FMO DATABASE

FMODB ID: JL169

Calculation Name: 3UL3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UL3

Chain ID: B

ChEMBL ID:

UniProt ID: Q8IDP4

Base Structure: X-ray

Registration Date: 2023-09-20

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-814597.270821
FMO2-HF: Nuclear repulsion	772273.68776
FMO2-HF: Total energy	-42323.58306
FMO2-MP2: Total energy	-42444.932028

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:54:ARG)

Summations of interaction energy for fragment #1(B:54: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.
98.558	97.961	10.331	-5.373	-4.361	-0.03

Interaction energy analysis for fragmet #1(B:54:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.001 / q_NPA : 0.998

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

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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	56	GLN	0	0.033	0.029	1.853	-10.826	-11.528	10.332	-5.363	-4.267	-0.030
4	B	57	GLN	0	0.045	0.026	4.811	1.026	1.131	-0.001	-0.010	-0.094	0.000
5	B	58	ASN	0	-0.063	-0.031	8.194	0.952	0.952	0.000	0.000	0.000	0.000
6	B	59	GLY	0	0.073	0.050	11.199	0.871	0.871	0.000	0.000	0.000	0.000
7	B	60	SER	0	0.003	-0.022	14.773	-0.181	-0.181	0.000	0.000	0.000	0.000
8	B	61	ASN	0	-0.044	-0.017	17.457	0.001	0.001	0.000	0.000	0.000	0.000
9	B	62	ILE	0	-0.056	-0.037	19.276	0.873	0.873	0.000	0.000	0.000	0.000
10	B	63	ILE	0	0.054	-0.012	18.971	-0.521	-0.521	0.000	0.000	0.000	0.000
11	B	64	ASN	0	0.003	0.006	18.557	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	65	GLY	0	0.016	0.010	16.273	-0.829	-0.829	0.000	0.000	0.000	0.000
13	B	66	VAL	0	-0.037	-0.025	12.581	0.738	0.738	0.000	0.000	0.000	0.000
14	B	67	ASN	0	0.072	0.042	12.338	-1.056	-1.056	0.000	0.000	0.000	0.000
15	B	68	MET	0	-0.001	0.020	14.256	0.243	0.243	0.000	0.000	0.000	0.000
16	B	69	LYS	1	0.917	0.933	16.790	14.799	14.799	0.000	0.000	0.000	0.000
17	B	70	ASN	0	0.034	0.026	20.588	-0.312	-0.312	0.000	0.000	0.000	0.000
18	B	71	THR	0	-0.034	-0.004	23.977	0.466	0.466	0.000	0.000	0.000	0.000
19	B	72	VAL	0	0.023	0.002	26.194	0.008	0.008	0.000	0.000	0.000	0.000
20	B	73	ILE	0	-0.003	0.007	21.745	-0.094	-0.094	0.000	0.000	0.000	0.000
21	B	74	VAL	0	-0.021	-0.026	24.998	0.377	0.377	0.000	0.000	0.000	0.000
22	B	75	LEU	0	0.005	0.006	22.210	-0.350	-0.350	0.000	0.000	0.000	0.000
23	B	76	TYR	0	0.008	-0.028	24.795	0.515	0.515	0.000	0.000	0.000	0.000
24	B	77	PHE	0	0.020	0.021	23.749	-0.437	-0.437	0.000	0.000	0.000	0.000
25	B	78	PHE	0	0.002	-0.035	23.182	0.524	0.524	0.000	0.000	0.000	0.000
26	B	79	ALA	0	0.090	0.044	26.531	-0.333	-0.333	0.000	0.000	0.000	0.000
27	B	80	LYS	1	0.767	0.863	24.134	12.599	12.599	0.000	0.000	0.000	0.000
28	B	81	TRP	0	0.013	0.003	28.795	0.412	0.412	0.000	0.000	0.000	0.000
29	B	82	CYS	0	-0.018	0.003	31.440	0.455	0.455	0.000	0.000	0.000	0.000
30	B	83	GLN	0	0.079	0.038	33.368	-0.136	-0.136	0.000	0.000	0.000	0.000
31	B	84	ALA	0	0.053	0.013	35.858	0.033	0.033	0.000	0.000	0.000	0.000
32	B	85	CYS	0	-0.022	-0.006	30.850	-0.066	-0.066	0.000	0.000	0.000	0.000
33	B	86	THR	0	-0.017	0.019	32.197	-0.031	-0.031	0.000	0.000	0.000	0.000
34	B	87	MET	0	0.068	0.019	33.260	0.009	0.009	0.000	0.000	0.000	0.000
35	B	88	GLN	0	0.034	0.014	31.770	0.133	0.133	0.000	0.000	0.000	0.000
36	B	89	SER	0	-0.027	-0.021	29.429	-0.342	-0.342	0.000	0.000	0.000	0.000
37	B	90	THR	0	0.058	0.044	30.857	-0.168	-0.168	0.000	0.000	0.000	0.000
38	B	91	GLU	-1	-0.801	-0.886	33.279	-8.323	-8.323	0.000	0.000	0.000	0.000
39	B	92	MET	0	-0.057	-0.022	28.632	-0.111	-0.111	0.000	0.000	0.000	0.000
40	B	93	ASP	-1	-0.843	-0.904	28.413	-10.899	-10.899	0.000	0.000	0.000	0.000
41	B	94	LYS	1	0.782	0.878	30.593	8.292	8.292	0.000	0.000	0.000	0.000
42	B	95	LEU	0	-0.013	-0.013	30.462	0.055	0.055	0.000	0.000	0.000	0.000
43	B	96	GLN	0	-0.011	-0.015	25.010	-0.466	-0.466	0.000	0.000	0.000	0.000
44	B	97	LYS	1	0.943	0.977	29.320	8.717	8.717	0.000	0.000	0.000	0.000
45	B	98	TYR	0	-0.013	0.009	31.311	0.113	0.113	0.000	0.000	0.000	0.000
46	B	99	TYR	0	0.018	0.002	30.582	0.182	0.182	0.000	0.000	0.000	0.000
47	B	100	GLY	0	0.011	0.014	28.698	-0.152	-0.152	0.000	0.000	0.000	0.000
48	B	101	LYS	1	0.945	0.957	25.373	11.224	11.224	0.000	0.000	0.000	0.000
49	B	102	ARG	1	0.933	0.965	26.453	9.222	9.222	0.000	0.000	0.000	0.000
50	B	103	ILE	0	-0.017	-0.014	26.904	0.100	0.100	0.000	0.000	0.000	0.000
51	B	104	TYR	0	0.010	0.010	17.376	-0.180	-0.180	0.000	0.000	0.000	0.000
52	B	105	LEU	0	0.004	0.021	23.338	0.306	0.306	0.000	0.000	0.000	0.000
53	B	106	LEU	0	0.003	0.006	18.253	-0.516	-0.516	0.000	0.000	0.000	0.000
54	B	107	LYS	1	0.913	0.978	21.157	12.324	12.324	0.000	0.000	0.000	0.000
55	B	108	VAL	0	0.024	-0.019	20.040	-0.647	-0.647	0.000	0.000	0.000	0.000
56	B	109	ASP	-1	-0.815	-0.894	21.297	-12.321	-12.321	0.000	0.000	0.000	0.000
57	B	110	LEU	0	0.090	0.034	22.355	-0.424	-0.424	0.000	0.000	0.000	0.000
58	B	111	ASP	-1	-0.817	-0.885	24.167	-11.667	-11.667	0.000	0.000	0.000	0.000
59	B	112	LYS	1	0.870	0.907	19.316	13.561	13.561	0.000	0.000	0.000	0.000
60	B	113	ASN	0	-0.052	-0.018	19.004	-0.417	-0.417	0.000	0.000	0.000	0.000
61	B	114	GLU	-1	-0.741	-0.850	21.135	-11.692	-11.692	0.000	0.000	0.000	0.000
62	B	115	SER	0	0.021	0.007	20.050	0.480	0.480	0.000	0.000	0.000	0.000
63	B	116	LEU	0	-0.003	-0.002	19.720	0.370	0.370	0.000	0.000	0.000	0.000
64	B	117	ALA	0	0.050	0.027	22.312	0.359	0.359	0.000	0.000	0.000	0.000
65	B	118	ARG	1	0.914	0.941	24.583	12.628	12.628	0.000	0.000	0.000	0.000
66	B	119	LYS	1	0.914	0.968	22.731	13.251	13.251	0.000	0.000	0.000	0.000
67	B	120	PHE	0	-0.047	-0.024	22.591	0.223	0.223	0.000	0.000	0.000	0.000
68	B	121	SER	0	-0.016	0.007	27.389	0.502	0.502	0.000	0.000	0.000	0.000
69	B	122	VAL	0	-0.064	-0.022	27.460	0.321	0.321	0.000	0.000	0.000	0.000
70	B	123	LYS	1	0.991	0.995	30.513	8.612	8.612	0.000	0.000	0.000	0.000
71	B	124	SER	0	-0.013	-0.024	32.781	0.188	0.188	0.000	0.000	0.000	0.000
72	B	125	LEU	0	-0.031	0.026	28.826	-0.383	-0.383	0.000	0.000	0.000	0.000
73	B	126	PRO	0	0.034	-0.012	31.222	0.232	0.232	0.000	0.000	0.000	0.000
74	B	127	THR	0	-0.009	-0.011	29.745	0.262	0.262	0.000	0.000	0.000	0.000
75	B	128	ILE	0	-0.019	-0.015	29.306	-0.410	-0.410	0.000	0.000	0.000	0.000
76	B	129	ILE	0	0.014	0.003	27.666	0.332	0.332	0.000	0.000	0.000	0.000
77	B	130	LEU	0	-0.020	0.003	28.177	-0.317	-0.317	0.000	0.000	0.000	0.000
78	B	131	LEU	0	0.026	0.022	24.327	0.222	0.222	0.000	0.000	0.000	0.000
79	B	132	LYS	1	0.953	0.970	27.048	10.748	10.748	0.000	0.000	0.000	0.000
80	B	133	ASN	0	0.011	0.005	25.448	-0.034	-0.034	0.000	0.000	0.000	0.000
81	B	134	LYN	0	-0.005	0.034	22.542	-0.093	-0.093	0.000	0.000	0.000	0.000
82	B	135	THR	0	0.029	0.045	25.844	0.225	0.225	0.000	0.000	0.000	0.000
83	B	136	MET	0	-0.019	-0.021	29.533	-0.102	-0.102	0.000	0.000	0.000	0.000
84	B	137	LEU	0	-0.062	-0.034	30.595	0.313	0.313	0.000	0.000	0.000	0.000
85	B	138	ALA	0	-0.008	-0.017	32.445	0.352	0.352	0.000	0.000	0.000	0.000
86	B	139	ARG	1	0.766	0.830	30.859	9.356	9.356	0.000	0.000	0.000	0.000
87	B	140	LYS	1	0.923	0.977	33.353	8.375	8.375	0.000	0.000	0.000	0.000
88	B	141	ASP	-1	-0.747	-0.842	33.594	-9.427	-9.427	0.000	0.000	0.000	0.000
89	B	142	HIS	0	0.036	0.031	35.323	0.133	0.133	0.000	0.000	0.000	0.000
90	B	143	PHE	0	0.024	0.009	35.902	-0.149	-0.149	0.000	0.000	0.000	0.000
91	B	144	VAL	0	-0.007	-0.010	34.755	0.217	0.217	0.000	0.000	0.000	0.000
92	B	145	SER	0	0.059	0.013	36.253	-0.213	-0.213	0.000	0.000	0.000	0.000
93	B	146	SER	0	0.027	0.007	35.140	-0.066	-0.066	0.000	0.000	0.000	0.000
94	B	147	ASN	0	0.024	-0.005	36.376	-0.225	-0.225	0.000	0.000	0.000	0.000
95	B	148	ASP	-1	-0.831	-0.873	38.872	-7.621	-7.621	0.000	0.000	0.000	0.000
96	B	149	LEU	0	-0.065	-0.042	32.849	-0.089	-0.089	0.000	0.000	0.000	0.000
97	B	150	ILE	0	-0.036	-0.019	35.567	-0.132	-0.132	0.000	0.000	0.000	0.000
98	B	151	ALA	0	0.016	0.023	36.751	-0.013	-0.013	0.000	0.000	0.000	0.000
99	B	152	LEU	0	-0.012	-0.015	36.109	0.034	0.034	0.000	0.000	0.000	0.000
100	B	153	ILE	0	-0.001	-0.013	31.535	-0.078	-0.078	0.000	0.000	0.000	0.000
101	B	154	LYS	1	0.872	0.942	34.871	7.958	7.958	0.000	0.000	0.000	0.000
102	B	155	LYS	1	0.946	0.990	37.243	7.787	7.787	0.000	0.000	0.000	0.000
103	B	156	HIS	1	0.921	0.964	33.927	8.804	8.804	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:54:ARG)