FMO DATABASE

FMODB ID: 5JZ3Z

Calculation Name: 1WRD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WRD

Chain ID: A

ChEMBL ID:

UniProt ID: O60784

Base Structure: X-ray

Registration Date: 2023-09-20

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-712335.347097
FMO2-HF: Nuclear repulsion	672216.004064
FMO2-HF: Total energy	-40119.343033
FMO2-MP2: Total energy	-40234.189356

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:210:GLY)

Summations of interaction energy for fragment #1(A:210:GLY)

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.
-25.089	-26.728	18.347	-8.499	-8.206	-0.022

Interaction energy analysis for fragmet #1(A:210:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : 0.004

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	212	LEU	0	0.027	0.017	3.582	1.260	2.721	0.002	-0.733	-0.729	0.001
4	A	213	GLY	0	0.039	0.034	3.098	2.489	3.050	0.033	-0.230	-0.364	0.000
5	A	214	SER	0	-0.007	-0.028	3.953	1.719	1.961	-0.001	-0.019	-0.222	0.000
6	A	215	GLU	-1	-0.839	-0.922	2.130	-15.922	-15.621	7.399	-3.943	-3.756	-0.045
7	A	216	GLN	0	-0.022	-0.035	1.983	-10.326	-14.536	10.915	-3.569	-3.136	0.022
8	A	217	ILE	0	0.034	0.027	4.679	-0.478	-0.472	-0.001	-0.005	0.001	0.000
9	A	218	GLY	0	0.027	0.020	7.315	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	219	LYS	1	0.903	0.951	7.054	-1.617	-1.617	0.000	0.000	0.000	0.000
11	A	220	LEU	0	0.031	0.008	5.555	-0.135	-0.135	0.000	0.000	0.000	0.000
12	A	221	ARG	1	0.832	0.876	8.719	0.233	0.233	0.000	0.000	0.000	0.000
13	A	222	SER	0	-0.015	-0.010	12.074	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	223	GLU	-1	-0.834	-0.900	9.456	0.419	0.419	0.000	0.000	0.000	0.000
15	A	224	LEU	0	0.040	0.005	11.371	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	225	GLU	-1	-0.984	-0.958	14.150	0.030	0.030	0.000	0.000	0.000	0.000
17	A	226	MET	0	0.056	0.028	16.658	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	227	VAL	0	-0.005	-0.013	15.364	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	228	SER	0	-0.017	-0.025	17.668	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	229	GLY	0	0.012	0.012	20.022	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	230	ASN	0	-0.031	-0.032	21.191	0.003	0.003	0.000	0.000	0.000	0.000
22	A	231	VAL	0	0.026	0.005	20.963	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	232	ARG	1	0.836	0.917	23.730	0.059	0.059	0.000	0.000	0.000	0.000
24	A	233	VAL	0	0.047	0.024	25.953	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	234	MET	0	-0.015	0.010	26.922	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	235	SER	0	0.019	-0.004	27.656	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	236	GLU	-1	-0.854	-0.913	29.544	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	237	MET	0	0.030	0.015	31.679	0.003	0.003	0.000	0.000	0.000	0.000
29	A	238	LEU	0	-0.051	-0.026	30.641	0.000	0.000	0.000	0.000	0.000	0.000
30	A	239	THR	0	-0.092	-0.050	33.409	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	240	GLU	-1	-0.929	-0.947	35.993	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	241	LEU	0	-0.037	-0.001	35.965	0.003	0.003	0.000	0.000	0.000	0.000
33	A	242	VAL	0	0.031	0.007	39.257	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	243	PRO	0	-0.010	-0.011	39.551	0.003	0.003	0.000	0.000	0.000	0.000
35	A	244	THR	0	-0.030	-0.025	41.359	0.003	0.003	0.000	0.000	0.000	0.000
36	A	245	GLN	0	-0.104	-0.061	43.955	0.003	0.003	0.000	0.000	0.000	0.000
37	A	246	ALA	0	0.000	0.032	39.852	0.002	0.002	0.000	0.000	0.000	0.000
38	A	247	GLU	-1	-0.854	-0.919	41.874	0.001	0.001	0.000	0.000	0.000	0.000
39	A	248	PRO	0	-0.045	-0.038	40.574	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	249	ALA	0	0.065	0.033	38.763	0.000	0.000	0.000	0.000	0.000	0.000
41	A	250	ASP	-1	-0.842	-0.923	36.884	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	251	LEU	0	-0.052	-0.027	35.544	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	252	GLU	-1	-0.948	-0.981	34.870	0.018	0.018	0.000	0.000	0.000	0.000
44	A	253	LEU	0	0.012	0.012	30.657	0.003	0.003	0.000	0.000	0.000	0.000
45	A	254	LEU	0	0.014	0.003	30.905	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	255	GLN	0	-0.030	-0.029	30.367	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	256	GLU	-1	-0.884	-0.923	27.953	0.047	0.047	0.000	0.000	0.000	0.000
48	A	257	LEU	0	-0.005	0.007	26.294	0.002	0.002	0.000	0.000	0.000	0.000
49	A	258	ASN	0	-0.007	-0.021	25.529	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	259	ARG	1	0.877	0.925	25.313	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	260	THR	0	-0.024	-0.017	21.859	0.005	0.005	0.000	0.000	0.000	0.000
52	A	261	CYS	0	0.007	-0.012	21.204	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	262	ARG	1	0.867	0.950	20.917	0.086	0.086	0.000	0.000	0.000	0.000
54	A	263	ALA	0	0.005	0.011	19.490	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	264	MET	0	-0.036	-0.001	16.775	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	265	GLN	0	-0.012	-0.007	16.311	-0.021	-0.021	0.000	0.000	0.000	0.000
57	A	266	GLN	0	-0.050	-0.033	16.150	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	267	ARG	1	0.827	0.906	7.818	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	268	VAL	0	-0.005	-0.011	12.110	-0.092	-0.092	0.000	0.000	0.000	0.000
60	A	269	LEU	0	-0.012	-0.014	12.773	-0.152	-0.152	0.000	0.000	0.000	0.000
61	A	270	GLU	-1	-0.889	-0.935	11.297	-0.200	-0.200	0.000	0.000	0.000	0.000
62	A	271	LEU	0	-0.072	-0.037	6.909	-0.183	-0.183	0.000	0.000	0.000	0.000
63	A	272	ILE	0	0.003	0.011	8.727	-0.446	-0.446	0.000	0.000	0.000	0.000
64	A	273	PRO	0	-0.025	-0.010	11.045	-0.159	-0.159	0.000	0.000	0.000	0.000
65	A	274	GLN	0	-0.062	-0.023	6.588	-0.164	-0.164	0.000	0.000	0.000	0.000
66	A	275	ILE	0	-0.046	-0.022	5.020	-1.695	-1.695	0.000	0.000	0.000	0.000
67	A	276	ALA	0	0.014	0.007	7.103	0.722	0.722	0.000	0.000	0.000	0.000
68	A	277	ASN	0	-0.043	-0.010	8.160	0.789	0.789	0.000	0.000	0.000	0.000
69	A	278	GLU	-1	-0.850	-0.921	9.797	-0.877	-0.877	0.000	0.000	0.000	0.000
70	A	279	GLN	0	-0.005	-0.005	13.323	0.118	0.118	0.000	0.000	0.000	0.000
71	A	280	LEU	0	-0.021	-0.007	6.892	0.092	0.092	0.000	0.000	0.000	0.000
72	A	281	THR	0	0.012	-0.009	10.858	0.031	0.031	0.000	0.000	0.000	0.000
73	A	282	GLU	-1	-0.894	-0.949	12.083	-0.442	-0.442	0.000	0.000	0.000	0.000
74	A	283	GLU	-1	-0.879	-0.900	13.201	-0.444	-0.444	0.000	0.000	0.000	0.000
75	A	284	LEU	0	-0.012	-0.009	9.206	0.116	0.116	0.000	0.000	0.000	0.000
76	A	285	LEU	0	0.022	0.016	13.871	0.104	0.104	0.000	0.000	0.000	0.000
77	A	286	ILE	0	0.057	0.028	16.966	0.088	0.088	0.000	0.000	0.000	0.000
78	A	287	VAL	0	-0.011	0.003	15.706	0.072	0.072	0.000	0.000	0.000	0.000
79	A	288	ASN	0	0.013	-0.008	17.513	0.081	0.081	0.000	0.000	0.000	0.000
80	A	289	ASP	-1	-0.864	-0.925	18.996	-0.304	-0.304	0.000	0.000	0.000	0.000
81	A	290	ASN	0	-0.088	-0.049	21.417	0.063	0.063	0.000	0.000	0.000	0.000
82	A	291	LEU	0	-0.004	0.005	18.618	0.032	0.032	0.000	0.000	0.000	0.000
83	A	292	ASN	0	-0.001	0.001	22.410	0.046	0.046	0.000	0.000	0.000	0.000
84	A	293	ASN	0	-0.056	-0.035	24.944	0.033	0.033	0.000	0.000	0.000	0.000
85	A	294	VAL	0	-0.002	0.008	25.055	0.016	0.016	0.000	0.000	0.000	0.000
86	A	295	PHE	0	0.015	-0.002	22.813	0.017	0.017	0.000	0.000	0.000	0.000
87	A	296	LEU	0	-0.028	-0.007	28.266	0.013	0.013	0.000	0.000	0.000	0.000
88	A	297	ARG	1	0.791	0.882	30.589	0.091	0.091	0.000	0.000	0.000	0.000
89	A	298	HIS	0	0.074	0.050	30.890	0.003	0.003	0.000	0.000	0.000	0.000
90	A	299	GLU	-1	-0.824	-0.879	32.250	-0.081	-0.081	0.000	0.000	0.000	0.000
91	A	300	ARG	1	0.979	0.981	33.458	0.107	0.107	0.000	0.000	0.000	0.000
92	A	301	PHE	0	0.015	0.014	35.620	0.004	0.004	0.000	0.000	0.000	0.000
93	A	302	GLU	-1	-0.766	-0.873	35.473	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	303	ARG	1	0.755	0.853	36.575	0.083	0.083	0.000	0.000	0.000	0.000
95	A	304	PHE	0	-0.030	-0.022	39.626	0.001	0.001	0.000	0.000	0.000	0.000
96	A	305	ARG	1	0.824	0.910	38.489	0.029	0.029	0.000	0.000	0.000	0.000
97	A	306	THR	0	-0.095	-0.054	41.678	0.004	0.004	0.000	0.000	0.000	0.000
98	A	307	GLY	0	-0.001	0.004	44.231	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:210:GLY)