FMO DATABASE

FMODB ID: 1NKNZ

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	OptAll
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	-1093412.28153
FMO2-HF: Nuclear repulsion	1044269.102567
FMO2-HF: Total energy	-49143.178962
FMO2-MP2: Total energy	-49288.270784

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.
-7.859	-5.681	9.346	-5.026	-6.495	-0.003

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 : 0.030 / q_NPA : 0.017

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	0.013	3.879	0.429	2.212	-0.020	-0.956	-0.807	0.002
4	A	3	SER	0	-0.004	-0.018	7.239	-0.253	-0.253	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.073	0.021	10.870	-0.024	-0.024	0.000	0.000	0.000	0.000
6	A	5	THR	0	0.006	-0.003	13.362	0.009	0.009	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.840	-0.869	11.016	0.282	0.282	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.014	-0.015	10.963	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.800	0.887	12.451	0.053	0.053	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.901	0.925	14.656	-0.134	-0.134	0.000	0.000	0.000	0.000
11	A	10	LEU	0	-0.010	0.009	11.223	0.012	0.012	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.025	0.000	14.898	0.005	0.005	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.797	-0.882	17.248	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.094	-0.058	17.263	0.015	0.015	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.005	0.003	19.650	0.008	0.008	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.022	0.001	16.539	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	PHE	0	0.053	0.030	15.928	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.027	-0.013	12.437	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.033	0.034	12.711	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.032	-0.012	11.728	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.019	0.009	10.523	0.041	0.041	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.784	-0.872	12.212	-0.466	-0.466	0.000	0.000	0.000	0.000
23	A	22	VAL	0	0.011	-0.001	11.422	0.017	0.017	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.725	0.831	14.473	0.284	0.284	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.004	0.000	17.307	0.029	0.029	0.000	0.000	0.000	0.000
26	A	25	GLN	0	-0.017	-0.031	20.490	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.062	0.035	23.391	0.000	0.000	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.818	-0.890	19.308	-0.307	-0.307	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.015	0.012	19.791	0.004	0.004	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.824	-0.897	22.526	-0.129	-0.129	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.068	-0.026	25.468	0.011	0.011	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.050	-0.003	23.487	0.006	0.006	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.940	0.954	20.781	0.117	0.117	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.021	0.021	16.631	0.015	0.015	0.000	0.000	0.000	0.000
35	A	34	PRO	0	-0.019	-0.023	20.202	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	35	HIS	0	0.033	0.020	16.685	0.016	0.016	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.059	-0.018	16.299	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.047	0.025	16.081	0.014	0.014	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.098	-0.061	16.091	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	39	ILE	0	0.040	0.017	14.931	0.030	0.030	0.000	0.000	0.000	0.000
41	A	40	PRO	0	-0.033	-0.005	15.181	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.066	0.019	11.893	0.007	0.007	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.894	0.954	14.955	0.210	0.210	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.042	-0.023	17.323	0.033	0.033	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.041	0.023	11.381	0.021	0.021	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.909	-0.977	14.719	-0.318	-0.318	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.747	0.853	16.347	0.169	0.169	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.804	0.875	14.748	0.055	0.055	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.795	-0.859	19.066	-0.098	-0.098	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.058	0.027	20.338	0.000	0.000	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.795	-0.888	22.205	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.024	-0.038	18.549	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.029	-0.016	16.251	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.812	0.907	18.441	0.057	0.057	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.031	0.024	19.843	0.006	0.006	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.031	-0.019	12.593	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.917	0.957	17.175	-0.039	-0.039	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.890	-0.953	19.018	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.007	0.003	17.891	0.007	0.007	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.036	-0.024	14.282	0.008	0.008	0.000	0.000	0.000	0.000
61	A	60	TRP	0	-0.024	-0.003	18.286	0.018	0.018	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.965	-0.982	21.958	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.831	-0.903	19.155	0.062	0.062	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.772	0.862	18.236	-0.102	-0.102	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.049	-0.008	21.875	0.011	0.011	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.001	0.002	22.993	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.107	-0.059	23.411	0.012	0.012	0.000	0.000	0.000	0.000
68	A	67	GLN	0	-0.010	-0.017	21.397	0.014	0.014	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.823	-0.895	18.949	0.143	0.143	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.045	-0.022	20.179	0.009	0.009	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.028	-0.026	15.428	0.033	0.033	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.017	0.006	11.530	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.039	0.014	12.669	0.001	0.001	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.002	-0.007	9.860	0.029	0.029	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.006	0.010	8.037	-0.086	-0.086	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.012	-0.003	7.167	-0.238	-0.238	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.018	0.017	6.809	0.128	0.128	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.023	-0.002	8.996	-0.178	-0.178	0.000	0.000	0.000	0.000
79	A	78	CYS	0	-0.037	0.032	11.473	0.053	0.053	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.935	0.972	14.045	0.249	0.249	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.022	0.002	14.926	0.031	0.031	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.049	0.027	10.560	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.032	0.001	9.939	-0.215	-0.215	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.815	-0.913	11.099	-0.630	-0.630	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.042	-0.018	8.693	0.130	0.130	0.000	0.000	0.000	0.000
86	A	85	GLN	0	-0.036	-0.017	5.626	-0.425	-0.425	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.829	0.905	6.298	0.554	0.554	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.065	0.027	8.634	0.092	0.092	0.000	0.000	0.000	0.000
89	A	88	VAL	0	-0.007	-0.003	2.394	-0.179	-0.154	1.494	-0.549	-0.969	-0.001
90	A	89	LYS	1	0.923	0.962	4.416	2.836	2.950	-0.001	-0.003	-0.109	0.000
91	A	90	ILE	0	0.003	0.025	6.746	0.255	0.255	0.000	0.000	0.000	0.000
92	A	91	LEU	0	0.028	0.013	7.500	0.098	0.098	0.000	0.000	0.000	0.000
93	A	92	GLN	0	-0.013	-0.026	1.937	-4.907	-7.529	6.982	-2.069	-2.291	0.011
94	A	93	SER	0	-0.042	-0.035	7.610	-0.024	-0.024	0.000	0.000	0.000	0.000
95	A	94	LEU	0	-0.018	-0.008	10.758	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.029	-0.014	10.225	0.025	0.025	0.000	0.000	0.000	0.000
97	A	96	ALA	0	-0.013	-0.006	10.612	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	97	ALA	0	-0.039	-0.019	12.492	-0.042	-0.042	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.040	-0.014	15.120	-0.050	-0.050	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.780	-0.845	16.023	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	100	LEU	0	-0.087	-0.052	12.395	-0.041	-0.041	0.000	0.000	0.000	0.000
102	A	101	ASP	-1	-0.811	-0.902	15.342	0.143	0.143	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.037	0.014	13.115	0.040	0.040	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.000	0.017	9.036	-0.066	-0.066	0.000	0.000	0.000	0.000
105	A	104	THR	0	-0.043	-0.025	6.522	0.326	0.326	0.000	0.000	0.000	0.000
106	A	105	VAL	0	0.001	0.018	4.343	-0.413	-0.300	-0.001	-0.024	-0.088	0.000
107	A	106	ARG	1	0.847	0.909	2.671	-4.328	-1.797	0.891	-1.375	-2.046	-0.015
108	A	107	ASP	-1	-0.732	-0.831	3.827	-1.519	-1.285	0.001	-0.050	-0.185	0.000
109	A	108	VAL	0	0.017	0.015	6.334	0.152	0.152	0.000	0.000	0.000	0.000
110	A	109	VAL	0	-0.044	-0.025	7.836	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.034	0.007	10.099	0.134	0.134	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.028	-0.012	12.471	0.044	0.044	0.000	0.000	0.000	0.000
113	A	112	LEU	0	0.006	0.000	13.932	0.063	0.063	0.000	0.000	0.000	0.000
114	A	113	MET	0	-0.047	-0.005	17.399	0.047	0.047	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.010	0.001	15.358	0.039	0.039	0.000	0.000	0.000	0.000
116	A	115	TRP	0	-0.016	-0.032	16.742	0.024	0.024	0.000	0.000	0.000	0.000
117	A	116	ALA	0	0.027	0.011	18.457	0.029	0.029	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.040	-0.015	20.389	0.019	0.019	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.875	0.936	16.533	0.105	0.105	0.000	0.000	0.000	0.000
120	A	119	ILE	0	-0.065	-0.019	17.414	0.020	0.020	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.738	-0.857	21.089	-0.092	-0.092	0.000	0.000	0.000	0.000
122	A	121	GLY	0	0.003	0.018	23.735	-0.015	-0.015	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.098	-0.069	26.003	0.002	0.002	0.000	0.000	0.000	0.000
124	A	123	PHE	0	0.003	-0.002	20.881	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	124	PRO	0	0.011	0.018	24.782	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	125	GLN	0	0.045	-0.007	23.075	-0.023	-0.023	0.000	0.000	0.000	0.000
127	A	126	TYR	0	-0.010	-0.038	20.213	-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)