FMO DATABASE

FMODB ID: V2491

Calculation Name: 1UB9-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-726970.799455
FMO2-HF: Nuclear repulsion	687186.471791
FMO2-HF: Total energy	-39784.327665
FMO2-MP2: Total energy	-39900.299089

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.
-2.157	3.071	1.569	-1.949	-4.849	-0.005

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 : 0.038 / q_NPA : -0.007

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	-0.804	-0.911	3.221	-5.331	-2.537	0.004	-1.224	-1.574	-0.004
4	A	4	LEU	0	-0.013	0.001	2.414	-0.415	0.883	1.526	-0.534	-2.291	-0.002
5	A	5	LYS	1	0.945	0.952	3.206	2.215	3.157	0.039	-0.180	-0.802	0.001
6	A	6	GLU	-1	-0.933	-0.950	5.298	-0.495	-0.397	0.000	-0.004	-0.093	0.000
7	A	7	ILE	0	0.008	0.013	7.905	0.381	0.381	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.051	-0.029	5.384	0.082	0.178	0.000	-0.007	-0.089	0.000
9	A	9	LYS	1	0.918	0.965	8.969	0.780	0.780	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.000	0.024	11.219	0.117	0.117	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.026	0.009	13.882	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.071	-0.041	16.150	0.045	0.045	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.032	-0.012	17.265	0.028	0.028	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.078	0.051	15.062	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.059	-0.024	15.941	0.039	0.039	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.092	0.036	17.900	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.017	0.016	20.063	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.867	0.925	20.624	0.176	0.176	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.046	0.045	17.474	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.062	0.030	21.193	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.030	-0.019	24.128	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.032	-0.011	22.901	0.014	0.014	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.019	0.016	20.784	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.034	-0.018	24.830	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.004	-0.019	28.222	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.011	0.017	22.804	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.030	-0.012	27.371	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.926	0.958	30.015	0.108	0.108	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.846	0.957	31.268	0.124	0.124	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.954	0.947	32.622	0.078	0.078	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.015	0.013	34.666	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.027	-0.009	36.359	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.078	0.030	34.247	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.012	-0.020	36.274	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.004	-0.005	37.478	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.036	0.027	31.370	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.044	-0.031	33.304	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.942	0.969	34.681	0.050	0.050	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.019	0.001	32.987	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.052	-0.031	28.440	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.923	-0.945	30.587	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.018	0.024	28.037	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.036	0.009	32.135	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.034	-0.010	33.480	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.046	0.026	34.466	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.027	0.004	29.257	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.015	0.013	29.603	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.822	-0.895	30.666	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.013	-0.005	28.913	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.016	0.005	23.780	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.014	0.009	27.008	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.905	0.926	29.443	0.075	0.075	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.077	-0.025	23.383	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.022	0.006	23.489	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.801	-0.873	26.121	-0.103	-0.103	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.905	0.956	25.980	0.122	0.122	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.066	-0.042	23.385	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.058	0.039	25.238	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.002	0.017	21.911	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.013	-0.023	26.224	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.918	0.975	29.506	0.105	0.105	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.079	-0.065	33.059	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.001	-0.014	35.773	0.005	0.005	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.879	0.940	39.537	0.057	0.057	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.033	0.016	42.405	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.006	-0.023	44.908	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.006	0.048	48.278	0.002	0.002	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.859	-0.968	50.294	-0.038	-0.038	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.915	0.944	48.351	0.043	0.043	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.021	-0.008	47.126	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.957	0.987	42.638	0.052	0.052	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.016	0.021	37.638	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.044	-0.003	37.277	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.035	0.018	31.456	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.869	-0.942	33.492	-0.092	-0.092	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.014	0.020	25.671	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.027	-0.031	28.457	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.817	-0.929	28.103	-0.130	-0.130	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.030	0.024	22.242	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.046	0.009	23.962	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.097	-0.056	23.515	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.915	-0.963	22.170	-0.210	-0.210	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.860	-0.915	19.390	-0.354	-0.354	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.015	-0.006	18.463	-0.040	-0.040	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.947	0.972	18.627	0.163	0.163	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.908	0.963	15.763	0.274	0.274	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.038	0.016	12.643	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.031	-0.035	13.995	-0.045	-0.045	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.050	-0.026	14.636	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.030	0.016	9.941	0.013	0.013	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.005	-0.022	9.799	-0.132	-0.132	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.891	0.958	11.603	0.300	0.300	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.034	0.029	9.316	0.036	0.036	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.020	-0.013	6.295	-0.060	-0.060	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.041	-0.028	8.226	0.133	0.133	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.899	-0.958	11.549	-0.259	-0.259	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.036	-0.007	8.621	0.051	0.051	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.119	-0.067	8.744	0.108	0.108	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.959	-0.957	10.919	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	100	LEU	-1	-1.017	-1.002	14.130	-0.004	-0.004	0.000	0.000	0.000	0.000

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Overview

Highlights

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