FMO DATABASE

FMODB ID: VQLQ1

Calculation Name: 3I2V-A-Xray372

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: 2023-09-23

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092616.577245
FMO2-HF: Nuclear repulsion	1043473.637948
FMO2-HF: Total energy	-49142.939297
FMO2-MP2: Total energy	-49288.111442

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.
-9.368	-4.958	6.422	-4.561	-6.27	-0.007

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 : 0 / q_Mulliken : 0.008 / q_NPA : 0.009

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	0.011	0.016	3.823	-0.237	1.611	-0.027	-0.927	-0.894	0.002
4	A	3	SER	0	-0.011	-0.023	7.026	-0.152	-0.152	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.078	0.015	10.519	-0.065	-0.065	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.002	0.008	13.258	0.002	0.002	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.849	-0.887	10.901	0.242	0.242	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.010	-0.009	11.212	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.807	0.888	12.689	0.080	0.080	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.898	0.930	14.662	-0.092	-0.092	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.003	0.008	11.678	0.007	0.007	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.021	0.006	15.337	0.007	0.007	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.807	-0.891	17.323	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.093	-0.057	17.721	0.016	0.016	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.006	0.006	19.895	0.010	0.010	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.025	0.003	16.825	0.002	0.002	0.000	0.000	0.000	0.000
17	A	16	PHE	0	0.076	0.035	15.793	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.045	-0.018	12.257	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.043	0.040	12.568	0.003	0.003	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.023	-0.003	11.616	-0.109	-0.109	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.010	0.003	10.867	0.055	0.055	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.775	-0.871	12.435	-0.510	-0.510	0.000	0.000	0.000	0.000
23	A	22	VAL	0	0.001	-0.016	11.283	0.021	0.021	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.739	0.838	14.415	0.312	0.312	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.016	0.004	17.131	0.024	0.024	0.000	0.000	0.000	0.000
26	A	25	GLN	0	0.000	-0.032	20.287	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.043	0.029	23.300	0.005	0.005	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.806	-0.890	19.768	-0.316	-0.316	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.006	0.010	19.964	0.008	0.008	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.825	-0.901	22.499	-0.152	-0.152	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.075	-0.022	25.170	0.014	0.014	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.058	-0.007	23.681	0.009	0.009	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.926	0.948	21.131	0.141	0.141	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.018	0.013	16.950	0.020	0.020	0.000	0.000	0.000	0.000
35	A	34	PRO	0	-0.012	-0.020	20.326	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	35	HIS	0	0.028	0.018	16.364	0.021	0.021	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.061	-0.014	16.375	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.042	0.027	16.229	0.024	0.024	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.070	-0.040	16.412	-0.037	-0.037	0.000	0.000	0.000	0.000
40	A	39	ILE	0	0.025	0.006	15.314	0.029	0.029	0.000	0.000	0.000	0.000
41	A	40	PRO	0	-0.035	0.000	15.468	-0.061	-0.061	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.055	0.013	11.894	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.917	0.963	14.895	0.242	0.242	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.014	-0.013	17.985	0.033	0.033	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.040	0.036	11.640	0.017	0.017	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.933	-0.988	14.825	-0.401	-0.401	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.786	0.877	16.424	0.223	0.223	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.818	0.891	15.094	0.178	0.178	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.816	-0.878	19.334	-0.148	-0.148	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.051	0.018	20.575	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.807	-0.898	22.437	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.041	-0.041	18.759	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.017	-0.005	16.533	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.834	0.915	18.889	0.097	0.097	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.049	0.032	19.839	0.005	0.005	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.041	-0.023	12.948	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.914	0.946	17.453	0.059	0.059	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.912	-0.959	19.274	-0.073	-0.073	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.013	0.010	17.951	0.008	0.008	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.030	-0.021	14.466	0.006	0.006	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.008	0.004	18.460	0.019	0.019	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.971	-0.981	22.039	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.869	-0.920	18.865	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.778	0.869	17.779	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.050	-0.021	21.883	0.015	0.015	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.010	0.009	22.695	0.004	0.004	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.105	-0.046	22.990	0.013	0.013	0.000	0.000	0.000	0.000
68	A	67	GLN	0	-0.020	-0.031	21.013	0.010	0.010	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.840	-0.897	18.747	0.076	0.076	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.026	-0.013	19.712	0.001	0.001	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.016	-0.016	14.872	0.034	0.034	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.032	-0.007	10.831	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.057	0.024	12.391	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.015	-0.004	9.325	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.008	0.007	8.017	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.012	-0.010	7.026	-0.341	-0.341	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.014	0.016	6.968	0.161	0.161	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.017	-0.002	9.163	-0.184	-0.184	0.000	0.000	0.000	0.000
79	A	78	CYS	0	-0.019	0.031	11.481	0.066	0.066	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.964	0.989	13.940	0.259	0.259	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.007	-0.011	14.933	0.029	0.029	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.035	0.018	10.863	0.019	0.019	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.033	0.006	9.836	-0.180	-0.180	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.833	-0.943	10.801	-0.706	-0.706	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.027	-0.023	8.472	0.082	0.082	0.000	0.000	0.000	0.000
86	A	85	GLN	0	-0.023	-0.009	5.750	-0.362	-0.362	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.880	0.938	6.344	0.448	0.448	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.050	0.029	8.982	0.096	0.096	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.011	-0.006	2.281	-0.190	-0.085	1.166	-0.422	-0.849	-0.002
90	A	89	LYS	1	0.911	0.955	4.917	3.242	3.242	0.000	0.000	0.000	0.000
91	A	90	ILE	0	0.002	0.016	6.910	0.302	0.302	0.000	0.000	0.000	0.000
92	A	91	LEU	0	0.025	0.009	7.838	0.128	0.128	0.000	0.000	0.000	0.000
93	A	92	GLN	0	-0.009	-0.023	2.104	-5.308	-5.639	3.728	-1.497	-1.900	0.014
94	A	93	SER	0	-0.032	-0.017	7.985	0.079	0.079	0.000	0.000	0.000	0.000
95	A	94	LEU	0	-0.027	-0.004	11.101	0.016	0.016	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.018	-0.003	10.172	0.057	0.057	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.000	0.001	10.771	0.001	0.001	0.000	0.000	0.000	0.000
98	A	97	ALA	0	-0.047	-0.015	12.603	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.039	-0.017	15.300	-0.036	-0.036	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.792	-0.867	16.415	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	100	LEU	0	-0.063	-0.049	12.956	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	101	ASP	-1	-0.839	-0.910	15.615	0.055	0.055	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.018	-0.002	12.847	0.008	0.008	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.009	0.012	8.976	-0.076	-0.076	0.000	0.000	0.000	0.000
105	A	104	THR	0	-0.046	-0.020	6.077	0.351	0.351	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.005	0.003	4.363	-0.484	-0.332	-0.001	-0.050	-0.100	0.000
107	A	106	ARG	1	0.865	0.924	2.442	-5.086	-2.687	1.554	-1.595	-2.358	-0.021
108	A	107	ASP	-1	-0.723	-0.810	3.760	-1.370	-1.133	0.002	-0.070	-0.169	0.000
109	A	108	VAL	0	0.008	0.011	6.338	0.161	0.161	0.000	0.000	0.000	0.000
110	A	109	VAL	0	-0.045	-0.024	7.351	0.034	0.034	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.030	0.004	9.580	0.096	0.096	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.026	-0.009	12.049	0.034	0.034	0.000	0.000	0.000	0.000
113	A	112	LEU	0	0.013	-0.004	13.674	0.064	0.064	0.000	0.000	0.000	0.000
114	A	113	MET	0	-0.035	-0.005	17.044	0.050	0.050	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.015	0.001	14.983	0.045	0.045	0.000	0.000	0.000	0.000
116	A	115	TRP	0	0.036	0.004	16.460	0.025	0.025	0.000	0.000	0.000	0.000
117	A	116	ALA	0	0.020	0.014	18.062	0.028	0.028	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.046	-0.015	19.935	0.021	0.021	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.876	0.933	16.329	0.045	0.045	0.000	0.000	0.000	0.000
120	A	119	ILE	0	-0.056	-0.021	17.476	0.018	0.018	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.813	-0.891	20.975	-0.097	-0.097	0.000	0.000	0.000	0.000
122	A	121	GLY	0	0.014	0.016	23.667	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.097	-0.069	25.867	0.000	0.000	0.000	0.000	0.000	0.000
124	A	123	PHE	0	-0.013	-0.013	20.930	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	124	PRO	0	0.015	0.015	24.678	0.002	0.002	0.000	0.000	0.000	0.000
126	A	125	GLN	0	0.038	-0.006	22.781	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	126	TYR	0	-0.027	-0.038	19.924	-0.005	-0.005	0.000	0.000	0.000	0.000

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