FMO DATABASE

FMODB ID: YV8V2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1092317.717305
FMO2-HF: Nuclear repulsion	1043175.292514
FMO2-HF: Total energy	-49142.424791
FMO2-MP2: Total energy	-49287.592272

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.
-9.236	-3.504	3.911	-3.944	-5.7	-0.005

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 : 0.015 / q_NPA : 0.004

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	0.013	0.014	3.823	-0.837	1.002	-0.026	-0.909	-0.903	0.002
4	A	3	SER	0	0.011	0.018	7.059	0.187	0.187	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.077	0.019	10.176	0.009	0.009	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.001	0.002	13.186	0.030	0.030	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.860	-0.931	10.998	-0.510	-0.510	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.041	-0.033	11.209	0.031	0.031	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.844	0.908	12.695	0.283	0.283	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.902	0.939	14.989	0.373	0.373	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.012	0.018	11.894	0.023	0.023	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.029	0.001	15.330	0.040	0.040	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.822	-0.905	17.387	-0.173	-0.173	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.112	-0.065	17.749	0.028	0.028	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.009	0.008	19.942	0.020	0.020	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.026	0.002	16.871	0.017	0.017	0.000	0.000	0.000	0.000
17	A	16	PHE	0	0.076	0.032	16.041	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.034	0.001	12.303	-0.057	-0.057	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.044	0.043	12.623	0.013	0.013	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.022	-0.005	11.586	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.005	0.000	10.901	0.059	0.059	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.768	-0.866	12.308	-0.279	-0.279	0.000	0.000	0.000	0.000
23	A	22	VAL	0	0.003	-0.018	11.399	0.037	0.037	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.746	0.845	14.488	0.195	0.195	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.046	0.017	17.164	0.017	0.017	0.000	0.000	0.000	0.000
26	A	25	GLN	0	0.006	-0.022	20.316	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.033	0.024	23.353	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.832	-0.908	19.598	-0.132	-0.132	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.004	0.009	20.025	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.841	-0.909	22.560	-0.063	-0.063	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.080	-0.021	25.141	0.003	0.003	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.053	-0.004	23.606	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.916	0.937	20.889	0.090	0.090	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.017	0.011	16.909	0.006	0.006	0.000	0.000	0.000	0.000
35	A	34	PRO	0	-0.015	-0.023	20.245	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	35	HIS	0	0.022	0.016	16.251	0.032	0.032	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.057	-0.012	16.273	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.049	0.032	16.066	0.024	0.024	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.077	-0.048	16.311	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	39	ILE	0	0.016	0.000	15.152	0.026	0.026	0.000	0.000	0.000	0.000
41	A	40	PRO	0	-0.037	0.000	15.515	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.064	0.020	11.846	0.019	0.019	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.918	0.960	14.937	0.044	0.044	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.008	-0.016	18.017	0.013	0.013	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.050	0.045	11.804	0.018	0.018	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.947	-0.998	14.914	0.076	0.076	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.795	0.887	16.456	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.939	0.983	14.874	-0.210	-0.210	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.841	-0.925	19.427	0.024	0.024	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.046	0.020	20.475	0.004	0.004	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.883	-0.944	22.355	0.035	0.035	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.031	-0.022	18.474	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	52	LEU	0	0.006	0.013	16.724	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.912	0.960	18.816	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.046	0.029	19.705	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.036	-0.021	13.071	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.952	0.964	17.423	-0.126	-0.126	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.911	-0.955	19.282	0.019	0.019	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.017	0.012	17.941	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.033	-0.019	14.560	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.016	-0.004	18.519	0.004	0.004	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.974	-0.985	22.106	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.946	-0.969	19.162	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.844	0.920	17.362	-0.053	-0.053	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.050	-0.017	22.003	0.012	0.012	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.007	0.009	22.800	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.084	-0.043	23.135	0.009	0.009	0.000	0.000	0.000	0.000
68	A	67	GLN	0	-0.037	-0.033	21.165	0.019	0.019	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.847	-0.903	19.167	0.059	0.059	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.001	-0.008	19.940	0.011	0.011	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.013	-0.015	15.005	0.018	0.018	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.032	-0.004	10.967	0.000	0.000	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.049	0.017	12.459	-0.053	-0.053	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.017	-0.002	9.478	0.042	0.042	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.018	0.012	7.918	-0.054	-0.054	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.009	-0.014	7.064	-0.353	-0.353	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.014	0.019	6.996	0.194	0.194	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.014	0.000	9.040	-0.203	-0.203	0.000	0.000	0.000	0.000
79	A	78	CYS	0	-0.019	0.034	11.477	0.099	0.099	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.994	1.004	13.953	0.101	0.101	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.002	-0.012	15.114	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.038	0.019	10.806	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.012	-0.001	10.040	0.013	0.013	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.866	-0.960	10.695	-0.083	-0.083	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.002	-0.051	8.154	0.092	0.092	0.000	0.000	0.000	0.000
86	A	85	GLN	0	-0.027	-0.012	5.675	0.170	0.170	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.958	0.976	6.275	0.151	0.151	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.054	0.032	8.967	0.080	0.080	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.006	-0.003	2.475	-0.329	-0.048	0.806	-0.332	-0.756	-0.001
90	A	89	LYS	1	0.905	0.959	4.699	-0.322	-0.226	-0.001	-0.001	-0.094	0.000
91	A	90	ILE	0	-0.014	0.004	6.930	0.111	0.111	0.000	0.000	0.000	0.000
92	A	91	LEU	0	0.034	0.011	7.779	0.033	0.033	0.000	0.000	0.000	0.000
93	A	92	GLN	0	-0.006	-0.018	2.259	-5.296	-4.603	1.993	-1.110	-1.576	0.013
94	A	93	SER	0	-0.024	-0.011	7.969	-0.044	-0.044	0.000	0.000	0.000	0.000
95	A	94	LEU	0	-0.023	-0.002	11.135	-0.051	-0.051	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.024	0.001	10.174	0.002	0.002	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.001	-0.005	10.855	-0.055	-0.055	0.000	0.000	0.000	0.000
98	A	97	ALA	0	-0.046	-0.014	12.650	-0.057	-0.057	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.042	-0.019	15.342	-0.082	-0.082	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.931	-0.961	16.427	0.196	0.196	0.000	0.000	0.000	0.000
101	A	100	LEU	0	-0.104	-0.062	12.796	-0.047	-0.047	0.000	0.000	0.000	0.000
102	A	101	ASP	-1	-0.841	-0.914	15.673	0.198	0.198	0.000	0.000	0.000	0.000
103	A	102	PRO	0	-0.008	-0.017	12.953	0.049	0.049	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.022	0.019	9.089	-0.094	-0.094	0.000	0.000	0.000	0.000
105	A	104	THR	0	-0.039	-0.017	6.196	0.349	0.349	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.004	0.006	4.345	-0.508	-0.384	-0.001	-0.038	-0.086	0.000
107	A	106	ARG	1	0.869	0.931	2.536	-2.701	-0.211	1.138	-1.493	-2.136	-0.019
108	A	107	ASP	-1	-0.716	-0.822	3.751	-0.150	0.059	0.002	-0.061	-0.149	0.000
109	A	108	VAL	0	0.008	0.007	6.262	-0.411	-0.411	0.000	0.000	0.000	0.000
110	A	109	VAL	0	-0.050	-0.027	7.031	0.224	0.224	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.027	0.004	9.328	0.069	0.069	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.025	-0.009	12.093	0.073	0.073	0.000	0.000	0.000	0.000
113	A	112	LEU	0	0.018	0.000	13.671	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	113	MET	0	-0.041	-0.009	17.054	0.032	0.032	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.017	-0.002	14.724	0.015	0.015	0.000	0.000	0.000	0.000
116	A	115	TRP	0	0.039	0.005	16.369	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	116	ALA	0	0.030	0.020	18.062	0.015	0.015	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.044	-0.014	19.559	0.014	0.014	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.870	0.931	15.526	0.344	0.344	0.000	0.000	0.000	0.000
120	A	119	ILE	0	-0.059	-0.023	17.561	0.001	0.001	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.812	-0.894	20.975	-0.136	-0.136	0.000	0.000	0.000	0.000
122	A	121	GLY	0	0.013	0.014	23.667	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.093	-0.057	25.840	0.011	0.011	0.000	0.000	0.000	0.000
124	A	123	PHE	0	-0.029	-0.022	21.005	0.003	0.003	0.000	0.000	0.000	0.000
125	A	124	PRO	0	0.017	0.018	24.657	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	125	GLN	0	0.040	-0.008	23.108	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	126	TYR	0	-0.035	-0.036	20.012	-0.002	-0.002	0.000	0.000	0.000	0.000

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