FMO DATABASE

FMODB ID: ZV8GN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-300124.541308
FMO2-HF: Nuclear repulsion	276345.949264
FMO2-HF: Total energy	-23778.592044
FMO2-MP2: Total energy	-23849.79325

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.
-14.02	-6.783	7.962	-5.713	-9.488	-0.042

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 : 0.019 / 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

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	3	ILE	0	0.014	0.009	3.675	-0.430	1.326	-0.006	-0.682	-1.068	0.003
4	A	4	ARG	1	0.812	0.876	6.055	0.014	0.014	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.015	0.005	9.775	0.061	0.061	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.014	0.016	12.558	0.004	0.004	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.036	-0.022	15.978	0.003	0.003	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.039	-0.031	18.764	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.906	-0.970	22.229	-0.099	-0.099	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.072	-0.033	24.016	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.835	0.924	20.113	0.185	0.185	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.002	-0.025	23.047	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.032	-0.010	21.210	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.022	0.009	20.018	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.782	-0.844	19.574	-0.225	-0.225	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.005	0.008	16.285	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.011	-0.006	15.284	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.006	0.002	14.902	-0.068	-0.068	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.013	-0.002	12.927	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.015	0.004	10.900	-0.072	-0.072	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.937	-0.961	9.951	-0.911	-0.911	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.071	0.032	10.619	-0.123	-0.123	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.047	-0.027	7.882	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.026	-0.019	6.200	-0.328	-0.328	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.007	7.072	-0.202	-0.202	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.008	-0.007	8.876	0.019	0.019	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.001	0.012	3.651	-0.093	0.112	0.005	-0.045	-0.165	0.000
28	A	28	HIS	0	-0.081	-0.046	5.464	0.101	0.101	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.899	-0.959	7.143	-0.463	-0.463	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.109	-0.073	7.689	0.147	0.147	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.051	-0.025	3.131	-0.314	0.213	0.098	-0.128	-0.497	-0.001
32	A	32	GLY	0	-0.004	0.016	6.142	0.092	0.092	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.037	-0.011	2.400	-2.197	-0.493	0.981	-0.844	-1.842	-0.007
34	A	34	PRO	0	0.023	0.008	5.121	-0.048	-0.006	-0.001	-0.007	-0.034	0.000
35	A	35	VAL	0	0.083	0.032	4.884	-0.874	-0.787	-0.001	-0.002	-0.084	0.000
36	A	36	GLU	-1	-0.838	-0.898	6.206	-1.464	-1.464	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.053	-0.022	3.474	-0.033	0.511	0.036	-0.198	-0.382	0.000
38	A	38	VAL	0	-0.038	-0.005	2.031	-9.866	-8.066	6.839	-3.706	-4.934	-0.037
39	A	39	ARG	1	0.801	0.885	3.584	3.249	3.821	0.011	-0.101	-0.482	0.000
40	A	40	VAL	0	0.040	0.019	5.680	-0.108	-0.108	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.043	-0.014	8.069	0.204	0.204	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.021	0.001	11.191	0.043	0.043	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.832	-0.898	14.052	-0.046	-0.046	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.814	-0.909	17.075	-0.160	-0.160	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.016	-0.009	20.328	0.024	0.024	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.010	0.031	22.873	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.002	-0.020	26.592	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.854	-0.950	28.116	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.910	0.948	26.269	0.039	0.039	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.021	0.039	18.717	0.009	0.009	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.005	-0.005	25.440	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.009	-0.007	25.235	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.010	0.000	27.728	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.001	-0.002	30.043	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.863	0.937	31.732	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.045	0.028	29.899	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.006	-0.018	26.019	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.012	0.003	29.423	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.782	-0.891	32.280	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.862	0.931	30.035	0.024	0.024	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.944	0.971	27.073	0.075	0.075	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.002	0.014	33.739	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.078	-0.045	36.446	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.003	0.014	35.055	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.016	0.001	36.492	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)