FMO DATABASE

FMODB ID: N1LYQ

Calculation Name: 3U28-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U28

Chain ID: C

ChEMBL ID:

UniProt ID: P33322

Base Structure: X-ray

Registration Date: 2023-03-14

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-646982.428454
FMO2-HF: Nuclear repulsion	610912.450528
FMO2-HF: Total energy	-36069.977926
FMO2-MP2: Total energy	-36174.431641

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(C:33:PRO)

Summations of interaction energy for fragment #1(C:33:PRO)

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.
-5.698	-0.318	1.568	-2.399	-4.549	-0.006

Interaction energy analysis for fragmet #1(C:33:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.013

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	C	35	ASP	-1	-0.827	-0.908	3.800	-3.199	-1.701	0.018	-0.660	-0.856	0.003
4	C	36	THR	0	-0.114	-0.060	6.059	0.045	0.045	0.000	0.000	0.000	0.000
5	C	37	VAL	0	-0.018	0.002	5.462	0.241	0.241	0.000	0.000	0.000	0.000
6	C	38	LEU	0	0.000	-0.010	7.510	-0.123	-0.123	0.000	0.000	0.000	0.000
7	C	39	GLU	-1	-0.848	-0.931	11.143	0.092	0.092	0.000	0.000	0.000	0.000
8	C	40	MET	0	-0.022	0.002	12.617	0.021	0.021	0.000	0.000	0.000	0.000
9	C	41	GLY	0	0.017	0.004	14.350	-0.014	-0.014	0.000	0.000	0.000	0.000
10	C	42	ALA	0	-0.002	0.004	15.848	-0.012	-0.012	0.000	0.000	0.000	0.000
11	C	43	PHE	0	0.021	0.000	18.188	0.008	0.008	0.000	0.000	0.000	0.000
12	C	44	LEU	0	-0.018	0.000	19.554	-0.012	-0.012	0.000	0.000	0.000	0.000
13	C	45	HIS	1	0.937	0.959	22.523	-0.088	-0.088	0.000	0.000	0.000	0.000
14	C	46	PRO	0	0.010	-0.001	21.758	0.011	0.011	0.000	0.000	0.000	0.000
15	C	47	CYS	0	-0.050	-0.031	22.540	-0.011	-0.011	0.000	0.000	0.000	0.000
16	C	48	GLU	-1	-0.933	-0.961	23.468	0.090	0.090	0.000	0.000	0.000	0.000
17	C	49	GLY	0	-0.011	0.004	21.739	0.004	0.004	0.000	0.000	0.000	0.000
18	C	50	ASP	-1	-0.875	-0.919	18.808	0.172	0.172	0.000	0.000	0.000	0.000
19	C	51	ILE	0	-0.058	-0.034	14.775	-0.024	-0.024	0.000	0.000	0.000	0.000
20	C	52	VAL	0	-0.014	-0.006	18.697	0.017	0.017	0.000	0.000	0.000	0.000
21	C	53	CYS	0	-0.013	0.008	17.173	-0.010	-0.010	0.000	0.000	0.000	0.000
22	C	54	ARG	1	0.904	0.950	19.818	-0.063	-0.063	0.000	0.000	0.000	0.000
23	C	55	SER	0	-0.011	-0.013	18.823	0.011	0.011	0.000	0.000	0.000	0.000
24	C	56	ILE	0	-0.053	-0.028	15.970	-0.020	-0.020	0.000	0.000	0.000	0.000
25	C	57	ASN	0	0.013	-0.002	14.989	-0.017	-0.017	0.000	0.000	0.000	0.000
26	C	58	THR	0	-0.008	-0.011	18.342	-0.007	-0.007	0.000	0.000	0.000	0.000
27	C	59	LYS	1	0.852	0.937	17.769	-0.121	-0.121	0.000	0.000	0.000	0.000
28	C	60	ILE	0	0.041	0.017	19.009	0.007	0.007	0.000	0.000	0.000	0.000
29	C	61	PRO	0	0.040	0.024	15.143	0.014	0.014	0.000	0.000	0.000	0.000
30	C	62	TYR	0	-0.035	-0.026	14.594	-0.031	-0.031	0.000	0.000	0.000	0.000
31	C	63	PHE	0	0.081	0.034	15.482	0.035	0.035	0.000	0.000	0.000	0.000
32	C	64	ASN	0	-0.049	-0.035	13.887	0.015	0.015	0.000	0.000	0.000	0.000
33	C	65	ALA	0	-0.015	0.000	11.566	0.089	0.089	0.000	0.000	0.000	0.000
34	C	66	PRO	0	-0.020	-0.014	6.414	-0.092	-0.092	0.000	0.000	0.000	0.000
35	C	67	ILE	0	0.012	0.015	8.415	0.017	0.017	0.000	0.000	0.000	0.000
36	C	68	TYR	0	-0.049	-0.029	2.542	-0.117	0.874	0.328	-0.313	-1.006	0.000
37	C	69	LEU	0	0.073	0.035	7.243	-0.087	-0.087	0.000	0.000	0.000	0.000
38	C	70	GLU	-1	-0.891	-0.943	7.237	-0.204	-0.204	0.000	0.000	0.000	0.000
39	C	71	ASN	0	-0.056	-0.031	7.481	-0.120	-0.120	0.000	0.000	0.000	0.000
40	C	72	LYS	1	0.840	0.906	2.218	0.104	1.141	0.754	-0.523	-1.268	0.000
41	C	73	THR	0	0.020	0.013	2.839	-2.208	-0.523	0.468	-0.876	-1.277	-0.009
42	C	74	GLN	0	-0.060	-0.027	3.989	0.307	0.476	0.000	-0.027	-0.142	0.000
43	C	75	VAL	0	0.011	0.002	5.469	-0.166	-0.166	0.000	0.000	0.000	0.000
44	C	76	GLY	0	0.073	0.031	8.822	-0.088	-0.088	0.000	0.000	0.000	0.000
45	C	77	LYS	1	0.856	0.947	9.311	-0.182	-0.182	0.000	0.000	0.000	0.000
46	C	78	VAL	0	-0.011	0.004	11.780	-0.076	-0.076	0.000	0.000	0.000	0.000
47	C	79	ASP	-1	-0.969	-0.983	14.737	0.217	0.217	0.000	0.000	0.000	0.000
48	C	80	GLU	-1	-0.919	-0.952	17.973	0.137	0.137	0.000	0.000	0.000	0.000
49	C	81	ILE	0	-0.033	-0.023	18.925	0.009	0.009	0.000	0.000	0.000	0.000
50	C	82	LEU	0	-0.010	-0.002	22.061	-0.013	-0.013	0.000	0.000	0.000	0.000
51	C	83	GLY	0	0.030	0.023	25.085	0.002	0.002	0.000	0.000	0.000	0.000
52	C	84	PRO	0	-0.008	0.004	27.748	0.002	0.002	0.000	0.000	0.000	0.000
53	C	85	LEU	0	0.034	-0.012	27.774	0.004	0.004	0.000	0.000	0.000	0.000
54	C	86	ASN	0	-0.076	-0.029	26.966	0.006	0.006	0.000	0.000	0.000	0.000
55	C	87	GLU	-1	-0.846	-0.921	26.076	0.058	0.058	0.000	0.000	0.000	0.000
56	C	88	VAL	0	-0.004	0.016	21.686	0.003	0.003	0.000	0.000	0.000	0.000
57	C	89	PHE	0	0.007	-0.008	22.120	-0.003	-0.003	0.000	0.000	0.000	0.000
58	C	90	PHE	0	-0.018	-0.014	14.821	0.010	0.010	0.000	0.000	0.000	0.000
59	C	91	THR	0	0.063	0.035	18.937	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	92	ILE	0	-0.019	-0.006	12.899	0.037	0.037	0.000	0.000	0.000	0.000
61	C	93	LYS	1	1.024	1.010	15.215	-0.253	-0.253	0.000	0.000	0.000	0.000
62	C	94	CYS	0	-0.049	-0.027	13.600	0.052	0.052	0.000	0.000	0.000	0.000
63	C	95	GLY	0	-0.011	-0.014	11.242	0.007	0.007	0.000	0.000	0.000	0.000
64	C	96	ASP	-1	-0.919	-0.973	12.305	0.087	0.087	0.000	0.000	0.000	0.000
65	C	97	GLY	0	-0.012	-0.001	12.871	-0.004	-0.004	0.000	0.000	0.000	0.000
66	C	98	VAL	0	-0.044	-0.001	11.242	-0.021	-0.021	0.000	0.000	0.000	0.000
67	C	99	GLN	0	0.019	0.006	14.523	0.003	0.003	0.000	0.000	0.000	0.000
68	C	100	ALA	0	0.063	0.022	17.707	-0.007	-0.007	0.000	0.000	0.000	0.000
69	C	101	THR	0	-0.057	-0.047	18.773	-0.004	-0.004	0.000	0.000	0.000	0.000
70	C	102	SER	0	-0.069	-0.027	17.439	-0.011	-0.011	0.000	0.000	0.000	0.000
71	C	103	PHE	0	0.003	0.015	13.362	-0.005	-0.005	0.000	0.000	0.000	0.000
72	C	104	LYS	1	0.910	0.956	19.074	0.003	0.003	0.000	0.000	0.000	0.000
73	C	105	GLU	-1	-0.921	-0.979	20.508	0.049	0.049	0.000	0.000	0.000	0.000
74	C	106	GLY	0	-0.051	-0.020	20.844	-0.009	-0.009	0.000	0.000	0.000	0.000
75	C	107	ASP	-1	-0.846	-0.912	16.316	0.009	0.009	0.000	0.000	0.000	0.000
76	C	108	LYS	1	0.899	0.950	14.129	0.001	0.001	0.000	0.000	0.000	0.000
77	C	109	PHE	0	-0.007	0.000	11.541	-0.007	-0.007	0.000	0.000	0.000	0.000
78	C	110	TYR	0	0.011	-0.001	8.103	-0.026	-0.026	0.000	0.000	0.000	0.000
79	C	111	ILE	0	0.014	0.003	8.715	0.183	0.183	0.000	0.000	0.000	0.000
80	C	112	ALA	0	0.052	0.030	7.201	-0.078	-0.078	0.000	0.000	0.000	0.000
81	C	113	ALA	0	0.039	0.002	8.611	-0.092	-0.092	0.000	0.000	0.000	0.000
82	C	114	ASP	-1	-0.931	-0.966	10.147	0.536	0.536	0.000	0.000	0.000	0.000
83	C	115	LYS	1	0.897	0.952	9.555	-0.676	-0.676	0.000	0.000	0.000	0.000
84	C	116	LEU	0	0.007	0.010	13.225	-0.019	-0.019	0.000	0.000	0.000	0.000
85	C	117	LEU	0	-0.020	-0.016	15.988	-0.023	-0.023	0.000	0.000	0.000	0.000
86	C	118	PRO	0	-0.007	0.004	19.767	-0.003	-0.003	0.000	0.000	0.000	0.000
87	C	119	ILE	0	0.102	0.033	22.507	0.002	0.002	0.000	0.000	0.000	0.000
88	C	120	GLU	-1	-0.933	-0.968	24.862	0.069	0.069	0.000	0.000	0.000	0.000
89	C	121	ARG	1	0.895	0.953	21.775	-0.130	-0.130	0.000	0.000	0.000	0.000
90	C	122	PHE	0	-0.018	-0.011	22.574	0.002	0.002	0.000	0.000	0.000	0.000
91	C	123	LEU	0	-0.039	-0.008	28.211	-0.005	-0.005	0.000	0.000	0.000	0.000
92	C	124	PRO	0	0.009	0.014	31.300	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:33:PRO)