FMO DATABASE

FMODB ID: 98VK2

Calculation Name: 2NML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NML

Chain ID: A

ChEMBL ID:

UniProt ID: P84090

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:

Apendix: None

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-784380.599696
FMO2-HF: Nuclear repulsion	741889.722945
FMO2-HF: Total energy	-42490.876752
FMO2-MP2: Total energy	-42612.018829

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-24.111	-19.752	15.193	-9.067	-10.484	-0.06

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.024

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	4	THR	0	-0.019	-0.036	3.861	0.025	1.586	-0.009	-0.758	-0.794	0.005
4	A	5	ILE	0	-0.006	0.001	6.142	0.398	0.398	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.011	-0.009	9.856	-0.005	-0.005	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.013	-0.010	12.414	0.115	0.115	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.047	0.008	15.682	0.000	0.000	0.000	0.000	0.000	0.000
8	A	9	GLN	0	-0.031	-0.031	19.002	0.030	0.030	0.000	0.000	0.000	0.000
9	A	10	PRO	0	0.041	0.024	22.671	0.016	0.016	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.057	0.031	24.728	0.016	0.016	0.000	0.000	0.000	0.000
11	A	12	LYS	1	1.006	0.983	27.352	0.185	0.185	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.816	0.893	29.583	0.187	0.187	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.035	0.031	27.002	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.773	-0.866	26.691	-0.206	-0.206	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.012	0.001	26.185	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.841	0.915	22.145	0.250	0.250	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.005	-0.005	19.532	0.013	0.013	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.015	-0.006	14.221	0.003	0.003	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.007	0.012	13.898	0.072	0.072	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.898	-0.939	9.499	-1.063	-1.063	0.000	0.000	0.000	0.000
21	A	22	TYR	0	0.037	0.027	7.071	0.345	0.345	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.882	-0.939	4.475	-1.884	-1.602	-0.001	-0.122	-0.158	0.000
23	A	24	SER	0	-0.083	-0.082	2.096	-9.920	-9.441	6.083	-3.360	-3.201	-0.033
24	A	25	VAL	0	0.042	0.005	3.173	2.480	2.208	0.057	0.662	-0.447	0.000
25	A	26	ASN	0	-0.015	0.003	5.338	0.825	0.897	-0.001	-0.001	-0.071	0.000
26	A	27	GLU	-1	-0.710	-0.833	6.080	-2.604	-2.604	0.000	0.000	0.000	0.000
27	A	28	CYS	0	-0.056	-0.001	7.635	0.311	0.311	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.042	-0.018	9.280	0.325	0.325	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.813	-0.899	11.132	-0.462	-0.462	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.018	0.000	12.169	0.128	0.128	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.011	-0.010	13.344	0.103	0.103	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.045	-0.011	15.441	0.065	0.065	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.928	0.947	13.967	0.701	0.701	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.051	-0.009	17.981	0.046	0.046	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.008	0.007	19.833	0.047	0.047	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.825	-0.905	19.997	-0.341	-0.341	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.797	-0.880	22.406	-0.228	-0.228	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.037	-0.015	23.991	0.025	0.025	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.011	0.001	25.290	0.028	0.028	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.818	0.907	26.744	0.200	0.200	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.793	0.876	26.234	0.274	0.274	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.014	-0.006	30.045	0.015	0.015	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.067	-0.020	30.507	0.022	0.022	0.000	0.000	0.000	0.000
44	A	45	PRO	0	0.029	0.021	32.628	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.007	-0.015	34.072	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	47	SER	0	0.017	0.015	32.272	0.010	0.010	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.005	-0.002	31.458	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.046	-0.034	28.946	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.001	0.007	26.683	0.009	0.009	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.027	-0.012	26.359	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.039	-0.038	20.137	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.805	-0.860	25.215	-0.195	-0.195	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.002	-0.018	19.134	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.049	-0.041	22.901	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.055	0.013	25.302	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.017	0.001	18.222	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.020	-0.035	18.708	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.853	-0.924	22.488	-0.242	-0.242	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.008	0.001	20.762	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.043	-0.030	17.947	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.825	-0.908	21.502	-0.353	-0.353	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.934	-0.962	24.149	-0.234	-0.234	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.106	-0.027	20.465	0.007	0.007	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.064	-0.035	23.724	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.868	-0.923	19.018	-0.495	-0.495	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.032	-0.009	16.272	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.030	-0.022	14.963	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	69	CYS	0	-0.058	-0.022	9.947	-0.123	-0.123	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.039	0.020	9.059	0.135	0.135	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.007	-0.006	3.204	-0.431	-0.067	0.067	-0.113	-0.319	-0.001
71	A	72	TYR	0	0.020	0.024	2.580	-3.988	-1.695	1.412	-1.371	-2.334	0.017
72	A	73	ARG	1	0.894	0.941	1.878	-10.844	-11.377	7.586	-3.985	-3.068	-0.048
73	A	74	ALA	0	0.056	0.022	4.223	0.643	0.756	-0.001	-0.019	-0.092	0.000
74	A	75	ASP	-1	-0.928	-0.962	6.138	0.249	0.249	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.033	-0.029	7.980	-0.081	-0.081	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.043	0.000	7.735	0.003	0.003	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.019	-0.004	7.382	-0.105	-0.105	0.000	0.000	0.000	0.000
78	A	79	TYR	0	-0.039	-0.049	6.122	0.029	0.029	0.000	0.000	0.000	0.000
79	A	80	GLN	0	-0.046	-0.014	6.482	0.366	0.366	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.006	0.007	8.407	-0.268	-0.268	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.005	-0.007	7.071	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.011	-0.019	12.222	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.904	0.952	14.815	0.316	0.316	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.777	-0.868	16.986	-0.414	-0.414	0.000	0.000	0.000	0.000
85	A	86	TRP	0	0.030	0.006	7.072	0.012	0.012	0.000	0.000	0.000	0.000
86	A	87	ILE	0	0.021	0.000	12.139	-0.066	-0.066	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.798	0.896	13.661	0.361	0.361	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.885	-0.947	14.995	-0.329	-0.329	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.758	0.886	9.597	0.821	0.821	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.066	0.021	12.319	0.017	0.017	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.026	0.021	14.402	0.074	0.074	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.047	-0.035	12.255	0.050	0.050	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.045	-0.001	11.225	0.066	0.066	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.079	0.032	13.559	0.075	0.075	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.860	0.918	17.215	0.178	0.178	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.826	0.924	10.307	0.312	0.312	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.037	-0.003	15.001	0.026	0.026	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.000	0.007	17.740	0.026	0.026	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.024	0.007	19.698	0.003	0.003	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.035	-0.011	15.138	-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:2:SER)