FMO DATABASE

FMODB ID: 1N3YZ

Calculation Name: 1UB4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UB4

Chain ID: A

ChEMBL ID:

UniProt ID: P0AE72

Base Structure: X-ray

Registration Date: 2023-09-23

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-749413.426913
FMO2-HF: Nuclear repulsion	709210.959516
FMO2-HF: Total energy	-40202.467397
FMO2-MP2: Total energy	-40317.232601

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-0.927	1.178	3.501	-1.449	-4.156	-0.002

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.003

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	A	4	ARG	1	0.904	0.930	2.311	-1.609	0.425	3.502	-1.432	-4.103	-0.002
4	A	5	TYR	0	-0.019	-0.021	4.658	-0.048	0.023	-0.001	-0.017	-0.053	0.000
5	A	6	VAL	0	-0.023	-0.013	8.395	-0.067	-0.067	0.000	0.000	0.000	0.000
6	A	7	PRO	0	-0.043	-0.009	10.852	0.049	0.049	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.813	-0.906	14.409	-0.224	-0.224	0.000	0.000	0.000	0.000
8	A	9	MET	0	-0.102	-0.047	17.444	0.017	0.017	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.002	-0.012	21.030	0.008	0.008	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.742	-0.850	16.180	-0.134	-0.134	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.024	-0.004	19.486	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	13	ILE	0	-0.003	-0.014	15.819	0.002	0.002	0.000	0.000	0.000	0.000
13	A	14	TRP	0	-0.023	-0.017	16.505	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.013	-0.012	15.934	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.809	-0.907	14.099	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	17	PHE	0	-0.084	-0.071	17.306	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.868	-0.909	19.656	-0.048	-0.048	0.000	0.000	0.000	0.000
18	A	19	PRO	0	-0.022	-0.015	18.776	0.001	0.001	0.000	0.000	0.000	0.000
19	A	27	GLY	0	0.031	0.014	20.752	0.002	0.002	0.000	0.000	0.000	0.000
20	A	28	HIS	1	0.938	0.956	18.754	0.019	0.019	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.861	0.949	20.628	0.062	0.062	0.000	0.000	0.000	0.000
22	A	30	PRO	0	-0.015	-0.015	20.816	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	31	ALA	0	0.024	0.014	20.756	0.000	0.000	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.057	0.034	21.210	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	33	VAL	0	-0.047	-0.020	17.650	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	34	LEU	0	0.023	0.002	21.045	0.009	0.009	0.000	0.000	0.000	0.000
27	A	35	SER	0	-0.001	-0.011	19.784	0.011	0.011	0.000	0.000	0.000	0.000
28	A	36	PRO	0	0.036	0.008	20.269	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	37	PHE	0	0.131	0.065	12.207	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	38	MET	0	-0.012	0.000	16.019	-0.047	-0.047	0.000	0.000	0.000	0.000
31	A	39	TYR	0	0.011	0.006	16.924	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	40	ASN	0	0.034	0.012	15.355	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	41	ASN	0	-0.002	-0.004	10.930	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	42	LYS	1	0.967	0.987	12.665	0.218	0.218	0.000	0.000	0.000	0.000
35	A	43	THR	0	-0.011	-0.013	15.133	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	44	GLY	0	-0.017	0.006	13.481	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	45	MET	0	-0.023	-0.001	14.391	0.027	0.027	0.000	0.000	0.000	0.000
38	A	46	CYS	0	-0.046	-0.014	17.272	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	47	LEU	0	0.044	0.027	19.142	0.012	0.012	0.000	0.000	0.000	0.000
40	A	48	CYS	0	-0.049	-0.016	21.143	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	49	VAL	0	0.079	0.053	23.243	0.003	0.003	0.000	0.000	0.000	0.000
42	A	50	PRO	0	0.007	0.018	24.914	0.000	0.000	0.000	0.000	0.000	0.000
43	A	51	CYS	0	0.005	0.010	25.255	0.003	0.003	0.000	0.000	0.000	0.000
44	A	52	THR	0	-0.067	-0.047	27.240	0.001	0.001	0.000	0.000	0.000	0.000
45	A	53	THR	0	0.050	0.024	29.484	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	54	GLN	0	-0.071	-0.034	31.782	0.001	0.001	0.000	0.000	0.000	0.000
47	A	55	SER	0	0.012	0.022	34.693	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	56	LYS	1	0.898	0.928	36.359	0.031	0.031	0.000	0.000	0.000	0.000
49	A	57	GLY	0	0.018	0.019	38.863	0.001	0.001	0.000	0.000	0.000	0.000
50	A	58	TYR	0	-0.083	-0.058	36.267	0.001	0.001	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.063	0.022	38.600	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	60	PHE	0	-0.018	-0.004	35.035	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.797	-0.887	34.081	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	62	VAL	0	-0.042	-0.020	31.629	0.002	0.002	0.000	0.000	0.000	0.000
55	A	63	VAL	0	0.022	0.002	31.930	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	64	LEU	0	-0.072	-0.023	26.619	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	65	SER	0	0.020	-0.009	30.318	0.004	0.004	0.000	0.000	0.000	0.000
58	A	66	GLY	0	-0.020	-0.012	29.175	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	67	GLN	0	-0.023	-0.003	24.390	0.002	0.002	0.000	0.000	0.000	0.000
60	A	68	GLU	-1	-0.939	-0.973	22.877	0.006	0.006	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.902	0.962	26.099	0.025	0.025	0.000	0.000	0.000	0.000
62	A	70	ASP	-1	-0.841	-0.912	29.068	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	71	GLY	0	-0.071	-0.064	29.997	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	72	VAL	0	-0.012	0.010	31.004	0.000	0.000	0.000	0.000	0.000	0.000
65	A	73	ALA	0	0.030	0.006	28.196	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.019	-0.018	29.474	0.003	0.003	0.000	0.000	0.000	0.000
67	A	75	ALA	0	0.012	-0.008	30.415	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	76	ASP	-1	-0.794	-0.885	31.456	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	77	GLN	0	-0.058	-0.023	29.787	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	78	VAL	0	0.008	0.006	27.047	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	79	LYS	1	0.942	0.970	23.688	0.115	0.115	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.018	0.004	22.758	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	81	ILE	0	-0.020	-0.036	18.123	0.007	0.007	0.000	0.000	0.000	0.000
74	A	82	ALA	0	0.066	0.019	16.551	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	83	TRP	0	-0.007	-0.022	9.593	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	84	ARG	1	0.884	0.951	9.177	0.763	0.763	0.000	0.000	0.000	0.000
77	A	85	ALA	0	-0.036	-0.021	10.806	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	86	ARG	1	0.872	0.930	12.962	0.159	0.159	0.000	0.000	0.000	0.000
79	A	87	GLY	0	0.022	0.027	10.703	0.026	0.026	0.000	0.000	0.000	0.000
80	A	88	ALA	0	-0.015	-0.001	11.665	0.036	0.036	0.000	0.000	0.000	0.000
81	A	89	THR	0	0.012	0.012	11.158	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	90	LYS	1	0.926	0.975	12.937	0.077	0.077	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.879	0.929	14.932	0.017	0.017	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.067	0.037	18.297	0.016	0.016	0.000	0.000	0.000	0.000
85	A	93	THR	0	-0.031	-0.009	19.456	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	94	VAL	0	-0.024	0.004	21.921	0.009	0.009	0.000	0.000	0.000	0.000
87	A	95	ALA	0	0.021	0.009	25.406	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	96	PRO	0	0.009	-0.014	27.613	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.875	-0.945	29.153	-0.034	-0.034	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.776	-0.876	28.927	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	99	LEU	0	-0.016	-0.022	25.128	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.008	-0.008	28.816	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	101	LEU	0	0.042	0.028	32.034	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.029	-0.014	27.915	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.923	0.948	26.621	0.087	0.087	0.000	0.000	0.000	0.000
96	A	104	ALA	0	0.009	0.014	31.591	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	105	LYS	1	0.859	0.927	34.560	0.040	0.040	0.000	0.000	0.000	0.000
98	A	106	ILE	0	0.022	0.009	29.358	0.000	0.000	0.000	0.000	0.000	0.000
99	A	107	ASN	0	-0.022	-0.018	33.782	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	108	VAL	0	-0.025	-0.004	35.907	0.001	0.001	0.000	0.000	0.000	0.000
101	A	109	LEU	0	-0.045	-0.019	35.458	0.001	0.001	0.000	0.000	0.000	0.000
102	A	110	ILE	0	-0.050	-0.024	31.440	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	111	GLY	0	-0.037	0.007	35.608	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)