FMO DATABASE

FMODB ID: 9QK32

Calculation Name: 6FOS-F-Xray547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | beta-carotene | phylloquinone | iron/sulfur cluster

Ligand 3-letter code: CLA | BCR | PQN | SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6FOS

Chain ID: F

ChEMBL ID:

UniProt ID: Q85FY7

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1183744.5258
FMO2-HF: Nuclear repulsion	1121798.520324
FMO2-HF: Total energy	-61946.005475
FMO2-MP2: Total energy	-62127.849562

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(F:31:LEU)

Summations of interaction energy for fragment #1(F:31:LEU)

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.
-47.449	-42.185	7.796	-4.875	-8.184	-0.033

Interaction energy analysis for fragmet #1(F:31:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.910

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	F	33	PRO	0	0.093	0.039	3.859	-0.049	1.602	-0.019	-0.674	-0.958	0.000
4	F	34	CYS	0	-0.012	0.000	4.602	2.201	2.381	-0.002	-0.018	-0.159	0.000
56	F	86	LEU	0	-0.021	-0.007	2.929	-2.714	-1.911	0.211	-0.219	-0.795	-0.002
57	F	88	GLY	0	0.055	0.028	2.113	-12.339	-10.834	2.250	-2.027	-1.728	-0.021
58	F	89	GLN	0	0.033	0.021	1.807	-6.278	-7.419	4.826	-0.987	-2.698	-0.001
59	F	90	ASP	-1	-0.846	-0.931	3.823	-31.022	-30.788	0.009	-0.054	-0.190	0.000
63	F	94	HIS	0	0.007	0.000	2.581	-7.064	-5.032	0.521	-0.896	-1.656	-0.009
5	F	35	GLN	0	0.071	0.030	8.176	0.517	0.517	0.000	0.000	0.000	0.000
6	F	36	GLN	0	-0.012	-0.014	8.558	0.749	0.749	0.000	0.000	0.000	0.000
7	F	37	SER	0	-0.009	0.021	5.911	0.689	0.689	0.000	0.000	0.000	0.000
8	F	38	GLU	-1	-0.824	-0.924	7.774	-26.209	-26.209	0.000	0.000	0.000	0.000
9	F	39	ALA	0	-0.062	-0.035	7.728	2.165	2.165	0.000	0.000	0.000	0.000
10	F	40	PHE	0	0.016	0.006	7.583	1.006	1.006	0.000	0.000	0.000	0.000
11	F	41	HIS	0	0.027	0.014	9.279	2.742	2.742	0.000	0.000	0.000	0.000
12	F	42	LYS	1	0.883	0.948	10.446	25.070	25.070	0.000	0.000	0.000	0.000
13	F	43	ARG	1	0.839	0.915	9.405	24.613	24.613	0.000	0.000	0.000	0.000
14	F	44	GLU	-1	-0.856	-0.910	13.725	-14.300	-14.300	0.000	0.000	0.000	0.000
15	F	45	ILE	0	0.072	0.028	16.052	0.914	0.914	0.000	0.000	0.000	0.000
16	F	46	ASN	0	-0.020	-0.012	16.733	1.410	1.410	0.000	0.000	0.000	0.000
17	F	47	GLU	-1	-0.941	-0.957	17.246	-13.559	-13.559	0.000	0.000	0.000	0.000
18	F	48	VAL	0	0.060	0.022	19.072	0.828	0.828	0.000	0.000	0.000	0.000
19	F	49	ARG	1	0.938	0.979	21.283	12.252	12.252	0.000	0.000	0.000	0.000
20	F	50	THR	0	-0.052	-0.041	21.019	0.601	0.601	0.000	0.000	0.000	0.000
21	F	51	LEU	0	-0.038	-0.013	23.314	0.542	0.542	0.000	0.000	0.000	0.000
22	F	52	GLU	-1	-0.847	-0.937	25.190	-10.019	-10.019	0.000	0.000	0.000	0.000
23	F	53	ASN	0	-0.014	-0.009	26.626	0.540	0.540	0.000	0.000	0.000	0.000
24	F	54	ARG	1	0.919	0.959	28.082	10.295	10.295	0.000	0.000	0.000	0.000
25	F	55	GLN	0	-0.079	-0.033	28.306	0.158	0.158	0.000	0.000	0.000	0.000
26	F	56	ALA	0	0.016	-0.004	31.010	0.282	0.282	0.000	0.000	0.000	0.000
27	F	57	ASN	0	-0.080	-0.038	32.625	0.397	0.397	0.000	0.000	0.000	0.000
28	F	58	TYR	0	-0.018	0.007	34.778	0.273	0.273	0.000	0.000	0.000	0.000
29	F	59	GLU	-1	-0.882	-0.938	36.708	-7.598	-7.598	0.000	0.000	0.000	0.000
30	F	60	ALA	0	0.018	0.002	35.583	0.052	0.052	0.000	0.000	0.000	0.000
31	F	61	ASN	0	-0.023	-0.015	37.196	-0.119	-0.119	0.000	0.000	0.000	0.000
32	F	62	SER	0	-0.012	0.005	39.737	0.231	0.231	0.000	0.000	0.000	0.000
33	F	63	PRO	0	0.019	0.004	39.248	-0.213	-0.213	0.000	0.000	0.000	0.000
34	F	64	SER	0	-0.034	-0.021	39.077	-0.080	-0.080	0.000	0.000	0.000	0.000
35	F	65	TYR	0	0.007	-0.009	35.028	-0.082	-0.082	0.000	0.000	0.000	0.000
36	F	66	LEU	0	0.031	0.028	34.548	-0.268	-0.268	0.000	0.000	0.000	0.000
37	F	67	ALA	0	0.009	0.012	33.834	-0.203	-0.203	0.000	0.000	0.000	0.000
38	F	68	LEU	0	-0.005	0.020	28.637	-0.311	-0.311	0.000	0.000	0.000	0.000
39	F	69	GLN	0	0.069	0.020	29.262	-0.316	-0.316	0.000	0.000	0.000	0.000
40	F	70	SER	0	-0.029	-0.026	29.330	-0.265	-0.265	0.000	0.000	0.000	0.000
41	F	71	GLN	0	0.014	0.010	26.166	-0.082	-0.082	0.000	0.000	0.000	0.000
42	F	72	ILE	0	0.022	-0.005	23.224	-0.574	-0.574	0.000	0.000	0.000	0.000
43	F	73	ASP	-1	-0.844	-0.926	24.149	-11.437	-11.437	0.000	0.000	0.000	0.000
44	F	74	GLN	0	-0.089	-0.051	24.539	-0.476	-0.476	0.000	0.000	0.000	0.000
45	F	75	VAL	0	-0.059	-0.013	19.762	-0.585	-0.585	0.000	0.000	0.000	0.000
46	F	76	HIS	1	0.889	0.932	19.753	12.552	12.552	0.000	0.000	0.000	0.000
47	F	77	LYS	1	0.829	0.929	19.930	10.835	10.835	0.000	0.000	0.000	0.000
48	F	78	ARG	1	0.956	0.999	17.043	15.027	15.027	0.000	0.000	0.000	0.000
49	F	79	PHE	0	0.002	-0.017	13.674	-0.858	-0.858	0.000	0.000	0.000	0.000
50	F	80	ASP	-1	-0.830	-0.916	14.121	-16.800	-16.800	0.000	0.000	0.000	0.000
51	F	81	LYS	1	0.908	0.952	15.118	13.589	13.589	0.000	0.000	0.000	0.000
52	F	82	TYR	0	0.017	0.016	9.639	0.388	0.388	0.000	0.000	0.000	0.000
53	F	83	GLY	0	0.013	0.012	10.486	-1.850	-1.850	0.000	0.000	0.000	0.000
54	F	84	THR	0	-0.096	-0.053	10.634	-0.919	-0.919	0.000	0.000	0.000	0.000
55	F	85	LEU	0	-0.034	-0.002	9.361	0.007	0.007	0.000	0.000	0.000	0.000
60	F	91	GLY	0	0.002	-0.001	5.613	4.305	4.305	0.000	0.000	0.000	0.000
61	F	92	LEU	0	-0.080	-0.037	6.257	3.303	3.303	0.000	0.000	0.000	0.000
62	F	93	PRO	0	-0.045	-0.027	5.852	-3.956	-3.956	0.000	0.000	0.000	0.000
64	F	95	LEU	0	0.013	0.013	6.246	1.266	1.266	0.000	0.000	0.000	0.000
65	F	96	ILE	0	-0.033	-0.016	6.686	-1.555	-1.555	0.000	0.000	0.000	0.000
66	F	97	THR	0	-0.025	-0.024	9.902	2.095	2.095	0.000	0.000	0.000	0.000
67	F	98	ASP	-1	-0.897	-0.949	11.548	-22.609	-22.609	0.000	0.000	0.000	0.000
68	F	99	GLY	0	0.001	-0.003	14.341	0.895	0.895	0.000	0.000	0.000	0.000
69	F	100	ASP	-1	-0.825	-0.876	12.003	-22.767	-22.767	0.000	0.000	0.000	0.000
70	F	101	TRP	0	0.041	0.001	14.323	-0.093	-0.093	0.000	0.000	0.000	0.000
71	F	102	ARG	1	0.789	0.872	10.225	26.685	26.685	0.000	0.000	0.000	0.000
72	F	103	HIS	0	-0.041	-0.039	8.411	-1.249	-1.249	0.000	0.000	0.000	0.000
73	F	104	ALA	0	0.015	0.026	13.014	0.463	0.463	0.000	0.000	0.000	0.000
74	F	105	ARG	1	0.923	0.944	15.812	17.967	17.967	0.000	0.000	0.000	0.000
75	F	106	GLU	-1	-0.787	-0.879	10.379	-25.854	-25.854	0.000	0.000	0.000	0.000
76	F	107	PHE	0	0.021	0.004	14.738	0.393	0.393	0.000	0.000	0.000	0.000
77	F	108	THR	0	0.025	0.005	16.644	0.731	0.731	0.000	0.000	0.000	0.000
78	F	109	ILE	0	0.029	0.016	19.390	0.772	0.772	0.000	0.000	0.000	0.000
79	F	110	PRO	0	-0.030	-0.004	19.522	0.537	0.537	0.000	0.000	0.000	0.000
80	F	111	ALA	0	0.018	-0.008	19.009	0.524	0.524	0.000	0.000	0.000	0.000
81	F	112	LEU	0	-0.002	0.029	19.951	0.416	0.416	0.000	0.000	0.000	0.000
82	F	113	LEU	0	0.038	0.011	22.227	0.635	0.635	0.000	0.000	0.000	0.000
83	F	114	PHE	0	0.009	0.007	25.031	0.472	0.472	0.000	0.000	0.000	0.000
84	F	115	LEU	0	0.019	0.049	24.584	0.469	0.469	0.000	0.000	0.000	0.000
85	F	116	TYR	0	0.007	-0.009	24.068	0.493	0.493	0.000	0.000	0.000	0.000
86	F	117	ILE	0	0.004	-0.001	28.234	0.403	0.403	0.000	0.000	0.000	0.000
87	F	118	THR	0	-0.032	-0.041	29.230	0.346	0.346	0.000	0.000	0.000	0.000
88	F	119	GLY	0	0.029	0.018	30.432	0.302	0.302	0.000	0.000	0.000	0.000
89	F	120	TRP	0	-0.015	-0.020	30.476	0.392	0.392	0.000	0.000	0.000	0.000
90	F	121	ILE	0	-0.004	0.007	33.942	0.264	0.264	0.000	0.000	0.000	0.000
91	F	122	GLY	0	0.028	0.021	35.329	0.272	0.272	0.000	0.000	0.000	0.000
92	F	123	TRP	0	-0.055	-0.045	32.132	0.370	0.370	0.000	0.000	0.000	0.000
93	F	124	VAL	0	0.041	0.025	36.988	0.190	0.190	0.000	0.000	0.000	0.000
94	F	125	GLY	0	0.041	0.042	39.400	0.228	0.228	0.000	0.000	0.000	0.000
95	F	126	ARG	1	0.921	0.953	37.998	7.956	7.956	0.000	0.000	0.000	0.000
96	F	127	SER	0	-0.047	-0.023	41.190	0.156	0.156	0.000	0.000	0.000	0.000
97	F	128	TYR	0	-0.019	-0.042	43.030	0.193	0.193	0.000	0.000	0.000	0.000
98	F	129	LEU	0	0.011	0.007	44.376	0.137	0.137	0.000	0.000	0.000	0.000
99	F	130	LYS	1	0.853	0.931	44.125	6.755	6.755	0.000	0.000	0.000	0.000
100	F	131	TYR	0	-0.011	-0.016	44.975	0.039	0.039	0.000	0.000	0.000	0.000
101	F	132	THR	0	-0.045	-0.008	49.353	0.080	0.080	0.000	0.000	0.000	0.000
102	F	133	LYS	1	0.933	0.974	49.421	5.953	5.953	0.000	0.000	0.000	0.000
103	F	134	GLU	-1	-0.893	-0.951	52.041	-5.699	-5.699	0.000	0.000	0.000	0.000
104	F	135	THR	0	0.012	0.005	55.138	0.128	0.128	0.000	0.000	0.000	0.000
105	F	136	LYS	1	0.915	0.942	58.223	4.954	4.954	0.000	0.000	0.000	0.000
106	F	137	ASN	0	-0.122	-0.046	56.752	0.095	0.095	0.000	0.000	0.000	0.000
107	F	138	PRO	0	0.055	0.026	58.478	-0.045	-0.045	0.000	0.000	0.000	0.000
108	F	139	THR	0	0.053	0.018	53.967	-0.045	-0.045	0.000	0.000	0.000	0.000
109	F	140	GLU	-1	-0.927	-0.960	53.191	-5.562	-5.562	0.000	0.000	0.000	0.000
110	F	141	GLN	0	-0.011	-0.016	53.458	-0.057	-0.057	0.000	0.000	0.000	0.000
111	F	142	GLU	-1	-0.801	-0.891	52.716	-5.760	-5.760	0.000	0.000	0.000	0.000
112	F	143	ILE	0	-0.090	-0.049	47.956	-0.171	-0.171	0.000	0.000	0.000	0.000
113	F	144	ILE	0	-0.043	-0.014	48.966	-0.134	-0.134	0.000	0.000	0.000	0.000
114	F	145	LEU	0	-0.075	-0.028	50.894	-0.054	-0.054	0.000	0.000	0.000	0.000
115	F	146	ASP	-1	-0.810	-0.905	50.028	-6.012	-6.012	0.000	0.000	0.000	0.000
116	F	147	VAL	0	-0.012	0.001	52.518	0.009	0.009	0.000	0.000	0.000	0.000
117	F	148	PRO	0	0.022	-0.006	50.778	-0.104	-0.104	0.000	0.000	0.000	0.000
118	F	149	MET	0	-0.035	-0.034	50.227	-0.150	-0.150	0.000	0.000	0.000	0.000
119	F	150	ALA	0	0.050	0.029	49.637	-0.082	-0.082	0.000	0.000	0.000	0.000
120	F	151	LEU	0	0.017	-0.005	46.073	-0.144	-0.144	0.000	0.000	0.000	0.000
121	F	152	LYS	1	0.883	0.948	45.763	6.212	6.212	0.000	0.000	0.000	0.000
122	F	153	TYR	0	0.032	0.016	46.708	-0.130	-0.130	0.000	0.000	0.000	0.000
123	F	154	MET	0	-0.003	0.006	42.276	-0.129	-0.129	0.000	0.000	0.000	0.000
124	F	155	LEU	0	-0.018	-0.010	41.805	-0.177	-0.177	0.000	0.000	0.000	0.000
125	F	156	SER	0	0.001	0.002	42.841	-0.061	-0.061	0.000	0.000	0.000	0.000
126	F	157	GLY	0	-0.007	-0.010	40.504	0.008	0.008	0.000	0.000	0.000	0.000
127	F	158	PHE	0	-0.040	-0.025	38.955	-0.227	-0.227	0.000	0.000	0.000	0.000
128	F	159	LEU	0	-0.024	-0.022	38.235	-0.221	-0.221	0.000	0.000	0.000	0.000
129	F	160	TRP	0	0.039	0.054	37.007	0.127	0.127	0.000	0.000	0.000	0.000
130	F	161	PRO	0	-0.020	0.003	34.959	0.095	0.095	0.000	0.000	0.000	0.000
131	F	162	LEU	0	0.033	0.001	37.284	0.022	0.022	0.000	0.000	0.000	0.000
132	F	163	SER	0	0.032	0.032	40.281	0.055	0.055	0.000	0.000	0.000	0.000
133	F	164	ALA	0	0.107	0.053	38.956	0.117	0.117	0.000	0.000	0.000	0.000
134	F	165	TRP	0	0.000	0.000	34.813	0.143	0.143	0.000	0.000	0.000	0.000
135	F	166	GLN	0	-0.095	-0.038	40.855	0.003	0.003	0.000	0.000	0.000	0.000
136	F	167	GLU	-1	-0.804	-0.880	43.994	-6.871	-6.871	0.000	0.000	0.000	0.000
137	F	168	TYR	0	0.028	-0.004	38.393	0.013	0.013	0.000	0.000	0.000	0.000
138	F	169	ARG	1	0.878	0.943	41.914	7.294	7.294	0.000	0.000	0.000	0.000
139	F	170	SER	0	-0.051	-0.040	45.249	0.142	0.142	0.000	0.000	0.000	0.000
140	F	171	GLY	0	0.009	0.003	46.345	0.122	0.122	0.000	0.000	0.000	0.000
141	F	172	GLN	0	0.033	0.001	41.992	0.140	0.140	0.000	0.000	0.000	0.000
142	F	173	LEU	0	-0.053	-0.020	46.768	0.098	0.098	0.000	0.000	0.000	0.000
143	F	174	LEU	0	-0.064	-0.047	50.028	0.139	0.139	0.000	0.000	0.000	0.000
144	F	175	ALA	0	-0.001	0.003	48.833	0.099	0.099	0.000	0.000	0.000	0.000
145	F	176	LYS	1	0.875	0.936	50.853	5.603	5.603	0.000	0.000	0.000	0.000
146	F	177	GLU	-1	-0.934	-0.944	49.445	-6.169	-6.169	0.000	0.000	0.000	0.000
147	F	178	ASP	-1	-0.934	-0.939	51.209	-5.610	-5.610	0.000	0.000	0.000	0.000
148	F	179	GLU	-1	-0.959	-1.000	47.909	-6.372	-6.372	0.000	0.000	0.000	0.000
149	F	180	ILE	0	-0.094	-0.048	47.825	0.122	0.122	0.000	0.000	0.000	0.000
150	F	181	THR	0	-0.020	-0.032	50.862	-0.070	-0.070	0.000	0.000	0.000	0.000
151	F	182	VAL	0	-0.081	-0.033	47.206	-0.035	-0.035	0.000	0.000	0.000	0.000
152	F	183	SER	-1	-0.898	-0.923	50.464	-5.808	-5.808	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(F:31:LEU)