FMO DATABASE

FMODB ID: 5J2KZ

Calculation Name: 3ILH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ILH

Chain ID: A

ChEMBL ID:

UniProt ID:

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:

Apendix: None

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1232808.029985
FMO2-HF: Nuclear repulsion	1179718.19431
FMO2-HF: Total energy	-53089.835675
FMO2-MP2: Total energy	-53244.310043

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:5:ARG)

Summations of interaction energy for fragment #1(A:5:ARG)

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.
-99.516	-96.248	0.956	-1.34	-2.883	-0.004

Interaction energy analysis for fragmet #1(A:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.963 / q_NPA : 0.966

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	7	ILE	0	0.033	0.032	3.858	-1.960	-0.608	-0.006	-0.692	-0.653	0.002
4	A	8	ASP	-1	-0.796	-0.878	6.694	-24.020	-24.020	0.000	0.000	0.000	0.000
5	A	9	SER	0	0.010	-0.026	9.084	1.501	1.501	0.000	0.000	0.000	0.000
6	A	10	VAL	0	-0.015	-0.004	12.256	-0.511	-0.511	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.007	0.004	14.656	0.496	0.496	0.000	0.000	0.000	0.000
8	A	12	LEU	0	-0.029	-0.024	17.312	-0.259	-0.259	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.036	-0.021	20.646	0.556	0.556	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.747	-0.889	24.284	-12.011	-12.011	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.832	-0.941	26.281	-9.897	-9.897	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.850	-0.898	27.971	-10.588	-10.588	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.927	-0.970	26.861	-10.981	-10.981	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.012	0.005	25.799	-0.513	-0.513	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.015	0.013	23.287	-0.713	-0.713	0.000	0.000	0.000	0.000
16	A	20	ASN	0	0.005	0.017	22.182	-1.223	-1.223	0.000	0.000	0.000	0.000
17	A	21	PHE	0	-0.026	-0.032	21.036	-0.908	-0.908	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.016	0.005	20.840	-0.745	-0.745	0.000	0.000	0.000	0.000
19	A	23	ASN	0	0.047	0.011	18.319	-1.170	-1.170	0.000	0.000	0.000	0.000
20	A	24	THR	0	0.020	0.028	16.594	-1.228	-1.228	0.000	0.000	0.000	0.000
21	A	25	THR	0	-0.024	-0.026	15.982	-1.034	-1.034	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.072	-0.021	14.491	-1.349	-1.349	0.000	0.000	0.000	0.000
23	A	27	ILE	0	0.032	0.005	11.336	-1.484	-1.484	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.945	0.980	11.200	14.654	14.654	0.000	0.000	0.000	0.000
25	A	29	MET	0	-0.079	-0.041	11.128	-1.435	-1.435	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.030	-0.008	7.692	-2.174	-2.174	0.000	0.000	0.000	0.000
27	A	31	HIS	0	-0.080	-0.054	6.853	-5.238	-5.238	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.839	0.932	2.302	47.888	49.485	0.958	-0.584	-1.971	-0.006
29	A	33	VAL	0	0.016	0.008	5.748	-1.543	-1.543	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.916	-0.941	7.037	-27.404	-27.404	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.921	-0.938	9.939	-14.765	-14.765	0.000	0.000	0.000	0.000
32	A	36	ILE	0	-0.048	-0.033	13.538	-0.319	-0.319	0.000	0.000	0.000	0.000
33	A	37	GLN	0	-0.026	-0.023	15.961	1.475	1.475	0.000	0.000	0.000	0.000
34	A	38	SER	0	-0.020	-0.001	19.567	-0.205	-0.205	0.000	0.000	0.000	0.000
35	A	39	VAL	0	-0.026	-0.010	22.486	0.420	0.420	0.000	0.000	0.000	0.000
36	A	40	THR	0	0.071	0.019	25.787	-0.187	-0.187	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.039	0.014	28.496	0.392	0.392	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.082	0.047	28.670	-0.276	-0.276	0.000	0.000	0.000	0.000
39	A	43	ASN	0	0.001	-0.007	29.343	-0.200	-0.200	0.000	0.000	0.000	0.000
40	A	44	ALA	0	-0.009	-0.004	29.183	-0.064	-0.064	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.004	0.003	25.249	-0.237	-0.237	0.000	0.000	0.000	0.000
42	A	46	ILE	0	0.048	0.020	25.722	-0.304	-0.304	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.041	-0.020	27.517	0.006	0.006	0.000	0.000	0.000	0.000
44	A	48	LYS	1	0.853	0.933	22.454	12.277	12.277	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.029	0.007	20.828	-0.317	-0.317	0.000	0.000	0.000	0.000
46	A	50	ASN	0	-0.011	-0.005	23.367	-0.241	-0.241	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.940	-0.960	23.646	-11.639	-11.639	0.000	0.000	0.000	0.000
48	A	52	LEU	0	-0.038	-0.049	18.875	-0.178	-0.178	0.000	0.000	0.000	0.000
49	A	53	TYR	0	0.031	0.035	21.028	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.059	-0.013	22.663	0.008	0.008	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.069	-0.036	20.046	0.149	0.149	0.000	0.000	0.000	0.000
52	A	56	GLY	0	0.012	0.004	17.500	-0.156	-0.156	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.876	0.923	16.127	13.759	13.759	0.000	0.000	0.000	0.000
54	A	58	TRP	0	0.123	0.040	15.926	1.018	1.018	0.000	0.000	0.000	0.000
55	A	59	PRO	0	-0.075	-0.005	15.062	-0.874	-0.874	0.000	0.000	0.000	0.000
56	A	60	SER	0	0.003	-0.024	9.465	0.188	0.188	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.038	-0.028	10.937	-0.290	-0.290	0.000	0.000	0.000	0.000
58	A	62	ILE	0	-0.008	-0.002	14.341	0.410	0.410	0.000	0.000	0.000	0.000
59	A	63	CYS	0	-0.042	-0.004	17.280	-0.306	-0.306	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.013	-0.002	20.113	0.337	0.337	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.788	-0.878	23.792	-11.356	-11.356	0.000	0.000	0.000	0.000
62	A	66	ILE	0	-0.037	-0.018	26.178	0.230	0.230	0.000	0.000	0.000	0.000
63	A	67	ASN	0	-0.086	-0.045	28.862	0.204	0.204	0.000	0.000	0.000	0.000
64	A	68	MET	0	0.052	0.038	28.514	-0.274	-0.274	0.000	0.000	0.000	0.000
65	A	69	PRO	0	-0.025	0.005	32.384	0.291	0.291	0.000	0.000	0.000	0.000
66	A	70	GLY	0	-0.044	-0.020	34.481	-0.130	-0.130	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.018	-0.009	32.021	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	72	ASN	0	0.029	-0.001	32.407	-0.501	-0.501	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.012	0.003	28.275	-0.090	-0.090	0.000	0.000	0.000	0.000
70	A	74	TRP	0	-0.014	-0.051	27.424	-0.208	-0.208	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.800	-0.879	30.564	-8.697	-8.697	0.000	0.000	0.000	0.000
72	A	76	LEU	0	-0.003	0.006	26.180	0.030	0.030	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.017	0.008	24.341	-0.063	-0.063	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.880	-0.947	27.753	-9.475	-9.475	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.021	-0.011	30.165	0.176	0.176	0.000	0.000	0.000	0.000
76	A	80	PHE	0	0.047	0.009	22.726	0.020	0.020	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.826	0.920	27.229	9.880	9.880	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.066	-0.033	28.785	0.326	0.326	0.000	0.000	0.000	0.000
79	A	83	HIS	0	-0.084	-0.023	28.856	0.429	0.429	0.000	0.000	0.000	0.000
80	A	84	PHE	0	-0.038	-0.040	24.324	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	85	GLN	0	0.084	0.050	24.471	-0.698	-0.698	0.000	0.000	0.000	0.000
82	A	86	PRO	0	-0.031	-0.012	23.967	-0.251	-0.251	0.000	0.000	0.000	0.000
83	A	87	MET	0	-0.022	-0.006	19.896	-0.469	-0.469	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.805	0.917	20.166	11.033	11.033	0.000	0.000	0.000	0.000
85	A	89	ASN	0	-0.005	-0.038	18.617	-0.272	-0.272	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.815	0.913	12.358	17.913	17.913	0.000	0.000	0.000	0.000
87	A	91	SER	0	0.008	-0.001	15.069	-0.563	-0.563	0.000	0.000	0.000	0.000
88	A	92	ILE	0	-0.046	0.004	12.651	0.195	0.195	0.000	0.000	0.000	0.000
89	A	93	VAL	0	0.000	-0.013	15.678	-0.163	-0.163	0.000	0.000	0.000	0.000
90	A	94	CYS	0	-0.031	-0.018	17.255	-0.071	-0.071	0.000	0.000	0.000	0.000
91	A	95	LEU	0	0.023	0.017	19.383	0.261	0.261	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.015	-0.014	19.804	-0.434	-0.434	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.031	0.016	23.634	0.599	0.599	0.000	0.000	0.000	0.000
94	A	98	SER	0	0.010	-0.008	26.329	-0.378	-0.378	0.000	0.000	0.000	0.000
95	A	99	SER	0	0.014	0.014	27.830	-0.078	-0.078	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.017	0.013	24.610	0.016	0.016	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.720	-0.860	28.528	-9.099	-9.099	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.016	0.006	29.935	-0.194	-0.194	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.797	0.872	30.925	8.711	8.711	0.000	0.000	0.000	0.000
100	A	104	ASP	-1	-0.748	-0.873	28.820	-10.209	-10.209	0.000	0.000	0.000	0.000
101	A	105	GLN	0	-0.043	-0.007	24.448	0.026	0.026	0.000	0.000	0.000	0.000
102	A	106	ALA	0	0.051	0.019	27.034	-0.277	-0.277	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.764	0.894	29.241	9.768	9.768	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.014	-0.018	24.219	-0.073	-0.073	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.975	-0.971	24.424	-12.301	-12.301	0.000	0.000	0.000	0.000
106	A	110	ALA	0	-0.055	-0.029	25.807	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	111	SER	0	-0.036	-0.023	25.543	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.772	-0.865	23.920	-11.738	-11.738	0.000	0.000	0.000	0.000
109	A	113	TRP	0	-0.073	-0.049	21.620	-0.450	-0.450	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.079	-0.028	21.542	-0.351	-0.351	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.753	-0.841	17.670	-16.469	-16.469	0.000	0.000	0.000	0.000
112	A	116	TYR	0	-0.035	-0.048	16.203	-1.133	-1.133	0.000	0.000	0.000	0.000
113	A	117	TYR	0	0.064	0.040	19.867	0.374	0.374	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.049	-0.022	18.484	-0.276	-0.276	0.000	0.000	0.000	0.000
115	A	119	SER	0	0.024	0.008	21.696	0.396	0.396	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.757	0.862	21.731	10.925	10.925	0.000	0.000	0.000	0.000
117	A	121	PRO	0	-0.043	-0.013	20.097	0.450	0.450	0.000	0.000	0.000	0.000
118	A	122	LEU	0	0.063	0.005	15.630	-0.219	-0.219	0.000	0.000	0.000	0.000
119	A	123	THR	0	0.042	0.025	16.094	-0.366	-0.366	0.000	0.000	0.000	0.000
120	A	124	ALA	0	0.066	0.012	11.309	-0.906	-0.906	0.000	0.000	0.000	0.000
121	A	125	ASN	0	-0.014	-0.005	11.094	-3.091	-3.091	0.000	0.000	0.000	0.000
122	A	126	ALA	0	0.001	0.010	11.923	-1.053	-1.053	0.000	0.000	0.000	0.000
123	A	127	LEU	0	0.059	0.026	10.449	-0.422	-0.422	0.000	0.000	0.000	0.000
124	A	128	ASN	0	-0.062	-0.028	6.403	-7.173	-7.173	0.000	0.000	0.000	0.000
125	A	129	ASN	0	0.001	-0.003	8.597	-3.006	-3.006	0.000	0.000	0.000	0.000
126	A	130	LEU	0	0.028	0.021	11.224	0.152	0.152	0.000	0.000	0.000	0.000
127	A	131	TYR	0	0.030	-0.001	6.338	-0.346	-0.346	0.000	0.000	0.000	0.000
128	A	132	ASN	0	-0.011	-0.037	6.711	-4.791	-4.791	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.865	0.957	8.931	19.828	19.828	0.000	0.000	0.000	0.000
130	A	134	VAL	0	0.014	0.004	7.552	0.569	0.569	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.049	-0.027	3.858	-1.948	-1.629	0.004	-0.064	-0.259	0.000
132	A	136	ASN	0	-0.110	-0.017	7.534	-0.782	-0.782	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.794	-0.880	9.817	-17.977	-17.977	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ARG)