FMO DATABASE

FMODB ID: ZY1KN

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	OptHSide
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	-1452231.45238
FMO2-HF: Nuclear repulsion	1392589.934211
FMO2-HF: Total energy	-59641.518169
FMO2-MP2: Total energy	-59813.475032

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.
-2.88	0.36	2.89	-2.987	-3.142	-0.012

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 : 0.013 / q_NPA : 0.007

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	3.796	-0.454	1.115	-0.015	-0.826	-0.727	0.004
4	B	0	MET	0	-0.028	-0.009	6.675	0.783	0.783	0.000	0.000	0.000	0.000
5	B	1	MET	0	0.028	-0.008	8.149	-0.382	-0.382	0.000	0.000	0.000	0.000
6	B	2	ASP	-1	-0.789	-0.877	10.672	-0.539	-0.539	0.000	0.000	0.000	0.000
7	B	3	ALA	0	0.087	0.044	12.794	0.074	0.074	0.000	0.000	0.000	0.000
8	B	4	ARG	1	0.814	0.892	14.157	0.624	0.624	0.000	0.000	0.000	0.000
9	B	5	ILE	0	0.037	0.021	10.918	0.051	0.051	0.000	0.000	0.000	0.000
10	B	6	VAL	0	0.012	0.013	15.048	0.063	0.063	0.000	0.000	0.000	0.000
11	B	7	ASN	0	-0.045	-0.040	17.186	0.082	0.082	0.000	0.000	0.000	0.000
12	B	8	ALA	0	0.029	0.034	17.589	0.040	0.040	0.000	0.000	0.000	0.000
13	B	9	LEU	0	0.016	0.021	16.791	0.039	0.039	0.000	0.000	0.000	0.000
14	B	10	ILE	0	-0.001	-0.018	19.328	0.036	0.036	0.000	0.000	0.000	0.000
15	B	11	GLY	0	-0.007	0.000	22.495	0.024	0.024	0.000	0.000	0.000	0.000
16	B	12	SER	0	-0.006	-0.027	21.251	0.026	0.026	0.000	0.000	0.000	0.000
17	B	13	VAL	0	-0.002	0.019	22.455	0.021	0.021	0.000	0.000	0.000	0.000
18	B	14	TYR	0	-0.027	-0.011	25.029	0.014	0.014	0.000	0.000	0.000	0.000
19	B	15	GLU	-1	-0.804	-0.877	27.021	-0.119	-0.119	0.000	0.000	0.000	0.000
20	B	16	THR	0	0.017	-0.007	25.609	0.013	0.013	0.000	0.000	0.000	0.000
21	B	17	ILE	0	-0.024	-0.014	27.588	0.010	0.010	0.000	0.000	0.000	0.000
22	B	18	ARG	1	0.850	0.926	30.124	0.091	0.091	0.000	0.000	0.000	0.000
23	B	19	ASP	-1	-0.875	-0.927	31.681	-0.067	-0.067	0.000	0.000	0.000	0.000
24	B	20	VAL	0	-0.042	-0.012	30.012	0.007	0.007	0.000	0.000	0.000	0.000
25	B	21	LEU	0	-0.029	-0.023	31.206	0.006	0.006	0.000	0.000	0.000	0.000
26	B	22	GLY	0	-0.005	0.011	34.633	0.003	0.003	0.000	0.000	0.000	0.000
27	B	23	ILE	0	-0.078	-0.044	34.575	0.000	0.000	0.000	0.000	0.000	0.000
28	B	24	GLU	-1	-0.851	-0.946	32.311	-0.104	-0.104	0.000	0.000	0.000	0.000
29	B	25	PRO	0	-0.047	0.005	29.072	0.001	0.001	0.000	0.000	0.000	0.000
30	B	26	LYS	1	0.816	0.876	30.713	0.105	0.105	0.000	0.000	0.000	0.000
31	B	27	THR	0	-0.046	-0.029	24.166	0.004	0.004	0.000	0.000	0.000	0.000
32	B	28	GLY	0	0.055	0.046	25.315	0.005	0.005	0.000	0.000	0.000	0.000
33	B	29	LYS	1	0.904	0.942	23.206	0.199	0.199	0.000	0.000	0.000	0.000
34	B	30	PRO	0	0.024	0.005	18.838	0.004	0.004	0.000	0.000	0.000	0.000
35	B	31	SER	0	-0.033	-0.014	18.444	-0.004	-0.004	0.000	0.000	0.000	0.000
36	B	32	THR	0	-0.005	0.008	12.679	0.004	0.004	0.000	0.000	0.000	0.000
37	B	33	VAL	0	-0.015	0.002	14.800	0.038	0.038	0.000	0.000	0.000	0.000
38	B	34	SER	0	-0.025	-0.028	14.169	-0.044	-0.044	0.000	0.000	0.000	0.000
39	B	35	HIS	0	-0.088	-0.056	14.297	0.014	0.014	0.000	0.000	0.000	0.000
40	B	36	ILE	0	0.026	0.016	15.095	-0.025	-0.025	0.000	0.000	0.000	0.000
41	B	37	GLU	-1	-0.835	-0.900	17.977	0.000	0.000	0.000	0.000	0.000	0.000
42	B	38	ILE	0	-0.017	-0.006	21.312	-0.012	-0.012	0.000	0.000	0.000	0.000
43	B	39	PRO	0	-0.025	-0.012	23.915	0.010	0.010	0.000	0.000	0.000	0.000
44	B	40	HIS	0	-0.055	-0.016	25.466	0.015	0.015	0.000	0.000	0.000	0.000
45	B	41	SER	0	0.014	0.012	28.006	0.005	0.005	0.000	0.000	0.000	0.000
46	B	42	LEU	0	0.014	-0.001	28.002	0.011	0.011	0.000	0.000	0.000	0.000
47	B	43	VAL	0	-0.019	-0.009	21.527	-0.011	-0.011	0.000	0.000	0.000	0.000
48	B	44	THR	0	0.008	0.021	22.703	0.018	0.018	0.000	0.000	0.000	0.000
49	B	45	VAL	0	-0.040	-0.020	17.140	-0.016	-0.016	0.000	0.000	0.000	0.000
50	B	46	ILE	0	0.041	0.035	17.851	0.016	0.016	0.000	0.000	0.000	0.000
51	B	47	GLY	0	-0.021	-0.012	14.800	-0.016	-0.016	0.000	0.000	0.000	0.000
52	B	48	ILE	0	-0.009	-0.009	12.261	-0.039	-0.039	0.000	0.000	0.000	0.000
53	B	49	THR	0	-0.029	-0.031	10.914	0.100	0.100	0.000	0.000	0.000	0.000
54	B	50	GLY	0	0.071	0.030	10.784	-0.105	-0.105	0.000	0.000	0.000	0.000
55	B	51	GLY	0	-0.009	-0.010	9.105	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	52	ILE	0	-0.056	-0.038	7.786	-0.318	-0.318	0.000	0.000	0.000	0.000
57	B	53	GLU	-1	-0.844	-0.874	5.356	2.872	2.872	0.000	0.000	0.000	0.000
58	B	54	GLY	0	-0.003	-0.026	7.375	-0.154	-0.154	0.000	0.000	0.000	0.000
59	B	55	SER	0	-0.048	-0.007	9.792	0.055	0.055	0.000	0.000	0.000	0.000
60	B	56	LEU	0	0.046	0.035	13.374	-0.090	-0.090	0.000	0.000	0.000	0.000
61	B	57	ILE	0	-0.021	-0.022	15.441	0.044	0.044	0.000	0.000	0.000	0.000
62	B	58	TYR	0	-0.020	-0.004	18.621	-0.029	-0.029	0.000	0.000	0.000	0.000
63	B	59	SER	0	0.002	-0.002	22.075	0.021	0.021	0.000	0.000	0.000	0.000
64	B	60	PHE	0	0.019	0.004	24.904	-0.011	-0.011	0.000	0.000	0.000	0.000
65	B	61	SER	0	0.042	-0.011	28.472	0.008	0.008	0.000	0.000	0.000	0.000
66	B	62	SER	0	0.033	0.008	31.756	0.001	0.001	0.000	0.000	0.000	0.000
67	B	63	GLU	-1	-0.834	-0.908	34.217	-0.015	-0.015	0.000	0.000	0.000	0.000
68	B	64	THR	0	-0.018	-0.016	31.176	0.001	0.001	0.000	0.000	0.000	0.000
69	B	65	ALA	0	0.020	0.023	31.900	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	66	LEU	0	-0.001	0.004	33.165	0.000	0.000	0.000	0.000	0.000	0.000
71	B	67	LYS	1	0.932	0.990	35.913	0.039	0.039	0.000	0.000	0.000	0.000
72	B	68	VAL	0	0.012	0.002	30.948	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	69	VAL	0	0.027	0.006	34.019	0.000	0.000	0.000	0.000	0.000	0.000
74	B	70	SER	0	-0.028	-0.025	35.810	0.000	0.000	0.000	0.000	0.000	0.000
75	B	71	ALA	0	-0.048	-0.028	36.152	0.000	0.000	0.000	0.000	0.000	0.000
76	B	72	MET	0	-0.061	-0.021	31.833	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	73	MET	0	-0.071	-0.029	36.437	0.003	0.003	0.000	0.000	0.000	0.000
78	B	74	GLY	0	0.000	0.002	39.893	0.002	0.002	0.000	0.000	0.000	0.000
79	B	75	GLY	0	-0.008	-0.001	41.275	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	76	MET	0	-0.084	-0.024	42.615	0.001	0.001	0.000	0.000	0.000	0.000
81	B	77	GLU	-1	-0.953	-0.966	42.629	-0.008	-0.008	0.000	0.000	0.000	0.000
82	B	78	TYR	0	-0.019	-0.037	39.513	0.002	0.002	0.000	0.000	0.000	0.000
83	B	79	ASN	0	0.006	-0.004	41.129	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	80	GLN	0	-0.020	-0.011	40.329	0.000	0.000	0.000	0.000	0.000	0.000
85	B	81	LEU	0	-0.003	-0.005	33.607	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	82	ASP	-1	-0.789	-0.884	36.334	0.022	0.022	0.000	0.000	0.000	0.000
87	B	83	GLU	-1	-0.902	-0.957	34.874	0.048	0.048	0.000	0.000	0.000	0.000
88	B	84	LEU	0	-0.039	-0.018	34.806	0.001	0.001	0.000	0.000	0.000	0.000
89	B	85	ALA	0	0.008	0.015	35.505	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	86	LEU	0	-0.015	-0.024	30.966	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	87	SER	0	0.022	0.017	30.379	0.003	0.003	0.000	0.000	0.000	0.000
92	B	88	ALA	0	-0.009	0.004	30.721	-0.002	-0.002	0.000	0.000	0.000	0.000
93	B	89	ILE	0	0.038	0.008	27.845	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	90	GLY	0	0.025	0.026	26.331	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	91	GLU	-1	-0.824	-0.907	26.080	0.000	0.000	0.000	0.000	0.000	0.000
96	B	92	LEU	0	0.012	0.013	27.188	-0.008	-0.008	0.000	0.000	0.000	0.000
97	B	93	GLY	0	0.026	-0.006	23.776	-0.014	-0.014	0.000	0.000	0.000	0.000
98	B	94	ASN	0	-0.071	-0.060	22.877	-0.005	-0.005	0.000	0.000	0.000	0.000
99	B	95	MET	0	0.008	0.019	23.630	-0.012	-0.012	0.000	0.000	0.000	0.000
100	B	96	THR	0	-0.030	-0.012	21.769	-0.015	-0.015	0.000	0.000	0.000	0.000
101	B	97	ALA	0	-0.033	-0.020	19.236	-0.025	-0.025	0.000	0.000	0.000	0.000
102	B	98	GLY	0	0.027	0.016	19.884	-0.009	-0.009	0.000	0.000	0.000	0.000
103	B	99	LYS	1	0.844	0.896	22.215	0.087	0.087	0.000	0.000	0.000	0.000
104	B	100	LEU	0	0.005	0.010	15.705	-0.020	-0.020	0.000	0.000	0.000	0.000
105	B	101	ALA	0	0.010	0.001	17.355	-0.034	-0.034	0.000	0.000	0.000	0.000
106	B	102	MET	0	-0.008	0.002	18.417	-0.013	-0.013	0.000	0.000	0.000	0.000
107	B	103	LYS	1	0.830	0.897	20.361	0.150	0.150	0.000	0.000	0.000	0.000
108	B	104	LEU	0	-0.010	-0.024	13.783	-0.040	-0.040	0.000	0.000	0.000	0.000
109	B	105	GLU	-1	-0.939	-0.958	16.814	-0.131	-0.131	0.000	0.000	0.000	0.000
110	B	106	HIS	0	-0.062	-0.027	18.360	0.021	0.021	0.000	0.000	0.000	0.000
111	B	107	LEU	0	-0.116	-0.050	16.255	-0.013	-0.013	0.000	0.000	0.000	0.000
112	B	108	GLY	0	0.018	0.008	15.768	-0.064	-0.064	0.000	0.000	0.000	0.000
113	B	109	LYS	1	0.798	0.918	7.820	0.978	0.978	0.000	0.000	0.000	0.000
114	B	110	HIS	0	0.048	0.031	13.693	0.039	0.039	0.000	0.000	0.000	0.000
115	B	111	VAL	0	-0.044	-0.014	12.168	0.007	0.007	0.000	0.000	0.000	0.000
116	B	112	ASP	-1	-0.810	-0.872	14.543	0.164	0.164	0.000	0.000	0.000	0.000
117	B	113	ILE	0	-0.024	-0.024	15.651	0.005	0.005	0.000	0.000	0.000	0.000
118	B	114	THR	0	-0.038	-0.011	17.573	0.012	0.012	0.000	0.000	0.000	0.000
119	B	115	PRO	0	0.036	0.003	19.389	-0.024	-0.024	0.000	0.000	0.000	0.000
120	B	116	PRO	0	-0.004	0.001	21.900	0.015	0.015	0.000	0.000	0.000	0.000
121	B	117	THR	0	-0.034	-0.009	21.099	0.004	0.004	0.000	0.000	0.000	0.000
122	B	118	VAL	0	0.007	-0.002	23.258	-0.006	-0.006	0.000	0.000	0.000	0.000
123	B	119	VAL	0	-0.010	-0.009	23.765	0.009	0.009	0.000	0.000	0.000	0.000
124	B	120	SER	0	0.031	0.022	26.414	-0.011	-0.011	0.000	0.000	0.000	0.000
125	B	121	GLY	0	-0.051	-0.043	29.450	0.009	0.009	0.000	0.000	0.000	0.000
126	B	122	ARG	1	0.935	0.946	30.197	-0.041	-0.041	0.000	0.000	0.000	0.000
127	B	123	ASP	-1	-0.897	-0.927	28.542	0.021	0.021	0.000	0.000	0.000	0.000
128	B	124	LEU	0	-0.040	-0.010	24.648	0.011	0.011	0.000	0.000	0.000	0.000
129	B	125	LYS	1	0.897	0.950	21.865	-0.017	-0.017	0.000	0.000	0.000	0.000
130	B	126	ILE	0	0.031	0.004	17.166	0.019	0.019	0.000	0.000	0.000	0.000
131	B	127	LYS	1	0.928	0.966	14.599	-0.162	-0.162	0.000	0.000	0.000	0.000
132	B	128	SER	0	0.056	0.024	12.124	0.066	0.066	0.000	0.000	0.000	0.000
133	B	129	PHE	0	-0.052	-0.031	7.948	0.031	0.031	0.000	0.000	0.000	0.000
134	B	130	GLY	0	0.018	-0.002	5.624	-0.017	-0.017	0.000	0.000	0.000	0.000
135	B	131	VAL	0	-0.027	-0.002	6.470	0.112	0.112	0.000	0.000	0.000	0.000
136	B	132	ILE	0	0.004	0.013	8.418	0.059	0.059	0.000	0.000	0.000	0.000
137	B	133	LEU	0	-0.022	-0.007	11.878	-0.032	-0.032	0.000	0.000	0.000	0.000
138	B	134	LYS	1	0.911	0.948	14.395	0.195	0.195	0.000	0.000	0.000	0.000
139	B	135	LEU	0	-0.025	-0.028	18.044	-0.031	-0.031	0.000	0.000	0.000	0.000
140	B	136	PRO	0	0.018	0.032	20.806	0.019	0.019	0.000	0.000	0.000	0.000
141	B	137	ILE	0	0.006	-0.016	23.089	-0.010	-0.010	0.000	0.000	0.000	0.000
142	B	138	SER	0	0.011	0.020	26.633	0.011	0.011	0.000	0.000	0.000	0.000
143	B	139	VAL	0	-0.021	-0.006	29.538	-0.003	-0.003	0.000	0.000	0.000	0.000
144	B	140	PHE	0	-0.012	-0.010	32.107	0.002	0.002	0.000	0.000	0.000	0.000
145	B	141	SER	0	-0.061	-0.042	34.079	0.003	0.003	0.000	0.000	0.000	0.000
146	B	142	GLU	-1	-0.845	-0.906	32.281	-0.106	-0.106	0.000	0.000	0.000	0.000
147	B	143	GLU	-1	-0.977	-1.001	27.196	-0.128	-0.128	0.000	0.000	0.000	0.000
148	B	144	ASP	-1	-0.794	-0.881	29.543	-0.064	-0.064	0.000	0.000	0.000	0.000
149	B	145	PHE	0	0.006	-0.013	24.691	0.011	0.011	0.000	0.000	0.000	0.000
150	B	146	ASP	-1	-0.802	-0.883	22.436	-0.119	-0.119	0.000	0.000	0.000	0.000
151	B	147	LEU	0	0.012	0.010	18.545	0.014	0.014	0.000	0.000	0.000	0.000
152	B	148	HIS	0	-0.036	-0.034	16.091	-0.040	-0.040	0.000	0.000	0.000	0.000
153	B	149	LEU	0	0.009	0.010	12.521	0.029	0.029	0.000	0.000	0.000	0.000
154	B	150	SER	0	-0.020	-0.005	10.508	-0.082	-0.082	0.000	0.000	0.000	0.000
155	B	151	VAL	0	0.035	0.008	6.544	0.056	0.056	0.000	0.000	0.000	0.000
156	B	152	LYS	1	0.942	0.964	3.722	-4.531	-4.342	0.003	-0.067	-0.125	0.000
157	B	153	SER	0	-0.066	-0.081	1.987	-3.654	-2.400	2.897	-2.049	-2.102	-0.016
158	B	154	GLY	0	0.102	0.054	3.664	0.793	1.021	0.005	-0.045	-0.188	0.000
159	B	155	GLY	0	-0.047	-0.027	5.414	0.570	0.570	0.000	0.000	0.000	0.000

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