FMO DATABASE

FMODB ID: QYGNY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-379258.289566
FMO2-HF: Nuclear repulsion	353479.628733
FMO2-HF: Total energy	-25778.660833
FMO2-MP2: Total energy	-25854.176916

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.
-26.089	-19.788	4.925	-4.755	-6.471	0.019

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 : 0.060 / q_NPA : 0.020

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	7	LEU	0	0.058	0.038	2.436	-6.082	-3.062	2.060	-2.120	-2.960	0.020
4	A	8	GLU	-1	-0.748	-0.858	2.301	-9.177	-6.922	2.856	-2.290	-2.821	0.001
5	A	9	LYS	1	0.842	0.891	3.667	-0.280	0.162	0.007	-0.080	-0.369	0.000
6	A	10	VAL	0	0.009	0.007	5.857	0.022	0.022	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.031	0.015	6.344	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.782	0.875	5.726	1.897	1.897	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.914	-0.942	9.201	0.434	0.434	0.000	0.000	0.000	0.000
10	A	14	TRP	0	-0.007	-0.009	11.387	0.074	0.074	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.819	0.913	12.145	0.732	0.732	0.000	0.000	0.000	0.000
12	A	16	GLY	0	-0.043	-0.022	14.108	0.047	0.047	0.000	0.000	0.000	0.000
13	A	17	HIS	0	-0.014	0.002	16.106	0.052	0.052	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.911	0.964	18.079	0.024	0.024	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.035	0.013	14.456	0.039	0.039	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.016	0.013	17.700	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.021	-0.007	14.694	0.017	0.017	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.051	-0.022	16.248	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.042	0.008	16.117	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	24	GLY	0	0.003	0.009	18.098	0.017	0.017	0.000	0.000	0.000	0.000
21	A	25	GLY	0	-0.069	-0.044	19.557	0.009	0.009	0.000	0.000	0.000	0.000
22	A	26	ASP	-1	-0.845	-0.906	20.407	0.076	0.076	0.000	0.000	0.000	0.000
23	A	27	HIS	0	-0.039	-0.004	20.682	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.011	-0.018	21.662	0.017	0.017	0.000	0.000	0.000	0.000
25	A	29	PHE	0	-0.014	0.010	20.939	0.004	0.004	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.015	-0.039	20.344	0.011	0.011	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.032	0.010	20.052	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.038	-0.009	19.278	0.021	0.021	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.019	0.018	11.577	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.791	-0.861	16.018	-0.314	-0.314	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.833	-0.930	12.819	-0.830	-0.830	0.000	0.000	0.000	0.000
32	A	36	PHE	0	-0.022	-0.018	6.721	0.195	0.195	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.857	-0.924	8.398	-1.601	-1.601	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.962	-0.979	3.925	-10.277	-9.693	0.002	-0.265	-0.321	-0.002
35	A	39	GLU	-1	-0.941	-0.950	6.865	-0.893	-0.893	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.067	-0.037	10.099	0.265	0.265	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.005	-0.008	9.990	-0.148	-0.148	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.029	-0.014	12.418	0.089	0.089	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.022	0.008	15.647	0.021	0.021	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.777	0.856	18.069	0.270	0.270	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.855	-0.918	21.474	-0.150	-0.150	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.022	0.026	21.372	0.014	0.014	0.000	0.000	0.000	0.000
43	A	47	VAL	0	-0.043	-0.034	23.930	0.009	0.009	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.742	-0.853	24.856	-0.074	-0.074	0.000	0.000	0.000	0.000
45	A	49	VAL	0	0.013	0.000	27.446	0.004	0.004	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.045	-0.017	29.991	0.005	0.005	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.000	0.001	30.711	0.002	0.002	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.018	-0.020	28.850	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.810	0.882	26.168	0.095	0.095	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.036	0.022	26.153	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.762	0.865	25.659	0.188	0.188	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.036	-0.037	21.176	0.008	0.008	0.000	0.000	0.000	0.000
53	A	57	MET	0	-0.022	0.005	19.527	0.034	0.034	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.006	0.016	16.321	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.030	-0.019	14.757	0.067	0.067	0.000	0.000	0.000	0.000
56	A	60	GLY	0	0.084	0.051	13.071	-0.100	-0.100	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.012	-0.018	6.245	0.124	0.124	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.935	-0.968	10.356	-0.766	-0.766	0.000	0.000	0.000	0.000
59	A	63	ASP	-1	-0.944	-0.969	12.611	-0.286	-0.286	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.023	-0.016	11.582	0.084	0.084	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.036	-0.003	13.120	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	TRP	0	-0.043	-0.041	12.790	0.088	0.088	0.000	0.000	0.000	0.000
63	A	67	ILE	0	0.035	0.022	9.802	-0.075	-0.075	0.000	0.000	0.000	0.000
64	A	68	MET	0	-0.032	-0.015	13.407	0.112	0.112	0.000	0.000	0.000	0.000
65	A	69	LEU	0	0.019	0.026	15.142	-0.057	-0.057	0.000	0.000	0.000	0.000
66	A	70	LEU	0	-0.090	-0.041	16.705	0.016	0.016	0.000	0.000	0.000	0.000

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