FMO DATABASE

FMODB ID: 3G9JL

Calculation Name: 7CZ3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a

Ligand 3-letter code: COA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7CZ3

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1597180.444974
FMO2-HF: Nuclear repulsion	1530926.209161
FMO2-HF: Total energy	-66254.235812
FMO2-MP2: Total energy	-66446.036444

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
35.829	41.716	11.352	-8.077	-9.163	-0.09

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.730 / q_NPA : 1.861

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	5	PHE	0	0.080	0.038	3.891	-8.125	-6.368	-0.014	-0.868	-0.875	-0.002
123	A	125	PRO	0	-0.059	-0.032	2.751	-8.055	-6.708	0.531	-0.381	-1.497	-0.001
124	A	126	GLN	0	0.058	0.028	3.236	0.057	1.317	0.055	-0.371	-0.944	-0.003
125	A	127	VAL	0	0.011	-0.002	1.948	-48.994	-49.314	9.378	-5.190	-3.868	-0.068
126	A	128	LEU	0	-0.048	-0.011	2.207	-6.951	-5.109	1.403	-1.262	-1.984	-0.016
127	A	129	PRO	0	0.023	0.014	4.927	1.704	1.705	-0.001	-0.005	0.005	0.000
4	A	6	MET	0	-0.005	0.030	6.454	3.710	3.710	0.000	0.000	0.000	0.000
5	A	7	ARG	1	1.025	1.025	9.138	45.542	45.542	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.895	-0.956	7.055	-76.786	-76.786	0.000	0.000	0.000	0.000
7	A	9	SER	0	-0.074	-0.038	10.073	2.261	2.261	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.874	0.946	11.868	36.795	36.795	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.029	-0.018	14.882	0.507	0.507	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.019	0.000	18.253	0.247	0.247	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.807	0.902	21.855	22.687	22.687	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.041	0.018	25.163	-0.165	-0.165	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.039	-0.017	28.575	0.017	0.017	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.994	0.998	31.727	16.352	16.352	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.041	0.034	35.035	-0.351	-0.351	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.003	-0.015	34.772	0.447	0.447	0.000	0.000	0.000	0.000
17	A	19	PRO	0	0.052	0.003	39.178	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.010	0.001	40.530	0.415	0.415	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.845	-0.891	36.026	-17.935	-17.935	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.048	-0.012	38.446	-0.328	-0.328	0.000	0.000	0.000	0.000
21	A	23	ASN	0	0.028	0.015	41.126	0.368	0.368	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.025	-0.011	43.079	0.121	0.121	0.000	0.000	0.000	0.000
23	A	25	HIS	0	-0.016	0.004	44.421	0.323	0.323	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.004	0.003	44.328	-0.260	-0.260	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.019	-0.009	39.185	-0.269	-0.269	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.032	-0.015	33.273	0.043	0.043	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.004	0.004	36.517	-0.091	-0.091	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.055	0.019	33.316	-0.491	-0.491	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.008	-0.005	31.781	-0.644	-0.644	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.853	0.914	31.441	18.440	18.440	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.034	0.016	28.787	-0.658	-0.658	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.021	0.005	27.264	-0.956	-0.956	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.012	0.013	26.377	-0.982	-0.982	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.817	-0.895	26.471	-22.867	-22.867	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.007	-0.009	22.530	-1.191	-1.191	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.831	-0.907	21.944	-28.654	-28.654	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.001	0.014	21.545	-1.800	-1.800	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.003	0.001	20.174	-1.359	-1.359	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.024	0.007	17.822	-2.012	-2.012	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.042	-0.022	16.775	-2.620	-2.620	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.002	-0.001	16.770	-2.306	-2.306	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.013	0.016	14.288	-2.327	-2.327	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.041	0.001	12.657	-4.716	-4.716	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.029	0.026	11.943	-4.448	-4.448	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.873	0.942	11.661	34.379	34.379	0.000	0.000	0.000	0.000
46	A	48	HIS	0	-0.039	-0.028	4.979	-1.776	-1.776	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.051	-0.060	7.280	-8.282	-8.282	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.892	0.958	7.259	58.026	58.026	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.843	0.907	7.807	59.981	59.981	0.000	0.000	0.000	0.000
50	A	52	HIS	0	0.104	0.063	11.831	-0.156	-0.156	0.000	0.000	0.000	0.000
51	A	53	CYS	0	-0.069	-0.032	13.923	-2.585	-2.585	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.019	0.014	16.283	1.800	1.800	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.016	-0.016	18.554	-2.103	-2.103	0.000	0.000	0.000	0.000
54	A	56	ALA	0	-0.077	-0.037	18.924	1.101	1.101	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.037	-0.030	20.240	1.165	1.165	0.000	0.000	0.000	0.000
56	A	58	ILE	0	0.031	0.012	20.834	-1.505	-1.505	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.804	-0.874	20.981	-27.326	-27.326	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.009	0.001	23.759	0.294	0.294	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.028	-0.021	25.506	-0.697	-0.697	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.905	-0.937	27.889	-19.353	-19.353	0.000	0.000	0.000	0.000
61	A	63	PHE	0	-0.053	-0.046	30.093	-0.433	-0.433	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.001	0.003	29.009	0.590	0.590	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.023	0.001	33.148	0.555	0.555	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.025	0.020	35.207	-0.344	-0.344	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.003	0.010	32.318	-0.219	-0.219	0.000	0.000	0.000	0.000
66	A	68	HIS	0	0.034	0.000	36.935	0.412	0.412	0.000	0.000	0.000	0.000
67	A	69	GLN	0	0.025	-0.008	38.996	-0.252	-0.252	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.030	-0.004	41.001	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.752	-0.850	35.963	-16.530	-16.530	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.074	-0.031	33.323	-0.170	-0.170	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.029	0.001	29.032	0.008	0.008	0.000	0.000	0.000	0.000
72	A	74	CYS	0	-0.047	-0.023	26.068	-0.549	-0.549	0.000	0.000	0.000	0.000
73	A	75	TYR	0	0.028	0.016	23.956	-0.069	-0.069	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.792	-0.894	19.274	-29.942	-29.942	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.012	0.005	17.817	0.112	0.112	0.000	0.000	0.000	0.000
76	A	78	PHE	0	0.032	-0.004	12.344	-0.840	-0.840	0.000	0.000	0.000	0.000
77	A	79	VAL	0	-0.022	-0.009	8.980	1.109	1.109	0.000	0.000	0.000	0.000
78	A	80	CYS	0	0.009	-0.002	10.320	-2.132	-2.132	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.062	0.043	9.608	-2.261	-2.261	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.028	-0.013	6.233	-4.442	-4.442	0.000	0.000	0.000	0.000
81	A	83	GLY	0	0.013	0.028	8.922	1.120	1.120	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.946	0.963	5.685	66.316	66.316	0.000	0.000	0.000	0.000
83	A	85	SER	0	0.015	-0.004	8.774	-3.793	-3.793	0.000	0.000	0.000	0.000
84	A	86	SER	0	0.007	0.008	11.102	-0.025	-0.025	0.000	0.000	0.000	0.000
85	A	87	MET	0	-0.034	0.001	9.630	-6.440	-6.440	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.789	-0.870	11.745	-33.253	-33.253	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.019	-0.014	12.731	-3.179	-3.179	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.068	0.031	14.960	2.307	2.307	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.028	-0.026	17.028	-0.782	-0.782	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.851	0.933	20.145	29.236	29.236	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.002	-0.001	22.515	-0.175	-0.175	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.000	-0.003	25.058	0.550	0.550	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.009	0.008	28.431	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.854	-0.929	31.881	-19.337	-19.337	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.030	0.025	34.082	0.251	0.251	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.026	-0.022	36.226	-0.133	-0.133	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.053	0.000	38.966	0.136	0.136	0.000	0.000	0.000	0.000
98	A	100	ALA	0	0.031	0.011	41.283	0.180	0.180	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.037	0.015	37.482	-0.304	-0.304	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.942	-0.959	36.283	-16.204	-16.204	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.887	0.914	27.569	20.258	20.258	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.764	0.863	32.221	17.011	17.011	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.018	-0.007	26.626	-0.377	-0.377	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.017	0.002	29.351	0.530	0.530	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.023	0.009	27.495	0.352	0.352	0.000	0.000	0.000	0.000
106	A	108	THR	0	-0.036	-0.015	22.585	-0.803	-0.803	0.000	0.000	0.000	0.000
107	A	109	CYS	0	-0.014	0.008	22.187	0.518	0.518	0.000	0.000	0.000	0.000
108	A	110	PHE	0	0.038	0.032	16.486	-1.330	-1.330	0.000	0.000	0.000	0.000
109	A	111	ILE	0	0.050	0.013	18.166	1.216	1.216	0.000	0.000	0.000	0.000
110	A	112	THR	0	-0.056	-0.016	15.690	-2.690	-2.690	0.000	0.000	0.000	0.000
111	A	113	PHE	0	0.059	0.028	14.988	0.817	0.817	0.000	0.000	0.000	0.000
112	A	114	VAL	0	-0.045	-0.041	14.305	-2.514	-2.514	0.000	0.000	0.000	0.000
113	A	115	ALA	0	0.034	0.025	11.182	1.473	1.473	0.000	0.000	0.000	0.000
114	A	116	ILE	0	-0.025	-0.023	13.258	-0.294	-0.294	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.884	0.952	10.517	43.077	43.077	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.839	-0.921	14.206	-28.019	-28.019	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.040	0.025	17.672	-0.065	-0.065	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.904	0.952	17.463	30.820	30.820	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.031	0.000	14.787	-1.606	-1.606	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.020	0.000	10.885	-1.609	-1.609	0.000	0.000	0.000	0.000
121	A	123	SER	0	-0.033	-0.022	6.483	-0.049	-0.049	0.000	0.000	0.000	0.000
122	A	124	VAL	0	0.019	0.017	6.849	-2.634	-2.634	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.929	-0.967	8.777	-50.983	-50.983	0.000	0.000	0.000	0.000
129	A	131	THR	0	-0.020	-0.031	10.985	3.387	3.387	0.000	0.000	0.000	0.000
130	A	132	GLN	0	0.044	0.017	13.984	-1.325	-1.325	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.878	-0.935	16.464	-29.790	-29.790	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.785	-0.896	11.396	-44.405	-44.405	0.000	0.000	0.000	0.000
133	A	135	HIS	0	-0.025	-0.039	11.979	-3.021	-3.021	0.000	0.000	0.000	0.000
134	A	136	TRP	0	-0.058	-0.023	13.433	-0.225	-0.225	0.000	0.000	0.000	0.000
135	A	137	LEU	0	0.009	0.001	14.255	0.435	0.435	0.000	0.000	0.000	0.000
136	A	138	HIS	0	-0.004	-0.002	7.190	2.214	2.214	0.000	0.000	0.000	0.000
137	A	139	LYS	1	0.919	0.977	12.421	27.002	27.002	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.052	0.012	15.517	0.725	0.725	0.000	0.000	0.000	0.000
139	A	141	GLY	0	0.023	0.021	13.521	0.884	0.884	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.041	-0.009	14.096	-0.209	-0.209	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.880	-0.946	15.372	-25.535	-25.535	0.000	0.000	0.000	0.000
142	A	144	ARG	1	0.876	0.919	18.166	27.226	27.226	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.006	-0.002	15.470	0.876	0.876	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.975	-0.988	17.601	-28.883	-28.883	0.000	0.000	0.000	0.000
145	A	147	ASN	0	-0.023	-0.019	20.335	1.433	1.433	0.000	0.000	0.000	0.000
146	A	148	ARG	1	0.824	0.890	16.437	33.520	33.520	0.000	0.000	0.000	0.000
147	A	149	LYS	1	0.908	0.958	18.285	31.739	31.739	0.000	0.000	0.000	0.000
148	A	150	LYS	1	0.970	0.984	22.023	21.593	21.593	0.000	0.000	0.000	0.000
149	A	151	GLY	0	0.041	0.021	25.126	0.884	0.884	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.950	0.967	21.631	28.077	28.077	0.000	0.000	0.000	0.000
151	A	153	LEU	0	-0.050	-0.011	25.661	0.351	0.351	0.000	0.000	0.000	0.000
152	A	154	LYS	1	1.043	1.026	27.908	19.267	19.267	0.000	0.000	0.000	0.000
153	A	155	SER	0	-0.010	-0.007	28.612	0.745	0.745	0.000	0.000	0.000	0.000
154	A	156	LYS	1	0.894	0.952	26.471	22.882	22.882	0.000	0.000	0.000	0.000
155	A	157	GLU	-1	-0.833	-0.931	30.789	-18.733	-18.733	0.000	0.000	0.000	0.000
156	A	158	MET	0	0.009	0.006	33.677	0.400	0.400	0.000	0.000	0.000	0.000
157	A	159	ALA	0	0.002	0.000	32.792	0.427	0.427	0.000	0.000	0.000	0.000
158	A	160	GLU	-1	-0.928	-0.970	32.687	-18.457	-18.457	0.000	0.000	0.000	0.000
159	A	161	VAL	0	-0.035	-0.014	36.303	0.441	0.441	0.000	0.000	0.000	0.000
160	A	162	LEU	0	-0.013	-0.006	37.204	0.430	0.430	0.000	0.000	0.000	0.000
161	A	163	THR	0	-0.060	-0.032	36.525	0.288	0.288	0.000	0.000	0.000	0.000
162	A	164	LEU	0	-0.070	-0.049	37.412	0.229	0.229	0.000	0.000	0.000	0.000
163	A	165	SER	0	-0.016	0.007	40.947	0.409	0.409	0.000	0.000	0.000	0.000
164	A	166	LYS	1	0.911	0.980	37.730	16.674	16.674	0.000	0.000	0.000	0.000
165	A	167	PRO	0	0.024	-0.003	43.265	-0.002	-0.002	0.000	0.000	0.000	0.000
166	A	168	TRP	0	0.009	-0.011	39.754	-0.364	-0.364	0.000	0.000	0.000	0.000
167	A	169	ASN	0	-0.091	-0.030	41.384	-0.520	-0.520	0.000	0.000	0.000	0.000
168	A	170	ILE	-1	-0.908	-0.943	36.576	-15.921	-15.921	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)