FMO DATABASE

FMODB ID: 3JV8L

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	OptH
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	-783310.408588
FMO2-HF: Nuclear repulsion	740820.206435
FMO2-HF: Total energy	-42490.202153
FMO2-MP2: Total energy	-42611.40361

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.
-30.403	-46.244	47.373	-19.879	-11.649	-0.091

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 : -0.097 / q_NPA : -0.092

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	-0.014	-0.029	3.813	1.904	3.157	0.000	-0.499	-0.753	0.003
4	A	5	ILE	0	0.002	0.009	5.851	-0.094	-0.094	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.006	-0.015	9.517	0.053	0.053	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.015	-0.010	12.065	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.046	0.006	15.352	0.011	0.011	0.000	0.000	0.000	0.000
8	A	9	GLN	0	-0.014	-0.018	18.421	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	10	PRO	0	0.020	0.013	22.039	0.005	0.005	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.079	0.040	24.276	0.004	0.004	0.000	0.000	0.000	0.000
11	A	12	LYS	1	1.011	0.986	26.673	0.004	0.004	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.827	0.905	28.976	0.016	0.016	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.042	0.024	26.646	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.816	-0.902	25.935	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.017	0.006	25.721	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.854	0.926	21.548	0.015	0.015	0.000	0.000	0.000	0.000
17	A	18	THR	0	0.006	0.007	19.077	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.014	-0.011	14.244	0.019	0.019	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.005	0.010	13.455	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.875	-0.932	9.129	-0.302	-0.302	0.000	0.000	0.000	0.000
21	A	22	TYR	0	0.007	0.005	6.733	0.105	0.105	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.871	-0.932	4.399	-2.150	-1.830	-0.001	-0.156	-0.163	0.000
23	A	24	SER	0	-0.041	-0.056	2.056	-11.616	-10.164	6.244	-4.410	-3.285	-0.041
24	A	25	VAL	0	0.043	0.013	3.066	-0.283	-0.422	0.052	0.565	-0.477	0.000
25	A	26	ASN	0	-0.002	-0.018	5.828	-0.570	-0.570	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.774	-0.851	5.936	-1.390	-1.390	0.000	0.000	0.000	0.000
27	A	28	CYS	0	-0.030	0.010	7.417	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.073	-0.042	9.041	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.904	-0.950	11.032	-0.178	-0.178	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.008	0.005	11.853	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.026	-0.019	13.416	0.007	0.007	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.019	-0.008	15.473	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.992	0.996	15.366	0.140	0.140	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.037	0.003	17.805	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.007	0.004	19.640	0.004	0.004	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.843	-0.928	20.480	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.873	-0.921	22.213	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.018	-0.015	24.008	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.013	0.002	25.413	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.851	0.938	26.758	0.032	0.032	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.828	0.890	25.736	0.045	0.045	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.035	-0.008	30.151	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.051	-0.008	30.666	0.004	0.004	0.000	0.000	0.000	0.000
44	A	45	PRO	0	0.039	0.002	32.605	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.016	-0.007	33.842	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.007	0.000	32.425	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.024	-0.016	30.955	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.008	-0.008	28.806	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.027	0.006	26.990	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.011	-0.004	26.592	0.001	0.001	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.043	-0.035	20.720	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.809	-0.884	25.820	0.019	0.019	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.010	-0.020	19.855	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.060	-0.039	23.390	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.094	0.054	25.885	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.038	-0.005	18.727	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.037	-0.048	18.994	0.001	0.001	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.839	-0.913	22.622	0.012	0.012	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.006	-0.002	20.971	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.034	-0.033	17.756	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.862	-0.925	21.477	0.018	0.018	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.943	-0.965	23.928	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.114	-0.030	20.020	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.059	-0.019	23.688	0.003	0.003	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.933	-0.974	19.998	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.018	-0.004	15.628	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.022	-0.002	14.277	0.007	0.007	0.000	0.000	0.000	0.000
68	A	69	CYS	0	-0.030	-0.007	9.265	0.009	0.009	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.028	0.010	8.468	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.004	0.002	2.611	-0.474	0.137	0.495	-0.311	-0.796	-0.001
71	A	72	TYR	0	0.041	0.045	2.458	-4.806	-2.422	1.692	-1.514	-2.562	0.014
72	A	73	ARG	1	0.894	0.959	1.485	-10.911	-32.801	38.892	-13.502	-3.499	-0.066
73	A	74	ALA	0	0.061	0.010	4.157	0.599	0.767	-0.001	-0.052	-0.114	0.000
74	A	75	ASP	-1	-0.934	-0.954	6.148	0.015	0.015	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.010	-0.009	8.152	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.035	-0.009	7.519	0.067	0.067	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.051	-0.021	7.313	-0.027	-0.027	0.000	0.000	0.000	0.000
78	A	79	TYR	0	-0.025	-0.059	5.905	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	80	GLN	0	-0.058	-0.023	6.128	0.038	0.038	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.002	0.011	7.999	0.014	0.014	0.000	0.000	0.000	0.000
81	A	82	TYR	0	0.006	0.009	6.870	-0.044	-0.044	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.061	0.016	11.910	0.010	0.010	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.933	0.938	14.521	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.867	-0.919	16.680	0.043	0.043	0.000	0.000	0.000	0.000
85	A	86	TRP	0	-0.008	-0.010	6.982	0.025	0.025	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.006	-0.016	11.833	0.043	0.043	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.876	0.935	13.489	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.898	-0.953	15.076	0.105	0.105	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.835	0.917	8.984	-0.303	-0.303	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.064	0.025	12.732	0.033	0.033	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.041	0.035	14.947	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.051	-0.046	12.705	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.060	-0.023	11.725	0.012	0.012	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.078	0.028	14.497	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.896	0.969	17.932	-0.117	-0.117	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.863	0.931	11.320	-0.288	-0.288	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.021	-0.005	14.611	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.013	0.016	18.254	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.051	-0.010	19.537	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.046	-0.009	15.394	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)