FMO DATABASE

FMODB ID: J4569

Calculation Name: 1VPM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a | phosphate ion

Ligand 3-letter code: COA | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VPM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KEQ1

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1420473.930668
FMO2-HF: Nuclear repulsion	1361052.565014
FMO2-HF: Total energy	-59421.365654
FMO2-MP2: Total energy	-59596.254274

3D Structure Molmil

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:2:ILE)

Summations of interaction energy for fragment #1(A:2:ILE)

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.
-14.412	-11.533	0.027	-1.239	-1.665	-0.003

Interaction energy analysis for fragmet #1(A:2:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.915

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

Sort

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	4	SER	0	0.019	0.014	3.356	-12.056	-9.937	0.014	-1.044	-1.089	-0.002
126	A	127	PRO	0	-0.042	0.002	4.665	-8.252	-8.185	-0.001	-0.010	-0.055	0.000
127	A	128	GLN	0	0.024	-0.003	3.080	1.030	1.720	0.015	-0.185	-0.520	-0.001
128	A	129	VAL	0	-0.023	-0.010	5.390	1.723	1.726	-0.001	0.000	-0.001	0.000
4	A	5	TYR	0	-0.018	-0.014	5.723	3.062	3.062	0.000	0.000	0.000	0.000
5	A	6	PRO	0	0.078	0.049	9.473	-0.220	-0.220	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.035	0.024	12.597	0.089	0.089	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.783	-0.845	14.363	-14.908	-14.908	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.815	0.917	12.102	25.023	25.023	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.037	-0.027	14.129	0.840	0.840	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.807	0.868	16.032	15.124	15.124	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.010	-0.003	19.181	0.328	0.328	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.035	0.021	22.307	0.075	0.075	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.002	0.010	26.004	0.282	0.282	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.010	-0.001	28.788	0.045	0.045	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.797	0.876	31.138	9.912	9.912	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.021	0.024	35.238	0.057	0.057	0.000	0.000	0.000	0.000
17	A	18	VAL	0	-0.007	0.010	38.181	-0.076	-0.076	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.021	0.008	40.237	0.271	0.271	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.047	0.014	43.031	-0.068	-0.068	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.002	-0.004	42.665	0.009	0.009	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.849	-0.908	39.344	-8.331	-8.331	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.056	-0.039	40.814	-0.098	-0.098	0.000	0.000	0.000	0.000
23	A	24	ASN	0	0.056	0.030	43.590	0.146	0.146	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.026	0.001	46.229	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.049	-0.023	48.492	0.142	0.142	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.026	0.026	47.020	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.007	-0.010	42.472	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.030	-0.014	36.859	0.020	0.020	0.000	0.000	0.000	0.000
29	A	30	PHE	0	0.010	0.001	39.272	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.057	0.021	36.229	-0.201	-0.201	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.014	-0.002	34.478	-0.289	-0.289	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.840	0.921	33.977	8.419	8.419	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.025	0.017	31.587	-0.237	-0.237	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.004	-0.002	29.925	-0.361	-0.361	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.006	0.012	29.042	-0.409	-0.409	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.012	0.002	29.057	-0.249	-0.249	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.013	0.003	25.491	-0.385	-0.385	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.854	-0.902	24.643	-13.294	-13.294	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.863	-0.907	24.149	-11.151	-11.151	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.017	-0.013	23.337	-0.432	-0.432	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.036	0.030	20.777	-0.761	-0.761	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.027	0.006	19.499	-1.083	-1.083	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.003	-0.001	19.636	-0.868	-0.868	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.047	-0.016	16.959	-0.703	-0.703	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.012	-0.007	15.241	-1.350	-1.350	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.049	-0.025	14.827	-1.278	-1.278	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.831	0.919	15.990	14.969	14.969	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.060	-0.037	8.345	1.596	1.596	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.014	-0.014	10.696	-2.341	-2.341	0.000	0.000	0.000	0.000
50	A	51	ASN	0	-0.033	0.023	11.740	-1.709	-1.709	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.014	-0.011	12.917	0.090	0.090	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.054	0.040	15.601	0.535	0.535	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.031	-0.026	15.862	-1.270	-1.270	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.016	0.011	18.303	0.940	0.940	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.001	-0.035	19.355	-1.180	-1.180	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.042	-0.012	19.285	0.452	0.452	0.000	0.000	0.000	0.000
57	A	58	SER	0	-0.046	-0.026	21.213	0.601	0.601	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.015	0.013	21.995	-0.629	-0.629	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.763	-0.841	22.775	-13.640	-13.640	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.005	-0.002	25.445	0.129	0.129	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.011	-0.016	28.068	-0.316	-0.316	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.882	-0.928	30.329	-9.405	-9.405	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.053	-0.029	32.992	-0.173	-0.173	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.864	0.928	30.301	10.425	10.425	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.006	-0.017	36.322	0.245	0.245	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.010	-0.005	37.484	-0.195	-0.195	0.000	0.000	0.000	0.000
67	A	68	ALA	0	0.026	0.010	37.942	-0.106	-0.106	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.056	-0.046	39.995	0.118	0.118	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.009	-0.021	42.627	-0.115	-0.115	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.023	-0.003	43.553	0.142	0.142	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.778	-0.861	40.289	-7.563	-7.563	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.007	-0.009	36.846	-0.078	-0.078	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.005	-0.010	33.635	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.836	-0.891	31.292	-9.590	-9.590	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.012	-0.011	27.333	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.784	-0.889	23.291	-12.999	-12.999	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.014	0.016	21.818	0.126	0.126	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.003	-0.022	17.191	-0.269	-0.269	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.000	-0.003	11.474	0.216	0.216	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.000	-0.028	14.452	-0.324	-0.324	0.000	0.000	0.000	0.000
81	A	82	HIS	0	-0.013	-0.014	11.314	-0.874	-0.874	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.003	0.010	7.353	-0.238	-0.238	0.000	0.000	0.000	0.000
83	A	84	GLY	0	-0.058	-0.025	8.929	-0.631	-0.631	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.967	0.975	7.596	23.843	23.843	0.000	0.000	0.000	0.000
85	A	86	THR	0	0.015	0.001	8.102	-2.331	-2.331	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.009	0.004	10.679	1.475	1.475	0.000	0.000	0.000	0.000
87	A	88	MET	0	0.006	0.017	10.868	-2.749	-2.749	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.744	-0.795	12.845	-15.868	-15.868	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.004	-0.005	14.987	-0.990	-0.990	0.000	0.000	0.000	0.000
90	A	91	TYR	0	-0.019	-0.011	17.653	0.698	0.698	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.001	-0.011	20.372	-0.234	-0.234	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.801	0.889	23.556	13.028	13.028	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.000	-0.010	26.758	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	95	HIS	0	0.006	-0.003	30.144	-0.153	-0.153	0.000	0.000	0.000	0.000
95	A	96	SER	0	0.018	0.018	33.312	-0.073	-0.073	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.053	-0.039	36.446	0.228	0.228	0.000	0.000	0.000	0.000
97	A	98	ASN	0	0.092	0.046	38.449	0.158	0.158	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.025	-0.016	40.103	0.040	0.040	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.041	-0.012	43.776	0.154	0.154	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.016	-0.015	44.906	0.069	0.069	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.001	0.011	41.958	0.016	0.016	0.000	0.000	0.000	0.000
102	A	103	GLU	-1	-0.985	-0.985	40.715	-7.589	-7.589	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.823	0.890	31.531	9.484	9.484	0.000	0.000	0.000	0.000
104	A	105	THR	0	0.040	0.025	37.328	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.038	-0.017	30.288	-0.176	-0.176	0.000	0.000	0.000	0.000
106	A	107	THR	0	-0.025	0.018	33.346	0.123	0.123	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.008	-0.049	29.991	0.012	0.012	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.824	-0.891	26.536	-11.405	-11.405	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.018	0.001	25.284	0.134	0.134	0.000	0.000	0.000	0.000
110	A	111	PHE	0	0.028	0.009	19.550	-0.427	-0.427	0.000	0.000	0.000	0.000
111	A	112	LEU	0	0.042	0.022	20.299	0.500	0.500	0.000	0.000	0.000	0.000
112	A	113	THR	0	-0.080	-0.040	16.244	-1.159	-1.159	0.000	0.000	0.000	0.000
113	A	114	MET	0	0.040	0.034	16.024	0.823	0.823	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.016	-0.026	14.874	-1.647	-1.647	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.021	0.026	12.274	0.976	0.976	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.020	-0.021	14.406	-0.444	-0.444	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.789	-0.872	15.454	-18.043	-18.043	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.873	-0.944	17.121	-16.251	-16.251	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.091	-0.065	19.391	0.804	0.804	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.005	0.005	20.521	0.544	0.544	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.820	0.909	14.980	18.824	18.824	0.000	0.000	0.000	0.000
122	A	123	PRO	0	-0.007	-0.008	15.083	-0.895	-0.895	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.885	0.937	11.383	21.514	21.514	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.035	-0.037	6.926	-0.264	-0.264	0.000	0.000	0.000	0.000
125	A	126	VAL	0	0.012	0.020	7.330	2.216	2.216	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.866	-0.920	8.794	-26.891	-26.891	0.000	0.000	0.000	0.000
130	A	131	PRO	0	-0.036	-0.020	10.301	1.910	1.910	0.000	0.000	0.000	0.000
131	A	132	GLN	0	-0.037	-0.040	13.767	0.976	0.976	0.000	0.000	0.000	0.000
132	A	133	THR	0	0.006	-0.016	16.532	1.017	1.017	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.812	-0.913	18.937	-15.447	-15.447	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.912	-0.930	21.089	-13.166	-13.166	0.000	0.000	0.000	0.000
135	A	136	GLU	-1	-0.764	-0.875	15.990	-18.010	-18.010	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.868	0.926	16.095	15.538	15.538	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.976	1.002	17.167	12.809	12.809	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.010	0.008	18.152	0.139	0.139	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.022	0.011	8.217	0.263	0.263	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.920	-0.964	14.881	-19.588	-19.588	0.000	0.000	0.000	0.000
141	A	142	THR	0	-0.046	-0.039	16.612	0.516	0.516	0.000	0.000	0.000	0.000
142	A	143	ALA	0	0.001	0.010	14.768	0.604	0.604	0.000	0.000	0.000	0.000
143	A	144	PRO	0	-0.025	-0.016	13.974	0.360	0.360	0.000	0.000	0.000	0.000
144	A	145	ALA	0	0.027	0.019	16.404	0.526	0.526	0.000	0.000	0.000	0.000
145	A	146	ARG	1	0.781	0.855	17.966	16.659	16.659	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.955	0.976	12.406	23.257	23.257	0.000	0.000	0.000	0.000
147	A	148	GLU	-1	-0.807	-0.888	18.351	-14.558	-14.558	0.000	0.000	0.000	0.000
148	A	149	ASN	0	-0.007	-0.015	20.709	0.776	0.776	0.000	0.000	0.000	0.000
149	A	150	ARG	1	0.719	0.823	17.840	16.253	16.253	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.810	0.894	18.948	15.093	15.093	0.000	0.000	0.000	0.000
151	A	152	LYS	1	0.955	0.969	22.583	11.621	11.621	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.836	0.901	23.509	13.174	13.174	0.000	0.000	0.000	0.000
153	A	154	ALA	0	-0.026	-0.005	24.587	0.289	0.289	0.000	0.000	0.000	0.000
154	A	155	ALA	0	-0.067	-0.020	26.714	-0.048	-0.048	0.000	0.000	0.000	0.000
155	A	156	LEU	-1	-0.931	-0.951	28.118	-9.628	-9.628	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ILE)