FMO DATABASE

FMODB ID: Y7Y22

Calculation Name: 6ZOO-P-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 | (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 | 1,2-diacyl-glycerol-3-sn-phosphate | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | (2~{r})-2-azanyl-3-(4-ethanoylsulfanyl-1~{h}-imidazol-5-yl)propanoic acid | calcium ion | copper (ii) ion

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

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6ZOO

Chain ID: P

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-658423.450776
FMO2-HF: Nuclear repulsion	621911.87245
FMO2-HF: Total energy	-36511.578326
FMO2-MP2: Total energy	-36617.544301

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:VAL)

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

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.
-264.928	-262.811	33.793	-17.441	-18.47	-0.172

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.754 / q_NPA : 0.853

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	VAL	0	-0.002	0.011	3.016	-0.562	2.267	0.224	-1.320	-1.733	-0.006
4	A	4	LEU	0	-0.046	-0.012	5.228	2.195	2.223	-0.001	-0.003	-0.024	0.000
19	A	19	LEU	0	-0.014	-0.014	2.147	-2.231	-3.520	4.516	-0.682	-2.546	-0.001
21	A	21	VAL	0	-0.043	-0.021	2.363	-4.483	-4.145	1.563	-0.382	-1.519	-0.001
22	A	22	SER	0	0.011	0.014	4.711	3.352	3.387	-0.001	-0.008	-0.026	0.000
25	A	25	GLU	-1	-0.848	-0.901	1.726	-114.662	-115.178	15.539	-8.906	-6.117	-0.101
26	A	26	THR	0	-0.107	-0.047	3.723	8.119	8.713	0.000	-0.264	-0.331	-0.001
27	A	27	ILE	0	0.015	0.011	1.828	-43.771	-44.513	11.938	-5.695	-5.501	-0.062
28	A	28	VAL	0	-0.017	-0.011	3.415	9.930	10.770	0.015	-0.181	-0.673	0.000
5	A	5	LEU	0	-0.007	-0.002	8.911	0.816	0.816	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.057	0.031	11.952	1.178	1.178	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.002	-0.006	13.726	-0.943	-0.943	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.001	-0.015	15.281	0.408	0.408	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.956	-0.979	17.534	-14.064	-14.064	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.022	-0.004	19.150	0.661	0.661	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.029	-0.009	18.583	0.140	0.140	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.014	0.002	16.767	-0.972	-0.972	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.021	0.006	13.951	0.231	0.231	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.016	0.018	8.959	-0.517	-0.517	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.037	0.001	8.922	1.287	1.287	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.002	-0.010	4.843	-2.255	-2.255	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.006	-0.005	7.548	-1.082	-1.082	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.000	0.003	9.361	0.310	0.310	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.885	-0.951	5.998	-25.587	-25.587	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.006	-0.017	6.401	-3.774	-3.774	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.049	-0.036	8.793	0.822	0.822	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.049	0.022	5.456	-2.604	-2.604	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.880	0.938	7.951	28.867	28.867	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.013	-0.011	10.378	0.184	0.184	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.059	-0.033	12.611	-0.867	-0.867	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.001	-0.001	14.670	1.237	1.237	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.011	0.005	17.128	-0.471	-0.471	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.029	0.027	17.315	0.157	0.157	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.013	-0.030	19.106	0.730	0.730	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.031	-0.019	15.072	0.633	0.633	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.009	-0.031	15.645	0.522	0.522	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.027	-0.015	9.874	-0.501	-0.501	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.007	0.009	13.163	0.133	0.133	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.003	-0.037	8.171	-1.282	-1.282	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.879	-0.959	14.149	-14.804	-14.804	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-1.000	-0.975	16.959	-12.531	-12.531	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.878	-0.940	19.039	-12.417	-12.417	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.998	-1.004	17.384	-16.780	-16.780	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.049	0.041	14.639	-1.253	-1.253	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.029	-0.010	13.914	1.041	1.041	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.034	-0.017	17.209	-0.110	-0.110	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.026	-0.024	19.157	0.754	0.754	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.059	-0.029	14.032	-0.461	-0.461	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.774	-0.850	17.470	-15.799	-15.799	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.121	0.049	17.111	-0.916	-0.916	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.061	-0.042	16.869	-0.625	-0.625	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.838	0.902	15.121	15.925	15.925	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.016	-0.010	11.688	-1.438	-1.438	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.027	0.009	12.473	-1.663	-1.663	0.000	0.000	0.000	0.000
57	A	57	MET	0	-0.010	0.029	14.548	-0.316	-0.316	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.021	-0.028	16.642	0.473	0.473	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.942	-0.968	19.877	-12.637	-12.637	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.978	-0.984	21.677	-11.285	-11.285	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.943	-0.971	19.663	-15.586	-15.586	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.051	-0.039	18.647	-0.471	-0.471	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.026	0.023	12.907	0.160	0.160	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.018	-0.020	17.360	1.020	1.020	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.005	-0.012	18.094	-0.743	-0.743	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.011	-0.003	18.077	-0.630	-0.630	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.033	-0.018	14.800	-0.959	-0.959	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.872	-0.920	14.395	-18.527	-18.527	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.029	-0.034	9.127	-0.435	-0.435	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.015	0.009	9.948	1.501	1.501	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.022	-0.013	7.320	-4.526	-4.526	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.019	0.013	6.764	3.911	3.911	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.857	0.920	6.488	27.664	27.664	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.010	0.008	6.029	-1.263	-1.263	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.816	-0.888	8.502	-28.746	-28.746	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.004	-0.001	10.396	2.236	2.236	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.781	0.886	12.125	20.885	20.885	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.026	0.018	12.432	1.387	1.387	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.013	-0.007	11.245	-2.442	-2.442	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.081	0.027	9.723	0.645	0.645	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.838	0.911	11.155	15.316	15.316	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.011	0.005	7.856	-0.238	-0.238	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.013	-0.011	12.703	0.221	0.221	0.000	0.000	0.000	0.000
84	A	84	CYS	-1	-0.747	-0.762	14.774	-17.756	-17.756	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.040	0.022	16.220	0.952	0.952	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.008	-0.002	18.872	0.607	0.607	0.000	0.000	0.000	0.000
87	A	87	HIS	1	0.806	0.831	17.937	16.166	16.166	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.029	0.039	18.889	0.335	0.335	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.001	-0.005	19.867	0.144	0.144	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.077	-0.042	21.101	0.508	0.508	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.008	0.000	19.431	-0.065	-0.065	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.034	0.006	13.547	-0.368	-0.368	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.010	-0.023	14.857	-0.190	-0.190	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.016	0.002	11.086	-0.199	-0.199	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.043	-0.013	10.308	2.130	2.130	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.005	0.000	4.828	-2.106	-2.106	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.040	-0.017	7.163	2.607	2.607	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.010	0.009	6.817	-2.434	-2.434	0.000	0.000	0.000	0.000
99	A	99	ASN	-1	-0.807	-0.903	8.857	-22.081	-22.081	0.000	0.000	0.000	0.000

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