FMO DATABASE

FMODB ID: 3963L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-814020.24956
FMO2-HF: Nuclear repulsion	771696.027193
FMO2-HF: Total energy	-42324.222367
FMO2-MP2: Total energy	-42445.760077

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.
98.717	98.104	8.999	-4.673	-3.713	-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 : 0.976 / q_NPA : 0.987

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	0.059	0.037	1.851	-9.078	-9.724	9.000	-4.667	-3.687	-0.030
4	B	57	GLN	0	0.058	0.037	5.005	0.061	0.094	-0.001	-0.006	-0.026	0.000
5	B	58	ASN	0	-0.046	-0.025	8.559	0.483	0.483	0.000	0.000	0.000	0.000
6	B	59	GLY	0	0.069	0.036	11.233	0.962	0.962	0.000	0.000	0.000	0.000
7	B	60	SER	0	0.007	-0.023	14.983	-0.191	-0.191	0.000	0.000	0.000	0.000
8	B	61	ASN	0	-0.047	-0.009	17.760	0.193	0.193	0.000	0.000	0.000	0.000
9	B	62	ILE	0	-0.007	-0.013	19.406	0.961	0.961	0.000	0.000	0.000	0.000
10	B	63	ILE	0	0.026	0.009	18.598	-0.784	-0.784	0.000	0.000	0.000	0.000
11	B	64	ASN	0	-0.012	-0.019	17.595	-0.201	-0.201	0.000	0.000	0.000	0.000
12	B	65	GLY	0	-0.003	-0.001	16.181	-0.475	-0.475	0.000	0.000	0.000	0.000
13	B	66	VAL	0	-0.017	-0.003	12.609	0.587	0.587	0.000	0.000	0.000	0.000
14	B	67	ASN	0	0.008	0.005	12.641	-0.819	-0.819	0.000	0.000	0.000	0.000
15	B	68	MET	0	0.044	0.059	14.123	-0.175	-0.175	0.000	0.000	0.000	0.000
16	B	69	LYS	1	0.899	0.917	16.955	15.243	15.243	0.000	0.000	0.000	0.000
17	B	70	ASN	0	0.044	0.027	20.761	-0.406	-0.406	0.000	0.000	0.000	0.000
18	B	71	THR	0	0.005	0.017	23.730	0.591	0.591	0.000	0.000	0.000	0.000
19	B	72	VAL	0	0.018	0.015	25.554	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	73	ILE	0	-0.027	-0.015	21.897	-0.350	-0.350	0.000	0.000	0.000	0.000
21	B	74	VAL	0	-0.003	-0.008	25.203	0.470	0.470	0.000	0.000	0.000	0.000
22	B	75	LEU	0	0.018	0.021	22.322	-0.372	-0.372	0.000	0.000	0.000	0.000
23	B	76	TYR	0	0.001	-0.028	24.740	0.621	0.621	0.000	0.000	0.000	0.000
24	B	77	PHE	0	0.041	0.025	23.684	-0.383	-0.383	0.000	0.000	0.000	0.000
25	B	78	PHE	0	0.018	-0.023	23.293	0.561	0.561	0.000	0.000	0.000	0.000
26	B	79	ALA	0	0.051	0.026	26.693	-0.346	-0.346	0.000	0.000	0.000	0.000
27	B	80	LYS	1	0.751	0.836	24.198	12.605	12.605	0.000	0.000	0.000	0.000
28	B	81	TRP	0	0.031	0.014	28.422	0.407	0.407	0.000	0.000	0.000	0.000
29	B	82	CYS	0	-0.011	0.025	31.340	0.460	0.460	0.000	0.000	0.000	0.000
30	B	83	GLN	0	0.098	0.047	33.276	-0.084	-0.084	0.000	0.000	0.000	0.000
31	B	84	ALA	0	0.058	0.032	35.813	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	85	CYS	0	-0.036	-0.019	30.366	-0.137	-0.137	0.000	0.000	0.000	0.000
33	B	86	THR	0	-0.029	-0.005	31.686	-0.175	-0.175	0.000	0.000	0.000	0.000
34	B	87	MET	0	0.046	0.024	33.323	-0.016	-0.016	0.000	0.000	0.000	0.000
35	B	88	GLN	0	0.017	-0.003	31.628	0.088	0.088	0.000	0.000	0.000	0.000
36	B	89	SER	0	-0.020	-0.028	29.426	-0.371	-0.371	0.000	0.000	0.000	0.000
37	B	90	THR	0	0.071	0.053	30.712	-0.164	-0.164	0.000	0.000	0.000	0.000
38	B	91	GLU	-1	-0.800	-0.873	33.325	-8.317	-8.317	0.000	0.000	0.000	0.000
39	B	92	MET	0	-0.040	-0.012	28.642	-0.096	-0.096	0.000	0.000	0.000	0.000
40	B	93	ASP	-1	-0.827	-0.904	27.863	-11.150	-11.150	0.000	0.000	0.000	0.000
41	B	94	LYS	1	0.788	0.865	30.226	8.308	8.308	0.000	0.000	0.000	0.000
42	B	95	LEU	0	-0.002	0.006	30.326	0.098	0.098	0.000	0.000	0.000	0.000
43	B	96	GLN	0	-0.075	-0.051	24.857	-0.400	-0.400	0.000	0.000	0.000	0.000
44	B	97	LYS	1	0.954	0.979	28.925	8.773	8.773	0.000	0.000	0.000	0.000
45	B	98	TYR	0	0.004	0.030	31.205	0.172	0.172	0.000	0.000	0.000	0.000
46	B	99	TYR	0	0.028	-0.006	30.484	0.156	0.156	0.000	0.000	0.000	0.000
47	B	100	GLY	0	0.074	0.055	28.741	-0.111	-0.111	0.000	0.000	0.000	0.000
48	B	101	LYS	1	0.835	0.893	25.436	11.338	11.338	0.000	0.000	0.000	0.000
49	B	102	ARG	1	0.944	0.974	26.323	9.226	9.226	0.000	0.000	0.000	0.000
50	B	103	ILE	0	-0.025	-0.008	27.014	0.154	0.154	0.000	0.000	0.000	0.000
51	B	104	TYR	0	0.021	0.009	17.334	-0.153	-0.153	0.000	0.000	0.000	0.000
52	B	105	LEU	0	0.006	0.007	23.642	0.226	0.226	0.000	0.000	0.000	0.000
53	B	106	LEU	0	0.016	0.017	18.503	-0.442	-0.442	0.000	0.000	0.000	0.000
54	B	107	LYS	1	0.915	0.965	21.719	12.138	12.138	0.000	0.000	0.000	0.000
55	B	108	VAL	0	-0.001	-0.010	19.820	-0.735	-0.735	0.000	0.000	0.000	0.000
56	B	109	ASP	-1	-0.765	-0.876	21.634	-12.185	-12.185	0.000	0.000	0.000	0.000
57	B	110	LEU	0	0.060	0.021	22.618	-0.479	-0.479	0.000	0.000	0.000	0.000
58	B	111	ASP	-1	-0.776	-0.864	24.533	-11.578	-11.578	0.000	0.000	0.000	0.000
59	B	112	LYS	1	0.862	0.919	19.416	13.535	13.535	0.000	0.000	0.000	0.000
60	B	113	ASN	0	-0.020	-0.009	19.293	-0.494	-0.494	0.000	0.000	0.000	0.000
61	B	114	GLU	-1	-0.753	-0.853	21.166	-11.961	-11.961	0.000	0.000	0.000	0.000
62	B	115	SER	0	0.031	0.003	20.815	0.558	0.558	0.000	0.000	0.000	0.000
63	B	116	LEU	0	-0.037	-0.006	19.621	0.175	0.175	0.000	0.000	0.000	0.000
64	B	117	ALA	0	0.034	0.007	22.355	0.394	0.394	0.000	0.000	0.000	0.000
65	B	118	ARG	1	0.902	0.937	25.037	12.538	12.538	0.000	0.000	0.000	0.000
66	B	119	LYS	1	0.944	0.986	22.330	13.399	13.399	0.000	0.000	0.000	0.000
67	B	120	PHE	0	-0.022	-0.012	22.426	0.168	0.168	0.000	0.000	0.000	0.000
68	B	121	SER	0	-0.004	0.008	27.379	0.495	0.495	0.000	0.000	0.000	0.000
69	B	122	VAL	0	-0.069	-0.022	27.612	0.357	0.357	0.000	0.000	0.000	0.000
70	B	123	LYS	1	0.913	0.946	30.654	8.879	8.879	0.000	0.000	0.000	0.000
71	B	124	SER	0	0.002	-0.010	33.159	0.182	0.182	0.000	0.000	0.000	0.000
72	B	125	LEU	0	-0.006	0.019	29.001	-0.360	-0.360	0.000	0.000	0.000	0.000
73	B	126	PRO	0	0.013	-0.015	31.311	0.225	0.225	0.000	0.000	0.000	0.000
74	B	127	THR	0	-0.037	-0.017	30.040	0.310	0.310	0.000	0.000	0.000	0.000
75	B	128	ILE	0	-0.019	-0.014	29.278	-0.459	-0.459	0.000	0.000	0.000	0.000
76	B	129	ILE	0	-0.012	-0.013	27.715	0.366	0.366	0.000	0.000	0.000	0.000
77	B	130	LEU	0	-0.013	0.007	27.946	-0.375	-0.375	0.000	0.000	0.000	0.000
78	B	131	LEU	0	0.009	0.003	24.295	0.145	0.145	0.000	0.000	0.000	0.000
79	B	132	LYS	1	0.932	0.942	26.773	10.785	10.785	0.000	0.000	0.000	0.000
80	B	133	ASN	0	0.014	0.015	25.896	0.117	0.117	0.000	0.000	0.000	0.000
81	B	134	LYN	0	-0.003	0.008	22.136	-0.196	-0.196	0.000	0.000	0.000	0.000
82	B	135	THR	0	0.033	0.042	25.990	0.233	0.233	0.000	0.000	0.000	0.000
83	B	136	MET	0	0.007	-0.008	29.317	-0.253	-0.253	0.000	0.000	0.000	0.000
84	B	137	LEU	0	-0.059	-0.027	30.641	0.342	0.342	0.000	0.000	0.000	0.000
85	B	138	ALA	0	0.005	-0.009	32.532	0.370	0.370	0.000	0.000	0.000	0.000
86	B	139	ARG	1	0.766	0.825	30.886	9.387	9.387	0.000	0.000	0.000	0.000
87	B	140	LYS	1	0.879	0.948	33.365	8.373	8.373	0.000	0.000	0.000	0.000
88	B	141	ASP	-1	-0.745	-0.813	33.814	-9.398	-9.398	0.000	0.000	0.000	0.000
89	B	142	HIS	0	0.069	0.037	35.275	0.201	0.201	0.000	0.000	0.000	0.000
90	B	143	PHE	0	0.039	0.015	35.969	-0.167	-0.167	0.000	0.000	0.000	0.000
91	B	144	VAL	0	-0.020	-0.004	35.146	0.247	0.247	0.000	0.000	0.000	0.000
92	B	145	SER	0	0.032	-0.004	36.348	-0.219	-0.219	0.000	0.000	0.000	0.000
93	B	146	SER	0	-0.004	-0.038	34.337	-0.110	-0.110	0.000	0.000	0.000	0.000
94	B	147	ASN	0	-0.003	-0.008	36.318	-0.213	-0.213	0.000	0.000	0.000	0.000
95	B	148	ASP	-1	-0.815	-0.860	38.380	-7.729	-7.729	0.000	0.000	0.000	0.000
96	B	149	LEU	0	-0.003	-0.007	32.779	-0.064	-0.064	0.000	0.000	0.000	0.000
97	B	150	ILE	0	-0.030	-0.010	35.376	-0.110	-0.110	0.000	0.000	0.000	0.000
98	B	151	ALA	0	0.028	0.016	36.778	-0.039	-0.039	0.000	0.000	0.000	0.000
99	B	152	LEU	0	-0.039	-0.025	35.621	0.031	0.031	0.000	0.000	0.000	0.000
100	B	153	ILE	0	-0.006	-0.012	31.205	-0.106	-0.106	0.000	0.000	0.000	0.000
101	B	154	LYS	1	0.934	0.973	34.620	8.029	8.029	0.000	0.000	0.000	0.000
102	B	155	LYS	1	0.948	0.984	37.276	7.742	7.742	0.000	0.000	0.000	0.000
103	B	156	HIS	1	0.881	0.954	33.705	8.691	8.691	0.000	0.000	0.000	0.000

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