FMO DATABASE

FMODB ID: GVVQ1

Calculation Name: 2O01-D-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: 2O01

Chain ID: D

ChEMBL ID:

UniProt ID: Q01667

Base Structure: X-ray

Registration Date: 2025-10-05

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1074306.174705
FMO2-HF: Nuclear repulsion	1020220.853961
FMO2-HF: Total energy	-54085.320743
FMO2-MP2: Total energy	-54244.004239

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:19:GLU)

Summations of interaction energy for fragment #1(A:19:GLU)

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.
-26.853	-31.696	5.987	3.12	-4.263	-0.064

Interaction energy analysis for fragmet #1(A:19:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.143 / q_NPA : -0.054

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	21	ASP	-1	-0.874	-0.926	2.186	-16.909	-24.475	4.775	5.124	-2.333	-0.035
4	A	22	PRO	0	0.083	0.023	2.379	-12.618	-9.895	1.212	-2.004	-1.930	-0.029
5	A	23	ASN	0	-0.155	-0.075	5.945	1.697	1.697	0.000	0.000	0.000	0.000
6	A	24	THR	0	0.066	0.020	7.984	-0.595	-0.595	0.000	0.000	0.000	0.000
7	A	25	PRO	0	-0.003	0.013	10.268	0.643	0.643	0.000	0.000	0.000	0.000
8	A	26	SER	0	-0.050	-0.057	13.318	-0.075	-0.075	0.000	0.000	0.000	0.000
9	A	27	PRO	0	0.051	-0.006	16.094	0.138	0.138	0.000	0.000	0.000	0.000
10	A	28	ILE	0	-0.004	0.027	12.745	-0.106	-0.106	0.000	0.000	0.000	0.000
11	A	29	PHE	0	0.035	0.008	14.926	0.118	0.118	0.000	0.000	0.000	0.000
12	A	30	ALA	0	0.015	0.018	12.592	0.070	0.070	0.000	0.000	0.000	0.000
13	A	31	GLY	0	-0.003	0.004	13.265	0.109	0.109	0.000	0.000	0.000	0.000
14	A	32	SER	0	0.021	0.006	13.901	0.147	0.147	0.000	0.000	0.000	0.000
15	A	33	THR	0	0.078	0.025	17.392	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	34	GLY	0	-0.009	0.012	18.981	0.080	0.080	0.000	0.000	0.000	0.000
17	A	35	GLY	0	-0.015	-0.025	20.155	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	36	LEU	0	-0.060	-0.017	15.332	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	37	LEU	0	0.040	0.022	17.251	0.026	0.026	0.000	0.000	0.000	0.000
20	A	38	ARG	1	0.969	0.964	14.107	-1.739	-1.739	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.855	0.921	17.022	-0.506	-0.506	0.000	0.000	0.000	0.000
22	A	40	ALA	0	0.039	0.032	19.429	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	41	GLN	0	-0.001	0.005	15.540	-0.139	-0.139	0.000	0.000	0.000	0.000
24	A	42	VAL	0	0.023	0.012	18.402	0.041	0.041	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.877	-0.935	21.554	0.516	0.516	0.000	0.000	0.000	0.000
26	A	44	GLU	-1	-0.758	-0.872	24.222	0.092	0.092	0.000	0.000	0.000	0.000
27	A	45	PHE	0	-0.074	-0.044	16.247	0.050	0.050	0.000	0.000	0.000	0.000
28	A	46	TYR	0	-0.002	-0.009	21.278	-0.096	-0.096	0.000	0.000	0.000	0.000
29	A	47	VAL	0	-0.014	-0.009	17.717	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	48	ILE	0	-0.049	-0.020	20.312	0.062	0.062	0.000	0.000	0.000	0.000
31	A	49	THR	0	0.009	-0.027	19.980	-0.085	-0.085	0.000	0.000	0.000	0.000
32	A	50	TRP	0	0.051	-0.002	22.225	0.067	0.067	0.000	0.000	0.000	0.000
33	A	51	GLU	-1	-0.830	-0.885	22.786	-0.744	-0.744	0.000	0.000	0.000	0.000
34	A	52	SER	0	0.003	-0.023	21.883	0.058	0.058	0.000	0.000	0.000	0.000
35	A	53	PRO	0	-0.031	-0.022	24.318	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	54	LYS	1	0.942	0.976	25.179	0.954	0.954	0.000	0.000	0.000	0.000
37	A	55	GLU	-1	-0.816	-0.921	19.380	-1.774	-1.774	0.000	0.000	0.000	0.000
38	A	56	GLN	0	-0.089	-0.052	22.886	0.013	0.013	0.000	0.000	0.000	0.000
39	A	57	ILE	0	0.029	0.023	22.123	0.046	0.046	0.000	0.000	0.000	0.000
40	A	58	PHE	0	-0.043	-0.027	22.559	0.109	0.109	0.000	0.000	0.000	0.000
41	A	59	GLU	-1	-0.839	-0.910	24.064	-0.516	-0.516	0.000	0.000	0.000	0.000
42	A	60	MET	0	-0.010	-0.013	18.189	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	61	PRO	0	0.004	-0.010	22.514	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	62	THR	0	-0.070	-0.018	18.532	0.026	0.026	0.000	0.000	0.000	0.000
45	A	63	GLY	0	0.070	0.031	21.829	0.042	0.042	0.000	0.000	0.000	0.000
46	A	64	GLY	0	-0.045	-0.015	20.461	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	65	ALA	0	-0.026	-0.010	21.230	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	66	ALA	0	-0.037	-0.028	19.194	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	67	ILE	0	0.005	0.023	17.321	0.113	0.113	0.000	0.000	0.000	0.000
50	A	68	MET	0	-0.051	0.019	18.856	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	69	ARG	1	0.964	0.971	13.474	2.421	2.421	0.000	0.000	0.000	0.000
52	A	70	GLU	-1	-0.809	-0.896	20.304	-1.318	-1.318	0.000	0.000	0.000	0.000
53	A	71	GLY	0	0.002	0.023	18.404	0.030	0.030	0.000	0.000	0.000	0.000
54	A	72	PRO	0	-0.033	0.007	16.295	0.121	0.121	0.000	0.000	0.000	0.000
55	A	73	ASN	0	-0.094	-0.088	18.238	0.042	0.042	0.000	0.000	0.000	0.000
56	A	74	LEU	0	0.006	0.009	14.440	0.071	0.071	0.000	0.000	0.000	0.000
57	A	75	LEU	0	-0.001	-0.003	14.106	-0.255	-0.255	0.000	0.000	0.000	0.000
58	A	76	LYS	1	0.964	0.980	11.003	0.880	0.880	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.012	-0.036	17.171	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	78	ALA	0	0.057	0.035	20.212	0.024	0.024	0.000	0.000	0.000	0.000
61	A	79	ARG	1	0.842	0.904	22.214	0.078	0.078	0.000	0.000	0.000	0.000
62	A	80	LYS	1	0.912	0.951	25.742	0.016	0.016	0.000	0.000	0.000	0.000
63	A	81	GLU	-1	-0.818	-0.877	27.257	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	82	GLN	0	0.031	0.002	22.830	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	83	CYS	0	-0.013	0.034	24.925	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	84	LEU	0	0.047	0.029	26.602	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	85	ALA	0	0.038	0.042	28.995	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	86	LEU	0	0.031	0.011	23.067	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	87	GLY	0	0.018	-0.026	27.238	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	88	THR	0	-0.028	-0.040	28.826	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	89	ARG	1	0.831	0.934	26.966	0.464	0.464	0.000	0.000	0.000	0.000
72	A	90	LEU	0	-0.048	-0.017	25.633	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	91	ARG	1	0.899	0.968	29.799	0.437	0.437	0.000	0.000	0.000	0.000
74	A	92	SER	0	0.044	0.017	33.433	0.003	0.003	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.865	0.927	28.901	0.530	0.530	0.000	0.000	0.000	0.000
76	A	94	TYR	0	0.040	0.012	32.674	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	95	LYS	1	0.861	0.963	29.153	0.642	0.642	0.000	0.000	0.000	0.000
78	A	96	ILE	0	0.074	0.021	30.370	0.040	0.040	0.000	0.000	0.000	0.000
79	A	97	LYS	1	0.826	0.898	27.296	0.563	0.563	0.000	0.000	0.000	0.000
80	A	98	TYR	0	0.000	0.002	27.014	-0.043	-0.043	0.000	0.000	0.000	0.000
81	A	99	GLN	0	0.013	0.018	25.138	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	100	PHE	0	-0.021	-0.019	24.278	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	101	TYR	0	0.017	0.010	22.238	0.022	0.022	0.000	0.000	0.000	0.000
84	A	102	ARG	1	0.739	0.841	22.830	-0.249	-0.249	0.000	0.000	0.000	0.000
85	A	103	VAL	0	-0.033	-0.002	18.456	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	104	PHE	0	0.062	0.003	20.629	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	105	PRO	0	-0.017	0.015	19.067	0.008	0.008	0.000	0.000	0.000	0.000
88	A	106	SER	0	0.018	-0.002	20.628	0.020	0.020	0.000	0.000	0.000	0.000
89	A	107	GLY	0	-0.078	-0.053	20.846	-0.060	-0.060	0.000	0.000	0.000	0.000
90	A	108	GLU	-1	-0.728	-0.819	22.363	0.233	0.233	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.058	0.039	25.855	-0.056	-0.056	0.000	0.000	0.000	0.000
92	A	110	GLN	0	0.015	0.004	26.614	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	111	TYR	0	-0.035	0.003	27.605	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	112	LEU	0	0.026	-0.030	29.543	0.021	0.021	0.000	0.000	0.000	0.000
95	A	113	HIS	0	-0.015	0.019	28.976	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	114	PRO	0	0.042	0.014	27.925	-0.026	-0.026	0.000	0.000	0.000	0.000
97	A	115	LYS	1	0.847	0.941	29.332	0.127	0.127	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.760	-0.880	31.767	-0.154	-0.154	0.000	0.000	0.000	0.000
99	A	117	GLY	0	0.012	0.005	32.939	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	118	VAL	0	-0.122	-0.061	33.822	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	119	TYR	0	0.040	0.005	35.578	0.002	0.002	0.000	0.000	0.000	0.000
102	A	120	PRO	0	-0.018	0.004	35.764	0.003	0.003	0.000	0.000	0.000	0.000
103	A	121	GLU	-1	-0.886	-0.933	38.714	-0.184	-0.184	0.000	0.000	0.000	0.000
104	A	122	LYS	1	0.947	0.984	39.730	0.215	0.215	0.000	0.000	0.000	0.000
105	A	123	VAL	0	-0.007	0.011	41.620	0.000	0.000	0.000	0.000	0.000	0.000
106	A	124	ASN	0	0.033	-0.017	41.760	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	125	PRO	0	-0.013	0.022	41.444	0.004	0.004	0.000	0.000	0.000	0.000
108	A	126	GLY	0	0.057	0.033	44.637	0.006	0.006	0.000	0.000	0.000	0.000
109	A	127	ARG	1	0.806	0.877	40.611	0.117	0.117	0.000	0.000	0.000	0.000
110	A	128	GLN	0	0.029	0.017	40.890	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	129	GLY	0	0.037	0.018	46.028	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	130	VAL	0	-0.014	-0.016	45.190	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	131	GLY	0	-0.007	0.005	48.309	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	132	LEU	0	-0.009	-0.011	50.016	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	133	ASN	0	0.047	0.032	52.247	0.004	0.004	0.000	0.000	0.000	0.000
116	A	134	MET	0	0.042	0.035	55.077	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	135	ARG	1	0.889	0.936	58.220	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	136	SER	0	0.055	0.002	57.624	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	137	ILE	0	-0.039	-0.025	55.631	0.000	0.000	0.000	0.000	0.000	0.000
120	A	138	GLY	0	0.047	0.023	58.386	0.004	0.004	0.000	0.000	0.000	0.000
121	A	139	LYS	0	-0.006	0.050	61.604	0.001	0.001	0.000	0.000	0.000	0.000
122	A	140	ASN	0	-0.071	-0.053	58.689	0.001	0.001	0.000	0.000	0.000	0.000
123	A	141	VAL	0	0.026	0.007	61.730	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	142	SER	0	0.017	-0.004	61.766	0.001	0.001	0.000	0.000	0.000	0.000
125	A	143	PRO	0	-0.020	0.013	58.609	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	144	ILE	0	0.019	0.002	60.861	0.005	0.005	0.000	0.000	0.000	0.000
127	A	145	GLU	-1	-0.953	-0.980	61.246	0.046	0.046	0.000	0.000	0.000	0.000
128	A	146	VAL	0	0.037	0.007	57.564	0.003	0.003	0.000	0.000	0.000	0.000
129	A	147	LYS	1	0.890	0.942	59.537	-0.061	-0.061	0.000	0.000	0.000	0.000
130	A	148	PHE	0	0.010	0.001	58.630	0.000	0.000	0.000	0.000	0.000	0.000
131	A	149	THR	0	-0.010	0.007	55.811	0.001	0.001	0.000	0.000	0.000	0.000
132	A	150	GLY	0	0.087	0.045	56.083	0.006	0.006	0.000	0.000	0.000	0.000
133	A	151	LYS	1	0.853	0.923	54.710	-0.098	-0.098	0.000	0.000	0.000	0.000
134	A	152	GLN	0	-0.053	-0.025	55.602	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	153	PRO	0	0.042	0.021	54.686	0.006	0.006	0.000	0.000	0.000	0.000
136	A	154	TYR	0	0.035	0.032	50.367	0.006	0.006	0.000	0.000	0.000	0.000
137	A	155	ASP	-1	-0.921	-0.966	49.812	0.098	0.098	0.000	0.000	0.000	0.000
138	A	156	LEU	-1	-1.009	-0.997	51.740	0.058	0.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLU)