FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: R8M88

Calculation Name: 4OPH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OPH

Chain ID: A

ChEMBL ID:

UniProt ID: Q20NS3

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079800.677632
FMO2-HF: Nuclear repulsion 1999336.059485
FMO2-HF: Total energy -80464.618147
FMO2-MP2: Total energy -80696.909814


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-26.824-27.3222.591-10.673-11.4230.093
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.801 / q_NPA : -0.901
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   
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].
3A4ASN00.009-0.0111.746-52.809-56.77720.925-8.913-8.0450.101
4A5THR00.0020.0122.426-15.502-12.3831.666-1.672-3.113-0.008
5A6VAL00.0300.0244.250-6.636-6.2830.000-0.088-0.2650.000
6A7SER0-0.013-0.0116.295-6.592-6.5920.0000.0000.0000.000
7A8SER00.007-0.0206.585-4.897-4.8970.0000.0000.0000.000
8A9PHE0-0.0080.0108.119-3.603-3.6030.0000.0000.0000.000
9A10GLN00.0510.0209.811-3.253-3.2530.0000.0000.0000.000
10A11VAL00.0290.02311.941-2.221-2.2210.0000.0000.0000.000
11A12ASP-1-0.814-0.86912.19021.44921.4490.0000.0000.0000.000
12A13CYS0-0.070-0.03913.057-1.766-1.7660.0000.0000.0000.000
13A14PHE00.0120.01815.810-1.553-1.5530.0000.0000.0000.000
14A15LEU00.0220.00416.530-1.195-1.1950.0000.0000.0000.000
15A16TRP0-0.023-0.02018.432-1.286-1.2860.0000.0000.0000.000
16A17HIS00.004-0.00120.026-0.880-0.8800.0000.0000.0000.000
17A18VAL0-0.002-0.00222.030-0.797-0.7970.0000.0000.0000.000
18A19ARG10.7910.88220.601-14.961-14.9610.0000.0000.0000.000
19A20LYS10.8390.91724.271-11.024-11.0240.0000.0000.0000.000
20A21ARG10.9690.98226.168-11.383-11.3830.0000.0000.0000.000
21A22PHE00.0120.00427.745-0.415-0.4150.0000.0000.0000.000
22A23ALA0-0.027-0.02028.774-0.372-0.3720.0000.0000.0000.000
23A24ASP-1-0.857-0.91829.69010.16110.1610.0000.0000.0000.000
24A25GLN0-0.098-0.03231.981-0.308-0.3080.0000.0000.0000.000
25A26GLU-1-0.971-0.99733.4487.9547.9540.0000.0000.0000.000
26A27LEU0-0.012-0.00833.075-0.125-0.1250.0000.0000.0000.000
27A28GLY0-0.085-0.02431.192-0.003-0.0030.0000.0000.0000.000
28A29ASP-1-0.787-0.89431.4479.7919.7910.0000.0000.0000.000
29A30ALA00.039-0.01031.6560.2620.2620.0000.0000.0000.000
30A31PRO00.0830.03429.5560.2790.2790.0000.0000.0000.000
31A32PHE0-0.021-0.00826.3400.5710.5710.0000.0000.0000.000
32A33LEU00.0540.03626.6730.4860.4860.0000.0000.0000.000
33A34ASP-1-0.853-0.91027.33410.33710.3370.0000.0000.0000.000
34A35ARG10.8990.93123.131-11.324-11.3240.0000.0000.0000.000
35A36LEU0-0.0100.01822.3430.6000.6000.0000.0000.0000.000
36A37ARG10.8640.91422.650-10.339-10.3390.0000.0000.0000.000
37A38ALA0-0.026-0.01922.1170.3200.3200.0000.0000.0000.000
38A39ASP-1-0.799-0.87918.55915.63415.6340.0000.0000.0000.000
39A40GLN00.0120.03617.9130.5940.5940.0000.0000.0000.000
40A41ALA0-0.044-0.02318.8920.3250.3250.0000.0000.0000.000
41A42SER00.007-0.00315.8390.6870.6870.0000.0000.0000.000
42A43LEU00.0040.01013.4641.0511.0510.0000.0000.0000.000
43A44ARG10.9000.94014.346-12.526-12.5260.0000.0000.0000.000
44A45GLY00.0000.00415.2550.2070.2070.0000.0000.0000.000
45A46ARG10.8540.8889.349-23.211-23.2110.0000.0000.0000.000
46A47GLY00.0150.00810.2311.4661.4660.0000.0000.0000.000
47A48SER00.0230.00112.064-0.259-0.2590.0000.0000.0000.000
48A49THR0-0.109-0.0579.709-0.069-0.0690.0000.0000.0000.000
49A50LEU0-0.058-0.0145.5650.6840.6840.0000.0000.0000.000
50A51GLY0-0.0070.0138.4500.8900.8900.0000.0000.0000.000
51A52LEU0-0.032-0.0118.6710.3460.3460.0000.0000.0000.000
52A53ASP-1-0.849-0.92112.28815.60915.6090.0000.0000.0000.000
53A54ILE0-0.016-0.02514.8320.6720.6720.0000.0000.0000.000
54A55GLU-1-0.839-0.89216.49114.65514.6550.0000.0000.0000.000
55A56THR00.039-0.01216.0790.5220.5220.0000.0000.0000.000
56A57ALA00.0170.02012.8050.6700.6700.0000.0000.0000.000
57A58THR00.001-0.01814.3250.9150.9150.0000.0000.0000.000
58A59ARG10.8370.91617.218-14.879-14.8790.0000.0000.0000.000
59A60ALA00.0040.00813.978-0.087-0.0870.0000.0000.0000.000
60A61GLY00.026-0.00114.7290.2930.2930.0000.0000.0000.000
61A62LYS10.7610.86315.674-14.315-14.3150.0000.0000.0000.000
62A63GLN00.0340.00417.059-0.517-0.5170.0000.0000.0000.000
63A64ILE0-0.045-0.01811.3550.1230.1230.0000.0000.0000.000
64A65VAL00.015-0.00115.377-0.231-0.2310.0000.0000.0000.000
65A66GLU-1-0.826-0.88217.57613.59413.5940.0000.0000.0000.000
66A67ARG10.8240.89016.629-18.624-18.6240.0000.0000.0000.000
67A68ILE0-0.009-0.01114.160-0.215-0.2150.0000.0000.0000.000
68A69LEU0-0.009-0.00618.438-0.550-0.5500.0000.0000.0000.000
69A70GLU-1-0.901-0.94121.42412.01512.0150.0000.0000.0000.000
70A71GLU-1-0.927-0.92418.28716.88916.8890.0000.0000.0000.000
71A72GLU-1-0.938-0.97621.49213.45813.4580.0000.0000.0000.000
72A73SER0-0.056-0.01523.3430.4790.4790.0000.0000.0000.000
73A74ASP-1-0.901-0.96225.78411.50811.5080.0000.0000.0000.000
74A75GLU-1-0.908-0.96827.67510.02210.0220.0000.0000.0000.000
75A76ALA0-0.062-0.03530.474-0.020-0.0200.0000.0000.0000.000
76A77LEU0-0.0120.01925.339-0.149-0.1490.0000.0000.0000.000
77A78LYS10.7850.88624.158-12.741-12.7410.0000.0000.0000.000
78A79MET0-0.022-0.00626.224-0.311-0.3110.0000.0000.0000.000
79A80THR0-0.013-0.01728.883-0.056-0.0560.0000.0000.0000.000
80A81ILE0-0.015-0.01927.381-0.240-0.2400.0000.0000.0000.000
81A82ALA00.0460.02730.2010.2170.2170.0000.0000.0000.000
82A83SER0-0.057-0.01531.013-0.256-0.2560.0000.0000.0000.000
83A84VAL00.011-0.01031.561-0.181-0.1810.0000.0000.0000.000
84A85PRO0-0.0010.01734.199-0.255-0.2550.0000.0000.0000.000
85A86ALA0-0.004-0.01635.4520.0280.0280.0000.0000.0000.000
86A87SER00.0020.01033.721-0.313-0.3130.0000.0000.0000.000
87A88ARG10.9270.97536.942-7.722-7.7220.0000.0000.0000.000
88A89TYR00.007-0.00833.2240.1540.1540.0000.0000.0000.000
89A90LEU0-0.052-0.01237.809-0.341-0.3410.0000.0000.0000.000
90A91THR0-0.030-0.02538.1750.2900.2900.0000.0000.0000.000
91A92ASP-1-0.717-0.78439.6537.9207.9200.0000.0000.0000.000
92A93MET0-0.070-0.02435.510-0.190-0.1900.0000.0000.0000.000
93A94THR00.0230.00840.6470.0680.0680.0000.0000.0000.000
94A95LEU00.039-0.01138.5500.1450.1450.0000.0000.0000.000
95A96GLU-1-0.882-0.92440.0317.5357.5350.0000.0000.0000.000
96A97GLU-1-0.766-0.84940.7997.6527.6520.0000.0000.0000.000
97A98MET0-0.065-0.03935.1550.2190.2190.0000.0000.0000.000
98A99SER0-0.108-0.04035.8510.3050.3050.0000.0000.0000.000
99A100ARG10.8740.92537.106-7.796-7.7960.0000.0000.0000.000
100A101ASP-1-0.931-0.95837.2258.2578.2570.0000.0000.0000.000
101A102TRP0-0.013-0.02531.800-0.081-0.0810.0000.0000.0000.000
102A103PHE0-0.051-0.02834.3440.2310.2310.0000.0000.0000.000
103A104MET0-0.0470.01229.5880.0240.0240.0000.0000.0000.000
104A105LEU0-0.007-0.00334.7670.0880.0880.0000.0000.0000.000
105A106MET0-0.073-0.02934.3890.1380.1380.0000.0000.0000.000
106A107PRO00.0310.01429.7380.0530.0530.0000.0000.0000.000
107A108LYS10.9070.96428.690-9.935-9.9350.0000.0000.0000.000
108A109GLN00.0160.00724.688-0.179-0.1790.0000.0000.0000.000
109A110LYS10.9400.97623.274-12.339-12.3390.0000.0000.0000.000
110A111VAL00.0240.00418.579-0.085-0.0850.0000.0000.0000.000
111A112ALA0-0.036-0.01520.4890.2980.2980.0000.0000.0000.000
112A113GLY00.0760.04520.269-0.271-0.2710.0000.0000.0000.000
113A114SER0-0.015-0.02418.239-0.094-0.0940.0000.0000.0000.000
114A115LEU00.0140.02320.032-0.463-0.4630.0000.0000.0000.000
115A116CYS0-0.042-0.01922.7300.3560.3560.0000.0000.0000.000
116A117ILE00.0070.00524.033-0.494-0.4940.0000.0000.0000.000
117A118ARG10.8540.91525.080-11.821-11.8210.0000.0000.0000.000
118A119MET00.0190.00529.099-0.242-0.2420.0000.0000.0000.000
119A120ASP-1-0.711-0.87032.2138.9468.9460.0000.0000.0000.000
120A121GLN0-0.086-0.05833.6980.1110.1110.0000.0000.0000.000
121A122ALA0-0.028-0.01735.526-0.189-0.1890.0000.0000.0000.000
122A123ILE00.005-0.00938.750-0.080-0.0800.0000.0000.0000.000
123A124MET0-0.056-0.01440.7750.0440.0440.0000.0000.0000.000
124A125ASP-1-0.879-0.93743.4236.7016.7010.0000.0000.0000.000
125A126LYS10.7890.89943.612-6.916-6.9160.0000.0000.0000.000
126A127ASN00.0280.00545.0340.0680.0680.0000.0000.0000.000
127A128ILE0-0.018-0.01339.6030.0000.0000.0000.0000.0000.000
128A129ILE0-0.035-0.02242.020-0.020-0.0200.0000.0000.0000.000
129A130LEU00.006-0.00535.3430.1320.1320.0000.0000.0000.000
130A131LYS10.8070.87738.431-7.808-7.8080.0000.0000.0000.000
131A132ALA0-0.002-0.02534.8310.2790.2790.0000.0000.0000.000
132A133ASN00.0420.03835.319-0.340-0.3400.0000.0000.0000.000
133A134PHE00.007-0.01733.4320.3900.3900.0000.0000.0000.000
134A135SER00.0180.01332.427-0.240-0.2400.0000.0000.0000.000
135A136VAL00.008-0.00534.1650.1560.1560.0000.0000.0000.000
136A137ILE00.0180.02333.179-0.148-0.1480.0000.0000.0000.000
137A138PHE0-0.035-0.02935.285-0.001-0.0010.0000.0000.0000.000
138A139ASP-1-0.817-0.88439.0458.1578.1570.0000.0000.0000.000
139A140ARG10.8580.89934.190-8.526-8.5260.0000.0000.0000.000
140A141LEU0-0.005-0.00732.5490.0470.0470.0000.0000.0000.000
141A142GLU-1-0.905-0.94729.57210.75110.7510.0000.0000.0000.000
142A143THR0-0.007-0.01427.9250.5680.5680.0000.0000.0000.000
143A144LEU0-0.026-0.01128.694-0.506-0.5060.0000.0000.0000.000
144A145ILE0-0.032-0.02228.8830.3670.3670.0000.0000.0000.000
145A146LEU0-0.031-0.02330.1580.2760.2760.0000.0000.0000.000
146A147LEU00.0050.01731.539-0.361-0.3610.0000.0000.0000.000
147A148ARG10.8190.90632.788-9.164-9.1640.0000.0000.0000.000
148A149ALA0-0.021-0.00435.430-0.195-0.1950.0000.0000.0000.000
149A150PHE00.015-0.01637.5700.0400.0400.0000.0000.0000.000
150A151THR0-0.011-0.03041.113-0.032-0.0320.0000.0000.0000.000
151A152GLU-1-0.888-0.94043.8386.4886.4880.0000.0000.0000.000
152A153GLU-1-0.950-0.96646.9126.8726.8720.0000.0000.0000.000
153A154GLY00.0310.04044.7790.1580.1580.0000.0000.0000.000
154A155ALA00.0430.01842.1530.0380.0380.0000.0000.0000.000
155A156ILE0-0.0140.00635.5550.0350.0350.0000.0000.0000.000
156A157VAL00.0620.03737.4080.0300.0300.0000.0000.0000.000
157A158GLY0-0.004-0.01733.5050.1890.1890.0000.0000.0000.000
158A159GLU-1-0.825-0.90729.96010.44510.4450.0000.0000.0000.000
159A160ILE00.0010.00227.4680.3080.3080.0000.0000.0000.000
160A161SER00.0180.00726.873-0.101-0.1010.0000.0000.0000.000
161A162PRO00.0230.01124.4590.4140.4140.0000.0000.0000.000
162A163LEU0-0.019-0.01619.3450.0620.0620.0000.0000.0000.000
163A164PRO0-0.0120.01418.0810.1180.1180.0000.0000.0000.000
164A165SER0-0.060-0.04715.2741.0851.0850.0000.0000.0000.000
165A166LEU0-0.053-0.00212.127-0.641-0.6410.0000.0000.0000.000
166A167PRO00.007-0.00514.1461.0721.0720.0000.0000.0000.000
167A168GLY00.0510.03517.3740.0070.0070.0000.0000.0000.000
168A169HIS00.0020.01120.512-0.384-0.3840.0000.0000.0000.000
169A170THR00.0370.00523.195-0.277-0.2770.0000.0000.0000.000
170A171ASP-1-0.745-0.88625.87710.63310.6330.0000.0000.0000.000
171A172GLU-1-0.982-0.99426.29311.25811.2580.0000.0000.0000.000
172A173ASP-1-0.825-0.90522.75813.83613.8360.0000.0000.0000.000
173A174VAL00.015-0.01125.601-0.066-0.0660.0000.0000.0000.000
174A175LYS10.7940.92228.610-10.505-10.5050.0000.0000.0000.000
175A176ASN0-0.027-0.02425.799-0.590-0.5900.0000.0000.0000.000
176A177ALA00.0070.01026.782-0.066-0.0660.0000.0000.0000.000
177A178ILE00.0050.00128.447-0.216-0.2160.0000.0000.0000.000
178A179GLY0-0.0040.00731.963-0.222-0.2220.0000.0000.0000.000
179A180VAL0-0.052-0.03927.396-0.140-0.1400.0000.0000.0000.000
180A181LEU0-0.019-0.00230.654-0.116-0.1160.0000.0000.0000.000
181A182ILE00.0340.00132.222-0.194-0.1940.0000.0000.0000.000
182A183GLY00.0100.02034.483-0.161-0.1610.0000.0000.0000.000
183A184GLY0-0.034-0.02433.346-0.115-0.1150.0000.0000.0000.000
184A185LEU00.003-0.02034.312-0.079-0.0790.0000.0000.0000.000
185A186GLU-1-0.889-0.93836.9617.6037.6030.0000.0000.0000.000
186A187TRP0-0.090-0.03535.014-0.209-0.2090.0000.0000.0000.000
187A188ASN0-0.024-0.00236.244-0.152-0.1520.0000.0000.0000.000
188A189ASP-1-0.886-0.92040.2237.2507.2500.0000.0000.0000.000
189A190ASN00.010-0.02940.018-0.188-0.1880.0000.0000.0000.000
190A191THR0-0.050-0.01642.854-0.046-0.0460.0000.0000.0000.000
191A192VAL0-0.009-0.00138.329-0.006-0.0060.0000.0000.0000.000
192A193ARG10.7800.89541.583-7.417-7.4170.0000.0000.0000.000
193A194VAL00.0330.02637.9880.1120.1120.0000.0000.0000.000
194A195SER00.031-0.00340.349-0.197-0.1970.0000.0000.0000.000
195A196GLU-1-0.774-0.89141.7517.4137.4130.0000.0000.0000.000
196A197THR0-0.018-0.03440.8010.0560.0560.0000.0000.0000.000
197A198LEU00.0840.03435.5420.1280.1280.0000.0000.0000.000
198A199GLN0-0.0150.02739.0420.0090.0090.0000.0000.0000.000
199A200ARG10.7120.84941.058-7.372-7.3720.0000.0000.0000.000
200A201PHE0-0.086-0.06437.701-0.093-0.0930.0000.0000.0000.000
201A202ALA0-0.0100.01435.4820.1370.1370.0000.0000.0000.000
202A203TRP00.0100.00434.8720.2720.2720.0000.0000.0000.000