FMO DATABASE

FMODB ID: J3929

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

Total energy (hartree)

FMO2-HF: Electronic energy	-484463.477916
FMO2-HF: Nuclear repulsion	443491.347726
FMO2-HF: Total energy	-40972.130189
FMO2-MP2: Total energy	-41090.805891

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.
-3.677	-0.962	7.416	-5.26	-4.872	-0.039

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 : -0.010 / q_NPA : -0.011

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	0.063	0.021	3.811	-1.712	-0.353	-0.016	-0.801	-0.542	0.005
4	A	1	MET	0	0.033	0.000	6.610	0.055	0.055	0.000	0.000	0.000	0.000
5	A	2	ASP	-1	-0.830	-0.909	2.200	-2.323	-1.352	7.432	-4.396	-4.007	-0.044
6	A	3	ALA	0	-0.035	-0.021	4.146	0.250	0.437	0.000	-0.026	-0.162	0.000
7	A	4	ILE	0	-0.003	-0.008	5.084	0.097	0.138	-0.001	-0.001	-0.039	0.000
8	A	5	LYS	1	0.958	0.973	6.990	0.022	0.022	0.000	0.000	0.000	0.000
9	A	6	LYS	1	0.951	0.979	3.639	-0.357	-0.200	0.001	-0.036	-0.122	0.000
10	A	7	LYS	1	0.980	0.981	7.970	0.331	0.331	0.000	0.000	0.000	0.000
11	A	8	MET	0	-0.007	0.007	10.773	0.014	0.014	0.000	0.000	0.000	0.000
12	A	9	GLN	0	-0.019	-0.018	9.727	0.008	0.008	0.000	0.000	0.000	0.000
13	A	10	MET	0	-0.005	0.000	11.718	0.003	0.003	0.000	0.000	0.000	0.000
14	A	11	LEU	0	0.048	0.031	14.268	0.005	0.005	0.000	0.000	0.000	0.000
15	A	12	LYS	1	0.861	0.949	15.982	0.022	0.022	0.000	0.000	0.000	0.000
16	A	13	LEU	0	0.047	0.020	16.460	0.006	0.006	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.890	-0.935	18.615	-0.084	-0.084	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.883	0.931	20.373	0.036	0.036	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.898	-0.960	20.370	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	17	ASN	0	0.074	0.047	22.370	0.006	0.006	0.000	0.000	0.000	0.000
21	A	18	ALA	0	-0.106	-0.058	24.755	0.002	0.002	0.000	0.000	0.000	0.000
22	A	19	LEU	0	-0.022	-0.027	24.979	0.002	0.002	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.817	-0.887	27.137	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	21	ARG	1	0.882	0.928	25.883	0.046	0.046	0.000	0.000	0.000	0.000
25	A	22	ALA	0	-0.034	-0.010	30.720	0.001	0.001	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.919	-0.961	30.542	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	24	GLN	0	-0.064	-0.022	33.500	0.001	0.001	0.000	0.000	0.000	0.000
28	A	25	ALA	0	0.013	0.013	35.230	0.001	0.001	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.888	-0.965	36.293	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	27	ALA	0	-0.020	-0.002	37.865	0.002	0.002	0.000	0.000	0.000	0.000
31	A	28	ASP	-1	-0.885	-0.956	39.202	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.830	0.931	39.715	0.018	0.018	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.952	0.975	42.723	0.010	0.010	0.000	0.000	0.000	0.000
34	A	31	ALA	0	0.017	0.014	43.906	0.001	0.001	0.000	0.000	0.000	0.000
35	A	32	ALA	0	0.001	-0.002	45.488	0.001	0.001	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.969	-0.989	46.766	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.902	-0.960	48.219	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.954	0.978	49.907	0.012	0.012	0.000	0.000	0.000	0.000
39	A	36	SER	0	-0.041	-0.026	51.206	0.000	0.000	0.000	0.000	0.000	0.000
40	A	37	LYS	1	0.939	0.978	51.337	0.010	0.010	0.000	0.000	0.000	0.000
41	A	38	GLN	0	-0.027	-0.009	53.864	0.000	0.000	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.035	-0.023	54.551	0.000	0.000	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.925	-0.961	56.293	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.890	-0.948	59.241	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.939	-0.966	59.941	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	43	ILE	0	0.000	-0.022	61.365	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	VAL	0	-0.012	0.030	63.587	0.000	0.000	0.000	0.000	0.000	0.000
48	A	45	GLN	0	-0.019	-0.029	64.752	0.001	0.001	0.000	0.000	0.000	0.000
49	A	46	LEU	0	-0.006	-0.017	65.674	0.000	0.000	0.000	0.000	0.000	0.000
50	A	47	GLU	-1	-0.896	-0.940	67.245	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	48	LYS	1	0.830	0.924	69.013	0.006	0.006	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.025	-0.018	70.829	0.000	0.000	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.007	-0.003	70.603	0.000	0.000	0.000	0.000	0.000	0.000
54	A	51	ARG	1	0.974	0.986	73.819	0.006	0.006	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.008	0.018	75.625	0.000	0.000	0.000	0.000	0.000	0.000
56	A	53	THR	0	-0.051	-0.032	76.191	0.000	0.000	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.965	-0.988	76.905	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	55	ASP	-1	-0.862	-0.917	79.919	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	56	SER	0	-0.086	-0.052	81.308	0.000	0.000	0.000	0.000	0.000	0.000
60	A	57	ARG	1	0.894	0.954	80.987	0.006	0.006	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.862	-0.954	83.832	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.027	-0.002	85.910	0.000	0.000	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.004	-0.007	86.696	0.000	0.000	0.000	0.000	0.000	0.000
64	A	61	LEU	0	-0.037	-0.015	86.692	0.000	0.000	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.922	-0.946	90.141	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.905	-0.968	91.964	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.062	-0.019	91.930	0.000	0.000	0.000	0.000	0.000	0.000
68	A	65	HIS	1	0.885	0.929	91.973	0.005	0.005	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.944	0.982	95.702	0.004	0.004	0.000	0.000	0.000	0.000
70	A	67	SER	0	-0.048	-0.015	97.522	0.000	0.000	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.892	-0.952	96.340	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.896	-0.949	100.134	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	70	SER	0	-0.082	-0.048	102.078	0.000	0.000	0.000	0.000	0.000	0.000
74	A	71	LEU	0	-0.039	-0.002	102.998	0.000	0.000	0.000	0.000	0.000	0.000
75	A	72	LEU	0	0.050	0.030	104.485	0.000	0.000	0.000	0.000	0.000	0.000
76	A	73	PHE	0	0.003	-0.008	104.917	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	ALA	0	-0.041	-0.011	107.744	0.000	0.000	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.899	-0.965	107.228	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	76	GLU	-1	-0.978	-0.983	110.396	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	77	ASN	0	-0.071	-0.056	111.828	0.000	0.000	0.000	0.000	0.000	0.000
81	A	78	ALA	0	-0.007	0.007	113.273	0.000	0.000	0.000	0.000	0.000	0.000
82	A	79	ALA	0	0.053	0.025	114.895	0.000	0.000	0.000	0.000	0.000	0.000
83	A	80	LYS	1	0.899	0.955	114.732	0.003	0.003	0.000	0.000	0.000	0.000
84	A	81	ALA	0	0.053	0.017	118.156	0.000	0.000	0.000	0.000	0.000	0.000
85	A	82	GLU	-1	-0.934	-0.950	118.565	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	83	SER	0	-0.057	-0.032	120.945	0.000	0.000	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.953	-0.983	121.920	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	85	VAL	0	0.007	0.001	123.117	0.000	0.000	0.000	0.000	0.000	0.000
89	A	86	ALA	0	-0.003	0.003	125.276	0.000	0.000	0.000	0.000	0.000	0.000
90	A	87	SER	0	-0.090	-0.054	127.022	0.000	0.000	0.000	0.000	0.000	0.000
91	A	88	LEU	0	0.017	-0.011	127.197	0.000	0.000	0.000	0.000	0.000	0.000
92	A	89	ASN	0	0.040	0.017	128.113	0.000	0.000	0.000	0.000	0.000	0.000
93	A	90	ARG	1	0.936	0.987	127.890	0.003	0.003	0.000	0.000	0.000	0.000
94	A	91	ARG	1	0.921	0.956	131.154	0.002	0.002	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.002	0.012	132.509	0.000	0.000	0.000	0.000	0.000	0.000
96	A	93	GLN	0	-0.043	-0.012	135.661	0.000	0.000	0.000	0.000	0.000	0.000
97	A	94	LEU	0	-0.025	-0.021	136.763	0.000	0.000	0.000	0.000	0.000	0.000
98	A	95	VAL	0	-0.007	-0.006	138.794	0.000	0.000	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-1.023	-1.007	140.140	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	97	GLU	-1	-0.919	-0.954	140.954	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	98	GLU	-1	-1.092	-1.032	142.969	-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)