FMO DATABASE

FMODB ID: LJMZ9

Calculation Name: 3NFG-H-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFG

Chain ID: H

ChEMBL ID:

UniProt ID: Q6FNZ9

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	121
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-846711.433391
FMO2-HF: Nuclear repulsion	799959.365517
FMO2-HF: Total energy	-46752.067875
FMO2-MP2: Total energy	-46889.448978

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(H:23:ACE )

Summations of interaction energy for fragment #1(H:23: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.
1.446	2.396	-0.007	-0.461	-0.482	0

Interaction energy analysis for fragmet #1(H:23:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.003

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].
3	H	25	TYR	0	-0.018	-0.003	3.812	0.834	1.784	-0.007	-0.461	-0.482
4	H	26	GLN	0	0.018	0.004	7.097	-0.053	-0.053	0.000	0.000	0.000
5	H	27	PRO	0	-0.038	-0.004	9.574	0.088	0.088	0.000	0.000	0.000
6	H	28	PRO	0	0.016	0.014	13.322	0.022	0.022	0.000	0.000	0.000
7	H	29	SER	0	0.004	-0.002	15.923	-0.011	-0.011	0.000	0.000	0.000
8	H	30	ASP	-1	-0.899	-0.947	17.013	-0.083	-0.083	0.000	0.000	0.000
9	H	31	TYR	0	-0.022	-0.001	17.423	-0.004	-0.004	0.000	0.000	0.000
10	H	32	LYS	1	0.963	0.975	17.482	0.124	0.124	0.000	0.000	0.000
11	H	33	GLN	0	-0.044	-0.029	15.463	-0.016	-0.016	0.000	0.000	0.000
12	H	34	CYS	0	0.003	0.007	18.344	0.026	0.026	0.000	0.000	0.000
13	H	35	LYS	1	0.998	0.982	16.929	0.280	0.280	0.000	0.000	0.000
14	H	36	HIS	0	-0.054	-0.023	21.691	0.008	0.008	0.000	0.000	0.000
15	H	37	LEU	0	0.014	0.019	22.029	0.016	0.016	0.000	0.000	0.000
16	H	38	LYS	1	0.914	0.952	25.990	0.112	0.112	0.000	0.000	0.000
17	H	39	SER	0	0.005	0.001	29.113	-0.005	-0.005	0.000	0.000	0.000
18	H	40	PHE	0	0.066	0.027	30.519	0.003	0.003	0.000	0.000	0.000
19	H	41	PRO	0	0.033	0.026	32.247	-0.005	-0.005	0.000	0.000	0.000
20	H	42	VAL	0	0.008	-0.010	30.060	0.003	0.003	0.000	0.000	0.000
21	H	43	SER	0	-0.054	-0.043	33.147	0.002	0.002	0.000	0.000	0.000
22	H	44	GLU	-1	-0.899	-0.952	36.356	-0.057	-0.057	0.000	0.000	0.000
23	H	45	LEU	0	-0.018	0.004	32.502	0.002	0.002	0.000	0.000	0.000
24	H	46	LYS	1	0.819	0.914	32.317	0.083	0.083	0.000	0.000	0.000
25	H	47	GLY	0	0.033	0.010	37.974	0.000	0.000	0.000	0.000	0.000
26	H	48	ASP	-1	-0.921	-0.950	41.714	-0.042	-0.042	0.000	0.000	0.000
27	H	49	ASN	0	-0.027	-0.020	44.232	-0.001	-0.001	0.000	0.000	0.000
28	H	50	LYS	1	0.886	0.958	40.712	0.052	0.052	0.000	0.000	0.000
29	H	51	GLU	-1	-0.717	-0.837	41.389	-0.039	-0.039	0.000	0.000	0.000
30	H	52	LEU	0	-0.113	-0.044	33.389	-0.003	-0.003	0.000	0.000	0.000
31	H	53	TRP	0	0.007	-0.025	38.053	0.002	0.002	0.000	0.000	0.000
32	H	54	LEU	0	-0.029	-0.009	33.024	-0.005	-0.005	0.000	0.000	0.000
33	H	55	MET	0	-0.009	0.004	36.493	0.005	0.005	0.000	0.000	0.000
34	H	56	LYS	1	0.951	0.993	35.679	0.037	0.037	0.000	0.000	0.000
35	H	57	VAL	0	0.031	0.004	37.616	0.003	0.003	0.000	0.000	0.000
36	H	58	PRO	0	-0.021	-0.003	38.580	-0.002	-0.002	0.000	0.000	0.000
37	H	59	ALA	0	0.017	-0.003	36.930	-0.001	-0.001	0.000	0.000	0.000
38	H	60	ASN	0	-0.086	-0.052	38.713	-0.002	-0.002	0.000	0.000	0.000
39	H	61	ILE	0	-0.007	0.010	41.797	0.001	0.001	0.000	0.000	0.000
40	H	62	ASP	-1	-0.818	-0.889	41.399	-0.047	-0.047	0.000	0.000	0.000
41	H	63	ILE	0	0.020	-0.014	39.837	0.001	0.001	0.000	0.000	0.000
42	H	64	SER	0	-0.073	-0.047	41.072	0.001	0.001	0.000	0.000	0.000
43	H	65	GLN	0	-0.051	-0.025	42.848	0.003	0.003	0.000	0.000	0.000
44	H	66	LEU	0	-0.041	-0.003	44.605	0.002	0.002	0.000	0.000	0.000
45	H	67	LYS	1	0.918	0.955	46.490	0.038	0.038	0.000	0.000	0.000
46	H	68	SER	0	-0.016	-0.015	48.778	-0.001	-0.001	0.000	0.000	0.000
47	H	69	LEU	0	0.043	0.023	43.378	0.000	0.000	0.000	0.000	0.000
48	H	70	PRO	0	-0.020	-0.002	48.079	0.000	0.000	0.000	0.000	0.000
49	H	71	LEU	0	-0.008	-0.012	44.607	0.001	0.001	0.000	0.000	0.000
50	H	72	ASP	-1	-0.873	-0.938	49.301	-0.026	-0.026	0.000	0.000	0.000
51	H	73	THR	0	-0.028	-0.033	48.121	-0.001	-0.001	0.000	0.000	0.000
52	H	74	ASP	-1	-0.908	-0.939	48.805	-0.027	-0.027	0.000	0.000	0.000
53	H	75	ALA	0	-0.035	-0.002	51.164	0.001	0.001	0.000	0.000	0.000
54	H	76	THR	0	-0.037	-0.018	47.290	-0.001	-0.001	0.000	0.000	0.000
55	H	77	VAL	0	0.012	-0.005	47.845	-0.001	-0.001	0.000	0.000	0.000
56	H	78	SER	0	0.012	0.007	49.987	0.001	0.001	0.000	0.000	0.000
57	H	79	THR	0	-0.050	-0.031	51.014	0.000	0.000	0.000	0.000	0.000
58	H	80	VAL	0	0.018	0.012	47.800	0.000	0.000	0.000	0.000	0.000
59	H	81	GLU	-1	-0.951	-0.978	51.030	-0.023	-0.023	0.000	0.000	0.000
60	H	82	LEU	0	-0.009	0.011	46.071	0.000	0.000	0.000	0.000	0.000
61	H	83	GLY	0	-0.013	-0.010	50.225	0.000	0.000	0.000	0.000	0.000
62	H	84	SER	0	-0.040	-0.024	50.977	0.001	0.001	0.000	0.000	0.000
63	H	85	LYS	1	0.992	0.990	49.120	0.028	0.028	0.000	0.000	0.000
64	H	86	ASN	0	0.041	0.017	51.438	-0.001	-0.001	0.000	0.000	0.000
65	H	87	PHE	0	-0.025	-0.007	46.516	0.000	0.000	0.000	0.000	0.000
66	H	88	ASN	0	0.011	0.000	47.921	0.001	0.001	0.000	0.000	0.000
67	H	89	VAL	0	0.017	0.004	45.617	-0.002	-0.002	0.000	0.000	0.000
68	H	90	LEU	0	0.020	0.012	43.017	0.002	0.002	0.000	0.000	0.000
69	H	91	GLN	0	0.003	0.010	43.461	-0.003	-0.003	0.000	0.000	0.000
70	H	92	ASN	0	0.019	-0.012	39.886	0.000	0.000	0.000	0.000	0.000
71	H	93	THR	0	0.051	0.028	39.542	0.001	0.001	0.000	0.000	0.000
72	H	94	SER	0	-0.013	0.020	42.064	0.000	0.000	0.000	0.000	0.000
73	H	95	THR	0	-0.024	-0.016	43.829	0.002	0.002	0.000	0.000	0.000
74	H	96	GLN	0	-0.003	-0.018	44.144	-0.002	-0.002	0.000	0.000	0.000
75	H	97	GLU	-1	-0.977	-0.978	41.439	-0.023	-0.023	0.000	0.000	0.000
76	H	98	GLY	0	-0.004	-0.008	38.960	-0.001	-0.001	0.000	0.000	0.000
77	H	99	SER	0	0.014	0.018	39.621	-0.003	-0.003	0.000	0.000	0.000
78	H	100	ASP	-1	-0.876	-0.916	34.888	-0.040	-0.040	0.000	0.000	0.000
79	H	101	ASN	0	-0.024	-0.029	34.167	-0.001	-0.001	0.000	0.000	0.000
80	H	102	THR	0	-0.062	-0.044	31.965	-0.006	-0.006	0.000	0.000	0.000
81	H	103	ASN	0	0.000	0.005	28.817	-0.002	-0.002	0.000	0.000	0.000
82	H	104	LEU	0	-0.060	-0.023	27.712	-0.007	-0.007	0.000	0.000	0.000
83	H	105	SER	0	0.041	0.018	25.409	-0.003	-0.003	0.000	0.000	0.000
84	H	106	LEU	0	0.020	0.018	26.684	-0.006	-0.006	0.000	0.000	0.000
85	H	107	LEU	0	-0.021	-0.016	21.148	-0.006	-0.006	0.000	0.000	0.000
86	H	108	ILE	0	0.018	0.007	24.993	0.005	0.005	0.000	0.000	0.000
87	H	109	PRO	0	0.029	0.011	23.766	-0.016	-0.016	0.000	0.000	0.000
88	H	110	SER	0	-0.058	-0.021	22.166	0.009	0.009	0.000	0.000	0.000
89	H	111	GLU	-1	-0.873	-0.971	24.222	-0.119	-0.119	0.000	0.000	0.000
90	H	112	LYS	1	0.878	0.949	21.919	0.177	0.177	0.000	0.000	0.000
91	H	113	LYS	1	0.997	1.002	17.843	0.259	0.259	0.000	0.000	0.000
92	H	114	LYS	1	0.998	1.008	21.382	0.130	0.130	0.000	0.000	0.000
93	H	115	GLU	-1	-0.902	-0.954	16.189	-0.361	-0.361	0.000	0.000	0.000
94	H	116	THR	0	-0.039	-0.015	16.254	-0.025	-0.025	0.000	0.000	0.000
95	H	117	LEU	0	0.027	0.001	19.016	0.026	0.026	0.000	0.000	0.000
96	H	118	LYS	1	0.916	0.960	19.803	0.116	0.116	0.000	0.000	0.000
97	H	119	VAL	0	0.065	0.035	22.179	0.009	0.009	0.000	0.000	0.000
98	H	120	ALA	0	-0.012	0.008	24.684	0.001	0.001	0.000	0.000	0.000
99	H	121	THR	0	0.021	0.016	26.481	0.004	0.004	0.000	0.000	0.000
100	H	122	SER	0	-0.033	-0.032	29.147	0.001	0.001	0.000	0.000	0.000
101	H	123	LYS	1	0.931	0.947	31.242	0.054	0.054	0.000	0.000	0.000
102	H	124	ASP	-1	-0.853	-0.909	32.170	-0.059	-0.059	0.000	0.000	0.000
103	H	125	ASN	0	-0.046	-0.028	27.244	-0.005	-0.005	0.000	0.000	0.000
104	H	126	LYS	1	0.965	0.988	29.961	0.053	0.053	0.000	0.000	0.000
105	H	127	SER	0	-0.002	-0.014	28.174	-0.007	-0.007	0.000	0.000	0.000
106	H	128	VAL	0	-0.029	-0.016	30.391	0.004	0.004	0.000	0.000	0.000
107	H	129	TYR	0	0.027	0.029	31.509	-0.005	-0.005	0.000	0.000	0.000
108	H	130	PHE	0	-0.034	-0.026	31.402	-0.001	-0.001	0.000	0.000	0.000
109	H	131	ASP	-1	-0.828	-0.901	36.022	-0.047	-0.047	0.000	0.000	0.000
110	H	132	ARG	1	0.809	0.902	39.647	0.039	0.039	0.000	0.000	0.000
111	H	133	VAL	0	-0.022	-0.022	36.919	-0.004	-0.004	0.000	0.000	0.000
112	H	134	PHE	0	0.008	-0.005	39.365	0.003	0.003	0.000	0.000	0.000
113	H	135	THR	0	-0.033	-0.026	39.260	-0.003	-0.003	0.000	0.000	0.000
114	H	136	ILE	0	-0.018	0.004	41.443	0.002	0.002	0.000	0.000	0.000
115	H	137	SER	0	0.021	-0.007	42.443	-0.001	-0.001	0.000	0.000	0.000
116	H	138	GLU	-1	-0.874	-0.935	44.446	-0.027	-0.027	0.000	0.000	0.000
117	H	139	THR	0	0.011	0.008	46.818	0.000	0.000	0.000	0.000	0.000
118	H	140	ALA	0	0.010	-0.002	49.658	0.000	0.000	0.000	0.000	0.000
119	H	141	ARG	1	0.886	0.947	48.295	0.024	0.024	0.000	0.000	0.000
120	H	142	ILE	0	-0.040	-0.015	50.319	0.000	0.000	0.000	0.000	0.000
121	H	143	PRO	-1	-0.930	-0.952	48.218	-0.014	-0.014	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:23:ACE )