FMO DATABASE

FMODB ID: N94VQ

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	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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-814439.434056
FMO2-HF: Nuclear repulsion	772117.707337
FMO2-HF: Total energy	-42321.726719
FMO2-MP2: Total energy	-42443.114558

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.
97.576	97.585	9.645	-5.269	-4.385	-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 : 1.002 / q_NPA : 0.999

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	56	GLN	0	0.030	0.026	1.880	-10.897	-10.992	9.646	-5.259	-4.293	-0.030
4	B	57	GLN	0	0.046	0.028	4.801	1.208	1.312	-0.001	-0.010	-0.092	0.000
5	B	58	ASN	0	-0.062	-0.032	8.155	0.893	0.893	0.000	0.000	0.000	0.000
6	B	59	GLY	0	0.069	0.046	11.195	0.848	0.848	0.000	0.000	0.000	0.000
7	B	60	SER	0	-0.019	-0.035	14.770	-0.169	-0.169	0.000	0.000	0.000	0.000
8	B	61	ASN	0	-0.025	-0.002	17.660	0.147	0.147	0.000	0.000	0.000	0.000
9	B	62	ILE	0	-0.038	-0.053	19.265	0.833	0.833	0.000	0.000	0.000	0.000
10	B	63	ILE	0	0.046	-0.010	18.959	-0.464	-0.464	0.000	0.000	0.000	0.000
11	B	64	ASN	0	-0.046	-0.023	18.787	0.061	0.061	0.000	0.000	0.000	0.000
12	B	65	GLY	0	0.017	0.010	16.513	-0.822	-0.822	0.000	0.000	0.000	0.000
13	B	66	VAL	0	-0.036	-0.023	12.723	0.674	0.674	0.000	0.000	0.000	0.000
14	B	67	ASN	0	0.064	0.033	12.220	-1.097	-1.097	0.000	0.000	0.000	0.000
15	B	68	MET	0	-0.017	0.006	14.298	0.181	0.181	0.000	0.000	0.000	0.000
16	B	69	LYS	1	0.971	0.966	16.777	14.175	14.175	0.000	0.000	0.000	0.000
17	B	70	ASN	0	0.040	0.024	20.575	-0.593	-0.593	0.000	0.000	0.000	0.000
18	B	71	THR	0	-0.059	-0.008	23.964	0.466	0.466	0.000	0.000	0.000	0.000
19	B	72	VAL	0	0.023	-0.004	26.179	-0.016	-0.016	0.000	0.000	0.000	0.000
20	B	73	ILE	0	0.016	0.011	21.754	-0.056	-0.056	0.000	0.000	0.000	0.000
21	B	74	VAL	0	-0.045	-0.036	25.171	0.369	0.369	0.000	0.000	0.000	0.000
22	B	75	LEU	0	-0.008	0.002	22.646	-0.331	-0.331	0.000	0.000	0.000	0.000
23	B	76	TYR	0	-0.008	-0.026	24.983	0.470	0.470	0.000	0.000	0.000	0.000
24	B	77	PHE	0	0.018	0.019	24.123	-0.449	-0.449	0.000	0.000	0.000	0.000
25	B	78	PHE	0	-0.019	-0.034	23.145	0.519	0.519	0.000	0.000	0.000	0.000
26	B	79	ALA	0	0.135	0.061	26.701	-0.305	-0.305	0.000	0.000	0.000	0.000
27	B	80	LYS	1	0.949	0.974	24.786	12.394	12.394	0.000	0.000	0.000	0.000
28	B	81	TRP	0	0.003	0.013	28.898	0.405	0.405	0.000	0.000	0.000	0.000
29	B	82	CYS	0	-0.013	0.008	31.557	0.449	0.449	0.000	0.000	0.000	0.000
30	B	83	GLN	0	0.090	0.031	33.494	-0.197	-0.197	0.000	0.000	0.000	0.000
31	B	84	ALA	0	0.046	0.009	35.930	0.033	0.033	0.000	0.000	0.000	0.000
32	B	85	CYS	0	-0.010	0.005	31.011	-0.124	-0.124	0.000	0.000	0.000	0.000
33	B	86	THR	0	-0.007	0.029	32.361	-0.059	-0.059	0.000	0.000	0.000	0.000
34	B	87	MET	0	0.065	0.019	33.383	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	88	GLN	0	0.017	0.009	31.997	0.072	0.072	0.000	0.000	0.000	0.000
36	B	89	SER	0	-0.053	-0.042	29.392	-0.308	-0.308	0.000	0.000	0.000	0.000
37	B	90	THR	0	0.061	0.044	30.966	-0.134	-0.134	0.000	0.000	0.000	0.000
38	B	91	GLU	-1	-0.817	-0.928	33.458	-8.298	-8.298	0.000	0.000	0.000	0.000
39	B	92	MET	0	-0.049	-0.023	28.789	-0.106	-0.106	0.000	0.000	0.000	0.000
40	B	93	ASP	-1	-0.846	-0.895	28.951	-10.747	-10.747	0.000	0.000	0.000	0.000
41	B	94	LYS	1	0.799	0.900	30.778	8.342	8.342	0.000	0.000	0.000	0.000
42	B	95	LEU	0	0.011	-0.005	30.198	0.042	0.042	0.000	0.000	0.000	0.000
43	B	96	GLN	0	0.005	-0.012	24.879	-0.562	-0.562	0.000	0.000	0.000	0.000
44	B	97	LYS	1	0.936	0.977	29.405	8.667	8.667	0.000	0.000	0.000	0.000
45	B	98	TYR	0	-0.033	-0.012	31.443	0.076	0.076	0.000	0.000	0.000	0.000
46	B	99	TYR	0	0.007	0.008	30.560	0.162	0.162	0.000	0.000	0.000	0.000
47	B	100	GLY	0	-0.008	0.006	28.821	-0.149	-0.149	0.000	0.000	0.000	0.000
48	B	101	LYS	1	0.976	0.975	25.588	10.907	10.907	0.000	0.000	0.000	0.000
49	B	102	ARG	1	0.912	0.953	26.488	9.235	9.235	0.000	0.000	0.000	0.000
50	B	103	ILE	0	-0.004	-0.014	27.015	0.093	0.093	0.000	0.000	0.000	0.000
51	B	104	TYR	0	0.005	0.013	17.532	-0.194	-0.194	0.000	0.000	0.000	0.000
52	B	105	LEU	0	0.030	0.026	23.399	0.311	0.311	0.000	0.000	0.000	0.000
53	B	106	LEU	0	0.009	0.007	18.265	-0.521	-0.521	0.000	0.000	0.000	0.000
54	B	107	LYS	1	0.942	0.986	21.272	12.514	12.514	0.000	0.000	0.000	0.000
55	B	108	VAL	0	-0.034	-0.036	20.548	-0.621	-0.621	0.000	0.000	0.000	0.000
56	B	109	ASP	-1	-0.868	-0.941	21.468	-12.292	-12.292	0.000	0.000	0.000	0.000
57	B	110	LEU	0	0.060	0.025	22.561	-0.373	-0.373	0.000	0.000	0.000	0.000
58	B	111	ASP	-1	-0.900	-0.940	24.406	-11.556	-11.556	0.000	0.000	0.000	0.000
59	B	112	LYS	1	0.906	0.931	19.505	13.858	13.858	0.000	0.000	0.000	0.000
60	B	113	ASN	0	-0.050	-0.037	18.555	-0.233	-0.233	0.000	0.000	0.000	0.000
61	B	114	GLU	-1	-0.756	-0.874	21.410	-11.449	-11.449	0.000	0.000	0.000	0.000
62	B	115	SER	0	0.005	-0.001	20.024	0.429	0.429	0.000	0.000	0.000	0.000
63	B	116	LEU	0	-0.013	-0.007	19.593	0.374	0.374	0.000	0.000	0.000	0.000
64	B	117	ALA	0	0.060	0.028	22.651	0.346	0.346	0.000	0.000	0.000	0.000
65	B	118	ARG	1	0.946	0.970	24.456	12.558	12.558	0.000	0.000	0.000	0.000
66	B	119	LYS	1	0.894	0.966	23.156	13.241	13.241	0.000	0.000	0.000	0.000
67	B	120	PHE	0	-0.033	-0.023	23.061	0.232	0.232	0.000	0.000	0.000	0.000
68	B	121	SER	0	-0.015	0.004	27.733	0.496	0.496	0.000	0.000	0.000	0.000
69	B	122	VAL	0	-0.067	-0.019	27.718	0.304	0.304	0.000	0.000	0.000	0.000
70	B	123	LYS	1	0.989	0.992	30.814	8.596	8.596	0.000	0.000	0.000	0.000
71	B	124	SER	0	-0.038	-0.025	33.028	0.172	0.172	0.000	0.000	0.000	0.000
72	B	125	LEU	0	0.004	0.042	29.145	-0.376	-0.376	0.000	0.000	0.000	0.000
73	B	126	PRO	0	0.050	0.002	31.402	0.232	0.232	0.000	0.000	0.000	0.000
74	B	127	THR	0	-0.027	-0.017	29.716	0.242	0.242	0.000	0.000	0.000	0.000
75	B	128	ILE	0	-0.034	-0.021	29.515	-0.424	-0.424	0.000	0.000	0.000	0.000
76	B	129	ILE	0	0.013	0.003	27.726	0.353	0.353	0.000	0.000	0.000	0.000
77	B	130	LEU	0	-0.030	-0.003	28.398	-0.314	-0.314	0.000	0.000	0.000	0.000
78	B	131	LEU	0	0.028	0.019	24.359	0.247	0.247	0.000	0.000	0.000	0.000
79	B	132	LYS	1	0.979	0.991	27.266	10.514	10.514	0.000	0.000	0.000	0.000
80	B	133	ASN	0	0.002	0.000	25.455	-0.135	-0.135	0.000	0.000	0.000	0.000
81	B	134	LYN	0	0.020	0.067	22.202	-0.146	-0.146	0.000	0.000	0.000	0.000
82	B	135	THR	0	0.017	0.029	25.833	0.248	0.248	0.000	0.000	0.000	0.000
83	B	136	MET	0	-0.018	-0.004	29.522	-0.063	-0.063	0.000	0.000	0.000	0.000
84	B	137	LEU	0	-0.061	-0.030	30.888	0.308	0.308	0.000	0.000	0.000	0.000
85	B	138	ALA	0	-0.016	-0.024	32.698	0.350	0.350	0.000	0.000	0.000	0.000
86	B	139	ARG	1	0.826	0.903	30.910	9.374	9.374	0.000	0.000	0.000	0.000
87	B	140	LYS	1	0.929	0.971	33.592	8.405	8.405	0.000	0.000	0.000	0.000
88	B	141	ASP	-1	-0.803	-0.901	33.826	-9.342	-9.342	0.000	0.000	0.000	0.000
89	B	142	HIS	0	0.044	0.022	35.565	0.158	0.158	0.000	0.000	0.000	0.000
90	B	143	PHE	0	0.021	0.011	36.073	-0.148	-0.148	0.000	0.000	0.000	0.000
91	B	144	VAL	0	-0.014	-0.009	35.359	0.197	0.197	0.000	0.000	0.000	0.000
92	B	145	SER	0	0.123	0.069	36.374	-0.232	-0.232	0.000	0.000	0.000	0.000
93	B	146	SER	0	-0.003	0.012	35.105	-0.158	-0.158	0.000	0.000	0.000	0.000
94	B	147	ASN	0	-0.014	-0.027	36.456	-0.219	-0.219	0.000	0.000	0.000	0.000
95	B	148	ASP	-1	-0.824	-0.909	39.244	-7.573	-7.573	0.000	0.000	0.000	0.000
96	B	149	LEU	0	-0.076	-0.049	33.038	-0.103	-0.103	0.000	0.000	0.000	0.000
97	B	150	ILE	0	-0.005	0.006	35.702	-0.131	-0.131	0.000	0.000	0.000	0.000
98	B	151	ALA	0	-0.013	0.001	36.856	-0.012	-0.012	0.000	0.000	0.000	0.000
99	B	152	LEU	0	0.000	-0.010	36.190	0.027	0.027	0.000	0.000	0.000	0.000
100	B	153	ILE	0	-0.016	-0.015	31.481	-0.066	-0.066	0.000	0.000	0.000	0.000
101	B	154	LYS	1	0.890	0.952	35.024	7.797	7.797	0.000	0.000	0.000	0.000
102	B	155	LYS	1	0.950	0.989	37.374	7.799	7.799	0.000	0.000	0.000	0.000
103	B	156	HIS	1	0.903	0.958	34.077	8.740	8.740	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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