FMO DATABASE

FMODB ID: ZYKZN

Calculation Name: 3G1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G1J

Chain ID: A

ChEMBL ID:

UniProt ID: D0VX16

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-693997.537641
FMO2-HF: Nuclear repulsion	655830.439809
FMO2-HF: Total energy	-38167.097832
FMO2-MP2: Total energy	-38275.546995

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-6.249	-2.775	2.092	-3.016	-2.551	-0.021

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.001

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	2	ASP	-1	-0.856	-0.940	3.855	-3.019	-1.749	-0.002	-0.654	-0.615	0.003
4	A	3	ARG	1	0.852	0.893	3.244	1.033	1.307	0.008	-0.082	-0.200	0.000
5	A	4	ASP	-1	-0.879	-0.925	7.628	-0.660	-0.660	0.000	0.000	0.000	0.000
6	A	5	TYR	0	-0.074	-0.023	10.101	0.270	0.270	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.101	-0.033	7.099	0.154	0.154	0.000	0.000	0.000	0.000
8	A	7	GLN	0	-0.028	-0.012	11.437	0.101	0.101	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.059	0.018	13.580	0.011	0.011	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.851	-0.914	14.636	-0.071	-0.071	0.000	0.000	0.000	0.000
11	A	10	TYR	0	0.021	0.006	16.674	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	11	GLY	0	0.020	0.013	18.569	0.030	0.030	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.017	0.012	20.798	0.001	0.001	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.040	0.017	15.700	0.027	0.027	0.000	0.000	0.000	0.000
15	A	14	LYS	1	0.890	0.914	17.116	0.057	0.057	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.033	0.012	12.669	0.054	0.054	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.011	-0.001	12.858	0.009	0.009	0.000	0.000	0.000	0.000
18	A	17	GLN	0	-0.016	0.003	14.151	0.062	0.062	0.000	0.000	0.000	0.000
19	A	18	CYS	0	0.002	-0.007	15.447	0.033	0.033	0.000	0.000	0.000	0.000
20	A	19	TYR	0	-0.024	-0.038	16.172	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.973	1.003	18.103	-0.119	-0.119	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.003	0.009	18.764	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.022	-0.030	21.291	0.007	0.007	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.818	0.906	24.134	-0.039	-0.039	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.038	0.016	23.187	0.007	0.007	0.000	0.000	0.000	0.000
26	A	25	PHE	0	-0.036	-0.004	17.272	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.887	0.929	19.964	-0.094	-0.094	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.764	-0.875	14.702	0.055	0.055	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.031	-0.022	17.040	0.004	0.004	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.874	0.933	11.289	0.197	0.197	0.000	0.000	0.000	0.000
31	A	30	ASN	0	-0.016	-0.003	17.141	0.043	0.043	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.030	0.028	14.349	0.026	0.026	0.000	0.000	0.000	0.000
33	A	32	ASN	0	0.004	-0.002	17.464	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.026	-0.033	13.567	0.085	0.085	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.923	-0.965	19.003	0.180	0.180	0.000	0.000	0.000	0.000
36	A	35	ARG	1	0.921	0.949	21.829	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	36	GLY	0	-0.012	-0.012	23.258	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.817	-0.901	17.040	0.437	0.437	0.000	0.000	0.000	0.000
39	A	38	VAL	0	-0.018	-0.009	17.476	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	39	MET	0	-0.040	-0.009	12.908	0.099	0.099	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.833	0.903	9.678	-0.811	-0.811	0.000	0.000	0.000	0.000
42	A	41	PHE	0	0.020	0.013	11.020	0.066	0.066	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.053	-0.032	5.790	0.058	0.058	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.067	0.038	9.693	-0.138	-0.138	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.074	-0.037	11.065	0.064	0.064	0.000	0.000	0.000	0.000
46	A	45	ASN	0	0.077	0.032	11.901	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.010	-0.012	13.694	0.083	0.083	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.064	0.051	15.722	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	48	PRO	0	0.002	-0.020	18.467	0.044	0.044	0.000	0.000	0.000	0.000
50	A	49	TYR	0	-0.010	0.005	22.010	0.030	0.030	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.879	-0.941	17.211	-0.382	-0.382	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.064	-0.040	21.342	0.039	0.039	0.000	0.000	0.000	0.000
53	A	52	GLY	0	0.022	0.019	17.764	0.031	0.031	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.044	-0.005	15.967	-0.055	-0.055	0.000	0.000	0.000	0.000
55	A	54	SER	0	0.008	-0.004	10.886	0.007	0.007	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.030	-0.022	12.541	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.047	0.013	6.301	0.048	0.048	0.000	0.000	0.000	0.000
58	A	57	PHE	0	0.013	-0.006	8.689	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.794	-0.876	7.669	1.583	1.583	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.854	0.916	8.949	-0.837	-0.837	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.013	-0.023	11.210	0.133	0.133	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.067	0.046	9.703	-0.078	-0.078	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.032	-0.001	7.591	0.721	0.721	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.789	-0.875	2.670	-4.627	-2.697	2.086	-2.280	-1.736	-0.024
65	A	64	ARG	1	0.914	0.950	5.655	-0.941	-0.941	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.045	0.035	7.346	-0.136	-0.136	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.016	0.011	8.767	0.050	0.050	0.000	0.000	0.000	0.000
68	A	67	MET	0	-0.026	0.005	12.553	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.005	-0.010	14.342	0.061	0.061	0.000	0.000	0.000	0.000
70	A	69	CYS	0	0.026	0.028	18.037	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	70	VAL	0	0.014	0.000	20.358	0.033	0.033	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.919	0.941	22.857	0.127	0.127	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.003	-0.022	26.131	0.008	0.008	0.000	0.000	0.000	0.000
74	A	73	GLH	0	0.022	0.021	27.371	0.003	0.003	0.000	0.000	0.000	0.000
75	A	74	PHE	0	-0.011	-0.003	23.188	0.002	0.002	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.103	0.048	20.362	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	76	MET	0	-0.031	0.000	22.945	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	GLU	-1	-0.746	-0.839	25.097	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	78	ILE	0	0.012	0.008	20.172	0.001	0.001	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.018	0.000	20.909	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	80	HIS	1	0.856	0.918	21.910	0.094	0.094	0.000	0.000	0.000	0.000
82	A	81	HIS	1	0.894	0.948	24.687	0.030	0.030	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.055	0.040	19.123	0.014	0.014	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.796	-0.897	22.598	0.008	0.008	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.054	-0.030	25.056	0.014	0.014	0.000	0.000	0.000	0.000
86	A	85	TYR	0	-0.115	-0.084	21.720	0.007	0.007	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.014	-0.001	16.375	0.024	0.024	0.000	0.000	0.000	0.000
88	A	87	CYS	0	0.014	0.018	21.384	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.921	0.962	20.315	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.032	-0.018	20.903	0.025	0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)