FMO DATABASE

FMODB ID: LJ379

Calculation Name: 3U1C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U1C

Chain ID: A

ChEMBL ID:

UniProt ID: P04268

Base Structure: X-ray

Registration Date: 2023-06-19

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-484503.547238
FMO2-HF: Nuclear repulsion	443530.091046
FMO2-HF: Total energy	-40973.456192
FMO2-MP2: Total energy	-41092.034665

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:ALA)

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

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.
-2.843	0.556	3.452	-3.259	-3.591	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.006

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	0	HIS	0	0.045	0.007	3.874	-1.277	0.048	-0.014	-0.783	-0.529	0.004
4	A	1	MET	0	0.035	0.006	6.944	0.055	0.055	0.000	0.000	0.000	0.000
5	A	2	ASP	-1	-0.797	-0.893	2.414	-1.489	0.270	3.465	-2.416	-2.808	-0.021
6	A	3	ALA	0	0.012	0.010	4.364	0.136	0.252	-0.001	-0.013	-0.101	0.000
7	A	4	ILE	0	-0.028	-0.018	5.830	0.107	0.107	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.955	0.974	7.213	-0.086	-0.086	0.000	0.000	0.000	0.000
9	A	6	LYS	1	0.916	0.957	3.667	-0.597	-0.398	0.002	-0.047	-0.153	0.000
10	A	7	LYS	1	0.967	0.988	8.648	0.322	0.322	0.000	0.000	0.000	0.000
11	A	8	MET	0	-0.014	-0.010	11.348	0.019	0.019	0.000	0.000	0.000	0.000
12	A	9	GLN	0	-0.019	-0.017	9.632	0.021	0.021	0.000	0.000	0.000	0.000
13	A	10	MET	0	0.000	0.011	12.336	0.002	0.002	0.000	0.000	0.000	0.000
14	A	11	LEU	0	0.061	0.027	14.835	0.007	0.007	0.000	0.000	0.000	0.000
15	A	12	LYS	1	0.729	0.850	16.401	0.004	0.004	0.000	0.000	0.000	0.000
16	A	13	LEU	0	0.038	0.025	17.334	0.005	0.005	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.874	-0.945	19.060	-0.073	-0.073	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.894	0.945	20.793	0.018	0.018	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.794	-0.885	20.555	0.000	0.000	0.000	0.000	0.000	0.000
20	A	17	ASN	0	0.059	0.043	22.761	0.000	0.000	0.000	0.000	0.000	0.000
21	A	18	ALA	0	-0.071	-0.035	25.085	0.000	0.000	0.000	0.000	0.000	0.000
22	A	19	LEU	0	-0.026	-0.015	25.929	0.002	0.002	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.852	-0.917	26.828	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	21	ARG	1	0.866	0.915	25.645	0.040	0.040	0.000	0.000	0.000	0.000
25	A	22	ALA	0	-0.024	-0.003	31.048	0.001	0.001	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.935	-0.975	31.388	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	24	GLN	0	-0.073	-0.037	33.822	0.001	0.001	0.000	0.000	0.000	0.000
28	A	25	ALA	0	0.026	0.011	35.477	0.001	0.001	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.832	-0.898	37.003	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	27	ALA	0	-0.006	0.003	38.369	0.001	0.001	0.000	0.000	0.000	0.000
31	A	28	ASP	-1	-0.865	-0.924	39.140	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.762	0.872	40.907	0.010	0.010	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.803	0.877	42.913	0.006	0.006	0.000	0.000	0.000	0.000
34	A	31	ALA	0	0.017	0.008	44.283	0.001	0.001	0.000	0.000	0.000	0.000
35	A	32	ALA	0	-0.002	-0.002	45.831	0.000	0.000	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.857	-0.911	46.006	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.849	-0.919	48.413	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.931	0.971	50.204	0.009	0.009	0.000	0.000	0.000	0.000
39	A	36	SER	0	-0.038	-0.030	51.189	0.000	0.000	0.000	0.000	0.000	0.000
40	A	37	LYS	1	0.801	0.892	52.824	0.007	0.007	0.000	0.000	0.000	0.000
41	A	38	GLN	0	-0.006	0.005	54.746	0.000	0.000	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.006	-0.001	54.692	0.000	0.000	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.867	-0.941	55.357	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.865	-0.919	59.405	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.898	-0.957	59.491	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	43	ILE	0	-0.021	-0.019	61.849	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	VAL	0	0.011	0.020	64.061	0.000	0.000	0.000	0.000	0.000	0.000
48	A	45	GLN	0	-0.061	-0.033	64.464	0.000	0.000	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.023	0.012	65.620	0.000	0.000	0.000	0.000	0.000	0.000
50	A	47	GLU	-1	-0.888	-0.942	68.009	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	48	LYS	1	0.806	0.893	68.554	0.004	0.004	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.017	0.001	71.421	0.000	0.000	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.012	0.013	71.060	0.000	0.000	0.000	0.000	0.000	0.000
54	A	51	ARG	1	0.839	0.891	74.302	0.004	0.004	0.000	0.000	0.000	0.000
55	A	52	VAL	0	0.033	0.018	76.058	0.000	0.000	0.000	0.000	0.000	0.000
56	A	53	THR	0	-0.062	-0.054	76.110	0.000	0.000	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.869	-0.923	77.760	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	55	ASP	-1	-0.821	-0.871	80.359	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	56	SER	0	-0.024	-0.014	81.852	0.000	0.000	0.000	0.000	0.000	0.000
60	A	57	ARG	1	0.713	0.817	80.850	0.005	0.005	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.792	-0.884	84.275	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.016	-0.001	86.297	0.000	0.000	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.017	-0.015	86.850	0.000	0.000	0.000	0.000	0.000	0.000
64	A	61	LEU	0	-0.026	-0.012	87.269	0.000	0.000	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.885	-0.940	90.497	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.893	-0.934	91.870	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.044	-0.008	92.490	0.000	0.000	0.000	0.000	0.000	0.000
68	A	65	HIS	1	0.861	0.916	92.266	0.004	0.004	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.875	0.929	94.585	0.003	0.003	0.000	0.000	0.000	0.000
70	A	67	SER	0	-0.020	0.004	97.907	0.000	0.000	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.893	-0.941	96.334	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.897	-0.946	100.351	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	70	SER	0	-0.081	-0.062	102.265	0.000	0.000	0.000	0.000	0.000	0.000
74	A	71	LEU	0	-0.053	-0.009	103.131	0.000	0.000	0.000	0.000	0.000	0.000
75	A	72	LEU	0	0.061	0.034	104.704	0.000	0.000	0.000	0.000	0.000	0.000
76	A	73	PHE	0	0.003	-0.012	105.151	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	ALA	0	-0.029	-0.002	108.001	0.000	0.000	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.922	-0.966	107.683	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	76	GLU	-1	-0.889	-0.930	110.848	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	77	ASN	0	-0.037	-0.045	111.673	0.000	0.000	0.000	0.000	0.000	0.000
81	A	78	ALA	0	-0.001	0.014	113.755	0.000	0.000	0.000	0.000	0.000	0.000
82	A	79	ALA	0	0.051	0.025	115.224	0.000	0.000	0.000	0.000	0.000	0.000
83	A	80	LYS	1	0.759	0.878	114.805	0.002	0.002	0.000	0.000	0.000	0.000
84	A	81	ALA	0	0.082	0.038	118.482	0.000	0.000	0.000	0.000	0.000	0.000
85	A	82	GLU	-1	-0.949	-0.966	118.870	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	83	SER	0	-0.007	-0.003	121.274	0.000	0.000	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.943	-0.972	121.201	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	85	VAL	0	0.025	0.004	123.421	0.000	0.000	0.000	0.000	0.000	0.000
89	A	86	ALA	0	0.013	0.011	125.442	0.000	0.000	0.000	0.000	0.000	0.000
90	A	87	SER	0	-0.056	-0.045	127.122	0.000	0.000	0.000	0.000	0.000	0.000
91	A	88	LEU	0	-0.062	-0.024	127.296	0.000	0.000	0.000	0.000	0.000	0.000
92	A	89	ASN	0	-0.022	-0.021	128.477	0.000	0.000	0.000	0.000	0.000	0.000
93	A	90	ARG	1	0.944	0.974	128.016	0.002	0.002	0.000	0.000	0.000	0.000
94	A	91	ARG	1	0.932	0.967	131.287	0.002	0.002	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.007	-0.003	132.384	0.000	0.000	0.000	0.000	0.000	0.000
96	A	93	GLN	0	-0.076	-0.045	135.816	0.000	0.000	0.000	0.000	0.000	0.000
97	A	94	LEU	0	-0.030	-0.021	136.945	0.000	0.000	0.000	0.000	0.000	0.000
98	A	95	VAL	0	-0.018	-0.007	138.919	0.000	0.000	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-1.030	-1.006	140.314	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	97	GLU	-1	-0.879	-0.928	141.002	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	98	GLU	-1	-1.063	-1.014	142.925	-0.002	-0.002	0.000	0.000	0.000	0.000

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