FMO DATABASE

FMODB ID: PLLY9

Calculation Name: 3I2V-A-Xray13

Preferred Name: Adenylyltransferase and sulfurtransferase MOCS3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3I2V

Chain ID: A

ChEMBL ID: CHEMBL4295684

UniProt ID: O95396

Base Structure: X-ray

Registration Date: 2018-03-01

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. 1.20181228

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1094067.651274
FMO2-HF: Nuclear repulsion	1044925.322
FMO2-HF: Total energy	-49142.329274
FMO2-MP2: Total energy	-49287.520003

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-35.877	-29.454	5.952	-5.728	-6.648	-0.061

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.912

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	2	VAL	0	0.028	0.028	3.823	0.163	2.033	-0.027	-0.908	-0.935	-0.003
4	A	3	SER	0	0.026	0.025	7.078	1.738	1.738	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.077	0.021	10.264	0.218	0.218	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.003	0.006	13.258	0.508	0.508	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.864	-0.937	11.016	-23.821	-23.821	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.044	-0.035	11.238	0.538	0.538	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.852	0.912	12.722	16.117	16.117	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.903	0.940	15.004	19.726	19.726	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.005	0.015	11.925	0.386	0.386	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.033	0.000	15.359	0.718	0.718	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.819	-0.902	17.391	-14.223	-14.223	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.106	-0.065	17.779	0.692	0.692	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.013	0.011	19.973	0.610	0.610	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.029	0.001	16.901	0.259	0.259	0.000	0.000	0.000	0.000
17	A	16	PHE	0	0.076	0.031	16.041	-0.994	-0.994	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.042	-0.002	12.305	-1.958	-1.958	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.054	0.047	12.625	1.001	1.001	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.023	-0.006	11.592	-2.479	-2.479	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.005	0.001	10.907	1.316	1.316	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.770	-0.868	12.315	-19.649	-19.649	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.002	-0.020	11.401	0.500	0.500	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.752	0.848	14.489	16.328	16.328	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.038	0.015	17.168	0.445	0.445	0.000	0.000	0.000	0.000
26	A	25	GLN	0	0.003	-0.023	20.318	-0.284	-0.284	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.031	0.022	23.355	0.107	0.107	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.825	-0.905	19.606	-15.952	-15.952	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.011	0.001	20.042	0.102	0.102	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.847	-0.913	22.565	-11.453	-11.453	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.064	-0.011	25.150	0.422	0.422	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.047	0.001	23.616	0.128	0.128	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.915	0.937	20.896	11.931	11.931	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.017	0.010	16.916	0.481	0.481	0.000	0.000	0.000	0.000
35	A	34	PRO	0	-0.016	-0.024	20.252	-0.391	-0.391	0.000	0.000	0.000	0.000
36	A	35	HIS	0	0.018	0.013	16.257	0.899	0.899	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.065	-0.014	16.280	-0.557	-0.557	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.053	0.032	16.072	0.836	0.836	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.068	-0.044	16.318	-0.715	-0.715	0.000	0.000	0.000	0.000
40	A	39	ILE	0	0.014	-0.002	15.157	0.564	0.564	0.000	0.000	0.000	0.000
41	A	40	PRO	0	-0.029	0.004	15.522	-1.242	-1.242	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.056	0.014	11.844	-0.350	-0.350	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.918	0.958	14.934	13.656	13.656	0.000	0.000	0.000	0.000
44	A	43	HIS	0	0.000	-0.012	18.014	0.953	0.953	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.044	0.042	11.799	0.100	0.100	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.948	-0.998	14.908	-18.625	-18.625	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.792	0.885	16.448	13.934	13.934	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.934	0.978	14.262	18.911	18.911	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.828	-0.914	19.277	-12.570	-12.570	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.042	0.018	20.478	-0.519	-0.519	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.880	-0.944	22.357	-11.621	-11.621	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.027	-0.022	18.477	-0.299	-0.299	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.003	0.010	16.704	-0.589	-0.589	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.912	0.961	18.818	10.909	10.909	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.053	0.035	19.709	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.036	-0.021	13.073	-0.286	-0.286	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.942	0.959	17.426	14.286	14.286	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.906	-0.953	19.283	-11.895	-11.895	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.015	0.009	17.943	0.233	0.233	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.032	-0.019	14.562	-0.168	-0.168	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.010	0.000	18.520	0.222	0.222	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.969	-0.981	22.106	-12.128	-12.128	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.952	-0.973	19.163	-13.806	-13.806	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.846	0.920	17.376	16.249	16.249	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.047	-0.016	22.002	0.619	0.619	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.010	0.010	22.797	0.360	0.360	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.095	-0.047	23.123	0.111	0.111	0.000	0.000	0.000	0.000
68	A	67	GLN	0	-0.042	-0.048	16.836	-0.566	-0.566	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.812	-0.883	19.844	-14.781	-14.781	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.037	-0.034	19.140	-0.634	-0.634	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.020	0.007	15.009	-0.445	-0.445	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.017	-0.002	10.964	0.078	0.078	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.057	0.021	12.460	-0.211	-0.211	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.012	-0.002	9.478	-2.877	-2.877	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.016	0.014	7.921	1.356	1.356	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.003	-0.018	7.068	-6.549	-6.549	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.018	0.019	7.001	2.326	2.326	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.008	-0.003	9.048	-2.790	-2.790	0.000	0.000	0.000	0.000
79	A	78	CYS	0	-0.019	0.034	11.486	1.028	1.028	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.975	0.992	13.961	14.318	14.318	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.014	-0.004	14.826	0.197	0.197	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.029	0.009	10.795	-0.909	-0.909	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.015	0.003	9.753	-3.994	-3.994	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.853	-0.953	10.701	-22.340	-22.340	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.003	-0.053	8.162	0.488	0.488	0.000	0.000	0.000	0.000
86	A	85	GLN	0	-0.049	-0.026	5.679	-5.533	-5.533	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.939	0.965	6.273	21.199	21.199	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.080	0.045	8.962	0.253	0.253	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.018	-0.010	2.475	-1.183	-0.836	0.812	-0.383	-0.777	-0.003
90	A	89	LYS	1	0.908	0.960	5.074	44.153	44.153	0.000	0.000	0.000	0.000
91	A	90	ILE	0	-0.007	0.010	6.836	1.909	1.909	0.000	0.000	0.000	0.000
92	A	91	LEU	0	0.044	0.016	7.781	1.202	1.202	0.000	0.000	0.000	0.000
93	A	92	GLN	0	0.003	-0.015	1.698	-3.657	-3.077	4.154	-2.406	-2.327	-0.029
94	A	93	SER	0	-0.018	-0.007	7.056	2.241	2.241	0.000	0.000	0.000	0.000
95	A	94	LEU	0	-0.011	0.006	10.182	1.369	1.369	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.032	-0.004	9.342	0.902	0.902	0.000	0.000	0.000	0.000
97	A	96	ALA	0	-0.004	-0.009	9.988	1.361	1.361	0.000	0.000	0.000	0.000
98	A	97	ALA	0	-0.044	-0.013	11.761	1.127	1.127	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.040	-0.019	14.428	1.731	1.731	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.927	-0.958	15.603	-15.989	-15.989	0.000	0.000	0.000	0.000
101	A	100	LEU	0	-0.098	-0.060	12.657	0.436	0.436	0.000	0.000	0.000	0.000
102	A	101	ASP	-1	-0.835	-0.910	15.192	-15.970	-15.970	0.000	0.000	0.000	0.000
103	A	102	PRO	0	-0.009	-0.015	12.489	-1.585	-1.585	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.021	0.018	9.077	-0.106	-0.106	0.000	0.000	0.000	0.000
105	A	104	THR	0	-0.043	-0.019	6.194	-1.947	-1.947	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.008	0.008	4.345	-0.163	-0.044	-0.001	-0.048	-0.070	0.000
107	A	106	ARG	1	0.847	0.914	2.535	23.722	27.040	1.012	-1.919	-2.411	-0.026
108	A	107	ASP	-1	-0.710	-0.816	3.757	-44.159	-43.970	0.002	-0.064	-0.128	0.000
109	A	108	VAL	0	0.016	0.008	6.271	-4.068	-4.068	0.000	0.000	0.000	0.000
110	A	109	VAL	0	-0.063	-0.034	7.177	1.486	1.486	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.030	0.005	9.436	2.245	2.245	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.028	-0.008	11.918	1.885	1.885	0.000	0.000	0.000	0.000
113	A	112	LEU	0	0.019	-0.003	13.553	0.460	0.460	0.000	0.000	0.000	0.000
114	A	113	MET	0	-0.005	0.009	17.066	1.148	1.148	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.036	-0.011	14.855	0.652	0.652	0.000	0.000	0.000	0.000
116	A	115	TRP	0	0.040	0.004	16.369	-0.126	-0.126	0.000	0.000	0.000	0.000
117	A	116	ALA	0	0.033	0.024	18.062	0.591	0.591	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.044	-0.015	19.708	0.617	0.617	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.869	0.930	15.654	19.381	19.381	0.000	0.000	0.000	0.000
120	A	119	ILE	0	-0.070	-0.027	17.638	0.129	0.129	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.816	-0.897	20.975	-12.179	-12.179	0.000	0.000	0.000	0.000
122	A	121	GLY	0	0.022	0.019	23.666	-0.239	-0.239	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.098	-0.059	25.867	0.381	0.381	0.000	0.000	0.000	0.000
124	A	123	PHE	0	-0.037	-0.028	21.014	-0.021	-0.021	0.000	0.000	0.000	0.000
125	A	124	PRO	0	0.012	0.014	24.665	-0.077	-0.077	0.000	0.000	0.000	0.000
126	A	125	GLN	0	0.004	-0.029	22.879	-0.787	-0.787	0.000	0.000	0.000	0.000
127	A	126	TYR	-1	-0.897	-0.960	20.043	-13.045	-13.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)