FMO DATABASE

FMODB ID: G54R1

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	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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-748934.400745
FMO2-HF: Nuclear repulsion	708731.503275
FMO2-HF: Total energy	-40202.89747
FMO2-MP2: Total energy	-40317.628631

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.
-1.982	1.635	2.324	-1.93	-4.011	0.004

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 : 0.052 / q_NPA : 0.027

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	0.908	0.932	2.313	-2.662	0.896	2.325	-1.917	-3.967	0.004
4	A	5	TYR	0	-0.023	-0.029	4.723	-0.206	-0.147	-0.001	-0.013	-0.044	0.000
5	A	6	VAL	0	-0.013	-0.010	8.463	0.042	0.042	0.000	0.000	0.000	0.000
6	A	7	PRO	0	-0.024	-0.001	10.879	0.007	0.007	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.802	-0.905	14.445	-0.384	-0.384	0.000	0.000	0.000	0.000
8	A	9	MET	0	0.006	0.062	17.489	0.043	0.043	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.012	-0.008	21.069	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.735	-0.837	16.222	-0.312	-0.312	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.021	0.000	19.553	0.014	0.014	0.000	0.000	0.000	0.000
12	A	13	ILE	0	-0.006	-0.015	15.806	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	14	TRP	0	-0.003	-0.006	16.565	0.024	0.024	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.018	-0.014	15.966	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.788	-0.900	15.182	0.008	0.008	0.000	0.000	0.000	0.000
16	A	17	PHE	0	-0.085	-0.061	17.301	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.877	-0.910	19.701	0.059	0.059	0.000	0.000	0.000	0.000
18	A	19	PRO	0	-0.011	-0.011	18.638	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	27	GLY	0	0.033	0.015	20.771	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	28	HIS	1	0.918	0.951	18.421	0.017	0.017	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.879	0.941	20.647	0.048	0.048	0.000	0.000	0.000	0.000
22	A	30	PRO	0	-0.019	-0.003	20.842	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	31	ALA	0	-0.008	-0.010	20.764	0.006	0.006	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.060	0.034	21.254	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	33	VAL	0	-0.046	-0.018	17.675	0.008	0.008	0.000	0.000	0.000	0.000
26	A	34	LEU	0	0.010	-0.004	21.072	0.000	0.000	0.000	0.000	0.000	0.000
27	A	35	SER	0	-0.012	-0.018	19.789	0.011	0.011	0.000	0.000	0.000	0.000
28	A	36	PRO	0	0.038	0.013	20.281	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	37	PHE	0	0.136	0.066	12.438	0.005	0.005	0.000	0.000	0.000	0.000
30	A	38	MET	0	-0.010	0.001	16.025	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	39	TYR	0	0.020	0.011	17.113	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	40	ASN	0	0.019	0.010	15.400	0.033	0.033	0.000	0.000	0.000	0.000
33	A	41	ASN	0	-0.003	-0.001	11.138	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	42	LYS	1	0.962	0.988	12.838	0.227	0.227	0.000	0.000	0.000	0.000
35	A	43	THR	0	0.001	-0.012	15.283	0.022	0.022	0.000	0.000	0.000	0.000
36	A	44	GLY	0	-0.019	0.007	13.414	0.027	0.027	0.000	0.000	0.000	0.000
37	A	45	MET	0	-0.036	-0.008	14.317	0.043	0.043	0.000	0.000	0.000	0.000
38	A	46	CYS	0	-0.026	-0.010	17.270	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	47	LEU	0	0.026	0.023	19.115	0.023	0.023	0.000	0.000	0.000	0.000
40	A	48	CYS	0	-0.064	-0.023	21.101	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	49	VAL	0	0.092	0.060	23.246	0.009	0.009	0.000	0.000	0.000	0.000
42	A	50	PRO	0	0.015	0.020	24.938	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	51	CYS	0	0.006	0.018	25.541	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	52	THR	0	-0.045	-0.033	27.279	0.007	0.007	0.000	0.000	0.000	0.000
45	A	53	THR	0	0.047	0.025	29.633	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	54	GLN	0	-0.042	-0.021	31.840	0.001	0.001	0.000	0.000	0.000	0.000
47	A	55	SER	0	0.013	0.022	34.739	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	56	LYS	1	0.856	0.904	36.409	0.034	0.034	0.000	0.000	0.000	0.000
49	A	57	GLY	0	0.021	0.023	38.910	0.002	0.002	0.000	0.000	0.000	0.000
50	A	58	TYR	0	-0.074	-0.062	36.150	0.001	0.001	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.065	0.024	38.636	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	60	PHE	0	-0.009	0.003	35.117	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.771	-0.869	34.117	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	62	VAL	0	-0.040	-0.013	31.733	0.001	0.001	0.000	0.000	0.000	0.000
55	A	63	VAL	0	0.023	0.004	31.987	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	64	LEU	0	-0.054	-0.013	26.579	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	65	SER	0	0.012	-0.016	30.395	0.008	0.008	0.000	0.000	0.000	0.000
58	A	66	GLY	0	-0.020	-0.014	29.273	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	67	GLN	0	-0.034	-0.006	24.646	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	68	GLU	-1	-0.861	-0.921	22.954	-0.053	-0.053	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.918	0.957	26.285	0.061	0.061	0.000	0.000	0.000	0.000
62	A	70	ASP	-1	-0.837	-0.906	29.160	-0.055	-0.055	0.000	0.000	0.000	0.000
63	A	71	GLY	0	-0.083	-0.070	30.063	0.004	0.004	0.000	0.000	0.000	0.000
64	A	72	VAL	0	-0.018	0.011	31.050	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	73	ALA	0	0.039	0.006	28.246	0.001	0.001	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.026	-0.020	29.505	0.004	0.004	0.000	0.000	0.000	0.000
67	A	75	ALA	0	0.012	-0.010	30.430	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	76	ASP	-1	-0.788	-0.882	31.463	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	77	GLN	0	-0.066	-0.026	29.845	0.002	0.002	0.000	0.000	0.000	0.000
70	A	78	VAL	0	0.011	0.002	27.082	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	79	LYS	1	0.936	0.970	23.892	0.076	0.076	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.010	0.007	22.723	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	81	ILE	0	-0.020	-0.033	18.193	0.017	0.017	0.000	0.000	0.000	0.000
74	A	82	ALA	0	0.075	0.022	16.659	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	83	TRP	0	0.000	-0.022	9.497	0.007	0.007	0.000	0.000	0.000	0.000
76	A	84	ARG	1	0.862	0.937	9.407	0.597	0.597	0.000	0.000	0.000	0.000
77	A	85	ALA	0	-0.027	-0.015	10.853	0.032	0.032	0.000	0.000	0.000	0.000
78	A	86	ARG	1	0.871	0.926	12.986	0.083	0.083	0.000	0.000	0.000	0.000
79	A	87	GLY	0	0.018	0.025	10.678	0.032	0.032	0.000	0.000	0.000	0.000
80	A	88	ALA	0	-0.037	-0.016	11.642	0.018	0.018	0.000	0.000	0.000	0.000
81	A	89	THR	0	0.025	0.015	11.195	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	90	LYS	1	0.836	0.922	13.032	0.326	0.326	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.789	0.875	15.019	0.084	0.084	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.059	0.032	18.393	0.012	0.012	0.000	0.000	0.000	0.000
85	A	93	THR	0	-0.035	-0.010	19.547	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	94	VAL	0	-0.020	0.003	22.011	0.014	0.014	0.000	0.000	0.000	0.000
87	A	95	ALA	0	0.028	0.016	25.487	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	96	PRO	0	0.034	-0.002	27.857	0.001	0.001	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.858	-0.931	29.229	-0.093	-0.093	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.774	-0.875	29.143	-0.094	-0.094	0.000	0.000	0.000	0.000
91	A	99	LEU	0	-0.012	-0.020	25.332	0.001	0.001	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.048	-0.028	28.870	0.003	0.003	0.000	0.000	0.000	0.000
93	A	101	LEU	0	0.035	0.024	32.083	0.005	0.005	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.030	-0.017	27.882	0.004	0.004	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.852	0.873	26.491	0.154	0.154	0.000	0.000	0.000	0.000
96	A	104	ALA	0	0.004	0.011	31.616	0.003	0.003	0.000	0.000	0.000	0.000
97	A	105	LYS	1	0.840	0.906	34.573	0.069	0.069	0.000	0.000	0.000	0.000
98	A	106	ILE	0	0.006	0.001	29.464	0.003	0.003	0.000	0.000	0.000	0.000
99	A	107	ASN	0	-0.026	-0.018	33.788	0.000	0.000	0.000	0.000	0.000	0.000
100	A	108	VAL	0	-0.011	0.002	35.910	0.003	0.003	0.000	0.000	0.000	0.000
101	A	109	LEU	0	-0.045	-0.015	35.390	0.003	0.003	0.000	0.000	0.000	0.000
102	A	110	ILE	0	-0.038	-0.021	31.395	0.001	0.001	0.000	0.000	0.000	0.000
103	A	111	GLY	0	-0.060	-0.004	35.585	-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)