FMO DATABASE

FMODB ID: J39M9

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	OptAll
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	-881561.813858
FMO2-HF: Nuclear repulsion	838756.171522
FMO2-HF: Total energy	-42805.642337
FMO2-MP2: Total energy	-42932.161383

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.
-68.139	-65.51	0.088	-1.119	-1.599	0.001

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 : 0.957 / q_NPA : 0.965

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	0.021	0.001	3.908	2.988	4.352	-0.009	-0.665	-0.691	0.003
4	A	7	LEU	0	-0.020	-0.007	6.374	1.147	1.147	0.000	0.000	0.000	0.000
5	A	8	SER	0	0.046	0.003	9.966	1.147	1.147	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.060	0.008	12.742	0.313	0.313	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.841	0.903	15.996	15.878	15.878	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.827	-0.873	12.220	-23.685	-23.685	0.000	0.000	0.000	0.000
9	A	12	ALA	0	0.024	0.007	12.636	0.288	0.288	0.000	0.000	0.000	0.000
10	A	13	ARG	1	0.916	0.972	14.114	15.033	15.033	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.805	-0.891	17.783	-13.679	-13.679	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.931	0.980	10.111	24.462	24.462	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.019	0.017	15.886	0.331	0.331	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.049	-0.026	17.053	0.699	0.699	0.000	0.000	0.000	0.000
15	A	18	ALA	0	0.016	-0.001	18.657	0.568	0.568	0.000	0.000	0.000	0.000
16	A	19	HIS	0	-0.009	0.001	16.578	0.048	0.048	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.810	0.890	18.763	12.722	12.722	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.040	-0.015	21.816	0.478	0.478	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.010	-0.010	22.337	0.400	0.400	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.832	-0.892	23.138	-11.727	-11.727	0.000	0.000	0.000	0.000
21	A	24	ALA	0	-0.020	-0.008	25.522	0.172	0.172	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.035	0.030	27.256	0.019	0.019	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.773	-0.879	29.303	-9.629	-9.629	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.050	0.021	30.184	-0.177	-0.177	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.011	0.006	28.012	0.012	0.012	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.011	0.018	24.176	-0.251	-0.251	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.840	0.900	26.246	9.034	9.034	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.005	-0.012	28.463	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.026	-0.026	23.267	-0.082	-0.082	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.864	0.918	23.013	12.300	12.300	0.000	0.000	0.000	0.000
31	A	34	TYR	0	-0.028	-0.030	25.306	-0.121	-0.121	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.886	0.955	25.396	10.287	10.287	0.000	0.000	0.000	0.000
33	A	36	LEU	0	0.022	0.005	19.441	-0.082	-0.082	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.781	0.886	22.389	10.135	10.135	0.000	0.000	0.000	0.000
35	A	38	HIS	0	-0.018	-0.011	24.660	0.016	0.016	0.000	0.000	0.000	0.000
36	A	39	PHE	0	0.035	0.014	17.405	-0.134	-0.134	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.038	-0.028	19.033	-0.409	-0.409	0.000	0.000	0.000	0.000
38	A	41	GLU	-1	-0.794	-0.876	20.915	-11.316	-11.316	0.000	0.000	0.000	0.000
39	A	42	TRP	0	0.012	0.009	20.015	-0.270	-0.270	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.004	-0.007	18.049	-0.124	-0.124	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.849	-0.921	18.300	-15.947	-15.947	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.954	-0.971	20.056	-11.845	-11.845	0.000	0.000	0.000	0.000
43	A	46	ARG	1	0.740	0.835	21.005	12.876	12.876	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.925	-0.950	18.204	-14.950	-14.950	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.073	-0.021	14.792	-1.103	-1.103	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.064	-0.046	12.006	-0.831	-0.831	0.000	0.000	0.000	0.000
47	A	50	ALA	0	-0.033	-0.034	9.015	-1.228	-1.228	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.010	0.000	10.788	1.212	1.212	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.809	0.879	3.421	36.537	37.063	0.080	-0.195	-0.410	0.000
50	A	53	GLU	-1	-0.818	-0.895	9.568	-20.240	-20.240	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.026	-0.009	12.657	1.735	1.735	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.070	0.016	13.975	-0.127	-0.127	0.000	0.000	0.000	0.000
53	A	56	GLY	0	0.065	0.020	16.679	0.434	0.434	0.000	0.000	0.000	0.000
54	A	57	TRP	0	-0.016	-0.001	19.774	0.528	0.528	0.000	0.000	0.000	0.000
55	A	58	LYS	1	0.874	0.949	15.774	18.292	18.292	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.006	-0.002	17.101	0.221	0.221	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.866	-0.910	20.857	-10.339	-10.339	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.769	-0.865	23.547	-11.946	-11.946	0.000	0.000	0.000	0.000
59	A	62	TYR	0	-0.044	-0.030	22.306	0.250	0.250	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.746	-0.860	24.323	-9.954	-9.954	0.000	0.000	0.000	0.000
61	A	64	THR	0	-0.036	-0.040	26.440	0.571	0.571	0.000	0.000	0.000	0.000
62	A	65	PHE	0	-0.022	0.001	26.525	0.316	0.316	0.000	0.000	0.000	0.000
63	A	66	ARG	1	0.785	0.870	26.809	10.611	10.611	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.786	0.869	28.943	10.046	10.046	0.000	0.000	0.000	0.000
65	A	68	GLY	0	-0.017	0.009	32.174	0.317	0.317	0.000	0.000	0.000	0.000
66	A	69	SER	0	-0.040	-0.033	32.769	0.009	0.009	0.000	0.000	0.000	0.000
67	A	70	ASP	-1	-0.889	-0.949	34.969	-7.986	-7.986	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.098	-0.035	31.663	0.116	0.116	0.000	0.000	0.000	0.000
69	A	72	SER	0	0.036	0.012	34.935	0.137	0.137	0.000	0.000	0.000	0.000
70	A	73	PRO	0	0.059	0.018	34.251	-0.224	-0.224	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.018	0.009	33.103	-0.228	-0.228	0.000	0.000	0.000	0.000
72	A	75	THR	0	-0.025	-0.016	31.830	-0.164	-0.164	0.000	0.000	0.000	0.000
73	A	76	LEU	0	0.050	0.035	28.741	-0.318	-0.318	0.000	0.000	0.000	0.000
74	A	77	ASN	0	0.022	0.013	28.414	-0.467	-0.467	0.000	0.000	0.000	0.000
75	A	78	GLY	0	0.023	0.012	27.711	-0.307	-0.307	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.804	-0.843	25.328	-11.178	-11.178	0.000	0.000	0.000	0.000
77	A	80	MET	0	0.031	0.025	23.340	-0.557	-0.557	0.000	0.000	0.000	0.000
78	A	81	GLN	0	0.010	-0.002	22.876	-0.206	-0.206	0.000	0.000	0.000	0.000
79	A	82	THR	0	-0.079	-0.054	22.087	-0.238	-0.238	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.006	0.002	18.247	-0.561	-0.561	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.854	0.928	18.217	12.159	12.159	0.000	0.000	0.000	0.000
82	A	85	ASN	0	0.030	0.012	17.758	-0.496	-0.496	0.000	0.000	0.000	0.000
83	A	86	TRP	0	-0.071	-0.042	15.356	-0.381	-0.381	0.000	0.000	0.000	0.000
84	A	87	LEU	0	0.043	0.008	13.336	-1.087	-1.087	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.801	-0.883	12.800	-14.516	-14.516	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.039	-0.028	13.309	-1.116	-1.116	0.000	0.000	0.000	0.000
87	A	90	LEU	0	-0.015	-0.025	10.131	-1.019	-1.019	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.060	0.043	8.550	-2.034	-2.034	0.000	0.000	0.000	0.000
89	A	92	ARG	1	0.850	0.930	8.669	16.903	16.903	0.000	0.000	0.000	0.000
90	A	93	ILE	0	-0.109	-0.055	8.280	0.544	0.544	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.846	-0.919	3.199	-36.551	-36.036	0.017	-0.172	-0.360	-0.002
92	A	95	VAL	0	-0.085	-0.035	3.956	-2.942	-2.718	0.000	-0.087	-0.138	0.000
93	A	96	VAL	0	-0.041	-0.028	6.143	-0.179	-0.179	0.000	0.000	0.000	0.000
94	A	97	ASP	-1	-0.798	-0.887	7.288	-26.837	-26.837	0.000	0.000	0.000	0.000
95	A	98	GLU	-1	-0.907	-0.965	8.526	-21.152	-21.152	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.836	-0.901	10.609	-15.800	-15.800	0.000	0.000	0.000	0.000
97	A	100	LEU	0	-0.003	0.006	12.520	0.983	0.983	0.000	0.000	0.000	0.000
98	A	101	PRO	0	-0.017	-0.027	13.024	0.929	0.929	0.000	0.000	0.000	0.000
99	A	102	GLU	-1	-0.944	-0.971	15.985	-12.933	-12.933	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.764	0.877	15.580	16.230	16.230	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.060	-0.017	17.914	0.166	0.166	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.031	-0.028	20.631	0.476	0.476	0.000	0.000	0.000	0.000
103	A	106	VAL	0	0.009	-0.009	23.814	-0.154	-0.154	0.000	0.000	0.000	0.000
104	A	107	PRO	0	-0.074	-0.017	26.428	0.629	0.629	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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