FMO DATABASE

FMODB ID: 1NYYZ

Calculation Name: 1GRW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GRW

Chain ID: A

ChEMBL ID:

UniProt ID: P53017

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1009627.230012
FMO2-HF: Nuclear repulsion	960850.059829
FMO2-HF: Total energy	-48777.170183
FMO2-MP2: Total energy	-48919.386935

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
0.838	1.561	0.001	-0.127	-0.596	0

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.280 / q_NPA : 0.182

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].
3	A	5	PRO	0	0.026	-0.013	4.647	-0.260	0.050	-0.001	-0.051	-0.257
4	A	6	PRO	0	-0.013	0.002	6.963	0.338	0.338	0.000	0.000	0.000
5	A	7	GLY	0	0.055	0.020	9.231	0.050	0.050	0.000	0.000	0.000
6	A	8	ASP	-1	-0.935	-0.988	12.295	-0.247	-0.247	0.000	0.000	0.000
7	A	9	ILE	0	-0.035	0.010	15.912	0.026	0.026	0.000	0.000	0.000
8	A	10	GLN	0	-0.036	-0.032	18.100	0.007	0.007	0.000	0.000	0.000
9	A	11	THR	0	0.020	0.001	21.854	-0.004	-0.004	0.000	0.000	0.000
10	A	12	GLN	0	-0.048	0.006	24.231	0.005	0.005	0.000	0.000	0.000
11	A	13	PRO	0	0.155	0.061	27.952	0.002	0.002	0.000	0.000	0.000
12	A	14	GLY	0	0.014	0.019	26.371	-0.007	-0.007	0.000	0.000	0.000
13	A	15	THR	0	-0.053	-0.048	25.995	-0.009	-0.009	0.000	0.000	0.000
14	A	16	LYS	1	0.907	0.964	28.048	0.054	0.054	0.000	0.000	0.000
15	A	17	ILE	0	-0.007	0.001	29.822	0.002	0.002	0.000	0.000	0.000
16	A	18	VAL	0	0.007	0.010	31.854	-0.001	-0.001	0.000	0.000	0.000
17	A	19	PHE	0	-0.011	-0.004	32.344	0.001	0.001	0.000	0.000	0.000
18	A	20	ASN	0	0.007	-0.003	37.387	0.000	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.030	0.040	41.114	0.000	0.000	0.000	0.000	0.000
20	A	22	PRO	0	0.006	-0.015	43.839	0.000	0.000	0.000	0.000	0.000
21	A	23	TYR	0	-0.051	-0.054	40.075	-0.001	-0.001	0.000	0.000	0.000
22	A	24	ASP	-1	-0.901	-0.949	43.577	-0.028	-0.028	0.000	0.000	0.000
23	A	25	ASP	-1	-0.869	-0.942	43.939	-0.026	-0.026	0.000	0.000	0.000
24	A	26	LYS	1	0.910	0.972	36.331	0.036	0.036	0.000	0.000	0.000
25	A	27	HIS	0	-0.006	0.013	38.756	0.001	0.001	0.000	0.000	0.000
26	A	28	THR	0	-0.032	-0.044	33.892	-0.004	-0.004	0.000	0.000	0.000
27	A	29	TYR	0	0.012	0.019	33.081	0.002	0.002	0.000	0.000	0.000
28	A	30	HIS	0	0.034	0.000	30.781	-0.002	-0.002	0.000	0.000	0.000
29	A	31	ILE	0	-0.032	-0.008	25.487	-0.002	-0.002	0.000	0.000	0.000
30	A	32	LYS	1	0.923	0.968	25.600	0.039	0.039	0.000	0.000	0.000
31	A	33	VAL	0	-0.007	-0.006	19.704	-0.008	-0.008	0.000	0.000	0.000
32	A	34	ILE	0	0.010	-0.001	20.879	0.011	0.011	0.000	0.000	0.000
33	A	35	ASN	0	0.040	0.039	13.828	-0.048	-0.048	0.000	0.000	0.000
34	A	36	SER	0	-0.020	-0.023	17.529	0.019	0.019	0.000	0.000	0.000
35	A	37	SER	0	-0.040	-0.020	12.719	0.017	0.017	0.000	0.000	0.000
36	A	38	ALA	0	0.025	-0.001	12.828	0.023	0.023	0.000	0.000	0.000
37	A	39	ARG	1	0.958	0.982	7.251	-0.525	-0.525	0.000	0.000	0.000
38	A	40	ARG	1	0.900	0.949	10.857	-0.138	-0.138	0.000	0.000	0.000
39	A	41	ILE	0	-0.038	-0.001	9.965	-0.037	-0.037	0.000	0.000	0.000
40	A	42	GLY	0	0.028	0.017	11.505	0.056	0.056	0.000	0.000	0.000
41	A	43	TYR	0	-0.005	-0.018	13.204	-0.051	-0.051	0.000	0.000	0.000
42	A	44	GLY	0	0.022	0.005	15.706	0.022	0.022	0.000	0.000	0.000
43	A	45	ILE	0	-0.013	-0.002	17.890	-0.013	-0.013	0.000	0.000	0.000
44	A	46	LYS	1	0.920	0.959	18.329	0.166	0.166	0.000	0.000	0.000
45	A	47	THR	0	0.040	0.023	22.920	-0.001	-0.001	0.000	0.000	0.000
46	A	48	THR	0	0.007	0.016	26.384	-0.003	-0.003	0.000	0.000	0.000
47	A	49	ASN	0	0.014	0.002	28.394	0.005	0.005	0.000	0.000	0.000
48	A	50	MET	0	0.004	0.007	28.221	0.000	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.943	0.980	30.843	0.047	0.047	0.000	0.000	0.000
50	A	52	ARG	1	0.930	0.989	34.458	0.052	0.052	0.000	0.000	0.000
51	A	53	LEU	0	-0.031	-0.026	30.467	0.000	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.008	0.011	29.786	-0.003	-0.003	0.000	0.000	0.000
53	A	55	VAL	0	-0.075	-0.048	25.170	0.000	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.926	-0.919	26.995	-0.050	-0.050	0.000	0.000	0.000
55	A	57	PRO	0	0.070	0.021	23.481	0.003	0.003	0.000	0.000	0.000
56	A	58	PRO	0	0.011	-0.006	23.369	-0.007	-0.007	0.000	0.000	0.000
57	A	59	CYS	0	-0.062	-0.042	18.455	-0.013	-0.013	0.000	0.000	0.000
58	A	60	GLY	0	0.020	0.012	18.166	0.017	0.017	0.000	0.000	0.000
59	A	61	VAL	0	-0.027	-0.019	14.070	-0.022	-0.022	0.000	0.000	0.000
60	A	62	LEU	0	-0.013	-0.006	15.277	0.010	0.010	0.000	0.000	0.000
61	A	63	ASP	-1	-0.788	-0.883	14.934	0.064	0.064	0.000	0.000	0.000
62	A	64	PRO	0	0.004	-0.005	13.896	-0.024	-0.024	0.000	0.000	0.000
63	A	65	LYS	1	0.945	0.964	16.196	-0.023	-0.023	0.000	0.000	0.000
64	A	66	GLU	-1	-0.837	-0.886	18.875	-0.007	-0.007	0.000	0.000	0.000
65	A	67	ALA	0	-0.044	-0.040	20.004	-0.016	-0.016	0.000	0.000	0.000
66	A	68	VAL	0	0.038	0.021	21.313	0.008	0.008	0.000	0.000	0.000
67	A	69	LEU	0	-0.051	-0.035	23.762	-0.006	-0.006	0.000	0.000	0.000
68	A	70	LEU	0	-0.038	-0.011	22.789	0.001	0.001	0.000	0.000	0.000
69	A	71	ALA	0	0.037	0.014	27.114	0.001	0.001	0.000	0.000	0.000
70	A	72	VAL	0	-0.015	-0.018	28.174	-0.004	-0.004	0.000	0.000	0.000
71	A	73	SER	0	-0.025	-0.011	30.668	0.003	0.003	0.000	0.000	0.000
72	A	74	CYS	0	-0.042	-0.026	33.270	-0.005	-0.005	0.000	0.000	0.000
73	A	75	ASP	-1	-0.916	-0.955	35.892	-0.035	-0.035	0.000	0.000	0.000
74	A	76	ALA	0	0.027	0.045	38.571	-0.001	-0.001	0.000	0.000	0.000
75	A	77	PHE	0	-0.089	-0.069	39.426	-0.002	-0.002	0.000	0.000	0.000
76	A	78	ALA	0	0.047	0.029	42.426	0.001	0.001	0.000	0.000	0.000
77	A	79	PHE	0	0.032	0.005	40.777	-0.001	-0.001	0.000	0.000	0.000
78	A	80	GLY	0	-0.044	-0.036	43.511	-0.001	-0.001	0.000	0.000	0.000
79	A	81	GLN	0	-0.076	-0.042	45.404	0.001	0.001	0.000	0.000	0.000
80	A	82	GLU	-1	-0.874	-0.919	40.472	-0.041	-0.041	0.000	0.000	0.000
81	A	83	ASP	-1	-0.879	-0.913	37.762	-0.046	-0.046	0.000	0.000	0.000
82	A	84	THR	0	-0.035	-0.047	36.967	-0.001	-0.001	0.000	0.000	0.000
83	A	85	ASN	0	-0.027	-0.014	36.218	-0.001	-0.001	0.000	0.000	0.000
84	A	86	ASN	0	-0.003	0.000	32.134	-0.006	-0.006	0.000	0.000	0.000
85	A	87	ASP	-1	-0.781	-0.852	30.934	-0.066	-0.066	0.000	0.000	0.000
86	A	88	ARG	1	0.930	0.958	24.131	0.111	0.111	0.000	0.000	0.000
87	A	89	ILE	0	0.032	0.030	24.401	0.000	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.077	-0.053	19.370	-0.002	-0.002	0.000	0.000	0.000
89	A	91	VAL	0	0.019	0.011	17.793	0.004	0.004	0.000	0.000	0.000
90	A	92	GLU	-1	-0.850	-0.929	14.654	-0.239	-0.239	0.000	0.000	0.000
91	A	93	TRP	0	-0.017	-0.026	12.208	0.035	0.035	0.000	0.000	0.000
92	A	94	THR	0	0.012	0.018	6.986	-0.093	-0.093	0.000	0.000	0.000
93	A	95	ASN	0	0.014	0.001	5.544	0.388	0.388	0.000	0.000	0.000
94	A	96	THR	0	-0.048	-0.018	7.010	-0.122	-0.122	0.000	0.000	0.000
95	A	97	PRO	0	-0.014	-0.017	5.671	0.128	0.128	0.000	0.000	0.000
96	A	98	ASP	-1	-0.902	-0.964	6.149	1.266	1.266	0.000	0.000	0.000
97	A	99	GLY	0	-0.015	0.004	8.074	-0.123	-0.123	0.000	0.000	0.000
98	A	100	ALA	0	0.008	0.024	10.827	-0.062	-0.062	0.000	0.000	0.000
99	A	101	ALA	0	0.007	-0.004	12.443	0.022	0.022	0.000	0.000	0.000
100	A	102	LYS	1	0.875	0.938	14.767	-0.022	-0.022	0.000	0.000	0.000
101	A	103	GLN	0	0.009	-0.016	16.259	0.001	0.001	0.000	0.000	0.000
102	A	104	PHE	0	-0.026	-0.006	14.436	-0.003	-0.003	0.000	0.000	0.000
103	A	105	ARG	1	0.974	0.996	13.942	0.096	0.096	0.000	0.000	0.000
104	A	106	ARG	1	1.000	0.987	13.739	0.077	0.077	0.000	0.000	0.000
105	A	107	GLU	-1	-0.852	-0.927	11.492	-0.191	-0.191	0.000	0.000	0.000
106	A	108	TRP	0	-0.037	-0.021	9.281	-0.035	-0.035	0.000	0.000	0.000
107	A	109	PHE	0	-0.066	-0.046	8.601	-0.098	-0.098	0.000	0.000	0.000
108	A	110	GLN	0	-0.076	-0.030	10.916	0.030	0.030	0.000	0.000	0.000
109	A	111	GLY	0	0.022	0.025	8.794	0.041	0.041	0.000	0.000	0.000
110	A	112	ASP	-1	-0.905	-0.938	5.579	-0.095	-0.095	0.000	0.000	0.000
111	A	113	GLY	0	-0.011	-0.020	3.703	-0.643	-0.388	0.002	-0.045	-0.212
112	A	114	MET	0	-0.030	-0.001	4.065	0.353	0.511	0.000	-0.031	-0.127
113	A	115	VAL	0	0.040	0.029	6.801	-0.015	-0.015	0.000	0.000	0.000
114	A	116	ARG	1	0.846	0.940	10.070	0.389	0.389	0.000	0.000	0.000
115	A	117	ARG	1	0.887	0.912	12.632	0.252	0.252	0.000	0.000	0.000
116	A	118	LYS	1	0.888	0.958	16.321	0.129	0.129	0.000	0.000	0.000
117	A	119	ASN	0	-0.058	-0.027	19.655	0.011	0.011	0.000	0.000	0.000
118	A	120	LEU	0	0.005	0.002	22.948	0.001	0.001	0.000	0.000	0.000
119	A	121	PRO	0	0.001	-0.010	26.068	0.002	0.002	0.000	0.000	0.000
120	A	122	ILE	0	0.000	0.004	28.998	0.001	0.001	0.000	0.000	0.000
121	A	123	GLU	-1	-0.892	-0.944	31.935	-0.055	-0.055	0.000	0.000	0.000
122	A	124	TYR	0	-0.041	-0.070	34.719	0.002	0.002	0.000	0.000	0.000
123	A	125	ASN	0	-0.040	-0.028	38.522	0.001	0.001	0.000	0.000	0.000
124	A	126	PRO	0	0.032	0.038	41.494	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)