FMO DATABASE

FMODB ID: J35M9

Calculation Name: 3NFG-H-Xray372

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: 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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-844833.782501
FMO2-HF: Nuclear repulsion	798232.122511
FMO2-HF: Total energy	-46601.659989
FMO2-MP2: Total energy	-46738.662359

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:24:GLY)

Summations of interaction energy for fragment #1(H:24: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.
-0.284	1.327	-0.007	-0.776	-0.828	0.004

Interaction energy analysis for fragmet #1(H:24:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.019

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

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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	H	26	GLN	0	0.010	0.000	3.844	0.046	1.657	-0.007	-0.776	-0.828	0.004
4	H	27	PRO	0	-0.038	-0.003	6.579	0.257	0.257	0.000	0.000	0.000	0.000
5	H	28	PRO	0	0.029	0.007	10.127	-0.042	-0.042	0.000	0.000	0.000	0.000
6	H	29	SER	0	0.011	0.007	13.276	0.013	0.013	0.000	0.000	0.000	0.000
7	H	30	ASP	-1	-0.908	-0.953	14.764	-0.500	-0.500	0.000	0.000	0.000	0.000
8	H	31	TYR	0	-0.032	-0.002	14.273	0.065	0.065	0.000	0.000	0.000	0.000
9	H	32	LYS	1	0.964	0.977	14.045	0.226	0.226	0.000	0.000	0.000	0.000
10	H	33	GLN	0	-0.013	-0.012	11.855	0.006	0.006	0.000	0.000	0.000	0.000
11	H	34	CYS	0	0.012	0.012	14.263	0.064	0.064	0.000	0.000	0.000	0.000
12	H	35	LYS	1	0.870	0.896	12.095	0.139	0.139	0.000	0.000	0.000	0.000
13	H	36	HIS	0	-0.056	-0.024	17.558	0.031	0.031	0.000	0.000	0.000	0.000
14	H	37	LEU	0	-0.004	0.008	17.693	-0.005	-0.005	0.000	0.000	0.000	0.000
15	H	38	LYS	1	0.934	0.963	21.882	0.103	0.103	0.000	0.000	0.000	0.000
16	H	39	SER	0	0.023	0.014	24.981	-0.001	-0.001	0.000	0.000	0.000	0.000
17	H	40	PHE	0	0.051	0.016	26.385	-0.007	-0.007	0.000	0.000	0.000	0.000
18	H	41	PRO	0	0.032	0.023	28.213	0.009	0.009	0.000	0.000	0.000	0.000
19	H	42	VAL	0	0.010	-0.013	26.103	0.000	0.000	0.000	0.000	0.000	0.000
20	H	43	SER	0	-0.045	-0.036	29.258	-0.001	-0.001	0.000	0.000	0.000	0.000
21	H	44	GLU	-1	-0.815	-0.900	32.554	-0.019	-0.019	0.000	0.000	0.000	0.000
22	H	45	LEU	0	-0.011	0.002	28.795	-0.001	-0.001	0.000	0.000	0.000	0.000
23	H	46	LYS	1	0.818	0.909	28.583	-0.009	-0.009	0.000	0.000	0.000	0.000
24	H	47	GLY	0	0.030	0.010	34.401	0.005	0.005	0.000	0.000	0.000	0.000
25	H	48	ASP	-1	-0.912	-0.942	38.095	-0.002	-0.002	0.000	0.000	0.000	0.000
26	H	49	ASN	0	-0.036	-0.025	40.538	-0.002	-0.002	0.000	0.000	0.000	0.000
27	H	50	LYS	1	0.794	0.901	36.832	0.020	0.020	0.000	0.000	0.000	0.000
28	H	51	GLU	-1	-0.697	-0.799	37.809	-0.034	-0.034	0.000	0.000	0.000	0.000
29	H	52	LEU	0	-0.122	-0.048	29.952	-0.004	-0.004	0.000	0.000	0.000	0.000
30	H	53	TRP	0	0.003	-0.034	34.389	-0.004	-0.004	0.000	0.000	0.000	0.000
31	H	54	LEU	0	-0.034	-0.010	29.623	-0.005	-0.005	0.000	0.000	0.000	0.000
32	H	55	MET	0	-0.005	0.004	33.005	0.005	0.005	0.000	0.000	0.000	0.000
33	H	56	LYS	1	0.950	0.996	33.185	0.114	0.114	0.000	0.000	0.000	0.000
34	H	57	VAL	0	0.030	0.005	34.332	0.007	0.007	0.000	0.000	0.000	0.000
35	H	58	PRO	0	-0.017	-0.005	35.242	-0.009	-0.009	0.000	0.000	0.000	0.000
36	H	59	ALA	0	0.023	-0.001	33.703	0.002	0.002	0.000	0.000	0.000	0.000
37	H	60	ASN	0	-0.086	-0.048	35.357	0.002	0.002	0.000	0.000	0.000	0.000
38	H	61	ILE	0	-0.005	0.014	38.314	0.006	0.006	0.000	0.000	0.000	0.000
39	H	62	ASP	-1	-0.782	-0.858	37.724	-0.086	-0.086	0.000	0.000	0.000	0.000
40	H	63	ILE	0	0.033	-0.012	35.830	0.006	0.006	0.000	0.000	0.000	0.000
41	H	64	SER	0	-0.063	-0.040	37.063	0.007	0.007	0.000	0.000	0.000	0.000
42	H	65	GLN	0	-0.013	-0.012	38.825	0.010	0.010	0.000	0.000	0.000	0.000
43	H	66	LEU	0	-0.045	-0.006	40.638	0.004	0.004	0.000	0.000	0.000	0.000
44	H	67	LYS	1	0.818	0.897	42.392	0.053	0.053	0.000	0.000	0.000	0.000
45	H	68	SER	0	0.006	-0.001	44.730	0.001	0.001	0.000	0.000	0.000	0.000
46	H	69	LEU	0	0.034	0.017	39.533	-0.003	-0.003	0.000	0.000	0.000	0.000
47	H	70	PRO	0	-0.035	-0.013	44.259	0.002	0.002	0.000	0.000	0.000	0.000
48	H	71	LEU	0	-0.012	-0.008	41.214	0.000	0.000	0.000	0.000	0.000	0.000
49	H	72	ASP	-1	-0.849	-0.920	45.719	-0.036	-0.036	0.000	0.000	0.000	0.000
50	H	73	THR	0	-0.019	-0.034	44.581	-0.003	-0.003	0.000	0.000	0.000	0.000
51	H	74	ASP	-1	-0.889	-0.931	45.498	-0.032	-0.032	0.000	0.000	0.000	0.000
52	H	75	ALA	0	-0.064	-0.013	48.044	0.000	0.000	0.000	0.000	0.000	0.000
53	H	76	THR	0	-0.025	-0.011	44.544	-0.002	-0.002	0.000	0.000	0.000	0.000
54	H	77	VAL	0	0.004	-0.012	44.890	-0.004	-0.004	0.000	0.000	0.000	0.000
55	H	78	SER	0	0.023	0.014	46.903	0.002	0.002	0.000	0.000	0.000	0.000
56	H	79	THR	0	-0.016	-0.012	47.889	-0.002	-0.002	0.000	0.000	0.000	0.000
57	H	80	VAL	0	-0.012	-0.003	44.224	0.002	0.002	0.000	0.000	0.000	0.000
58	H	81	GLU	-1	-0.892	-0.942	47.577	-0.050	-0.050	0.000	0.000	0.000	0.000
59	H	82	LEU	0	-0.015	0.002	42.463	0.001	0.001	0.000	0.000	0.000	0.000
60	H	83	GLY	0	-0.002	-0.001	46.551	-0.003	-0.003	0.000	0.000	0.000	0.000
61	H	84	SER	0	-0.041	-0.028	47.218	0.002	0.002	0.000	0.000	0.000	0.000
62	H	85	LYS	1	0.979	0.985	45.297	0.073	0.073	0.000	0.000	0.000	0.000
63	H	86	ASN	0	-0.016	-0.017	47.947	-0.002	-0.002	0.000	0.000	0.000	0.000
64	H	87	PHE	0	-0.027	-0.006	43.017	-0.004	-0.004	0.000	0.000	0.000	0.000
65	H	88	ASN	0	0.010	0.000	45.109	0.002	0.002	0.000	0.000	0.000	0.000
66	H	89	VAL	0	0.018	0.003	42.485	-0.004	-0.004	0.000	0.000	0.000	0.000
67	H	90	LEU	0	0.010	0.007	40.526	0.003	0.003	0.000	0.000	0.000	0.000
68	H	91	GLN	0	-0.007	-0.002	40.430	-0.004	-0.004	0.000	0.000	0.000	0.000
69	H	92	ASN	0	0.022	-0.011	37.032	0.001	0.001	0.000	0.000	0.000	0.000
70	H	93	THR	0	0.066	0.037	36.769	-0.001	-0.001	0.000	0.000	0.000	0.000
71	H	94	SER	0	-0.018	0.013	39.213	0.003	0.003	0.000	0.000	0.000	0.000
72	H	95	THR	0	-0.027	-0.019	41.131	0.001	0.001	0.000	0.000	0.000	0.000
73	H	96	GLN	0	0.009	-0.012	41.649	-0.001	-0.001	0.000	0.000	0.000	0.000
74	H	97	GLU	-1	-0.968	-0.972	39.286	-0.072	-0.072	0.000	0.000	0.000	0.000
75	H	98	GLY	0	-0.009	-0.007	36.509	-0.004	-0.004	0.000	0.000	0.000	0.000
76	H	99	SER	0	0.013	0.018	36.988	-0.001	-0.001	0.000	0.000	0.000	0.000
77	H	100	ASP	-1	-0.867	-0.899	32.741	-0.060	-0.060	0.000	0.000	0.000	0.000
78	H	101	ASN	0	-0.033	-0.038	31.615	-0.013	-0.013	0.000	0.000	0.000	0.000
79	H	102	THR	0	-0.065	-0.057	29.567	-0.002	-0.002	0.000	0.000	0.000	0.000
80	H	103	ASN	0	-0.008	-0.002	26.561	0.007	0.007	0.000	0.000	0.000	0.000
81	H	104	LEU	0	-0.061	-0.019	25.193	-0.019	-0.019	0.000	0.000	0.000	0.000
82	H	105	SER	0	0.027	0.012	22.291	0.012	0.012	0.000	0.000	0.000	0.000
83	H	106	LEU	0	0.029	0.023	23.408	-0.015	-0.015	0.000	0.000	0.000	0.000
84	H	107	LEU	0	-0.019	-0.018	17.425	0.017	0.017	0.000	0.000	0.000	0.000
85	H	108	ILE	0	0.018	0.008	21.276	-0.005	-0.005	0.000	0.000	0.000	0.000
86	H	109	PRO	0	0.015	0.004	19.713	0.007	0.007	0.000	0.000	0.000	0.000
87	H	110	SER	0	-0.057	-0.021	18.388	0.028	0.028	0.000	0.000	0.000	0.000
88	H	111	GLU	-1	-0.800	-0.917	20.349	0.025	0.025	0.000	0.000	0.000	0.000
89	H	112	LYS	1	0.940	0.974	19.263	-0.165	-0.165	0.000	0.000	0.000	0.000
90	H	113	LYS	1	1.013	1.011	13.729	-0.272	-0.272	0.000	0.000	0.000	0.000
91	H	114	LYS	1	0.892	0.943	17.613	-0.050	-0.050	0.000	0.000	0.000	0.000
92	H	115	GLU	-1	-0.821	-0.892	12.546	-0.052	-0.052	0.000	0.000	0.000	0.000
93	H	116	THR	0	-0.065	-0.026	12.340	-0.020	-0.020	0.000	0.000	0.000	0.000
94	H	117	LEU	0	0.032	0.004	14.966	0.020	0.020	0.000	0.000	0.000	0.000
95	H	118	LYS	1	0.898	0.959	15.957	-0.033	-0.033	0.000	0.000	0.000	0.000
96	H	119	VAL	0	0.075	0.041	18.501	-0.011	-0.011	0.000	0.000	0.000	0.000
97	H	120	ALA	0	0.004	0.025	21.284	0.025	0.025	0.000	0.000	0.000	0.000
98	H	121	THR	0	0.011	-0.008	23.348	0.005	0.005	0.000	0.000	0.000	0.000
99	H	122	SER	0	-0.028	-0.021	25.949	0.001	0.001	0.000	0.000	0.000	0.000
100	H	123	LYS	1	0.941	0.951	28.300	-0.036	-0.036	0.000	0.000	0.000	0.000
101	H	124	ASP	-1	-0.796	-0.864	29.706	0.038	0.038	0.000	0.000	0.000	0.000
102	H	125	ASN	0	-0.030	-0.019	24.794	-0.003	-0.003	0.000	0.000	0.000	0.000
103	H	126	LYS	1	0.883	0.932	27.305	-0.026	-0.026	0.000	0.000	0.000	0.000
104	H	127	SER	0	-0.006	-0.017	24.924	0.003	0.003	0.000	0.000	0.000	0.000
105	H	128	VAL	0	-0.034	-0.018	27.515	-0.004	-0.004	0.000	0.000	0.000	0.000
106	H	129	TYR	0	0.021	0.028	28.360	-0.006	-0.006	0.000	0.000	0.000	0.000
107	H	130	PHE	0	-0.014	-0.021	27.886	0.002	0.002	0.000	0.000	0.000	0.000
108	H	131	ASP	-1	-0.819	-0.894	32.775	-0.034	-0.034	0.000	0.000	0.000	0.000
109	H	132	ARG	1	0.799	0.879	36.310	0.039	0.039	0.000	0.000	0.000	0.000
110	H	133	VAL	0	-0.026	-0.017	33.645	-0.004	-0.004	0.000	0.000	0.000	0.000
111	H	134	PHE	0	0.005	-0.005	36.178	0.002	0.002	0.000	0.000	0.000	0.000
112	H	135	THR	0	-0.033	-0.023	36.722	-0.010	-0.010	0.000	0.000	0.000	0.000
113	H	136	ILE	0	-0.027	-0.001	38.318	0.004	0.004	0.000	0.000	0.000	0.000
114	H	137	SER	0	0.014	-0.008	39.256	-0.006	-0.006	0.000	0.000	0.000	0.000
115	H	138	GLU	-1	-0.833	-0.905	41.394	-0.081	-0.081	0.000	0.000	0.000	0.000
116	H	139	THR	0	0.039	0.030	43.798	-0.001	-0.001	0.000	0.000	0.000	0.000
117	H	140	ALA	0	0.001	-0.005	46.872	-0.003	-0.003	0.000	0.000	0.000	0.000
118	H	141	ARG	1	0.835	0.900	45.121	0.079	0.079	0.000	0.000	0.000	0.000
119	H	142	ILE	0	0.004	0.008	47.815	-0.004	-0.004	0.000	0.000	0.000	0.000
120	H	143	PRO	0	-0.001	0.008	45.815	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:24:GLY)