FMO DATABASE

FMODB ID: 226NR

Calculation Name: 3NRY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRY

Chain ID: A

ChEMBL ID:

UniProt ID: O43663

Base Structure: X-ray

Registration Date: 2023-06-20

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107837.028112
FMO2-HF: Nuclear repulsion	1052324.270507
FMO2-HF: Total energy	-55512.757605
FMO2-MP2: Total energy	-55674.35203

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-0.438	1.907	0.3	-1.088	-1.559	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.017

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	ALA	0	-0.011	0.003	3.729	-0.496	0.862	-0.004	-0.650	-0.704	0.001
4	A	4	ALA	0	0.071	0.026	2.500	-1.295	-0.606	0.305	-0.347	-0.648	0.000
5	A	5	LEU	0	0.011	0.008	4.023	-0.065	0.233	-0.001	-0.091	-0.207	0.000
6	A	6	LYS	1	0.960	0.979	5.805	0.812	0.812	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.036	0.016	7.722	0.172	0.172	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.014	0.019	7.952	0.102	0.102	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.007	-0.030	9.590	0.144	0.144	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.964	-0.973	11.732	-0.167	-0.167	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.060	0.038	12.871	0.047	0.047	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.035	-0.010	13.901	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.954	0.972	15.703	0.218	0.218	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.899	-0.946	17.460	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.042	-0.011	17.292	0.025	0.025	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.016	-0.019	20.013	0.014	0.014	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.907	-0.958	21.757	-0.118	-0.118	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.008	-0.004	23.182	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.020	-0.009	23.869	0.011	0.011	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.013	0.001	26.057	0.018	0.018	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.945	0.993	27.751	0.065	0.065	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.058	-0.041	28.967	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.703	-0.821	30.428	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.954	-0.974	32.160	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.063	-0.050	33.271	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	TRP	0	-0.006	-0.002	34.877	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.835	0.900	35.174	0.075	0.075	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.007	0.007	37.700	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.028	-0.014	39.439	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.016	-0.004	39.662	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.863	-0.881	42.598	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.015	-0.034	43.456	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.794	-0.862	44.047	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.864	0.905	43.688	0.045	0.045	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.940	0.970	48.698	0.032	0.032	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.018	-0.010	49.730	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.066	-0.037	50.472	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.868	-0.925	52.349	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.037	-0.013	54.455	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.046	0.019	57.643	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.848	0.913	55.432	0.025	0.025	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.012	-0.002	58.596	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.006	0.011	61.950	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.033	0.030	57.418	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.901	0.946	61.277	0.020	0.020	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.020	0.005	57.712	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.037	0.015	56.612	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.004	-0.014	57.811	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.013	0.017	53.868	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.010	0.023	53.530	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.899	0.947	52.017	0.016	0.016	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.877	-0.961	48.957	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.832	-0.921	48.069	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.958	0.984	47.601	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.028	0.033	42.292	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.880	0.924	43.364	0.027	0.027	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.014	-0.004	43.321	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.789	0.899	38.950	0.035	0.035	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	-0.015	38.422	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.030	0.023	38.319	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.939	0.966	38.981	0.018	0.018	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.028	-0.013	34.242	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.009	0.014	34.077	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.068	0.035	33.134	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.815	0.907	29.466	0.035	0.035	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.048	-0.038	29.536	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.791	-0.881	28.249	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.902	-0.940	28.070	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.856	-0.921	25.848	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.039	-0.013	22.770	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.929	0.958	23.196	0.050	0.050	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.015	0.019	23.274	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.925	0.960	19.485	0.061	0.061	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.005	-0.008	18.464	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.861	-0.930	18.688	-0.089	-0.089	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.019	-0.017	16.560	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.009	0.009	12.561	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.867	-0.950	14.144	-0.209	-0.209	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.061	-0.032	15.867	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.957	-0.961	9.471	-0.110	-0.110	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.059	-0.034	8.780	-0.172	-0.172	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.041	-0.009	11.760	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.867	0.937	11.856	0.602	0.602	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.022	0.019	16.345	0.023	0.023	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.019	-0.020	18.453	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.069	-0.029	20.029	0.028	0.028	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.003	-0.009	22.445	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.050	-0.029	25.035	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.011	0.011	26.270	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.004	-0.005	26.860	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	LYS	1	1.015	1.012	23.820	0.107	0.107	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.057	0.026	24.895	0.011	0.011	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.026	0.005	25.714	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.939	-0.965	28.289	-0.090	-0.090	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.037	-0.043	29.566	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.007	-0.007	29.901	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.016	-0.009	32.281	0.006	0.006	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.875	-0.934	34.266	-0.074	-0.074	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.010	0.010	34.583	0.008	0.008	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.029	-0.035	35.384	0.007	0.007	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.803	-0.875	38.630	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.016	-0.009	38.120	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.037	-0.022	41.132	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.781	0.872	42.743	0.039	0.039	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.021	-0.021	43.577	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.897	-0.930	45.614	-0.039	-0.039	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.864	0.923	46.172	0.035	0.035	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.980	-0.994	48.978	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.994	0.992	46.911	0.040	0.040	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.053	0.039	51.608	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.871	0.927	52.441	0.027	0.027	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.014	0.007	54.462	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.924	-0.955	55.953	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.957	0.969	55.111	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	GLN	0	-0.037	-0.007	59.362	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.037	0.004	59.462	0.001	0.001	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.972	1.002	61.891	0.025	0.025	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.005	-0.014	63.303	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.960	0.990	65.184	0.018	0.018	0.000	0.000	0.000	0.000
120	A	120	LYS	1	1.016	1.004	66.093	0.023	0.023	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.007	0.010	67.842	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.045	-0.033	69.740	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.971	-0.989	70.807	-0.019	-0.019	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.009	-0.019	71.527	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.959	-0.972	73.657	-0.016	-0.016	0.000	0.000	0.000	0.000
126	A	126	MET	0	-0.058	-0.034	75.642	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.047	-0.015	74.687	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.045	-0.028	74.620	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.024	0.044	79.025	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.047	-0.024	80.174	0.000	0.000	0.000	0.000	0.000	0.000

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