FMO DATABASE

FMODB ID: ZVZ7N

Calculation Name: 2NWU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NWU

Chain ID: A

ChEMBL ID:

UniProt ID: Q97Z89

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	OptHSide
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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1226782.955209
FMO2-HF: Nuclear repulsion	1173677.833231
FMO2-HF: Total energy	-53105.121978
FMO2-MP2: Total energy	-53261.450551

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:ASP)

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

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.
-56.955	-52.082	28.527	-16.455	-16.943	0.091

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.840 / q_NPA : -0.913

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	VAL	0	-0.009	0.013	3.818	-3.106	-0.365	-0.037	-1.461	-1.243	0.005
4	A	5	MET	0	0.003	0.000	7.155	-1.447	-1.447	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.002	-0.009	9.784	-0.593	-0.593	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.004	0.008	13.390	-0.520	-0.520	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.002	-0.001	15.952	-0.421	-0.421	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.832	-0.897	19.705	12.007	12.007	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.004	-0.009	22.810	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.832	0.911	25.486	-10.732	-10.732	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.066	0.023	28.825	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.007	0.011	31.797	-0.134	-0.134	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.868	-0.917	27.299	10.785	10.785	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.736	-0.849	29.667	9.912	9.912	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.068	0.021	23.670	0.248	0.248	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.008	-0.018	24.775	0.692	0.692	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.875	0.923	26.059	-9.283	-9.283	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.012	-0.004	21.852	0.208	0.208	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.028	0.012	20.041	0.534	0.534	0.000	0.000	0.000	0.000
20	A	21	SER	0	0.002	0.016	21.537	0.400	0.400	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.016	-0.008	22.918	0.180	0.180	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.033	-0.012	16.806	0.296	0.296	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.008	-0.005	18.657	0.674	0.674	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.044	-0.003	19.997	0.051	0.051	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.025	-0.042	17.688	0.010	0.010	0.000	0.000	0.000	0.000
26	A	27	PHE	0	-0.029	-0.030	10.385	0.863	0.863	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.866	-0.903	14.007	15.360	15.360	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.028	-0.022	13.028	1.292	1.292	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.792	-0.905	9.654	27.145	27.145	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.819	0.897	11.204	-22.355	-22.355	0.000	0.000	0.000	0.000
31	A	32	MET	0	-0.006	-0.002	14.274	0.484	0.484	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.028	-0.006	14.439	0.603	0.603	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.046	0.016	17.490	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.816	0.889	19.698	-12.719	-12.719	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.876	0.927	22.554	-10.460	-10.460	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.852	-0.913	22.010	12.785	12.785	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.048	0.051	25.817	-0.340	-0.340	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.003	-0.017	28.907	0.066	0.066	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.052	-0.039	25.245	-0.120	-0.120	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.812	-0.877	23.896	11.044	11.044	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.005	-0.006	18.077	0.063	0.063	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.016	-0.009	19.013	0.095	0.095	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.023	0.006	12.691	0.360	0.360	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.019	-0.015	14.051	-0.168	-0.168	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.800	-0.903	8.256	26.495	26.495	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.005	0.014	8.659	-1.700	-1.700	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.960	0.981	2.565	-69.664	-67.571	3.367	-2.178	-3.283	0.015
48	A	49	THR	0	-0.038	-0.027	4.610	4.995	4.992	-0.001	-0.010	0.014	0.000
49	A	50	LEU	0	0.069	0.039	5.102	-3.272	-3.272	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.908	0.951	7.576	-30.619	-30.619	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.012	0.002	8.806	-2.102	-2.102	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.030	0.009	9.377	-1.411	-1.411	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.005	0.000	12.570	-0.891	-0.891	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.815	0.912	15.064	-16.011	-16.011	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.018	0.013	15.090	-0.870	-0.870	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.018	-0.010	15.133	-1.154	-1.154	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.950	0.971	17.060	-13.207	-13.207	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.030	0.010	20.315	-0.692	-0.692	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.012	0.003	17.798	-0.571	-0.571	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.776	0.883	18.025	-16.399	-16.399	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.033	-0.026	23.464	-0.368	-0.368	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.922	-0.955	25.321	10.310	10.310	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.831	0.916	26.170	-10.545	-10.545	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.033	0.024	23.183	-0.234	-0.234	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.013	0.003	20.792	0.373	0.373	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.792	-0.877	21.999	12.619	12.619	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.030	-0.013	23.456	0.257	0.257	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.050	0.021	18.771	0.263	0.263	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.820	0.879	18.116	-15.725	-15.725	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.925	0.974	18.866	-11.352	-11.352	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.054	-0.042	18.886	0.077	0.077	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.009	0.013	13.440	0.466	0.466	0.000	0.000	0.000	0.000
73	A	74	MET	0	-0.013	-0.008	14.808	1.359	1.359	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.896	0.948	16.537	-13.408	-13.408	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.039	0.026	14.815	-0.246	-0.246	0.000	0.000	0.000	0.000
76	A	77	ILE	0	-0.076	-0.029	11.439	1.167	1.167	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.942	-0.942	11.898	17.118	17.118	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.023	0.008	11.376	-0.866	-0.866	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.031	-0.021	5.841	-3.380	-3.380	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.027	0.005	6.063	5.533	5.533	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.024	-0.005	7.952	-2.309	-2.309	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.016	-0.009	10.053	0.511	0.511	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.006	0.003	12.131	-1.377	-1.377	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.010	-0.010	15.510	0.136	0.136	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.003	0.006	18.071	-0.263	-0.263	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.020	-0.004	20.501	0.081	0.081	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.846	0.912	23.086	-11.568	-11.568	0.000	0.000	0.000	0.000
88	A	89	GLN	0	0.043	0.009	24.414	-0.042	-0.042	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.007	0.010	25.937	-0.167	-0.167	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.063	0.032	22.443	-0.096	-0.096	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.045	-0.033	24.433	0.077	0.077	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.077	-0.032	26.666	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.011	0.013	25.666	-0.202	-0.202	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.018	-0.004	26.023	0.160	0.160	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.025	-0.001	19.165	0.212	0.212	0.000	0.000	0.000	0.000
96	A	97	SER	0	0.024	0.006	23.315	-0.358	-0.358	0.000	0.000	0.000	0.000
97	A	98	PHE	0	-0.004	-0.004	17.286	0.151	0.151	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.032	-0.011	21.096	-0.713	-0.713	0.000	0.000	0.000	0.000
99	A	109	ALA	0	0.000	-0.016	21.688	-0.121	-0.121	0.000	0.000	0.000	0.000
100	A	110	ILE	0	-0.008	0.010	17.379	0.120	0.120	0.000	0.000	0.000	0.000
101	A	111	LYS	1	0.874	0.932	15.541	-14.065	-14.065	0.000	0.000	0.000	0.000
102	A	112	PHE	0	0.033	0.021	12.072	0.215	0.215	0.000	0.000	0.000	0.000
103	A	113	TYR	0	0.009	-0.009	9.299	-0.926	-0.926	0.000	0.000	0.000	0.000
104	A	114	ILE	0	-0.026	-0.013	5.587	0.490	0.490	0.000	0.000	0.000	0.000
105	A	115	GLU	-1	-0.903	-0.950	2.849	35.011	36.566	0.423	-0.912	-1.065	-0.002
106	A	116	TYR	0	-0.014	-0.043	2.165	0.551	3.612	9.835	-6.897	-5.999	0.008
107	A	117	GLN	0	-0.017	-0.026	1.774	-30.546	-35.492	14.939	-4.931	-5.061	0.065
108	A	118	ASN	0	-0.046	-0.013	4.948	-7.061	-7.090	-0.001	-0.008	0.039	0.000
109	A	119	PRO	0	0.050	0.021	7.544	-1.285	-1.285	0.000	0.000	0.000	0.000
110	A	120	LYS	1	0.964	0.958	9.015	-20.662	-20.662	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.811	-0.889	9.720	30.255	30.255	0.000	0.000	0.000	0.000
112	A	122	ILE	0	0.013	0.008	6.540	-1.949	-1.949	0.000	0.000	0.000	0.000
113	A	123	VAL	0	-0.007	-0.009	10.724	-2.287	-2.287	0.000	0.000	0.000	0.000
114	A	124	ASP	-1	-0.799	-0.878	14.238	17.347	17.347	0.000	0.000	0.000	0.000
115	A	125	TRP	0	-0.001	0.020	10.262	-0.540	-0.540	0.000	0.000	0.000	0.000
116	A	126	LEU	0	-0.012	-0.013	12.175	-1.573	-1.573	0.000	0.000	0.000	0.000
117	A	127	ALA	0	-0.032	-0.021	15.496	-1.265	-1.265	0.000	0.000	0.000	0.000
118	A	128	PRO	0	0.027	0.036	18.322	-0.178	-0.178	0.000	0.000	0.000	0.000
119	A	129	LYS	1	0.846	0.929	20.307	-12.559	-12.559	0.000	0.000	0.000	0.000
120	A	130	THR	0	-0.063	-0.050	23.267	-0.282	-0.282	0.000	0.000	0.000	0.000
121	A	131	ALA	0	0.038	0.009	26.392	-0.211	-0.211	0.000	0.000	0.000	0.000
122	A	132	HIS	0	-0.003	-0.009	29.973	-0.249	-0.249	0.000	0.000	0.000	0.000
123	A	133	GLY	0	0.024	0.019	29.635	-0.183	-0.183	0.000	0.000	0.000	0.000
124	A	134	VAL	0	0.002	0.013	28.131	0.121	0.121	0.000	0.000	0.000	0.000
125	A	135	PRO	0	0.016	-0.004	22.930	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	136	LEU	0	-0.019	-0.006	24.544	-0.285	-0.285	0.000	0.000	0.000	0.000
127	A	137	TRP	0	-0.070	-0.043	18.302	-0.483	-0.483	0.000	0.000	0.000	0.000
128	A	138	ASP	-1	-0.875	-0.942	19.964	15.285	15.285	0.000	0.000	0.000	0.000
129	A	139	ASN	0	-0.009	0.012	15.549	-0.699	-0.699	0.000	0.000	0.000	0.000
130	A	140	PRO	0	0.032	0.017	14.491	-0.200	-0.200	0.000	0.000	0.000	0.000
131	A	141	VAL	0	-0.030	-0.027	10.303	0.591	0.591	0.000	0.000	0.000	0.000
132	A	142	PRO	0	0.027	0.019	7.779	-0.143	-0.143	0.000	0.000	0.000	0.000
133	A	143	PRO	0	0.008	0.011	7.728	0.159	0.159	0.000	0.000	0.000	0.000
134	A	144	ASP	-1	-0.872	-0.905	4.117	56.680	57.081	0.002	-0.058	-0.345	0.000

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