FMO DATABASE

FMODB ID: MNJ1Z

Calculation Name: 3NX6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NX6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5GUT0

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	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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-421041.55444
FMO2-HF: Nuclear repulsion	393884.945903
FMO2-HF: Total energy	-27156.608537
FMO2-MP2: Total energy	-27238.296216

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.
-6.953	-5.388	-0.012	-0.662	-0.89	0.002

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 : 0.024 / q_NPA : 0.001

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	A	4	LYS	1	1.036	1.020	3.878	-2.128	-0.943	-0.009	-0.600	-0.576	0.002
4	A	5	PRO	0	-0.056	-0.006	6.410	0.161	0.161	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.026	-0.009	9.822	-0.267	-0.267	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.015	-0.014	12.938	0.075	0.075	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.784	-0.895	15.820	0.334	0.334	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.899	0.960	12.960	-0.577	-0.577	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.049	0.019	12.030	-0.050	-0.050	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.041	-0.019	6.966	0.080	0.080	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.050	0.028	9.949	-0.178	-0.178	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.956	0.985	10.132	-0.606	-0.606	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.030	0.016	11.926	-0.174	-0.174	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.079	-0.019	14.907	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	35	SER	0	-0.010	-0.025	23.950	0.002	0.002	0.000	0.000	0.000	0.000
16	A	36	THR	0	-0.080	-0.032	20.282	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	37	LYS	1	1.022	0.994	20.329	-0.249	-0.249	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.010	-0.006	16.245	0.037	0.037	0.000	0.000	0.000	0.000
19	A	39	GLU	-1	-0.967	-0.972	12.807	0.266	0.266	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.014	-0.010	11.661	0.174	0.174	0.000	0.000	0.000	0.000
21	A	41	VAL	0	0.007	0.005	6.562	-0.094	-0.094	0.000	0.000	0.000	0.000
22	A	42	ALA	0	-0.008	-0.015	6.201	-0.170	-0.170	0.000	0.000	0.000	0.000
23	A	43	ILE	0	0.008	0.006	8.352	0.141	0.141	0.000	0.000	0.000	0.000
24	A	44	GLY	0	-0.020	0.002	10.867	-0.096	-0.096	0.000	0.000	0.000	0.000
25	A	45	ALA	0	-0.016	-0.023	12.848	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	46	GLY	0	0.085	0.044	15.189	-0.022	-0.022	0.000	0.000	0.000	0.000
27	A	47	LYS	1	0.894	0.950	18.059	-0.220	-0.220	0.000	0.000	0.000	0.000
28	A	48	PRO	0	-0.010	-0.007	19.607	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	49	LEU	0	-0.012	-0.011	22.580	0.019	0.019	0.000	0.000	0.000	0.000
30	A	50	ASP	-1	-0.889	-0.943	26.256	0.085	0.085	0.000	0.000	0.000	0.000
31	A	51	ASN	0	-0.062	-0.005	29.215	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	52	GLY	0	0.019	0.017	27.197	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	53	SER	0	-0.035	-0.032	25.257	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	54	LEU	0	-0.032	-0.027	19.022	0.010	0.010	0.000	0.000	0.000	0.000
35	A	55	HIS	0	-0.005	-0.004	21.923	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	56	ALA	0	0.002	-0.003	20.258	0.014	0.014	0.000	0.000	0.000	0.000
37	A	57	PRO	0	0.001	-0.002	16.076	0.009	0.009	0.000	0.000	0.000	0.000
38	A	58	VAL	0	-0.041	-0.014	18.857	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	59	VAL	0	-0.049	-0.022	15.410	0.011	0.011	0.000	0.000	0.000	0.000
40	A	60	LYS	1	0.922	0.960	15.146	-0.137	-0.137	0.000	0.000	0.000	0.000
41	A	61	VAL	0	-0.018	-0.016	9.931	0.048	0.048	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.032	0.018	12.701	-0.079	-0.079	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.891	-0.929	14.523	0.200	0.200	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.957	0.970	15.920	-0.134	-0.134	0.000	0.000	0.000	0.000
45	A	65	VAL	0	0.013	0.001	16.469	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	66	ILE	0	-0.041	-0.022	19.366	0.016	0.016	0.000	0.000	0.000	0.000
47	A	67	TYR	0	0.106	0.045	16.548	0.018	0.018	0.000	0.000	0.000	0.000
48	A	68	GLY	0	0.078	0.037	21.157	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	69	GLN	0	0.028	0.017	20.900	0.077	0.077	0.000	0.000	0.000	0.000
50	A	70	TYR	0	-0.066	-0.052	20.761	0.051	0.051	0.000	0.000	0.000	0.000
51	A	71	ALA	0	0.028	0.042	19.852	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	72	GLY	0	0.039	0.012	17.104	0.062	0.062	0.000	0.000	0.000	0.000
53	A	73	SER	0	-0.054	-0.020	13.837	-0.053	-0.053	0.000	0.000	0.000	0.000
54	A	74	SER	0	-0.005	-0.005	13.159	0.112	0.112	0.000	0.000	0.000	0.000
55	A	75	TYR	0	0.001	-0.012	4.640	-1.949	-1.830	-0.001	-0.027	-0.090	0.000
56	A	76	LYS	1	0.987	0.987	8.970	-0.547	-0.547	0.000	0.000	0.000	0.000
57	A	77	SER	0	0.011	-0.005	3.968	0.496	0.646	-0.001	-0.034	-0.115	0.000
58	A	78	GLU	-1	-0.924	-0.943	5.085	-2.124	-2.013	-0.001	-0.001	-0.109	0.000
59	A	79	GLY	0	-0.028	-0.020	7.779	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	80	VAL	0	-0.040	0.003	8.441	-0.134	-0.134	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.956	-0.992	9.413	1.238	1.238	0.000	0.000	0.000	0.000
62	A	82	TYR	0	-0.030	-0.013	6.748	-0.163	-0.163	0.000	0.000	0.000	0.000
63	A	83	LYS	1	0.965	0.979	10.622	-0.853	-0.853	0.000	0.000	0.000	0.000
64	A	84	VAL	0	-0.018	-0.006	9.838	0.104	0.104	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.005	0.009	12.554	-0.129	-0.129	0.000	0.000	0.000	0.000
66	A	86	ARG	1	0.846	0.912	15.153	-0.365	-0.365	0.000	0.000	0.000	0.000
67	A	87	GLU	-1	-0.807	-0.906	17.761	0.262	0.262	0.000	0.000	0.000	0.000
68	A	88	ASP	-1	-0.933	-0.968	18.779	0.266	0.266	0.000	0.000	0.000	0.000
69	A	89	ASP	-1	-0.867	-0.923	19.135	0.506	0.506	0.000	0.000	0.000	0.000
70	A	90	ILE	0	-0.119	-0.066	16.871	0.015	0.015	0.000	0.000	0.000	0.000
71	A	91	LEU	0	-0.013	0.002	20.711	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	92	ALA	0	0.006	-0.001	22.791	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	93	VAL	0	0.052	0.029	19.983	0.036	0.036	0.000	0.000	0.000	0.000
74	A	94	ILE	0	-0.069	-0.029	21.785	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	95	GLY	0	-0.024	-0.006	20.089	-0.013	-0.013	0.000	0.000	0.000	0.000

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