FMO DATABASE

FMODB ID: 1NYGZ

Calculation Name: 2D2A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D2A

Chain ID: A

ChEMBL ID:

UniProt ID: P77667

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-833699.105727
FMO2-HF: Nuclear repulsion	789844.023244
FMO2-HF: Total energy	-43855.082483
FMO2-MP2: Total energy	-43981.547209

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:9:ASN)

Summations of interaction energy for fragment #1(A:9:ASN)

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.
-2.026	1.289	0.019	-1.518	-1.815	-0.003

Interaction energy analysis for fragmet #1(A:9:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.008

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	11	GLN	0	0.001	-0.011	4.103	-2.594	-0.019	-0.005	-1.386	-1.184	-0.003
4	A	12	ASP	-1	-0.860	-0.918	5.911	1.817	1.817	0.000	0.000	0.000	0.000
5	A	13	PHE	0	-0.032	-0.035	3.711	0.285	0.850	0.026	-0.121	-0.470	0.000
6	A	14	ALA	0	-0.073	-0.022	8.489	-0.263	-0.263	0.000	0.000	0.000	0.000
7	A	15	TRP	0	-0.007	0.007	4.705	-0.101	-0.040	-0.001	-0.002	-0.057	0.000
8	A	16	GLN	0	-0.102	-0.049	11.628	0.074	0.074	0.000	0.000	0.000	0.000
9	A	17	GLY	0	0.030	0.007	13.951	0.035	0.035	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.099	-0.039	13.934	-0.079	-0.079	0.000	0.000	0.000	0.000
11	A	19	THR	0	-0.003	-0.038	17.463	0.033	0.033	0.000	0.000	0.000	0.000
12	A	20	LEU	0	0.023	0.038	21.134	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	21	THR	0	0.012	-0.014	24.247	0.027	0.027	0.000	0.000	0.000	0.000
14	A	22	PRO	0	0.060	-0.001	27.156	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.032	0.038	30.467	0.004	0.004	0.000	0.000	0.000	0.000
16	A	24	ALA	0	-0.016	-0.002	26.477	0.000	0.000	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.050	0.017	28.212	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.010	-0.008	29.210	0.007	0.007	0.000	0.000	0.000	0.000
19	A	27	HIS	1	0.843	0.903	30.744	0.195	0.195	0.000	0.000	0.000	0.000
20	A	28	ILE	0	0.032	0.029	25.638	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.872	0.917	30.000	0.108	0.108	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.885	-0.918	32.729	-0.140	-0.140	0.000	0.000	0.000	0.000
23	A	31	LEU	0	-0.094	-0.060	30.481	0.006	0.006	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.064	0.013	30.467	0.002	0.002	0.000	0.000	0.000	0.000
25	A	33	ALA	0	-0.037	0.026	33.188	0.008	0.008	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.829	0.895	36.256	0.163	0.163	0.000	0.000	0.000	0.000
27	A	35	GLN	0	-0.019	-0.004	33.306	0.001	0.001	0.000	0.000	0.000	0.000
28	A	36	PRO	0	0.088	0.053	34.423	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	37	GLY	0	-0.016	-0.025	33.536	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	38	MET	0	-0.064	0.020	28.468	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	39	VAL	0	-0.025	-0.013	26.149	0.015	0.015	0.000	0.000	0.000	0.000
32	A	40	GLY	0	-0.015	-0.016	25.860	0.015	0.015	0.000	0.000	0.000	0.000
33	A	41	VAL	0	0.002	0.018	23.328	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	42	ARG	1	0.858	0.890	17.108	0.523	0.523	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.029	-0.004	16.948	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	44	GLY	0	0.035	0.021	15.783	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	45	VAL	0	-0.039	-0.039	12.055	0.049	0.049	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.908	0.982	15.295	0.583	0.583	0.000	0.000	0.000	0.000
39	A	47	GLN	0	0.080	0.035	13.163	0.103	0.103	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.056	-0.036	16.581	0.129	0.129	0.000	0.000	0.000	0.000
41	A	49	GLY	0	0.045	0.020	18.569	-0.052	-0.052	0.000	0.000	0.000	0.000
42	A	50	CYS	0	-0.038	-0.011	19.352	0.020	0.020	0.000	0.000	0.000	0.000
43	A	51	ALA	0	0.012	-0.002	13.723	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	52	GLY	0	0.010	0.007	14.016	-0.154	-0.154	0.000	0.000	0.000	0.000
45	A	53	PHE	0	0.014	-0.012	10.899	-0.139	-0.139	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.068	-0.001	15.731	0.081	0.081	0.000	0.000	0.000	0.000
47	A	55	TYR	0	0.062	0.006	15.711	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	56	VAL	0	-0.046	-0.040	18.892	0.054	0.054	0.000	0.000	0.000	0.000
49	A	57	LEU	0	0.001	0.016	20.257	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	58	ASP	-1	-0.857	-0.917	22.614	-0.347	-0.347	0.000	0.000	0.000	0.000
51	A	59	SER	0	0.012	0.004	24.253	0.014	0.014	0.000	0.000	0.000	0.000
52	A	60	VAL	0	-0.023	-0.008	22.882	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	61	SER	0	-0.032	-0.054	25.821	0.019	0.019	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.887	-0.929	24.311	-0.231	-0.231	0.000	0.000	0.000	0.000
55	A	63	PRO	0	-0.068	-0.021	21.451	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	64	ASP	-1	-0.770	-0.882	18.073	-0.347	-0.347	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.756	0.837	18.175	0.298	0.298	0.000	0.000	0.000	0.000
58	A	66	ASP	-1	-0.844	-0.930	13.455	-0.567	-0.567	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.864	-0.902	14.517	-0.483	-0.483	0.000	0.000	0.000	0.000
60	A	68	LEU	0	-0.024	-0.002	12.354	0.096	0.096	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.009	-0.008	16.531	-0.059	-0.059	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.007	0.011	14.546	0.042	0.042	0.000	0.000	0.000	0.000
63	A	71	GLU	-1	-0.853	-0.932	20.660	-0.107	-0.107	0.000	0.000	0.000	0.000
64	A	72	HIS	0	0.017	0.016	24.368	0.014	0.014	0.000	0.000	0.000	0.000
65	A	73	ASP	-1	-0.845	-0.909	26.577	-0.102	-0.102	0.000	0.000	0.000	0.000
66	A	74	GLY	0	-0.040	-0.025	29.353	0.000	0.000	0.000	0.000	0.000	0.000
67	A	75	ALA	0	-0.046	-0.017	27.572	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.819	0.885	24.397	0.103	0.103	0.000	0.000	0.000	0.000
69	A	77	LEU	0	0.029	0.040	19.382	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	78	PHE	0	-0.021	-0.023	19.263	0.025	0.025	0.000	0.000	0.000	0.000
71	A	79	VAL	0	-0.004	-0.026	13.494	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	80	PRO	0	0.097	0.048	13.207	0.043	0.043	0.000	0.000	0.000	0.000
73	A	81	LEU	0	0.055	0.043	9.652	-0.160	-0.160	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.058	-0.023	6.750	0.039	0.039	0.000	0.000	0.000	0.000
75	A	83	ALA	0	-0.039	-0.044	9.148	-0.414	-0.414	0.000	0.000	0.000	0.000
76	A	84	MET	0	0.008	0.024	8.340	-0.133	-0.133	0.000	0.000	0.000	0.000
77	A	85	PRO	0	-0.035	-0.027	4.173	-0.072	0.042	-0.001	-0.009	-0.104	0.000
78	A	86	PHE	0	-0.004	0.027	6.305	0.005	0.005	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.048	-0.029	9.112	0.320	0.320	0.000	0.000	0.000	0.000
80	A	88	ASP	-1	-0.710	-0.864	9.885	-0.179	-0.179	0.000	0.000	0.000	0.000
81	A	89	GLY	0	0.001	-0.007	11.602	-0.045	-0.045	0.000	0.000	0.000	0.000
82	A	90	THR	0	-0.073	-0.022	14.843	0.021	0.021	0.000	0.000	0.000	0.000
83	A	91	GLU	-1	-0.890	-0.905	17.056	-0.197	-0.197	0.000	0.000	0.000	0.000
84	A	92	VAL	0	-0.035	-0.036	20.365	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.760	-0.857	22.579	-0.193	-0.193	0.000	0.000	0.000	0.000
86	A	94	PHE	0	-0.094	-0.081	26.176	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	95	VAL	0	-0.004	0.029	29.275	0.015	0.015	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.950	0.954	32.243	0.146	0.146	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.899	-0.947	35.536	-0.138	-0.138	0.000	0.000	0.000	0.000
90	A	98	GLY	0	-0.020	-0.017	38.376	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	99	LEU	0	-0.044	-0.030	39.789	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	100	ASN	0	-0.004	0.010	33.947	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	101	GLN	0	-0.040	-0.028	33.810	0.010	0.010	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.063	-0.042	28.168	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	103	PHE	0	0.064	0.041	25.281	0.014	0.014	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.895	0.957	24.928	0.322	0.322	0.000	0.000	0.000	0.000
97	A	105	PHE	0	-0.032	-0.051	19.538	0.003	0.003	0.000	0.000	0.000	0.000
98	A	106	HIS	0	0.047	0.044	20.810	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	107	ASN	0	0.078	0.031	13.093	0.065	0.065	0.000	0.000	0.000	0.000
100	A	108	PRO	0	0.012	-0.004	15.314	0.020	0.020	0.000	0.000	0.000	0.000
101	A	109	LYS	1	0.805	0.908	10.153	0.873	0.873	0.000	0.000	0.000	0.000
102	A	110	ALA	0	-0.028	-0.007	15.243	-0.035	-0.035	0.000	0.000	0.000	0.000
103	A	111	GLN	0	0.001	0.008	17.308	0.010	0.010	0.000	0.000	0.000	0.000
104	A	112	ASN	0	-0.075	-0.061	18.672	-0.054	-0.054	0.000	0.000	0.000	0.000
105	A	113	GLU	-1	-0.807	-0.874	22.157	-0.431	-0.431	0.000	0.000	0.000	0.000
106	A	114	CYS	0	-0.086	-0.050	23.175	0.027	0.027	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.023	0.016	24.983	0.028	0.028	0.000	0.000	0.000	0.000
108	A	116	CYM	-1	-0.872	-0.921	26.936	-0.354	-0.354	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.042	-0.011	29.031	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-1.007	-1.030	30.336	-0.278	-0.278	0.000	0.000	0.000	0.000
111	A	119	SER	0	-0.061	-0.039	29.482	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	120	PHE	0	0.008	-0.001	31.539	0.009	0.009	0.000	0.000	0.000	0.000
113	A	121	GLY	0	0.037	0.051	32.042	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	122	VAL	0	0.016	0.006	32.833	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASN)