FMO DATABASE

FMODB ID: 4JZYN

Calculation Name: 3NR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H063

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	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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1653324.86021
FMO2-HF: Nuclear repulsion	1587950.141853
FMO2-HF: Total energy	-65374.718357
FMO2-MP2: Total energy	-65563.606668

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-100.657	-100.922	34.634	-15.323	-19.044	-0.025

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : 0.000

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	2	LYS	1	0.953	0.971	3.426	-4.189	-1.630	0.366	-1.148	-1.777	0.000
4	A	3	LEU	0	0.038	0.030	5.925	0.217	0.217	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.096	-0.053	8.138	0.610	0.610	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.926	-0.956	11.716	-0.564	-0.564	0.000	0.000	0.000	0.000
7	A	6	ASN	0	0.000	-0.021	14.704	0.113	0.113	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.040	0.023	17.650	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.015	0.003	20.624	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	9	PHE	0	-0.020	-0.020	15.325	0.000	0.000	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.890	-0.936	17.817	-0.673	-0.673	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.018	0.013	19.733	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.026	-0.004	21.362	0.017	0.017	0.000	0.000	0.000	0.000
14	A	13	ASN	0	0.011	-0.004	16.758	0.001	0.001	0.000	0.000	0.000	0.000
15	A	14	SER	0	-0.055	-0.023	20.857	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	15	GLN	0	-0.068	-0.058	23.594	0.054	0.054	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.060	0.002	20.857	0.035	0.035	0.000	0.000	0.000	0.000
18	A	17	THR	0	0.031	0.011	23.561	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.007	-0.005	25.857	0.042	0.042	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.874	-0.928	24.755	-0.606	-0.606	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.117	-0.087	29.029	0.034	0.034	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.053	-0.006	31.668	0.013	0.013	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.986	-0.972	30.979	-0.434	-0.434	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.065	0.001	28.653	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	24	HIS	0	-0.012	-0.006	24.981	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.003	0.003	20.012	0.020	0.020	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.024	-0.001	22.784	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.060	-0.009	19.324	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.838	0.918	12.549	1.697	1.697	0.000	0.000	0.000	0.000
30	A	29	ILE	0	-0.027	-0.021	15.775	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.753	-0.821	10.586	-2.663	-2.663	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.010	-0.036	12.195	0.067	0.067	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.012	-0.020	6.025	-0.451	-0.451	0.000	0.000	0.000	0.000
34	A	33	SER	0	0.000	0.002	7.062	0.225	0.225	0.000	0.000	0.000	0.000
35	A	34	CYS	0	-0.039	-0.017	5.134	0.155	0.155	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.857	0.920	1.716	-52.670	-59.627	24.376	-7.606	-9.812	0.064
37	A	36	PRO	0	0.012	0.005	3.808	-1.217	-0.996	-0.001	-0.014	-0.205	0.000
38	A	37	LEU	0	0.023	0.031	3.922	0.309	0.525	0.000	-0.025	-0.191	0.000
39	A	38	SER	0	0.017	0.001	6.879	-0.234	-0.234	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.778	-0.899	10.156	0.689	0.689	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.870	0.934	13.204	-0.830	-0.830	0.000	0.000	0.000	0.000
42	A	41	CYS	0	-0.020	0.019	8.658	-0.135	-0.135	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.028	0.004	11.911	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.958	0.968	12.571	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.895	0.937	8.993	-0.779	-0.779	0.000	0.000	0.000	0.000
46	A	45	THR	0	0.029	0.022	8.551	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.022	0.021	10.048	-0.134	-0.134	0.000	0.000	0.000	0.000
48	A	47	PHE	0	0.020	0.008	3.512	-0.568	-0.219	0.009	-0.086	-0.272	0.000
49	A	48	TYR	0	-0.019	-0.051	3.693	-0.530	-0.255	0.002	-0.036	-0.241	0.000
50	A	49	LEU	0	-0.024	0.017	6.626	-0.587	-0.587	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.068	0.037	7.695	-0.308	-0.308	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.033	-0.014	2.601	-1.084	-0.496	0.251	-0.243	-0.596	-0.002
53	A	52	THR	0	-0.061	-0.051	4.292	-2.322	-2.169	-0.001	-0.049	-0.103	0.000
54	A	53	LEU	0	-0.010	0.015	6.452	-0.295	-0.295	0.000	0.000	0.000	0.000
55	A	54	ASN	0	0.021	0.010	5.471	0.179	0.179	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.874	-0.924	1.899	-39.469	-37.344	9.634	-6.096	-5.662	-0.087
57	A	56	SER	0	-0.056	-0.040	5.182	0.775	0.800	-0.001	-0.003	-0.021	0.000
58	A	57	PHE	0	0.025	0.005	8.722	0.386	0.386	0.000	0.000	0.000	0.000
59	A	58	ARG	1	0.836	0.950	3.676	9.869	10.050	-0.001	-0.017	-0.164	0.000
60	A	59	PRO	0	-0.090	-0.065	9.455	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.888	-0.944	11.475	-1.335	-1.335	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.004	-0.008	12.660	0.213	0.213	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.837	-0.902	10.187	-1.878	-1.878	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.041	0.005	10.197	0.250	0.250	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.093	-0.075	9.846	0.191	0.191	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.072	-0.039	10.987	0.187	0.187	0.000	0.000	0.000	0.000
67	A	66	ALA	0	-0.011	0.021	12.981	0.086	0.086	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.943	0.966	14.742	0.434	0.434	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.066	-0.057	16.254	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	69	HIS	0	-0.117	-0.080	17.244	0.017	0.017	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.700	-0.817	16.982	-0.655	-0.655	0.000	0.000	0.000	0.000
72	A	71	PHE	0	-0.040	-0.023	12.216	-0.074	-0.074	0.000	0.000	0.000	0.000
73	A	72	SER	0	0.006	0.014	17.295	0.081	0.081	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.804	0.884	18.742	0.134	0.134	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.829	-0.903	20.024	-0.373	-0.373	0.000	0.000	0.000	0.000
76	A	75	PRO	0	-0.053	-0.032	22.330	0.022	0.022	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.006	-0.008	25.096	0.022	0.022	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.091	0.049	23.285	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	78	SER	0	0.008	-0.010	25.449	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	79	TRP	0	-0.028	-0.002	25.725	0.008	0.008	0.000	0.000	0.000	0.000
81	A	80	VAL	0	0.058	0.035	21.758	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.001	0.008	25.118	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.026	-0.023	26.626	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	83	ALA	0	0.048	0.036	25.854	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	VAL	0	0.008	0.014	22.541	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	85	ASN	0	0.005	-0.002	25.527	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	86	CYS	0	-0.077	-0.039	28.709	0.015	0.015	0.000	0.000	0.000	0.000
88	A	87	SER	0	0.008	0.000	26.232	0.006	0.006	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.014	-0.005	23.677	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	89	PHE	0	-0.043	-0.010	27.723	0.011	0.011	0.000	0.000	0.000	0.000
91	A	90	SER	0	-0.028	-0.012	30.722	0.016	0.016	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.039	-0.010	27.992	0.010	0.010	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.024	0.011	27.584	0.001	0.001	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.871	0.923	30.652	0.291	0.291	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.859	-0.933	33.822	-0.250	-0.250	0.000	0.000	0.000	0.000
96	A	95	ASP	-1	-0.871	-0.918	32.402	-0.295	-0.295	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.036	-0.027	26.999	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.769	0.884	31.440	0.218	0.218	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.832	-0.924	32.868	-0.222	-0.222	0.000	0.000	0.000	0.000
100	A	99	LEU	0	0.064	0.048	25.374	0.002	0.002	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.932	0.981	27.673	0.247	0.247	0.000	0.000	0.000	0.000
102	A	101	PRO	0	-0.014	-0.023	27.869	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	102	GLN	0	0.041	0.044	25.980	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.019	0.001	21.612	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	104	TRP	0	-0.035	-0.040	22.621	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	105	ASN	0	-0.012	-0.001	24.616	0.011	0.011	0.000	0.000	0.000	0.000
107	A	106	ALA	0	0.044	0.031	21.852	0.017	0.017	0.000	0.000	0.000	0.000
108	A	107	VAL	0	0.002	-0.009	19.000	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	108	ASP	-1	-0.870	-0.943	20.358	-0.171	-0.171	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.955	-0.972	22.346	-0.158	-0.158	0.000	0.000	0.000	0.000
111	A	110	GLU	-1	-0.865	-0.875	15.587	-0.306	-0.306	0.000	0.000	0.000	0.000
112	A	111	ILE	0	-0.057	-0.044	14.193	0.055	0.055	0.000	0.000	0.000	0.000
113	A	112	CYS	0	-0.042	-0.008	18.161	0.044	0.044	0.000	0.000	0.000	0.000
114	A	113	LEU	0	0.096	0.028	20.379	0.008	0.008	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.056	-0.023	22.051	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.798	-0.850	19.645	0.081	0.081	0.000	0.000	0.000	0.000
117	A	116	CYS	0	-0.116	-0.024	17.979	0.006	0.006	0.000	0.000	0.000	0.000
118	A	117	ASP	-1	-0.816	-0.879	16.177	-0.087	-0.087	0.000	0.000	0.000	0.000
119	A	118	ILE	0	0.013	-0.001	16.679	-0.058	-0.058	0.000	0.000	0.000	0.000
120	A	119	TYR	0	-0.036	-0.028	14.849	0.099	0.099	0.000	0.000	0.000	0.000
121	A	120	SER	0	0.022	-0.014	17.269	-0.053	-0.053	0.000	0.000	0.000	0.000
122	A	121	TYR	0	-0.042	-0.036	14.744	-0.040	-0.040	0.000	0.000	0.000	0.000
123	A	122	ASN	0	-0.047	-0.032	16.886	-0.029	-0.029	0.000	0.000	0.000	0.000
124	A	123	PRO	0	0.033	0.033	18.464	0.038	0.038	0.000	0.000	0.000	0.000
125	A	124	ASP	-1	-0.820	-0.893	19.887	-0.347	-0.347	0.000	0.000	0.000	0.000
126	A	125	LEU	0	-0.007	-0.024	22.509	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	126	ASP	-1	-0.950	-0.956	23.910	-0.393	-0.393	0.000	0.000	0.000	0.000
128	A	127	SER	0	-0.090	-0.058	19.658	0.003	0.003	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.858	-0.928	19.290	-0.801	-0.801	0.000	0.000	0.000	0.000
130	A	129	PRO	0	-0.037	-0.022	15.845	0.028	0.028	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.082	-0.041	15.440	-0.033	-0.033	0.000	0.000	0.000	0.000
132	A	131	GLY	0	-0.006	0.016	20.296	0.035	0.035	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.987	-0.999	23.670	-0.391	-0.391	0.000	0.000	0.000	0.000
134	A	133	ASP	-1	-0.771	-0.850	23.779	-0.610	-0.610	0.000	0.000	0.000	0.000
135	A	134	GLY	0	-0.039	-0.018	26.629	0.010	0.010	0.000	0.000	0.000	0.000
136	A	135	SER	0	-0.100	-0.057	25.432	0.020	0.020	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.040	-0.030	27.720	0.023	0.023	0.000	0.000	0.000	0.000
138	A	137	TRP	0	-0.030	-0.014	23.244	0.006	0.006	0.000	0.000	0.000	0.000
139	A	138	SER	0	0.019	-0.003	21.405	-0.048	-0.048	0.000	0.000	0.000	0.000
140	A	139	PHE	0	-0.014	-0.010	19.510	0.054	0.054	0.000	0.000	0.000	0.000
141	A	140	ASN	0	0.048	0.024	15.336	-0.165	-0.165	0.000	0.000	0.000	0.000
142	A	141	TYR	0	-0.012	-0.002	16.976	0.052	0.052	0.000	0.000	0.000	0.000
143	A	142	PHE	0	0.001	-0.009	10.510	-0.091	-0.091	0.000	0.000	0.000	0.000
144	A	143	PHE	0	0.011	0.003	14.707	0.148	0.148	0.000	0.000	0.000	0.000
145	A	144	TYR	0	-0.006	-0.014	9.178	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	145	ASN	0	0.045	0.013	13.837	0.149	0.149	0.000	0.000	0.000	0.000
147	A	146	LYS	1	0.885	0.912	12.981	0.099	0.099	0.000	0.000	0.000	0.000
148	A	147	ARG	1	0.782	0.857	13.780	-0.021	-0.021	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.027	-0.025	14.634	0.116	0.116	0.000	0.000	0.000	0.000
150	A	149	LYS	1	0.854	0.944	9.365	-0.556	-0.556	0.000	0.000	0.000	0.000
151	A	150	ARG	1	0.909	0.960	9.743	0.205	0.205	0.000	0.000	0.000	0.000
152	A	151	ILE	0	0.009	-0.010	8.306	0.050	0.050	0.000	0.000	0.000	0.000
153	A	152	VAL	0	0.021	0.023	11.337	-0.157	-0.157	0.000	0.000	0.000	0.000
154	A	153	PHE	0	-0.026	-0.017	10.947	0.072	0.072	0.000	0.000	0.000	0.000
155	A	154	PHE	0	0.031	-0.004	12.996	0.007	0.007	0.000	0.000	0.000	0.000
156	A	155	SER	0	-0.021	-0.008	14.986	0.053	0.053	0.000	0.000	0.000	0.000
157	A	156	CYS	0	-0.013	0.012	16.895	-0.005	-0.005	0.000	0.000	0.000	0.000
158	A	157	ARG	1	0.915	0.938	20.376	0.757	0.757	0.000	0.000	0.000	0.000
159	A	158	SER	0	0.036	0.046	23.062	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)