FMO DATABASE

FMODB ID: KG733

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	OptH
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	-710077.716633
FMO2-HF: Nuclear repulsion	669959.058741
FMO2-HF: Total energy	-40118.657892
FMO2-MP2: Total energy	-40233.643016

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.
-12.41	-12.51	12.143	-7.083	-4.958	0

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 : -0.011

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	0.035	0.023	3.642	0.920	2.277	0.001	-0.674	-0.683	0.001
4	A	213	GLY	0	0.064	0.035	3.578	0.949	1.150	0.003	-0.058	-0.145	0.000
5	A	214	SER	0	-0.030	-0.027	4.920	1.056	1.157	-0.001	-0.007	-0.093	0.000
6	A	215	GLU	-1	-0.826	-0.903	2.232	-4.654	-6.563	8.180	-4.261	-2.010	-0.013
7	A	216	GLN	0	-0.030	-0.030	2.227	-6.028	-5.873	3.961	-2.082	-2.034	0.012
8	A	217	ILE	0	0.063	0.036	5.211	-0.650	-0.655	-0.001	-0.001	0.007	0.000
9	A	218	GLY	0	0.010	0.009	7.946	-0.096	-0.096	0.000	0.000	0.000	0.000
10	A	219	LYS	1	0.957	0.970	6.981	-1.248	-1.248	0.000	0.000	0.000	0.000
11	A	220	LEU	0	0.022	0.004	7.028	-0.122	-0.122	0.000	0.000	0.000	0.000
12	A	221	ARG	1	0.836	0.900	9.190	0.087	0.087	0.000	0.000	0.000	0.000
13	A	222	SER	0	0.002	0.004	12.503	-0.050	-0.050	0.000	0.000	0.000	0.000
14	A	223	GLU	-1	-0.822	-0.875	10.388	-0.156	-0.156	0.000	0.000	0.000	0.000
15	A	224	LEU	0	0.025	-0.007	11.921	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	225	GLU	-1	-0.975	-0.965	14.711	0.043	0.043	0.000	0.000	0.000	0.000
17	A	226	MET	0	0.081	0.038	17.104	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	227	VAL	0	-0.024	-0.024	15.634	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	228	SER	0	-0.009	-0.023	18.320	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	229	GLY	0	-0.005	0.009	20.539	0.001	0.001	0.000	0.000	0.000	0.000
21	A	230	ASN	0	-0.023	-0.024	21.436	0.003	0.003	0.000	0.000	0.000	0.000
22	A	231	VAL	0	0.015	0.004	21.741	0.000	0.000	0.000	0.000	0.000	0.000
23	A	232	ARG	1	0.869	0.940	24.390	0.054	0.054	0.000	0.000	0.000	0.000
24	A	233	VAL	0	0.051	0.031	26.563	0.002	0.002	0.000	0.000	0.000	0.000
25	A	234	MET	0	0.013	0.018	27.653	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	235	SER	0	-0.052	-0.039	28.274	0.000	0.000	0.000	0.000	0.000	0.000
27	A	236	GLU	-1	-0.879	-0.959	30.033	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	237	MET	0	0.014	0.019	32.174	0.004	0.004	0.000	0.000	0.000	0.000
29	A	238	LEU	0	-0.059	-0.029	31.333	0.000	0.000	0.000	0.000	0.000	0.000
30	A	239	THR	0	-0.087	-0.038	34.340	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	240	GLU	-1	-0.928	-0.940	36.401	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	241	LEU	0	-0.018	0.000	36.652	0.002	0.002	0.000	0.000	0.000	0.000
33	A	242	VAL	0	0.031	0.015	39.689	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	243	PRO	0	-0.021	-0.017	40.357	0.003	0.003	0.000	0.000	0.000	0.000
35	A	244	THR	0	-0.031	-0.042	42.132	0.002	0.002	0.000	0.000	0.000	0.000
36	A	245	GLN	0	-0.081	-0.044	44.555	0.004	0.004	0.000	0.000	0.000	0.000
37	A	246	ALA	0	-0.006	0.030	40.448	0.002	0.002	0.000	0.000	0.000	0.000
38	A	247	GLU	-1	-0.829	-0.917	42.483	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	248	PRO	0	-0.064	-0.036	41.130	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	249	ALA	0	0.063	0.026	39.578	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	250	ASP	-1	-0.844	-0.923	37.575	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	251	LEU	0	-0.052	-0.041	36.220	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	252	GLU	-1	-0.970	-0.982	35.574	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	253	LEU	0	0.034	0.024	31.171	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	254	LEU	0	0.000	0.001	31.470	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	255	GLN	0	-0.003	-0.012	30.839	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	256	GLU	-1	-1.007	-0.986	28.513	0.000	0.000	0.000	0.000	0.000	0.000
48	A	257	LEU	0	0.020	-0.005	26.987	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	258	ASN	0	-0.012	-0.011	25.969	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	259	ARG	1	0.961	0.975	25.765	0.013	0.013	0.000	0.000	0.000	0.000
51	A	260	THR	0	0.003	0.004	22.022	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	261	CYS	0	0.001	-0.012	21.573	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	262	ARG	1	0.870	0.948	21.361	0.117	0.117	0.000	0.000	0.000	0.000
54	A	263	ALA	0	0.005	0.009	19.938	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	264	MET	0	-0.043	-0.005	17.210	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	265	GLN	0	-0.019	-0.021	16.629	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	266	GLN	0	-0.048	-0.011	16.970	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	267	ARG	1	0.828	0.892	7.967	0.306	0.306	0.000	0.000	0.000	0.000
59	A	268	VAL	0	-0.012	-0.018	12.636	-0.137	-0.137	0.000	0.000	0.000	0.000
60	A	269	LEU	0	-0.017	-0.019	13.330	-0.137	-0.137	0.000	0.000	0.000	0.000
61	A	270	GLU	-1	-0.929	-0.961	12.066	-0.508	-0.508	0.000	0.000	0.000	0.000
62	A	271	LEU	0	-0.080	-0.048	7.288	-0.223	-0.223	0.000	0.000	0.000	0.000
63	A	272	ILE	0	-0.008	0.000	9.260	-0.389	-0.389	0.000	0.000	0.000	0.000
64	A	273	PRO	0	-0.024	-0.008	11.140	-0.147	-0.147	0.000	0.000	0.000	0.000
65	A	274	GLN	0	-0.047	-0.016	6.655	-0.149	-0.149	0.000	0.000	0.000	0.000
66	A	275	ILE	0	-0.060	-0.021	5.764	-1.337	-1.337	0.000	0.000	0.000	0.000
67	A	276	ALA	0	0.013	0.010	7.169	0.646	0.646	0.000	0.000	0.000	0.000
68	A	277	ASN	0	-0.049	-0.018	8.357	0.658	0.658	0.000	0.000	0.000	0.000
69	A	278	GLU	-1	-0.851	-0.936	10.202	-0.730	-0.730	0.000	0.000	0.000	0.000
70	A	279	GLN	0	-0.015	-0.002	13.599	0.080	0.080	0.000	0.000	0.000	0.000
71	A	280	LEU	0	-0.042	-0.023	7.644	0.064	0.064	0.000	0.000	0.000	0.000
72	A	281	THR	0	0.033	0.006	11.354	0.011	0.011	0.000	0.000	0.000	0.000
73	A	282	GLU	-1	-0.903	-0.952	12.675	-0.398	-0.398	0.000	0.000	0.000	0.000
74	A	283	GLU	-1	-0.843	-0.896	13.875	-0.305	-0.305	0.000	0.000	0.000	0.000
75	A	284	LEU	0	-0.025	-0.025	9.850	0.076	0.076	0.000	0.000	0.000	0.000
76	A	285	LEU	0	0.025	0.012	14.477	0.065	0.065	0.000	0.000	0.000	0.000
77	A	286	ILE	0	0.033	0.035	17.425	0.068	0.068	0.000	0.000	0.000	0.000
78	A	287	VAL	0	-0.044	-0.024	16.029	0.055	0.055	0.000	0.000	0.000	0.000
79	A	288	ASN	0	0.029	0.004	17.811	0.057	0.057	0.000	0.000	0.000	0.000
80	A	289	ASP	-1	-0.902	-0.942	19.473	-0.290	-0.290	0.000	0.000	0.000	0.000
81	A	290	ASN	0	-0.060	-0.044	21.573	0.041	0.041	0.000	0.000	0.000	0.000
82	A	291	LEU	0	-0.020	0.002	18.947	0.030	0.030	0.000	0.000	0.000	0.000
83	A	292	ASN	0	0.073	0.036	23.197	0.038	0.038	0.000	0.000	0.000	0.000
84	A	293	ASN	0	-0.018	-0.006	25.436	0.021	0.021	0.000	0.000	0.000	0.000
85	A	294	VAL	0	-0.017	-0.010	25.657	0.017	0.017	0.000	0.000	0.000	0.000
86	A	295	PHE	0	-0.006	-0.004	23.374	0.019	0.019	0.000	0.000	0.000	0.000
87	A	296	LEU	0	0.030	0.012	28.718	0.012	0.012	0.000	0.000	0.000	0.000
88	A	297	ARG	1	0.819	0.893	31.184	0.101	0.101	0.000	0.000	0.000	0.000
89	A	298	HIS	0	0.082	0.063	31.417	0.002	0.002	0.000	0.000	0.000	0.000
90	A	299	GLU	-1	-0.924	-0.964	32.912	-0.109	-0.109	0.000	0.000	0.000	0.000
91	A	300	ARG	1	0.907	0.957	34.031	0.109	0.109	0.000	0.000	0.000	0.000
92	A	301	PHE	0	0.007	0.005	36.213	0.005	0.005	0.000	0.000	0.000	0.000
93	A	302	GLU	-1	-0.767	-0.872	36.284	-0.050	-0.050	0.000	0.000	0.000	0.000
94	A	303	ARG	1	0.873	0.954	37.615	0.102	0.102	0.000	0.000	0.000	0.000
95	A	304	PHE	0	-0.042	-0.022	40.743	0.002	0.002	0.000	0.000	0.000	0.000
96	A	305	ARG	1	0.814	0.902	39.850	0.050	0.050	0.000	0.000	0.000	0.000
97	A	306	THR	0	-0.111	-0.055	42.142	0.003	0.003	0.000	0.000	0.000	0.000
98	A	307	GLY	0	0.019	0.010	44.528	-0.001	-0.001	0.000	0.000	0.000	0.000

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