FMO DATABASE

FMODB ID: 1NYMZ

Calculation Name: 1RIY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RIY

Chain ID: A

ChEMBL ID:

UniProt ID: P36206

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-385543.983463
FMO2-HF: Nuclear repulsion	358282.489112
FMO2-HF: Total energy	-27261.494351
FMO2-MP2: Total energy	-27342.907627

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:MET)

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

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.
-19.255	-11.645	11.937	-6.899	-12.65	-0.022

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.028

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	LYS	1	0.924	0.939	2.930	-2.107	1.405	0.184	-2.010	-1.686	-0.001
4	A	4	LYS	1	0.887	0.932	5.570	0.960	0.960	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.772	-0.882	2.307	-7.170	-4.347	3.448	-2.724	-3.548	-0.024
6	A	6	LEU	0	-0.001	0.009	2.934	1.206	3.374	1.944	-1.197	-2.916	0.001
7	A	7	ILE	0	0.003	0.004	3.768	0.482	0.154	0.023	0.641	-0.336	-0.001
8	A	8	ASP	-1	-0.755	-0.864	6.928	0.687	0.687	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.846	0.899	2.753	-5.843	-6.408	6.338	-1.609	-4.164	0.003
10	A	10	VAL	0	-0.014	-0.008	6.107	-0.657	-0.657	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.006	0.000	8.152	-0.445	-0.445	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.956	0.976	9.729	-1.319	-1.319	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.913	0.946	4.989	-2.930	-2.930	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.011	0.013	10.838	-0.156	-0.156	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.027	0.039	13.725	-0.124	-0.124	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.002	0.012	13.870	-0.107	-0.107	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.956	0.959	14.503	-0.278	-0.278	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.905	0.939	10.926	-0.788	-0.788	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.899	0.949	13.074	-0.256	-0.256	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.818	-0.900	15.831	0.291	0.291	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.017	0.010	9.915	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.937	0.973	11.724	0.116	0.116	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.017	0.016	12.641	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.043	0.033	14.368	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.002	-0.002	8.175	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.818	-0.926	12.445	-0.161	-0.161	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.049	0.020	14.367	-0.069	-0.069	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.033	0.002	14.110	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.053	-0.037	10.519	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.867	-0.917	15.061	-0.205	-0.205	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.017	-0.003	18.470	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.067	-0.042	15.405	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.016	-0.016	17.620	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.898	-0.952	20.030	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.030	-0.013	22.113	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.033	-0.024	18.427	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.023	-0.009	22.988	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.844	0.906	25.390	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.086	-0.033	26.364	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.817	-0.888	25.468	0.011	0.011	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.853	0.919	23.553	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.046	0.025	19.660	0.020	0.020	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.011	-0.019	20.036	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.029	0.023	15.636	0.013	0.013	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.069	0.024	18.148	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.021	0.010	16.813	0.045	0.045	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.036	-0.012	10.469	0.046	0.046	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.039	0.002	15.184	-0.057	-0.057	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.055	-0.019	17.692	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.057	0.030	12.979	-0.041	-0.041	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.788	-0.865	18.922	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.041	0.030	21.517	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.822	0.895	24.139	0.089	0.089	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.996	0.985	26.488	0.082	0.082	0.000	0.000	0.000	0.000
55	A	74	ARG	1	1.039	1.010	28.014	0.158	0.158	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.909	0.980	26.501	0.122	0.122	0.000	0.000	0.000	0.000
57	A	76	VAL	0	0.043	0.023	22.142	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.038	0.012	18.726	0.031	0.031	0.000	0.000	0.000	0.000
59	A	78	LYS	1	0.952	0.979	19.018	0.131	0.131	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.033	0.018	13.795	0.033	0.033	0.000	0.000	0.000	0.000
61	A	80	LYS	1	0.829	0.908	17.329	0.027	0.027	0.000	0.000	0.000	0.000
62	A	81	PRO	0	0.040	0.036	15.122	0.044	0.044	0.000	0.000	0.000	0.000
63	A	82	GLY	0	0.035	0.002	17.081	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.870	0.926	17.951	-0.074	-0.074	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.063	0.024	16.806	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	85	LEU	0	-0.022	-0.008	11.040	0.033	0.033	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.913	0.943	14.541	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	87	GLU	-1	-0.764	-0.857	17.123	0.049	0.049	0.000	0.000	0.000	0.000
69	A	88	LYS	1	0.939	0.986	10.239	-0.565	-0.565	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.023	-0.006	10.972	0.025	0.025	0.000	0.000	0.000	0.000
71	A	90	LYS	1	0.856	0.923	13.554	-0.092	-0.092	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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