FMO DATABASE

FMODB ID: G7GY1

Calculation Name: 1JBO-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phycocyanobilin | n-methyl asparagine

Ligand 3-letter code: CYC | MEN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JBO

Chain ID: A

ChEMBL ID:

UniProt ID: P50032

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1425905.549967
FMO2-HF: Nuclear repulsion	1363943.639743
FMO2-HF: Total energy	-61961.910224
FMO2-MP2: Total energy	-62140.122474

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:MET)

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

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.
-173.918	-161.487	15.494	-10.857	-17.065	-0.123

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.925

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	THR	0	0.045	0.014	3.329	3.208	5.835	0.073	-1.107	-1.593	-0.004
4	A	4	PRO	0	0.072	0.026	5.238	-0.349	-0.343	-0.001	-0.005	0.001	0.000
6	A	6	THR	0	-0.019	-0.021	4.165	4.290	4.671	-0.001	-0.167	-0.213	0.000
101	A	101	ALA	0	-0.026	-0.019	4.110	-0.242	0.157	0.066	-0.116	-0.349	0.000
102	A	102	GLY	0	-0.035	-0.020	5.866	-1.020	-1.053	-0.001	-0.004	0.039	0.000
105	A	105	GLY	0	-0.017	0.011	2.298	-0.231	-0.320	1.757	-0.682	-0.985	0.000
106	A	106	PRO	0	-0.018	-0.033	2.515	-7.625	-7.624	5.642	-0.912	-4.731	-0.007
107	A	107	MET	0	0.014	0.015	3.467	2.148	2.141	0.038	0.254	-0.284	0.000
108	A	108	ASP	-1	-0.766	-0.851	4.758	-36.118	-36.080	-0.001	-0.004	-0.033	0.000
109	A	109	GLU	-1	-0.889	-0.953	1.979	-121.187	-113.485	6.014	-7.182	-6.533	-0.099
110	A	110	TYR	0	-0.053	-0.042	2.869	1.164	2.570	1.908	-0.932	-2.384	-0.013
5	A	5	ILE	0	-0.011	0.003	8.125	1.707	1.707	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.907	-0.950	7.220	-26.383	-26.383	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.021	0.008	9.328	1.958	1.958	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.003	-0.010	9.601	1.634	1.634	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.034	0.023	8.412	1.574	1.574	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.001	0.018	10.562	1.829	1.829	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.015	-0.001	13.618	1.582	1.582	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.901	-0.953	12.595	-21.541	-21.541	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.039	-0.032	12.672	0.785	0.785	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.104	-0.058	15.023	2.013	2.013	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.000	0.003	17.778	0.975	0.975	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.848	0.935	18.460	15.552	15.552	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.020	0.008	17.972	-0.860	-0.860	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.015	-0.007	14.308	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.062	-0.062	18.405	1.224	1.224	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.001	-0.029	20.066	-0.409	-0.409	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.027	0.016	18.712	0.100	0.100	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.772	-0.854	15.774	-17.260	-17.260	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.002	-0.005	16.077	-0.776	-0.776	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.001	0.003	18.043	0.115	0.115	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.010	0.018	14.138	0.124	0.124	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.016	-0.004	12.753	-0.656	-0.656	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.805	-0.895	14.587	-14.092	-14.092	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.032	0.020	16.945	0.281	0.281	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.872	0.943	8.403	23.528	23.528	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.009	-0.019	13.091	-0.427	-0.427	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.811	0.891	15.559	13.988	13.988	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.803	0.880	14.427	15.993	15.993	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.018	0.009	13.721	0.147	0.147	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.000	0.011	14.757	0.043	0.043	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.030	0.015	17.796	0.207	0.207	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.004	-0.029	12.406	0.160	0.160	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.001	0.008	12.926	-0.090	-0.090	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.937	-0.969	15.050	-12.134	-12.134	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.036	0.009	15.602	0.248	0.248	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.011	0.008	12.532	0.072	0.072	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.912	0.953	14.335	14.235	14.235	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.012	0.021	17.069	0.363	0.363	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.022	0.003	15.166	0.382	0.382	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.035	-0.033	14.384	-0.209	-0.209	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.051	-0.032	16.473	0.078	0.078	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.031	-0.012	20.143	0.769	0.769	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.031	0.020	17.388	0.183	0.183	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.051	-0.038	19.275	-0.279	-0.279	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.030	0.013	21.976	0.185	0.185	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.032	-0.010	19.685	0.158	0.158	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.009	-0.002	17.525	-0.092	-0.092	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.842	-0.915	21.316	-10.868	-10.868	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.000	-0.007	25.045	0.281	0.281	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.011	0.006	22.059	0.200	0.200	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.000	-0.004	23.864	0.070	0.070	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.024	-0.017	25.102	0.462	0.462	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.004	0.015	26.319	0.291	0.291	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.008	-0.008	23.863	0.231	0.231	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.023	-0.025	25.915	0.264	0.264	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.019	-0.015	30.210	0.274	0.274	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.792	0.914	29.241	10.285	10.285	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.014	-0.009	26.996	0.083	0.083	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.076	0.052	31.589	-0.085	-0.085	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.061	0.039	29.900	0.081	0.081	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.011	-0.013	28.431	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.045	-0.041	30.876	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.041	-0.032	32.893	0.164	0.164	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.034	0.006	33.716	0.124	0.124	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.019	0.006	34.065	-0.310	-0.310	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.042	0.016	32.439	0.036	0.036	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.048	-0.022	28.627	-0.036	-0.036	0.000	0.000	0.000	0.000
73	A	73	GLN	0	-0.008	-0.006	26.300	-0.202	-0.202	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.007	0.004	26.662	-0.301	-0.301	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.012	0.003	27.327	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.012	0.001	29.017	0.187	0.187	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.030	-0.034	31.005	0.189	0.189	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.008	-0.016	30.928	-0.163	-0.163	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.839	-0.909	27.642	-9.745	-9.745	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.042	0.025	26.128	-0.468	-0.468	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.844	0.908	25.704	8.865	8.865	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.003	0.010	24.476	-0.359	-0.359	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.906	0.956	21.636	12.022	12.022	0.000	0.000	0.000	0.000
84	A	84	CYS	0	0.045	0.035	20.662	-0.496	-0.496	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.058	0.018	20.886	-0.452	-0.452	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.819	0.893	16.949	14.744	14.744	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.786	-0.862	16.414	-15.707	-15.707	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.028	0.019	15.891	-0.963	-0.963	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.030	0.013	16.409	-0.415	-0.415	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.058	-0.045	12.253	-0.949	-0.949	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.083	0.036	11.579	-1.293	-1.293	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.015	0.017	12.513	-0.884	-0.884	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.894	0.956	9.086	21.318	21.318	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.018	0.023	6.986	-2.106	-2.106	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.046	0.036	8.487	-1.475	-1.475	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.067	-0.043	10.471	-0.230	-0.230	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.012	-0.004	5.199	-0.195	-0.195	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.044	-0.005	6.361	-1.639	-1.639	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.042	0.002	7.388	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.023	-0.012	7.699	0.486	0.486	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.001	-0.017	6.309	0.336	0.336	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.010	-0.030	5.777	-0.077	-0.077	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.053	-0.019	6.716	3.405	3.405	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.030	0.011	9.254	1.928	1.928	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.015	-0.001	9.021	1.984	1.984	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.042	0.031	10.941	0.266	0.266	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.011	0.003	13.955	1.416	1.416	0.000	0.000	0.000	0.000
116	A	116	SER	0	0.030	0.007	15.714	1.037	1.037	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.857	-0.920	17.214	-17.315	-17.315	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.018	0.000	16.383	0.993	0.993	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.002	-0.012	18.416	0.832	0.832	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.022	-0.023	21.107	0.870	0.870	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.095	-0.051	22.294	0.656	0.656	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.084	-0.052	20.199	0.463	0.463	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.857	-0.901	24.352	-10.349	-10.349	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.029	-0.003	20.399	0.266	0.266	0.000	0.000	0.000	0.000
125	A	125	SER	0	0.016	0.001	23.220	-0.150	-0.150	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.051	0.019	20.862	-0.042	-0.042	0.000	0.000	0.000	0.000
127	A	127	SER	0	0.017	-0.006	21.837	-0.179	-0.179	0.000	0.000	0.000	0.000
128	A	128	TRP	0	-0.016	-0.005	23.318	0.111	0.111	0.000	0.000	0.000	0.000
129	A	129	TYR	0	0.017	-0.010	18.388	0.115	0.115	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.021	0.023	20.062	-0.115	-0.115	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.851	-0.922	21.591	-10.503	-10.503	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.021	0.006	20.643	0.186	0.186	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.015	-0.007	15.794	-0.049	-0.049	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.929	0.964	19.919	11.480	11.480	0.000	0.000	0.000	0.000
135	A	135	TYR	0	-0.002	0.015	23.307	0.179	0.179	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.033	0.004	17.739	0.178	0.178	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.760	0.857	20.638	13.119	13.119	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.047	-0.013	22.059	0.215	0.215	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.070	-0.038	24.430	0.656	0.656	0.000	0.000	0.000	0.000
140	A	140	HIS	0	0.011	0.004	20.223	0.312	0.312	0.000	0.000	0.000	0.000
141	A	143	GLY	0	0.000	0.011	22.816	-0.026	-0.026	0.000	0.000	0.000	0.000
142	A	144	LEU	0	-0.051	-0.007	19.029	0.142	0.142	0.000	0.000	0.000	0.000
143	A	145	THR	0	0.003	-0.009	23.502	0.314	0.314	0.000	0.000	0.000	0.000
144	A	146	GLY	0	0.033	0.013	23.535	-0.360	-0.360	0.000	0.000	0.000	0.000
145	A	147	GLN	0	0.060	0.012	20.222	-0.713	-0.713	0.000	0.000	0.000	0.000
146	A	148	ALA	0	0.065	0.049	18.733	-0.651	-0.651	0.000	0.000	0.000	0.000
147	A	149	ALA	0	0.029	0.017	18.797	-0.540	-0.540	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.048	-0.016	18.481	-0.323	-0.323	0.000	0.000	0.000	0.000
149	A	161	GLU	-1	-0.796	-0.863	13.821	-18.434	-18.434	0.000	0.000	0.000	0.000
150	A	162	ALA	0	0.026	0.005	14.894	-0.907	-0.907	0.000	0.000	0.000	0.000
151	A	163	ASN	0	0.016	0.001	16.177	-0.568	-0.568	0.000	0.000	0.000	0.000
152	A	164	ALA	0	0.017	0.028	14.727	-0.155	-0.155	0.000	0.000	0.000	0.000
153	A	165	TYR	0	0.016	-0.006	9.078	-1.340	-1.340	0.000	0.000	0.000	0.000
154	A	166	ILE	0	0.000	0.001	13.076	-0.515	-0.515	0.000	0.000	0.000	0.000
155	A	167	ASP	-1	-0.754	-0.875	15.985	-13.767	-13.767	0.000	0.000	0.000	0.000
156	A	168	TYR	0	-0.108	-0.061	9.221	1.161	1.161	0.000	0.000	0.000	0.000
157	A	169	ALA	0	0.045	0.006	13.326	-0.242	-0.242	0.000	0.000	0.000	0.000
158	A	170	ILE	0	-0.033	-0.017	14.396	0.483	0.483	0.000	0.000	0.000	0.000
159	A	171	ASN	0	-0.054	-0.036	16.698	0.871	0.871	0.000	0.000	0.000	0.000
160	A	172	ALA	0	-0.033	-0.007	13.667	0.154	0.154	0.000	0.000	0.000	0.000
161	A	173	LEU	0	-0.102	-0.045	15.739	-0.009	-0.009	0.000	0.000	0.000	0.000
162	A	174	SER	-1	-0.961	-0.972	18.741	-12.993	-12.993	0.000	0.000	0.000	0.000

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