FMO DATABASE

FMODB ID: RMY38

Calculation Name: 3QB9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | fe (iii) ion

Ligand 3-letter code: HEM | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3QB9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPQ9

Base Structure: X-ray

Registration Date: 2025-10-04

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1603587.500619
FMO2-HF: Nuclear repulsion	1538436.444561
FMO2-HF: Total energy	-65151.056058
FMO2-MP2: Total energy	-65338.842108

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.
-263.903	-259.107	12.162	-8.635	-8.323	-0.102

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 : 0.747 / q_NPA : 0.868

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	GLY	0	0.032	0.016	3.833	4.766	6.050	-0.014	-0.445	-0.825	0.000
61	A	61	ARG	1	0.781	0.868	4.509	28.266	28.332	-0.001	-0.002	-0.063	0.000
64	A	64	LEU	0	-0.054	-0.019	2.441	-6.946	-6.763	1.279	-0.246	-1.216	-0.003
65	A	65	LEU	0	-0.062	-0.028	3.062	-16.969	-14.918	0.231	-0.870	-1.412	-0.006
66	A	66	ASP	-1	-0.835	-0.920	1.861	-121.178	-120.066	10.668	-7.064	-4.717	-0.093
67	A	67	GLY	0	0.006	0.012	4.981	6.197	6.297	-0.001	-0.008	-0.090	0.000
4	A	4	ASP	-1	-0.739	-0.874	5.503	-21.298	-21.298	0.000	0.000	0.000	0.000
5	A	5	PRO	0	-0.005	-0.007	9.090	0.326	0.326	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.828	-0.891	11.736	-17.952	-17.952	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.002	-0.002	9.829	1.032	1.032	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.014	0.006	7.443	1.246	1.246	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.805	0.908	11.199	19.965	19.965	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.041	0.032	14.810	0.877	0.877	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.015	0.007	9.719	0.909	0.909	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.035	0.003	13.566	1.740	1.740	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-1.004	-1.002	16.221	-14.502	-14.502	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.082	0.032	16.946	0.917	0.917	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.004	0.010	15.716	0.625	0.625	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.009	0.015	18.346	0.722	0.722	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.041	0.033	21.554	0.826	0.826	0.000	0.000	0.000	0.000
18	A	18	GLU	0	-0.061	-0.056	19.033	0.453	0.453	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.002	0.001	20.750	0.564	0.564	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.046	-0.044	23.796	0.605	0.605	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.035	0.024	25.158	0.494	0.494	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.001	0.018	22.404	0.419	0.419	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.010	0.000	26.897	0.373	0.373	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.035	-0.025	29.706	0.277	0.277	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.020	-0.028	27.697	0.445	0.445	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.014	0.011	30.697	0.385	0.385	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.014	0.001	32.502	0.327	0.327	0.000	0.000	0.000	0.000
28	A	28	HIS	0	0.035	0.001	34.956	0.419	0.419	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.055	-0.020	34.720	0.250	0.250	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.801	0.876	36.140	8.332	8.332	0.000	0.000	0.000	0.000
31	A	31	MET	0	-0.051	-0.017	38.635	0.144	0.144	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.066	0.035	37.713	0.155	0.155	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.842	-0.916	40.231	-7.465	-7.465	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.085	-0.035	42.249	0.210	0.210	0.000	0.000	0.000	0.000
35	A	35	TRP	0	-0.069	-0.030	42.339	0.133	0.133	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.055	0.041	45.950	0.152	0.152	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.054	-0.034	43.468	0.082	0.082	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.020	-0.018	42.381	-0.163	-0.163	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.883	-0.927	41.095	-7.271	-7.271	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.015	-0.003	38.771	-0.169	-0.169	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.007	0.010	37.942	-0.267	-0.267	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.031	-0.025	36.596	-0.306	-0.306	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.026	-0.006	32.743	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.022	-0.042	33.262	-0.341	-0.341	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.931	0.962	32.375	8.840	8.840	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.040	-0.016	30.550	-0.362	-0.362	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.786	-0.899	28.586	-10.398	-10.398	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.062	-0.032	27.233	-0.502	-0.502	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.031	-0.056	26.165	-0.397	-0.397	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.821	-0.880	24.251	-11.644	-11.644	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.776	-0.845	22.490	-13.131	-13.131	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.083	-0.034	21.406	-0.726	-0.726	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.871	0.929	19.634	11.308	11.308	0.000	0.000	0.000	0.000
54	A	54	HIS	1	0.860	0.939	17.695	13.081	13.081	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.005	0.000	16.713	-0.990	-0.990	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.945	-0.941	15.877	-17.596	-17.596	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.854	-0.932	13.371	-17.942	-17.942	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.038	-0.026	11.783	-2.000	-2.000	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.028	-0.020	11.669	-1.782	-1.782	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.871	-0.934	9.886	-26.024	-26.024	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.035	-0.021	6.883	-4.118	-4.118	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.003	0.003	7.894	-4.357	-4.357	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.014	-0.022	8.681	0.883	0.883	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.020	0.025	11.732	1.118	1.118	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.021	-0.033	14.335	1.559	1.559	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.025	-0.012	16.667	1.019	1.019	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.067	-0.020	20.471	1.072	1.072	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.813	0.905	19.339	16.236	16.236	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.022	0.016	23.459	-0.313	-0.313	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.018	0.009	26.058	0.107	0.107	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.062	-0.050	27.955	0.139	0.139	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.011	0.014	30.120	0.065	0.065	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.845	0.931	30.823	9.990	9.990	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.014	0.006	34.662	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.025	0.024	37.609	0.202	0.202	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.056	-0.055	40.126	0.090	0.090	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.016	-0.005	43.392	0.126	0.126	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.030	0.004	41.981	-0.179	-0.179	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.827	0.900	41.087	6.598	6.598	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.816	-0.904	40.793	-7.409	-7.409	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.035	-0.014	37.858	-0.232	-0.232	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.058	0.026	36.450	-0.254	-0.254	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.876	-0.945	36.040	-7.670	-7.670	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.050	-0.030	35.562	-0.217	-0.217	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.794	-0.896	32.253	-9.525	-9.525	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.035	0.028	31.275	-0.378	-0.378	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.051	-0.023	31.594	-0.244	-0.244	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.063	-0.029	26.794	-0.262	-0.262	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.745	-0.835	27.092	-11.330	-11.330	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.028	-0.055	27.098	-0.459	-0.459	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.910	-0.922	25.645	-12.257	-12.257	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.001	0.003	21.839	-0.519	-0.519	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.015	0.001	23.053	-0.525	-0.525	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.043	-0.028	24.605	-0.146	-0.146	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.791	0.884	19.983	13.285	13.285	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.002	-0.012	17.883	-0.681	-0.681	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.871	0.946	19.967	10.806	10.806	0.000	0.000	0.000	0.000
103	A	103	PRO	0	-0.017	-0.003	21.616	-0.184	-0.184	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.034	0.006	18.270	-0.510	-0.510	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.016	0.012	16.278	-1.177	-1.177	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.018	-0.003	16.480	-0.574	-0.574	0.000	0.000	0.000	0.000
107	A	107	MET	0	0.014	0.023	14.649	-0.907	-0.907	0.000	0.000	0.000	0.000
108	A	108	CYS	0	-0.055	-0.034	12.410	-1.337	-1.337	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.805	0.869	12.793	14.576	14.576	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.959	-0.974	14.973	-14.721	-14.721	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.727	0.841	11.675	20.784	20.784	0.000	0.000	0.000	0.000
112	A	112	GLN	0	-0.045	-0.020	11.150	-2.340	-2.340	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.736	-0.810	7.642	-30.915	-30.915	0.000	0.000	0.000	0.000
114	A	114	THR	0	0.012	-0.022	9.565	0.657	0.657	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.040	-0.013	7.106	0.767	0.767	0.000	0.000	0.000	0.000
116	A	116	SER	0	0.013	-0.028	8.387	0.402	0.402	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.003	0.014	10.326	1.262	1.262	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.017	0.004	12.647	0.855	0.855	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.028	0.001	11.476	0.612	0.612	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.037	0.000	13.738	0.927	0.927	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.796	-0.892	16.175	-14.403	-14.403	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.854	0.935	15.138	16.675	16.675	0.000	0.000	0.000	0.000
123	A	123	ILE	0	0.039	0.029	16.634	0.433	0.433	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.028	-0.023	20.026	0.501	0.501	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.023	0.015	22.163	0.449	0.449	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.851	-0.927	21.707	-12.310	-12.310	0.000	0.000	0.000	0.000
127	A	127	GLU	0	-0.042	-0.052	23.350	0.333	0.333	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.908	-0.950	26.046	-10.447	-10.447	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.937	-0.962	27.864	-9.604	-9.604	0.000	0.000	0.000	0.000
130	A	130	HIS	1	0.839	0.920	28.334	10.537	10.537	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.013	-0.022	29.144	0.239	0.239	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.903	-0.937	31.970	-8.121	-8.121	0.000	0.000	0.000	0.000
133	A	133	TYR	0	0.009	0.010	33.206	0.307	0.307	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.013	0.000	32.515	0.291	0.291	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.831	-0.899	35.691	-8.257	-8.257	0.000	0.000	0.000	0.000
136	A	136	THR	0	-0.014	-0.012	37.770	0.326	0.326	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.038	-0.006	37.937	0.407	0.407	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.007	0.008	39.002	0.218	0.218	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.853	-0.927	42.011	-6.920	-6.920	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.075	-0.038	42.594	0.238	0.238	0.000	0.000	0.000	0.000
141	A	141	MET	0	-0.041	-0.019	44.270	0.116	0.116	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.863	-0.909	46.436	-6.494	-6.494	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.769	0.878	44.778	6.920	6.920	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.068	-0.024	47.811	0.143	0.143	0.000	0.000	0.000	0.000
145	A	145	GLY	0	0.036	0.034	50.560	0.147	0.147	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.810	-0.906	47.952	-6.575	-6.575	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.908	-0.944	49.237	-5.975	-5.975	0.000	0.000	0.000	0.000
148	A	148	LEU	0	-0.042	-0.015	51.420	-0.011	-0.011	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.027	-0.008	41.348	-0.016	-0.016	0.000	0.000	0.000	0.000
150	A	150	SER	0	0.023	-0.013	46.914	-0.136	-0.136	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.069	-0.038	47.973	-0.036	-0.036	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.120	-0.065	46.270	0.056	0.056	0.000	0.000	0.000	0.000
153	A	153	CYS	0	-0.032	-0.001	43.929	-0.174	-0.174	0.000	0.000	0.000	0.000
154	A	154	VAL	0	-0.034	-0.003	44.660	-0.095	-0.095	0.000	0.000	0.000	0.000
155	A	155	SER	0	0.042	0.026	46.867	0.015	0.015	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.880	0.943	48.202	5.958	5.958	0.000	0.000	0.000	0.000
157	A	157	PRO	0	-0.047	-0.040	51.766	0.043	0.043	0.000	0.000	0.000	0.000
158	A	158	PRO	0	0.029	0.013	50.098	-0.069	-0.069	0.000	0.000	0.000	0.000
159	A	159	THR	-1	-0.947	-0.952	47.431	-6.495	-6.495	0.000	0.000	0.000	0.000

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