FMO DATABASE

FMODB ID: P59ZZ

Calculation Name: 3CCD-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CCD

Chain ID: A

ChEMBL ID:

UniProt ID: P0AA04

Base Structure: X-ray

Registration Date: 2017-12-04

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20171117

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandCharge	SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-555156.031162
FMO2-HF: Nuclear repulsion	522556.854107
FMO2-HF: Total energy	-32599.177056
FMO2-MP2: Total energy	-32693.321033

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:1:MET)

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

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.
-346.862	-331.62	19.673	-17.556	-17.36	-0.221

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.709 / q_NPA : 0.853

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

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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	3	GLU	-1	-0.898	-0.969	2.810	-38.188	-34.723	0.330	-1.216	-2.579	-0.005
4	A	4	GLN	0	-0.020	-0.007	4.821	2.650	2.707	-0.001	-0.008	-0.048	0.000
5	A	5	GLU	-1	-0.935	-0.959	8.129	-19.512	-19.512	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.019	-0.015	10.730	0.432	0.432	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.023	-0.008	14.064	0.432	0.432	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.001	0.010	17.314	0.046	0.046	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.028	-0.001	19.379	0.382	0.382	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.055	0.048	22.491	0.502	0.502	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.053	-0.017	24.502	0.102	0.102	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.083	-0.046	27.257	0.471	0.471	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.026	-0.020	23.247	-0.082	-0.082	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.020	-0.003	17.804	0.067	0.067	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.825	-0.908	21.976	-11.073	-11.073	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.008	-0.031	24.066	-0.307	-0.307	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.868	0.955	24.796	9.358	9.358	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.137	0.095	22.644	-0.267	-0.267	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.010	-0.008	20.331	-0.708	-0.708	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.017	-0.021	20.145	-0.650	-0.650	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.060	-0.025	21.759	0.149	0.149	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.051	0.018	13.154	-0.667	-0.667	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.008	0.008	16.778	-0.932	-0.932	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.899	0.952	17.544	12.112	12.112	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.835	-0.912	17.713	-15.584	-15.584	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.025	0.017	13.159	-0.935	-0.935	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.772	0.869	13.795	14.424	14.424	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.040	0.000	16.233	0.179	0.179	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.036	0.003	10.929	-0.231	-0.231	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.034	-0.038	11.582	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.055	-0.036	6.469	-2.148	-2.148	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.987	-0.985	6.714	-25.445	-25.445	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.002	-0.008	6.150	-4.462	-4.462	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.040	-0.020	6.551	4.451	4.451	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.032	0.022	8.287	-1.189	-1.189	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.018	0.003	8.449	1.057	1.057	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.003	-0.016	11.204	0.160	0.160	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.008	-0.013	14.436	0.312	0.312	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.012	0.012	12.500	0.463	0.463	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.859	0.946	13.568	13.920	13.920	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.017	-0.015	9.923	-0.260	-0.260	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.032	-0.014	12.115	1.031	1.031	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.003	0.006	11.048	-0.558	-0.558	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.067	0.015	11.109	1.432	1.432	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.854	0.944	11.639	24.982	24.982	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.075	-0.063	14.792	0.761	0.761	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.086	0.041	17.315	-0.249	-0.249	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.022	0.008	19.886	0.088	0.088	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.952	0.972	15.028	17.257	17.257	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.040	0.060	14.676	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.014	-0.024	17.344	0.143	0.143	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.093	-0.059	18.831	0.445	0.445	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.042	-0.021	14.066	0.393	0.393	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.006	0.019	18.729	0.571	0.571	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.034	0.019	17.047	-0.732	-0.732	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.025	0.023	20.269	0.299	0.299	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.042	0.010	21.495	-0.235	-0.235	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.041	-0.018	21.749	0.346	0.346	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.085	-0.036	16.806	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.000	0.005	13.461	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.030	-0.011	12.662	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.019	0.012	6.269	0.432	0.432	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.032	-0.016	8.259	0.655	0.655	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.048	0.013	3.296	-2.304	-1.818	0.069	-0.126	-0.428	0.000
65	A	65	ALA	0	-0.041	-0.016	3.575	5.723	6.182	0.005	-0.128	-0.337	0.000
66	A	66	GLU	-1	-0.847	-0.931	2.007	-136.897	-129.025	8.929	-8.534	-8.267	-0.112
67	A	67	GLY	0	0.034	0.002	3.524	13.623	13.778	0.013	-0.023	-0.145	-0.001
68	A	68	GLU	-1	-0.963	-0.977	5.607	-29.522	-29.522	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.810	-0.891	8.122	-28.338	-28.338	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.781	-0.882	1.850	-126.574	-123.826	10.328	-7.521	-5.556	-0.103
71	A	71	GLN	0	-0.004	-0.008	5.851	4.124	4.124	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.977	0.987	7.512	25.692	25.692	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.007	0.011	8.219	2.489	2.489	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.026	-0.012	5.827	2.738	2.738	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.926	-0.969	9.233	-23.695	-23.695	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.100	-0.062	12.159	1.734	1.734	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.005	-0.011	11.169	1.600	1.600	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.010	0.001	11.349	1.462	1.462	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.931	0.960	14.049	16.330	16.330	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.007	0.000	16.922	0.882	0.882	0.000	0.000	0.000	0.000
81	A	81	MET	0	0.001	0.005	15.233	1.134	1.134	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.058	-0.026	18.433	0.712	0.712	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-1.018	-1.004	21.175	-12.888	-12.888	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.075	-0.027	19.425	0.391	0.391	0.000	0.000	0.000	0.000
85	A	85	GLU	-2	-1.775	-1.924	23.274	-22.453	-22.453	0.000	0.000	0.000	0.000
86	A	6577	SO4	-2	-1.758	-1.852	19.896	-28.455	-28.455	0.000	0.000	0.000	0.000

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