FMO DATABASE

FMODB ID: Z7Z8N

Calculation Name: 1C52-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1C52

Chain ID: A

ChEMBL ID:

UniProt ID: P04164

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1109861.119988
FMO2-HF: Nuclear repulsion	1060518.359619
FMO2-HF: Total energy	-49342.760368
FMO2-MP2: Total energy	-49487.528302

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:GLN)

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

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.
26.521	32.337	3.709	-4.895	-4.63	-0.066

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.893

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	ASP	-1	-0.757	-0.861	3.788	-26.257	-24.742	-0.011	-0.431	-1.072	-0.001
76	A	76	LYS	1	0.905	0.927	4.548	43.650	43.737	-0.001	-0.005	-0.082	0.000
78	A	78	GLU	-1	-0.882	-0.957	2.070	-106.870	-102.656	3.721	-4.459	-3.476	-0.065
4	A	4	GLY	0	0.041	-0.002	5.788	1.953	1.953	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.030	0.016	8.984	2.240	2.240	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.909	0.956	6.869	23.728	23.728	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.050	-0.016	5.719	0.852	0.852	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.003	-0.024	9.230	1.816	1.816	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.000	0.002	12.125	1.544	1.544	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.011	-0.009	9.982	1.777	1.777	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.023	-0.005	14.586	0.574	0.574	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.031	-0.007	16.447	1.045	1.045	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.047	0.032	18.311	0.681	0.681	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.036	-0.001	20.626	0.509	0.509	0.000	0.000	0.000	0.000
15	A	15	HIS	1	0.858	0.892	19.788	14.265	14.265	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.038	0.042	21.476	0.092	0.092	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.071	0.023	15.213	-0.671	-0.671	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.018	0.018	19.808	-0.670	-0.670	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.054	0.027	21.389	0.220	0.220	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.000	-0.022	22.179	0.082	0.082	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.045	-0.008	24.419	0.360	0.360	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.021	0.004	25.729	0.141	0.141	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.046	0.010	28.788	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.028	0.023	31.994	0.154	0.154	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.040	-0.002	29.526	0.098	0.098	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.005	-0.017	24.988	-0.326	-0.326	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.012	0.022	25.565	0.041	0.041	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.013	0.004	25.032	-0.555	-0.555	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.038	-0.027	19.462	-0.116	-0.116	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.044	0.031	23.168	-0.090	-0.090	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.061	-0.045	24.041	0.675	0.675	0.000	0.000	0.000	0.000
32	A	32	HIS	0	0.018	0.003	25.448	0.557	0.557	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.017	0.008	19.667	0.085	0.085	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.000	-0.017	23.149	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.861	-0.920	24.892	-9.967	-9.967	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.038	-0.016	23.702	0.269	0.269	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.031	-0.027	19.665	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.033	0.001	24.124	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.841	0.934	27.100	10.314	10.314	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.864	-0.929	26.639	-11.709	-11.709	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.015	0.010	25.299	0.230	0.230	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.020	0.001	24.425	-0.306	-0.306	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.765	0.826	16.457	16.901	16.901	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.833	-0.936	19.348	-15.000	-15.000	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.010	0.000	20.800	-0.326	-0.326	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.014	0.002	18.768	-0.151	-0.151	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.024	0.014	15.440	-0.691	-0.691	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.038	-0.019	17.721	-0.232	-0.232	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.009	-0.001	20.764	0.159	0.159	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.001	-0.002	14.598	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.030	-0.001	15.067	-0.469	-0.469	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.043	-0.024	18.159	0.200	0.200	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.034	0.036	21.287	0.557	0.557	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.052	-0.045	22.759	0.216	0.216	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.005	-0.007	26.011	0.333	0.333	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.036	0.032	29.443	0.130	0.130	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.033	-0.019	32.053	-0.164	-0.164	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.041	-0.020	28.765	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.803	-0.881	33.052	-8.336	-8.336	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.039	-0.022	28.428	-0.345	-0.345	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.861	0.919	28.050	11.021	11.021	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.076	0.056	33.499	0.117	0.117	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.027	-0.001	33.565	0.117	0.117	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.897	0.923	34.043	8.149	8.149	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.010	0.006	30.192	-0.115	-0.115	0.000	0.000	0.000	0.000
66	A	66	ASN	0	0.005	-0.016	32.682	-0.184	-0.184	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.074	0.048	30.225	0.179	0.179	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.036	-0.027	26.633	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.010	0.012	19.019	0.007	0.007	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.030	0.015	19.587	0.369	0.369	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.033	-0.035	19.019	-0.593	-0.593	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.002	-0.014	14.369	0.146	0.146	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.016	0.012	13.984	-1.706	-1.706	0.000	0.000	0.000	0.000
74	A	74	GLN	0	0.053	0.039	13.173	-0.393	-0.393	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.045	-0.001	9.236	-1.829	-1.829	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.780	-0.889	8.614	-26.749	-26.749	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.833	-0.905	5.248	-41.415	-41.415	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.021	0.013	7.249	2.932	2.932	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.027	0.015	8.402	1.856	1.856	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.002	0.004	6.824	2.371	2.371	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.007	-0.004	8.944	2.605	2.605	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.009	-0.001	11.742	2.048	2.048	0.000	0.000	0.000	0.000
85	A	85	ASN	0	0.002	-0.011	10.612	3.432	3.432	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.009	0.037	12.106	1.403	1.403	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.036	-0.014	14.135	1.432	1.432	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.023	0.019	16.602	1.182	1.182	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.079	-0.068	15.129	0.580	0.580	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.012	0.014	16.579	0.792	0.792	0.000	0.000	0.000	0.000
91	A	91	TRP	0	0.005	0.010	18.398	0.564	0.564	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.025	0.008	21.230	0.697	0.697	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.814	-0.906	21.274	-12.644	-12.644	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.045	0.016	18.824	0.518	0.518	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.913	0.959	20.973	11.957	11.957	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.859	0.938	23.849	12.721	12.721	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.008	0.024	22.756	0.375	0.375	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.966	0.977	24.388	10.499	10.499	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.016	0.008	24.414	0.163	0.163	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.016	0.009	16.208	-0.283	-0.283	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.954	0.979	18.115	15.607	15.607	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.046	0.026	12.997	0.152	0.152	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.021	0.011	12.945	0.665	0.665	0.000	0.000	0.000	0.000
104	A	104	THR	0	0.012	-0.019	11.013	-2.404	-2.404	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.034	0.000	7.903	0.771	0.771	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.914	-0.961	10.027	-20.990	-20.990	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.763	-0.834	13.320	-17.839	-17.839	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.001	-0.001	11.680	1.279	1.279	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.971	0.990	12.501	24.384	24.384	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.933	0.969	14.563	15.683	15.683	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.003	-0.003	17.386	1.274	1.274	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.799	0.880	11.760	23.904	23.904	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.039	-0.017	18.525	0.565	0.565	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.902	0.952	21.729	13.451	13.451	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.936	0.968	22.720	13.460	13.460	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.012	0.027	24.032	0.484	0.484	0.000	0.000	0.000	0.000
117	A	117	THR	0	0.067	0.026	25.374	-0.321	-0.321	0.000	0.000	0.000	0.000
118	A	118	PRO	0	0.032	0.011	25.675	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	119	GLN	0	0.043	0.012	27.298	-0.122	-0.122	0.000	0.000	0.000	0.000
120	A	120	GLN	0	0.042	0.027	28.495	0.031	0.031	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.016	0.019	23.968	0.090	0.090	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.034	-0.018	26.928	0.044	0.044	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.023	-0.018	29.894	0.275	0.275	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.831	-0.910	26.642	-10.688	-10.688	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.871	0.932	28.160	10.782	10.782	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.926	0.962	29.205	9.297	9.297	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.841	0.909	30.302	10.538	10.538	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.029	0.004	26.582	0.068	0.068	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.027	0.027	30.826	0.056	0.056	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.107	-0.059	28.277	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	131	LYS	0	-0.027	-0.011	32.404	0.759	0.759	0.000	0.000	0.000	0.000

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