FMO DATABASE

FMODB ID: MVRGZ

Calculation Name: 1NO4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NO4

Chain ID: A

ChEMBL ID:

UniProt ID: P13848

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	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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-384279.039308
FMO2-HF: Nuclear repulsion	353642.834145
FMO2-HF: Total energy	-30636.205163
FMO2-MP2: Total energy	-30727.557204

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:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-18.076	-12.456	14.095	-6.566	-13.15	-0.066

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.039

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	0.833	0.897	3.872	0.588	1.887	-0.010	-0.575	-0.715	0.002
4	A	5	PRO	0	-0.011	-0.026	6.390	-0.036	-0.036	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.769	-0.869	9.129	0.174	0.174	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.855	-0.915	6.521	-0.712	-0.712	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.002	-0.010	6.449	0.044	0.044	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.922	-0.967	8.364	0.308	0.308	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.895	-0.953	12.017	0.004	0.004	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.067	-0.030	8.597	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.023	-0.015	11.616	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.025	-0.014	14.023	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.821	0.898	15.433	0.028	0.028	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.041	-0.035	13.770	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.049	-0.003	17.592	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.850	-0.918	20.216	0.021	0.021	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.031	-0.009	22.727	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.916	-0.971	25.248	0.016	0.016	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.055	0.001	19.220	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.018	0.000	23.665	0.000	0.000	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.070	0.024	21.267	0.003	0.003	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.007	0.011	21.345	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.816	-0.892	18.678	-0.072	-0.072	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.844	0.917	17.390	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.049	-0.048	16.967	0.009	0.009	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.927	-0.967	14.093	-0.166	-0.166	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.037	0.028	13.013	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.001	-0.012	11.931	0.008	0.008	0.000	0.000	0.000	0.000
29	A	30	GLN	0	0.010	0.020	11.986	0.025	0.025	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.010	0.002	9.062	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.022	0.020	7.412	-0.124	-0.124	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.864	0.925	7.483	0.142	0.142	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.021	-0.015	5.657	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.059	0.041	1.998	-3.729	-5.769	6.072	-1.951	-2.081	-0.022
35	A	36	TYR	0	0.005	0.002	3.220	-1.124	-0.033	0.072	-0.460	-0.703	-0.004
36	A	37	GLY	0	0.001	0.000	5.553	0.128	0.128	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.043	-0.029	2.412	-0.557	0.623	1.288	-0.841	-1.626	0.001
38	A	39	PHE	0	0.026	0.015	2.263	-2.700	-0.472	3.257	-1.676	-3.809	-0.003
39	A	40	VAL	0	0.001	-0.010	2.844	1.592	-0.205	0.248	1.804	-0.255	0.002
40	A	41	SER	0	-0.069	-0.039	5.984	0.046	0.046	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.795	-0.893	2.544	-11.710	-8.051	3.168	-2.867	-3.961	-0.042
42	A	43	TYR	0	-0.007	0.006	6.057	0.172	0.172	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.022	-0.005	7.875	0.012	0.012	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.885	-0.933	9.287	-0.360	-0.360	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.028	0.001	8.987	0.024	0.024	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.030	-0.024	10.973	0.026	0.026	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.782	0.865	13.567	-0.069	-0.069	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.044	-0.035	13.146	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.009	-0.002	15.108	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.775	-0.884	16.853	0.069	0.069	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.787	0.879	19.016	0.038	0.038	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.020	0.006	17.528	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.018	-0.002	21.035	0.002	0.002	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.011	0.006	22.899	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.814	-0.892	22.914	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.844	0.913	24.710	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.818	-0.904	26.586	0.049	0.049	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.925	-0.955	29.080	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.031	0.010	27.673	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.028	-0.001	29.283	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.002	-0.010	32.613	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.054	-0.032	34.315	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	ASN	0	0.032	-0.007	33.134	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.006	0.025	36.520	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.876	0.952	37.415	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.058	0.030	38.085	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.033	0.013	36.457	0.000	0.000	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.880	0.930	40.588	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.030	-0.006	44.181	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ILE	0	0.041	0.024	43.827	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.082	0.049	45.953	0.000	0.000	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.059	-0.038	47.740	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.014	-0.014	49.523	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.894	-0.937	48.478	0.006	0.006	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.788	0.887	51.723	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.089	-0.039	53.604	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.986	-0.983	54.988	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:PRO)