FMO DATABASE

FMODB ID: 2NQ5R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-299613.306645
FMO2-HF: Nuclear repulsion	275835.429144
FMO2-HF: Total energy	-23777.877501
FMO2-MP2: Total energy	-23849.224521

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.
-13.393	-4.535	5.383	-5.098	-9.144	-0.035

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 : 0.049 / q_NPA : 0.012

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	0.021	0.007	3.505	-0.611	1.675	-0.015	-0.996	-1.275	0.003
4	A	4	ARG	1	0.849	0.908	5.617	0.174	0.174	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.011	0.003	9.317	0.104	0.104	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.003	0.011	11.932	0.018	0.018	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.016	-0.001	15.513	0.018	0.018	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.043	-0.035	18.206	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.930	-0.979	21.725	-0.149	-0.149	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.000	0.007	23.667	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.866	0.949	19.775	0.240	0.240	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.001	-0.004	22.910	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.053	-0.005	21.636	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.005	0.003	20.635	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.805	-0.887	20.146	-0.273	-0.273	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.006	0.011	16.152	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.011	-0.012	15.757	-0.073	-0.073	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.012	0.006	15.747	-0.067	-0.067	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.029	-0.016	12.850	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.012	0.008	11.284	-0.090	-0.090	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.928	-0.958	10.652	-0.951	-0.951	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.074	0.034	11.303	-0.109	-0.109	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.082	-0.047	8.185	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.008	-0.013	6.585	-0.348	-0.348	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.031	0.028	7.015	-0.186	-0.186	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.008	0.009	8.774	0.053	0.053	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.001	-0.005	3.168	-0.178	0.117	0.025	-0.075	-0.245	0.000
28	A	28	HIS	0	-0.101	-0.068	5.298	0.157	0.250	-0.001	-0.001	-0.091	0.000
29	A	29	GLU	-1	-0.863	-0.936	6.807	-0.398	-0.398	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.140	-0.075	7.625	0.184	0.184	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.061	-0.027	2.976	-0.275	0.281	0.206	-0.137	-0.625	-0.001
32	A	32	GLY	0	0.008	0.018	6.596	0.171	0.171	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.062	-0.018	2.413	-2.165	-0.507	1.477	-0.998	-2.137	-0.009
34	A	34	PRO	0	0.059	0.024	5.070	-0.158	-0.108	-0.001	-0.006	-0.043	0.000
35	A	35	VAL	0	0.093	0.028	4.942	-0.892	-0.808	-0.001	-0.001	-0.082	0.000
36	A	36	GLU	-1	-0.930	-0.950	6.140	-1.443	-1.443	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.120	-0.057	3.596	0.058	0.453	0.021	-0.117	-0.299	0.000
38	A	38	VAL	0	-0.060	-0.023	2.225	-9.351	-6.444	3.656	-2.706	-3.858	-0.028
39	A	39	ARG	1	0.970	1.001	3.500	3.499	4.033	0.016	-0.061	-0.489	0.000
40	A	40	VAL	0	0.058	0.016	5.486	-0.327	-0.327	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.060	-0.022	8.049	0.263	0.263	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.012	-0.003	10.951	0.034	0.034	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.859	-0.910	13.644	-0.145	-0.145	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.882	-0.954	16.332	-0.259	-0.259	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.038	-0.025	19.718	0.027	0.027	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.042	0.029	22.061	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.002	-0.018	25.801	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.882	-0.955	27.340	-0.069	-0.069	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.914	0.952	25.661	0.075	0.075	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.016	0.028	18.587	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.007	-0.008	25.071	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.013	-0.004	25.019	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.003	-0.002	27.431	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.004	-0.007	29.626	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.975	1.004	30.987	0.032	0.032	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.070	0.045	29.211	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.015	-0.029	25.474	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.001	0.005	28.895	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.902	-0.953	31.678	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.881	0.930	28.728	0.051	0.051	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.932	0.967	26.820	0.107	0.107	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.011	0.004	33.384	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.058	-0.020	36.340	0.005	0.005	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.005	0.010	34.824	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.023	-0.004	36.531	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)