FMO DATABASE

FMODB ID: 66VJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-727276.528826
FMO2-HF: Nuclear repulsion	687490.938187
FMO2-HF: Total energy	-39785.590638
FMO2-MP2: Total energy	-39901.542781

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.
-7.357	-0.36	2.154	-3.248	-5.901	-0.027

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 : 0.041 / q_NPA : -0.004

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	-0.800	-0.914	2.462	-10.540	-5.857	0.824	-2.556	-2.950	-0.026
4	A	4	LEU	0	-0.001	0.004	2.523	-0.389	0.969	1.305	-0.513	-2.150	-0.001
5	A	5	LYS	1	0.849	0.911	3.208	1.899	2.768	0.026	-0.175	-0.720	0.000
6	A	6	GLU	-1	-0.906	-0.919	5.523	-0.276	-0.276	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.014	0.006	7.999	0.304	0.304	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.035	-0.024	5.504	0.029	0.116	-0.001	-0.004	-0.081	0.000
9	A	9	LYS	1	0.909	0.962	9.139	0.730	0.730	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.002	0.025	11.303	0.099	0.099	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.027	0.008	14.137	0.024	0.024	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.075	-0.041	16.258	0.039	0.039	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.034	-0.007	17.640	0.025	0.025	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.075	0.046	15.360	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.060	-0.022	16.274	0.036	0.036	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.095	0.035	17.907	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.008	0.010	20.167	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.879	0.925	21.090	0.155	0.155	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.042	0.043	17.617	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.058	0.029	21.461	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.031	-0.022	24.321	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.033	-0.006	23.029	0.011	0.011	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.016	0.012	20.679	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.027	-0.016	24.834	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.006	-0.012	28.185	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.020	0.017	23.149	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.005	-0.006	27.370	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.916	0.954	30.016	0.075	0.075	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.823	0.927	31.396	0.097	0.097	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.890	0.910	32.620	0.061	0.061	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.021	0.018	34.711	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.030	-0.007	36.509	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.062	0.018	34.241	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.004	-0.016	36.601	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.006	-0.001	37.670	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.034	0.025	31.631	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.046	-0.035	33.536	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.940	0.971	34.781	0.039	0.039	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.015	-0.001	33.057	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.051	-0.027	28.666	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.927	-0.943	30.659	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.020	0.024	28.235	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.045	0.013	32.200	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.036	-0.011	33.569	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.044	0.027	34.553	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.009	-0.001	29.311	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.003	0.014	29.726	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.800	-0.885	30.846	-0.074	-0.074	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.007	-0.004	29.182	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.026	0.014	24.336	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.016	0.008	27.240	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.868	0.914	29.696	0.071	0.071	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.076	-0.030	23.515	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.030	0.015	23.655	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.805	-0.868	26.397	-0.089	-0.089	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.913	0.961	26.674	0.114	0.114	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.068	-0.044	23.342	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.055	0.037	25.542	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.004	0.010	22.259	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.023	-0.032	26.462	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.875	0.939	29.757	0.083	0.083	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.081	-0.077	33.363	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.014	-0.008	36.124	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.863	0.920	39.889	0.050	0.050	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.036	0.016	42.617	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.020	-0.011	45.192	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.025	0.058	48.528	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.859	-0.949	50.516	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.869	0.905	48.760	0.034	0.034	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.001	0.006	47.472	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.953	0.984	42.932	0.041	0.041	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.010	0.022	38.030	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.040	0.002	37.489	0.001	0.001	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.041	0.019	31.798	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.803	-0.878	33.561	-0.071	-0.071	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.023	0.023	25.578	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.025	-0.020	28.458	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.790	-0.902	28.095	-0.102	-0.102	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.038	0.030	22.503	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.052	0.014	23.951	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.096	-0.056	23.508	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.885	-0.926	22.035	-0.167	-0.167	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.832	-0.902	19.303	-0.286	-0.286	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.020	-0.008	18.456	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.944	0.973	18.625	0.126	0.126	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.834	0.911	15.803	0.212	0.212	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.039	0.018	12.794	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.031	-0.033	13.995	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.048	-0.032	14.633	0.020	0.020	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.006	-0.023	9.870	0.026	0.026	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.014	-0.018	9.802	-0.088	-0.088	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.794	0.882	11.614	0.211	0.211	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.021	0.017	9.363	0.042	0.042	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.005	-0.004	5.849	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.038	-0.026	8.240	0.142	0.142	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.845	-0.902	11.567	-0.123	-0.123	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.012	0.006	8.637	0.040	0.040	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.100	-0.056	8.407	0.120	0.120	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.934	-0.945	10.892	0.085	0.085	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.070	-0.027	13.925	0.025	0.025	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

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