FMO DATABASE

FMODB ID: 899MY

Calculation Name: 1NQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NQ3

Chain ID: A

ChEMBL ID:

UniProt ID: P80601

Base Structure: X-ray

Registration Date: 2023-09-21

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1036889.788847
FMO2-HF: Nuclear repulsion	988840.520151
FMO2-HF: Total energy	-48049.268696
FMO2-MP2: Total energy	-48191.407946

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
0.211	1.98	-0.016	-0.87	-0.882	0.004

Interaction energy analysis for fragmet #1(A:3:SER)

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 : 0.018

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	5	VAL	0	0.020	0.019	3.863	0.441	2.176	-0.015	-0.867	-0.853	0.004
4	A	6	ARG	1	0.982	0.982	5.291	0.606	0.640	-0.001	-0.003	-0.029	0.000
5	A	7	ARG	1	0.903	0.953	8.243	1.223	1.223	0.000	0.000	0.000	0.000
6	A	8	ILE	0	0.029	0.013	11.271	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.021	0.000	14.894	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.024	-0.020	17.866	0.048	0.048	0.000	0.000	0.000	0.000
9	A	11	THR	0	0.057	0.023	20.983	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.015	0.016	24.100	0.014	0.014	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.842	0.902	27.375	0.161	0.161	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.072	0.052	26.539	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	15	PRO	0	-0.003	0.020	28.352	0.005	0.005	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.019	0.017	26.785	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.002	0.004	23.555	0.005	0.005	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.035	-0.013	25.300	0.014	0.014	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.033	0.005	26.040	0.004	0.004	0.000	0.000	0.000	0.000
18	A	20	PRO	0	-0.030	0.000	23.198	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	21	TYR	0	-0.003	-0.003	21.177	0.004	0.004	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.008	-0.013	18.804	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	GLN	0	0.016	0.006	20.825	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.050	0.026	18.949	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.050	-0.016	13.315	0.019	0.019	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.019	0.022	11.530	0.002	0.002	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.025	-0.030	8.004	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.892	-0.945	8.145	-2.430	-2.430	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.864	0.921	9.269	1.207	1.207	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.017	0.007	12.709	0.177	0.177	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.022	-0.019	14.157	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.009	0.003	13.876	0.077	0.077	0.000	0.000	0.000	0.000
31	A	33	ILE	0	-0.007	-0.015	18.657	0.009	0.009	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.006	-0.021	21.861	0.017	0.017	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.020	0.018	23.793	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.069	-0.038	26.012	0.016	0.016	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.062	0.022	29.505	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	GLY	0	0.034	0.025	32.915	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	39	MET	0	-0.050	-0.005	31.635	0.011	0.011	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.757	-0.872	33.754	-0.100	-0.100	0.000	0.000	0.000	0.000
39	A	41	PRO	0	-0.035	-0.030	31.066	0.004	0.004	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.035	-0.016	31.698	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.027	-0.027	34.226	0.006	0.006	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.031	0.019	33.941	0.007	0.007	0.000	0.000	0.000	0.000
43	A	45	GLN	0	-0.047	-0.013	34.761	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.025	-0.009	37.210	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.016	0.013	38.598	0.005	0.005	0.000	0.000	0.000	0.000
46	A	48	PRO	0	-0.022	-0.007	40.338	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.033	-0.003	44.022	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.000	0.019	43.441	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	VAL	0	0.052	0.007	40.174	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	52	VAL	0	0.023	0.019	40.204	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.772	-0.870	40.353	-0.101	-0.101	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.799	-0.908	37.782	-0.083	-0.083	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.028	0.011	36.070	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.833	0.896	35.276	0.091	0.091	0.000	0.000	0.000	0.000
55	A	57	GLN	0	-0.010	0.016	33.092	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	58	ALA	0	0.002	0.003	32.064	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.006	-0.010	30.573	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.007	-0.023	30.395	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.018	-0.009	28.861	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	62	ILE	0	0.002	-0.004	25.572	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.022	0.014	25.576	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.806	-0.896	26.206	-0.241	-0.241	0.000	0.000	0.000	0.000
63	A	65	ILE	0	-0.034	-0.011	21.479	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.022	-0.013	21.495	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.851	0.912	21.580	0.195	0.195	0.000	0.000	0.000	0.000
66	A	68	ALA	0	-0.039	-0.019	21.001	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.040	-0.013	17.559	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.031	-0.001	17.880	-0.086	-0.086	0.000	0.000	0.000	0.000
69	A	71	CYS	0	-0.105	-0.049	19.110	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.794	-0.882	21.972	-0.301	-0.301	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.031	0.003	24.807	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	74	THR	0	-0.062	-0.048	26.496	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.018	-0.009	20.834	0.011	0.011	0.000	0.000	0.000	0.000
74	A	76	VAL	0	-0.033	-0.014	22.093	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.005	0.001	20.438	0.013	0.013	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.819	0.911	23.056	0.236	0.236	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.028	0.015	24.973	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.086	-0.076	27.347	0.010	0.010	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.031	-0.019	29.713	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.025	0.022	30.101	0.009	0.009	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.012	0.001	34.093	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.033	0.016	37.832	0.004	0.004	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.822	-0.909	40.391	-0.052	-0.052	0.000	0.000	0.000	0.000
84	A	86	ILE	0	0.021	0.010	40.559	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	87	ASN	0	-0.058	-0.043	42.689	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.795	-0.878	42.001	-0.072	-0.072	0.000	0.000	0.000	0.000
87	A	89	PHE	0	-0.012	-0.008	37.197	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.019	0.004	40.791	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	91	ALA	0	0.061	0.038	42.747	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.024	0.013	36.945	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.002	0.006	38.213	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.836	-0.905	39.290	-0.112	-0.112	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.000	0.014	37.238	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	TYR	0	0.023	-0.009	31.055	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.772	0.850	35.378	0.107	0.107	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.055	-0.018	37.319	0.001	0.001	0.000	0.000	0.000	0.000
97	A	99	TYR	0	-0.031	-0.006	32.088	0.001	0.001	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.030	-0.011	28.681	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	101	GLN	0	-0.014	-0.014	33.368	0.016	0.016	0.000	0.000	0.000	0.000
100	A	102	SER	0	0.003	-0.006	32.871	0.005	0.005	0.000	0.000	0.000	0.000
101	A	103	SER	0	-0.026	-0.018	28.624	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	104	PHE	0	0.011	0.012	28.894	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.008	0.019	26.850	0.000	0.000	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.009	0.019	26.343	0.024	0.024	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.860	0.920	27.998	0.147	0.147	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.003	0.011	30.555	0.010	0.010	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.003	-0.011	32.174	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	110	TYR	0	0.002	0.004	31.026	0.001	0.001	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.005	0.011	36.731	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	112	VAL	0	-0.020	-0.015	34.217	0.001	0.001	0.000	0.000	0.000	0.000
111	A	113	ALA	0	-0.010	-0.010	37.694	0.001	0.001	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.002	-0.004	38.047	0.003	0.003	0.000	0.000	0.000	0.000
113	A	115	LEU	0	0.001	0.020	33.788	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.034	0.011	32.041	0.008	0.008	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.788	0.852	33.865	0.051	0.051	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.007	0.023	38.099	0.001	0.001	0.000	0.000	0.000	0.000
117	A	119	GLY	0	-0.022	0.010	37.877	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.781	0.841	38.884	0.064	0.064	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.020	-0.013	35.189	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.895	-0.955	29.981	-0.095	-0.095	0.000	0.000	0.000	0.000
121	A	123	ILE	0	-0.018	-0.006	29.168	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.801	-0.848	24.933	-0.201	-0.201	0.000	0.000	0.000	0.000
123	A	125	ALA	0	0.019	-0.011	24.398	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.024	-0.007	18.767	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.026	0.017	19.722	0.026	0.026	0.000	0.000	0.000	0.000
126	A	128	VAL	0	0.001	0.000	16.021	-0.062	-0.062	0.000	0.000	0.000	0.000
127	A	129	GLN	0	0.017	0.004	14.063	-0.079	-0.079	0.000	0.000	0.000	0.000
128	A	130	GLY	0	0.014	0.034	17.379	-0.052	-0.052	0.000	0.000	0.000	0.000
129	A	131	PRO	0	0.012	-0.004	17.578	-0.077	-0.077	0.000	0.000	0.000	0.000
130	A	132	LEU	0	0.004	-0.013	19.543	-0.067	-0.067	0.000	0.000	0.000	0.000
131	A	133	THR	0	-0.018	-0.009	21.935	0.022	0.022	0.000	0.000	0.000	0.000
132	A	134	THR	0	0.019	0.017	24.427	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	135	ALA	0	0.004	0.014	26.877	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)