FMO DATABASE

FMODB ID: 1NLJZ

Calculation Name: 1WPA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WPA

Chain ID: A

ChEMBL ID:

UniProt ID: Q16625

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-791239.220837
FMO2-HF: Nuclear repulsion	745946.220864
FMO2-HF: Total energy	-45292.999973
FMO2-MP2: Total energy	-45425.372881

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:416:TRP)

Summations of interaction energy for fragment #1(A:416:TRP)

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.
-34.685	-13.969	12.228	-9.381	-23.563	-0.011

Interaction energy analysis for fragmet #1(A:416:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / 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	418	ARG	1	0.946	0.960	3.704	-6.080	-3.883	-0.009	-0.944	-1.245	0.003
4	A	419	GLU	-1	-0.822	-0.899	2.614	-10.271	-5.504	1.530	-2.481	-3.816	-0.031
5	A	420	TYR	0	-0.049	-0.044	3.200	-0.449	0.773	0.029	-0.343	-0.908	0.000
6	A	421	PRO	0	0.052	0.043	5.330	-0.206	-0.159	-0.001	-0.003	-0.043	0.000
7	A	422	PRO	0	0.050	0.019	7.711	-0.090	-0.090	0.000	0.000	0.000	0.000
8	A	423	ILE	0	-0.073	-0.020	10.257	0.040	0.040	0.000	0.000	0.000	0.000
9	A	424	THR	0	0.002	-0.003	12.458	0.005	0.005	0.000	0.000	0.000	0.000
10	A	425	SER	0	0.049	0.027	15.670	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	426	ASP	-1	-0.665	-0.822	16.211	0.021	0.021	0.000	0.000	0.000	0.000
12	A	427	GLN	0	0.035	0.013	17.316	0.000	0.000	0.000	0.000	0.000	0.000
13	A	428	GLN	0	0.036	0.036	10.696	0.007	0.007	0.000	0.000	0.000	0.000
14	A	429	ARG	1	0.785	0.882	12.719	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	430	GLN	0	0.000	-0.005	13.475	0.004	0.004	0.000	0.000	0.000	0.000
16	A	431	LEU	0	-0.019	0.002	11.072	0.007	0.007	0.000	0.000	0.000	0.000
17	A	432	TYR	0	0.018	-0.025	7.860	0.030	0.030	0.000	0.000	0.000	0.000
18	A	433	LYS	1	0.818	0.896	10.393	0.031	0.031	0.000	0.000	0.000	0.000
19	A	434	ARG	1	1.003	1.001	12.916	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	435	ASN	0	-0.015	0.004	9.037	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	436	PHE	0	-0.034	-0.014	9.075	0.076	0.076	0.000	0.000	0.000	0.000
22	A	437	ASP	-1	-0.770	-0.878	10.517	0.043	0.043	0.000	0.000	0.000	0.000
23	A	438	THR	0	-0.019	-0.008	12.080	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	439	GLY	0	0.048	0.027	9.760	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	440	LEU	0	-0.033	-0.025	10.567	-0.092	-0.092	0.000	0.000	0.000	0.000
26	A	441	GLN	0	0.007	0.005	12.871	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	442	GLU	-1	-0.835	-0.899	9.356	-0.116	-0.116	0.000	0.000	0.000	0.000
28	A	443	TYR	0	-0.011	-0.010	9.437	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	444	LYS	1	0.939	0.964	11.777	0.058	0.058	0.000	0.000	0.000	0.000
30	A	445	SER	0	-0.016	-0.002	15.401	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	446	LEU	0	0.040	0.019	11.029	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	447	GLN	0	-0.065	-0.041	13.934	-0.071	-0.071	0.000	0.000	0.000	0.000
33	A	448	SER	0	-0.028	-0.033	15.434	0.004	0.004	0.000	0.000	0.000	0.000
34	A	449	GLU	-1	-0.798	-0.864	17.305	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	450	LEU	0	-0.072	-0.044	13.687	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	451	ASP	-1	-0.858	-0.921	18.263	-0.243	-0.243	0.000	0.000	0.000	0.000
37	A	452	GLU	-1	-0.903	-0.941	20.517	-0.143	-0.143	0.000	0.000	0.000	0.000
38	A	453	ILE	0	0.086	0.042	22.057	0.004	0.004	0.000	0.000	0.000	0.000
39	A	454	ASN	0	-0.043	-0.019	19.563	0.010	0.010	0.000	0.000	0.000	0.000
40	A	455	LYS	1	0.831	0.898	22.301	0.190	0.190	0.000	0.000	0.000	0.000
41	A	456	GLU	-1	-0.925	-0.961	26.246	-0.120	-0.120	0.000	0.000	0.000	0.000
42	A	457	LEU	0	-0.021	-0.012	24.650	0.003	0.003	0.000	0.000	0.000	0.000
43	A	458	SER	0	0.017	0.011	27.573	0.008	0.008	0.000	0.000	0.000	0.000
44	A	459	ARG	1	0.891	0.938	28.894	0.122	0.122	0.000	0.000	0.000	0.000
45	A	460	LEU	0	0.061	0.036	30.956	0.004	0.004	0.000	0.000	0.000	0.000
46	A	461	ASP	-1	-0.846	-0.907	30.174	-0.130	-0.130	0.000	0.000	0.000	0.000
47	A	462	LYS	1	0.880	0.934	31.117	0.124	0.124	0.000	0.000	0.000	0.000
48	A	463	GLU	-1	-0.858	-0.911	35.831	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	464	LEU	0	-0.073	-0.031	34.663	0.004	0.004	0.000	0.000	0.000	0.000
50	A	465	ASP	-1	-0.973	-0.975	36.941	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	466	ASP	-1	-0.987	-0.989	39.623	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	467	TYR	0	-0.146	-0.087	39.975	0.006	0.006	0.000	0.000	0.000	0.000
53	A	468	ARG	1	0.877	0.915	43.549	0.053	0.053	0.000	0.000	0.000	0.000
54	A	469	GLU	-1	-0.858	-0.922	43.067	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	470	GLU	-1	-0.899	-0.927	44.908	-0.054	-0.054	0.000	0.000	0.000	0.000
56	A	471	SER	0	-0.089	-0.053	45.239	0.001	0.001	0.000	0.000	0.000	0.000
57	A	472	GLU	-1	-0.917	-0.965	45.107	-0.053	-0.053	0.000	0.000	0.000	0.000
58	A	473	GLU	-1	-0.906	-0.966	42.993	-0.060	-0.060	0.000	0.000	0.000	0.000
59	A	474	TYR	0	0.022	0.021	40.033	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	475	MET	0	-0.009	-0.002	39.907	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	476	ALA	0	-0.013	-0.003	39.427	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	477	ALA	0	0.040	0.022	36.614	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	478	ALA	0	0.032	0.013	35.186	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	479	ASP	-1	-0.897	-0.939	34.822	-0.086	-0.086	0.000	0.000	0.000	0.000
65	A	480	GLU	-1	-0.844	-0.917	31.800	-0.106	-0.106	0.000	0.000	0.000	0.000
66	A	481	TYR	0	-0.003	-0.024	29.917	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	482	ASN	0	-0.028	-0.035	29.811	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	483	ARG	1	0.806	0.892	29.733	0.080	0.080	0.000	0.000	0.000	0.000
69	A	484	LEU	0	0.053	0.022	26.738	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	485	LYS	1	0.807	0.911	25.356	0.115	0.115	0.000	0.000	0.000	0.000
71	A	486	GLN	0	-0.033	-0.005	24.960	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	487	VAL	0	0.040	0.027	22.674	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	488	LYS	1	0.889	0.959	20.545	0.210	0.210	0.000	0.000	0.000	0.000
74	A	489	GLY	0	-0.033	-0.022	20.053	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	490	SER	0	0.011	-0.003	21.018	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	491	ALA	0	0.028	-0.003	18.166	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	492	ASP	-1	-0.807	-0.875	16.505	-0.263	-0.263	0.000	0.000	0.000	0.000
78	A	493	TYR	0	0.056	0.031	15.997	-0.052	-0.052	0.000	0.000	0.000	0.000
79	A	494	LYS	1	0.839	0.913	15.457	0.190	0.190	0.000	0.000	0.000	0.000
80	A	495	SER	0	-0.035	-0.025	12.439	-0.079	-0.079	0.000	0.000	0.000	0.000
81	A	496	LYS	1	0.880	0.913	11.106	0.116	0.116	0.000	0.000	0.000	0.000
82	A	497	LYS	1	0.981	0.996	11.340	0.367	0.367	0.000	0.000	0.000	0.000
83	A	498	ASN	0	-0.127	-0.068	7.997	-0.234	-0.234	0.000	0.000	0.000	0.000
84	A	499	HIS	0	0.045	0.003	6.433	-0.531	-0.531	0.000	0.000	0.000	0.000
85	A	500	CYS	0	0.005	0.007	6.790	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	501	LYS	1	0.922	0.954	7.075	0.928	0.928	0.000	0.000	0.000	0.000
87	A	502	GLN	0	0.015	0.026	2.921	-2.718	-1.392	0.233	-0.351	-1.208	-0.001
88	A	503	LEU	0	0.025	0.020	2.895	-0.165	1.144	0.486	-0.590	-1.204	-0.006
89	A	504	LYS	1	0.926	0.962	5.434	1.260	1.260	0.000	0.000	0.000	0.000
90	A	505	SER	0	-0.044	-0.033	2.216	-1.319	-0.098	1.603	-1.062	-1.763	-0.002
91	A	506	LYS	1	0.851	0.945	2.733	-8.731	-2.328	5.969	-3.466	-8.906	0.032
92	A	507	LEU	0	-0.015	-0.005	3.646	-1.601	-1.991	0.108	1.133	-0.851	0.002
93	A	508	SER	0	-0.011	-0.011	5.717	-0.170	-0.170	0.000	0.000	0.000	0.000
94	A	509	HIS	0	-0.063	-0.035	2.788	-3.704	-1.307	2.281	-1.258	-3.420	-0.008
95	A	510	ILE	0	0.011	0.007	4.347	-0.385	-0.168	-0.001	-0.016	-0.199	0.000
96	A	511	LYS	1	0.961	0.985	6.306	0.076	0.076	0.000	0.000	0.000	0.000
97	A	512	LYS	1	0.856	0.919	7.653	0.308	0.308	0.000	0.000	0.000	0.000
98	A	513	MET	0	-0.023	-0.001	6.274	0.100	0.100	0.000	0.000	0.000	0.000
99	A	514	VAL	0	0.014	-0.004	9.146	0.046	0.046	0.000	0.000	0.000	0.000
100	A	515	GLY	0	-0.002	0.003	11.902	0.010	0.010	0.000	0.000	0.000	0.000
101	A	516	ASP	-1	-0.794	-0.880	11.296	-0.161	-0.161	0.000	0.000	0.000	0.000
102	A	517	TYR	0	-0.033	-0.025	13.505	0.022	0.022	0.000	0.000	0.000	0.000
103	A	518	ASP	-1	-0.767	-0.892	15.300	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	519	ARG	1	0.823	0.899	14.194	0.112	0.112	0.000	0.000	0.000	0.000
105	A	520	GLN	0	-0.052	-0.034	15.710	0.019	0.019	0.000	0.000	0.000	0.000
106	A	521	LYS	1	0.817	0.926	18.867	0.002	0.002	0.000	0.000	0.000	0.000
107	A	522	THR	0	-0.051	-0.012	21.862	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:416:TRP)