FMO DATABASE

FMODB ID: GNRN1

Calculation Name: 1X8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X8Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LNF2

Base Structure: X-ray

Registration Date: 2023-03-13

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204611.649874
FMO2-HF: Nuclear repulsion	1145288.962241
FMO2-HF: Total energy	-59322.687633
FMO2-MP2: Total energy	-59488.620189

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:-1:MET)

Summations of interaction energy for fragment #1(A:-1:MET)

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.
-16.944	-13.644	20.848	-6.856	-17.291	-0.03

Interaction energy analysis for fragmet #1(A:-1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.016

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	1	SER	0	0.019	-0.008	2.745	-2.268	-0.306	0.472	-0.933	-1.501	-0.009
4	A	2	SER	0	0.020	0.027	5.022	0.577	0.762	-0.001	-0.015	-0.169	0.000
5	A	3	GLU	-1	-0.863	-0.906	2.699	-7.084	-5.316	0.416	-0.678	-1.506	-0.005
6	A	4	MET	0	-0.016	-0.015	1.985	1.008	-4.649	16.134	-3.218	-7.258	0.001
7	A	5	SER	0	0.012	-0.011	3.110	1.391	0.907	0.072	0.790	-0.379	0.000
8	A	6	THR	0	-0.063	-0.046	5.854	0.327	0.327	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.032	-0.010	2.370	-0.049	0.253	0.644	-0.141	-0.805	0.000
10	A	8	CYS	0	0.016	0.017	6.133	0.625	0.625	0.000	0.000	0.000	0.000
11	A	9	ASP	-1	-0.900	-0.931	7.900	-0.365	-0.365	0.000	0.000	0.000	0.000
12	A	10	LYS	1	0.853	0.910	9.451	0.725	0.725	0.000	0.000	0.000	0.000
13	A	11	THR	0	-0.049	-0.010	9.328	0.080	0.080	0.000	0.000	0.000	0.000
14	A	12	LEU	0	-0.012	-0.019	12.132	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	13	ASN	0	0.013	-0.013	13.476	0.003	0.003	0.000	0.000	0.000	0.000
16	A	14	PRO	0	0.079	0.048	10.769	0.113	0.113	0.000	0.000	0.000	0.000
17	A	15	SER	0	0.022	0.020	10.588	0.156	0.156	0.000	0.000	0.000	0.000
18	A	16	PHE	0	-0.023	-0.005	11.747	0.139	0.139	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.080	0.021	6.702	0.675	0.675	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.937	0.974	7.520	-0.177	-0.177	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.045	-0.014	7.845	0.035	0.035	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.061	0.008	3.176	-1.972	-0.644	0.525	-0.403	-1.450	0.004
23	A	22	ASN	0	0.080	0.030	4.369	-0.302	0.060	0.003	-0.071	-0.293	0.000
24	A	23	THR	0	-0.134	-0.066	5.393	-0.780	-0.747	-0.001	0.000	-0.031	0.000
25	A	24	LYS	1	0.860	0.928	6.756	-1.380	-1.380	0.000	0.000	0.000	0.000
26	A	25	PHE	0	-0.031	-0.004	2.454	-1.488	-0.259	0.990	-0.539	-1.680	0.000
27	A	26	ALA	0	0.041	0.029	2.315	-7.137	-5.091	1.596	-1.629	-2.014	-0.021
28	A	27	SER	0	0.003	0.006	4.434	0.898	1.100	-0.001	-0.018	-0.184	0.000
29	A	28	PRO	0	-0.008	0.000	5.307	-0.485	-0.461	-0.001	-0.001	-0.021	0.000
30	A	29	ASN	0	0.050	0.035	8.533	-0.154	-0.154	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.084	0.011	11.820	0.050	0.050	0.000	0.000	0.000	0.000
32	A	31	GLN	0	0.032	0.011	15.095	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.014	-0.005	12.183	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.000	0.007	11.262	0.022	0.022	0.000	0.000	0.000	0.000
35	A	34	ALA	0	0.040	0.031	14.350	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.852	0.899	16.781	-0.412	-0.412	0.000	0.000	0.000	0.000
37	A	36	THR	0	-0.012	0.001	14.291	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	37	THR	0	-0.033	-0.036	16.874	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	38	LEU	0	0.052	0.026	19.075	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.800	-0.863	19.583	0.324	0.324	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.066	-0.040	19.244	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	41	THR	0	-0.020	-0.026	21.830	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	42	GLN	0	0.054	0.028	24.612	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	43	ALA	0	-0.023	0.003	24.484	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.883	0.945	23.728	-0.193	-0.193	0.000	0.000	0.000	0.000
46	A	45	ALA	0	0.073	0.028	27.545	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	46	THR	0	0.025	0.011	29.682	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	47	GLN	0	-0.078	-0.046	26.594	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	48	THR	0	-0.027	-0.020	31.526	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.059	0.046	33.818	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.951	0.970	33.217	-0.129	-0.129	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.858	0.940	35.675	-0.081	-0.081	0.000	0.000	0.000	0.000
53	A	52	LEU	0	0.008	-0.002	37.668	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	53	GLN	0	0.080	0.033	39.800	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.033	0.009	40.375	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	55	ILE	0	-0.062	-0.038	39.585	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.039	-0.019	43.420	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.936	-0.968	45.002	0.062	0.062	0.000	0.000	0.000	0.000
59	A	58	GLY	0	-0.080	-0.025	46.331	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	59	GLY	0	-0.057	-0.016	47.982	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	60	VAL	0	-0.007	-0.009	46.526	0.000	0.000	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.867	-0.939	49.963	0.038	0.038	0.000	0.000	0.000	0.000
63	A	62	PRO	0	0.019	-0.018	51.336	0.002	0.002	0.000	0.000	0.000	0.000
64	A	63	ARG	1	0.909	0.956	49.203	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.010	0.003	46.980	0.002	0.002	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.920	0.961	47.059	-0.046	-0.046	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.032	0.000	47.828	0.002	0.002	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.060	0.033	44.979	0.002	0.002	0.000	0.000	0.000	0.000
69	A	68	TYR	0	0.036	-0.009	41.009	0.003	0.003	0.000	0.000	0.000	0.000
70	A	69	ARG	1	0.959	0.974	42.938	-0.049	-0.049	0.000	0.000	0.000	0.000
71	A	70	SER	0	0.046	0.043	43.794	0.001	0.001	0.000	0.000	0.000	0.000
72	A	71	CYS	0	-0.050	0.003	36.762	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.052	-0.025	39.306	0.006	0.006	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.859	-0.918	39.823	0.073	0.073	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.929	-0.966	38.231	0.079	0.079	0.000	0.000	0.000	0.000
76	A	75	TYR	0	-0.068	-0.092	32.179	0.011	0.011	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.951	-0.965	35.397	0.091	0.091	0.000	0.000	0.000	0.000
78	A	77	SER	0	0.017	0.016	36.680	0.004	0.004	0.000	0.000	0.000	0.000
79	A	78	ALA	0	-0.042	-0.017	32.697	0.006	0.006	0.000	0.000	0.000	0.000
80	A	79	ILE	0	-0.048	-0.030	31.686	0.010	0.010	0.000	0.000	0.000	0.000
81	A	80	GLY	0	0.066	0.044	31.765	0.009	0.009	0.000	0.000	0.000	0.000
82	A	81	ASN	0	0.018	-0.003	32.179	0.003	0.003	0.000	0.000	0.000	0.000
83	A	82	LEU	0	-0.049	-0.042	27.026	0.010	0.010	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.937	-0.958	27.979	0.156	0.156	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.889	-0.952	29.071	0.124	0.124	0.000	0.000	0.000	0.000
86	A	85	ALA	0	-0.039	-0.032	26.801	0.004	0.004	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.069	-0.028	21.597	0.021	0.021	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.920	-0.950	25.309	0.155	0.155	0.000	0.000	0.000	0.000
89	A	88	HIS	0	-0.038	-0.026	27.032	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.019	-0.009	19.543	0.007	0.007	0.000	0.000	0.000	0.000
91	A	90	ALA	0	-0.053	-0.011	22.701	0.013	0.013	0.000	0.000	0.000	0.000
92	A	91	SER	0	-0.039	-0.035	23.950	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	92	GLY	0	-0.023	0.011	23.211	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	93	ASP	-1	-0.840	-0.912	24.195	0.117	0.117	0.000	0.000	0.000	0.000
95	A	94	GLY	0	-0.001	-0.015	24.879	0.003	0.003	0.000	0.000	0.000	0.000
96	A	95	MET	0	-0.027	-0.011	25.464	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.048	0.013	29.041	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	97	MET	0	-0.051	-0.025	21.537	0.005	0.005	0.000	0.000	0.000	0.000
99	A	98	ASN	0	-0.041	-0.014	26.435	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	99	MET	0	-0.019	0.001	28.079	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.998	0.991	29.998	-0.115	-0.115	0.000	0.000	0.000	0.000
102	A	101	VAL	0	0.004	-0.004	25.436	0.000	0.000	0.000	0.000	0.000	0.000
103	A	102	SER	0	-0.031	-0.020	28.806	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	103	ALA	0	0.032	0.028	31.210	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	104	ALA	0	-0.005	0.000	30.000	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.070	-0.027	28.768	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.861	-0.928	31.312	0.082	0.082	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.080	0.043	34.975	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	108	ALA	0	-0.055	-0.041	31.770	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.893	-0.966	33.802	0.069	0.069	0.000	0.000	0.000	0.000
111	A	110	THR	0	0.053	0.036	35.367	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.080	-0.058	33.838	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.880	-0.939	38.119	0.052	0.052	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.888	-0.946	41.191	0.056	0.056	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.031	-0.032	39.465	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.881	0.955	41.303	-0.048	-0.048	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.860	0.928	42.756	-0.036	-0.036	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.036	0.015	44.047	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.900	0.951	45.739	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.022	-0.005	44.500	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.047	0.028	40.233	0.001	0.001	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.776	-0.885	37.812	0.069	0.069	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.033	-0.001	35.137	0.003	0.003	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.039	-0.003	33.177	0.006	0.006	0.000	0.000	0.000	0.000
125	A	125	VAL	0	0.072	0.027	33.189	0.008	0.008	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.009	0.021	34.588	0.004	0.004	0.000	0.000	0.000	0.000
127	A	127	ASN	0	-0.042	-0.041	30.011	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.080	0.035	29.411	0.015	0.015	0.000	0.000	0.000	0.000
129	A	129	SER	0	0.082	0.050	29.691	0.011	0.011	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.927	0.965	30.258	-0.067	-0.067	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.071	-0.032	24.739	0.008	0.008	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.025	0.006	25.798	0.017	0.017	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.881	0.953	26.994	-0.079	-0.079	0.000	0.000	0.000	0.000
134	A	134	ASN	0	-0.024	-0.009	23.866	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.043	-0.021	20.936	0.012	0.012	0.000	0.000	0.000	0.000
136	A	136	CYS	0	0.009	0.003	22.822	0.014	0.014	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.057	0.032	24.975	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.024	-0.016	18.191	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.003	-0.005	20.956	0.009	0.009	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.016	0.023	22.118	0.000	0.000	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.007	0.010	20.053	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	142	ILE	0	0.025	-0.006	16.779	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	143	SER	0	-0.024	-0.022	19.814	-0.015	-0.015	0.000	0.000	0.000	0.000
144	A	144	ASN	0	-0.019	-0.026	22.761	-0.013	-0.013	0.000	0.000	0.000	0.000
145	A	145	MET	0	-0.058	-0.031	17.611	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	146	LEU	0	-0.048	0.006	19.520	0.005	0.005	0.000	0.000	0.000	0.000
147	A	147	PRO	0	-0.028	-0.016	19.827	-0.018	-0.018	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.916	0.972	22.880	-0.117	-0.117	0.000	0.000	0.000	0.000
149	A	149	ASN	0	0.012	0.014	26.641	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:MET)