FMO DATABASE

FMODB ID: R9MR8

Calculation Name: 3NXA-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXA

Chain ID: C

ChEMBL ID:

UniProt ID: Q96FQ6

Base Structure: X-ray

Registration Date: 2023-06-22

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-692516.679139
FMO2-HF: Nuclear repulsion	653616.128785
FMO2-HF: Total energy	-38900.550354
FMO2-MP2: Total energy	-39015.942108

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(C:5:TYR)

Summations of interaction energy for fragment #1(C:5:TYR)

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.
-5.26	-5.463	-0.005	1.341	-1.134	0.003

Interaction energy analysis for fragmet #1(C:5:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.021

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	C	7	GLU	-1	-0.948	-1.009	3.241	6.672	5.412	-0.034	1.727	-0.433	0.000
4	C	8	LEU	0	0.068	0.035	5.453	0.047	0.047	0.000	0.000	0.000	0.000
5	C	9	GLU	-1	-0.881	-0.922	4.528	-4.596	-4.453	-0.001	-0.055	-0.087	0.000
6	C	10	LYS	1	0.985	0.977	3.413	-6.541	-5.627	0.030	-0.331	-0.614	0.003
7	C	11	ALA	0	0.016	0.021	6.458	-0.430	-0.430	0.000	0.000	0.000	0.000
8	C	12	VAL	0	0.032	0.013	9.585	-0.128	-0.128	0.000	0.000	0.000	0.000
9	C	13	ILE	0	-0.031	0.008	6.542	-0.110	-0.110	0.000	0.000	0.000	0.000
10	C	14	VAL	0	0.014	0.000	9.746	-0.187	-0.187	0.000	0.000	0.000	0.000
11	C	15	LEU	0	0.037	0.016	11.991	-0.166	-0.166	0.000	0.000	0.000	0.000
12	C	16	VAL	0	-0.009	0.008	13.022	-0.086	-0.086	0.000	0.000	0.000	0.000
13	C	17	GLU	-1	-0.908	-0.946	12.397	0.189	0.189	0.000	0.000	0.000	0.000
14	C	18	ASN	0	-0.071	-0.063	15.255	-0.037	-0.037	0.000	0.000	0.000	0.000
15	C	19	PHE	0	-0.006	0.016	17.620	-0.044	-0.044	0.000	0.000	0.000	0.000
16	C	20	TYR	0	-0.045	-0.055	17.127	-0.042	-0.042	0.000	0.000	0.000	0.000
17	C	21	LYS	1	0.808	0.940	19.160	-0.348	-0.348	0.000	0.000	0.000	0.000
18	C	22	TYR	0	-0.114	-0.135	20.873	-0.019	-0.019	0.000	0.000	0.000	0.000
19	C	23	VAL	0	-0.010	0.017	22.664	-0.020	-0.020	0.000	0.000	0.000	0.000
20	C	24	SER	0	-0.087	-0.064	25.098	0.008	0.008	0.000	0.000	0.000	0.000
21	C	25	LYS	1	0.983	1.011	26.510	-0.102	-0.102	0.000	0.000	0.000	0.000
22	C	26	TYR	0	-0.002	-0.017	29.415	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	27	SER	0	-0.012	0.024	28.231	-0.008	-0.008	0.000	0.000	0.000	0.000
24	C	28	LEU	0	0.074	0.012	30.369	-0.008	-0.008	0.000	0.000	0.000	0.000
25	C	29	VAL	0	0.022	0.016	28.735	-0.010	-0.010	0.000	0.000	0.000	0.000
26	C	30	LYS	1	0.916	0.925	24.824	0.039	0.039	0.000	0.000	0.000	0.000
27	C	31	ASN	0	0.022	0.031	22.789	0.006	0.006	0.000	0.000	0.000	0.000
28	C	32	LYS	1	0.957	0.995	24.338	0.016	0.016	0.000	0.000	0.000	0.000
29	C	33	ILE	0	0.051	0.053	23.918	0.002	0.002	0.000	0.000	0.000	0.000
30	C	34	SER	0	-0.015	-0.018	26.979	-0.007	-0.007	0.000	0.000	0.000	0.000
31	C	35	LYS	1	0.901	0.914	29.502	-0.035	-0.035	0.000	0.000	0.000	0.000
32	C	36	SER	0	-0.052	-0.004	31.295	0.006	0.006	0.000	0.000	0.000	0.000
33	C	37	SER	0	0.082	0.048	27.134	0.003	0.003	0.000	0.000	0.000	0.000
34	C	38	PHE	0	0.003	-0.010	24.148	0.015	0.015	0.000	0.000	0.000	0.000
35	C	39	ARG	1	0.916	0.943	27.312	-0.063	-0.063	0.000	0.000	0.000	0.000
36	C	40	GLU	-1	-0.916	-0.950	28.259	0.123	0.123	0.000	0.000	0.000	0.000
37	C	41	MET	0	0.026	0.025	22.437	0.011	0.011	0.000	0.000	0.000	0.000
38	C	42	LEU	0	-0.058	0.001	24.673	0.023	0.023	0.000	0.000	0.000	0.000
39	C	43	GLN	0	-0.022	-0.043	26.351	0.022	0.022	0.000	0.000	0.000	0.000
40	C	44	LYS	1	0.914	0.962	23.943	-0.279	-0.279	0.000	0.000	0.000	0.000
41	C	45	GLU	-1	-0.775	-0.811	20.895	0.375	0.375	0.000	0.000	0.000	0.000
42	C	46	LEU	0	-0.024	-0.028	20.840	0.034	0.034	0.000	0.000	0.000	0.000
43	C	47	ASN	0	0.010	0.017	23.755	-0.007	-0.007	0.000	0.000	0.000	0.000
44	C	48	HIS	0	0.031	-0.001	22.301	-0.037	-0.037	0.000	0.000	0.000	0.000
45	C	49	MET	0	-0.052	-0.038	19.883	-0.020	-0.020	0.000	0.000	0.000	0.000
46	C	50	LEU	0	0.006	0.016	24.438	-0.021	-0.021	0.000	0.000	0.000	0.000
47	C	51	SER	0	-0.022	0.011	28.003	-0.020	-0.020	0.000	0.000	0.000	0.000
48	C	52	ASP	-1	-0.830	-0.912	30.063	0.116	0.116	0.000	0.000	0.000	0.000
49	C	53	THR	0	0.024	0.005	31.987	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	54	GLY	0	-0.025	-0.024	34.895	-0.005	-0.005	0.000	0.000	0.000	0.000
51	C	55	ASN	0	0.047	0.005	29.375	-0.015	-0.015	0.000	0.000	0.000	0.000
52	C	56	ARG	1	0.949	0.995	30.856	-0.138	-0.138	0.000	0.000	0.000	0.000
53	C	57	LYS	1	0.923	0.960	31.800	-0.080	-0.080	0.000	0.000	0.000	0.000
54	C	58	ALA	0	-0.058	-0.008	31.948	-0.008	-0.008	0.000	0.000	0.000	0.000
55	C	59	ALA	0	0.038	0.009	29.006	-0.007	-0.007	0.000	0.000	0.000	0.000
56	C	60	ASP	-1	-0.848	-0.939	30.793	0.085	0.085	0.000	0.000	0.000	0.000
57	C	61	LYS	1	0.909	0.952	33.271	-0.067	-0.067	0.000	0.000	0.000	0.000
58	C	62	LEU	0	-0.005	-0.010	28.952	-0.010	-0.010	0.000	0.000	0.000	0.000
59	C	63	ILE	0	-0.014	0.019	29.111	-0.008	-0.008	0.000	0.000	0.000	0.000
60	C	64	GLN	0	-0.042	-0.016	32.363	-0.005	-0.005	0.000	0.000	0.000	0.000
61	C	65	ASN	0	-0.032	-0.036	35.155	-0.008	-0.008	0.000	0.000	0.000	0.000
62	C	66	LEU	0	-0.005	0.022	29.623	-0.005	-0.005	0.000	0.000	0.000	0.000
63	C	67	ASP	-1	-0.776	-0.882	33.451	0.007	0.007	0.000	0.000	0.000	0.000
64	C	68	ALA	0	-0.088	-0.049	33.248	0.001	0.001	0.000	0.000	0.000	0.000
65	C	69	ASN	0	-0.102	-0.045	30.717	-0.011	-0.011	0.000	0.000	0.000	0.000
66	C	70	HIS	0	0.121	0.050	30.927	0.004	0.004	0.000	0.000	0.000	0.000
67	C	71	ASP	-1	-0.960	-0.979	33.287	0.000	0.000	0.000	0.000	0.000	0.000
68	C	72	GLY	0	0.042	0.018	34.703	0.005	0.005	0.000	0.000	0.000	0.000
69	C	73	ARG	1	0.770	0.898	30.194	-0.016	-0.016	0.000	0.000	0.000	0.000
70	C	74	ILE	0	0.034	0.010	25.698	-0.007	-0.007	0.000	0.000	0.000	0.000
71	C	75	SER	0	0.003	-0.016	25.326	0.004	0.004	0.000	0.000	0.000	0.000
72	C	76	PHE	0	0.081	0.018	16.365	0.018	0.018	0.000	0.000	0.000	0.000
73	C	77	ASP	-1	-0.875	-0.933	21.674	-0.048	-0.048	0.000	0.000	0.000	0.000
74	C	78	GLU	-1	-0.841	-0.901	23.052	0.022	0.022	0.000	0.000	0.000	0.000
75	C	79	TYR	0	-0.084	-0.093	17.467	0.024	0.024	0.000	0.000	0.000	0.000
76	C	80	TRP	0	0.053	0.032	15.090	0.026	0.026	0.000	0.000	0.000	0.000
77	C	81	THR	0	-0.024	-0.016	21.239	0.006	0.006	0.000	0.000	0.000	0.000
78	C	82	LEU	0	-0.008	0.009	24.467	0.008	0.008	0.000	0.000	0.000	0.000
79	C	83	ILE	0	0.034	0.014	20.129	0.010	0.010	0.000	0.000	0.000	0.000
80	C	84	GLY	0	-0.010	0.015	22.399	0.012	0.012	0.000	0.000	0.000	0.000
81	C	85	GLY	0	-0.013	-0.023	23.230	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	86	ILE	0	0.019	0.015	24.308	-0.002	-0.002	0.000	0.000	0.000	0.000
83	C	87	THR	0	0.012	0.020	20.040	0.017	0.017	0.000	0.000	0.000	0.000
84	C	88	GLY	0	-0.104	-0.078	23.332	-0.002	-0.002	0.000	0.000	0.000	0.000
85	C	89	PRO	0	-0.017	-0.018	24.973	-0.003	-0.003	0.000	0.000	0.000	0.000
86	C	90	ILE	0	0.033	0.035	23.967	-0.004	-0.004	0.000	0.000	0.000	0.000
87	C	91	ALA	0	0.047	0.019	22.091	0.020	0.020	0.000	0.000	0.000	0.000
88	C	92	LYS	1	0.946	0.963	22.586	-0.077	-0.077	0.000	0.000	0.000	0.000
89	C	93	LEU	0	0.063	0.068	24.701	0.007	0.007	0.000	0.000	0.000	0.000
90	C	94	ILE	0	-0.014	-0.025	19.500	0.011	0.011	0.000	0.000	0.000	0.000
91	C	95	HIS	0	-0.010	-0.014	19.637	0.043	0.043	0.000	0.000	0.000	0.000
92	C	96	GLU	-1	-0.998	-1.018	21.394	0.144	0.144	0.000	0.000	0.000	0.000
93	C	97	GLN	0	-0.108	-0.045	22.391	-0.006	-0.006	0.000	0.000	0.000	0.000
94	C	98	GLU	-1	-0.910	-0.970	17.376	0.464	0.464	0.000	0.000	0.000	0.000
95	C	99	GLN	0	-0.048	-0.001	20.386	-0.008	-0.008	0.000	0.000	0.000	0.000
96	C	100	GLN	0	-0.063	-0.044	22.313	0.005	0.005	0.000	0.000	0.000	0.000
97	C	101	SER	0	-0.038	0.011	20.741	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:5:TYR)