FMO DATABASE

FMODB ID: 6Y2RZ

Calculation Name: 3RY0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RY0

Chain ID: A

ChEMBL ID:

UniProt ID: C0LTT5

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-299665.304536
FMO2-HF: Nuclear repulsion	275886.9833
FMO2-HF: Total energy	-23778.321236
FMO2-MP2: Total energy	-23849.625915

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:1:PRO)

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

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.
-12.438	-4.318	5.009	-4.779	-8.353	-0.032

Interaction energy analysis for fragmet #1(A:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.009

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	3	ILE	0	0.016	0.008	3.652	-0.544	1.670	-0.018	-0.959	-1.237	0.002
4	A	4	ARG	1	0.820	0.892	5.814	0.133	0.133	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.016	0.005	9.536	0.100	0.100	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.003	0.008	12.120	0.019	0.019	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.018	-0.003	15.720	0.016	0.016	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.044	-0.031	18.379	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.916	-0.980	21.874	-0.136	-0.136	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.015	0.007	23.821	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.843	0.930	20.124	0.219	0.219	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.009	-0.032	23.000	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.051	-0.002	21.680	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.007	-0.001	20.641	-0.031	-0.031	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.785	-0.844	20.185	-0.251	-0.251	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.006	0.011	16.273	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.014	-0.015	15.770	-0.068	-0.068	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.009	0.008	15.697	-0.062	-0.062	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.020	-0.013	12.872	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.009	0.007	11.280	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.940	-0.962	10.586	-0.875	-0.875	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.073	0.033	11.455	-0.096	-0.096	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.073	-0.044	8.166	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.012	-0.010	6.581	-0.323	-0.323	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.031	0.025	7.367	-0.157	-0.157	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.008	0.009	9.173	0.040	0.040	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.009	0.005	3.760	-0.086	0.089	0.001	-0.032	-0.144	0.000
28	A	28	HIS	0	-0.089	-0.058	5.550	0.144	0.144	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.885	-0.945	7.220	-0.384	-0.384	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.117	-0.073	7.664	0.148	0.148	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.068	-0.032	2.616	-0.445	0.101	0.419	-0.183	-0.782	-0.002
32	A	32	GLY	0	0.010	0.021	6.222	0.185	0.185	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.053	-0.015	2.652	-2.100	-0.482	0.906	-0.785	-1.740	-0.007
34	A	34	PRO	0	0.048	0.014	4.969	-0.095	-0.052	-0.001	-0.005	-0.036	0.000
35	A	35	VAL	0	0.089	0.031	5.284	-0.652	-0.652	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.866	-0.909	6.380	-1.428	-1.428	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.063	-0.026	3.601	0.038	0.368	0.009	-0.096	-0.244	0.000
38	A	38	VAL	0	-0.053	-0.019	2.206	-9.079	-6.421	3.681	-2.642	-3.698	-0.025
39	A	39	ARG	1	0.835	0.913	3.482	3.662	4.198	0.012	-0.077	-0.472	0.000
40	A	40	VAL	0	0.058	0.018	5.527	-0.273	-0.273	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.059	-0.022	8.114	0.242	0.242	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.015	0.002	11.081	0.040	0.040	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.839	-0.898	13.781	-0.131	-0.131	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.850	-0.946	16.511	-0.232	-0.232	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.047	-0.028	19.891	0.026	0.026	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.029	0.032	22.264	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.002	-0.020	26.012	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.857	-0.948	27.542	-0.063	-0.063	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.914	0.955	25.861	0.071	0.071	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.017	0.029	18.769	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.001	-0.013	25.306	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.001	0.001	25.046	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.008	0.010	27.573	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.000	-0.005	29.630	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.880	0.937	31.125	0.029	0.029	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.063	0.041	29.444	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.010	-0.026	25.690	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.011	0.001	29.104	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.804	-0.893	31.880	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.870	0.923	29.747	0.043	0.043	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.924	0.966	26.848	0.099	0.099	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.009	0.005	33.567	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.061	-0.026	36.537	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.004	0.014	35.038	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.021	-0.002	36.708	0.001	0.001	0.000	0.000	0.000	0.000

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