FMO DATABASE

FMODB ID: YY6Z2

Calculation Name: 3NRW-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRW

Chain ID: A

ChEMBL ID:

UniProt ID: Q5V4F9

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	106
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-885259.843434
FMO2-HF: Nuclear repulsion	842284.3967
FMO2-HF: Total energy	-42975.446734
FMO2-MP2: Total energy	-43102.524298

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:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
1.813	3.945	0.47	-1.177	-1.425	-0.005

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.035

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	5	PRO	0	0.007	0.021	3.321	0.292	1.338	0.025	-0.501	-0.569	0.000
4	A	6	SER	0	0.016	0.007	5.418	0.311	0.311	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.008	0.004	8.040	-0.012	-0.012	0.000	0.000	0.000	0.000
6	A	8	SER	0	0.063	0.043	11.266	0.061	0.061	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.093	0.023	14.156	0.015	0.015	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.962	0.984	16.101	0.017	0.017	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.854	-0.920	14.358	-0.083	-0.083	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.025	0.013	12.991	0.002	0.002	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.880	0.944	14.811	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.894	-0.950	18.343	0.013	0.013	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.919	0.970	12.593	0.022	0.022	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.022	0.012	16.664	0.005	0.005	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.054	-0.034	17.824	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.034	0.018	19.914	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	19	HIS	0	-0.041	-0.016	17.498	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.974	0.987	19.628	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.054	-0.012	22.255	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.020	-0.020	22.439	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.956	-0.966	23.224	0.068	0.068	0.000	0.000	0.000	0.000
22	A	24	ALA	0	-0.022	-0.016	25.927	0.005	0.005	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.028	0.020	27.780	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.819	-0.924	29.788	0.027	0.027	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.040	-0.029	30.836	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.005	-0.003	28.001	0.001	0.001	0.000	0.000	0.000	0.000
27	A	29	ILE	0	0.036	0.038	24.844	0.006	0.006	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.940	0.970	26.798	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	31	SER	0	-0.004	0.004	28.825	0.001	0.001	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.022	-0.013	23.452	0.005	0.005	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.975	0.988	24.425	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	34	TYR	0	-0.040	-0.043	25.656	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.903	0.954	25.250	-0.075	-0.075	0.000	0.000	0.000	0.000
34	A	36	LEU	0	0.037	0.015	19.578	0.003	0.003	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.883	0.961	22.362	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.028	0.016	24.631	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.028	0.010	16.603	0.000	0.000	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.042	-0.031	19.322	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.897	-0.940	20.972	0.037	0.037	0.000	0.000	0.000	0.000
40	A	42	TRP	0	0.017	0.015	18.786	0.000	0.000	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.014	-0.027	17.661	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.977	-0.999	19.703	0.013	0.013	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.918	-0.961	20.948	0.015	0.015	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.747	0.901	20.582	-0.071	-0.071	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.909	-0.949	19.901	0.022	0.022	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.072	-0.020	14.329	0.005	0.005	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.029	-0.029	14.542	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.018	-0.016	9.529	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	51	MET	0	-0.022	-0.010	10.444	0.029	0.029	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.850	0.900	3.222	-2.593	-1.816	0.419	-0.537	-0.659	-0.004
51	A	53	GLU	-1	-0.877	-0.937	8.022	0.089	0.089	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.052	-0.022	10.995	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.058	0.020	11.702	0.046	0.046	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.062	0.016	14.268	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	57	TRP	0	0.013	0.015	17.253	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.947	0.979	15.088	-0.153	-0.153	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.004	-0.004	15.439	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.884	-0.935	18.974	0.102	0.102	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.893	-0.950	21.701	0.070	0.070	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.052	-0.025	21.023	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.813	-0.904	22.943	0.106	0.106	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.027	-0.023	24.842	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	65	PHE	0	-0.020	-0.005	25.805	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.819	0.883	25.708	-0.074	-0.074	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.912	0.972	28.415	-0.083	-0.083	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.024	-0.003	30.745	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.081	-0.044	31.572	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	70	ASP	-1	-0.882	-0.945	33.471	0.037	0.037	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.079	-0.030	31.180	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.010	-0.003	34.518	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.073	0.021	33.370	0.003	0.003	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.020	0.008	32.321	0.005	0.005	0.000	0.000	0.000	0.000
73	A	75	THR	0	-0.039	-0.021	31.341	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.060	0.036	27.639	0.003	0.003	0.000	0.000	0.000	0.000
75	A	77	ASN	0	0.063	0.012	27.681	0.010	0.010	0.000	0.000	0.000	0.000
76	A	78	GLY	0	-0.002	0.001	27.045	0.008	0.008	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.854	-0.906	25.062	0.081	0.081	0.000	0.000	0.000	0.000
78	A	80	MET	0	0.045	0.022	22.182	0.007	0.007	0.000	0.000	0.000	0.000
79	A	81	GLN	0	-0.011	0.004	22.180	0.011	0.011	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.041	-0.024	21.994	0.005	0.005	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.016	0.015	17.812	0.008	0.008	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.969	0.995	17.817	-0.184	-0.184	0.000	0.000	0.000	0.000
83	A	85	ASN	0	0.018	0.004	17.267	0.032	0.032	0.000	0.000	0.000	0.000
84	A	86	TRP	0	-0.094	-0.043	15.865	0.019	0.019	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.037	0.001	12.810	0.018	0.018	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.900	-0.941	12.336	0.300	0.300	0.000	0.000	0.000	0.000
87	A	89	TYR	0	-0.061	-0.032	12.663	0.023	0.023	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.003	-0.026	10.146	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	91	ALA	0	0.035	0.037	8.234	0.102	0.102	0.000	0.000	0.000	0.000
90	A	92	ARG	1	0.929	0.975	7.838	-0.072	-0.072	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.132	-0.057	8.609	-0.052	-0.052	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.850	-0.923	3.233	0.206	0.413	0.024	-0.096	-0.135	-0.001
93	A	95	VAL	0	-0.077	-0.034	4.120	0.340	0.442	0.002	-0.043	-0.062	0.000
94	A	96	VAL	0	-0.067	-0.045	6.566	-0.109	-0.109	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.867	-0.924	5.951	1.688	1.688	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.899	-0.963	6.734	1.409	1.409	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.936	-0.960	9.085	0.464	0.464	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.023	-0.013	10.718	-0.115	-0.115	0.000	0.000	0.000	0.000
99	A	101	PRO	0	-0.011	-0.012	11.921	-0.093	-0.093	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.944	-0.983	14.788	0.268	0.268	0.000	0.000	0.000	0.000
101	A	103	LYS	1	0.904	0.953	13.304	-0.425	-0.425	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.059	-0.015	16.911	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	105	HIS	0	-0.054	-0.044	19.428	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.042	-0.032	22.848	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	107	PRO	0	-0.018	0.020	25.292	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	108	NME	0	-0.029	-0.013	28.671	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )