FMO DATABASE

FMODB ID: YVZL2

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1234180.333314
FMO2-HF: Nuclear repulsion	1181089.097418
FMO2-HF: Total energy	-53091.235896
FMO2-MP2: Total energy	-53245.541485

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.
-94.794	-91.867	0.123	-1.063	-1.986	-0.001

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 : 0.967 / q_NPA : 0.967

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	-0.006	0.007	3.853	-2.314	-0.948	-0.002	-0.675	-0.688	0.001
4	A	8	ASP	-1	-0.812	-0.896	6.753	-23.280	-23.280	0.000	0.000	0.000	0.000
5	A	9	SER	0	-0.004	-0.018	9.047	1.454	1.454	0.000	0.000	0.000	0.000
6	A	10	VAL	0	-0.017	-0.007	12.229	-0.589	-0.589	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.011	-0.003	14.670	0.596	0.596	0.000	0.000	0.000	0.000
8	A	12	LEU	0	-0.049	-0.020	17.920	-0.111	-0.111	0.000	0.000	0.000	0.000
9	A	13	ILE	0	0.011	-0.007	20.864	0.465	0.465	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.766	-0.887	24.224	-11.788	-11.788	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.849	-0.931	26.588	-10.012	-10.012	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.813	-0.891	27.688	-10.676	-10.676	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.875	-0.939	26.786	-10.954	-10.954	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.046	-0.017	26.038	-0.486	-0.486	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.015	0.003	23.097	-0.654	-0.654	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.041	-0.021	22.373	-1.265	-1.265	0.000	0.000	0.000	0.000
17	A	21	PHE	0	0.008	0.004	21.170	-0.871	-0.871	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.009	0.005	20.728	-0.773	-0.773	0.000	0.000	0.000	0.000
19	A	23	ASN	0	0.053	0.030	18.243	-1.196	-1.196	0.000	0.000	0.000	0.000
20	A	24	THR	0	0.035	0.021	16.675	-1.211	-1.211	0.000	0.000	0.000	0.000
21	A	25	THR	0	-0.036	-0.026	16.002	-0.980	-0.980	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.016	-0.018	14.200	-1.118	-1.118	0.000	0.000	0.000	0.000
23	A	27	ILE	0	0.003	-0.004	11.593	-1.684	-1.684	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.884	0.936	11.151	14.637	14.637	0.000	0.000	0.000	0.000
25	A	29	MET	0	-0.051	-0.021	11.589	-1.025	-1.025	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.040	-0.008	7.885	-2.011	-2.011	0.000	0.000	0.000	0.000
27	A	31	HIS	0	-0.018	-0.004	6.971	-5.298	-5.298	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.768	0.879	3.238	47.594	48.559	0.043	-0.197	-0.811	-0.001
29	A	33	VAL	0	0.027	0.012	5.829	-1.318	-1.318	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.870	-0.911	7.423	-27.883	-27.883	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.860	-0.909	10.238	-14.317	-14.317	0.000	0.000	0.000	0.000
32	A	36	ILE	0	-0.026	-0.027	13.568	-0.652	-0.652	0.000	0.000	0.000	0.000
33	A	37	GLN	0	-0.022	-0.010	16.136	1.401	1.401	0.000	0.000	0.000	0.000
34	A	38	SER	0	-0.038	-0.034	19.766	-0.282	-0.282	0.000	0.000	0.000	0.000
35	A	39	VAL	0	0.003	-0.003	22.718	0.393	0.393	0.000	0.000	0.000	0.000
36	A	40	THR	0	0.041	0.025	26.074	-0.171	-0.171	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.063	0.019	28.877	0.400	0.400	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.081	0.040	28.724	-0.267	-0.267	0.000	0.000	0.000	0.000
39	A	43	ASN	0	0.027	0.002	29.417	-0.182	-0.182	0.000	0.000	0.000	0.000
40	A	44	ALA	0	-0.002	0.012	29.056	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.028	0.018	25.275	-0.217	-0.217	0.000	0.000	0.000	0.000
42	A	46	ILE	0	0.036	0.017	25.938	-0.251	-0.251	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.063	-0.039	27.757	0.083	0.083	0.000	0.000	0.000	0.000
44	A	48	LYS	1	0.813	0.899	22.511	12.101	12.101	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.004	-0.003	21.191	-0.397	-0.397	0.000	0.000	0.000	0.000
46	A	50	ASN	0	-0.039	-0.034	23.709	-0.136	-0.136	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.896	-0.928	23.780	-11.515	-11.515	0.000	0.000	0.000	0.000
48	A	52	LEU	0	-0.061	-0.034	18.471	-0.175	-0.175	0.000	0.000	0.000	0.000
49	A	53	TYR	0	0.040	0.007	21.251	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.049	-0.003	22.751	0.161	0.161	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.039	-0.018	20.851	0.198	0.198	0.000	0.000	0.000	0.000
52	A	56	GLY	0	-0.012	-0.009	18.069	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.831	0.911	16.153	13.858	13.858	0.000	0.000	0.000	0.000
54	A	58	TRP	0	0.069	0.010	15.853	0.989	0.989	0.000	0.000	0.000	0.000
55	A	59	PRO	0	-0.068	-0.015	14.946	-0.886	-0.886	0.000	0.000	0.000	0.000
56	A	60	SER	0	0.014	-0.010	9.759	0.104	0.104	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.020	-0.020	10.677	-0.426	-0.426	0.000	0.000	0.000	0.000
58	A	62	ILE	0	0.010	0.010	14.142	0.399	0.399	0.000	0.000	0.000	0.000
59	A	63	CYS	0	-0.083	-0.034	17.151	-0.540	-0.540	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.019	0.007	19.831	0.329	0.329	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.799	-0.906	23.622	-11.106	-11.106	0.000	0.000	0.000	0.000
62	A	66	ILE	0	-0.034	-0.021	26.524	0.252	0.252	0.000	0.000	0.000	0.000
63	A	67	ASN	0	-0.086	-0.049	29.289	0.205	0.205	0.000	0.000	0.000	0.000
64	A	68	MET	0	0.012	0.036	28.257	0.138	0.138	0.000	0.000	0.000	0.000
65	A	69	PRO	0	-0.007	0.002	32.134	0.267	0.267	0.000	0.000	0.000	0.000
66	A	70	GLY	0	-0.058	-0.021	34.510	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.050	-0.019	31.940	0.016	0.016	0.000	0.000	0.000	0.000
68	A	72	ASN	0	0.040	-0.001	32.291	-0.523	-0.523	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.015	0.000	28.272	-0.082	-0.082	0.000	0.000	0.000	0.000
70	A	74	TRP	0	-0.046	-0.054	27.568	-0.223	-0.223	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.786	-0.875	30.219	-8.682	-8.682	0.000	0.000	0.000	0.000
72	A	76	LEU	0	-0.027	-0.002	26.027	0.083	0.083	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.052	0.029	24.044	-0.108	-0.108	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.891	-0.952	27.575	-9.386	-9.386	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.020	-0.011	30.094	0.133	0.133	0.000	0.000	0.000	0.000
76	A	80	PHE	0	-0.001	-0.013	22.539	0.022	0.022	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.853	0.929	27.124	9.879	9.879	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.073	-0.029	28.818	0.329	0.329	0.000	0.000	0.000	0.000
79	A	83	HIS	0	-0.056	-0.016	29.144	0.363	0.363	0.000	0.000	0.000	0.000
80	A	84	PHE	0	0.001	-0.002	24.202	-0.053	-0.053	0.000	0.000	0.000	0.000
81	A	85	GLN	0	0.067	0.038	24.349	-0.761	-0.761	0.000	0.000	0.000	0.000
82	A	86	PRO	0	-0.030	-0.021	24.235	-0.257	-0.257	0.000	0.000	0.000	0.000
83	A	87	MET	0	-0.003	0.005	19.804	-0.483	-0.483	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.820	0.901	19.801	10.732	10.732	0.000	0.000	0.000	0.000
85	A	89	ASN	0	-0.025	-0.010	18.475	-0.130	-0.130	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.793	0.876	12.443	17.648	17.648	0.000	0.000	0.000	0.000
87	A	91	SER	0	0.018	0.017	14.946	-0.376	-0.376	0.000	0.000	0.000	0.000
88	A	92	ILE	0	-0.039	0.003	12.272	0.434	0.434	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.018	-0.021	15.281	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	94	CYS	0	-0.055	-0.029	17.653	-0.189	-0.189	0.000	0.000	0.000	0.000
91	A	95	LEU	0	0.026	0.019	19.592	0.308	0.308	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.033	-0.028	20.535	-0.529	-0.529	0.000	0.000	0.000	0.000
93	A	97	SER	0	0.088	0.026	24.158	0.550	0.550	0.000	0.000	0.000	0.000
94	A	98	SER	0	0.008	-0.007	26.629	-0.444	-0.444	0.000	0.000	0.000	0.000
95	A	99	SER	0	-0.024	-0.008	28.709	0.088	0.088	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.018	0.018	24.933	0.074	0.074	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.736	-0.853	28.666	-8.974	-8.974	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.028	0.003	30.288	-0.216	-0.216	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.825	0.900	31.607	8.719	8.719	0.000	0.000	0.000	0.000
100	A	104	ASP	-1	-0.733	-0.858	29.671	-9.960	-9.960	0.000	0.000	0.000	0.000
101	A	105	GLN	0	-0.076	-0.044	25.850	-0.205	-0.205	0.000	0.000	0.000	0.000
102	A	106	ALA	0	0.002	0.002	27.716	-0.258	-0.258	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.771	0.877	29.566	9.662	9.662	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.020	-0.005	24.389	-0.065	-0.065	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.890	-0.949	24.789	-12.160	-12.160	0.000	0.000	0.000	0.000
106	A	110	ALA	0	-0.053	-0.014	25.917	-0.038	-0.038	0.000	0.000	0.000	0.000
107	A	111	SER	0	-0.012	-0.003	25.710	0.439	0.439	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.808	-0.889	23.437	-11.664	-11.664	0.000	0.000	0.000	0.000
109	A	113	TRP	0	-0.075	-0.052	21.404	-0.280	-0.280	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.044	-0.021	21.115	-0.118	-0.118	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.769	-0.856	16.869	-16.407	-16.407	0.000	0.000	0.000	0.000
112	A	116	TYR	0	-0.035	-0.040	16.389	-1.045	-1.045	0.000	0.000	0.000	0.000
113	A	117	TYR	0	0.066	0.036	20.145	0.422	0.422	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.045	-0.015	18.617	-0.318	-0.318	0.000	0.000	0.000	0.000
115	A	119	SER	0	0.017	0.005	22.018	0.507	0.507	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.782	0.904	22.086	10.726	10.726	0.000	0.000	0.000	0.000
117	A	121	PRO	0	-0.015	-0.008	20.114	0.387	0.387	0.000	0.000	0.000	0.000
118	A	122	LEU	0	0.045	0.007	16.018	-0.282	-0.282	0.000	0.000	0.000	0.000
119	A	123	THR	0	0.025	0.003	16.030	-0.394	-0.394	0.000	0.000	0.000	0.000
120	A	124	ALA	0	0.062	0.018	11.277	-0.781	-0.781	0.000	0.000	0.000	0.000
121	A	125	ASN	0	0.007	0.008	11.013	-3.151	-3.151	0.000	0.000	0.000	0.000
122	A	126	ALA	0	0.009	0.014	12.313	-0.826	-0.826	0.000	0.000	0.000	0.000
123	A	127	LEU	0	0.032	0.016	10.840	-0.436	-0.436	0.000	0.000	0.000	0.000
124	A	128	ASN	0	-0.003	-0.005	6.456	-6.603	-6.603	0.000	0.000	0.000	0.000
125	A	129	ASN	0	-0.013	-0.010	9.151	-2.910	-2.910	0.000	0.000	0.000	0.000
126	A	130	LEU	0	0.019	0.022	11.797	0.597	0.597	0.000	0.000	0.000	0.000
127	A	131	TYR	0	0.067	0.010	6.687	-0.048	-0.048	0.000	0.000	0.000	0.000
128	A	132	ASN	0	-0.024	-0.014	6.880	-5.679	-5.679	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.854	0.945	8.909	19.801	19.801	0.000	0.000	0.000	0.000
130	A	134	VAL	0	0.056	0.035	7.424	0.761	0.761	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.079	-0.051	3.227	-1.310	-0.714	0.082	-0.191	-0.487	-0.001
132	A	136	ASN	0	-0.100	-0.044	6.871	-0.122	-0.122	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.825	-0.867	10.241	-17.771	-17.771	0.000	0.000	0.000	0.000

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