FMO DATABASE

FMODB ID: Z7Z3N

Calculation Name: 1CPC-A-Xray547

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: 1CPC

Chain ID: A

ChEMBL ID:

UniProt ID: P07122

Base Structure: X-ray

Registration Date: 2025-09-02

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1394765.070707
FMO2-HF: Nuclear repulsion	1334376.190274
FMO2-HF: Total energy	-60388.880433
FMO2-MP2: Total energy	-60565.526002

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.
-170.143	-159.466	21.901	-12.667	-19.912	-0.142

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 : 0.803 / q_NPA : 0.916

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	0.021	0.000	2.640	4.146	6.745	0.355	-0.965	-1.990	-0.004
4	A	4	PRO	0	0.042	0.015	4.887	0.096	0.114	-0.001	-0.009	-0.008	0.000
6	A	6	THR	0	-0.018	-0.022	3.710	4.752	5.327	0.001	-0.264	-0.312	0.000
101	A	101	VAL	0	-0.045	-0.024	3.054	-0.631	0.097	1.053	-0.368	-1.413	0.001
102	A	102	GLY	0	-0.034	-0.013	6.370	-0.339	-0.373	-0.001	-0.002	0.038	0.000
105	A	105	GLY	0	0.017	0.023	2.336	0.107	-0.355	2.508	-0.878	-1.169	0.000
106	A	106	PRO	0	-0.024	-0.030	2.732	-5.296	-5.255	3.796	0.090	-3.927	-0.006
107	A	107	LEU	0	0.013	0.002	3.621	2.894	3.048	0.015	0.026	-0.195	0.000
108	A	108	ASP	-1	-0.791	-0.853	4.515	-37.631	-37.581	-0.001	-0.005	-0.044	0.000
109	A	109	ASP	-1	-0.835	-0.930	1.953	-131.812	-125.682	11.716	-9.526	-8.319	-0.122
110	A	110	TYR	0	-0.059	-0.040	2.564	0.678	1.556	2.460	-0.766	-2.573	-0.011
5	A	5	LEU	0	-0.009	0.001	7.767	1.994	1.994	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.839	-0.911	6.742	-38.571	-38.571	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.007	0.010	8.906	2.418	2.418	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.002	-0.005	9.670	1.889	1.889	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.027	0.014	8.144	1.586	1.586	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.014	0.001	10.279	1.829	1.829	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.012	-0.001	13.249	1.415	1.415	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.918	-0.960	12.373	-21.524	-21.524	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.066	-0.028	13.287	1.519	1.519	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.054	-0.024	15.013	1.908	1.908	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.002	0.003	17.625	1.035	1.035	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.855	0.932	18.274	15.541	15.541	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.017	0.005	18.025	-0.841	-0.841	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.010	-0.005	14.552	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.033	-0.038	18.587	1.167	1.167	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.012	-0.015	20.087	-0.367	-0.367	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.014	0.018	18.406	0.032	0.032	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.758	-0.854	15.378	-17.808	-17.808	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.004	0.010	15.728	-0.713	-0.713	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.007	-0.009	17.850	0.104	0.104	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.021	-0.005	12.521	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.010	-0.005	13.470	-0.584	-0.584	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.028	-0.025	14.521	0.175	0.175	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.013	0.015	16.087	0.468	0.468	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.828	0.912	9.719	22.235	22.235	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.002	-0.021	13.124	0.137	0.137	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.934	0.971	15.478	13.116	13.116	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.007	-0.008	14.173	1.055	1.055	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.004	0.000	13.291	0.207	0.207	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.005	0.003	14.489	0.192	0.192	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.005	0.000	17.370	0.369	0.369	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.015	-0.028	12.360	0.147	0.147	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.018	0.002	11.479	-0.176	-0.176	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.031	-0.005	14.545	0.359	0.359	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.031	0.016	15.602	0.365	0.365	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.015	0.009	12.391	0.119	0.119	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.929	0.974	14.201	13.439	13.439	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.044	0.028	16.911	0.288	0.288	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.004	-0.010	14.909	0.346	0.346	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.055	-0.047	14.486	-0.134	-0.134	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.987	-0.987	16.533	-11.159	-11.159	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.935	0.970	20.113	11.822	11.822	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.027	0.025	17.036	0.285	0.285	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.002	-0.004	18.917	0.022	0.022	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.022	0.000	21.482	0.261	0.261	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.011	0.008	19.650	0.158	0.158	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.032	0.011	19.092	0.046	0.046	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.012	-0.032	20.983	0.279	0.279	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.006	0.008	24.586	0.312	0.312	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.014	0.003	22.068	0.227	0.227	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.002	-0.002	23.689	0.110	0.110	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.004	-0.007	24.995	0.270	0.270	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.010	0.017	26.468	0.345	0.345	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.018	0.008	24.016	0.233	0.233	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.009	-0.016	26.671	0.144	0.144	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.034	-0.027	30.344	0.380	0.380	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.808	0.906	29.445	10.319	10.319	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.027	-0.011	26.993	0.142	0.142	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.067	0.051	31.670	-0.119	-0.119	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.036	0.025	30.321	0.019	0.019	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.013	-0.017	28.417	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.019	-0.029	30.822	-0.180	-0.180	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.044	-0.021	33.052	0.149	0.149	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.018	0.018	34.061	0.061	0.061	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.032	-0.009	34.550	-0.287	-0.287	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.098	0.037	32.664	0.023	0.023	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.057	-0.025	28.887	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.022	-0.009	26.642	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	74	PHE	0	0.018	0.019	27.056	-0.248	-0.248	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.013	0.006	27.397	0.010	0.010	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.014	-0.010	29.188	0.161	0.161	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.018	-0.006	30.274	0.278	0.278	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.025	0.008	30.027	-0.217	-0.217	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.035	0.007	26.799	-0.195	-0.195	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.038	0.022	26.037	-0.451	-0.451	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.853	0.919	25.659	8.844	8.844	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.881	-0.943	24.820	-10.835	-10.835	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.910	0.944	21.699	11.844	11.844	0.000	0.000	0.000	0.000
84	A	84	CYS	0	0.025	0.033	20.774	-0.720	-0.720	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.027	0.004	20.877	-0.513	-0.513	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.808	0.894	17.355	14.515	14.515	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.785	-0.861	16.476	-15.744	-15.744	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.010	0.011	15.729	-1.036	-1.036	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.033	0.017	16.213	-0.470	-0.470	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.056	-0.040	12.138	-0.818	-0.818	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.065	0.028	11.457	-1.649	-1.649	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.005	0.011	12.082	-0.956	-0.956	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.910	0.963	8.966	21.166	21.166	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.025	0.024	7.138	-1.699	-1.699	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.066	0.041	8.111	-1.574	-1.574	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.080	-0.049	10.301	-0.041	-0.041	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.022	0.002	5.057	0.054	0.054	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.039	-0.004	6.307	-1.549	-1.549	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.022	0.009	7.393	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.023	-0.012	7.287	0.715	0.715	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.005	-0.019	5.873	0.116	0.116	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.009	-0.030	5.796	0.488	0.488	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.056	-0.015	6.556	3.617	3.617	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.039	0.008	9.401	1.904	1.904	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.007	0.007	9.568	1.861	1.861	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.035	0.029	10.855	0.228	0.228	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.030	-0.016	13.946	1.581	1.581	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.028	0.019	15.675	1.236	1.236	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.879	-0.954	17.427	-16.539	-16.539	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.002	0.017	15.130	1.076	1.076	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.014	0.000	18.711	0.911	0.911	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.944	0.978	21.215	14.571	14.571	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.093	-0.062	22.439	0.693	0.693	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.069	-0.042	20.617	0.479	0.479	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.906	-0.938	24.575	-10.432	-10.432	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.004	0.010	20.837	0.316	0.316	0.000	0.000	0.000	0.000
125	A	125	SER	0	0.034	0.022	23.321	-0.409	-0.409	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.052	0.014	21.031	-0.128	-0.128	0.000	0.000	0.000	0.000
127	A	127	SER	0	-0.023	-0.016	21.951	-0.110	-0.110	0.000	0.000	0.000	0.000
128	A	128	TRP	0	0.018	-0.005	23.451	0.003	0.003	0.000	0.000	0.000	0.000
129	A	129	TYR	0	0.014	-0.012	18.394	0.041	0.041	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.043	0.028	19.964	-0.227	-0.227	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.875	-0.927	21.478	-10.641	-10.641	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.021	0.003	20.710	0.170	0.170	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.019	-0.010	15.607	-0.063	-0.063	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.949	0.973	19.703	11.845	11.845	0.000	0.000	0.000	0.000
135	A	135	TYR	0	0.012	0.018	23.018	0.192	0.192	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.033	0.005	17.525	0.211	0.211	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.767	0.864	20.414	13.613	13.613	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.031	-0.001	21.637	0.194	0.194	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.064	-0.038	24.086	0.664	0.664	0.000	0.000	0.000	0.000
140	A	140	HIS	0	0.012	0.012	19.795	0.437	0.437	0.000	0.000	0.000	0.000
141	A	143	GLY	0	0.000	0.007	22.534	0.117	0.117	0.000	0.000	0.000	0.000
142	A	144	LEU	0	-0.052	-0.016	18.423	0.131	0.131	0.000	0.000	0.000	0.000
143	A	145	SER	0	-0.014	-0.017	22.893	0.327	0.327	0.000	0.000	0.000	0.000
144	A	146	GLY	0	0.049	0.016	22.880	-0.272	-0.272	0.000	0.000	0.000	0.000
145	A	147	ASP	-1	-0.850	-0.933	19.049	-13.171	-13.171	0.000	0.000	0.000	0.000
146	A	148	PRO	0	-0.049	-0.022	17.896	-0.707	-0.707	0.000	0.000	0.000	0.000
147	A	149	ALA	0	0.023	0.013	17.920	-0.561	-0.561	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.019	0.000	18.357	-0.350	-0.350	0.000	0.000	0.000	0.000
149	A	161	GLU	-1	-0.725	-0.819	11.662	-20.253	-20.253	0.000	0.000	0.000	0.000
150	A	162	ALA	0	0.020	0.004	14.194	-0.972	-0.972	0.000	0.000	0.000	0.000
151	A	163	ASN	0	0.024	0.006	15.475	-0.569	-0.569	0.000	0.000	0.000	0.000
152	A	164	SER	0	-0.005	0.022	13.982	-0.152	-0.152	0.000	0.000	0.000	0.000
153	A	165	TYR	0	-0.015	-0.040	9.248	-1.187	-1.187	0.000	0.000	0.000	0.000
154	A	166	ILE	0	-0.006	0.000	12.605	-0.443	-0.443	0.000	0.000	0.000	0.000
155	A	167	ASP	-1	-0.764	-0.878	15.510	-14.177	-14.177	0.000	0.000	0.000	0.000
156	A	168	TYR	0	-0.104	-0.058	8.947	1.322	1.322	0.000	0.000	0.000	0.000
157	A	169	ALA	0	0.018	0.003	12.941	-0.250	-0.250	0.000	0.000	0.000	0.000
158	A	170	ILE	0	-0.024	-0.021	14.190	0.577	0.577	0.000	0.000	0.000	0.000
159	A	171	ASN	0	-0.054	-0.039	16.725	1.035	1.035	0.000	0.000	0.000	0.000
160	A	172	ALA	0	-0.023	0.008	13.858	0.032	0.032	0.000	0.000	0.000	0.000
161	A	173	LEU	0	-0.116	-0.060	15.974	0.136	0.136	0.000	0.000	0.000	0.000
162	A	174	SER	-1	-0.964	-0.971	18.968	-13.008	-13.008	0.000	0.000	0.000	0.000

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