FMO DATABASE

FMODB ID: Z65NN

Calculation Name: 1YCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZN2

Base Structure: X-ray

Registration Date: 2023-09-19

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-378295.532044
FMO2-HF: Nuclear repulsion	352517.514903
FMO2-HF: Total energy	-25778.017141
FMO2-MP2: Total energy	-25853.587091

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-18.047	-15.672	9.304	-4.378	-7.299	0.009

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.018

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	7	LEU	0	0.063	0.037	2.221	-6.090	-4.868	5.176	-2.368	-4.030	0.023
4	A	8	GLU	-1	-0.736	-0.871	1.798	-6.327	-5.927	4.116	-1.967	-2.549	-0.014
5	A	9	LYS	1	0.885	0.940	3.483	0.397	0.926	0.014	-0.033	-0.509	0.000
6	A	10	VAL	0	0.050	0.022	5.388	0.124	0.253	-0.001	-0.008	-0.119	0.000
7	A	11	LEU	0	0.042	0.033	6.488	0.074	0.074	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.758	0.861	5.876	1.855	1.855	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.996	-1.000	9.459	0.434	0.434	0.000	0.000	0.000	0.000
10	A	14	TRP	0	0.026	0.001	11.064	0.060	0.060	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.902	0.979	11.972	0.766	0.766	0.000	0.000	0.000	0.000
12	A	16	GLY	0	-0.047	-0.010	13.983	0.044	0.044	0.000	0.000	0.000	0.000
13	A	17	HIS	0	-0.042	-0.017	15.621	0.049	0.049	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.962	0.980	17.525	0.028	0.028	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.014	0.005	14.725	0.029	0.029	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.015	0.016	17.902	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.041	0.012	14.776	0.012	0.012	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.005	0.033	16.588	0.002	0.002	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.034	0.003	16.414	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	24	GLY	0	0.003	0.013	18.028	0.016	0.016	0.000	0.000	0.000	0.000
21	A	25	GLY	0	-0.082	-0.055	19.936	0.016	0.016	0.000	0.000	0.000	0.000
22	A	26	ASP	-1	-0.865	-0.934	20.135	0.060	0.060	0.000	0.000	0.000	0.000
23	A	27	HIS	0	-0.019	0.010	21.019	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.011	-0.023	21.905	0.013	0.013	0.000	0.000	0.000	0.000
25	A	29	PHE	0	-0.024	0.001	21.345	0.005	0.005	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.028	-0.045	20.648	0.011	0.011	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.024	-0.005	20.302	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.026	0.001	19.041	0.011	0.011	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.019	0.018	11.244	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.845	-0.920	15.699	-0.339	-0.339	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.883	-0.978	13.352	-0.770	-0.770	0.000	0.000	0.000	0.000
32	A	36	PHE	0	-0.049	-0.020	6.495	0.121	0.121	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.882	-0.948	8.533	-1.343	-1.343	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.941	-0.973	5.139	-6.071	-5.976	-0.001	-0.002	-0.092	0.000
35	A	39	GLU	-1	-0.934	-0.940	7.727	-0.914	-0.914	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.035	-0.010	10.717	0.215	0.215	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.018	-0.016	10.711	-0.120	-0.120	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.048	-0.018	13.248	0.091	0.091	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.000	-0.010	16.083	0.014	0.014	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.831	0.896	18.609	0.274	0.274	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.937	-0.976	21.649	-0.154	-0.154	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.025	0.024	21.999	0.012	0.012	0.000	0.000	0.000	0.000
43	A	47	VAL	0	-0.047	-0.044	24.549	0.010	0.010	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.798	-0.900	25.410	-0.080	-0.080	0.000	0.000	0.000	0.000
45	A	49	VAL	0	-0.004	-0.013	27.844	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.078	-0.030	30.147	0.006	0.006	0.000	0.000	0.000	0.000
47	A	51	GLY	0	-0.007	-0.008	31.051	0.002	0.002	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.028	-0.012	29.519	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.946	0.961	26.862	0.111	0.111	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.014	0.017	26.903	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.817	0.914	25.546	0.190	0.190	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.034	-0.025	22.073	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	57	MET	0	-0.002	0.012	19.791	0.031	0.031	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.035	0.027	16.820	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.019	-0.016	15.021	0.060	0.060	0.000	0.000	0.000	0.000
56	A	60	GLY	0	0.069	0.051	13.519	-0.087	-0.087	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.002	-0.028	6.910	0.123	0.123	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.939	-0.967	10.750	-0.819	-0.819	0.000	0.000	0.000	0.000
59	A	63	ASP	-1	-0.977	-0.979	12.511	-0.274	-0.274	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.008	-0.012	11.485	0.076	0.076	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.086	-0.032	12.832	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	TRP	0	-0.039	-0.045	12.668	0.073	0.073	0.000	0.000	0.000	0.000
63	A	67	ILE	0	0.024	0.020	9.834	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	68	MET	0	-0.031	-0.017	13.225	0.104	0.104	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.016	0.015	15.049	-0.053	-0.053	0.000	0.000	0.000	0.000
66	A	70	LEU	0	-0.044	-0.019	16.799	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)