FMO DATABASE

FMODB ID: 3ZYGL

Calculation Name: 6YAC-N-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (1~{s})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{s})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | fe2/s2 (inorganic) cluster | calcium ion

Ligand 3-letter code: CLA | CHL | CL0 | DGD | XAT | C7Z | LUT | BCR | LMG | LHG | LMT | PQN | SF4 | FES | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6YAC

Chain ID: N

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-659810.934273
FMO2-HF: Nuclear repulsion	622443.815546
FMO2-HF: Total energy	-37367.118727
FMO2-MP2: Total energy	-37472.982525

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:1:ALA)

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

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.
-338.639	-333.447	11.461	-7.681	-8.97	-0.094

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.773 / q_NPA : 0.881

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	3	TYR	0	-0.038	-0.006	2.357	-22.054	-21.465	9.830	-4.555	-5.864	-0.051
4	A	4	LYS	1	0.853	0.937	4.971	29.460	29.534	-0.001	-0.009	-0.063	0.000
19	A	19	PRO	0	-0.055	-0.031	4.036	-9.660	-9.424	0.001	-0.140	-0.097	0.000
20	A	20	SER	0	0.004	-0.018	2.207	-17.645	-13.643	1.634	-2.908	-2.728	-0.043
21	A	21	ASP	-1	-0.956	-0.967	4.213	-35.629	-35.402	-0.001	-0.062	-0.164	0.000
82	A	82	THR	0	0.040	0.010	4.759	-12.848	-12.857	-0.001	-0.006	0.017	0.000
83	A	83	SER	0	-0.050	-0.024	5.161	-6.090	-6.017	-0.001	-0.001	-0.071	0.000
5	A	5	VAL	0	0.001	-0.007	8.733	-0.437	-0.437	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.847	0.934	11.078	22.223	22.223	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.019	0.010	14.614	-0.055	-0.055	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.005	-0.005	17.346	0.723	0.723	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.014	-0.010	20.819	-0.137	-0.137	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.031	-0.031	23.228	0.318	0.318	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.897	-0.936	24.585	-12.387	-12.387	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.011	0.000	24.776	0.282	0.282	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.080	-0.048	19.205	-0.250	-0.250	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.057	-0.029	18.763	0.367	0.367	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.785	-0.905	14.057	-21.718	-21.718	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.016	0.002	11.371	1.150	1.150	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.905	-0.957	7.417	-38.304	-38.304	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.006	-0.001	7.215	3.328	3.328	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.029	-0.011	7.166	4.976	4.976	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.019	0.004	9.069	-2.078	-2.078	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.007	-0.003	10.843	0.032	0.032	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.034	-0.010	12.253	0.495	0.495	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.824	-0.917	14.027	-18.684	-18.684	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.029	0.003	9.060	1.109	1.109	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.019	0.000	13.379	0.384	0.384	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.858	-0.920	16.113	-14.472	-14.472	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.990	-0.984	14.146	-19.149	-19.149	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.082	-0.046	14.784	0.632	0.632	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.027	0.003	17.616	0.882	0.882	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.089	-0.041	17.833	0.760	0.760	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.898	-0.958	20.062	-13.345	-13.345	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.019	-0.021	17.710	-0.095	-0.095	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.047	-0.002	22.239	0.275	0.275	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.033	0.000	21.852	-0.456	-0.456	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.012	-0.015	23.869	0.583	0.583	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.109	-0.073	23.844	-0.172	-0.172	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.780	0.861	18.306	16.078	16.078	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.038	0.008	20.411	-0.557	-0.557	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.050	0.028	20.878	0.269	0.269	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.020	-0.028	21.391	0.429	0.429	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.030	0.017	24.559	0.543	0.543	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.065	0.036	24.372	-0.624	-0.624	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.007	-0.014	25.256	-0.203	-0.203	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.081	-0.037	20.079	0.119	0.119	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.009	0.023	20.085	-0.955	-0.955	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.033	0.007	19.095	0.151	0.151	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.890	0.957	19.372	14.795	14.795	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.000	0.018	14.671	-0.353	-0.353	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.041	-0.018	17.149	0.978	0.978	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.059	-0.043	15.337	0.646	0.646	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.013	0.006	11.648	-1.451	-1.451	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.964	-0.984	11.303	-25.116	-25.116	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.011	-0.012	10.186	-2.899	-2.899	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.875	-0.925	9.415	-24.686	-24.686	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.050	-0.005	11.311	-0.943	-0.943	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.020	-0.014	13.857	1.553	1.553	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.964	-0.980	15.280	-16.497	-16.497	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.002	0.011	17.128	0.350	0.350	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.059	-0.040	18.931	0.740	0.740	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.051	-0.037	22.756	0.078	0.078	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.019	0.017	21.046	0.016	0.016	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.892	-0.939	25.165	-10.476	-10.476	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.955	-0.983	25.287	-11.957	-11.957	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.888	-0.948	25.509	-12.071	-12.071	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.002	-0.007	23.225	-0.882	-0.882	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.037	-0.024	17.883	-0.595	-0.595	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-1.005	-0.996	19.403	-14.060	-14.060	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.034	-0.018	21.956	0.028	0.028	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.063	-0.030	19.605	0.147	0.147	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.023	0.010	19.608	-0.577	-0.577	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.000	0.001	14.810	-0.505	-0.505	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.026	0.016	17.904	0.595	0.595	0.000	0.000	0.000	0.000
76	A	76	THR	0	0.035	-0.004	15.494	-0.834	-0.834	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.034	-0.011	14.943	-0.848	-0.848	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.002	0.011	15.408	0.227	0.227	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.006	0.017	12.831	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.023	0.022	7.827	-0.183	-0.183	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.016	0.013	5.953	0.232	0.232	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.898	-0.939	6.441	-30.265	-30.265	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.011	0.009	8.174	2.522	2.522	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.068	-0.040	10.999	0.811	0.811	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.029	0.014	12.174	0.263	0.263	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.858	-0.929	16.581	-15.435	-15.435	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.015	-0.009	18.742	-0.529	-0.529	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.021	-0.009	21.270	0.259	0.259	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.757	0.897	22.357	13.340	13.340	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.798	-0.889	24.856	-11.396	-11.396	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.910	-0.946	27.022	-10.345	-10.345	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.824	-0.904	26.893	-11.932	-11.932	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.056	-0.021	24.788	-0.135	-0.135	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.103	-0.081	27.574	0.135	0.135	0.000	0.000	0.000	0.000
97	A	97	ALA	-1	-1.002	-0.983	30.715	-8.919	-8.919	0.000	0.000	0.000	0.000

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