FMO DATABASE

FMODB ID: 4JR3N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-709659.618884
FMO2-HF: Nuclear repulsion	669540.432527
FMO2-HF: Total energy	-40119.186357
FMO2-MP2: Total energy	-40234.089539

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.
-15.742	-17.321	13.823	-7.229	-5.016	0.002

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 : 0.001 / q_NPA : 0.005

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	0.028	0.020	3.616	0.837	2.186	0.000	-0.672	-0.678	0.001
4	A	213	GLY	0	0.069	0.035	3.543	0.924	1.103	0.003	-0.042	-0.139	0.000
5	A	214	SER	0	-0.026	-0.023	4.929	1.058	1.162	-0.001	-0.007	-0.096	0.000
6	A	215	GLU	-1	-0.841	-0.920	2.212	-5.100	-5.335	5.067	-3.087	-1.746	-0.012
7	A	216	GLN	0	-0.025	-0.035	2.034	-9.266	-12.238	8.755	-3.420	-2.364	0.013
8	A	217	ILE	0	0.061	0.035	5.164	-0.662	-0.666	-0.001	-0.001	0.007	0.000
9	A	218	GLY	0	0.009	0.011	7.913	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	219	LYS	1	0.920	0.957	7.055	-0.882	-0.882	0.000	0.000	0.000	0.000
11	A	220	LEU	0	0.024	0.003	6.507	-0.128	-0.128	0.000	0.000	0.000	0.000
12	A	221	ARG	1	0.834	0.883	9.163	0.135	0.135	0.000	0.000	0.000	0.000
13	A	222	SER	0	-0.001	0.002	12.474	-0.042	-0.042	0.000	0.000	0.000	0.000
14	A	223	GLU	-1	-0.838	-0.899	10.073	-0.091	-0.091	0.000	0.000	0.000	0.000
15	A	224	LEU	0	0.043	0.003	12.039	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	225	GLU	-1	-0.986	-0.962	14.695	0.023	0.023	0.000	0.000	0.000	0.000
17	A	226	MET	0	0.073	0.036	17.056	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	227	VAL	0	-0.022	-0.019	15.612	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	228	SER	0	-0.016	-0.032	18.250	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	229	GLY	0	0.004	0.013	20.527	0.003	0.003	0.000	0.000	0.000	0.000
21	A	230	ASN	0	-0.038	-0.036	21.453	0.007	0.007	0.000	0.000	0.000	0.000
22	A	231	VAL	0	0.027	0.009	21.757	0.001	0.001	0.000	0.000	0.000	0.000
23	A	232	ARG	1	0.843	0.919	24.384	0.065	0.065	0.000	0.000	0.000	0.000
24	A	233	VAL	0	0.044	0.027	26.553	0.003	0.003	0.000	0.000	0.000	0.000
25	A	234	MET	0	0.001	0.012	27.560	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	235	SER	0	-0.014	-0.027	28.155	0.001	0.001	0.000	0.000	0.000	0.000
27	A	236	GLU	-1	-0.851	-0.925	30.029	-0.051	-0.051	0.000	0.000	0.000	0.000
28	A	237	MET	0	0.013	0.020	32.165	0.005	0.005	0.000	0.000	0.000	0.000
29	A	238	LEU	0	-0.052	-0.025	31.349	0.001	0.001	0.000	0.000	0.000	0.000
30	A	239	THR	0	-0.093	-0.038	34.085	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	240	GLU	-1	-0.928	-0.937	36.397	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	241	LEU	0	-0.023	-0.002	36.454	0.003	0.003	0.000	0.000	0.000	0.000
33	A	242	VAL	0	0.038	0.013	39.684	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	243	PRO	0	-0.017	-0.009	40.317	0.003	0.003	0.000	0.000	0.000	0.000
35	A	244	THR	0	-0.015	-0.027	42.133	0.002	0.002	0.000	0.000	0.000	0.000
36	A	245	GLN	0	-0.101	-0.062	44.562	0.004	0.004	0.000	0.000	0.000	0.000
37	A	246	ALA	0	-0.018	0.022	40.409	0.003	0.003	0.000	0.000	0.000	0.000
38	A	247	GLU	-1	-0.854	-0.922	42.393	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	248	PRO	0	-0.030	-0.035	41.124	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	249	ALA	0	0.054	0.031	39.571	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	250	ASP	-1	-0.839	-0.921	37.570	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	251	LEU	0	-0.054	-0.039	36.213	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	252	GLU	-1	-0.957	-0.979	35.571	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	253	LEU	0	0.007	0.009	31.161	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	254	LEU	0	0.014	0.009	31.463	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	255	GLN	0	-0.011	-0.018	30.838	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	256	GLU	-1	-0.895	-0.922	28.523	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	257	LEU	0	0.006	0.000	26.980	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	258	ASN	0	-0.003	-0.017	25.967	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	259	ARG	1	0.893	0.929	25.769	0.020	0.020	0.000	0.000	0.000	0.000
51	A	260	THR	0	-0.012	-0.005	22.062	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	261	CYS	0	-0.003	-0.016	21.573	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	262	ARG	1	0.885	0.957	21.367	0.135	0.135	0.000	0.000	0.000	0.000
54	A	263	ALA	0	0.002	0.008	20.001	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	264	MET	0	-0.036	-0.002	17.213	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	265	GLN	0	-0.018	-0.015	16.637	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	266	GLN	0	-0.065	-0.033	16.629	-0.046	-0.046	0.000	0.000	0.000	0.000
58	A	267	ARG	1	0.874	0.921	8.077	0.387	0.387	0.000	0.000	0.000	0.000
59	A	268	VAL	0	-0.010	-0.016	12.653	-0.143	-0.143	0.000	0.000	0.000	0.000
60	A	269	LEU	0	-0.019	-0.017	13.354	-0.140	-0.140	0.000	0.000	0.000	0.000
61	A	270	GLU	-1	-0.907	-0.936	11.804	-0.544	-0.544	0.000	0.000	0.000	0.000
62	A	271	LEU	0	-0.085	-0.048	7.274	-0.233	-0.233	0.000	0.000	0.000	0.000
63	A	272	ILE	0	-0.008	-0.003	9.295	-0.394	-0.394	0.000	0.000	0.000	0.000
64	A	273	PRO	0	-0.017	-0.003	11.178	-0.140	-0.140	0.000	0.000	0.000	0.000
65	A	274	GLN	0	-0.062	-0.025	6.624	-0.162	-0.162	0.000	0.000	0.000	0.000
66	A	275	ILE	0	-0.058	-0.020	5.687	-1.356	-1.356	0.000	0.000	0.000	0.000
67	A	276	ALA	0	0.020	0.014	7.168	0.657	0.657	0.000	0.000	0.000	0.000
68	A	277	ASN	0	-0.049	-0.022	8.310	0.681	0.681	0.000	0.000	0.000	0.000
69	A	278	GLU	-1	-0.845	-0.924	10.156	-0.746	-0.746	0.000	0.000	0.000	0.000
70	A	279	GLN	0	-0.023	-0.008	13.593	0.096	0.096	0.000	0.000	0.000	0.000
71	A	280	LEU	0	-0.032	-0.016	7.609	0.062	0.062	0.000	0.000	0.000	0.000
72	A	281	THR	0	0.033	0.001	11.445	0.005	0.005	0.000	0.000	0.000	0.000
73	A	282	GLU	-1	-0.898	-0.947	12.700	-0.419	-0.419	0.000	0.000	0.000	0.000
74	A	283	GLU	-1	-0.857	-0.891	13.907	-0.335	-0.335	0.000	0.000	0.000	0.000
75	A	284	LEU	0	-0.017	-0.018	9.823	0.081	0.081	0.000	0.000	0.000	0.000
76	A	285	LEU	0	0.034	0.018	14.490	0.069	0.069	0.000	0.000	0.000	0.000
77	A	286	ILE	0	0.051	0.036	17.446	0.074	0.074	0.000	0.000	0.000	0.000
78	A	287	VAL	0	-0.025	-0.004	16.286	0.059	0.059	0.000	0.000	0.000	0.000
79	A	288	ASN	0	0.021	0.001	17.921	0.056	0.056	0.000	0.000	0.000	0.000
80	A	289	ASP	-1	-0.894	-0.942	19.489	-0.310	-0.310	0.000	0.000	0.000	0.000
81	A	290	ASN	0	-0.109	-0.076	21.883	0.059	0.059	0.000	0.000	0.000	0.000
82	A	291	LEU	0	-0.010	0.006	19.083	0.030	0.030	0.000	0.000	0.000	0.000
83	A	292	ASN	0	0.024	0.014	22.808	0.039	0.039	0.000	0.000	0.000	0.000
84	A	293	ASN	0	-0.015	-0.007	25.452	0.026	0.026	0.000	0.000	0.000	0.000
85	A	294	VAL	0	-0.014	-0.003	25.677	0.018	0.018	0.000	0.000	0.000	0.000
86	A	295	PHE	0	0.007	-0.001	23.265	0.017	0.017	0.000	0.000	0.000	0.000
87	A	296	LEU	0	-0.005	0.001	28.729	0.013	0.013	0.000	0.000	0.000	0.000
88	A	297	ARG	1	0.819	0.890	31.198	0.107	0.107	0.000	0.000	0.000	0.000
89	A	298	HIS	0	0.074	0.055	31.486	0.003	0.003	0.000	0.000	0.000	0.000
90	A	299	GLU	-1	-0.819	-0.873	32.932	-0.109	-0.109	0.000	0.000	0.000	0.000
91	A	300	ARG	1	0.964	0.974	34.191	0.119	0.119	0.000	0.000	0.000	0.000
92	A	301	PHE	0	-0.004	0.001	36.237	0.005	0.005	0.000	0.000	0.000	0.000
93	A	302	GLU	-1	-0.752	-0.856	36.244	-0.055	-0.055	0.000	0.000	0.000	0.000
94	A	303	ARG	1	0.748	0.853	36.880	0.109	0.109	0.000	0.000	0.000	0.000
95	A	304	PHE	0	-0.055	-0.031	40.420	0.002	0.002	0.000	0.000	0.000	0.000
96	A	305	ARG	1	0.813	0.891	39.495	0.056	0.056	0.000	0.000	0.000	0.000
97	A	306	THR	0	-0.108	-0.054	42.138	0.004	0.004	0.000	0.000	0.000	0.000
98	A	307	GLY	0	0.021	0.013	44.537	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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