FMO DATABASE

FMODB ID: 4N4NN

Calculation Name: 1GPR-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GPR

Chain ID: A

ChEMBL ID:

UniProt ID: P20166

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1485807.821106
FMO2-HF: Nuclear repulsion	1426662.808953
FMO2-HF: Total energy	-59145.012153
FMO2-MP2: Total energy	-59319.293715

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:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
0.013	1.187	-0.004	-0.543	-0.628	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.037

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	5	PRO	0	-0.006	0.000	3.836	0.444	1.618	-0.004	-0.543	-0.628	-0.002
4	A	6	LEU	0	-0.003	0.024	5.827	0.138	0.138	0.000	0.000	0.000	0.000
5	A	7	GLN	0	-0.003	-0.008	8.222	0.175	0.175	0.000	0.000	0.000	0.000
6	A	8	ASN	0	0.056	0.029	10.168	0.037	0.037	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.906	-0.952	13.006	0.012	0.012	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.080	-0.040	15.344	0.027	0.027	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.065	-0.037	11.961	0.013	0.013	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.938	-0.963	12.835	-0.051	-0.051	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.850	-0.889	10.359	-0.539	-0.539	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.035	-0.031	11.791	0.035	0.035	0.000	0.000	0.000	0.000
13	A	15	PHE	0	0.017	-0.011	13.831	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.035	0.002	16.983	0.031	0.031	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.002	-0.007	19.467	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	18	PRO	0	0.042	0.048	22.430	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.010	-0.006	23.429	0.004	0.004	0.000	0.000	0.000	0.000
18	A	20	THR	0	0.037	0.032	27.208	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.019	0.006	29.737	0.002	0.002	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.929	-0.937	31.791	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.016	0.005	26.825	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	HIS	1	0.757	0.843	31.018	0.064	0.064	0.000	0.000	0.000	0.000
23	A	25	PRO	0	0.080	0.022	30.925	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	26	ILE	0	0.009	0.003	29.178	0.001	0.001	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.016	-0.023	31.919	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.827	-0.878	35.279	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.009	-0.003	32.918	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	PRO	0	-0.057	-0.015	36.208	0.002	0.002	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.805	-0.925	36.907	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	32	GLN	0	-0.010	-0.016	36.889	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.015	0.008	33.700	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	PHE	0	0.019	-0.009	30.324	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.006	0.002	32.877	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.040	-0.015	35.058	0.003	0.003	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.895	0.944	30.415	0.056	0.056	0.000	0.000	0.000	0.000
36	A	38	MET	0	-0.044	-0.008	31.117	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	MET	0	-0.041	-0.010	27.988	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.045	0.020	26.328	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.848	-0.924	25.742	-0.065	-0.065	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.014	-0.017	25.377	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.037	-0.007	23.241	0.010	0.010	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.031	0.009	28.219	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	45	ILE	0	0.009	0.007	26.372	0.004	0.004	0.000	0.000	0.000	0.000
44	A	46	LEU	0	0.012	0.013	30.739	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	47	PRO	0	-0.032	-0.016	32.190	0.002	0.002	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.037	-0.036	33.273	0.005	0.005	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.871	-0.900	31.691	-0.078	-0.078	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.003	0.004	32.327	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.000	0.003	27.053	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.009	-0.003	24.664	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.000	-0.006	21.831	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	54	SER	0	-0.029	-0.028	16.485	0.013	0.013	0.000	0.000	0.000	0.000
53	A	55	PRO	0	0.051	0.032	18.677	0.002	0.002	0.000	0.000	0.000	0.000
54	A	56	VAL	0	0.016	0.008	13.698	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.963	0.997	7.872	1.107	1.107	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.034	0.008	11.479	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	59	LYS	1	0.871	0.944	12.433	0.342	0.342	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.012	0.008	14.968	0.040	0.040	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.046	-0.036	17.176	0.003	0.003	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.023	-0.007	20.353	0.022	0.022	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.017	0.020	23.963	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.015	0.020	26.278	0.012	0.012	0.000	0.000	0.000	0.000
63	A	65	PRO	0	-0.010	-0.032	29.754	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.060	-0.089	32.663	0.002	0.002	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.923	0.963	29.781	0.120	0.120	0.000	0.000	0.000	0.000
66	A	68	HIS	0	0.078	0.111	30.599	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.022	0.006	28.344	0.001	0.001	0.000	0.000	0.000	0.000
68	A	70	ILE	0	-0.026	-0.008	22.309	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.003	0.012	22.500	0.005	0.005	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.014	-0.012	17.402	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	73	GLN	0	-0.022	-0.005	13.454	0.015	0.015	0.000	0.000	0.000	0.000
72	A	74	SER	0	-0.045	-0.032	12.674	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.746	-0.843	7.131	-1.516	-1.516	0.000	0.000	0.000	0.000
74	A	76	GLY	0	-0.039	-0.034	8.616	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	77	GLY	0	-0.026	-0.008	9.841	0.120	0.120	0.000	0.000	0.000	0.000
76	A	78	ARG	1	0.863	0.938	12.665	0.239	0.239	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.963	-0.983	15.819	-0.263	-0.263	0.000	0.000	0.000	0.000
78	A	80	ILE	0	-0.019	-0.011	17.169	0.026	0.026	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.002	0.004	20.726	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.001	-0.003	22.133	0.009	0.009	0.000	0.000	0.000	0.000
81	A	83	HIS	0	-0.015	-0.019	25.733	0.000	0.000	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.033	-0.008	29.406	0.007	0.007	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.014	0.021	31.429	0.004	0.004	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.002	0.000	34.451	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.890	-0.968	37.116	-0.056	-0.056	0.000	0.000	0.000	0.000
86	A	88	THR	0	0.002	-0.013	34.797	0.003	0.003	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.001	0.015	36.217	0.000	0.000	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.025	-0.028	37.602	0.001	0.001	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.006	0.002	38.780	0.003	0.003	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.857	0.929	38.950	0.058	0.058	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.052	0.018	36.035	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-1.016	-0.987	36.968	-0.066	-0.066	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.069	0.034	37.974	0.001	0.001	0.000	0.000	0.000	0.000
94	A	96	PHE	0	-0.053	-0.022	32.458	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	97	THR	0	0.001	0.003	31.090	0.002	0.002	0.000	0.000	0.000	0.000
96	A	98	SER	0	0.024	0.004	26.907	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	99	PHE	0	-0.090	-0.049	25.353	0.008	0.008	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.000	0.005	21.010	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.036	-0.014	22.454	0.028	0.028	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.866	-0.940	21.475	-0.188	-0.188	0.000	0.000	0.000	0.000
101	A	103	GLY	0	-0.091	-0.056	18.211	0.007	0.007	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.830	-0.907	17.227	-0.287	-0.287	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.786	0.851	8.940	1.142	1.142	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.052	-0.019	14.300	0.048	0.048	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.919	-0.974	12.638	-0.636	-0.636	0.000	0.000	0.000	0.000
106	A	108	PRO	0	0.016	-0.010	13.072	0.047	0.047	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.067	0.036	16.204	0.015	0.015	0.000	0.000	0.000	0.000
108	A	110	GLN	0	-0.008	0.019	17.539	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.905	0.958	20.141	0.128	0.128	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.029	-0.014	20.298	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.004	-0.009	24.012	0.006	0.006	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.991	-1.000	27.743	-0.099	-0.099	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.011	0.005	30.931	0.002	0.002	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.887	-0.944	33.939	-0.062	-0.062	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.023	-0.018	35.071	0.002	0.002	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.931	-0.959	38.466	-0.052	-0.052	0.000	0.000	0.000	0.000
117	A	119	ALA	0	-0.034	-0.003	40.441	0.003	0.003	0.000	0.000	0.000	0.000
118	A	120	VAL	0	-0.005	-0.016	37.237	0.001	0.001	0.000	0.000	0.000	0.000
119	A	121	LYS	1	0.930	0.974	40.334	0.054	0.054	0.000	0.000	0.000	0.000
120	A	122	PRO	0	-0.053	-0.040	41.758	0.002	0.002	0.000	0.000	0.000	0.000
121	A	123	ASN	0	-0.081	-0.030	42.905	0.004	0.004	0.000	0.000	0.000	0.000
122	A	124	VAL	0	0.019	0.027	39.031	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	125	PRO	0	-0.003	0.006	41.248	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.002	-0.007	38.662	0.001	0.001	0.000	0.000	0.000	0.000
125	A	127	LEU	0	0.034	0.017	36.217	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.068	-0.034	33.999	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	129	THR	0	0.021	0.008	28.875	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	130	PRO	0	-0.019	0.006	29.575	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	131	ILE	0	-0.020	-0.009	23.101	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	132	VAL	0	-0.014	0.001	25.239	0.008	0.008	0.000	0.000	0.000	0.000
131	A	133	PHE	0	0.022	0.001	18.824	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	134	THR	0	0.014	-0.012	21.905	0.011	0.011	0.000	0.000	0.000	0.000
133	A	135	ASN	0	-0.057	-0.018	16.789	0.014	0.014	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.021	-0.006	19.832	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	137	ALA	0	-0.020	-0.019	19.894	0.009	0.009	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.949	-0.979	21.715	-0.030	-0.030	0.000	0.000	0.000	0.000
137	A	139	GLY	0	-0.033	-0.019	24.402	0.005	0.005	0.000	0.000	0.000	0.000
138	A	140	GLU	-1	-0.846	-0.902	19.034	-0.094	-0.094	0.000	0.000	0.000	0.000
139	A	141	THR	0	-0.053	-0.020	23.617	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.008	-0.009	23.065	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	143	SER	0	0.007	0.000	24.775	0.007	0.007	0.000	0.000	0.000	0.000
142	A	144	ILE	0	-0.060	-0.019	25.465	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	145	LYS	1	0.824	0.875	21.515	0.058	0.058	0.000	0.000	0.000	0.000
144	A	146	ALA	0	-0.041	-0.002	26.685	0.006	0.006	0.000	0.000	0.000	0.000
145	A	147	SER	0	-0.016	-0.022	28.230	0.001	0.001	0.000	0.000	0.000	0.000
146	A	148	GLY	0	0.020	0.017	31.955	0.000	0.000	0.000	0.000	0.000	0.000
147	A	149	SER	0	-0.017	-0.026	32.614	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.029	0.004	27.109	0.001	0.001	0.000	0.000	0.000	0.000
149	A	151	ASN	0	0.005	-0.012	27.414	0.002	0.002	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.831	0.877	24.990	0.102	0.102	0.000	0.000	0.000	0.000
151	A	153	GLU	-1	-0.938	-1.002	20.618	-0.155	-0.155	0.000	0.000	0.000	0.000
152	A	154	GLN	0	-0.010	0.019	21.475	0.002	0.002	0.000	0.000	0.000	0.000
153	A	155	GLU	-1	-0.885	-0.968	18.009	-0.107	-0.107	0.000	0.000	0.000	0.000
154	A	156	ASP	-1	-0.861	-0.902	19.512	-0.046	-0.046	0.000	0.000	0.000	0.000
155	A	157	ILE	0	0.012	0.011	21.109	0.013	0.013	0.000	0.000	0.000	0.000
156	A	158	VAL	0	-0.021	0.005	21.169	0.009	0.009	0.000	0.000	0.000	0.000
157	A	159	LYS	1	0.912	0.963	21.092	0.021	0.021	0.000	0.000	0.000	0.000
158	A	160	ILE	0	0.008	0.011	18.572	0.000	0.000	0.000	0.000	0.000	0.000
159	A	161	GLU	-1	-0.929	-0.965	20.509	-0.025	-0.025	0.000	0.000	0.000	0.000
160	A	162	NME	0	0.035	0.021	23.149	-0.005	-0.005	0.000	0.000	0.000	0.000

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