FMO DATABASE

FMODB ID: 3Q1NL

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	OptAll
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	-848132.566014
FMO2-HF: Nuclear repulsion	801530.464173
FMO2-HF: Total energy	-46602.101842
FMO2-MP2: Total energy	-46739.128949

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.
-0.567	1.057	-0.002	-0.831	-0.79	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 : 0.039 / 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

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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	0.008	-0.002	3.856	-0.143	1.481	-0.002	-0.831	-0.790	0.004
4	H	27	PRO	0	-0.033	-0.002	6.689	0.249	0.249	0.000	0.000	0.000	0.000
5	H	28	PRO	0	0.030	0.005	10.359	-0.086	-0.086	0.000	0.000	0.000	0.000
6	H	29	SER	0	-0.021	-0.019	13.413	0.012	0.012	0.000	0.000	0.000	0.000
7	H	30	ASP	-1	-0.876	-0.926	15.110	-0.528	-0.528	0.000	0.000	0.000	0.000
8	H	31	TYR	0	-0.031	-0.002	14.352	0.059	0.059	0.000	0.000	0.000	0.000
9	H	32	LYS	1	0.968	0.972	14.183	0.240	0.240	0.000	0.000	0.000	0.000
10	H	33	GLN	0	-0.002	0.000	11.889	0.008	0.008	0.000	0.000	0.000	0.000
11	H	34	CYS	0	0.035	0.016	14.141	0.062	0.062	0.000	0.000	0.000	0.000
12	H	35	LYS	1	0.804	0.862	11.912	0.111	0.111	0.000	0.000	0.000	0.000
13	H	36	HIS	0	-0.041	-0.015	17.143	0.034	0.034	0.000	0.000	0.000	0.000
14	H	37	LEU	0	0.025	0.027	17.942	-0.007	-0.007	0.000	0.000	0.000	0.000
15	H	38	LYS	1	0.883	0.929	21.787	0.091	0.091	0.000	0.000	0.000	0.000
16	H	39	SER	0	0.024	0.018	25.349	-0.002	-0.002	0.000	0.000	0.000	0.000
17	H	40	PHE	0	0.073	0.023	26.888	-0.007	-0.007	0.000	0.000	0.000	0.000
18	H	41	PRO	0	0.061	0.042	28.573	0.010	0.010	0.000	0.000	0.000	0.000
19	H	42	VAL	0	-0.022	-0.029	26.280	0.000	0.000	0.000	0.000	0.000	0.000
20	H	43	SER	0	-0.026	-0.021	29.554	0.001	0.001	0.000	0.000	0.000	0.000
21	H	44	GLU	-1	-0.790	-0.897	32.884	-0.016	-0.016	0.000	0.000	0.000	0.000
22	H	45	LEU	0	-0.049	-0.015	28.921	-0.001	-0.001	0.000	0.000	0.000	0.000
23	H	46	LYS	1	0.799	0.902	29.067	-0.009	-0.009	0.000	0.000	0.000	0.000
24	H	47	GLY	0	0.038	0.020	34.760	0.006	0.006	0.000	0.000	0.000	0.000
25	H	48	ASP	-1	-0.898	-0.944	38.511	-0.001	-0.001	0.000	0.000	0.000	0.000
26	H	49	ASN	0	-0.046	-0.018	41.044	-0.001	-0.001	0.000	0.000	0.000	0.000
27	H	50	LYS	1	0.785	0.890	37.232	0.017	0.017	0.000	0.000	0.000	0.000
28	H	51	GLU	-1	-0.720	-0.813	37.774	-0.033	-0.033	0.000	0.000	0.000	0.000
29	H	52	LEU	0	-0.117	-0.056	29.791	-0.003	-0.003	0.000	0.000	0.000	0.000
30	H	53	TRP	0	-0.002	-0.027	34.402	-0.006	-0.006	0.000	0.000	0.000	0.000
31	H	54	LEU	0	-0.035	-0.012	29.991	-0.005	-0.005	0.000	0.000	0.000	0.000
32	H	55	MET	0	-0.013	-0.008	33.423	0.005	0.005	0.000	0.000	0.000	0.000
33	H	56	LYS	1	0.957	0.998	33.624	0.111	0.111	0.000	0.000	0.000	0.000
34	H	57	VAL	0	0.030	0.001	34.753	0.008	0.008	0.000	0.000	0.000	0.000
35	H	58	PRO	0	-0.020	-0.006	35.709	-0.009	-0.009	0.000	0.000	0.000	0.000
36	H	59	ALA	0	0.018	0.004	34.081	0.003	0.003	0.000	0.000	0.000	0.000
37	H	60	ASN	0	-0.080	-0.041	35.836	0.000	0.000	0.000	0.000	0.000	0.000
38	H	61	ILE	0	-0.019	-0.002	38.460	0.007	0.007	0.000	0.000	0.000	0.000
39	H	62	ASP	-1	-0.788	-0.855	37.945	-0.085	-0.085	0.000	0.000	0.000	0.000
40	H	63	ILE	0	0.028	-0.009	35.914	0.006	0.006	0.000	0.000	0.000	0.000
41	H	64	SER	0	-0.071	-0.043	37.183	0.007	0.007	0.000	0.000	0.000	0.000
42	H	65	GLN	0	-0.006	-0.023	38.984	0.010	0.010	0.000	0.000	0.000	0.000
43	H	66	LEU	0	-0.030	0.006	40.656	0.005	0.005	0.000	0.000	0.000	0.000
44	H	67	LYS	1	0.825	0.894	42.674	0.053	0.053	0.000	0.000	0.000	0.000
45	H	68	SER	0	-0.011	0.001	44.882	0.002	0.002	0.000	0.000	0.000	0.000
46	H	69	LEU	0	0.038	0.007	39.945	-0.003	-0.003	0.000	0.000	0.000	0.000
47	H	70	PRO	0	-0.026	0.002	44.668	0.001	0.001	0.000	0.000	0.000	0.000
48	H	71	LEU	0	-0.017	-0.015	41.456	-0.001	-0.001	0.000	0.000	0.000	0.000
49	H	72	ASP	-1	-0.835	-0.910	45.930	-0.037	-0.037	0.000	0.000	0.000	0.000
50	H	73	THR	0	-0.003	-0.016	44.630	-0.003	-0.003	0.000	0.000	0.000	0.000
51	H	74	ASP	-1	-0.896	-0.930	45.498	-0.031	-0.031	0.000	0.000	0.000	0.000
52	H	75	ALA	0	-0.059	-0.023	48.039	0.000	0.000	0.000	0.000	0.000	0.000
53	H	76	THR	0	0.000	-0.007	44.526	-0.002	-0.002	0.000	0.000	0.000	0.000
54	H	77	VAL	0	-0.022	-0.017	44.913	-0.004	-0.004	0.000	0.000	0.000	0.000
55	H	78	SER	0	0.013	0.009	46.981	0.002	0.002	0.000	0.000	0.000	0.000
56	H	79	THR	0	-0.005	-0.009	47.867	-0.003	-0.003	0.000	0.000	0.000	0.000
57	H	80	VAL	0	-0.020	-0.006	44.276	0.002	0.002	0.000	0.000	0.000	0.000
58	H	81	GLU	-1	-0.863	-0.924	47.683	-0.050	-0.050	0.000	0.000	0.000	0.000
59	H	82	LEU	0	0.004	0.012	42.632	0.002	0.002	0.000	0.000	0.000	0.000
60	H	83	GLY	0	0.021	-0.002	46.749	-0.003	-0.003	0.000	0.000	0.000	0.000
61	H	84	SER	0	-0.051	-0.033	47.645	0.003	0.003	0.000	0.000	0.000	0.000
62	H	85	LYS	1	0.937	0.977	44.814	0.074	0.074	0.000	0.000	0.000	0.000
63	H	86	ASN	0	-0.021	-0.011	48.047	-0.002	-0.002	0.000	0.000	0.000	0.000
64	H	87	PHE	0	-0.016	-0.007	43.397	-0.003	-0.003	0.000	0.000	0.000	0.000
65	H	88	ASN	0	0.030	0.006	45.466	0.002	0.002	0.000	0.000	0.000	0.000
66	H	89	VAL	0	0.008	-0.003	42.651	-0.004	-0.004	0.000	0.000	0.000	0.000
67	H	90	LEU	0	0.021	0.020	40.569	0.003	0.003	0.000	0.000	0.000	0.000
68	H	91	GLN	0	0.009	-0.002	40.717	-0.004	-0.004	0.000	0.000	0.000	0.000
69	H	92	ASN	0	0.044	0.013	37.283	0.001	0.001	0.000	0.000	0.000	0.000
70	H	93	THR	0	0.067	0.054	36.772	-0.001	-0.001	0.000	0.000	0.000	0.000
71	H	94	SER	0	-0.018	0.001	39.215	0.003	0.003	0.000	0.000	0.000	0.000
72	H	95	THR	0	-0.067	-0.035	40.610	0.001	0.001	0.000	0.000	0.000	0.000
73	H	96	GLN	0	0.003	-0.006	41.338	-0.001	-0.001	0.000	0.000	0.000	0.000
74	H	97	GLU	-1	-0.960	-0.982	39.480	-0.072	-0.072	0.000	0.000	0.000	0.000
75	H	98	GLY	0	-0.013	-0.003	36.434	-0.006	-0.006	0.000	0.000	0.000	0.000
76	H	99	SER	0	0.009	0.016	37.083	-0.001	-0.001	0.000	0.000	0.000	0.000
77	H	100	ASP	-1	-0.846	-0.903	32.919	-0.059	-0.059	0.000	0.000	0.000	0.000
78	H	101	ASN	0	-0.031	-0.036	31.829	-0.012	-0.012	0.000	0.000	0.000	0.000
79	H	102	THR	0	-0.049	-0.049	29.409	-0.005	-0.005	0.000	0.000	0.000	0.000
80	H	103	ASN	0	-0.040	-0.013	26.519	0.007	0.007	0.000	0.000	0.000	0.000
81	H	104	LEU	0	-0.057	-0.017	25.594	-0.019	-0.019	0.000	0.000	0.000	0.000
82	H	105	SER	0	0.018	0.002	22.982	0.012	0.012	0.000	0.000	0.000	0.000
83	H	106	LEU	0	0.030	0.031	23.803	-0.014	-0.014	0.000	0.000	0.000	0.000
84	H	107	LEU	0	-0.018	-0.014	17.844	0.014	0.014	0.000	0.000	0.000	0.000
85	H	108	ILE	0	0.010	0.007	21.673	-0.003	-0.003	0.000	0.000	0.000	0.000
86	H	109	PRO	0	0.020	0.006	20.150	0.006	0.006	0.000	0.000	0.000	0.000
87	H	110	SER	0	-0.044	-0.023	17.930	0.029	0.029	0.000	0.000	0.000	0.000
88	H	111	GLU	-1	-0.785	-0.890	20.466	0.034	0.034	0.000	0.000	0.000	0.000
89	H	112	LYS	1	0.962	0.973	19.939	-0.177	-0.177	0.000	0.000	0.000	0.000
90	H	113	LYS	1	0.967	0.989	13.534	-0.274	-0.274	0.000	0.000	0.000	0.000
91	H	114	LYS	1	0.874	0.942	17.679	-0.058	-0.058	0.000	0.000	0.000	0.000
92	H	115	GLU	-1	-0.818	-0.881	12.807	-0.021	-0.021	0.000	0.000	0.000	0.000
93	H	116	THR	0	-0.043	-0.026	12.927	-0.023	-0.023	0.000	0.000	0.000	0.000
94	H	117	LEU	0	0.026	0.005	15.517	0.014	0.014	0.000	0.000	0.000	0.000
95	H	118	LYS	1	0.842	0.928	16.418	-0.024	-0.024	0.000	0.000	0.000	0.000
96	H	119	VAL	0	0.102	0.053	18.872	-0.010	-0.010	0.000	0.000	0.000	0.000
97	H	120	ALA	0	0.019	0.023	21.479	0.026	0.026	0.000	0.000	0.000	0.000
98	H	121	THR	0	0.004	0.000	23.841	0.006	0.006	0.000	0.000	0.000	0.000
99	H	122	SER	0	0.005	-0.010	26.448	-0.001	-0.001	0.000	0.000	0.000	0.000
100	H	123	LYS	1	0.939	0.956	28.400	-0.039	-0.039	0.000	0.000	0.000	0.000
101	H	124	ASP	-1	-0.790	-0.867	30.059	0.038	0.038	0.000	0.000	0.000	0.000
102	H	125	ASN	0	-0.029	-0.019	25.000	-0.003	-0.003	0.000	0.000	0.000	0.000
103	H	126	LYS	1	0.899	0.935	27.450	-0.028	-0.028	0.000	0.000	0.000	0.000
104	H	127	SER	0	-0.018	-0.009	25.767	0.002	0.002	0.000	0.000	0.000	0.000
105	H	128	VAL	0	-0.053	-0.027	27.551	-0.002	-0.002	0.000	0.000	0.000	0.000
106	H	129	TYR	0	-0.006	0.002	28.341	-0.008	-0.008	0.000	0.000	0.000	0.000
107	H	130	PHE	0	0.003	-0.022	27.691	0.002	0.002	0.000	0.000	0.000	0.000
108	H	131	ASP	-1	-0.798	-0.884	32.732	-0.033	-0.033	0.000	0.000	0.000	0.000
109	H	132	ARG	1	0.801	0.885	36.078	0.039	0.039	0.000	0.000	0.000	0.000
110	H	133	VAL	0	-0.009	-0.012	33.692	-0.005	-0.005	0.000	0.000	0.000	0.000
111	H	134	PHE	0	0.002	0.006	36.298	0.002	0.002	0.000	0.000	0.000	0.000
112	H	135	THR	0	-0.047	-0.036	36.785	-0.011	-0.011	0.000	0.000	0.000	0.000
113	H	136	ILE	0	-0.001	0.009	38.534	0.005	0.005	0.000	0.000	0.000	0.000
114	H	137	SER	0	-0.023	-0.029	39.410	-0.007	-0.007	0.000	0.000	0.000	0.000
115	H	138	GLU	-1	-0.815	-0.897	41.649	-0.079	-0.079	0.000	0.000	0.000	0.000
116	H	139	THR	0	0.025	0.032	43.747	-0.002	-0.002	0.000	0.000	0.000	0.000
117	H	140	ALA	0	-0.010	-0.004	47.198	-0.002	-0.002	0.000	0.000	0.000	0.000
118	H	141	ARG	1	0.826	0.885	45.186	0.079	0.079	0.000	0.000	0.000	0.000
119	H	142	ILE	0	0.017	0.011	48.252	-0.003	-0.003	0.000	0.000	0.000	0.000
120	H	143	PRO	0	-0.012	0.006	45.779	0.002	0.002	0.000	0.000	0.000	0.000

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