FMO DATABASE

FMODB ID: 8967Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-749162.232308
FMO2-HF: Nuclear repulsion	708959.05884
FMO2-HF: Total energy	-40203.173467
FMO2-MP2: Total energy	-40317.907092

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.
-0.995	2.207	2.099	-1.71	-3.59	0

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 : 0.056 / q_NPA : 0.030

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].
3	A	4	ARG	1	0.898	0.932	2.400	-1.786	1.365	2.100	-1.702	-3.549
4	A	5	TYR	0	-0.012	-0.020	4.888	-0.110	-0.059	-0.001	-0.008	-0.041
5	A	6	VAL	0	-0.018	-0.015	8.650	-0.053	-0.053	0.000	0.000	0.000
6	A	7	PRO	0	-0.002	0.022	11.205	0.028	0.028	0.000	0.000	0.000
7	A	8	ASP	-1	-0.786	-0.889	14.790	-0.399	-0.399	0.000	0.000	0.000
8	A	9	MET	0	0.042	0.045	17.826	0.039	0.039	0.000	0.000	0.000
9	A	10	GLY	0	0.040	0.026	21.651	0.006	0.006	0.000	0.000	0.000
10	A	11	ASP	-1	-0.758	-0.850	16.653	-0.350	-0.350	0.000	0.000	0.000
11	A	12	LEU	0	-0.006	0.009	20.073	0.011	0.011	0.000	0.000	0.000
12	A	13	ILE	0	-0.023	-0.020	16.411	-0.020	-0.020	0.000	0.000	0.000
13	A	14	TRP	0	0.017	0.001	17.153	0.030	0.030	0.000	0.000	0.000
14	A	15	VAL	0	0.007	-0.008	16.470	-0.027	-0.027	0.000	0.000	0.000
15	A	16	ASP	-1	-0.819	-0.930	15.678	-0.097	-0.097	0.000	0.000	0.000
16	A	17	PHE	0	-0.095	-0.054	17.787	-0.013	-0.013	0.000	0.000	0.000
17	A	18	ASP	-1	-0.851	-0.914	20.059	-0.006	-0.006	0.000	0.000	0.000
18	A	19	PRO	0	-0.020	0.000	19.020	-0.004	-0.004	0.000	0.000	0.000
19	A	27	GLY	0	0.039	0.021	21.320	0.000	0.000	0.000	0.000	0.000
20	A	28	HIS	1	0.910	0.951	18.248	0.075	0.075	0.000	0.000	0.000
21	A	29	ARG	1	0.875	0.943	20.959	0.093	0.093	0.000	0.000	0.000
22	A	30	PRO	0	0.009	0.012	21.186	-0.013	-0.013	0.000	0.000	0.000
23	A	31	ALA	0	-0.022	-0.022	21.219	0.010	0.010	0.000	0.000	0.000
24	A	32	VAL	0	0.059	0.030	21.764	-0.012	-0.012	0.000	0.000	0.000
25	A	33	VAL	0	-0.033	-0.011	18.043	0.008	0.008	0.000	0.000	0.000
26	A	34	LEU	0	-0.007	-0.013	21.355	0.007	0.007	0.000	0.000	0.000
27	A	35	SER	0	-0.013	-0.010	19.852	0.018	0.018	0.000	0.000	0.000
28	A	36	PRO	0	0.031	0.022	20.348	-0.017	-0.017	0.000	0.000	0.000
29	A	37	PHE	0	0.119	0.036	12.157	-0.005	-0.005	0.000	0.000	0.000
30	A	38	MET	0	-0.020	-0.006	16.003	-0.043	-0.043	0.000	0.000	0.000
31	A	39	TYR	0	0.005	0.005	17.173	-0.007	-0.007	0.000	0.000	0.000
32	A	40	ASN	0	0.007	0.002	15.374	0.027	0.027	0.000	0.000	0.000
33	A	41	ASN	0	0.009	0.006	10.519	-0.068	-0.068	0.000	0.000	0.000
34	A	42	LYS	1	0.947	0.986	12.805	0.241	0.241	0.000	0.000	0.000
35	A	43	THR	0	0.005	-0.007	15.353	0.028	0.028	0.000	0.000	0.000
36	A	44	GLY	0	-0.026	-0.008	13.289	0.020	0.020	0.000	0.000	0.000
37	A	45	MET	0	-0.022	0.005	14.119	0.037	0.037	0.000	0.000	0.000
38	A	46	CYS	0	-0.038	-0.021	17.392	-0.034	-0.034	0.000	0.000	0.000
39	A	47	LEU	0	0.031	0.018	19.230	0.023	0.023	0.000	0.000	0.000
40	A	48	CYS	0	-0.071	-0.031	21.397	-0.013	-0.013	0.000	0.000	0.000
41	A	49	VAL	0	0.092	0.055	23.494	0.012	0.012	0.000	0.000	0.000
42	A	50	PRO	0	0.010	0.016	25.309	-0.008	-0.008	0.000	0.000	0.000
43	A	51	CYS	0	-0.006	0.019	25.916	0.002	0.002	0.000	0.000	0.000
44	A	52	THR	0	-0.032	-0.018	27.629	0.006	0.006	0.000	0.000	0.000
45	A	53	THR	0	0.081	0.036	30.104	-0.004	-0.004	0.000	0.000	0.000
46	A	54	GLN	0	-0.031	-0.001	32.361	0.002	0.002	0.000	0.000	0.000
47	A	55	SER	0	-0.009	-0.001	35.310	-0.001	-0.001	0.000	0.000	0.000
48	A	56	LYS	1	0.861	0.907	36.661	0.056	0.056	0.000	0.000	0.000
49	A	57	GLY	0	0.031	0.026	39.443	0.003	0.003	0.000	0.000	0.000
50	A	58	TYR	0	-0.066	-0.055	36.208	0.003	0.003	0.000	0.000	0.000
51	A	59	PRO	0	0.036	0.012	38.898	-0.004	-0.004	0.000	0.000	0.000
52	A	60	PHE	0	0.013	0.010	35.413	-0.003	-0.003	0.000	0.000	0.000
53	A	61	GLU	-1	-0.765	-0.864	34.457	-0.069	-0.069	0.000	0.000	0.000
54	A	62	VAL	0	-0.045	-0.018	32.014	0.002	0.002	0.000	0.000	0.000
55	A	63	VAL	0	0.020	0.009	32.039	-0.004	-0.004	0.000	0.000	0.000
56	A	64	LEU	0	-0.041	-0.014	26.733	-0.006	-0.006	0.000	0.000	0.000
57	A	65	SER	0	0.017	-0.018	30.390	0.007	0.007	0.000	0.000	0.000
58	A	66	GLY	0	-0.025	-0.018	29.254	-0.008	-0.008	0.000	0.000	0.000
59	A	67	GLN	0	-0.039	-0.014	24.712	-0.014	-0.014	0.000	0.000	0.000
60	A	68	GLU	-1	-0.845	-0.914	23.134	-0.097	-0.097	0.000	0.000	0.000
61	A	69	ARG	1	0.817	0.888	26.636	0.093	0.093	0.000	0.000	0.000
62	A	70	ASP	-1	-0.838	-0.899	29.231	-0.074	-0.074	0.000	0.000	0.000
63	A	71	GLY	0	-0.023	-0.013	31.205	0.001	0.001	0.000	0.000	0.000
64	A	72	VAL	0	-0.023	0.000	31.541	-0.003	-0.003	0.000	0.000	0.000
65	A	73	ALA	0	0.050	0.008	28.354	-0.001	-0.001	0.000	0.000	0.000
66	A	74	LEU	0	-0.050	-0.029	29.692	0.007	0.007	0.000	0.000	0.000
67	A	75	ALA	0	0.015	-0.004	30.798	-0.005	-0.005	0.000	0.000	0.000
68	A	76	ASP	-1	-0.730	-0.850	32.106	-0.082	-0.082	0.000	0.000	0.000
69	A	77	GLN	0	-0.101	-0.045	30.141	-0.001	-0.001	0.000	0.000	0.000
70	A	78	VAL	0	-0.004	-0.007	27.726	-0.008	-0.008	0.000	0.000	0.000
71	A	79	LYS	1	0.939	0.971	24.275	0.117	0.117	0.000	0.000	0.000
72	A	80	SER	0	0.005	0.010	22.849	-0.020	-0.020	0.000	0.000	0.000
73	A	81	ILE	0	-0.025	-0.031	18.550	0.018	0.018	0.000	0.000	0.000
74	A	82	ALA	0	0.077	0.024	16.808	-0.023	-0.023	0.000	0.000	0.000
75	A	83	TRP	0	0.011	-0.017	9.729	-0.008	-0.008	0.000	0.000	0.000
76	A	84	ARG	1	0.863	0.935	9.489	0.766	0.766	0.000	0.000	0.000
77	A	85	ALA	0	-0.017	-0.013	10.981	0.007	0.007	0.000	0.000	0.000
78	A	86	ARG	1	0.865	0.928	13.467	0.159	0.159	0.000	0.000	0.000
79	A	87	GLY	0	0.012	0.029	10.557	0.031	0.031	0.000	0.000	0.000
80	A	88	ALA	0	-0.032	-0.018	11.561	0.016	0.016	0.000	0.000	0.000
81	A	89	THR	0	0.003	0.002	11.719	-0.061	-0.061	0.000	0.000	0.000
82	A	90	LYS	1	0.814	0.905	13.266	0.384	0.384	0.000	0.000	0.000
83	A	91	LYS	1	0.764	0.859	15.308	0.142	0.142	0.000	0.000	0.000
84	A	92	GLY	0	0.059	0.035	18.788	0.018	0.018	0.000	0.000	0.000
85	A	93	THR	0	-0.038	-0.015	20.038	-0.031	-0.031	0.000	0.000	0.000
86	A	94	VAL	0	-0.014	0.011	22.660	0.014	0.014	0.000	0.000	0.000
87	A	95	ALA	0	0.038	0.019	26.152	-0.009	-0.009	0.000	0.000	0.000
88	A	96	PRO	0	0.030	-0.006	28.496	-0.001	-0.001	0.000	0.000	0.000
89	A	97	GLU	-1	-0.845	-0.914	29.865	-0.105	-0.105	0.000	0.000	0.000
90	A	98	GLU	-1	-0.773	-0.860	29.624	-0.112	-0.112	0.000	0.000	0.000
91	A	99	LEU	0	-0.012	-0.013	25.879	0.000	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.053	-0.034	29.285	0.002	0.002	0.000	0.000	0.000
93	A	101	LEU	0	0.018	0.011	32.616	0.004	0.004	0.000	0.000	0.000
94	A	102	ILE	0	-0.017	-0.011	28.143	0.004	0.004	0.000	0.000	0.000
95	A	103	LYS	1	0.835	0.874	26.627	0.172	0.172	0.000	0.000	0.000
96	A	104	ALA	0	0.014	0.016	32.082	0.003	0.003	0.000	0.000	0.000
97	A	105	LYS	1	0.831	0.893	34.871	0.083	0.083	0.000	0.000	0.000
98	A	106	ILE	0	0.016	0.007	29.681	0.002	0.002	0.000	0.000	0.000
99	A	107	ASN	0	-0.016	-0.010	34.016	0.000	0.000	0.000	0.000	0.000
100	A	108	VAL	0	-0.029	-0.012	36.317	0.003	0.003	0.000	0.000	0.000
101	A	109	LEU	0	-0.039	-0.005	35.530	0.004	0.004	0.000	0.000	0.000
102	A	110	ILE	0	-0.043	-0.024	31.587	0.001	0.001	0.000	0.000	0.000
103	A	111	GLY	0	-0.063	-0.009	35.976	-0.001	-0.001	0.000	0.000	0.000

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