FMO DATABASE

FMODB ID: 668KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1451199.861509
FMO2-HF: Nuclear repulsion	1391559.341292
FMO2-HF: Total energy	-59640.520217
FMO2-MP2: Total energy	-59812.488151

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.
-3.435	-0.090000000000002	1.258	-2.122	-2.481	-0.006

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 : -0.012 / 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	B	-1	HIS	0	0.029	0.017	3.796	-0.635	0.314	-0.013	-0.434	-0.502	0.002
4	B	0	MET	0	-0.021	-0.011	6.675	0.486	0.486	0.000	0.000	0.000	0.000
5	B	1	MET	0	0.013	-0.011	8.149	-0.004	-0.004	0.000	0.000	0.000	0.000
6	B	2	ASP	-1	-0.833	-0.925	10.675	0.030	0.030	0.000	0.000	0.000	0.000
7	B	3	ALA	0	0.066	0.034	13.211	0.038	0.038	0.000	0.000	0.000	0.000
8	B	4	ARG	1	0.894	0.950	15.673	-0.100	-0.100	0.000	0.000	0.000	0.000
9	B	5	ILE	0	0.038	0.025	11.637	0.015	0.015	0.000	0.000	0.000	0.000
10	B	6	VAL	0	0.013	0.011	15.520	0.011	0.011	0.000	0.000	0.000	0.000
11	B	7	ASN	0	-0.014	-0.018	17.300	0.002	0.002	0.000	0.000	0.000	0.000
12	B	8	ALA	0	0.022	0.028	18.285	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	9	LEU	0	0.021	0.023	16.696	0.009	0.009	0.000	0.000	0.000	0.000
14	B	10	ILE	0	-0.004	-0.017	19.487	-0.005	-0.005	0.000	0.000	0.000	0.000
15	B	11	GLY	0	-0.010	-0.005	22.510	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	12	SER	0	-0.032	-0.044	21.644	0.000	0.000	0.000	0.000	0.000	0.000
17	B	13	VAL	0	0.018	0.022	22.446	0.002	0.002	0.000	0.000	0.000	0.000
18	B	14	TYR	0	-0.022	-0.010	25.033	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	15	GLU	-1	-0.850	-0.934	27.557	0.091	0.091	0.000	0.000	0.000	0.000
20	B	16	THR	0	0.019	-0.003	25.890	0.002	0.002	0.000	0.000	0.000	0.000
21	B	17	ILE	0	-0.009	0.006	27.665	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	18	ARG	1	0.909	0.960	30.128	-0.060	-0.060	0.000	0.000	0.000	0.000
23	B	19	ASP	-1	-0.912	-0.961	31.989	0.067	0.067	0.000	0.000	0.000	0.000
24	B	20	VAL	0	-0.048	-0.011	30.097	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	21	LEU	0	-0.031	-0.025	31.592	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	22	GLY	0	-0.008	0.011	34.636	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	23	ILE	0	-0.071	-0.043	34.274	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	24	GLU	-1	-0.890	-0.958	32.410	0.046	0.046	0.000	0.000	0.000	0.000
29	B	25	PRO	0	-0.053	0.000	29.055	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	26	LYS	1	0.932	0.963	30.716	-0.010	-0.010	0.000	0.000	0.000	0.000
31	B	27	THR	0	-0.011	-0.012	24.192	0.001	0.001	0.000	0.000	0.000	0.000
32	B	28	GLY	0	0.023	0.020	25.327	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	29	LYS	1	0.907	0.939	23.364	0.045	0.045	0.000	0.000	0.000	0.000
34	B	30	PRO	0	0.022	0.006	18.846	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	31	SER	0	-0.033	-0.013	18.455	-0.020	-0.020	0.000	0.000	0.000	0.000
36	B	32	THR	0	0.004	0.003	12.756	0.000	0.000	0.000	0.000	0.000	0.000
37	B	33	VAL	0	-0.015	0.007	14.787	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	34	SER	0	-0.025	-0.032	14.169	-0.017	-0.017	0.000	0.000	0.000	0.000
39	B	35	HIS	0	-0.042	-0.022	14.295	-0.010	-0.010	0.000	0.000	0.000	0.000
40	B	36	ILE	0	0.025	0.015	15.296	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	37	GLU	-1	-0.956	-0.973	17.977	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	38	ILE	0	-0.022	-0.010	21.699	0.001	0.001	0.000	0.000	0.000	0.000
43	B	39	PRO	0	-0.014	-0.006	23.916	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	40	HIS	0	-0.031	0.002	25.681	0.000	0.000	0.000	0.000	0.000	0.000
45	B	41	SER	0	0.015	0.012	28.006	0.001	0.001	0.000	0.000	0.000	0.000
46	B	42	LEU	0	0.014	-0.001	28.003	0.004	0.004	0.000	0.000	0.000	0.000
47	B	43	VAL	0	-0.009	-0.006	21.577	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	44	THR	0	0.005	0.018	22.714	0.000	0.000	0.000	0.000	0.000	0.000
49	B	45	VAL	0	-0.023	-0.013	17.149	0.008	0.008	0.000	0.000	0.000	0.000
50	B	46	ILE	0	0.030	0.025	17.868	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	47	GLY	0	-0.027	-0.017	14.802	0.025	0.025	0.000	0.000	0.000	0.000
52	B	48	ILE	0	-0.004	-0.002	12.495	-0.045	-0.045	0.000	0.000	0.000	0.000
53	B	49	THR	0	0.004	0.000	11.590	0.122	0.122	0.000	0.000	0.000	0.000
54	B	50	GLY	0	0.077	0.030	11.420	-0.083	-0.083	0.000	0.000	0.000	0.000
55	B	51	GLY	0	-0.016	-0.013	10.010	0.224	0.224	0.000	0.000	0.000	0.000
56	B	52	ILE	0	-0.063	-0.046	8.783	0.205	0.205	0.000	0.000	0.000	0.000
57	B	53	GLU	-1	-0.875	-0.930	6.278	2.295	2.295	0.000	0.000	0.000	0.000
58	B	54	GLY	0	-0.017	-0.027	7.379	0.105	0.105	0.000	0.000	0.000	0.000
59	B	55	SER	0	-0.067	-0.019	9.795	-0.051	-0.051	0.000	0.000	0.000	0.000
60	B	56	LEU	0	0.064	0.038	13.377	-0.011	-0.011	0.000	0.000	0.000	0.000
61	B	57	ILE	0	-0.033	-0.026	15.286	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	58	TYR	0	-0.039	-0.028	18.623	-0.011	-0.011	0.000	0.000	0.000	0.000
63	B	59	SER	0	-0.013	-0.011	22.078	0.004	0.004	0.000	0.000	0.000	0.000
64	B	60	PHE	0	0.033	0.010	24.906	-0.004	-0.004	0.000	0.000	0.000	0.000
65	B	61	SER	0	0.086	0.043	28.474	0.003	0.003	0.000	0.000	0.000	0.000
66	B	62	SER	0	0.045	0.004	31.758	0.005	0.005	0.000	0.000	0.000	0.000
67	B	63	GLU	-1	-0.898	-0.958	34.219	0.035	0.035	0.000	0.000	0.000	0.000
68	B	64	THR	0	-0.016	-0.013	31.262	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	65	ALA	0	0.031	0.022	31.825	0.002	0.002	0.000	0.000	0.000	0.000
70	B	66	LEU	0	-0.001	0.008	33.167	0.002	0.002	0.000	0.000	0.000	0.000
71	B	67	LYS	1	0.924	0.984	35.877	-0.032	-0.032	0.000	0.000	0.000	0.000
72	B	68	VAL	0	0.021	0.009	31.048	0.000	0.000	0.000	0.000	0.000	0.000
73	B	69	VAL	0	0.023	0.004	34.078	0.002	0.002	0.000	0.000	0.000	0.000
74	B	70	SER	0	-0.032	-0.020	35.813	0.000	0.000	0.000	0.000	0.000	0.000
75	B	71	ALA	0	-0.036	-0.024	36.316	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	72	MET	0	-0.061	-0.025	32.017	0.001	0.001	0.000	0.000	0.000	0.000
77	B	73	MET	0	-0.075	-0.023	36.441	0.001	0.001	0.000	0.000	0.000	0.000
78	B	74	GLY	0	0.004	0.003	39.896	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	75	GLY	0	-0.009	-0.001	41.274	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	76	MET	0	-0.091	-0.031	42.638	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	77	GLU	-1	-0.957	-0.974	42.632	0.033	0.033	0.000	0.000	0.000	0.000
82	B	78	TYR	0	0.015	-0.005	39.352	0.002	0.002	0.000	0.000	0.000	0.000
83	B	79	ASN	0	-0.009	-0.013	41.132	0.000	0.000	0.000	0.000	0.000	0.000
84	B	80	GLN	0	-0.018	-0.011	40.331	0.000	0.000	0.000	0.000	0.000	0.000
85	B	81	LEU	0	-0.002	-0.003	33.339	0.001	0.001	0.000	0.000	0.000	0.000
86	B	82	ASP	-1	-0.813	-0.916	36.335	0.060	0.060	0.000	0.000	0.000	0.000
87	B	83	GLU	-1	-0.913	-0.970	35.233	0.079	0.079	0.000	0.000	0.000	0.000
88	B	84	LEU	0	-0.032	-0.006	34.808	0.006	0.006	0.000	0.000	0.000	0.000
89	B	85	ALA	0	0.009	0.018	35.508	0.003	0.003	0.000	0.000	0.000	0.000
90	B	86	LEU	0	-0.012	-0.023	31.029	0.004	0.004	0.000	0.000	0.000	0.000
91	B	87	SER	0	-0.001	0.008	30.382	0.011	0.011	0.000	0.000	0.000	0.000
92	B	88	ALA	0	0.031	0.024	30.724	0.007	0.007	0.000	0.000	0.000	0.000
93	B	89	ILE	0	0.036	0.009	27.698	0.004	0.004	0.000	0.000	0.000	0.000
94	B	90	GLY	0	0.023	0.042	26.334	0.007	0.007	0.000	0.000	0.000	0.000
95	B	91	GLU	-1	-0.870	-0.940	26.084	0.140	0.140	0.000	0.000	0.000	0.000
96	B	92	LEU	0	0.000	0.009	27.112	0.005	0.005	0.000	0.000	0.000	0.000
97	B	93	GLY	0	0.036	-0.010	23.770	0.004	0.004	0.000	0.000	0.000	0.000
98	B	94	ASN	0	-0.005	-0.018	22.881	0.033	0.033	0.000	0.000	0.000	0.000
99	B	95	MET	0	0.007	0.020	23.870	0.014	0.014	0.000	0.000	0.000	0.000
100	B	96	THR	0	-0.009	0.006	21.428	0.002	0.002	0.000	0.000	0.000	0.000
101	B	97	ALA	0	-0.027	-0.019	19.325	0.009	0.009	0.000	0.000	0.000	0.000
102	B	98	GLY	0	0.028	0.017	20.377	0.024	0.024	0.000	0.000	0.000	0.000
103	B	99	LYS	1	0.839	0.914	22.975	-0.121	-0.121	0.000	0.000	0.000	0.000
104	B	100	LEU	0	0.025	0.020	15.887	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	101	ALA	0	0.014	0.005	18.303	0.012	0.012	0.000	0.000	0.000	0.000
106	B	102	MET	0	-0.003	0.002	19.336	0.000	0.000	0.000	0.000	0.000	0.000
107	B	103	LYS	1	0.819	0.907	21.173	-0.118	-0.118	0.000	0.000	0.000	0.000
108	B	104	LEU	0	-0.007	-0.023	14.751	-0.006	-0.006	0.000	0.000	0.000	0.000
109	B	105	GLU	-1	-0.952	-0.966	17.813	0.218	0.218	0.000	0.000	0.000	0.000
110	B	106	HIS	0	-0.041	-0.002	19.366	-0.037	-0.037	0.000	0.000	0.000	0.000
111	B	107	LEU	0	-0.144	-0.066	17.250	-0.023	-0.023	0.000	0.000	0.000	0.000
112	B	108	GLY	0	0.015	0.000	16.491	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	109	LYS	1	0.857	0.939	9.270	-0.766	-0.766	0.000	0.000	0.000	0.000
114	B	110	HIS	0	0.064	0.042	14.676	-0.056	-0.056	0.000	0.000	0.000	0.000
115	B	111	VAL	0	-0.054	-0.018	13.194	0.103	0.103	0.000	0.000	0.000	0.000
116	B	112	ASP	-1	-0.870	-0.908	15.437	0.357	0.357	0.000	0.000	0.000	0.000
117	B	113	ILE	0	-0.032	-0.038	16.294	0.054	0.054	0.000	0.000	0.000	0.000
118	B	114	THR	0	-0.045	-0.008	17.580	-0.025	-0.025	0.000	0.000	0.000	0.000
119	B	115	PRO	0	0.039	-0.001	19.536	-0.010	-0.010	0.000	0.000	0.000	0.000
120	B	116	PRO	0	0.002	0.007	21.903	0.011	0.011	0.000	0.000	0.000	0.000
121	B	117	THR	0	-0.044	-0.012	21.195	-0.015	-0.015	0.000	0.000	0.000	0.000
122	B	118	VAL	0	0.027	0.008	23.260	0.004	0.004	0.000	0.000	0.000	0.000
123	B	119	VAL	0	-0.022	-0.013	23.640	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	120	SER	0	0.027	0.017	26.415	-0.004	-0.004	0.000	0.000	0.000	0.000
125	B	121	GLY	0	-0.055	-0.049	29.454	0.000	0.000	0.000	0.000	0.000	0.000
126	B	122	ARG	1	0.944	0.947	30.197	-0.039	-0.039	0.000	0.000	0.000	0.000
127	B	123	ASP	-1	-0.919	-0.934	28.518	0.025	0.025	0.000	0.000	0.000	0.000
128	B	124	LEU	0	-0.045	-0.009	24.647	0.002	0.002	0.000	0.000	0.000	0.000
129	B	125	LYS	1	1.007	1.005	22.077	-0.022	-0.022	0.000	0.000	0.000	0.000
130	B	126	ILE	0	0.036	0.010	16.989	0.010	0.010	0.000	0.000	0.000	0.000
131	B	127	LYS	1	0.916	0.959	14.989	-0.049	-0.049	0.000	0.000	0.000	0.000
132	B	128	SER	0	0.052	0.034	12.135	0.046	0.046	0.000	0.000	0.000	0.000
133	B	129	PHE	0	-0.045	-0.028	7.974	-0.045	-0.045	0.000	0.000	0.000	0.000
134	B	130	GLY	0	0.017	0.002	5.622	0.117	0.117	0.000	0.000	0.000	0.000
135	B	131	VAL	0	-0.030	0.003	6.341	-0.083	-0.083	0.000	0.000	0.000	0.000
136	B	132	ILE	0	0.014	0.013	8.419	0.151	0.151	0.000	0.000	0.000	0.000
137	B	133	LEU	0	-0.025	-0.001	11.879	-0.063	-0.063	0.000	0.000	0.000	0.000
138	B	134	LYS	1	0.979	0.988	14.397	0.038	0.038	0.000	0.000	0.000	0.000
139	B	135	LEU	0	-0.035	-0.030	18.046	-0.017	-0.017	0.000	0.000	0.000	0.000
140	B	136	PRO	0	0.011	0.041	20.808	0.011	0.011	0.000	0.000	0.000	0.000
141	B	137	ILE	0	0.033	-0.011	23.293	0.000	0.000	0.000	0.000	0.000	0.000
142	B	138	SER	0	0.028	0.031	26.636	-0.003	-0.003	0.000	0.000	0.000	0.000
143	B	139	VAL	0	-0.042	-0.015	29.588	0.001	0.001	0.000	0.000	0.000	0.000
144	B	140	PHE	0	-0.021	-0.020	32.110	-0.003	-0.003	0.000	0.000	0.000	0.000
145	B	141	SER	0	-0.062	-0.043	34.048	-0.004	-0.004	0.000	0.000	0.000	0.000
146	B	142	GLU	-1	-0.945	-0.976	32.162	0.008	0.008	0.000	0.000	0.000	0.000
147	B	143	GLU	-1	-1.008	-1.012	27.456	-0.002	-0.002	0.000	0.000	0.000	0.000
148	B	144	ASP	-1	-0.779	-0.872	29.545	0.038	0.038	0.000	0.000	0.000	0.000
149	B	145	PHE	0	-0.001	-0.014	25.144	0.008	0.008	0.000	0.000	0.000	0.000
150	B	146	ASP	-1	-0.891	-0.940	22.341	0.028	0.028	0.000	0.000	0.000	0.000
151	B	147	LEU	0	-0.001	0.002	18.405	0.015	0.015	0.000	0.000	0.000	0.000
152	B	148	HIS	0	-0.025	-0.033	16.028	-0.035	-0.035	0.000	0.000	0.000	0.000
153	B	149	LEU	0	0.007	0.007	12.359	0.022	0.022	0.000	0.000	0.000	0.000
154	B	150	SER	0	-0.020	-0.013	10.283	-0.090	-0.090	0.000	0.000	0.000	0.000
155	B	151	VAL	0	0.036	0.008	6.439	0.131	0.131	0.000	0.000	0.000	0.000
156	B	152	LYS	1	0.935	0.958	3.726	-1.900	-1.741	0.002	-0.058	-0.102	0.000
157	B	153	SER	0	-0.024	-0.029	2.662	-2.026	0.021	1.266	-1.582	-1.732	-0.008
158	B	154	GLY	0	0.094	0.058	4.213	-1.839	-1.649	0.003	-0.048	-0.145	0.000
159	B	155	GLY	0	-0.072	-0.033	6.308	-0.614	-0.614	0.000	0.000	0.000	0.000

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