FMO DATABASE

FMODB ID: 2NL9R

Calculation Name: 5DYM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DYM

Chain ID: A

ChEMBL ID:

UniProt ID: C9YK90

Base Structure: X-ray

Registration Date: 2023-09-22

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-740825.807965
FMO2-HF: Nuclear repulsion	700013.978107
FMO2-HF: Total energy	-40811.829858
FMO2-MP2: Total energy	-40930.420288

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:10:GLY)

Summations of interaction energy for fragment #1(A:10:GLY)

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.
-6.356	-3.266	0.373	-1.373	-2.089	0.01

Interaction energy analysis for fragmet #1(A:10:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.005

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	12	ILE	0	0.003	-0.001	2.922	-3.847	-1.162	0.374	-1.308	-1.751	0.010
4	A	13	ASP	-1	-0.756	-0.881	4.215	-0.910	-0.609	-0.001	-0.035	-0.265	0.000
5	A	14	ILE	0	0.035	0.012	6.241	0.002	0.002	0.000	0.000	0.000	0.000
6	A	15	LEU	0	-0.009	0.005	7.271	0.007	0.007	0.000	0.000	0.000	0.000
7	A	16	ILE	0	0.006	-0.003	8.084	-0.116	-0.116	0.000	0.000	0.000	0.000
8	A	17	VAL	0	0.012	-0.002	10.385	-0.084	-0.084	0.000	0.000	0.000	0.000
9	A	18	SER	0	-0.048	-0.013	12.086	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.054	-0.028	12.355	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.039	-0.025	13.927	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	21	GLU	-1	-0.846	-0.892	16.784	0.019	0.019	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.855	0.914	18.642	-0.086	-0.086	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.859	0.904	20.464	-0.199	-0.199	0.000	0.000	0.000	0.000
15	A	24	ASP	-1	-0.692	-0.781	19.842	0.151	0.151	0.000	0.000	0.000	0.000
16	A	25	CYS	0	-0.064	-0.022	17.496	0.000	0.000	0.000	0.000	0.000	0.000
17	A	26	TYR	0	0.057	0.023	18.552	0.008	0.008	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.030	-0.004	15.823	0.022	0.022	0.000	0.000	0.000	0.000
19	A	28	TYR	0	0.017	0.008	16.063	0.055	0.055	0.000	0.000	0.000	0.000
20	A	29	GLU	-1	-0.780	-0.885	17.950	0.237	0.237	0.000	0.000	0.000	0.000
21	A	30	ILE	0	-0.008	-0.003	12.376	0.013	0.013	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.028	-0.006	13.093	0.067	0.067	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.795	0.890	14.168	-0.223	-0.223	0.000	0.000	0.000	0.000
24	A	33	GLN	0	0.044	0.027	15.561	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	34	VAL	0	-0.021	-0.015	9.348	0.011	0.011	0.000	0.000	0.000	0.000
26	A	35	ARG	1	0.873	0.950	12.662	-0.566	-0.566	0.000	0.000	0.000	0.000
27	A	36	GLU	-1	-0.794	-0.874	14.729	0.219	0.219	0.000	0.000	0.000	0.000
28	A	37	ARG	1	0.869	0.938	15.209	-0.313	-0.313	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.098	-0.066	11.230	0.039	0.039	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.830	-0.910	11.913	0.212	0.212	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.077	-0.031	4.825	0.338	0.338	0.000	0.000	0.000	0.000
32	A	41	GLU	-1	-0.833	-0.905	9.854	0.447	0.447	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.058	-0.046	7.653	0.126	0.126	0.000	0.000	0.000	0.000
34	A	43	LYS	1	0.944	0.959	9.210	-0.599	-0.599	0.000	0.000	0.000	0.000
35	A	44	GLU	-1	-0.821	-0.905	10.134	0.540	0.540	0.000	0.000	0.000	0.000
36	A	45	GLY	0	0.004	-0.007	11.786	0.023	0.023	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.022	0.004	5.361	-0.118	-0.118	0.000	0.000	0.000	0.000
38	A	47	MET	0	-0.009	0.013	7.638	0.233	0.233	0.000	0.000	0.000	0.000
39	A	48	TYR	0	0.012	-0.003	9.591	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	49	LEU	0	0.003	0.008	8.438	-0.087	-0.087	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.016	-0.011	6.103	-0.103	-0.103	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.004	0.002	7.532	-0.216	-0.216	0.000	0.000	0.000	0.000
43	A	52	LYS	1	0.885	0.944	10.980	-0.304	-0.304	0.000	0.000	0.000	0.000
44	A	53	ARG	1	0.885	0.927	4.126	-1.064	-0.960	0.000	-0.030	-0.073	0.000
45	A	54	MET	0	-0.021	-0.009	8.328	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	55	GLU	-1	-0.746	-0.828	10.787	0.166	0.166	0.000	0.000	0.000	0.000
47	A	56	SER	0	-0.040	-0.015	12.935	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	57	LYS	1	0.863	0.942	6.996	0.265	0.265	0.000	0.000	0.000	0.000
49	A	58	ASN	0	0.017	0.021	13.815	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.044	0.046	10.324	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.050	-0.030	12.276	0.020	0.020	0.000	0.000	0.000	0.000
52	A	61	LYS	1	0.947	0.970	15.609	-0.102	-0.102	0.000	0.000	0.000	0.000
53	A	62	SER	0	-0.035	-0.039	18.155	0.002	0.002	0.000	0.000	0.000	0.000
54	A	63	TYR	0	-0.106	-0.080	19.818	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	64	TYR	0	0.035	0.005	22.303	0.024	0.024	0.000	0.000	0.000	0.000
56	A	65	SER	0	0.019	0.030	25.448	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	66	ASN	0	0.052	0.012	27.798	0.001	0.001	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.801	-0.889	31.208	0.097	0.097	0.000	0.000	0.000	0.000
59	A	68	GLN	0	0.007	0.002	32.398	0.002	0.002	0.000	0.000	0.000	0.000
60	A	69	SER	0	-0.073	-0.031	30.608	0.000	0.000	0.000	0.000	0.000	0.000
61	A	70	SER	0	0.038	0.012	31.731	0.004	0.004	0.000	0.000	0.000	0.000
62	A	71	GLY	0	0.004	0.001	28.457	0.001	0.001	0.000	0.000	0.000	0.000
63	A	72	GLY	0	0.026	0.027	28.603	0.008	0.008	0.000	0.000	0.000	0.000
64	A	73	ARG	1	0.812	0.894	26.407	-0.101	-0.101	0.000	0.000	0.000	0.000
65	A	74	ARG	1	0.896	0.955	23.133	-0.161	-0.161	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.842	0.907	16.717	-0.250	-0.250	0.000	0.000	0.000	0.000
67	A	76	TYR	0	-0.020	-0.011	19.839	0.035	0.035	0.000	0.000	0.000	0.000
68	A	77	TYR	0	0.005	-0.016	15.494	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	78	ASN	0	-0.014	-0.014	18.291	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	79	LEU	0	0.008	0.019	14.819	0.003	0.003	0.000	0.000	0.000	0.000
71	A	80	THR	0	0.025	-0.003	17.265	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	81	ASN	0	0.031	0.000	18.803	0.003	0.003	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.817	-0.898	16.974	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	83	GLY	0	-0.005	-0.011	14.623	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.813	0.898	15.285	-0.053	-0.053	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.867	-0.922	17.871	-0.064	-0.064	0.000	0.000	0.000	0.000
77	A	86	PHE	0	-0.029	-0.026	8.404	-0.042	-0.042	0.000	0.000	0.000	0.000
78	A	87	LEU	0	-0.019	-0.010	13.686	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	88	GLU	-1	-0.821	-0.905	14.666	-0.076	-0.076	0.000	0.000	0.000	0.000
80	A	89	ILE	0	0.051	0.022	14.835	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.779	0.877	9.824	0.482	0.482	0.000	0.000	0.000	0.000
82	A	91	LYS	1	0.859	0.923	13.473	0.004	0.004	0.000	0.000	0.000	0.000
83	A	92	GLN	0	-0.064	-0.031	16.145	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.767	-0.863	12.515	-0.473	-0.473	0.000	0.000	0.000	0.000
85	A	94	TRP	0	0.006	0.003	13.587	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	95	ARG	1	0.818	0.886	15.224	0.111	0.111	0.000	0.000	0.000	0.000
87	A	96	PHE	0	0.011	0.012	17.604	0.014	0.014	0.000	0.000	0.000	0.000
88	A	97	ILE	0	0.049	0.013	12.790	0.012	0.012	0.000	0.000	0.000	0.000
89	A	98	LYS	1	0.929	0.973	16.783	0.101	0.101	0.000	0.000	0.000	0.000
90	A	99	LYS	1	0.952	0.985	17.875	0.118	0.118	0.000	0.000	0.000	0.000
91	A	100	VAL	0	0.009	0.004	19.257	0.013	0.013	0.000	0.000	0.000	0.000
92	A	101	MET	0	0.035	0.004	15.460	0.000	0.000	0.000	0.000	0.000	0.000
93	A	102	ASN	0	0.003	0.005	18.867	0.005	0.005	0.000	0.000	0.000	0.000
94	A	103	GLN	0	-0.053	-0.016	21.039	0.016	0.016	0.000	0.000	0.000	0.000
95	A	104	PHE	0	-0.022	-0.017	21.474	0.009	0.009	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.019	-0.007	16.764	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	106	GLY	0	-0.067	-0.008	20.723	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:GLY)