FMO DATABASE

FMODB ID: GNL61

Calculation Name: 3NRH-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRH

Chain ID: A

ChEMBL ID:

UniProt ID: Q64XJ4

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	162
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1627680.177428
FMO2-HF: Nuclear repulsion	1562854.380264
FMO2-HF: Total energy	-64825.797165
FMO2-MP2: Total energy	-65012.607854

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:5:ACE )

Summations of interaction energy for fragment #1(A:5: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.
18.467	5.129	28.096	-10.481	-4.278	-0.035

Interaction energy analysis for fragmet #1(A:5:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.085 / q_NPA : -0.001

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	7	VAL	0	0.067	0.029	3.614	0.792	1.459	-0.006	-0.124	-0.537	0.000
4	A	8	ILE	0	0.010	0.024	3.293	-0.332	0.095	0.113	-0.176	-0.364	0.000
5	A	9	PHE	0	-0.007	-0.001	2.578	0.341	0.506	0.465	-0.158	-0.472	0.001
6	A	10	ASP	-1	-0.894	-0.957	7.549	-0.370	-0.370	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.944	0.958	10.093	0.484	0.484	0.000	0.000	0.000	0.000
8	A	12	ASN	0	0.001	-0.007	13.512	0.084	0.084	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.031	0.029	9.209	0.071	0.071	0.000	0.000	0.000	0.000
10	A	14	ILE	0	0.000	0.008	10.506	0.085	0.085	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.891	-0.945	13.456	-0.130	-0.130	0.000	0.000	0.000	0.000
12	A	16	PHE	0	0.002	-0.001	14.428	0.033	0.033	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.036	0.020	12.269	0.032	0.032	0.000	0.000	0.000	0.000
14	A	18	THR	0	-0.039	-0.014	15.580	0.028	0.028	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.017	-0.010	18.640	0.016	0.016	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.024	0.015	17.732	0.014	0.014	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.033	0.013	18.873	0.015	0.015	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.964	-0.976	20.582	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	23	PHE	0	-0.046	-0.038	23.046	0.004	0.004	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.028	-0.001	21.660	0.008	0.008	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.048	0.029	24.317	0.004	0.004	0.000	0.000	0.000	0.000
22	A	26	PHE	0	-0.075	-0.049	26.099	0.001	0.001	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.013	-0.013	27.164	0.001	0.001	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.766	-0.853	24.963	0.035	0.035	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.896	0.957	29.388	0.003	0.003	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.044	0.023	32.138	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.941	-0.970	34.378	0.015	0.015	0.000	0.000	0.000	0.000
28	A	32	SER	0	-0.096	-0.035	35.670	0.000	0.000	0.000	0.000	0.000	0.000
29	A	33	MET	0	-0.064	-0.015	33.178	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.942	0.969	38.744	0.003	0.003	0.000	0.000	0.000	0.000
31	A	35	ARG	1	0.951	0.975	39.638	0.001	0.001	0.000	0.000	0.000	0.000
32	A	36	SER	0	-0.026	-0.010	39.769	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	37	THR	0	0.043	0.016	36.553	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	38	PHE	0	0.075	0.030	32.909	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	39	VAL	0	0.018	0.009	35.019	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	40	ASP	-1	-0.864	-0.925	35.906	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	41	THR	0	-0.051	-0.030	31.175	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	42	THR	0	0.050	0.023	30.673	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.039	-0.019	30.996	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.887	0.950	31.098	0.029	0.029	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.022	0.005	25.748	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.022	0.019	26.322	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	47	PRO	0	0.011	0.004	26.547	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.011	0.001	23.459	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.047	0.018	20.787	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	50	TYR	0	0.019	0.007	21.752	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.036	-0.011	22.677	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.863	0.903	18.644	0.136	0.136	0.000	0.000	0.000	0.000
49	A	53	ALA	0	0.043	0.032	17.997	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	54	SER	0	-0.066	-0.042	18.315	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	55	MET	0	-0.112	-0.042	18.397	0.002	0.002	0.000	0.000	0.000	0.000
52	A	56	LEU	0	-0.020	0.012	13.151	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	57	PRO	0	-0.033	-0.001	10.840	0.024	0.024	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.935	0.961	12.964	0.258	0.258	0.000	0.000	0.000	0.000
55	A	59	CYS	0	-0.002	0.014	10.019	-0.107	-0.107	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.946	-0.966	9.340	0.023	0.023	0.000	0.000	0.000	0.000
57	A	61	MET	0	-0.061	-0.023	9.606	0.051	0.051	0.000	0.000	0.000	0.000
58	A	62	ILE	0	-0.045	-0.009	6.865	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	63	GLY	0	-0.052	-0.028	10.253	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.959	-0.973	11.731	0.589	0.589	0.000	0.000	0.000	0.000
61	A	65	GLU	-1	-0.972	-0.995	12.802	0.426	0.426	0.000	0.000	0.000	0.000
62	A	66	SER	0	-0.065	-0.034	13.211	0.009	0.009	0.000	0.000	0.000	0.000
63	A	67	PRO	0	0.016	-0.003	12.255	0.014	0.014	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.926	-0.955	14.359	0.200	0.200	0.000	0.000	0.000	0.000
65	A	69	THR	0	-0.037	-0.021	16.993	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	70	TYR	0	-0.067	-0.031	19.735	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	71	VAL	0	-0.038	-0.024	21.721	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.002	0.013	24.525	0.001	0.001	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.861	-0.955	27.555	0.040	0.040	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.925	-0.964	30.863	0.037	0.037	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.049	-0.016	26.492	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	76	TYR	0	-0.022	-0.042	28.359	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.773	-0.873	30.103	0.023	0.023	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.020	0.000	32.944	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.019	0.000	28.472	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	80	ARG	1	0.866	0.904	32.457	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	81	ILE	0	0.012	0.004	34.204	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	82	ASN	0	0.024	0.018	34.314	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.042	-0.024	31.386	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	84	ALA	0	0.022	0.010	36.047	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	85	SER	0	-0.056	-0.026	39.009	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.081	-0.020	37.186	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	87	LEU	0	-0.022	-0.020	36.818	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.001	0.000	40.851	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.871	-0.960	43.508	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.794	0.899	41.725	0.004	0.004	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.725	-0.822	38.264	0.004	0.004	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.876	-0.918	39.778	0.005	0.005	0.000	0.000	0.000	0.000
89	A	93	TYR	0	-0.121	-0.080	35.401	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	94	LEU	0	-0.090	-0.051	41.645	0.001	0.001	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.906	-0.969	38.201	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	96	NME	0	0.011	0.024	38.692	0.001	0.001	0.000	0.000	0.000	0.000
93	A	107	ACE	0	0.014	-0.002	43.219	0.000	0.000	0.000	0.000	0.000	0.000
94	A	108	ILE	0	-0.022	-0.021	38.199	0.002	0.002	0.000	0.000	0.000	0.000
95	A	109	LYS	1	0.931	0.963	41.775	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	110	LYS	1	0.971	1.000	34.947	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	111	ASN	0	0.069	0.031	37.380	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	112	ILE	0	-0.004	-0.009	34.449	0.000	0.000	0.000	0.000	0.000	0.000
99	A	113	SER	0	-0.089	-0.090	33.783	0.001	0.001	0.000	0.000	0.000	0.000
100	A	114	GLU	-1	-0.938	-0.965	33.018	0.018	0.018	0.000	0.000	0.000	0.000
101	A	115	ASP	-1	-0.851	-0.899	31.272	0.003	0.003	0.000	0.000	0.000	0.000
102	A	116	LEU	0	-0.066	-0.051	29.341	0.000	0.000	0.000	0.000	0.000	0.000
103	A	117	ALA	0	0.015	0.016	28.105	0.001	0.001	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.804	-0.888	27.423	0.027	0.027	0.000	0.000	0.000	0.000
105	A	119	ILE	0	-0.086	-0.038	24.091	0.002	0.002	0.000	0.000	0.000	0.000
106	A	120	TYR	0	-0.084	-0.083	23.380	0.003	0.003	0.000	0.000	0.000	0.000
107	A	121	GLN	0	0.026	0.017	22.949	0.001	0.001	0.000	0.000	0.000	0.000
108	A	122	ASP	-1	-0.839	-0.916	20.232	0.055	0.055	0.000	0.000	0.000	0.000
109	A	123	ILE	0	-0.089	-0.051	18.823	0.004	0.004	0.000	0.000	0.000	0.000
110	A	124	LYS	1	0.888	0.931	18.428	-0.050	-0.050	0.000	0.000	0.000	0.000
111	A	125	ASP	-1	-0.772	-0.896	18.240	0.110	0.110	0.000	0.000	0.000	0.000
112	A	126	PHE	0	-0.004	-0.004	11.053	0.013	0.013	0.000	0.000	0.000	0.000
113	A	127	ILE	0	-0.036	-0.031	14.027	0.023	0.023	0.000	0.000	0.000	0.000
114	A	128	PHE	0	-0.035	-0.006	15.378	0.008	0.008	0.000	0.000	0.000	0.000
115	A	129	VAL	0	0.062	0.029	11.404	0.020	0.020	0.000	0.000	0.000	0.000
116	A	130	PHE	0	-0.054	-0.026	8.200	0.062	0.062	0.000	0.000	0.000	0.000
117	A	131	GLN	0	-0.048	-0.030	11.010	0.022	0.022	0.000	0.000	0.000	0.000
118	A	132	LEU	0	-0.035	-0.015	13.036	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	133	GLY	0	-0.045	-0.016	9.804	0.008	0.008	0.000	0.000	0.000	0.000
120	A	134	LEU	0	0.006	0.021	8.757	0.130	0.130	0.000	0.000	0.000	0.000
121	A	135	ASN	0	0.046	0.030	1.859	14.414	-0.135	27.524	-10.010	-2.965	-0.036
122	A	136	GLU	-1	-0.887	-0.961	5.064	1.813	1.815	0.000	-0.009	0.006	0.000
123	A	137	THR	0	0.104	0.058	6.637	-0.245	-0.245	0.000	0.000	0.000	0.000
124	A	138	MET	0	-0.054	0.001	6.217	-0.099	-0.099	0.000	0.000	0.000	0.000
125	A	139	ASN	0	-0.077	-0.039	4.662	-0.482	-0.532	0.000	-0.004	0.054	0.000
126	A	140	ASP	-1	-0.722	-0.880	6.694	0.301	0.301	0.000	0.000	0.000	0.000
127	A	141	SER	0	-0.021	-0.013	10.040	-0.125	-0.125	0.000	0.000	0.000	0.000
128	A	142	LEU	0	-0.022	-0.014	8.623	-0.073	-0.073	0.000	0.000	0.000	0.000
129	A	143	ALA	0	-0.006	-0.009	10.599	-0.048	-0.048	0.000	0.000	0.000	0.000
130	A	144	ILE	0	0.026	0.011	12.240	-0.025	-0.025	0.000	0.000	0.000	0.000
131	A	145	CYS	0	-0.017	0.009	14.665	-0.029	-0.029	0.000	0.000	0.000	0.000
132	A	146	GLN	0	-0.026	-0.045	14.156	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	147	GLU	-1	-0.917	-0.959	16.271	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	148	ASN	0	0.031	-0.012	18.170	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	149	PHE	0	-0.081	-0.018	19.552	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	150	GLY	0	-0.021	-0.013	21.054	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	151	LEU	0	-0.067	-0.008	21.917	0.002	0.002	0.000	0.000	0.000	0.000
138	A	152	LEU	0	-0.045	-0.035	24.090	0.002	0.002	0.000	0.000	0.000	0.000
139	A	153	TRP	0	0.075	0.027	18.480	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	154	GLY	0	0.045	0.023	24.236	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	155	GLN	0	-0.038	-0.029	25.320	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	156	LYS	1	0.949	0.974	27.749	-0.011	-0.011	0.000	0.000	0.000	0.000
143	A	157	LEU	0	0.005	0.029	25.102	0.000	0.000	0.000	0.000	0.000	0.000
144	A	158	VAL	0	-0.003	-0.007	28.570	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	159	ASN	0	0.003	-0.002	30.914	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	160	THR	0	0.048	0.012	31.441	0.002	0.002	0.000	0.000	0.000	0.000
147	A	161	MET	0	-0.036	-0.014	30.446	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	162	ARG	1	0.850	0.946	33.529	0.014	0.014	0.000	0.000	0.000	0.000
149	A	163	ALA	0	0.054	0.037	36.528	0.000	0.000	0.000	0.000	0.000	0.000
150	A	164	LEU	0	0.030	-0.004	33.564	0.000	0.000	0.000	0.000	0.000	0.000
151	A	165	HIS	0	-0.015	0.002	37.387	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.909	-0.959	38.797	-0.015	-0.015	0.000	0.000	0.000	0.000
153	A	167	VAL	0	-0.047	-0.025	40.315	0.001	0.001	0.000	0.000	0.000	0.000
154	A	168	LYS	1	0.794	0.895	39.644	0.021	0.021	0.000	0.000	0.000	0.000
155	A	169	TYR	0	-0.047	-0.038	39.235	0.000	0.000	0.000	0.000	0.000	0.000
156	A	170	SER	0	0.004	0.025	44.362	0.000	0.000	0.000	0.000	0.000	0.000
157	A	171	PRO	0	-0.019	-0.003	46.387	0.001	0.001	0.000	0.000	0.000	0.000
158	A	172	LYS	1	0.854	0.913	45.696	0.012	0.012	0.000	0.000	0.000	0.000
159	A	173	ALA	0	0.004	0.002	51.143	0.000	0.000	0.000	0.000	0.000	0.000
160	A	174	ARG	1	0.958	0.989	47.931	0.007	0.007	0.000	0.000	0.000	0.000
161	A	175	DLE	0	-0.009	-0.017	53.734	0.001	0.001	0.000	0.000	0.000	0.000
162	A	176	NME	0	0.034	0.035	54.076	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:5:ACE )