FMO DATABASE

FMODB ID: ZY5MN

Calculation Name: 1UB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UB9

Chain ID: A

ChEMBL ID:

UniProt ID: O58788

Base Structure: X-ray

Registration Date: 2023-06-20

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-727798.532866
FMO2-HF: Nuclear repulsion	688012.754252
FMO2-HF: Total energy	-39785.778614
FMO2-MP2: Total energy	-39901.694421

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-12.815	-10.978	11.087	-5.428	-7.496	-0.056

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.012

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	3	GLU	-1	-0.762	-0.895	1.878	-15.225	-15.386	8.855	-4.461	-4.233	-0.057
4	A	4	LEU	0	0.013	0.009	2.500	-0.189	0.867	2.193	-0.762	-2.486	0.000
5	A	5	LYS	1	0.815	0.890	3.086	1.111	1.973	0.040	-0.201	-0.702	0.001
6	A	6	GLU	-1	-0.886	-0.908	5.970	-0.285	-0.285	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.002	0.005	7.090	0.305	0.305	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.037	-0.026	5.791	0.074	0.154	-0.001	-0.004	-0.075	0.000
9	A	9	LYS	1	0.921	0.967	9.219	0.589	0.589	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.003	0.014	11.484	0.082	0.082	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.003	-0.007	13.980	0.032	0.032	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.075	-0.039	16.180	0.033	0.033	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.012	-0.007	17.056	0.028	0.028	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.069	0.031	15.202	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.041	-0.015	16.089	0.032	0.032	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.078	0.035	18.369	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.019	0.015	20.538	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.889	0.934	21.354	0.128	0.128	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.054	0.039	17.215	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.035	0.021	21.102	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.021	-0.020	24.201	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.043	-0.010	22.468	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.030	0.015	20.318	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.021	-0.011	24.525	0.008	0.008	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.004	-0.010	27.781	0.006	0.006	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.005	0.013	22.773	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.024	-0.012	26.939	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.899	0.944	29.365	0.071	0.071	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.785	0.893	30.973	0.091	0.091	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.876	0.904	32.093	0.057	0.057	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.033	0.026	34.225	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.014	-0.010	36.024	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.048	0.020	34.355	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.000	-0.014	36.243	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.002	-0.001	37.078	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.036	0.017	31.099	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.042	-0.038	33.070	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.921	0.971	34.973	0.035	0.035	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.015	-0.005	32.399	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.035	-0.019	28.088	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.931	-0.943	30.562	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.019	0.018	28.524	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.058	0.024	32.462	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.032	-0.007	33.684	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.059	0.032	34.648	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.008	0.002	29.303	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.005	0.020	29.950	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.806	-0.889	30.923	-0.064	-0.064	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.014	-0.010	29.562	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.014	0.015	24.859	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.009	0.006	27.108	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.888	0.909	29.306	0.060	0.060	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.075	-0.025	23.648	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.036	0.016	23.013	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.816	-0.879	26.051	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.897	0.945	27.176	0.096	0.096	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.043	-0.024	23.176	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.054	0.037	25.268	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	0.028	21.688	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.028	-0.032	25.762	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.887	0.943	29.011	0.077	0.077	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.071	-0.068	32.686	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.000	-0.021	35.578	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.867	0.916	39.331	0.044	0.044	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.029	0.018	42.029	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.028	-0.008	44.579	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.030	0.040	48.010	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.863	-0.938	50.089	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.874	0.926	48.498	0.031	0.031	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.023	0.021	47.292	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.921	0.965	42.471	0.037	0.037	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.008	0.011	37.691	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.051	-0.004	37.098	0.001	0.001	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.045	0.019	31.548	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.786	-0.867	32.771	-0.065	-0.065	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.017	0.022	24.836	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.029	-0.042	27.665	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.767	-0.871	27.336	-0.097	-0.097	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.065	0.041	21.846	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.062	0.024	23.259	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.081	-0.046	22.954	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.877	-0.899	21.245	-0.160	-0.160	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.822	-0.914	18.463	-0.274	-0.274	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.031	-0.013	17.850	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.884	0.930	18.157	0.131	0.131	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.820	0.904	15.273	0.199	0.199	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.058	0.032	12.139	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.022	-0.021	13.274	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.040	-0.023	13.846	0.020	0.020	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.015	-0.034	9.110	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.027	-0.019	9.147	-0.101	-0.101	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.815	0.888	10.992	0.225	0.225	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.017	0.012	8.628	0.043	0.043	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.002	-0.003	5.380	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.052	-0.029	7.886	0.195	0.195	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.829	-0.895	11.526	-0.139	-0.139	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.025	-0.007	8.368	0.056	0.056	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.074	-0.045	7.923	0.124	0.124	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.939	-0.951	10.872	0.074	0.074	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.085	-0.030	13.545	0.011	0.011	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

Support

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