FMO DATABASE

FMODB ID: 76Q1K

Calculation Name: 1NG6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NG6

Chain ID: A

ChEMBL ID:

UniProt ID: P54464

Base Structure: X-ray

Registration Date: 2023-09-23

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1328885.060484
FMO2-HF: Nuclear repulsion	1269349.886557
FMO2-HF: Total energy	-59535.173927
FMO2-MP2: Total energy	-59706.15826

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:1:MET)

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

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.
-16.337	-9.138	9.816	-5.184	-11.834	-0.029

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	LEU	0	0.074	0.032	2.782	-3.294	0.005	0.401	-1.874	-1.826	-0.002
4	A	4	LEU	0	0.053	0.012	5.411	1.021	1.021	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.857	-0.875	2.267	-4.570	-3.420	4.177	-2.032	-3.296	-0.010
6	A	6	ARG	1	0.920	0.962	2.322	3.486	5.667	2.803	-1.488	-3.496	-0.003
7	A	7	LEU	0	0.039	0.021	3.078	1.582	0.564	0.055	1.414	-0.452	-0.001
8	A	8	ASN	0	-0.028	-0.026	6.427	0.115	0.115	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.018	-0.007	2.601	-5.603	-4.016	2.380	-1.204	-2.764	-0.013
10	A	10	ASP	-1	-0.767	-0.868	5.857	-0.776	-0.776	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.075	-0.029	7.278	-0.190	-0.190	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.973	0.977	9.273	-1.405	-1.405	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.000	0.017	7.699	-0.113	-0.113	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.044	0.003	9.612	-0.060	-0.060	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.035	-0.003	12.813	-0.048	-0.048	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.875	0.944	12.497	-0.625	-0.625	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.028	-0.028	12.749	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.940	0.975	15.812	-0.278	-0.278	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.776	-0.855	14.757	0.019	0.019	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.905	0.939	16.187	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.841	-0.932	18.216	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.892	0.932	13.375	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.008	0.003	13.563	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.064	-0.039	14.740	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.052	0.038	14.038	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.028	0.020	9.498	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.922	0.949	12.195	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.049	-0.020	14.117	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.071	0.040	11.994	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.898	0.947	10.416	-0.230	-0.230	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.015	-0.008	12.298	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.032	-0.036	15.775	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.002	0.004	10.255	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.008	-0.015	13.005	0.040	0.040	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.001	-0.007	15.183	0.044	0.044	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.798	-0.871	17.115	-0.412	-0.412	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.036	0.020	15.634	0.016	0.016	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.029	0.014	17.780	0.048	0.048	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.819	0.904	20.428	0.398	0.398	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.051	-0.028	19.556	0.028	0.028	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.836	0.926	22.237	0.238	0.238	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.849	0.916	17.627	0.652	0.652	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.905	-0.947	14.865	-0.392	-0.392	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.044	-0.024	11.541	0.017	0.017	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.030	-0.012	12.970	0.121	0.121	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.006	-0.021	12.660	-0.174	-0.174	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.852	-0.947	7.618	-2.797	-2.797	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.795	-0.882	11.914	-0.955	-0.955	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.807	-0.869	15.439	-0.636	-0.636	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.883	-0.952	9.365	-2.149	-2.149	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.021	0.011	12.820	0.116	0.116	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.058	-0.012	15.039	0.140	0.140	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.018	-0.008	15.215	0.089	0.089	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.022	0.010	11.030	0.093	0.093	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.010	-0.014	15.545	0.086	0.086	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.829	0.916	18.710	0.520	0.520	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.830	-0.892	16.502	-0.314	-0.314	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.016	0.006	17.511	0.060	0.060	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.784	0.870	19.570	0.319	0.319	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.002	0.007	21.227	0.026	0.026	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.830	0.903	18.616	0.323	0.323	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.958	0.982	21.792	0.399	0.399	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.817	-0.892	25.105	-0.232	-0.232	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.003	-0.013	26.060	0.021	0.021	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.018	0.005	25.381	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.000	-0.004	28.119	0.009	0.009	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.940	-0.969	30.949	-0.139	-0.139	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.019	-0.030	27.669	0.013	0.013	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.016	0.003	32.278	0.011	0.011	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.047	-0.013	33.848	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.043	-0.020	35.387	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.046	-0.014	36.570	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.817	0.883	33.214	0.067	0.067	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.091	0.017	32.512	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.760	-0.835	30.983	-0.063	-0.063	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.055	-0.027	28.792	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.005	0.015	27.648	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.805	-0.891	26.926	-0.095	-0.095	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.821	0.911	23.746	0.112	0.112	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.024	-0.022	22.915	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.009	-0.006	22.279	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.868	0.920	20.764	0.064	0.064	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.880	-0.929	18.336	-0.192	-0.192	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.021	-0.005	17.420	-0.049	-0.049	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.816	-0.896	17.550	-0.245	-0.245	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.091	-0.041	13.367	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.024	-0.023	13.073	-0.068	-0.068	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.888	-0.951	13.216	-0.517	-0.517	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.025	0.008	9.657	-0.078	-0.078	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.184	-0.132	6.661	-0.169	-0.169	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.046	-0.007	10.069	-0.229	-0.229	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.042	-0.005	13.017	0.019	0.019	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.893	-0.950	14.910	-0.367	-0.367	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.078	-0.062	17.356	0.027	0.027	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.016	-0.001	20.393	0.029	0.029	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.005	-0.034	23.890	0.013	0.013	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.793	-0.910	26.940	-0.225	-0.225	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.918	-0.959	29.575	-0.183	-0.183	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.782	-0.852	26.471	-0.297	-0.297	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.022	-0.014	25.803	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.838	0.884	28.329	0.205	0.205	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.015	0.002	30.599	0.012	0.012	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.028	0.012	24.994	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.020	-0.004	29.190	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.010	0.007	31.031	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	GLH	0	-0.023	-0.034	29.481	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.001	-0.006	28.614	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.012	-0.009	31.120	0.005	0.005	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.022	-0.012	34.348	0.009	0.009	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.807	-0.848	29.435	-0.276	-0.276	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.036	-0.016	31.260	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.013	0.005	34.377	0.005	0.005	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.092	-0.028	35.793	0.005	0.005	0.000	0.000	0.000	0.000
114	A	114	SER	0	0.004	0.003	37.758	0.007	0.007	0.000	0.000	0.000	0.000
115	A	115	SER	0	0.027	0.031	40.496	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.927	0.943	38.086	0.167	0.167	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.009	0.013	37.810	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.792	-0.902	36.453	-0.187	-0.187	0.000	0.000	0.000	0.000
119	A	119	MET	0	0.004	-0.006	32.620	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.005	0.002	31.515	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.859	0.934	30.377	0.181	0.181	0.000	0.000	0.000	0.000
122	A	122	VAL	0	0.017	0.010	30.414	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.002	-0.011	26.708	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.001	0.003	26.022	-0.033	-0.033	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.009	0.006	25.219	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.004	0.006	25.619	-0.017	-0.017	0.000	0.000	0.000	0.000
127	A	127	MET	0	0.021	0.010	21.224	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	128	PRO	0	-0.032	-0.014	19.738	-0.060	-0.060	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.781	0.868	19.576	0.285	0.285	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.013	-0.002	21.485	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.840	0.918	15.492	0.931	0.931	0.000	0.000	0.000	0.000
132	A	132	GLY	0	0.018	0.003	16.612	-0.064	-0.064	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.923	0.970	17.571	0.589	0.589	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.039	0.023	19.916	0.062	0.062	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.813	-0.895	22.168	-0.415	-0.415	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.051	0.017	23.190	0.022	0.022	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.030	-0.031	24.763	0.026	0.026	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.038	-0.011	26.986	0.025	0.025	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.040	0.028	23.466	0.023	0.023	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.019	-0.027	27.133	0.028	0.028	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.939	0.985	30.211	0.246	0.246	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.042	-0.023	30.271	0.021	0.021	0.000	0.000	0.000	0.000
143	A	143	VAL	0	0.039	0.022	29.960	0.013	0.013	0.000	0.000	0.000	0.000
144	A	144	SER	0	0.011	-0.008	33.050	0.019	0.019	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.093	-0.070	35.725	0.015	0.015	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.043	-0.012	35.996	0.017	0.017	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.034	0.013	35.015	0.006	0.006	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.004	-0.020	38.935	0.002	0.002	0.000	0.000	0.000	0.000

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