0.014	10.081	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	52	ILE	0	-0.067	-0.044	7.796	-0.366	-0.366	0.000	0.000	0.000	0.000
57	B	53	GLU	-1	-0.821	-0.852	4.862	3.093	3.225	-0.001	-0.005	-0.125	0.000
58	B	54	GLY	0	0.001	-0.038	6.852	-0.230	-0.230	0.000	0.000	0.000	0.000
59	B	55	SER	0	-0.025	-0.002	9.288	0.081	0.081	0.000	0.000	0.000	0.000
60	B	56	LEU	0	0.006	0.024	12.930	-0.081	-0.081	0.000	0.000	0.000	0.000
61	B	57	ILE	0	0.000	-0.010	15.240	0.045	0.045	0.000	0.000	0.000	0.000
62	B	58	TYR	0	-0.034	-0.035	18.269	-0.034	-0.034	0.000	0.000	0.000	0.000
63	B	59	SER	0	0.011	0.003	21.800	0.023	0.023	0.000	0.000	0.000	0.000
64	B	60	PHE	0	0.027	0.017	24.788	-0.013	-0.013	0.000	0.000	0.000	0.000
65	B	61	SER	0	0.009	-0.021	28.459	0.008	0.008	0.000	0.000	0.000	0.000
66	B	62	SER	0	0.047	0.017	31.727	0.000	0.000	0.000	0.000	0.000	0.000
67	B	63	GLU	-1	-0.829	-0.891	34.136	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	64	THR	0	0.012	0.004	31.425	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	65	ALA	0	0.005	0.016	31.756	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	66	LEU	0	-0.006	0.005	32.883	0.000	0.000	0.000	0.000	0.000	0.000
71	B	67	LYS	1	0.833	0.926	34.911	0.035	0.035	0.000	0.000	0.000	0.000
72	B	68	VAL	0	-0.008	-0.001	30.555	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	69	VAL	0	0.012	0.007	33.817	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	70	SER	0	-0.025	-0.026	35.597	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	71	ALA	0	-0.015	-0.007	35.618	0.000	0.000	0.000	0.000	0.000	0.000
76	B	72	MET	0	-0.060	-0.021	31.040	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	73	MET	0	-0.074	-0.028	35.866	0.004	0.004	0.000	0.000	0.000	0.000
78	B	74	GLY	0	-0.008	-0.002	39.329	0.001	0.001	0.000	0.000	0.000	0.000
79	B	75	GLY	0	-0.020	-0.007	40.817	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	76	MET	0	-0.069	-0.017	42.205	0.001	0.001	0.000	0.000	0.000	0.000
81	B	77	GLU	-1	-0.883	-0.921	42.502	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	78	TYR	0	-0.035	-0.055	39.025	0.001	0.001	0.000	0.000	0.000	0.000
83	B	79	ASN	0	-0.037	-0.028	40.806	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	80	GLN	0	-0.024	-0.021	40.209	0.000	0.000	0.000	0.000	0.000	0.000
85	B	81	LEU	0	0.001	-0.003	33.350	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	82	ASP	-1	-0.785	-0.868	36.090	0.030	0.030	0.000	0.000	0.000	0.000
87	B	83	GLU	-1	-0.881	-0.942	34.200	0.059	0.059	0.000	0.000	0.000	0.000
88	B	84	LEU	0	-0.044	-0.014	34.179	0.001	0.001	0.000	0.000	0.000	0.000
89	B	85	ALA	0	0.020	0.003	34.709	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	86	LEU	0	-0.018	-0.019	30.525	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	87	SER	0	0.014	0.006	29.962	0.002	0.002	0.000	0.000	0.000	0.000
92	B	88	ALA	0	-0.031	-0.012	30.189	-0.003	-0.003	0.000	0.000	0.000	0.000
93	B	89	ILE	0	0.023	-0.001	27.842	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	90	GLY	0	0.018	0.029	25.972	-0.006	-0.006	0.000	0.000	0.000	0.000
95	B	91	GLU	-1	-0.819	-0.903	25.637	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	92	LEU	0	0.017	0.008	26.897	-0.009	-0.009	0.000	0.000	0.000	0.000
97	B	93	GLY	0	0.036	0.020	23.322	-0.017	-0.017	0.000	0.000	0.000	0.000
98	B	94	ASN	0	-0.079	-0.059	22.415	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	95	MET	0	-0.006	0.003	23.383	-0.014	-0.014	0.000	0.000	0.000	0.000
100	B	96	THR	0	-0.038	-0.019	21.183	-0.018	-0.018	0.000	0.000	0.000	0.000
101	B	97	ALA	0	-0.019	-0.018	18.763	-0.027	-0.027	0.000	0.000	0.000	0.000
102	B	98	GLY	0	0.025	0.021	19.696	-0.014	-0.014	0.000	0.000	0.000	0.000
103	B	99	LYS	1	0.823	0.893	22.212	0.083	0.083	0.000	0.000	0.000	0.000
104	B	100	LEU	0	-0.007	0.003	15.682	-0.024	-0.024	0.000	0.000	0.000	0.000
105	B	101	ALA	0	0.010	-0.007	17.763	-0.037	-0.037	0.000	0.000	0.000	0.000
106	B	102	MET	0	-0.016	-0.001	18.805	-0.015	-0.015	0.000	0.000	0.000	0.000
107	B	103	LYS	1	0.814	0.899	20.540	0.153	0.153	0.000	0.000	0.000	0.000
108	B	104	LEU	0	-0.036	-0.024	14.046	-0.049	-0.049	0.000	0.000	0.000	0.000
109	B	105	GLU	-1	-0.887	-0.939	17.380	-0.172	-0.172	0.000	0.000	0.000	0.000
110	B	106	HIS	0	-0.047	-0.020	18.964	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	107	LEU	0	-0.080	-0.029	17.038	-0.019	-0.019	0.000	0.000	0.000	0.000
112	B	108	GLY	0	0.003	0.010	16.760	-0.074	-0.074	0.000	0.000	0.000	0.000
113	B	109	LYS	1	0.757	0.883	9.007	1.099	1.099	0.000	0.000	0.000	0.000
114	B	110	HIS	0	0.040	0.009	14.656	0.052	0.052	0.000	0.000	0.000	0.000
115	B	111	VAL	0	-0.060	-0.023	12.420	-0.017	-0.017	0.000	0.000	0.000	0.000
116	B	112	ASP	-1	-0.814	-0.874	14.632	0.138	0.138	0.000	0.000	0.000	0.000
117	B	113	ILE	0	-0.029	-0.020	15.259	0.006	0.006	0.000	0.000	0.000	0.000
118	B	114	THR	0	-0.057	-0.021	16.435	0.034	0.034	0.000	0.000	0.000	0.000
119	B	115	PRO	0	0.019	-0.007	18.714	-0.021	-0.021	0.000	0.000	0.000	0.000
120	B	116	PRO	0	0.010	0.016	21.343	0.017	0.017	0.000	0.000	0.000	0.000
121	B	117	THR	0	-0.035	-0.012	20.742	0.002	0.002	0.000	0.000	0.000	0.000
122	B	118	VAL	0	0.023	0.006	22.925	-0.006	-0.006	0.000	0.000	0.000	0.000
123	B	119	VAL	0	-0.008	-0.008	23.810	0.009	0.009	0.000	0.000	0.000	0.000
124	B	120	SER	0	0.052	0.033	26.476	-0.010	-0.010	0.000	0.000	0.000	0.000
125	B	121	GLY	0	-0.036	-0.035	28.979	0.011	0.011	0.000	0.000	0.000	0.000
126	B	122	ARG	1	0.918	0.945	29.868	-0.058	-0.058	0.000	0.000	0.000	0.000
127	B	123	ASP	-1	-0.864	-0.924	27.785	0.045	0.045	0.000	0.000	0.000	0.000
128	B	124	LEU	0	-0.023	-0.004	24.670	0.016	0.016	0.000	0.000	0.000	0.000
129	B	125	LYS	1	0.835	0.925	22.021	-0.046	-0.046	0.000	0.000	0.000	0.000
130	B	126	ILE	0	0.035	0.010	17.519	0.020	0.020	0.000	0.000	0.000	0.000
131	B	127	LYS	1	0.908	0.950	14.493	-0.240	-0.240	0.000	0.000	0.000	0.000
132	B	128	SER	0	0.050	0.023	11.943	0.083	0.083	0.000	0.000	0.000	0.000
133	B	129	PHE	0	-0.042	-0.030	8.109	0.065	0.065	0.000	0.000	0.000	0.000
134	B	130	GLY	0	0.022	0.008	5.541	0.083	0.083	0.000	0.000	0.000	0.000
135	B	131	VAL	0	-0.035	0.004	6.533	0.092	0.092	0.000	0.000	0.000	0.000
136	B	132	ILE	0	0.010	0.005	8.479	0.088	0.088	0.000	0.000	0.000	0.000
137	B	133	LEU	0	-0.042	-0.016	11.932	-0.035	-0.035	0.000	0.000	0.000	0.000
138	B	134	LYS	1	0.886	0.918	14.611	0.178	0.178	0.000	0.000	0.000	0.000
139	B	135	LEU	0	-0.013	-0.025	18.266	-0.041	-0.041	0.000	0.000	0.000	0.000
140	B	136	PRO	0	0.030	0.045	20.781	0.019	0.019	0.000	0.000	0.000	0.000
141	B	137	ILE	0	0.002	-0.016	23.192	-0.014	-0.014	0.000	0.000	0.000	0.000
142	B	138	SER	0	-0.016	0.010	26.783	0.013	0.013	0.000	0.000	0.000	0.000
143	B	139	VAL	0	-0.038	-0.013	29.525	-0.005	-0.005	0.000	0.000	0.000	0.000
144	B	140	PHE	0	0.015	-0.012	32.221	0.002	0.002	0.000	0.000	0.000	0.000
145	B	141	SER	0	-0.053	-0.025	34.057	0.005	0.005	0.000	0.000	0.000	0.000
146	B	142	GLU	-1	-0.824	-0.887	32.408	-0.101	-0.101	0.000	0.000	0.000	0.000
147	B	143	GLU	-1	-0.974	-1.003	27.511	-0.120	-0.120	0.000	0.000	0.000	0.000
148	B	144	ASP	-1	-0.806	-0.904	29.183	-0.053	-0.053	0.000	0.000	0.000	0.000
149	B	145	PHE	0	0.016	0.000	24.233	0.012	0.012	0.000	0.000	0.000	0.000
150	B	146	ASP	-1	-0.781	-0.872	23.036	-0.105	-0.105	0.000	0.000	0.000	0.000
151	B	147	LEU	0	-0.013	-0.003	18.557	0.013	0.013	0.000	0.000	0.000	0.000
152	B	148	HIS	0	0.005	0.004	16.269	-0.032	-0.032	0.000	0.000	0.000	0.000
153	B	149	LEU	0	-0.007	0.002	12.249	0.026	0.026	0.000	0.000	0.000	0.000
154	B	150	SER	0	0.000	0.014	10.508	-0.079	-0.079	0.000	0.000	0.000	0.000
155	B	151	VAL	0	0.009	-0.003	5.896	0.057	0.057	0.000	0.000	0.000	0.000
156	B	152	LYS	1	0.950	0.984	3.438	-7.930	-7.623	0.010	-0.147	-0.170	0.000
157	B	153	SER	0	-0.062	-0.090	2.303	-2.332	-1.598	5.001	-3.258	-2.477	-0.022
158	B	154	GLY	0	0.075	0.050	3.265	1.054	1.005	0.074	0.181	-0.205	-0.001
159	B	155	GLY	0	0.001	0.001	5.861	0.479	0.479	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:-3:GLY)