FMO DATABASE

FMODB ID: N1G3Q

Calculation Name: 3NRW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRW

Chain ID: A

ChEMBL ID:

UniProt ID: Q5V4F9

Base Structure: X-ray

Registration Date: 2023-06-19

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-880165.118976
FMO2-HF: Nuclear repulsion	837359.702978
FMO2-HF: Total energy	-42805.415998
FMO2-MP2: Total energy	-42931.972179

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
-67.83	-65.27	0.081	-1.06	-1.579	0

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.944 / q_NPA : 0.964

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	6	SER	0	0.025	0.001	3.824	3.870	5.349	-0.012	-0.644	-0.822	0.002
4	A	7	LEU	0	-0.019	-0.004	6.345	1.825	1.825	0.000	0.000	0.000	0.000
5	A	8	SER	0	0.054	0.002	10.038	1.290	1.290	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.085	0.019	12.680	0.266	0.266	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.842	0.907	15.787	15.944	15.944	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.821	-0.867	12.123	-23.924	-23.924	0.000	0.000	0.000	0.000
9	A	12	ALA	0	0.009	0.003	12.287	0.290	0.290	0.000	0.000	0.000	0.000
10	A	13	ARG	1	0.875	0.928	13.863	15.238	15.238	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.808	-0.899	17.544	-13.893	-13.893	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.923	0.981	10.262	24.022	24.022	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.025	0.013	15.973	0.476	0.476	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.039	-0.026	17.079	0.692	0.692	0.000	0.000	0.000	0.000
15	A	18	ALA	0	0.028	0.015	18.732	0.590	0.590	0.000	0.000	0.000	0.000
16	A	19	HIS	0	-0.030	-0.015	16.723	0.162	0.162	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.848	0.921	18.867	12.550	12.550	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.052	-0.014	21.745	0.413	0.413	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.024	-0.024	22.172	0.222	0.222	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.843	-0.904	23.523	-11.488	-11.488	0.000	0.000	0.000	0.000
21	A	24	ALA	0	-0.019	-0.009	25.594	0.209	0.209	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.022	0.022	27.443	0.044	0.044	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.790	-0.911	29.269	-9.786	-9.786	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.012	0.002	30.154	-0.166	-0.166	0.000	0.000	0.000	0.000
25	A	28	SER	0	0.006	0.008	27.912	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.023	0.029	24.049	-0.251	-0.251	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.886	0.940	26.142	8.972	8.972	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.013	-0.006	28.232	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.024	-0.020	23.029	-0.103	-0.103	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.901	0.946	22.706	12.287	12.287	0.000	0.000	0.000	0.000
31	A	34	TYR	0	-0.029	-0.034	25.064	-0.128	-0.128	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.888	0.951	25.284	10.263	10.263	0.000	0.000	0.000	0.000
33	A	36	LEU	0	0.018	0.006	19.230	-0.099	-0.099	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.779	0.893	22.281	10.289	10.289	0.000	0.000	0.000	0.000
35	A	38	HIS	0	-0.023	-0.013	24.572	0.066	0.066	0.000	0.000	0.000	0.000
36	A	39	PHE	0	0.026	0.011	17.102	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.030	-0.025	18.840	-0.417	-0.417	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.790	-0.877	20.941	-11.309	-11.309	0.000	0.000	0.000	0.000
39	A	42	TRP	0	0.022	0.017	19.948	-0.258	-0.258	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.006	-0.022	17.975	-0.134	-0.134	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.870	-0.931	18.277	-15.832	-15.832	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.934	-0.963	19.856	-11.962	-11.962	0.000	0.000	0.000	0.000
43	A	46	ARG	1	0.701	0.835	20.856	12.742	12.742	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.924	-0.955	17.985	-15.041	-15.041	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.080	-0.028	14.724	-1.031	-1.031	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.054	-0.047	11.823	-0.387	-0.387	0.000	0.000	0.000	0.000
47	A	50	ALA	0	-0.032	-0.028	8.627	-1.371	-1.371	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.014	-0.007	10.438	1.381	1.381	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.840	0.913	3.477	35.827	36.384	0.090	-0.214	-0.433	0.000
50	A	53	GLU	-1	-0.825	-0.900	9.216	-21.083	-21.083	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.044	-0.014	12.286	1.720	1.720	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.074	0.020	13.636	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	56	GLY	0	0.075	0.025	16.334	0.428	0.428	0.000	0.000	0.000	0.000
54	A	57	TRP	0	-0.020	-0.003	19.374	0.501	0.501	0.000	0.000	0.000	0.000
55	A	58	LYS	1	0.902	0.955	15.406	18.499	18.499	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.005	-0.006	16.885	0.323	0.323	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.894	-0.939	20.540	-10.546	-10.546	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.767	-0.859	23.375	-11.769	-11.769	0.000	0.000	0.000	0.000
59	A	62	TYR	0	-0.060	-0.040	22.205	0.316	0.316	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.779	-0.875	24.178	-9.976	-9.976	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.001	-0.006	26.157	0.591	0.591	0.000	0.000	0.000	0.000
62	A	65	PHE	0	-0.018	0.003	26.393	0.322	0.322	0.000	0.000	0.000	0.000
63	A	66	ARG	1	0.812	0.876	26.476	10.661	10.661	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.781	0.884	29.268	9.984	9.984	0.000	0.000	0.000	0.000
65	A	68	GLY	0	-0.011	0.004	31.899	0.309	0.309	0.000	0.000	0.000	0.000
66	A	69	SER	0	-0.078	-0.041	32.398	0.112	0.112	0.000	0.000	0.000	0.000
67	A	70	ASP	-1	-0.888	-0.946	34.315	-7.944	-7.944	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.083	-0.030	31.886	0.162	0.162	0.000	0.000	0.000	0.000
69	A	72	SER	0	0.028	0.009	35.170	0.165	0.165	0.000	0.000	0.000	0.000
70	A	73	PRO	0	0.076	0.020	34.325	-0.240	-0.240	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.008	0.007	33.189	-0.223	-0.223	0.000	0.000	0.000	0.000
72	A	75	THR	0	-0.031	-0.025	31.861	-0.139	-0.139	0.000	0.000	0.000	0.000
73	A	76	LEU	0	0.058	0.038	28.739	-0.301	-0.301	0.000	0.000	0.000	0.000
74	A	77	ASN	0	0.039	0.015	28.464	-0.423	-0.423	0.000	0.000	0.000	0.000
75	A	78	GLY	0	0.013	0.008	27.763	-0.299	-0.299	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.800	-0.850	25.353	-11.149	-11.149	0.000	0.000	0.000	0.000
77	A	80	MET	0	0.056	0.028	23.358	-0.584	-0.584	0.000	0.000	0.000	0.000
78	A	81	GLN	0	-0.009	-0.004	22.955	-0.181	-0.181	0.000	0.000	0.000	0.000
79	A	82	THR	0	-0.062	-0.038	21.972	-0.248	-0.248	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.009	0.013	18.325	-0.566	-0.566	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.892	0.941	18.345	12.036	12.036	0.000	0.000	0.000	0.000
82	A	85	ASN	0	0.018	0.007	17.907	-0.467	-0.467	0.000	0.000	0.000	0.000
83	A	86	TRP	0	-0.078	-0.040	15.255	-0.450	-0.450	0.000	0.000	0.000	0.000
84	A	87	LEU	0	0.049	0.006	13.424	-1.009	-1.009	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.827	-0.894	12.934	-14.405	-14.405	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.054	-0.031	13.331	-1.089	-1.089	0.000	0.000	0.000	0.000
87	A	90	LEU	0	-0.007	-0.024	10.039	-1.065	-1.065	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.033	0.034	8.623	-1.976	-1.976	0.000	0.000	0.000	0.000
89	A	92	ARG	1	0.915	0.968	8.810	16.383	16.383	0.000	0.000	0.000	0.000
90	A	93	ILE	0	-0.121	-0.056	8.487	-0.279	-0.279	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.859	-0.923	3.620	-34.187	-33.899	0.002	-0.075	-0.214	-0.001
92	A	95	VAL	0	-0.077	-0.041	3.810	-4.430	-4.194	0.001	-0.127	-0.110	-0.001
93	A	96	VAL	0	-0.063	-0.042	6.285	-0.357	-0.357	0.000	0.000	0.000	0.000
94	A	97	ASP	-1	-0.821	-0.908	7.766	-25.932	-25.932	0.000	0.000	0.000	0.000
95	A	98	GLU	-1	-0.886	-0.954	9.050	-21.404	-21.404	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.846	-0.903	10.869	-16.185	-16.185	0.000	0.000	0.000	0.000
97	A	100	LEU	0	-0.004	0.000	12.621	0.926	0.926	0.000	0.000	0.000	0.000
98	A	101	PRO	0	0.005	-0.010	13.214	0.938	0.938	0.000	0.000	0.000	0.000
99	A	102	GLU	-1	-0.962	-0.981	16.124	-13.008	-13.008	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.770	0.879	15.348	16.574	16.574	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.063	-0.019	18.262	0.262	0.262	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.033	-0.029	20.930	0.486	0.486	0.000	0.000	0.000	0.000
103	A	106	VAL	0	-0.049	-0.028	23.983	0.014	0.014	0.000	0.000	0.000	0.000
104	A	107	PRO	0	-0.015	0.010	26.531	0.365	0.365	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)