FMO DATABASE

FMODB ID: MNNJZ

Calculation Name: 5IX3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IX3

Chain ID: A

ChEMBL ID:

UniProt ID: U5NVV0

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1862270.944603
FMO2-HF: Nuclear repulsion	1793189.835569
FMO2-HF: Total energy	-69081.109034
FMO2-MP2: Total energy	-69284.431728

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-17.827	-17.212	12.21	-6.567	-6.257	-0.063

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.032

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	2	LYS	1	0.809	0.891	3.838	0.001	1.568	-0.009	-0.794	-0.763	0.003
4	A	3	LEU	0	-0.011	0.005	6.337	0.225	0.225	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.759	0.857	9.904	0.298	0.298	0.000	0.000	0.000	0.000
6	A	5	ALA	0	0.026	0.006	11.784	0.069	0.069	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.015	-0.002	15.494	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.903	-0.956	17.425	-0.194	-0.194	0.000	0.000	0.000	0.000
9	A	8	TYR	0	-0.042	-0.039	19.673	0.006	0.006	0.000	0.000	0.000	0.000
10	A	9	SER	0	-0.014	-0.011	18.094	0.010	0.010	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.794	-0.874	16.495	-0.245	-0.245	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.013	0.011	19.063	0.023	0.023	0.000	0.000	0.000	0.000
13	A	12	LEU	0	0.023	0.014	21.867	0.016	0.016	0.000	0.000	0.000	0.000
14	A	13	PHE	0	0.019	0.009	15.869	0.011	0.011	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.001	-0.003	19.866	0.024	0.024	0.000	0.000	0.000	0.000
16	A	15	HIS	0	0.018	0.017	21.413	0.011	0.011	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.865	-0.926	20.063	0.035	0.035	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.004	-0.007	17.467	0.018	0.018	0.000	0.000	0.000	0.000
19	A	18	ASN	0	-0.020	-0.011	21.449	0.026	0.026	0.000	0.000	0.000	0.000
20	A	19	ASN	0	-0.045	-0.025	24.491	0.001	0.001	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.873	-0.911	21.822	0.094	0.094	0.000	0.000	0.000	0.000
22	A	21	TYR	0	-0.098	-0.038	21.053	0.021	0.021	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.057	-0.028	27.372	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.074	-0.048	28.883	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	24	MET	0	0.004	0.010	30.211	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	25	SER	0	0.031	0.014	26.980	0.005	0.005	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.023	-0.022	28.432	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	27	TRP	0	0.000	-0.009	22.965	0.000	0.000	0.000	0.000	0.000	0.000
29	A	28	PHE	0	-0.023	-0.031	25.988	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.917	-0.952	30.263	0.009	0.009	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.836	-0.869	32.560	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	31	PRO	0	-0.021	-0.016	31.983	0.000	0.000	0.000	0.000	0.000	0.000
33	A	32	TYR	0	-0.056	-0.038	25.608	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.949	-0.978	31.083	0.014	0.014	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.084	-0.081	30.632	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	35	LEU	0	0.016	0.001	25.645	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	36	THR	0	-0.004	0.001	28.806	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.752	-0.850	31.942	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	38	LEU	0	0.004	0.017	24.584	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.039	-0.018	26.999	0.001	0.001	0.000	0.000	0.000	0.000
41	A	40	HIS	0	0.020	0.017	28.936	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.026	-0.015	30.450	0.000	0.000	0.000	0.000	0.000	0.000
43	A	42	PHE	0	-0.005	-0.010	22.610	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.835	-0.924	28.017	-0.076	-0.076	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.750	0.859	30.309	0.020	0.020	0.000	0.000	0.000	0.000
46	A	45	HIS	1	0.749	0.846	29.472	0.026	0.026	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.019	0.032	25.833	0.000	0.000	0.000	0.000	0.000	0.000
48	A	47	LEU	0	-0.057	-0.037	26.875	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.789	-0.844	28.808	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.822	-0.896	26.924	-0.036	-0.036	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.042	-0.030	27.415	0.006	0.006	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.769	-0.860	25.441	0.013	0.013	0.000	0.000	0.000	0.000
53	A	52	ARG	1	0.753	0.849	21.094	0.024	0.024	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.779	0.862	19.366	0.022	0.022	0.000	0.000	0.000	0.000
55	A	54	PHE	0	-0.042	-0.020	13.862	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	55	ILE	0	0.008	0.020	12.596	0.048	0.048	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.012	-0.008	9.715	-0.055	-0.055	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.783	-0.880	8.162	-0.724	-0.724	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.759	-0.859	4.122	-0.023	0.320	-0.001	-0.069	-0.274	0.000
60	A	59	GLU	-1	-0.916	-0.966	1.890	-17.612	-19.057	12.221	-5.694	-5.081	-0.066
61	A	60	ASN	0	-0.088	-0.032	4.932	0.391	0.541	-0.001	-0.010	-0.139	0.000
62	A	61	GLN	0	-0.037	-0.038	7.965	0.216	0.216	0.000	0.000	0.000	0.000
63	A	62	VAL	0	0.010	0.024	9.223	-0.071	-0.071	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.030	-0.018	9.553	0.070	0.070	0.000	0.000	0.000	0.000
65	A	64	GLY	0	0.025	-0.015	12.457	0.087	0.087	0.000	0.000	0.000	0.000
66	A	65	ILE	0	-0.016	0.015	14.492	-0.070	-0.070	0.000	0.000	0.000	0.000
67	A	66	VAL	0	0.002	-0.011	14.218	0.051	0.051	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.794	-0.879	17.078	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.027	-0.012	19.890	0.021	0.021	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.088	0.029	22.700	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.852	-0.927	26.422	0.034	0.034	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.080	-0.041	24.235	0.005	0.005	0.000	0.000	0.000	0.000
73	A	72	ASN	0	0.050	0.036	28.385	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	73	TYR	0	-0.008	-0.040	26.191	0.005	0.005	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.045	-0.013	31.067	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	HIS	0	-0.022	-0.024	33.982	0.002	0.002	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.821	0.907	27.438	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.048	-0.039	28.131	0.008	0.008	0.000	0.000	0.000	0.000
79	A	78	CYS	0	0.023	0.024	24.406	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.806	-0.868	26.427	0.071	0.071	0.000	0.000	0.000	0.000
81	A	80	ILE	0	-0.067	-0.042	18.534	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	81	GLN	0	-0.029	-0.023	21.864	0.011	0.011	0.000	0.000	0.000	0.000
83	A	82	ILE	0	-0.027	-0.016	15.577	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.007	0.013	17.782	0.020	0.020	0.000	0.000	0.000	0.000
85	A	84	ILE	0	-0.041	-0.026	12.952	0.006	0.006	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.822	0.901	15.461	-0.088	-0.088	0.000	0.000	0.000	0.000
87	A	86	PRO	0	0.036	0.028	16.598	0.067	0.067	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.829	-0.905	16.054	0.195	0.195	0.000	0.000	0.000	0.000
89	A	88	PHE	0	-0.004	-0.012	10.875	0.073	0.073	0.000	0.000	0.000	0.000
90	A	89	SER	0	-0.025	-0.018	13.854	0.103	0.103	0.000	0.000	0.000	0.000
91	A	90	GLY	0	-0.023	-0.019	15.785	0.020	0.020	0.000	0.000	0.000	0.000
92	A	91	LYS	1	0.821	0.908	10.636	-0.527	-0.527	0.000	0.000	0.000	0.000
93	A	92	GLY	0	0.026	0.014	10.171	0.295	0.295	0.000	0.000	0.000	0.000
94	A	93	TYR	0	-0.017	-0.057	7.169	0.071	0.071	0.000	0.000	0.000	0.000
95	A	94	ALA	0	0.032	0.018	10.620	-0.106	-0.106	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.835	0.892	12.753	-0.596	-0.596	0.000	0.000	0.000	0.000
97	A	96	PHE	0	0.016	0.011	5.614	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	97	ALA	0	0.025	0.008	10.221	-0.117	-0.117	0.000	0.000	0.000	0.000
99	A	98	PHE	0	0.032	0.008	12.166	-0.075	-0.075	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.791	-0.863	10.960	0.650	0.650	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.819	0.898	8.130	-0.694	-0.694	0.000	0.000	0.000	0.000
102	A	101	ALA	0	0.043	0.038	12.733	-0.060	-0.060	0.000	0.000	0.000	0.000
103	A	102	ILE	0	-0.009	0.005	15.906	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	103	ILE	0	-0.029	-0.006	13.315	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	104	TYR	0	0.024	0.010	15.780	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	105	ALA	0	0.059	0.027	17.493	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	106	PHE	0	-0.011	-0.005	20.560	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	107	ASN	0	-0.030	-0.029	18.179	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	108	ILE	0	-0.030	-0.004	16.354	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	109	LEU	0	-0.004	0.012	20.730	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	110	ASN	0	-0.048	-0.016	23.315	0.007	0.007	0.000	0.000	0.000	0.000
112	A	111	MET	0	0.020	0.037	24.546	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	112	HIS	0	-0.014	-0.017	26.276	0.006	0.006	0.000	0.000	0.000	0.000
114	A	113	LYS	1	0.799	0.885	27.371	-0.070	-0.070	0.000	0.000	0.000	0.000
115	A	114	ILE	0	0.018	0.019	22.095	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	115	TYR	0	-0.043	-0.055	25.391	0.010	0.010	0.000	0.000	0.000	0.000
117	A	116	LEU	0	0.022	0.026	23.189	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	117	TYR	0	0.051	0.025	26.793	0.000	0.000	0.000	0.000	0.000	0.000
119	A	118	VAL	0	-0.025	-0.017	26.111	0.008	0.008	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.792	-0.868	28.524	0.093	0.093	0.000	0.000	0.000	0.000
121	A	120	ALA	0	0.052	0.014	30.006	0.011	0.011	0.000	0.000	0.000	0.000
122	A	121	ASP	-1	-0.831	-0.895	31.760	0.106	0.106	0.000	0.000	0.000	0.000
123	A	122	ASN	0	-0.048	-0.013	24.828	0.020	0.020	0.000	0.000	0.000	0.000
124	A	123	LYS	1	0.870	0.903	26.203	-0.116	-0.116	0.000	0.000	0.000	0.000
125	A	124	LYS	1	0.985	0.990	21.255	-0.222	-0.222	0.000	0.000	0.000	0.000
126	A	125	ALA	0	-0.027	0.000	21.723	0.027	0.027	0.000	0.000	0.000	0.000
127	A	126	ILE	0	0.033	0.015	22.455	0.009	0.009	0.000	0.000	0.000	0.000
128	A	127	HIS	0	-0.031	-0.033	23.283	0.001	0.001	0.000	0.000	0.000	0.000
129	A	128	ILE	0	-0.038	0.000	17.373	0.022	0.022	0.000	0.000	0.000	0.000
130	A	129	TYR	0	0.046	0.020	19.717	0.014	0.014	0.000	0.000	0.000	0.000
131	A	130	GLU	-1	-0.834	-0.912	21.734	0.178	0.178	0.000	0.000	0.000	0.000
132	A	131	SER	0	-0.140	-0.079	18.768	0.015	0.015	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.827	-0.909	16.151	0.417	0.417	0.000	0.000	0.000	0.000
134	A	133	GLY	0	-0.009	-0.006	19.629	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	134	PHE	0	-0.057	-0.034	20.765	-0.020	-0.020	0.000	0.000	0.000	0.000
136	A	135	LYS	1	0.841	0.905	24.960	-0.109	-0.109	0.000	0.000	0.000	0.000
137	A	136	THR	0	-0.016	-0.015	28.660	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.803	-0.856	31.192	0.080	0.080	0.000	0.000	0.000	0.000
139	A	138	GLY	0	-0.002	-0.002	33.894	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	139	LEU	0	-0.045	-0.016	34.429	0.006	0.006	0.000	0.000	0.000	0.000
141	A	140	LEU	0	0.015	0.016	34.491	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	141	LYS	1	0.871	0.892	37.251	-0.061	-0.061	0.000	0.000	0.000	0.000
143	A	142	GLU	-1	-0.983	-1.001	39.649	0.045	0.045	0.000	0.000	0.000	0.000
144	A	143	GLN	0	-0.014	0.014	35.717	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	144	PHE	0	0.039	0.029	32.440	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	145	TYR	0	0.004	0.000	36.434	0.001	0.001	0.000	0.000	0.000	0.000
147	A	146	THR	0	0.021	0.006	32.980	0.001	0.001	0.000	0.000	0.000	0.000
148	A	147	LYS	1	0.971	0.975	31.503	-0.084	-0.084	0.000	0.000	0.000	0.000
149	A	148	GLY	0	0.004	0.006	37.082	0.001	0.001	0.000	0.000	0.000	0.000
150	A	149	LYS	1	0.876	0.945	39.204	-0.058	-0.058	0.000	0.000	0.000	0.000
151	A	150	TYR	0	0.094	0.049	38.837	0.001	0.001	0.000	0.000	0.000	0.000
152	A	151	LYS	1	0.734	0.829	33.635	-0.086	-0.086	0.000	0.000	0.000	0.000
153	A	152	ASP	-1	-0.792	-0.872	36.663	0.066	0.066	0.000	0.000	0.000	0.000
154	A	153	ALA	0	-0.018	-0.010	31.977	0.005	0.005	0.000	0.000	0.000	0.000
155	A	154	TYR	0	-0.020	-0.002	30.342	-0.007	-0.007	0.000	0.000	0.000	0.000
156	A	155	PHE	0	0.024	0.027	30.581	0.004	0.004	0.000	0.000	0.000	0.000
157	A	156	MET	0	-0.023	-0.021	26.259	0.003	0.003	0.000	0.000	0.000	0.000
158	A	157	SER	0	-0.034	-0.051	26.649	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	158	LEU	0	0.029	0.031	21.819	0.006	0.006	0.000	0.000	0.000	0.000
160	A	159	LEU	0	0.010	0.006	25.983	-0.010	-0.010	0.000	0.000	0.000	0.000
161	A	160	LYS	1	0.877	0.935	24.705	-0.050	-0.050	0.000	0.000	0.000	0.000
162	A	161	SER	0	-0.025	-0.034	25.770	0.004	0.004	0.000	0.000	0.000	0.000
163	A	162	GLU	-1	-0.835	-0.904	26.848	0.108	0.108	0.000	0.000	0.000	0.000
164	A	163	TYR	0	0.039	0.009	16.535	-0.001	-0.001	0.000	0.000	0.000	0.000
165	A	164	ILE	0	-0.055	-0.015	22.185	0.011	0.011	0.000	0.000	0.000	0.000
166	A	165	LEU	0	-0.061	-0.012	24.206	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)