FMO DATABASE

FMODB ID: N3RZQ

Calculation Name: 3U1C-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-484466.877113
FMO2-HF: Nuclear repulsion	443495.323041
FMO2-HF: Total energy	-40971.554072
FMO2-MP2: Total energy	-41090.23357

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.
-3.646	1.712	6.523	-6.374	-5.506	-0.069

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 : 1 / q_Mulliken : 0.837 / q_NPA : 0.908

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	0.096	0.042	3.811	-1.694	-0.577	-0.010	-0.576	-0.531	0.001
4	A	1	MET	0	0.058	0.014	6.609	1.754	1.754	0.000	0.000	0.000	0.000
5	A	2	ASP	-1	-0.830	-0.915	2.183	-74.800	-70.905	6.531	-5.745	-4.681	-0.070
6	A	3	ALA	0	-0.036	-0.021	4.148	4.270	4.455	0.001	-0.028	-0.157	0.000
7	A	4	ILE	0	0.010	0.000	5.080	4.162	4.198	0.000	-0.002	-0.033	0.000
8	A	5	LYS	1	0.961	0.974	6.992	28.420	28.420	0.000	0.000	0.000	0.000
9	A	6	LYS	1	0.946	0.976	3.642	45.920	46.045	0.001	-0.023	-0.104	0.000
10	A	7	LYS	1	0.986	0.984	7.968	26.651	26.651	0.000	0.000	0.000	0.000
11	A	8	MET	0	0.000	0.010	10.769	1.214	1.214	0.000	0.000	0.000	0.000
12	A	9	GLN	0	-0.022	-0.019	9.727	0.114	0.114	0.000	0.000	0.000	0.000
13	A	10	MET	0	-0.004	0.000	11.715	0.817	0.817	0.000	0.000	0.000	0.000
14	A	11	LEU	0	0.050	0.032	14.265	0.940	0.940	0.000	0.000	0.000	0.000
15	A	12	LYS	1	0.861	0.949	15.980	15.862	15.862	0.000	0.000	0.000	0.000
16	A	13	LEU	0	0.047	0.020	16.458	0.613	0.613	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.888	-0.935	18.613	-14.168	-14.168	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.888	0.933	20.371	13.331	13.331	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.902	-0.961	20.370	-13.805	-13.805	0.000	0.000	0.000	0.000
20	A	17	ASN	0	0.074	0.047	22.369	0.620	0.620	0.000	0.000	0.000	0.000
21	A	18	ALA	0	-0.105	-0.057	24.752	0.514	0.514	0.000	0.000	0.000	0.000
22	A	19	LEU	0	-0.020	-0.027	24.978	0.318	0.318	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.819	-0.888	27.136	-10.583	-10.583	0.000	0.000	0.000	0.000
24	A	21	ARG	1	0.884	0.929	25.879	11.140	11.140	0.000	0.000	0.000	0.000
25	A	22	ALA	0	-0.033	-0.010	30.718	0.333	0.333	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.920	-0.961	30.542	-9.558	-9.558	0.000	0.000	0.000	0.000
27	A	24	GLN	0	-0.064	-0.022	33.498	0.101	0.101	0.000	0.000	0.000	0.000
28	A	25	ALA	0	0.013	0.013	35.228	0.285	0.285	0.000	0.000	0.000	0.000
29	A	26	GLU	-1	-0.889	-0.965	36.290	-7.732	-7.732	0.000	0.000	0.000	0.000
30	A	27	ALA	0	-0.020	-0.002	37.864	0.256	0.256	0.000	0.000	0.000	0.000
31	A	28	ASP	-1	-0.885	-0.956	39.200	-7.582	-7.582	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.831	0.931	39.714	7.811	7.811	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.953	0.975	42.722	6.849	6.849	0.000	0.000	0.000	0.000
34	A	31	ALA	0	0.017	0.014	43.905	0.186	0.186	0.000	0.000	0.000	0.000
35	A	32	ALA	0	0.000	-0.002	45.486	0.186	0.186	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.968	-0.989	46.765	-6.444	-6.444	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.903	-0.960	48.218	-6.066	-6.066	0.000	0.000	0.000	0.000
38	A	35	ARG	1	0.955	0.978	49.905	6.036	6.036	0.000	0.000	0.000	0.000
39	A	36	SER	0	-0.041	-0.026	51.195	0.148	0.148	0.000	0.000	0.000	0.000
40	A	37	LYS	1	0.937	0.978	51.336	6.104	6.104	0.000	0.000	0.000	0.000
41	A	38	GLN	0	-0.027	-0.009	53.863	0.030	0.030	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.037	-0.024	54.549	0.085	0.085	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.923	-0.960	56.291	-5.445	-5.445	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.890	-0.948	59.240	-5.136	-5.136	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.940	-0.967	59.939	-5.138	-5.138	0.000	0.000	0.000	0.000
46	A	43	ILE	0	-0.001	-0.022	61.363	0.110	0.110	0.000	0.000	0.000	0.000
47	A	44	VAL	0	-0.012	0.030	63.586	0.112	0.112	0.000	0.000	0.000	0.000
48	A	45	GLN	0	-0.019	-0.029	64.751	0.190	0.190	0.000	0.000	0.000	0.000
49	A	46	LEU	0	-0.005	-0.017	65.671	0.097	0.097	0.000	0.000	0.000	0.000
50	A	47	GLU	-1	-0.897	-0.940	67.241	-4.528	-4.528	0.000	0.000	0.000	0.000
51	A	48	LYS	1	0.832	0.924	69.011	4.645	4.645	0.000	0.000	0.000	0.000
52	A	49	GLN	0	-0.025	-0.019	70.827	0.090	0.090	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.006	-0.004	70.601	0.071	0.071	0.000	0.000	0.000	0.000
54	A	51	ARG	1	0.975	0.986	73.817	4.216	4.216	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.011	0.017	75.623	0.064	0.064	0.000	0.000	0.000	0.000
56	A	53	THR	0	-0.050	-0.031	76.187	0.067	0.067	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.965	-0.988	76.903	-4.085	-4.085	0.000	0.000	0.000	0.000
58	A	55	ASP	-1	-0.861	-0.917	79.917	-3.902	-3.902	0.000	0.000	0.000	0.000
59	A	56	SER	0	-0.087	-0.052	81.306	0.077	0.077	0.000	0.000	0.000	0.000
60	A	57	ARG	1	0.894	0.954	80.983	3.926	3.926	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.862	-0.954	83.830	-3.757	-3.757	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.027	-0.002	85.908	0.026	0.026	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.005	-0.008	86.694	0.052	0.052	0.000	0.000	0.000	0.000
64	A	61	LEU	0	-0.038	-0.016	86.690	0.047	0.047	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.920	-0.945	90.138	-3.430	-3.430	0.000	0.000	0.000	0.000
66	A	63	GLU	-1	-0.905	-0.968	91.962	-3.354	-3.354	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.063	-0.019	91.929	0.040	0.040	0.000	0.000	0.000	0.000
68	A	65	HIS	1	0.884	0.929	91.970	3.465	3.465	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.946	0.982	95.700	3.377	3.377	0.000	0.000	0.000	0.000
70	A	67	SER	0	-0.050	-0.015	97.519	0.055	0.055	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.892	-0.952	96.337	-3.303	-3.303	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.894	-0.948	100.132	-3.155	-3.155	0.000	0.000	0.000	0.000
73	A	70	SER	0	-0.083	-0.048	102.076	0.044	0.044	0.000	0.000	0.000	0.000
74	A	71	LEU	0	-0.041	-0.003	102.996	0.034	0.034	0.000	0.000	0.000	0.000
75	A	72	LEU	0	0.051	0.031	104.482	0.037	0.037	0.000	0.000	0.000	0.000
76	A	73	PHE	0	0.003	-0.008	104.914	0.036	0.036	0.000	0.000	0.000	0.000
77	A	74	ALA	0	-0.043	-0.011	107.742	0.040	0.040	0.000	0.000	0.000	0.000
78	A	75	GLU	-1	-0.899	-0.965	107.225	-2.974	-2.974	0.000	0.000	0.000	0.000
79	A	76	GLU	-1	-0.979	-0.984	110.393	-2.874	-2.874	0.000	0.000	0.000	0.000
80	A	77	ASN	0	-0.069	-0.055	111.826	0.051	0.051	0.000	0.000	0.000	0.000
81	A	78	ALA	0	-0.008	0.007	113.270	0.031	0.031	0.000	0.000	0.000	0.000
82	A	79	ALA	0	0.052	0.025	114.892	0.031	0.031	0.000	0.000	0.000	0.000
83	A	80	LYS	1	0.899	0.955	114.730	2.826	2.826	0.000	0.000	0.000	0.000
84	A	81	ALA	0	0.052	0.017	118.153	0.029	0.029	0.000	0.000	0.000	0.000
85	A	82	GLU	-1	-0.933	-0.950	118.562	-2.685	-2.685	0.000	0.000	0.000	0.000
86	A	83	SER	0	-0.058	-0.032	120.941	0.041	0.041	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.952	-0.984	121.917	-2.618	-2.618	0.000	0.000	0.000	0.000
88	A	85	VAL	0	0.004	0.000	123.116	0.031	0.031	0.000	0.000	0.000	0.000
89	A	86	ALA	0	-0.004	0.002	125.273	0.027	0.027	0.000	0.000	0.000	0.000
90	A	87	SER	0	-0.089	-0.054	127.019	0.035	0.035	0.000	0.000	0.000	0.000
91	A	88	LEU	0	0.015	-0.012	127.194	0.028	0.028	0.000	0.000	0.000	0.000
92	A	89	ASN	0	0.037	0.015	128.110	0.032	0.032	0.000	0.000	0.000	0.000
93	A	90	ARG	1	0.933	0.985	127.887	2.515	2.515	0.000	0.000	0.000	0.000
94	A	91	ARG	1	0.923	0.956	131.151	2.462	2.462	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.007	0.010	132.506	0.017	0.017	0.000	0.000	0.000	0.000
96	A	93	GLN	0	-0.052	-0.017	135.659	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	94	LEU	0	-0.030	-0.025	136.761	0.012	0.012	0.000	0.000	0.000	0.000
98	A	95	VAL	0	-0.009	-0.005	138.792	0.012	0.012	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-1.041	-1.017	140.140	-2.258	-2.258	0.000	0.000	0.000	0.000
100	A	97	GLU	-1	-0.950	-0.974	140.951	-2.285	-2.285	0.000	0.000	0.000	0.000
101	A	98	GLU	-2	-2.009	-1.985	142.967	-4.451	-4.451	0.000	0.000	0.000	0.000

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